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Sample records for oligonucleotide array design

  1. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Wernersson, Rasmus; Knudsen, Steen

    2003-01-01

    with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added......Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer...... to the program to extend the default parameters: homology, DeltaTm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/....

  2. Combining gene expression data from different generations of oligonucleotide arrays

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    Kong Sek

    2004-10-01

    Full Text Available Abstract Background One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. Results We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis. Conclusions Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different

  3. Efficient oligonucleotide probe selection for pan-genomic tiling arrays

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    Zhang Wei

    2009-09-01

    Full Text Available Abstract Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole-genome tiling requires that the genome sequence is known in advance. For the accurate analysis of uncharacterized bacteria, an array must query a fully representative set of sequences from the species' pan-genome. Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome. Results This paper presents a new probe selection algorithm (PanArray that can tile multiple whole genomes using a minimal number of probes. Unlike arrays built on clustered gene families, PanArray uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments. Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. The viability of the algorithm is demonstrated by array designs for seven different bacterial pan-genomes and, in particular, the design of a 385,000 probe array that fully tiles the genomes of 20 different Listeria monocytogenes strains with overlapping probes at greater than twofold coverage. Conclusion PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on

  4. Identification of clinically relevant viridans streptococci by an oligonucleotide array.

    Science.gov (United States)

    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.

  5. Spatially Defined Oligonucleotide Arrays. Technical Report for Phase II; FINAL

    International Nuclear Information System (INIS)

    None

    2000-01-01

    The goal of the Human Genome Project is to sequence all 3 billion base pairs of the human genome. Progress in this has been rapid; GenBank(reg s ign) finished 1994 with 286 million bases of sequence and grew by 2470 in the first quarter of 1995. The challenge to the scientific community is to understand the biological relevance of this genetic information. In most cases the sequence being generated for any single region of the genome represents the genotype of a single individual. A complete understanding of the function of specific genes and other regions of the genome and their role in human disease and development will only become apparent when the sequence of many more individuals is known. Access to genetic information is ultimately limited by the ability to screen DNA sequence. Although the pioneering sequencing methods of Sanger et al. (15) and Maxam and Gilbert (11) have become standard in virtually all molecular biology laboratories, the basic protocols remain largely unchanged. The throughput of this sequencing technology is now becoming the rate-limiting step in both large-scale sequencing projects such as the Human Genome Project and the subsequent efforts to understand genetic diversity. This has inspired the development of advanced DNA sequencing technologies (9), Incremental improvements to Sanger sequencing have been made in DNA labeling and detection. High-speed electrophoresis methods using ultrathin gels or capillary arrays are now being more widely employed. However, these methods are throughput-limited by their sequential nature and the speed and resolution of separations. This limitation will become more pronounced as the need to rapidly screen newly discovered genes for biologically relevant polymorphisms increases. An alternative to gel-based sequencing is to use high-density oligonucleotide probe arrays. Oligonucleotide probe arrays display specific oligonucleotide probes at precise locations in a high density, information-rich format (5

  6. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

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    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  7. Correction of Spatial Bias in Oligonucleotide Array Data

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    Philippe Serhal

    2013-01-01

    Full Text Available 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.

  8. Correction of Spatial Bias in Oligonucleotide Array Data

    Science.gov (United States)

    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

  9. Analysis of oligonucleotide array experiments with repeated measures using mixed models

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    Getchell Thomas V

    2004-12-01

    Full Text Available Abstract Background Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease or absence (Control of the disease, and brain regions including olfactory bulb (OB or cerebellum (CER. In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. Results In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH procedure of controlling false discovery rate (FDR at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the α-level (αnew = 0.0033 determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD procedure at the level of αnew to control the family-wise error rate (FWER for each gene examined. Conclusions A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

  10. A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray

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    Fairbanks Benjamin D

    2006-04-01

    Full Text Available Abstract Background DNA microarrays have proven powerful for functional genomics studies. Several technologies exist for the generation of whole-genome arrays. It is well documented that 25mer probes directed against different regions of the same gene produce variable signal intensity values. However, the extent to which this is true for probes of greater length (60mers is not well characterized. Moreover, this information has not previously been reported for whole-genome arrays designed against bacteria, whose genomes may differ substantially in characteristics directly affecting microarray performance. Results We report here an analysis of alternative 60mer probe designs for an in-situ synthesized oligonucleotide array for the GC rich, β-proteobacterium Burkholderia cenocepacia. Probes were designed using the ArrayOligoSel3.5 software package and whole-genome microarrays synthesized by Agilent, Inc. using their in-situ, ink-jet technology platform. We first validated the quality of the microarrays as demonstrated by an average signal to noise ratio of >1000. Next, we determined that the variance of replicate probes (1178 total probes examined of identical sequence was 3.8% whereas the variance of alternative probes (558 total alternative probes examined designs was 9.5%. We determined that depending upon the definition, about 2.4% of replicate and 7.8% of alternative probes produced outlier conclusions. Finally, we determined none of the probe design subscores (GC content, internal repeat, binding energy and self annealment produced by ArrayOligoSel3.5 were predictive or probes that produced outlier signals. Conclusion Our analysis demonstrated that the use of multiple probes per target sequence is not essential for in-situ synthesized 60mer oligonucleotide arrays designed against bacteria. Although probes producing outlier signals were identified, the use of ratios results in less than 10% of such outlier conclusions. We also determined that

  11. Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

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    Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

    2014-01-01

    Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

  12. Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

    Directory of Open Access Journals (Sweden)

    Laia Ramos

    Full Text Available Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb. Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14(q10;q10. Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

  13. Oligonucleotide Arrays vs. Metaphase-Comparative Genomic Hybridisation and BAC Arrays for Single-Cell Analysis: First Applications to Preimplantation Genetic Diagnosis for Robertsonian Translocation Carriers

    Science.gov (United States)

    Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

    2014-01-01

    Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers. PMID:25415307

  14. Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

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    Jee Justin

    2008-12-01

    Full Text Available Abstract Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S. cerevisiae and H. sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions. Results We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C→A, C→G and T→A (yielding purine-purine mispairs are most disruptive, whereas A→X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa. This skew is small in highly-expressed regions (± 0.5% of total intensity range and large (± 2% or more elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM. Conclusion We investigate several parameters for oligonucleotide design, including the effects of each central nucleotide substitution on array signal intensity and of multiple MM per oligo. To avoid GC skew, individual substitutions should not alter probe GC content. RNA sample mixture complexity may increase the amount of nonspecific hybridization, magnify GC skew and boost the intensity of MM oligos at all levels.

  15. Whole genome DNA copy number changes identified by high density oligonucleotide arrays

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    Huang Jing

    2004-05-01

    Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

  16. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR.

    Science.gov (United States)

    Qin, Li-Xuan; Beyer, Richard P; Hudson, Francesca N; Linford, Nancy J; Morris, Daryl E; Kerr, Kathleen F

    2006-01-17

    There are currently many different methods for processing and summarizing probe-level data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are most effective. There is no single best way to do this validation, and a variety of approaches is needed. Moreover, gene expression data are collected to answer a variety of scientific questions, and the same method may not be best for all questions. Only a handful of validation studies have been done so far, most of which rely on spike-in datasets and focus on the question of detecting differential expression. Here we seek methods that excel at estimating relative expression. We evaluate methods by identifying those that give the strongest linear association between expression measurements by array and the "gold-standard" assay. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is generally considered the "gold-standard" assay for measuring gene expression by biologists and is often used to confirm findings from microarray data. Here we use qRT-PCR measurements to validate methods for the components of processing oligo array data: background adjustment, normalization, mismatch adjustment, and probeset summary. An advantage of our approach over spike-in studies is that methods are validated on a real dataset that was collected to address a scientific question. We initially identify three of six popular methods that consistently produced the best agreement between oligo array and RT-PCR data for medium- and high-intensity genes. The three methods are generally known as MAS5, gcRMA, and the dChip mismatch mode. For medium- and high-intensity genes, we identified use of data from mismatch probes (as in MAS5 and dChip mismatch) and a sequence-based method of background adjustment (as in gcRMA) as the most important factors in methods' performances. However, we found poor reliability for methods using mismatch probes for low-intensity genes

  17. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR

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    Morris Daryl E

    2006-01-01

    Full Text Available Abstract Background There are currently many different methods for processing and summarizing probe-level data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are most effective. There is no single best way to do this validation, and a variety of approaches is needed. Moreover, gene expression data are collected to answer a variety of scientific questions, and the same method may not be best for all questions. Only a handful of validation studies have been done so far, most of which rely on spike-in datasets and focus on the question of detecting differential expression. Here we seek methods that excel at estimating relative expression. We evaluate methods by identifying those that give the strongest linear association between expression measurements by array and the "gold-standard" assay. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR is generally considered the "gold-standard" assay for measuring gene expression by biologists and is often used to confirm findings from microarray data. Here we use qRT-PCR measurements to validate methods for the components of processing oligo array data: background adjustment, normalization, mismatch adjustment, and probeset summary. An advantage of our approach over spike-in studies is that methods are validated on a real dataset that was collected to address a scientific question. Results We initially identify three of six popular methods that consistently produced the best agreement between oligo array and RT-PCR data for medium- and high-intensity genes. The three methods are generally known as MAS5, gcRMA, and the dChip mismatch mode. For medium- and high-intensity genes, we identified use of data from mismatch probes (as in MAS5 and dChip mismatch and a sequence-based method of background adjustment (as in gcRMA as the most important factors in methods' performances. However, we found poor reliability for methods

  18. Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida.

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    Ping Gong

    Full Text Available High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome-scale expressed sequence tags (ESTs. Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59% probed targets. We validated and made publicly available 63.5K oligo probes so the earthworm research community can use them to pursue ecological, toxicological, and other functional genomics questions. Our approach is efficient, cost-effective and robust because it (1 does not require a major genomics core facility; (2 allows new probes to be easily added and old probes modified or eliminated when new sequence information becomes available, (3 is not bioinformatics-intensive upfront but does provide opportunities for more in-depth annotation of biological functions for target genes; and (4 if desired, EST orthologs to the UniGene clusters of a reference genome can be identified and selected in order to improve the target gene specificity of designed probes. This approach is

  19. Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

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    Townsend Henrik J

    2005-11-01

    Full Text Available Abstract High-density oligonucleotide (oligo arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L. Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ and may be used to facilitate transcriptomic analyses of a wide range of plant and animal

  20. Programmable Array Logic Design

    International Nuclear Information System (INIS)

    Demon Handoyo; Djen Djen Djainal

    2007-01-01

    Good digital circuit design that part of a complex system, often becoming a separate problem. To produce finishing design according to wanted performance is often given on to considerations which each other confuse, hence thereby analyse optimization become important in this case. To realization is made design logic program, the first are determined global diagram block, then are decided contents of these block diagram, and then determined its interconnection in the form of logic expression, continued with election of component. These steps are done to be obtained the design with low price, easy in its interconnection, minimal volume, low power and certainty god work. (author)

  1. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

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    Magness Charles L

    2007-01-01

    Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

  2. Template-Directed Ligation of Peptides to Oligonucleotides

    Science.gov (United States)

    Bruick, Richard K.; Dawson, Philip E.; Kent, Stephen BH; Usman, Nassim; Joyce, Gerald F.

    1996-01-01

    Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

  3. Subclassification and Detection of New Markers for the Discrimination of Primary Liver Tumors by Gene Expression Analysis Using Oligonucleotide Arrays.

    Science.gov (United States)

    Hass, Holger G; Vogel, Ulrich; Scheurlen, Michael; Jobst, Jürgen

    2017-12-26

    The failure to correctly differentiate between intrahepatic cholangiocarcinoma [CC] and hepatocellular carcinoma [HCC] is a significant clinical problem, particularly in terms of the different treatment goals for both cancers. In this study a specific gene expression profile to discriminate these two subgroups of liver cancer was established and potential diagnostic markers for clinical use were analyzed. To evaluate the gene expression profiles of HCC and intrahepatic CC, Oligonucleotide arrays ( Affymetrix U133A) were used. Overexpressed genes were checked for their potential use as new markers for discrimination and their expression values were validated by reverse transcription polymerase chain reaction and immunohistochemistry analyses. 695 genes/expressed sequence tags (ESTs) in HCC (245 up-/450 down-regulated) and 552 genes/ESTs in CC (221 up-/331 down-regulated) were significantly dysregulated (p〈0.05, fold change >2, ≥70%). Using a supervised learning method, and one-way analysis of variance a specific 270-gene expression profile that enabled rapid, reproducible differentiation between both tumors and non-malignant liver tissues was established. A panel of 12 genes (e.g. HSP90β, ERG1, GPC3, TKT, ACLY, and NME1 for HCC; SPT2, T4S3, CNX43, TTD1, HBD01 for CC) were detected and partly described for the first time as potential discrimination markers. A specific gene expression profile for discrimination of primary liver cancer was identified and potential marker genes with feasible clinical impact were described.

  4. Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE.

    Science.gov (United States)

    Quintin, Michael; Ma, Natalie J; Ahmed, Samir; Bhatia, Swapnil; Lewis, Aaron; Isaacs, Farren J; Densmore, Douglas

    2016-06-17

    Genome engineering technologies now enable precise manipulation of organism genotype, but can be limited in scalability by their design requirements. Here we describe Merlin ( http://merlincad.org ), an open-source web-based tool to assist biologists in designing experiments using multiplex automated genome engineering (MAGE). Merlin provides methods to generate pools of single-stranded DNA oligonucleotides (oligos) for MAGE experiments by performing free energy calculation and BLAST scoring on a sliding window spanning the targeted site. These oligos are designed not only to improve recombination efficiency, but also to minimize off-target interactions. The application further assists experiment planning by reporting predicted allelic replacement rates after multiple MAGE cycles, and enables rapid result validation by generating primer sequences for multiplexed allele-specific colony PCR. Here we describe the Merlin oligo and primer design procedures and validate their functionality compared to OptMAGE by eliminating seven AvrII restriction sites from the Escherichia coli genome.

  5. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L. reveals patterns of SNP variation associated with breeding

    Directory of Open Access Journals (Sweden)

    Zhu Tong

    2009-10-01

    Full Text Available Abstract Background Cultivated tomato (Solanum lycopersicum L. has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market, OH9242 (processing, and PI114490 (cherry were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α used to define the confidence interval (CI, and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace, and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka to synonymous substitutions (Ks for 20 loci with multiple SNPs (≥ 4 per

  6. [Sequencing by hybridization methods to generate large arrays of oligonucleotides]. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    The subject of this project is to address a pressing need for custom DNA microarrays (chips) which can be easily and at low cost formatted and revised for research. In this sense, the term custom means chips for which there is need for limited quantities (less than hundreds) of any particular chip design which contains a large number of different, users defined sequences. Of the three principal approaches to fabricate DNA microarrays, the two which have been commercialized (a and b below) are not particularly suited to research purposes because of the significant time and costs required, once a result is obtained, to utilize that result in the design of a new and better chip: (a) the photodeprotection scheme used by Affymetrix; and (b) the spotting of pre-synthesized oligos or c-DNA onto surfaces.

  7. 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.

    Science.gov (United States)

    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

    2011-04-01

    Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

  8. Design of circular differential microphone arrays

    CERN Document Server

    Benesty, Jacob; Cohen, Israel

    2015-01-01

    Recently, we proposed a completely novel and efficient way to design differential beamforming algorithms for linear microphone arrays. Thanks to this very flexible approach, any order of differential arrays can be designed. Moreover, they can be made robust against white noise amplification, which is the main inconvenience in these types of arrays. The other well-known problem with linear arrays is that electronic steering is not really feasible.  In this book, we extend all these fundamental ideas to circular microphone arrays and show that we can design small and compact differential arrays of any order that can be electronically steered in many different directions and offer a good degree of control of the white noise amplification problem, high directional gain, and frequency-independent response. We also present a number of practical examples, demonstrating that differential beamforming with circular microphone arrays is likely one of the best candidates for applications involving speech enhancement (i....

  9. Flat-plate photovoltaic array design optimization

    Science.gov (United States)

    Ross, R. G., Jr.

    1980-01-01

    An analysis is presented which integrates the results of specific studies in the areas of photovoltaic structural design optimization, optimization of array series/parallel circuit design, thermal design optimization, and optimization of environmental protection features. The analysis is based on minimizing the total photovoltaic system life-cycle energy cost including repair and replacement of failed cells and modules. This approach is shown to be a useful technique for array optimization, particularly when time-dependent parameters such as array degradation and maintenance are involved.

  10. Experimental design, modeling and optimization of polyplex formation between DNA oligonucleotides and branched polyethylenimine.

    Science.gov (United States)

    Clima, Lilia; Ursu, Elena L; Cojocaru, Corneliu; Rotaru, Alexandru; Barboiu, Mihail; Pinteala, Mariana

    2015-09-28

    The complexes formed by DNA and polycations have received great attention owing to their potential application in gene therapy. In this study, the binding efficiency between double-stranded oligonucleotides (dsDNA) and branched polyethylenimine (B-PEI) has been quantified by processing of the images captured from the gel electrophoresis assays. The central composite experimental design has been employed to investigate the effects of controllable factors on the binding efficiency. On the basis of experimental data and the response surface methodology, a multivariate regression model has been constructed and statistically validated. The model has enabled us to predict the binding efficiency depending on experimental factors, such as concentrations of dsDNA and B-PEI as well as the initial pH of solution. The optimization of the binding process has been performed using simplex and gradient methods. The optimal conditions determined for polyplex formation have yielded a maximal binding efficiency close to 100%. In order to reveal the mechanism of complex formation at the atomic-scale, a molecular dynamic simulation has been carried out. According to the computation results, B-PEI amine hydrogen atoms have interacted with oxygen atoms from dsDNA phosphate groups. These interactions have led to the formation of hydrogen bonds between macromolecules, stabilizing the polyplex structure.

  11. CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Ishikawa Shumpei

    2006-02-01

    Full Text Available Abstract Background DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell. Results We describe a novel algorithm called CARAT (Copy Number Analysis with Regression And Tree that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods. Conclusion Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.

  12. Designing Flat-Plate Photovoltaic Arrays

    Science.gov (United States)

    Ross, R. G., Jr.

    1984-01-01

    Report presents overview of state of art in design techniques for flat-plate solar photovoltaic modules and arrays. Paper discusses design requirements, design analyses, and test methods identified and developed for this technology over past several years in effort to reduce cost and improve utility and reliability for broad spectrum of terrestrial applications.

  13. Design and analysis of effects of triplet repeat oligonucleotides in cell models for myotonic dystrophy

    NARCIS (Netherlands)

    Gonzalez-Barriga, A.; Mulders, S.A.M.; Giessen, J. van der; Hooijer, J.D.; Bijl, S.; Kessel, I.D.G. van; Beers, J. van; Deutekom, J.C. van; Fransen, J.A.M.; Wieringa, B.; Wansink, D.G.

    2013-01-01

    Myotonic dystrophy type 1 (DM1) is caused by DM protein kinase (DMPK) transcripts containing an expanded (CUG)n repeat. Antisense oligonucleotide (AON)-mediated suppression of these mutant RNAs is considered a promising therapeutic strategy for this severe disorder. Earlier, we identified a

  14. Study and Design of Differential Microphone Arrays

    CERN Document Server

    Benesty, Jacob

    2013-01-01

    Microphone arrays have attracted a lot of interest over the last few decades since they have the potential to solve many important problems such as noise reduction/speech enhancement, source separation, dereverberation, spatial sound recording, and source localization/tracking, to name a few. However, the design and implementation of microphone arrays with beamforming algorithms is not a trivial task when it comes to processing broadband signals such as speech. Indeed, in most sensor arrangements, the beamformer tends to have a frequency-dependent response. One exception, perhaps, is the family of differential microphone arrays (DMAs) that have the promise to form frequency-independent responses. Moreover, they have the potential to attain high directional gains with small and compact apertures. As a result, this type of microphone arrays has drawn much research and development attention recently. This book is intended to provide a systematic study of DMAs from a signal processing perspective. The primary obj...

  15. Simulation of sparse matrix array designs

    Science.gov (United States)

    Boehm, Rainer; Heckel, Thomas

    2018-04-01

    Matrix phased array probes are becoming more prominently used in industrial applications. The main drawbacks, using probes incorporating a very large number of transducer elements, are needed for an appropriate cabling and an ultrasonic device offering many parallel channels. Matrix arrays designed for extended functionality feature at least 64 or more elements. Typical arrangements are square matrices, e.g., 8 by 8 or 11 by 11 or rectangular matrixes, e.g., 8 by 16 or 10 by 12 to fit a 128-channel phased array system. In some phased array systems, the number of simultaneous active elements is limited to a certain number, e.g., 32 or 64. Those setups do not allow running the probe with all elements active, which may cause a significant change in the directivity pattern of the resulting sound beam. When only a subset of elements can be used during a single acquisition, different strategies may be applied to collect enough data for rebuilding the missing information from the echo signal. Omission of certain elements may be one approach, overlay of subsequent shots with different active areas may be another one. This paper presents the influence of a decreased number of active elements on the sound field and their distribution on the array. Solutions using subsets with different element activity patterns on matrix arrays and their advantages and disadvantages concerning the sound field are evaluated using semi-analytical simulation tools. Sound field criteria are discussed, which are significant for non-destructive testing results and for the system setup.

  16. A novel method to design sparse linear arrays for ultrasonic phased array.

    Science.gov (United States)

    Yang, Ping; Chen, Bin; Shi, Ke-Ren

    2006-12-22

    In ultrasonic phased array testing, a sparse array can increase the resolution by enlarging the aperture without adding system complexity. Designing a sparse array involves choosing the best or a better configuration from a large number of candidate arrays. We firstly designed sparse arrays by using a genetic algorithm, but found that the arrays have poor performance and poor consistency. So, a method based on the Minimum Redundancy Linear Array was then adopted. Some elements are determined by the minimum-redundancy array firstly in order to ensure spatial resolution and then a genetic algorithm is used to optimize the remaining elements. Sparse arrays designed by this method have much better performance and consistency compared to the arrays designed only by a genetic algorithm. Both simulation and experiment confirm the effectiveness.

  17. Conformal array design on arbitrary polygon surface with transformation optics

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Li, E-mail: dengl@bupt.edu.cn; Hong, Weijun, E-mail: hongwj@bupt.edu.cn; Zhu, Jianfeng; Peng, Biao; Li, Shufang [Beijing Key Laboratory of Network System Architecture and Convergence, School of Information and Communication Engineering, Beijing University of Posts and Telecommunications, 100876 Beijing (China); Wu, Yongle, E-mail: wuyongle138@gmail.com [Beijing Key Laboratory of Work Safety Intelligent Monitoring, School of Electronic Engineering, Beijing University of Posts and Telecommunications, 100876 Beijing (China)

    2016-06-15

    A transformation-optics based method to design a conformal antenna array on an arbitrary polygon surface is proposed and demonstrated in this paper. This conformal antenna array can be adjusted to behave equivalently as a uniformly spaced linear array by applying an appropriate transformation medium. An typical example of general arbitrary polygon conformal arrays, not limited to circular array, is presented, verifying the proposed approach. In summary, the novel arbitrary polygon surface conformal array can be utilized in array synthesis and beam-forming, maintaining all benefits of linear array.

  18. Conformal array design on arbitrary polygon surface with transformation optics

    International Nuclear Information System (INIS)

    Deng, Li; Hong, Weijun; Zhu, Jianfeng; Peng, Biao; Li, Shufang; Wu, Yongle

    2016-01-01

    A transformation-optics based method to design a conformal antenna array on an arbitrary polygon surface is proposed and demonstrated in this paper. This conformal antenna array can be adjusted to behave equivalently as a uniformly spaced linear array by applying an appropriate transformation medium. An typical example of general arbitrary polygon conformal arrays, not limited to circular array, is presented, verifying the proposed approach. In summary, the novel arbitrary polygon surface conformal array can be utilized in array synthesis and beam-forming, maintaining all benefits of linear array.

  19. Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides.

    Science.gov (United States)

    Wang, Fenghua; Zhang, Hefei; Gao, Jingxia; Chen, Fengjiao; Chen, Sijie; Zhang, Cuizhen; Peng, Gang

    2016-01-01

    Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.

  20. Design & fabrication of cantilever array biosensors

    DEFF Research Database (Denmark)

    Boisen, Anja; Thundat, T

    2009-01-01

    Surface immobilization of functional receptors on microfabricated cantilever arrays offers a new paradigm for the development of biosensors based on nanomechanics. Microcantilever-based systems are capable of real-time, multiplexed detection of unlabeled disease markers in extremely small volumes......, electronic processing, and even local telemetry on a single chip have the potential of satisfying the need for highly sensitive and selective multiple-target detection in very small samples. Here we will review the design and fabrication process of cantilever-based biosensors....

  1. A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH.

    Directory of Open Access Journals (Sweden)

    Birte Möhlendick

    Full Text Available Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH of single cells. The protocol is based on an established adapter-linker PCR (WGAM and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost- effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.

  2. A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment

    NARCIS (Netherlands)

    Aguirre von Wobeser, E.; Huisman, J.; Ibelings, B.; Matthijs, H.C.P.; Matthijs, H.C.P.

    2005-01-01

    A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment Eneas Aguirre-von-Wobeser 1, Jef Huisman1, Bas Ibelings2 and Hans C.P. Matthijs1 1 Universiteit van Amsterdam, Amsterdam, The

  3. Phased-array design for MST and ST radars

    Science.gov (United States)

    Ecklund, W. L.

    1986-01-01

    All of the existing radar systems fully dedicated to clear-air radar studies use some type of phased-array antennas. The effects of beam-steering techniques including feed networks and phase shifters; sidelobe control; ground-clutter suppression; low altitude coverage; arrays with integrated radiating elements and feed networks; analysis of coaxial-collinear antennas; use of arrays with multiple beams; and array testing and measure on structural design of the antenna are discussed.

  4. Application of oligonucleotide array CGH to the simultaneous detection of a deletion in the nuclear TK2 gene and mtDNA depletion.

    Science.gov (United States)

    Zhang, Shulin; Li, Fang-Yuan; Bass, Harold N; Pursley, Amber; Schmitt, Eric S; Brown, Blaire L; Brundage, Ellen K; Mardach, Rebecca; Wong, Lee-Jun

    2010-01-01

    Thymidine kinase 2 (TK2), encoded by the TK2 gene on chromosome 16q22, is one of the deoxyribonucleoside kinases responsible for the maintenance of mitochondrial deoxyribonucleotide pools. Defects in TK2 mainly cause a myopathic form of the mitochondrial DNA depletion syndrome (MDDS). Currently, only point mutations and small insertions and deletions have been reported in TK2 gene; gross rearrangements of TK2 gene and possible hepatic involvement in patients with TK2 mutations have not been described. We report a non-consanguineous Jordanian family with three deceased siblings due to mtDNA depletion. Sequence analysis of the father detected a heterozygous c.761T>A (p.I254N) mutation in his TK2 gene; however, point mutations in the mother were not detected. Subsequent gene dosage analysis using oligonucleotide array CGH identified an intragenic approximately 5.8-kb deletion encompassing the 5'UTR to intron 2 of her TK2 gene. Sequence analysis confirmed that the deletion spans c.1-495 to c.283-2899 of the TK2 gene (nucleotide 65,136,256-65,142,086 of chromosome 16). Analysis of liver and muscle specimens from one of the deceased infants in this family revealed compound heterozygosity for the paternal point mutation and maternal intragenic deletion. In addition, a significant reduction of the mtDNA content in liver and muscle was detected (10% and 20% of age- and tissue-matched controls, respectively). Prenatal diagnosis was performed in the third pregnancy. The fetus was found to carry both the point mutation and the deletion. This child died 6months after birth due to myopathy. A serum specimen demonstrated elevated liver transaminases in two of the infants from whom results were available. This report expands the mutation spectrum associated with TK2 deficiency. While the myopathic form of MDDS appears to be the main phenotype of TK2 mutations, liver dysfunction may also be a part of the mitochondrial depletion syndrome caused by TK2 gene defects.

  5. G4-DNA formation in the HRAS promoter and rational design of decoy oligonucleotides for cancer therapy.

    Directory of Open Access Journals (Sweden)

    Alexandro Membrino

    Full Text Available HRAS is a proto-oncogene involved in the tumorigenesis of urinary bladder cancer. In the HRAS promoter we identified two G-rich elements, hras-1 and hras-2, that fold, respectively, into an antiparallel and a parallel quadruplex (qhras-1, qhras-2. When we introduced in sequence hras-1 or hras-2 two point mutations that block quadruplex formation, transcription increased 5-fold, but when we stabilized the G-quadruplexes by guanidinium phthalocyanines, transcription decreased to 20% of control. By ChIP we found that sequence hras-1 is bound only by MAZ, while hras-2 is bound by MAZ and Sp1: two transcription factors recognizing guanine boxes. We also discovered by EMSA that recombinant MAZ-GST binds to both HRAS quadruplexes, while Sp1-GST only binds to qhras-1. The over-expression of MAZ and Sp1 synergistically activates HRAS transcription, while silencing each gene by RNAi results in a strong down-regulation of transcription. All these data indicate that the HRAS G-quadruplexes behave as transcription repressors. Finally, we designed decoy oligonucleotides mimicking the HRAS quadruplexes, bearing (R-1-O-[4-(1-Pyrenylethynyl phenylmethyl] glycerol and LNA modifications to increase their stability and nuclease resistance (G4-decoys. The G4-decoys repressed HRAS transcription and caused a strong antiproliferative effect, mediated by apoptosis, in T24 bladder cancer cells where HRAS is mutated.

  6. Design of a trichromatic cone array.

    Directory of Open Access Journals (Sweden)

    Patrick Garrigan

    2010-02-01

    Full Text Available Cones with peak sensitivity to light at long (L, medium (M and short (S wavelengths are unequal in number on the human retina: S cones are rare (<10% while increasing in fraction from center to periphery, and the L/M cone proportions are highly variable between individuals. What optical properties of the eye, and statistical properties of natural scenes, might drive this organization? We found that the spatial-chromatic structure of natural scenes was largely symmetric between the L, M and S sensitivity bands. Given this symmetry, short wavelength attenuation by ocular media gave L/M cones a modest signal-to-noise advantage, which was amplified, especially in the denser central retina, by long-wavelength accommodation of the lens. Meanwhile, total information represented by the cone mosaic remained relatively insensitive to L/M proportions. Thus, the observed cone array design along with a long-wavelength accommodated lens provides a selective advantage: it is maximally informative.

  7. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

    DEFF Research Database (Denmark)

    Bonde, Mads; Klausen, Michael Schantz; Anderson, Mads Valdemar

    2014-01-01

    Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well......, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating...

  8. Fluorescence detection of natural RNA using rationally designed "clickable" oligonucleotide probes

    DEFF Research Database (Denmark)

    Okholm, Anders; Kjems, Jørgen; Astakhova, Kira

    2014-01-01

    Herein a reliable approach to the design of effective fluorescent probes for RNA detection is described. The fluorescence signalling of hybridization by internally positioned polyaromatic hydrocarbons and rhodamine dyes was achieved with a low fluorescence background signal, high fluorescence qua...... quantum yields at ambient and elevated temperature, high selectivity and signal specificity of the probes when binding to miR-7 and circRNA targets....

  9. Design of two easily-testable VLSI array multipliers

    Energy Technology Data Exchange (ETDEWEB)

    Ferguson, J.; Shen, J.P.

    1983-01-01

    Array multipliers are well-suited to VLSI implementation because of the regularity in their iterative structure. However, most VLSI circuits are very difficult to test. This paper shows that, with appropriate cell design, array multipliers can be designed to be very easily testable. An array multiplier is called c-testable if all its adder cells can be exhaustively tested while requiring only a constant number of test patterns. The testability of two well-known array multiplier structures are studied. The conventional design of the carry-save array multipler is shown to be not c-testable. However, a modified design, using a modified adder cell, is generated and shown to be c-testable and requires only 16 test patterns. Similar results are obtained for the baugh-wooley two's complement array multiplier. A modified design of the baugh-wooley array multiplier is shown to be c-testable and requires 55 test patterns. The implementation of a practical c-testable 16*16 array multiplier is also presented. 10 references.

  10. Design of a new electrode array for cochlear implants

    International Nuclear Information System (INIS)

    Kha, H.; Chen, B.

    2010-01-01

    Full text: This study aims to design a new electrode array which can be precisely located beneath the basilar membrane within the cochlear scala tympani. This placement of the electrode array is beneficial for increasing the effectiveness of the electrical stimulation of the audi tory nerves and maximising the growth factors delivered into the cochlea for regenerating the progressively lost auditory neurons, thereby significantly improving performance of the cochlear implant systems. Methods The design process involved two steps. First, the biocom patible nitinol-based shape memory alloy, of which mechanical deformation can be controlled using electrical cUTents/fields act vated by body temperature, was selected. Second, five different designs of the electrode array with embedded nitinol actuators were studied (Table I). The finite element method was employed to predict final positions of these electrode arrays. Results The electrode array with three 6 mm actuators at 2-8, 8-J4 and 14-20 mm from the tip (Fig. I) was found to be located most closely to the basilar membrane, compared with those in the other four cases. Conclusions A new nitinol cochlear implant electrode array with three embedded nitinol actuators has been designed. This electrode array is expected to be located beneath the basilar membrane for maximising the delivery of growth factors. Future research will involve the manufacturing of a prototype of this electrode array for use in insertion experiments and neurotrophin release tests.

  11. Multispectral linear array (MLA) focal plane mechanical and thermal design

    Science.gov (United States)

    Mitchell, A. S.; Kaminski, E. F.

    1982-01-01

    The mechanical and thermal design of an integrated focal plane subsystem of a Multispectral Linear Array (MLA) instrument is discussed in terms of focal-plane alignment, thermoelastic performance, and thermal requirements. The modular construction and thermal control of the focal plane array are discussed.

  12. Probe design for expression arrays using OligoWiz

    DEFF Research Database (Denmark)

    Wernersson, Rasmus

    2014-01-01

    Since all measurements from a DNA microarray is dependant on the probes used, a good choice of probes is of vital importa nce when designing custom micro-arrays. This chapter describes how to de sign expression arrays using the “ OligoWiz ” software suite. The general desired features of good...... probes and the issues which probe design must address are introduced and a conceptual (rather than mathematical) description of how OligoWiz scores the quality of th e potential probes is presented. This is followed by a detailed step-by-step guide to designing expression arrays with OligoWiz....

  13. Challenging aspects of contemporary cochlear implant electrode array design.

    Science.gov (United States)

    Mistrík, Pavel; Jolly, Claude; Sieber, Daniel; Hochmair, Ingeborg

    2017-12-01

    A design comparison of current perimodiolar and lateral wall electrode arrays of the cochlear implant (CI) is provided. The focus is on functional features such as acoustic frequency coverage and tonotopic mapping, battery consumption and dynamic range. A traumacity of their insertion is also evaluated. Review of up-to-date literature. Perimodiolar electrode arrays are positioned in the basal turn of the cochlea near the modiolus. They are designed to initiate the action potential in the proximity to the neural soma located in spiral ganglion. On the other hand, lateral wall electrode arrays can be inserted deeper inside the cochlea, as they are located along the lateral wall and such insertion trajectory is less traumatic. This class of arrays targets primarily surviving neural peripheral processes. Due to their larger insertion depth, lateral wall arrays can deliver lower acoustic frequencies in manner better corresponding to cochlear tonotopicity. In fact, spiral ganglion sections containing auditory nerve fibres tuned to low acoustic frequencies are located deeper than 1 and half turn inside the cochlea. For this reason, a significant frequency mismatch might be occurring for apical electrodes in perimodiolar arrays, detrimental to speech perception. Tonal languages such as Mandarin might be therefore better treated with lateral wall arrays. On the other hand, closer proximity to target tissue results in lower psychophysical threshold levels for perimodiolar arrays. However, the maximal comfort level is also lower, paradoxically resulting in narrower dynamic range than that of lateral wall arrays. Battery consumption is comparable for both types of arrays. Lateral wall arrays are less likely to cause trauma to cochlear structures. As the current trend in cochlear implantation is the maximal protection of residual acoustic hearing, the lateral wall arrays seem more suitable for hearing preservation CI surgeries. Future development could focus on combining the

  14. 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

    Science.gov (United States)

    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

  15. APRON: A Cellular Processor Array Simulation and Hardware Design Tool

    Science.gov (United States)

    Barr, David R. W.; Dudek, Piotr

    2009-12-01

    We present a software environment for the efficient simulation of cellular processor arrays (CPAs). This software (APRON) is used to explore algorithms that are designed for massively parallel fine-grained processor arrays, topographic multilayer neural networks, vision chips with SIMD processor arrays, and related architectures. The software uses a highly optimised core combined with a flexible compiler to provide the user with tools for the design of new processor array hardware architectures and the emulation of existing devices. We present performance benchmarks for the software processor array implemented on standard commodity microprocessors. APRON can be configured to use additional processing hardware if necessary and can be used as a complete graphical user interface and development environment for new or existing CPA systems, allowing more users to develop algorithms for CPA systems.

  16. APRON: A Cellular Processor Array Simulation and Hardware Design Tool

    Directory of Open Access Journals (Sweden)

    David R. W. Barr

    2009-01-01

    Full Text Available We present a software environment for the efficient simulation of cellular processor arrays (CPAs. This software (APRON is used to explore algorithms that are designed for massively parallel fine-grained processor arrays, topographic multilayer neural networks, vision chips with SIMD processor arrays, and related architectures. The software uses a highly optimised core combined with a flexible compiler to provide the user with tools for the design of new processor array hardware architectures and the emulation of existing devices. We present performance benchmarks for the software processor array implemented on standard commodity microprocessors. APRON can be configured to use additional processing hardware if necessary and can be used as a complete graphical user interface and development environment for new or existing CPA systems, allowing more users to develop algorithms for CPA systems.

  17. Introduction to embedded system design using field programmable gate arrays

    CERN Document Server

    Dubey, Rahul

    2009-01-01

    Offers information on the use of field programmable gate arrays (FPGAs) in the design of embedded systems. This text considers a hypothetical robot controller as an embedded application and weaves around it related concepts of FPGA-based digital design. It is suitable for both students and designers who have worked with microprocessors.

  18. Heat-rejection design for large concentrating solar arrays

    Science.gov (United States)

    French, E. P.

    1980-01-01

    This paper considers the effect of heat rejection devices (radiators) on the performance and cost of large concentrating solar arrays for space application. Overall array characteristics are derived from the weight, cost, and performance of four major components; namely primary structure, optics/secondary structure, radiator, and solar panel. An ideal concentrator analysis is used to establish general cost and performance trends independent of specific array design. Both passive and heat-pipe radiation are evaluated, with an incremental cost-of-power approach used in the evaluation. Passive radiators are found to be more cost effective with silicon than with gallium arsenide (GaAs) arrays. Representative concentrating arrays have been evaluated for both near-term and advanced solar cell technology. Minimum cost of power is achieved at geometric concentration ratios in the range 2 to 6.

  19. Phased-array radar design application of radar fundamentals

    CERN Document Server

    Jeffrey, Thomas

    2009-01-01

    Phased-Array Radar Design is a text-reference designed for electrical engineering graduate students in colleges and universities as well as for corporate in-house training programs for radar design engineers, especially systems engineers and analysts who would like to gain hands-on, practical knowledge and skills in radar design fundamentals, advanced radar concepts, trade-offs for radar design and radar performance analysis.

  20. A study into the design of steerable microphone arrays

    CERN Document Server

    Lai, Chiong Ching; Leung, Yee Hong

    2017-01-01

    The book covers the design formulations for broadband beamformer targeting nearfield and farfield sources. The book content includes background information on the acoustic environment, including propagation medium, the array geometries, signal models and basic beamformer designs. Subsequently it introduces design formulation for nearfield, farfield and mixed nearfield-farfield beamformers and extends the design formulation into electronically steerable beamformers. In addition, a robust formulation is introduced for all the designs mentioned.

  1. Design and control of phased ICRF antenna arrays

    International Nuclear Information System (INIS)

    Goulding, R.H.; Baity, F.W.; Hoffman, D.J.

    1993-01-01

    Phased antenna arrays operating in the ion cyclotron range of frequencies (ICRF) are used to produce highly directional wave spectra, primarily for use in current drive experiments. RF current drive using phased antennas has been demonstrated in both the JET and DIII-D tokamaks, and both devices are planning to operate new four-element arrays beginning early next year. Features of antenna design that are relevant to phased operation and production of directional spectra are reviewed. Recent advances in the design of the feed circuits and the related control systems for these arrays should substantially improve their performance, by reducing the coupling seen by the matching networks and rf power supplies caused by the mutual impedance of the array elements. The feed circuit designs for the DIII-D and JET phased antenna arrays are compared. The two configurations differ significantly due to the fact that one power amplifier is used for the entire array in the former case, and one per element in the latter. The JET system uses automatic feedback control of matching, phase and amplitude of antenna currents, and the transmitter power balance. The design of this system is discussed, and a time dependent model used to predict its behavior is described

  2. Coil Array Design Inspired on the Kepler's Lenten Pretzel

    International Nuclear Information System (INIS)

    Vazquez, F.; Solis, S. E.; Rodriguez, A. O.

    2008-01-01

    The RF coil arrays are an important part in Magnetic Resonance Imaging, since they are the main device for transmission and reception of the magnetic resonance signal. An RF coil array with a new configuration based on the Kepler's Lenten pretzel for the geocentric path of Mars is proposed in this work. The evenly distributed trajectories may serve as the basic configuration to form a coil array to adequately cover a region of interest for magnetic resonance experiments. The main goal is to investigate the electromagnetic properties of this coil array geometry to obtain an optimal design for its further construction. Hence, the electromagnetic properties of the coil array were numerical simulated using the finite element method and the quasi-static approach. Resulting simulations showed that there is an important concentration of magnetic field lines at the centre of the coil array. This is an advantage over other coil arrays where the magnetic field usually decreased at their geometrical centre. Both the electric and magnetic fields had also a very good uniformity. These characteristics made this coil design a good candidate for applications where the use of multi-coil technology is mandatory

  3. Array design and expression evaluation in POOMA II

    Energy Technology Data Exchange (ETDEWEB)

    Karmesin, S.; Crotinger, J.; Cummings, J.; Haney, S.; Humphrey, W.; Reynders, J.; Smith, S.; Williams, T.J.

    1998-12-31

    POOMA is a templated C++ class library for use in the development of large-scale scientific simulations on serial and parallel computers. POOMA II is a new design and implementation of POOMA intended to add richer capabilities and greater flexibility to the framework. The new design employs a generic Array class that acts as an interface to, or view on, a wide variety of data representation objects referred to as engines. This design separates the interface and the representation of multidimensional arrays. The separation is achieved using compile-time techniques rather than virtual functions, and thus code efficiency is maintained. POOMA II uses PETE, the Portable Expression Template Engine, to efficiently represent complex mathematical expressions involving arrays and other objects. The representation of expressions is kept separate from expression evaluation, allowing the use of multiple evaluator mechanisms that can support nested where-block constructs, hardware-specific optimizations and different run-time environments.

  4. Design of nested Halbach cylinder arrays for magnetic refrigeration applications

    Energy Technology Data Exchange (ETDEWEB)

    Trevizoli, Paulo V., E-mail: trevizoli@polo.ufsc.br; Lozano, Jaime A.; Peixer, Guilherme F.; Barbosa Jr, Jader R.

    2015-12-01

    We present an experimentally validated analytical procedure to design nested Halbach cylinder arrays for magnetic cooling applications. The procedure aims at maximizing the magnetic flux density variation in the core of the array for a given set of design parameters, namely the inner diameter of the internal magnet, the air gap between the magnet cylinders, the number of segments of each magnet and the remanent flux density of the Nd{sub 2}Fe{sub 14}B magnet grade. The design procedure was assisted and verified by 3-D numerical modeling using a commercial software package. An important aspect of the optimal design is to maintain an uniform axial distribution of the magnetic flux density in the region of the inner gap occupied by the active magnetocaloric regenerator. An optimal nested Halbach cylinder array was manufactured and experimentally evaluated for the magnetic flux density in the inner gap. The analytically calculated magnetic flux density variation agreed to within 5.6% with the experimental value for the center point of the magnet gap. - Highlights: • An analytical procedure to design nested Halbach cylinder arrays is proposed. • An optimal magnet configuration was built based on the analytical procedure. • The procedure was validated with 3D COMSOL simulations and experimental data.

  5. Design considerations for large roof-integrated photovoltaic arrays

    Energy Technology Data Exchange (ETDEWEB)

    Ropp, M.E.; Begovic, M.; Rohatgi, A. [Georgia Inst. of Tech., Atlanta, GA (United States); Long, R. [Georgia Institute of Technology, Atlanta (United States). Office of Facilities

    1997-01-01

    This paper describes calculations and modeling used in the design of the photovoltaic (PV) array built on the roof of the Georgia Tech Aquatic Center, the aquatic sports venue for the 1996 Olympic and Paralympic Games. The software package PVFORM (version 3.3) was extensively utilized; because of its importance to this work, it is thoroughly reviewed here. Procedures required to adapt PVFORM to this particular installation are described. The expected behavior and performance of the system, including maximum power output, annual energy output and maximum expected temperature, are then presented, and the use of this information in making informed design decisions is described. Finally, since the orientation of the PV array is not optimal, the effect of the unoptimized array orientation on the system`s performance is quantified. (author)

  6. Laser beam shaping design based on micromirror array

    Science.gov (United States)

    Fang, Han; Su, Bida; Liu, Jiaguo; Fan, Xiaoli; Jing, Wang

    2017-10-01

    In the practical application of the laser, it is necessary to use the laser beam shaping technology to shape the output beam of laser device to the uniform light intensity distribution. The shaping divergent optical system of compound eye integrator way is composed of beam expanding mirror group and lens array. Its working principle is to expand the output laser to a certain size of caliber, and then divide the beam with lens array into multiple sub beam, where the lens unit of lens array can control the divergence angle of sub beam through the design of focal length, with mutual superposition of the sub beam in far field, to make up for the nonuniformity of beam, so that the radiant exitance on the radiated surface may become uniform. In this paper, we use a reflective microlens array to realize the laser beam shaping. By through of the practical optical path model established, the ray tracing is carried out and the simulation results for single-mode Gaussian beam with noise circumstance is provided. The analysis results show that the laser beam shaping under different inputs can be effectively realized by use of microlens array. All the energy is within the signal window, with a high energy efficiency of more than 90%; The measured surface has a better uniformity, and the uniformity is better than 99.5% at 150m.

  7. Electromagnetic linear machines with dual Halbach array design and analysis

    CERN Document Server

    Yan, Liang; Peng, Juanjuan; Zhang, Lei; Jiao, Zongxia

    2017-01-01

    This book extends the conventional two-dimensional (2D) magnet arrangement into 3D pattern for permanent magnet linear machines for the first time, and proposes a novel dual Halbach array. It can not only effectively increase the radial component of magnetic flux density and output force of tubular linear machines, but also significantly reduce the axial flux density, radial force and thus system vibrations and noises. The book is also the first to address the fundamentals and provide a summary of conventional arrays, as well as novel concepts for PM pole design in electric linear machines. It covers theoretical study, numerical simulation, design optimization and experimental works systematically. The design concept and analytical approaches can be implemented to other linear and rotary machines with similar structures. The book will be of interest to academics, researchers, R&D engineers and graduate students in electronic engineering and mechanical engineering who wish to learn the core principles, met...

  8. Design of photovoltaic central power station concentrator array

    Energy Technology Data Exchange (ETDEWEB)

    1984-02-01

    A design for a photovoltaic central power station using tracking concentrators has been developed. The 100 MW plant is assumed to be located adjacent to the Saguaro Power Station of Arizona Public Service. The design assumes an advanced Martin Marietta two-axis tracking fresnel lens concentrator. The concentrators are arrayed in 5 MW subfields, each with its own power conditioning unit. The photovoltaic plant output is connected to the existing 115 kV switchyard. The site specific design allows detailed cost estimates for engineering, site preparation, and installation. Collector and power conditioning costs have been treated parametrically.

  9. Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry

    Energy Technology Data Exchange (ETDEWEB)

    Jafari, Safiye [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Faridbod, Farnoush, E-mail: faridbodf@khayam.ut.ac.ir [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Biosensor Research Center, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Norouzi, Parviz [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Biosensor Research Center, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of); Dezfuli, Amin Shiralizadeh [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Ajloo, Davood [School of Chemistry, Damghan University, Damghan (Iran, Islamic Republic of); Mohammadipanah, Fatemeh [Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran (Iran, Islamic Republic of); Ganjali, Mohammad Reza [Center of Excellence in Electrochemistry, University of Tehran, Tehran (Iran, Islamic Republic of); Biosensor Research Center, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran (Iran, Islamic Republic of)

    2015-10-01

    A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO{sub 2}NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy){sub 3}]{sup 2+/3+} redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy){sub 3}]{sup 2+/3+} FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10{sup −15} to 1 × 10{sup −8} mol L{sup −1}. The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL{sup −1} with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy){sub 3}]{sup 2+/3+} interaction with ssDNA before and after hybridization. - Highlights: • New DNA biosensor is designed for sub-femtomolar detection of Aeromonas hydrophila DNA sequence. • Reduced graphene oxide decorated Ceria nanoparticles was used as a new immobilization platform. • Biosensor was successfully used to detect A. hydrophila DNA sequence in fish pond water.

  10. Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry

    International Nuclear Information System (INIS)

    Jafari, Safiye; Faridbod, Farnoush; Norouzi, Parviz; Dezfuli, Amin Shiralizadeh; Ajloo, Davood; Mohammadipanah, Fatemeh; Ganjali, Mohammad Reza

    2015-01-01

    A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO_2NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy)_3]"2"+"/"3"+ redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy)_3]"2"+"/"3"+ FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10"−"1"5 to 1 × 10"−"8 mol L"−"1. The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL"−"1 with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy)_3]"2"+"/"3"+ interaction with ssDNA before and after hybridization. - Highlights: • New DNA biosensor is designed for sub-femtomolar detection of Aeromonas hydrophila DNA sequence. • Reduced graphene oxide decorated Ceria nanoparticles was used as a new immobilization platform. • Biosensor was successfully used to detect A. hydrophila DNA sequence in fish pond water.

  11. High Performance Systolic Array Core Architecture Design for DNA Sequencer

    Directory of Open Access Journals (Sweden)

    Saiful Nurdin Dayana

    2018-01-01

    Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

  12. Design and Analysis of MEMS Linear Phased Array

    Directory of Open Access Journals (Sweden)

    Guoxiang Fan

    2016-01-01

    Full Text Available A structure of micro-electro-mechanical system (MEMS linear phased array based on “multi-cell” element is designed to increase radiation sound pressure of transducer working in bending vibration mode at high frequency. In order to more accurately predict the resonant frequency of an element, the theoretical analysis of the dynamic equation of a fixed rectangular composite plate and finite element method simulation are adopted. The effects of the parameters both in the lateral and elevation direction on the three-dimensional beam directivity characteristics are comprehensively analyzed. The key parameters in the analysis include the “cell” number of element, “cell” size, “inter-cell” spacing and the number of elements, element width. The simulation results show that optimizing the linear array parameters both in the lateral and elevation direction can greatly improve the three-dimensional beam focusing for MEMS linear phased array, which is obviously different from the traditional linear array.

  13. A CMOS ASIC Design for SiPM Arrays.

    Science.gov (United States)

    Dey, Samrat; Banks, Lushon; Chen, Shaw-Pin; Xu, Wenbin; Lewellen, Thomas K; Miyaoka, Robert S; Rudell, Jacques C

    2011-12-01

    Our lab has previously reported on novel board-level readout electronics for an 8×8 silicon photomultiplier (SiPM) array featuring row/column summation technique to reduce the hardware requirements for signal processing. We are taking the next step by implementing a monolithic CMOS chip which is based on the row-column architecture. In addition, this paper explores the option of using diagonal summation as well as calibration to compensate for temperature and process variations. Further description of a timing pickoff signal which aligns all of the positioning (spatial channels) pulses in the array is described. The ASIC design is targeted to be scalable with the detector size and flexible to accommodate detectors from different vendors. This paper focuses on circuit implementation issues associated with the design of the ASIC to interface our Phase II MiCES FPGA board with a SiPM array. Moreover, a discussion is provided for strategies to eventually integrate all the analog and mixed-signal electronics with the SiPM, on either a single-silicon substrate or multi-chip module (MCM).

  14. 1024x1024 resistive emitter array design and fabrication status

    Science.gov (United States)

    Bryant, Paul T.; Oleson, Jim; McHugh, Stephen W.; Beuville, Eric; Schlesselmann, John D.; Woolaway, James T.; Barskey, Steve; Solomon, Steven L.; Joyner, Thomas W.

    2002-07-01

    Santa Barbara Infrared (SBIR) is producing a high performance 1,024 x 1,024 Large Format Resistive emitter Array (LFRA) for use in the next generation of IR Scene Projectors (IRSPs). LFRA requirements were developed through close cooperation with the Tri-Service IR Scene Projector working group, and through detailed trade studies sponsored by the OSD Central T&E Investment Program (CTEIP) and a Phase I US Navy Small Business Innovative Research (SBIR) contract. The CMOS Read-In Integrated Circuit (RIIC) is being designed by SBIR and Indigo Systems under a Small Business Innovative Research (SBIR) contract. Performance and features include 750 K MWIR maximum apparent temperature, 5 ms radiance rise time, 200 Hz full frame update, and 400 Hz window mode operation. Ten 8-inch CMOS wafers will be fabricated and characterized in mid-2002, followed by emitter fabrication in late 2002. This paper discusses array performance, requirements flow-down, array design, fabrication of 2 X 2-inch CMOS devices, and plans for subsequent RIIC wafer test and emitter pixel fabrication.

  15. Solar cell array design handbook - The principles and technology of photovoltaic energy conversion

    Science.gov (United States)

    Rauschenbach, H. S.

    1980-01-01

    Photovoltaic solar cell array design and technology for ground-based and space applications are discussed from the user's point of view. Solar array systems are described, with attention given to array concepts, historical development, applications and performance, and the analysis of array characteristics, circuits, components, performance and reliability is examined. Aspects of solar cell array design considered include the design process, photovoltaic system and detailed array design, and the design of array thermal, radiation shielding and electromagnetic components. Attention is then given to the characteristics and design of the separate components of solar arrays, including the solar cells, optical elements and mechanical elements, and the fabrication, testing, environmental conditions and effects and material properties of arrays and their components are discussed.

  16. Nanoparticle array based optical frequency selective surfaces: theory and design.

    Science.gov (United States)

    Saeidi, Chiya; van der Weide, Daniel

    2013-07-01

    We demonstrate a synthesis procedure for designing a bandstop optical frequency selective surface (FSS) composed of nanoparticle (NP) elements. The proposed FSS uses two-dimensional (2-D) periodic arrays of NPs with subwavelength unit-cell dimensions. We derive equivalent circuit for a nanoparticle array (NPA) using the closed-form solution for a 2-D NPA excited by a plane wave in the limit of the dipole approximation, which includes contribution from both individual and collective plasmon modes. Using the extracted equivalent circuit, we demonstrate synthesis of an optical FSS using cascaded NPA layers as coupled resonators, which we validate with both circuit model and full-wave simulation for a third-order Butterworth bandstop prototype.

  17. Reconfigurable signal processor designs for advanced digital array radar systems

    Science.gov (United States)

    Suarez, Hernan; Zhang, Yan (Rockee); Yu, Xining

    2017-05-01

    The new challenges originated from Digital Array Radar (DAR) demands a new generation of reconfigurable backend processor in the system. The new FPGA devices can support much higher speed, more bandwidth and processing capabilities for the need of digital Line Replaceable Unit (LRU). This study focuses on using the latest Altera and Xilinx devices in an adaptive beamforming processor. The field reprogrammable RF devices from Analog Devices are used as analog front end transceivers. Different from other existing Software-Defined Radio transceivers on the market, this processor is designed for distributed adaptive beamforming in a networked environment. The following aspects of the novel radar processor will be presented: (1) A new system-on-chip architecture based on Altera's devices and adaptive processing module, especially for the adaptive beamforming and pulse compression, will be introduced, (2) Successful implementation of generation 2 serial RapidIO data links on FPGA, which supports VITA-49 radio packet format for large distributed DAR processing. (3) Demonstration of the feasibility and capabilities of the processor in a Micro-TCA based, SRIO switching backplane to support multichannel beamforming in real-time. (4) Application of this processor in ongoing radar system development projects, including OU's dual-polarized digital array radar, the planned new cylindrical array radars, and future airborne radars.

  18. Thermal design of spacecraft solar arrays using a polyimide foam

    International Nuclear Information System (INIS)

    Bianco, N; Iasiello, M; Naso, V

    2015-01-01

    The design of the Thermal Control System (TCS) of spacecraft solar arrays plays a fundamental role. Indeed, the spacecraft components must operate within a certain range of temperature. If this doesn't occur, their performance is reduced and they may even break. Solar arrays, which are employed to recharge batteries, are directly exposed to the solar heat flux, and they need to be insulated from the earth's surface irradiation. Insulation is currently provided either with a white paint coating or with a Multi Layer Insulation (MLI) system [1]. A configuration based on an open-cell polyimide foam has also been recently proposed [2]. Using polyimide foams in TCSs looks very attractive in terms of costs, weight and assembling. An innovative thermal analysis of the above cited TCS configurations is carried out in this paper, by solving the porous media energy equation, under the assumption of Local Thermal Equilibrium (LTE) between the two phases. Radiation effects through the solar array are also considered by using the Rosseland approximation. Under a stationary daylight condition, temperature profiles are obtained by means of the finite-element based code COMSOL Multiphysics ® . Finally, since the weight plays an important role in aerospace applications, weights of the three TCS configurations are compared. (paper)

  19. Thermal design of spacecraft solar arrays using a polyimide foam

    Science.gov (United States)

    Bianco, N.; Iasiello, M.; Naso, V.

    2015-11-01

    The design of the Thermal Control System (TCS) of spacecraft solar arrays plays a fundamental role. Indeed, the spacecraft components must operate within a certain range of temperature. If this doesn't occur, their performance is reduced and they may even break. Solar arrays, which are employed to recharge batteries, are directly exposed to the solar heat flux, and they need to be insulated from the earth's surface irradiation. Insulation is currently provided either with a white paint coating or with a Multi Layer Insulation (MLI) system [1]. A configuration based on an open-cell polyimide foam has also been recently proposed [2]. Using polyimide foams in TCSs looks very attractive in terms of costs, weight and assembling. An innovative thermal analysis of the above cited TCS configurations is carried out in this paper, by solving the porous media energy equation, under the assumption of Local Thermal Equilibrium (LTE) between the two phases. Radiation effects through the solar array are also considered by using the Rosseland approximation. Under a stationary daylight condition, temperature profiles are obtained by means of the finite-element based code COMSOL Multiphysics®. Finally, since the weight plays an important role in aerospace applications, weights of the three TCS configurations are compared.

  20. Low Complexity Beampattern Design in MIMO Radars Using Planar Array

    KAUST Repository

    Bouchoucha, Taha

    2015-01-07

    In multiple-input multiple-output radar systems, it is usually desirable to steer transmitted power in the region-of-interest. To do this, conventional methods optimize the waveform covariance matrix, R, for the desired beampattern, which is then used to generate actual transmitted waveforms. Both steps require constrained optimization, therefore, use iterative and expensive algorithms. In this paper, we provide a closed-form solution to design covariance matrix for the given beampattern using the planar array, which is then used to derive a novel closed-form algorithm to directly design the finite-alphabet constant-envelope (FACE) waveforms. The proposed algorithm exploits the two-dimensional fast-Fourier-transform. The performance of our proposed algorithm is compared with existing methods that are based on semi-definite quadratic programming with the advantage of a considerably reduced complexity.

  1. Therapeutic Oligonucleotides Targeting Liver Disease: TTR Amyloidosis

    Directory of Open Access Journals (Sweden)

    Christoph Niemietz

    2015-09-01

    Full Text Available The liver has become an increasingly interesting target for oligonucleotide therapy. Mutations of the gene encoding transthyretin (TTR, expressed in vast amounts by the liver, result in a complex degenerative disease, termed familial amyloid polyneuropathy (FAP. Misfolded variants of TTR are linked to the establishment of extracellular protein deposition in various tissues, including the heart and the peripheral nervous system. Recent progress in the chemistry and formulation of antisense (ASO and small interfering RNA (siRNA designed for a knockdown of TTR mRNA in the liver has allowed to address the issue of gene-specific molecular therapy in a clinical setting of FAP. The two therapeutic oligonucleotides bind to RNA in a sequence specific manner but exploit different mechanisms. Here we describe major developments that have led to the advent of therapeutic oligonucleotides for treatment of TTR-related disease.

  2. Analysis of neighborhood behavior in lead optimization and array design.

    Science.gov (United States)

    Papadatos, George; Cooper, Anthony W J; Kadirkamanathan, Visakan; Macdonald, Simon J F; McLay, Iain M; Pickett, Stephen D; Pritchard, John M; Willett, Peter; Gillet, Valerie J

    2009-02-01

    Neighborhood behavior describes the extent to which small structural changes defined by a molecular descriptor are likely to lead to small property changes. This study evaluates two methods for the quantification of neighborhood behavior: the optimal diagonal method of Patterson et al. and the optimality criterion method of Horvath and Jeandenans. The methods are evaluated using twelve different types of fingerprint (both 2D and 3D) with screening data derived from several lead optimization projects at GlaxoSmithKline. The principal focus of the work is the design of chemical arrays during lead optimization, and the study hence considers not only biological activity but also important drug properties such as metabolic stability, permeability, and lipophilicity. Evidence is provided to suggest that the optimality criterion method may provide a better quantitative description of neighborhood behavior than the optimal diagonal method.

  3. Design of Circularly-Polarised, Crossed Drooping Dipole, Phased Array Antenna Using Genetic Algorithm Optimisation

    DEFF Research Database (Denmark)

    Larsen, Niels Vesterdal

    2007-01-01

    A printed drooping dipole array is designed and constructed. The design is based on a genetic algorithm optimisation procedure used in conjunction with the software programme AWAS. By optimising the array G/T for specific combinations of scan angles and frequencies an optimum design is obtained...

  4. Algorithms and Array Design Criteria for Robust Imaging in Interferometry

    Science.gov (United States)

    Kurien, Binoy George

    Optical interferometry is a technique for obtaining high-resolution imagery of a distant target by interfering light from multiple telescopes. Image restoration from interferometric measurements poses a unique set of challenges. The first challenge is that the measurement set provides only a sparse-sampling of the object's Fourier Transform and hence image formation from these measurements is an inherently ill-posed inverse problem. Secondly, atmospheric turbulence causes severe distortion of the phase of the Fourier samples. We develop array design conditions for unique Fourier phase recovery, as well as a comprehensive algorithmic framework based on the notion of redundant-spaced-calibration (RSC), which together achieve reliable image reconstruction in spite of these challenges. Within this framework, we see that classical interferometric observables such as the bispectrum and closure phase can limit sensitivity, and that generalized notions of these observables can improve both theoretical and empirical performance. Our framework leverages techniques from lattice theory to resolve integer phase ambiguities in the interferometric phase measurements, and from graph theory, to select a reliable set of generalized observables. We analyze the expected shot-noise-limited performance of our algorithm for both pairwise and Fizeau interferometric architectures and corroborate this analysis with simulation results. We apply techniques from the field of compressed sensing to perform image reconstruction from the estimates of the object's Fourier coefficients. The end result is a comprehensive strategy to achieve well-posed and easily-predictable reconstruction performance in optical interferometry.

  5. Low-cost modular array-field designs for flat-panel and concentrator photovoltaic systems

    Science.gov (United States)

    Post, H. N.; Carmichael, D. C.; Alexander, G.; Castle, J. A.

    1982-09-01

    Described are the design and development of low-cost, modular array fields for flat-panel and concentrator photovoltaic (PV) systems. The objective of the work was to reduce substantially the cost of the array-field Balance-of-System (BOS) subsystems and site-specific design costs as compared to previous PV installations. These subsystems include site preparation, foundations, support structures, electrical writing, grounding, lightning protection, electromagnetic interference considerations, and controls. To reduce these BOS and design costs, standardized modular (building-block) designs for flat-panel and concentrator array fields have been developed that are fully integrated and optimized for lowest life-cycle costs. Using drawings and specifications now available, these building-block designs can be used in multiples to install various size array fields. The developed designs are immediately applicable (1982) and reduce the array-field BOS costs to a fraction of previous costs.

  6. Improved Design of Microphone-Array Hearing Aids

    National Research Council Canada - National Science Library

    Greenberg, Julie

    1994-01-01

    ...). Research on microphone array hearing aids is motivated by the lack of success of single-microphone systems, as well as the documented advantages of binaural hearing and multiple-element sensing systems...

  7. Quasi-optical antenna-mixer-array design for terahertz frequencies

    Science.gov (United States)

    Guo, Yong; Potter, Kent A.; Rutledge, David B.

    1992-01-01

    A new quasi-optical antenna-mixer-array design for terahertz frequencies is presented. In the design, antenna and mixer are combined into an entity, based on the technology in which millimeter-wave horn antenna arrays have been fabricated in silicon wafers. It consists of a set of forward- and backward-looking horns made with a set of silicon wafers. The front side is used to receive incoming signal, and the back side is used to feed local oscillator signal. Intermediate frequency is led out from the side of the array. Signal received by the horn array is picked up by antenna probes suspended on thin silicon-oxynitride membranes inside the horns. Mixer diodes will be located on the membranes inside the horns. Modeling of such an antenna-mixer-array design is done on a scaled model at microwave frequencies. The impedance matching, RF and LO isolation, and patterns of the array have been tested and analyzed.

  8. Physical analysis for designing nested-wire arrays on Z-pinch implosion

    International Nuclear Information System (INIS)

    Yang Zhenhua; Liu Quan; Ding Ning; Ning Cheng

    2005-01-01

    Z-pinch experiments have demonstrated that the X-ray power increases 40% with a nested-wire array compared with that with a single-layered wire array. The design of the nested-wire array on Z accelerator is studied through the implosion dynamics and the growth of RT instabilities. The analysis shows that the nested-wire array does not produce more total X-ray radiation energy than the single-layered wire array, but it obviously increases the X-ray power. The radius of the outer array of the nested-wire array could be determined based on the radius of the optimized single-layered. The masses of the outer and inner arrays could be determined by the implosion time of the nested-wire array, which is roughly the same as that of the single-layered wire array. Some suggestions are put forward which may be helpful in the nested-wire array design for Z-pinch experiments. (authors)

  9. Fully automated parallel oligonucleotide synthesizer

    Czech Academy of Sciences Publication Activity Database

    Lebl, M.; Burger, Ch.; Ellman, B.; Heiner, D.; Ibrahim, G.; Jones, A.; Nibbe, M.; Thompson, J.; Mudra, Petr; Pokorný, Vít; Poncar, Pavel; Ženíšek, Karel

    2001-01-01

    Roč. 66, č. 8 (2001), s. 1299-1314 ISSN 0010-0765 Institutional research plan: CEZ:AV0Z4055905 Keywords : automated oligonucleotide synthesizer Subject RIV: CC - Organic Chemistry Impact factor: 0.778, year: 2001

  10. Computer-aided engineering system for design of sequence arrays and lithographic masks

    Science.gov (United States)

    Hubbell, Earl A.; Morris, MacDonald S.; Winkler, James L.

    1996-01-01

    An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system (100) is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files (104) to design and/or generate lithographic masks (110).

  11. Design structure for in-system redundant array repair in integrated circuits

    Science.gov (United States)

    Bright, Arthur A.; Crumley, Paul G.; Dombrowa, Marc; Douskey, Steven M.; Haring, Rudolf A.; Oakland, Steven F.; Quellette, Michael R.; Strissel, Scott A.

    2008-11-25

    A design structure for repairing an integrated circuit during operation of the integrated circuit. The integrated circuit comprising of a multitude of memory arrays and a fuse box holding control data for controlling redundancy logic of the arrays. The design structure provides the integrated circuit with a control data selector for passing the control data from the fuse box to the memory arrays; providing a source of alternate control data, external of the integrated circuit; and connecting the source of alternate control data to the control data selector. The design structure further passes the alternate control data from the source thereof, through the control data selector and to the memory arrays to control the redundancy logic of the memory arrays.

  12. A Compact Design of Planar Array Antenna with Fractal Elements for Future Generation Applications

    DEFF Research Database (Denmark)

    Ojaroudiparchin, Naser; Shen, Ming; Pedersen, Gert F.

    2016-01-01

    In this paper, a planar phased array fractal antenna for the future fifth generation (5G) applications is presented. The proposed array antenna is designed to operate at 22 GHz. 64 patch antenna elements with coaxial-probe feeds have been used for the proposed design. The antenna elements are based...... on Vicsek fractal geometry where the third iteration patches operate over a wide bandwidth and contribute to improve the efficiency and realized gain performance. The designed planar array has more than 22 dB realized gain and -0.3 dB total efficiency when its beam is tilted to 0 degrees elevation...

  13. A design concept for an MMIC (Monolithic Microwave Integrated Circuit) microstrip phased array

    Science.gov (United States)

    Lee, Richard Q.; Smetana, Jerry; Acosta, Roberto

    1987-01-01

    A conceptual design for a microstrip phased array with monolithic microwave integrated circuit (MMIC) amplitude and phase controls is described. The MMIC devices used are 20 GHz variable power amplifiers and variable phase shifters recently developed by NASA contractors for applications in future Ka proposed design, which concept is for a general NxN element array of rectangular lattice geometry. Subarray excitation is incorporated in the MMIC phased array design to reduce the complexity of the beam forming network and the number of MMIC components required.

  14. Design and optimization of a self-developing single axis tracking PV array

    International Nuclear Information System (INIS)

    Colozza, A.J.

    1992-01-01

    This paper reports on a study performed in order to design a tracking PV array and optimize the design for maximum specific power. The design considerations were minimal deployment time, high reliability and small stowage volume. The array design was self-deployable, from a compact stowage configuration, using a passive pressurized gas deployment mechanism. The array structural components consist of a combination of beams, columns and cables used to deploy and orient a flexible PV blanket. Each structural component of the design was analyzed to determine the size necessary to withstand the various forces it would be subjected to. An optimization was performed to determine the array dimensions and blanket geometry which produce the maximum specific power

  15. Mechanical Design and Development of TES Bolometer Detector Arrays for the Advanced ACTPol Experiment

    Science.gov (United States)

    Ward, Jonathan T.; Austermann, Jason; Beall, James A.; Choi, Steve K.; Crowley, Kevin T.; Devlin, Mark J.; Duff, Shannon M.; Gallardo, Patricio M.; Henderson, Shawn W.; Ho, Shuay-Pwu Patty; hide

    2016-01-01

    The next generation Advanced ACTPol (AdvACT) experiment is currently underway and will consist of four Transition Edge Sensor (TES) bolometer arrays, with three operating together, totaling 5800 detectors on the sky. Building on experience gained with the ACTPol detector arrays, AdvACT will utilize various new technologies, including 150 mm detector wafers equipped with multichroic pixels, allowing for a more densely packed focal plane. Each set of detectors includes a feedhorn array of stacked silicon wafers which form a spline pro le leading to each pixel. This is then followed by a waveguide interface plate, detector wafer, back short cavity plate, and backshort cap. Each array is housed in a custom designed structure manufactured from high purity copper and then gold plated. In addition to the detector array assembly, the array package also encloses cryogenic readout electronics. We present the full mechanical design of the AdvACT high frequency (HF) detector array package along with a detailed look at the detector array stack assemblies. This experiment will also make use of extensive hardware and software previously developed for ACT, which will be modi ed to incorporate the new AdvACT instruments. Therefore, we discuss the integration of all AdvACT arrays with pre-existing ACTPol infrastructure.

  16. Design and Analysis Tools for Deployable Solar Array Systems, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Large, lightweight, deployable solar array structures have been identified as a key enabling technology for NASA with analysis and design of these structures being...

  17. Design of Robust Adaptive Array Processors for Non-Stationary Ocean Environments

    National Research Council Canada - National Science Library

    Wage, Kathleen E

    2009-01-01

    The overall goal of this project is to design adaptive array processing algorithms that have good transient performance, are robust to mismatch, work with low sample support, and incorporate waveguide...

  18. Design and Analysis Tools for Deployable Solar Array Systems, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Large, lightweight, deployable solar array structures have been identified as a key enabling technology for NASA with analysis and design of these structures being...

  19. Proceedings of the Flat-Plate Solar Array Project Research Forum on the Design of Flat-Plate Photovoltaic Arrays for Central Stations

    Science.gov (United States)

    1983-01-01

    The Flat Plate Solar Array Project, focuses on advancing technologies relevant to the design and construction of megawatt level central station systems. Photovoltaic modules and arrays for flat plate central station or other large scale electric power production facilities require the establishment of a technical base that resolves design issues and results in practical and cost effective configurations. Design, qualification and maintenance issues related to central station arrays derived from the engineering and operating experiences of early applications and parallel laboratory reserch activities are investigated. Technical issues are examined from the viewpoint of the utility engineer, architect/engineer and laboratory researcher. Topics on optimum source circuit designs, module insulation design for high system voltages, array safety, structural interface design, measurements, and array operation and maintenance are discussed.

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

    Directory of Open Access Journals (Sweden)

    Michael A Cook

    Full Text Available 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.

  1. Low power and reliable SRAM memory cell and array design

    CERN Document Server

    Ishibashi, Koichiro

    2011-01-01

    Success in the development of recent advanced semiconductor device technologies is due to the success of SRAM memory cells. This book addresses various issues for designing SRAM memory cells for advanced CMOS technology. To study LSI design, SRAM cell design is the best materials subject because issues about variability, leakage and reliability have to be taken into account for the design.

  2. Practical Consideration Factors to Design Array Configuration of Direction Finding System for Airborne Signal Intelligence

    Directory of Open Access Journals (Sweden)

    Jong-Hwan Lee

    2018-01-01

    Full Text Available Airborne signal intelligence (SIGINT systems must be capable of locating radio signal sources. Direction finding (DF to support this capability is an important factor. There are some practical considerations to be taken when designing the array configuration of a DF system for airborne SIGINT systems. This paper summarizes the practical factors when designing the array configuration of the DF system for airborne SIGINT. In particular, it focuses on four areas: antenna consideration factors when installing the DF system for airborne SIGINT from a practical point of view, array configuration methods for airborne communications intelligence and electronic intelligence, and a numerical analysis to select the optimum antenna position for airborne SIGINT.

  3. Design and testing of a combustion-heated nineteen-converter SAVTEC array

    International Nuclear Information System (INIS)

    Nyren, T.; Fitzpatrick, G.O.; Korringa, M.; McVey, J.; Sahines, T.

    1984-01-01

    The SAVTEC (Self-Adjusting Versatile Thermionic Energy Converter) is a new design approach for achieving very close (<12μ) interelectrode spacing in a thermionic converter. Techniques were developed for fabricating an array of nineteen SAVTEC converters. The array was incorporated in an SiC protective ''hot shell'' which also served as a radiant heat source for the emitter of each converter. The completed assembly was tested with a specially constructed combustion heat source. Electric output was generated by sixteen of the nineteen converters, despite poor thermal contact in a cooling block, which resulted in high collector temperatures. Details of the array design and test results are described

  4. A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Chen Feng

    2010-10-01

    Full Text Available Abstract Background Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators. Results Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals and Plasmodium falciparum (a related parasite responsible for severe human malaria, we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at

  5. 2D array design based on Fermat spiral for ultrasound imaging.

    Science.gov (United States)

    Martínez-Graullera, Oscar; Martín, Carlos J; Godoy, Gregorio; Ullate, Luis G

    2010-02-01

    The main challenge faced by 3D ultrasonic imaging with 2D array transducers is the large number of elements required to achieve an acceptable level of quality in the images. Therefore, the optimisation of the array layout, in order to reduce the number of active elements in the aperture, has been a research topic in the last years. Nowadays, array technology has made viable the production of 2D arrays with larger flexibility on elements size, shape and position, allowing to study other configurations different to the classical matrix organisation, such as circular, archimedes spiral or polygonal layout between others. In this work, the problem of designing an imaging system array with large apertures and a very limited number of active elements (N(e)=128 and N(e)=256) using the Fermat spiral layout has been studied. As summary, a general discussion about the most interesting cases is presented.

  6. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

    DEFF Research Database (Denmark)

    Lou, Chenguang; Christensen, Niels Johan; Martos Maldonado, Manuel Cristo

    2017-01-01

    by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex......, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12nm) in solution was revealed to be independent of concentration. The topological folding...

  7. Peptide-LNA oligonucleotide conjugates

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Hansen, Lykke Haastrup; Vester, Birte

    2013-01-01

    properties, peptides were introduced into oligonucleotides via a 2'-alkyne-2'-amino-LNA scaffold. Derivatives of methionine- and leucine-enkephalins were chosen as model peptides of mixed amino acid content, which were singly and doubly incorporated into LNA/DNA strands using highly efficient copper......(i)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry. DNA/RNA target binding affinity and selectivity of the resulting POCs were improved in comparison to LNA/DNA mixmers and unmodified DNA controls. This clearly demonstrates that internal attachment of peptides to oligonucleotides can significantly...

  8. Design of a Compact Wideband Antenna Array for Microwave Imaging Applications

    Directory of Open Access Journals (Sweden)

    J. Puskely

    2013-12-01

    Full Text Available In the paper, wideband antenna arrays aimed at microwave imaging applications and SAR applications operating at Ka band were designed. The antenna array feeding network is realized by a low-loss SIW technology. Moreover, we have replaced the large feed network comprised of various T and Y junctions by a simple broadband network of compact size to more reduce losses in the substrate integrated waveguide and also save space on the PCB. The designed power 8-way divider is complemented by a wideband substrate integrated waveguide to a grounded coplanar waveguide transition and directly connected to the antenna elements. The measured results of antenna array are consistent with our simulation. Obtained results of the developed array demonstrated improvement compared to previously developed binary feed networks with microstrip or SIW splitters.

  9. Design and analysis of high gain array antenna for wireless communication applications

    Directory of Open Access Journals (Sweden)

    Sri Jaya LAKSHMI

    2015-05-01

    Full Text Available The array of antennas generally used for directing the radiated power towards a desired angular sector. Arrays can be used to synthesize a required pattern that cannot be achieved with a single element. The geometrical arrangement, number of elements, phases of the array elements and relative amplitudes depends on the angular pattern. This paper is focused on the issues related to the design and implementation of 4×1 array microstrip antenna with aperture coupled corporate feed for wireless local area network applications. Parametric analysis with change in element spacing is attempted in this work to understand the directional characteristics of the radiation pattern. Gain of more than 14 db and the efficiency more than 93% is achieved from the current design at desired frequency band.

  10. Electronic Structures of LNA Phosphorothioate Oligonucleotides

    DEFF Research Database (Denmark)

    Bohr, Henrik G.; Shim, Irene; Stein, Cy

    2017-01-01

    Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces...

  11. Low Complexity Beampattern Design in MIMO Radars Using Planar Array

    KAUST Repository

    Bouchoucha, Taha; Ahmed, Sajid; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim

    2015-01-01

    is then used to generate actual transmitted waveforms. Both steps require constrained optimization, therefore, use iterative and expensive algorithms. In this paper, we provide a closed-form solution to design covariance matrix for the given beampattern using

  12. Highly Directive Reflect Array Antenna Design for Wireless Power Transfer

    Science.gov (United States)

    2017-04-14

    61102F 6.  AUTHOR(S) Siddhartha Prakash Duttagupta 5d.  PROJECT NUMBER 5e.  TASK NUMBER 5f.   WORK UNIT NUMBER 7.  PERFORMING ORGANIZATION NAME(S) AND...this study by Asian Office of Aerospace Research and Development (AOARD), USA 06 March, 2017 DISTRIBUTION A. Approved for public release...D parabolic design. These include suitability for manufacturing, ease of testing, and flexibility of RAA design for different frequencies

  13. Design of 3x3 Focusing Array for Heavy Ion Driver Final Report on CRADA TC-02082-04

    Energy Technology Data Exchange (ETDEWEB)

    Martovetsky, N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-09-28

    This memo presents a design of a 3x3 quadrupole array for HIF. It contains 3 D magnetic field computations of the array build with racetrack coils with and without different shields. It is shown that it is possible to have a low error magnetic field in the cells and shield the stray fields to acceptable levels. The array design seems to be a practical solution to any size array for future multi-beam heavy ion fusion drivers.

  14. Magnetic design consideration of a Magnetic Lead Screw with Halbach Array

    DEFF Research Database (Denmark)

    Holm, Rasmus Koldborg; Berg, Nick Ilsø; Rasmussen, Peter Omand

    This paper presents the novel design of a Magnetic Lead Screw (MLS) with magnetic thread of Halbach Arrays. The MLS where designed and build, tests indicated a stall force which where 12 % lower than calculated in 3D FE. This is explained by demagnetization of the magnet during stall, the behavio...

  15. Design considerations on a sparse array antenna for Ka-band spaceborne SAR applications

    NARCIS (Netherlands)

    Jacobs, S.; Bekers, D.; Monni, S.; Otten, M.; Van Rossum, W.; Gerini, G.; Germani, C.; Fortini, D.; Toso, G.

    2015-01-01

    This contribution addresses the problem of designing a sparse active array antenna for spaceborne SAR applications at Ka-band. The main driver for the design is limiting the recurring manufacturing costs associated to the number of active modules, while preserving main performance and insuring a

  16. Thermodynamics of Oligonucleotide Duplex Melting

    Science.gov (United States)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-01-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply…

  17. Robust design of microlenses arrays employing dielectric resonators metasurfaces

    NARCIS (Netherlands)

    Silvestri, F.; Gerini, G.; Bäumer, S.M.B.

    2017-01-01

    In the last years, much interest has grown around the concept of optical surfaces employing high contrast dielectric resonators. However, a systematic approach for the design of this optical surfaces under particular requirements has never been proposed. In this contribution, we describe this

  18. Analysis and design of arrayed waveguide gratings with MMI couplers.

    Science.gov (United States)

    Munoz, P; Pastor, D; Capmany, J

    2001-09-24

    We present an extension of the AWG model and design procedure described in [1] to incorporate multimode interference, MMI, couplers. For the first time to our knowledge, a closed formula for the passing bands bandwidth and crosstalk estimation plots are derived.

  19. Design of Small CRPA Arrays with Circular Microstrip Loops for Electromagnetically Coupled Feed

    Directory of Open Access Journals (Sweden)

    Jun Hur

    2018-04-01

    Full Text Available This paper proposes a design of small controlled reception pattern antenna (CRPA arrays using circular microstrip loops with frequencyinsensitive characteristics. The proposed array consists of seven identical upper and lower circular loops that are electromagnetically coupled, which results in a frequency-insensitive behavior. To demonstrate the feasibility of the proposed feeding mechanism, the proposed array is fabricated, and its antenna characteristics are measured in a full-anechoic chamber. The operating principle of the proposed feeding mechanism is then interpreted using an equivalent circuit model, and the effectiveness of the circular loop shape is demonstrated by calculating near electromagnetic fields in proximity to the radiator. The results confirm that the proposed feeding mechanism is suitable to have frequency-insensitive behavior and induces strong electric and magnetic field strengths for higher radiation gain in extremely small antenna arrays.

  20. Design of UAV-Embedded Microphone Array System for Sound Source Localization in Outdoor Environments

    Directory of Open Access Journals (Sweden)

    Kotaro Hoshiba

    2017-11-01

    Full Text Available In search and rescue activities, unmanned aerial vehicles (UAV should exploit sound information to compensate for poor visual information. This paper describes the design and implementation of a UAV-embedded microphone array system for sound source localization in outdoor environments. Four critical development problems included water-resistance of the microphone array, efficiency in assembling, reliability of wireless communication, and sufficiency of visualization tools for operators. To solve these problems, we developed a spherical microphone array system (SMAS consisting of a microphone array, a stable wireless network communication system, and intuitive visualization tools. The performance of SMAS was evaluated with simulated data and a demonstration in the field. Results confirmed that the SMAS provides highly accurate localization, water resistance, prompt assembly, stable wireless communication, and intuitive information for observers and operators.

  1. Design of UAV-Embedded Microphone Array System for Sound Source Localization in Outdoor Environments †

    Science.gov (United States)

    Hoshiba, Kotaro; Washizaki, Kai; Wakabayashi, Mizuho; Ishiki, Takahiro; Bando, Yoshiaki; Gabriel, Daniel; Nakadai, Kazuhiro; Okuno, Hiroshi G.

    2017-01-01

    In search and rescue activities, unmanned aerial vehicles (UAV) should exploit sound information to compensate for poor visual information. This paper describes the design and implementation of a UAV-embedded microphone array system for sound source localization in outdoor environments. Four critical development problems included water-resistance of the microphone array, efficiency in assembling, reliability of wireless communication, and sufficiency of visualization tools for operators. To solve these problems, we developed a spherical microphone array system (SMAS) consisting of a microphone array, a stable wireless network communication system, and intuitive visualization tools. The performance of SMAS was evaluated with simulated data and a demonstration in the field. Results confirmed that the SMAS provides highly accurate localization, water resistance, prompt assembly, stable wireless communication, and intuitive information for observers and operators. PMID:29099790

  2. Design of UAV-Embedded Microphone Array System for Sound Source Localization in Outdoor Environments.

    Science.gov (United States)

    Hoshiba, Kotaro; Washizaki, Kai; Wakabayashi, Mizuho; Ishiki, Takahiro; Kumon, Makoto; Bando, Yoshiaki; Gabriel, Daniel; Nakadai, Kazuhiro; Okuno, Hiroshi G

    2017-11-03

    In search and rescue activities, unmanned aerial vehicles (UAV) should exploit sound information to compensate for poor visual information. This paper describes the design and implementation of a UAV-embedded microphone array system for sound source localization in outdoor environments. Four critical development problems included water-resistance of the microphone array, efficiency in assembling, reliability of wireless communication, and sufficiency of visualization tools for operators. To solve these problems, we developed a spherical microphone array system (SMAS) consisting of a microphone array, a stable wireless network communication system, and intuitive visualization tools. The performance of SMAS was evaluated with simulated data and a demonstration in the field. Results confirmed that the SMAS provides highly accurate localization, water resistance, prompt assembly, stable wireless communication, and intuitive information for observers and operators.

  3. Micro solar concentrators: Design and fabrication for microcells arrays

    Science.gov (United States)

    Jutteau, Sébastien; Paire, Myriam; Proise, Florian; Lombez, Laurent; Guillemoles, Jean-François

    2015-09-01

    In this work we look at a micro-concentrating system adapted to a new type of concentrator photovoltaic material, well known for flate-plate applications, Cu(In,Ga)Se2. Cu(In,Ga)Se2 solar cells are polycrystalline thin film devices that can be deposited by a variety of techniques. We proposed to use a microcell architecture [1], [2], with lateral dimensions varying from a few μm to hundreds of μm, to adapt the film cell to concentration conditions. A 5% absolute efficiency increase on Cu(In,Ga)Se2 microcells at 475 suns has been observed for a final efficiency of 21.3%[3]. We study micro-concentrating systems adapted to the low and middle concentration range, where thin film concentrator cells will lean to substrate fabrication simplification and cost savings. Our study includes optical design, fabrication and experimental tests of prototypes.

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

    Science.gov (United States)

    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.

  5. Challenges to oligonucleotides-based therapeutics for Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Goyenvalle Aurélie

    2011-02-01

    Full Text Available Abstract Antisense oligonucleotides are short nucleic acids designed to bind to specific messenger RNAs in order to modulate splicing patterns or inhibit protein translation. As such, they represent promising therapeutic tools for many disorders and have been actively developed for more than 20 years as a form of molecular medicine. Although significant progress has been made in developing these agents as drugs, they are yet not recognized as effective therapeutics and several hurdles remain to be overcome. Within the last few years, however, the prospect of successful oligonucleotides-based therapies has moved a step closer, in particular for Duchenne muscular dystrophy. Clinical trials have recently been conducted for this myopathy, where exon skipping is being used to achieve therapeutic outcomes. In this review, the recent developments and clinical trials using antisense oligonucleotides for Duchenne muscular dystrophy are discussed, with emphasis on the challenges ahead for this type of therapy, especially with regards to delivery and regulatory issues.

  6. Optimization of ultrasonic arrays design and setting using a differential evolution

    International Nuclear Information System (INIS)

    Puel, B.; Chatillon, S.; Calmon, P.; Lesselier, D.

    2011-01-01

    Optimization of both design and setting of phased arrays could be not so easy when they are performed manually via parametric studies. An optimization method based on an Evolutionary Algorithm and numerical simulation is proposed and evaluated. The Randomized Adaptive Differential Evolution has been adapted to meet the specificities of the non-destructive testing applications. In particular, the solution of multi-objective problems is aimed at with the implementation of the concept of pareto-optimal sets of solutions. The algorithm has been implemented and connected to the ultrasonic simulation modules of the CIVA software used as forward model. The efficiency of the method is illustrated on two realistic cases of application: optimization of the position and delay laws of a flexible array inspecting a nozzle, considered as a mono-objective problem; and optimization of the design of a surrounded array and its delay laws, considered as a constrained bi-objective problem. (authors)

  7. Recommendations of the Oligonucleotide Safety Working Group's Formulated Oligonucleotide Subcommittee for the Safety Assessment of Formulated Oligonucleotide-Based Therapeutics.

    Science.gov (United States)

    Marlowe, Jennifer L; Akopian, Violetta; Karmali, Priya; Kornbrust, Douglas; Lockridge, Jennifer; Semple, Sean

    2017-08-01

    The use of lipid formulations has greatly improved the ability to effectively deliver oligonucleotides and has been instrumental in the rapid expansion of therapeutic development programs using oligonucleotide drugs. However, the development of such complex multicomponent therapeutics requires the implementation of unique, scientifically sound approaches to the nonclinical development of these drugs, based upon a hybrid of knowledge and experiences drawn from small molecule, protein, and oligonucleotide therapeutic drug development. The relative paucity of directly applicable regulatory guidance documents for oligonucleotide therapeutics in general has resulted in the generation of multiple white papers from oligonucleotide drug development experts and members of the Oligonucleotide Safety Working Group (OSWG). The members of the Formulated Oligonucleotide Subcommittee of the OSWG have utilized their collective experience working with a variety of formulations and their associated oligonucleotide payloads, as well as their insights into regulatory considerations and expectations, to generate a series of consensus recommendations for the pharmacokinetic characterization and nonclinical safety assessment of this unique class of therapeutics. It should be noted that the focus of Subcommittee discussions was on lipid nanoparticle and other types of particulate formulations of therapeutic oligonucleotides and not on conjugates or other types of modifications of oligonucleotide structure intended to facilitate delivery.

  8. Effects of design on cost of flat-plate solar photovoltaic arrays for terrestrial central station power applications

    Science.gov (United States)

    Tsou, P.; Stolte, W.

    1978-01-01

    The paper examines the impact of module and array designs on the balance-of-plant costs for flat-plate terrestrial central station power applications. Consideration is given to the following types of arrays: horizontal, tandem, augmented, tilt adjusted, and E-W tracking. The life-cycle cost of a 20-year plant life serves as the costing criteria for making design and cost tradeoffs. A tailored code of accounts is developed for determining consistent photovoltaic power plant costs and providing credible photovoltaic system cost baselines for flat-plate module and array designs by costing several varying array design approaches.

  9. Improved Titanium Billet Inspection Sensitivity through Optimized Phased Array Design, Part I: Design Technique, Modeling and Simulation

    International Nuclear Information System (INIS)

    Lupien, Vincent; Hassan, Waled; Dumas, Philippe

    2006-01-01

    Reductions in the beam diameter and pulse duration of focused ultrasound for titanium inspections are believed to result in a signal-to-noise ratio improvement for embedded defect detection. It has been inferred from this result that detection limits could be extended to smaller defects through a larger diameter, higher frequency transducer resulting in a reduced beamwidth and pulse duration. Using Continuum Probe Designer TM (Pat. Pending), a transducer array was developed for full coverage inspection of 8 inch titanium billets. The main challenge in realizing a large aperture phased array transducer for billet inspection is ensuring that the number of elements remains within the budget allotted by the driving electronics. The optimization technique implemented by Continuum Probe Designer TM yields an array with twice the aperture but the same number of elements as existing phased arrays for the same application. The unequal area element design was successfully manufactured and validated both numerically and experimentally. Part I of this two-part series presents the design, simulation and modeling steps, while Part II presents the experimental validation and comparative study to multizone

  10. Implementation of the first student-designed PV array in Canada

    International Nuclear Information System (INIS)

    Hadlock, C.; DeLoyde, J.; Dhir, T.

    2004-01-01

    This paper is a culmination of a 2-year project involving students, faculty, staff member, and private industry. Solar Technology Education Project (STEP) became the first student-led group to successfully install a 36-panel photovoltaic (PV) array on a Canadian University campus. The fundraising, design, and assembly of the PV array was entirely student driven. The project was completed in January 2004 with the installation of a 2 kW photovoltaic grid-tied array mounted to the roof of the University of Waterloo's Federation Hall, the largest student-run pub in North America. The photovoltaic array was a demonstration project to raise awareness about solar technology and the need for energy efficiency in buildings. It took two years to complete the project, which was implemented in three phases. The first phase was aimed at raising the required capital. The second phase included design and fabrication of the array. The third phase, still ongoing today, is the community outreach phase, which involves educating the surrounding communities about the project, solar technology, and the role of individuals in combating global warming. This paper examines the steps required for the implementation of a successful educational photovoltaic project, using the students' experience as a roadmap. A section highlighting what's next for STEP is also presented as the students attempt to build on the momentum from the project. The aim is to launch a solar thermal project on another University of Waterloo building to move one step closer to the ultimate goal of a sustainable campus

  11. Spatio-spectral color filter array design for optimal image recovery.

    Science.gov (United States)

    Hirakawa, Keigo; Wolfe, Patrick J

    2008-10-01

    In digital imaging applications, data are typically obtained via a spatial subsampling procedure implemented as a color filter array-a physical construction whereby only a single color value is measured at each pixel location. Owing to the growing ubiquity of color imaging and display devices, much recent work has focused on the implications of such arrays for subsequent digital processing, including in particular the canonical demosaicking task of reconstructing a full color image from spatially subsampled and incomplete color data acquired under a particular choice of array pattern. In contrast to the majority of the demosaicking literature, we consider here the problem of color filter array design and its implications for spatial reconstruction quality. We pose this problem formally as one of simultaneously maximizing the spectral radii of luminance and chrominance channels subject to perfect reconstruction, and-after proving sub-optimality of a wide class of existing array patterns-provide a constructive method for its solution that yields robust, new panchromatic designs implementable as subtractive colors. Empirical evaluations on multiple color image test sets support our theoretical results, and indicate the potential of these patterns to increase spatial resolution for fixed sensor size, and to contribute to improved reconstruction fidelity as well as significantly reduced hardware complexity.

  12. An unified approach for the design of focal-plane arrays in satellite communication

    NARCIS (Netherlands)

    Zamanifekri, A.; Smolders, A.B.

    2012-01-01

    The aim of this paper is to present a hybrid approach for designing focal plane arrays using commercially available software, considering the fact that the main trade-off in the EM simulation is the accuracy versus computational power. The presented approach is hybrid method based on FDTD/PO. The

  13. Direct Closed-Form Design of Finite Alphabet Constant Envelope Waveforms for Planar Array Beampatterns

    KAUST Repository

    Bouchoucha, Taha

    2015-01-01

    them hard to use in practice especially for real time radar applications. In this paper, we provide a closed-form solution to design the covariance matrix for a given beampattern in the three dimensional space using planar arrays, which is then used

  14. Design of a ring resonator-based optical beam forming network for phased array receive antennas

    NARCIS (Netherlands)

    van 't Klooster, J.W.J.R.; Roeloffzen, C.G.H.; Meijerink, Arjan; Zhuang, L.; Marpaung, D.A.I.; van Etten, Wim; Heideman, Rene; Leinse, Arne; Schippers, H.; Verpoorte, J.; Wintels, M.

    2008-01-01

    A novel squint-free ring resonator-based optical beam forming network (OBFN) for phased array antennas (PAA) is proposed. It is intended to provide broadband connectivity to airborne platforms via geostationary satellites. In this paper, we present the design of the OBFN and its control system. Our

  15. Mechanical design of a low concentration ratio solar array for a space station application

    Science.gov (United States)

    Biss, M. S.; Hsu, L.

    1983-01-01

    This paper describes a preliminary study and conceptual design of a low concentration ratio solar array for a space station application with approximately a 100 kW power requirement. The baseline design calls for a multiple series of inverted, truncated, pyramidal optical elements with a geometric concentration ratio (GCR) of 6. It also calls for low life cycle cost, simple on-orbit maintainability, 1984 technology readiness date, and gallium arsenide (GaAs) of silicon (Si) solar cell interchangeability. Due to the large area needed to produce the amount of power required for the baseline space station, a symmetrical wing design, making maximum use of the commonality of parts approach, was taken. This paper will describe the mechanical and structural design of a mass-producible solar array that is very easy to tailor to the needs of the individual user requirement.

  16. Design of a dielectric resonator receive array at 7 Tesla using detunable ceramic resonators

    Science.gov (United States)

    Ruytenberg, Thomas; Webb, Andrew G.

    2017-11-01

    Ceramic-based dielectric resonators can be used for high frequency magnetic resonance imaging and microscopy. When used as elements in a transmit array, the intrinsically low inter-element coupling allows flexibility in designing different geometric arrangements for different regions-of-interest. However, without being able to detune such resonators, they cannot be used as elements in a receive-only array. Here, we propose and implement a method, based on mode-disruption, for detuning ceramic-based dielectric resonators to enable them to be used as receive-only elements.

  17. Impacts on the Electrical System Economics from Critical Design Factors of Wave Energy Converters and Arrays

    OpenAIRE

    Sharkey, Fergus; Conlon, Michael; Gaughan, Kevin

    2013-01-01

    It is expected that ultimately, like offshore wind farms, electrical systems will make up to a quarter of the overall Capex of wave farms. This is a significant element of cost and consideration must be taken in the design of both individual wave energy converters (WECs) and arrays of WECs to ensure that these costs can be minimised. In a worst case scenario design decisions could increase the cost of the electrical system by several orders and ultimately make the technology uncompetitive. ...

  18. Design and Deployment of a Multichroic Polarimeter Array on the Atacama Cosmology Telescope

    Science.gov (United States)

    Datta, R.; Austermann, J.; Beall, J. A.; Becker, D.; Coughlin, K. P.; Duff, S. M.; Gallardo, P.A.; Grace, E.; Hasselfield, M.; Henderson, S. W.; hide

    2016-01-01

    We present the design and the preliminary on-sky performance with respect to beams and pass bands of a multichroic polarimeter array covering the 90 and 146 GHz cosmic microwave background bands and its enabling broad-band optical system recently deployed on the Atacama Cosmology Telescope (ACT). The constituent pixels are feedhorn-coupled multichroic polarimeters fabricated at NIST. This array is coupled to the ACT telescope via a set of three silicon lenses incorporating novel broad-band metamaterial anti-reflection coatings. This receiver represents the first multichroic detector array deployed for a CMB experiment and paves the way for the extensive use of multichroic detectors and broad-band optical systems in the next generation of CMB experiments.

  19. Design and Deployment of a Multichroic Polarimeter Array on the Atacama Cosmology Telescope

    Science.gov (United States)

    Datta, R.; Austermann, J.; Beall, J. A.; Becker, D.; Coughlin, K. P.; Duff, S. M.; Gallardo, P. A.; Grace, E.; Hasselfield, M.; Henderson, S. W.; Hilton, G. C.; Ho, S. P.; Hubmayr, J.; Koopman, B. J.; Lanen, J. V.; Li, D.; McMahon, J.; Munson, C. D.; Nati, F.; Niemack, M. D.; Page, L.; Pappas, C. G.; Salatino, M.; Schmitt, B. L.; Schillaci, A.; Simon, S. M.; Staggs, S. T.; Stevens, J. R.; Vavagiakis, E. M.; Ward, J. T.; Wollack, E. J.

    2016-08-01

    We present the design and the preliminary on-sky performance with respect to beams and passbands of a multichroic polarimeter array covering the 90 and 146 GHz cosmic microwave background bands and its enabling broad-band optical system recently deployed on the Atacama Cosmology Telescope (ACT). The constituent pixels are feedhorn-coupled multichroic polarimeters fabricated at NIST. This array is coupled to the ACT telescope via a set of three silicon lenses incorporating novel broad-band metamaterial anti-reflection coatings. This receiver represents the first multichroic detector array deployed for a CMB experiment and paves the way for the extensive use of multichroic detectors and broad-band optical systems in the next generation of CMB experiments.

  20. Design of a Solar Motor Drive System Fed by a Direct-Connected Photovoltaic Array

    Directory of Open Access Journals (Sweden)

    AYDOGMUS, O.

    2012-08-01

    Full Text Available A solar motor pump drive system is modeled and simulated. The proposed drive system does not require any kind of energy storage system and dc-dc converter. The system is connected directly to a photovoltaic (PV array. Thus, a low cost solar system can be achieved. A vector controlled Permanent Magnet Synchronous Motor (PMSM is used as a solar motor to increase the efficiency of system. The motor is designed for a low rated voltage level about 24V. The hill climbing MPPT method is used for balanced the motor power and PV power to obtain a high efficiency. The results are performed by using MATLAB/SimPowerSystem blocks. In addition, the PV array is modeled to allow for the possibility of running as on-line adjustable in simulation environment without using lookup table. The performances of motor, MPPT and drive system are analyzed in different conditions as temperature and irradiation of PV array.

  1. Design and fabrication of magnetically functionalized flexible micropillar arrays for rapid and controllable microfluidic mixing

    KAUST Repository

    Zhou, BingPu; Xu, Wei; Syed, Ahad; Chau, Yeungyeung; Chen, Longqing; Chew, Basil; Yassine, Omar; Wu, Xiaoxiao; Gao, Yibo; Zhang, Jingxian; Xiao, Xiao; Kosel, Jü rgen; Zhang, Xixiang; Yao, Zhaohui; Wen, Weijia

    2015-01-01

    Magnetically functionalized PDMS-based micropillar arrays have been successfully designed, fabricated and implanted for controllable microfluidic mixing. The arrangement of PDMS micropillar arrays inside the microchannel can be flexibly controlled by an external magnetic field. As a consequence, the flow fields inside the microchannel can be regulated at will via magnetic activation conveniently. When a microchannel is implanted with such micropillar arrays, two microstreams can be mixed easily and controllably upon the simple application of an on/off magnetic signal. Mixing efficiencies based on micropillar arrays with different densities were investigated and compared. It was found that micropillar arrays with higher density (i.e. smaller pillar pitch) would render better mixing performance. Our microfluidic system is capable of generating highly reproducible results within many cycles of mixing/non-mixing conversion. We believe that the simple mixing-triggering method together with rapid and controllable mixing control will be extraordinarily valuable for various biological or chemical applications in the future. This journal is © The Royal Society of Chemistry 2015.

  2. Design and fabrication of magnetically functionalized flexible micropillar arrays for rapid and controllable microfluidic mixing

    KAUST Repository

    Zhou, BingPu

    2015-03-25

    Magnetically functionalized PDMS-based micropillar arrays have been successfully designed, fabricated and implanted for controllable microfluidic mixing. The arrangement of PDMS micropillar arrays inside the microchannel can be flexibly controlled by an external magnetic field. As a consequence, the flow fields inside the microchannel can be regulated at will via magnetic activation conveniently. When a microchannel is implanted with such micropillar arrays, two microstreams can be mixed easily and controllably upon the simple application of an on/off magnetic signal. Mixing efficiencies based on micropillar arrays with different densities were investigated and compared. It was found that micropillar arrays with higher density (i.e. smaller pillar pitch) would render better mixing performance. Our microfluidic system is capable of generating highly reproducible results within many cycles of mixing/non-mixing conversion. We believe that the simple mixing-triggering method together with rapid and controllable mixing control will be extraordinarily valuable for various biological or chemical applications in the future. This journal is © The Royal Society of Chemistry 2015.

  3. Design of micro, flexible light-emitting diode arrays and fabrication of flexible electrodes

    International Nuclear Information System (INIS)

    Gao, Dan; Wang, Weibiao; Liang, Zhongzhu; Liang, Jingqiu; Qin, Yuxin; Lv, Jinguang

    2016-01-01

    In this study, we design micro, flexible light-emitting diode (LED) array devices. Using theoretical calculations and finite element simulations, we analyze the deformation of the conventional single electrode bar. Through structure optimization, we obtain a three-dimensional (3D), chain-shaped electrode structure, which has a greater bending degree. The optimized electrodes not only have a bigger bend but can also be made to spin. When the supporting body is made of polydimethylsiloxane (PDMS), the maximum bending degree of the micro, flexible LED arrays (4  ×  1 arrays) was approximately 230 µ m; this was obtained using the finite element method. The device (4  ×  1 arrays) can stretch to 15%. This paper describes the fabrication of micro, flexible LED arrays using microelectromechancial (MEMS) technology combined with electroplating technology. Specifically, the isolated grooves are made by dry etching which can isolate and protect the light-emitting units. A combination of MEMS technology and wet etching is used to fabricate the large size spacing. (paper)

  4. Design Concept of Array ECT Sensor for Steam Generator Tubing Inspection

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Chan Hee; Lee, Tae Hun; Yoo, Hyun Ju [Korea Hydro and Nuclear Power Co. Ltd. CRI, Daejeon (Korea, Republic of)

    2015-05-15

    The eddy current testing, which is one of the nondestructive examination methods, is widely used for the inspection of heat exchangers including steam generator tubing in the nuclear power plant. It uses electromagnetic induction to detect flaws in conductive materials. Two types of eddy current probes are conventionally used for the inspection of steam generator tubing according to the main purpose. One is the bobbin probe technology and the other is the rotating probe. During the inspection, they have restrictions for the flaw detection or the inspection speed. An array probe can be alternative to the bobbin and rotating probes. The design concept of array coils with high sensitivity is described in this paper. It is expected that the eddy current testing using this type of array sensors may provide high detectability and resolution for flaws in steam generator tubing. Eddy current technology has some barriers for the inspection of steam generator tubing in the nuclear power plant. Bobbin probes offer poor circumferential crack detection and rotating probes are time and money consuming due to the mechanical rotation. Array probe inspection technique can replace bobbin and rotating probe techniques due to its sensitivity for flaw detection and inspection speed. In general, circular-shaped coils are considered in an array eddy current probe.

  5. The Implications of Encoder/Modulator/ Phased Array Designs for Future Broadband LEO Communications

    Science.gov (United States)

    Vanderaar, Mark; Jensen, Chris A.; Terry, John D.

    1997-01-01

    In this paper we summarize the effects of modulation and channel coding on the design of wide angle scan, broadband, phased army antennas. In the paper we perform several trade studies. First, we investigate the amplifier back-off requirement as a function of variability of modulation envelope. Specifically, we contrast constant and non-constant envelope modulations, as well as single and multiple carrier schemes. Additionally, we address the issues an(f concerns of using pulse shaping filters with the above modulation types. Second, we quantify the effects of beam steering on the quality of data, recovery using selected modulation techniques. In particular, we show that the frequency response of the array introduces intersymbol interference for broadband signals and that the mode of operation for the beam steering controller may introduce additional burst or random errors. Finally, we show that the encoder/modulator design must be performed in conjunction with the phased array antenna design.

  6. The design of a second harmonic tangential array interferometer for C-Mod

    International Nuclear Information System (INIS)

    Bretz, N.; Jobes, F.; Irby, J.

    1997-01-01

    A design for a tangential array interferometer for C-Mod operating at 1.06 and 0.53 μm is presented. This is a special type of two color interferometer in which a Nd:YAG laser is frequency doubled in a nonlinear crystal. Because the doubling efficiency is imperfect, two frequencies propagate collinearly through the plasma after which the 1.06 μm ray is doubled again mixing in the optical domain with the undoubled ray. The resulting interference is insensitive to path length but is affected by plasma dispersion in the usual way. A typical central fringe shift in C-Mod is expected to be 0.1 endash 1.0, but the absolute and relative accuracy in n e l measurements can be as high as in a conventional interferometer. This design uses a repetitively pulsed laser which is converted to a fan beam crossing the horizontal midplane. The chordal array is defined by internal retroreflectors on the C-Mod midplane which return the beam to the second doubler and a detector array. This interferometer design has beam diameters of a few millimeters and element spacings of a few centimeters, uses a repetitively pulsed, TEM 00 Nd:YAG laser, fiber optic beam transport, commercial components, and a compact optical design which minimizes port space requirements. An optical system design is presented which is based on the performance of a tabletop prototype at Princeton Plasma Physics Laboratory. copyright 1997 American Institute of Physics

  7. The Medicinal Chemistry of Therapeutic Oligonucleotides.

    Science.gov (United States)

    Wan, W Brad; Seth, Punit P

    2016-11-10

    Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.

  8. Design and performance of single photon APD focal plane arrays for 3-D LADAR imaging

    Science.gov (United States)

    Itzler, Mark A.; Entwistle, Mark; Owens, Mark; Patel, Ketan; Jiang, Xudong; Slomkowski, Krystyna; Rangwala, Sabbir; Zalud, Peter F.; Senko, Tom; Tower, John; Ferraro, Joseph

    2010-08-01

    ×We describe the design, fabrication, and performance of focal plane arrays (FPAs) for use in 3-D LADAR imaging applications requiring single photon sensitivity. These 32 × 32 FPAs provide high-efficiency single photon sensitivity for three-dimensional LADAR imaging applications at 1064 nm. Our GmAPD arrays are designed using a planarpassivated avalanche photodiode device platform with buried p-n junctions that has demonstrated excellent performance uniformity, operational stability, and long-term reliability. The core of the FPA is a chip stack formed by hybridizing the GmAPD photodiode array to a custom CMOS read-out integrated circuit (ROIC) and attaching a precision-aligned GaP microlens array (MLA) to the back-illuminated detector array. Each ROIC pixel includes an active quenching circuit governing Geiger-mode operation of the corresponding avalanche photodiode pixel as well as a pseudo-random counter to capture per-pixel time-of-flight timestamps in each frame. The FPA has been designed to operate at frame rates as high as 186 kHz for 2 μs range gates. Effective single photon detection efficiencies as high as 40% (including all optical transmission and MLA losses) are achieved for dark count rates below 20 kHz. For these planar-geometry diffused-junction GmAPDs, isolation trenches are used to reduce crosstalk due to hot carrier luminescence effects during avalanche events, and we present details of the crosstalk performance for different operating conditions. Direct measurement of temporal probability distribution functions due to cumulative timing uncertainties of the GmAPDs and ROIC circuitry has demonstrated a FWHM timing jitter as low as 265 ps (standard deviation is ~100 ps).

  9. Design and Implementation of PIR-Array to Reduce Power Consumption for Iraq's Households

    Directory of Open Access Journals (Sweden)

    Nidhal Yousif Nasser

    2016-12-01

    Full Text Available The purpose of this study is to design and implement a model using PIR-sensors for motion detection to reduce the electrical power for designing smart home requirements for Iraq households. Reducing energy consumption of home appliances plays an important role in modern designs of smart homes. The PIR (passive infrared sensor has been designed to detect human motion and has many applications especially in security fields. The main concept of the proposed work in this paper has focused on controlling the electrical devices (appliances, based on the location of a person movement inside the home. The design of the circuit control has also been designed to run specific devices located closed to person position in a room by designing PIR sensor array mounted in different angles. The proposed work has been compared with normal state by finding consumption in power (kWh and tariffs belong to MoE-Iraq.

  10. Design of a photovoltaic central power station: flat-plate array

    Energy Technology Data Exchange (ETDEWEB)

    1984-02-01

    A design for a photovoltaic central power station using fixed flat-panel arrays has been developed. The 100 MW plant is assumed to be located adjacent to the Saguaro Power Station of Arizona Public Service. The design assumes high-efficiency photovoltaic modules using dendritic web cells. The modules are arranged in 5 MW subfields, each with its own power conditioning unit. The photovoltaic output is connected to the existing 115 kV utility switchyard. The site specific design allows detailed cost estimates for engineering, site preparation, and installation. Collector and power conditioning costs have been treated parametrically.

  11. Design of data acquisition system for 2D-ARRAY ionization chamber detector

    International Nuclear Information System (INIS)

    He Chaohui; Xing Guilai; Wu Zhifang; Wang Zhentao

    2012-01-01

    The introduction is given on the design and development of data acquisition system for 2D-ARRAY ionization chamber detector, which is used for dose verification of tumor radiotherapy. The paper describes the structure and the principle of the 2D-ARRAY ionization chamber detector system in detail, and focuses on the discussion on the design process of the detector's data acquisition system and the development of data acquisition system which is constituted by preamplifier, preamplifier control board and data acquisition board. The client can setup the parameters of the detector system via TCP/IP and do data processing such as high speed data collection and acquisition, further operation and so on. (authors)

  12. A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent

    Directory of Open Access Journals (Sweden)

    Lykke Pedersen

    2014-01-01

    Full Text Available Antisense oligonucleotides complementary to RNA targets promise generality and ease of drug design. The first systemically administered antisense drug was recently approved for treatment and others are in clinical development. Chemical modifications that increase the hybridization affinity of oligonucleotides are reasoned to confer higher potency, i.e., modified oligonucleotides can be dosed at lower concentrations to achieve the same effect. Surprisingly, shorter and less affine oligonucleotides sometimes display increased potency. To explain this apparent contradiction, increased uptake or decreased propensity to form structures have been suggested as possible mechanisms. Here, we provide an alternative explanation that invokes only the kinetics behind oligonucleotide-mediated cleavage of RNA targets. A model based on the law of mass action predicts, and experiments support, the existence of an optimal binding affinity. Exaggerated affinity, and not length per se, is detrimental to potency. This finding clarifies how to optimally apply high-affinity modifications in the discovery of potent antisense oligonucleotide drugs.

  13. Design, modeling and testing of the Askaryan Radio Array South Pole autonomous renewable power stations

    Energy Technology Data Exchange (ETDEWEB)

    Besson, D.Z., E-mail: zedlam@ku.edu [Department of Physics and Astronomy, University of Kansas, 1082 Malott Hall, 1251 Wescoe Hall Drive, Lawrence, KS 66045-7582 (United States); Moscow Engineering and Physics Institute, 31 Kashirskaya Highway, Moscow 115409 (Russian Federation); Kennedy, D.M., E-mail: dmkennedy@ku.edu [Department of Physics and Astronomy, University of Kansas, 1082 Malott Hall, 1251 Wescoe Hall Drive, Lawrence, KS 66045-7582 (United States); Ratzlaff, K., E-mail: ratzlaff@ku.edu [Instrumentation Design Laboratory, University of Kansas, 6042 Malott Hall, 1251 Wescoe Hall Drive, Lawrence, KS 66045-7582 (United States); Young, R., E-mail: rwyoung@ku.edu [Instrumentation Design Laboratory, University of Kansas, 6042 Malott Hall, 1251 Wescoe Hall Drive, Lawrence, KS 66045-7582 (United States)

    2014-11-01

    We describe the design, construction and operation of the Askaryan Radio Array (ARA) Autonomous Renewable Power Stations, initially installed at the South Pole in December, 2010 with the goal of providing an independently operating 100 W power source capable of year-round operation in extreme environments. In addition to particle astrophysics applications at the South Pole, such a station can easily be, and has since been, extended to operation elsewhere, as described herein.

  14. Design of a K-Band Transmit Phased Array For Low Earth Orbit Satellite Communications

    Science.gov (United States)

    Watson, Thomas; Miller, Stephen; Kershner, Dennis; Anzic, Godfrey

    2000-01-01

    The design of a light weight, low cost phased array antenna is presented. Multilayer printed wiring board (PWB) technology is utilized for Radio Frequencies (RF) and DC/Logic manifold distribution. Transmit modules are soldered on one side and patch antenna elements are on the other, allowing the use of automated assembly processes. The 19 GHz antenna has two independently steerable beams, each capable of transferring data at 622 Mbps. A passive, self-contained phase change thermal management system is also presented.

  15. Design of redundant array of independent DVD libraries based on iSCSI

    Science.gov (United States)

    Chen, Yupeng; Pan, Longfa

    2003-04-01

    This paper presents a new approach to realize the redundant array of independent DVD libraries (RAID-LoIP) by using the iSCSI technology and traditional RAID algorithms. Our design reaches the high performance of optical storage system with following features: large storage size, highly accessing rate, random access, long distance of DVD libraries, block I/O storage, long storage life. Our RAID-LoIP system can be a good solution for broadcasting media asset storage system.

  16. Design, modeling and testing of the Askaryan Radio Array South Pole autonomous renewable power stations

    International Nuclear Information System (INIS)

    Besson, D.Z.; Kennedy, D.M.; Ratzlaff, K.; Young, R.

    2014-01-01

    We describe the design, construction and operation of the Askaryan Radio Array (ARA) Autonomous Renewable Power Stations, initially installed at the South Pole in December, 2010 with the goal of providing an independently operating 100 W power source capable of year-round operation in extreme environments. In addition to particle astrophysics applications at the South Pole, such a station can easily be, and has since been, extended to operation elsewhere, as described herein

  17. Camera trap arrays improve detection probability of wildlife: Investigating study design considerations using an empirical dataset.

    Science.gov (United States)

    O'Connor, Kelly M; Nathan, Lucas R; Liberati, Marjorie R; Tingley, Morgan W; Vokoun, Jason C; Rittenhouse, Tracy A G

    2017-01-01

    Camera trapping is a standard tool in ecological research and wildlife conservation. Study designs, particularly for small-bodied or cryptic wildlife species often attempt to boost low detection probabilities by using non-random camera placement or baited cameras, which may bias data, or incorrectly estimate detection and occupancy. We investigated the ability of non-baited, multi-camera arrays to increase detection probabilities of wildlife. Study design components were evaluated for their influence on wildlife detectability by iteratively parsing an empirical dataset (1) by different sizes of camera arrays deployed (1-10 cameras), and (2) by total season length (1-365 days). Four species from our dataset that represented a range of body sizes and differing degrees of presumed detectability based on life history traits were investigated: white-tailed deer (Odocoileus virginianus), bobcat (Lynx rufus), raccoon (Procyon lotor), and Virginia opossum (Didelphis virginiana). For all species, increasing from a single camera to a multi-camera array significantly improved detection probability across the range of season lengths and number of study sites evaluated. The use of a two camera array increased survey detection an average of 80% (range 40-128%) from the detection probability of a single camera across the four species. Species that were detected infrequently benefited most from a multiple-camera array, where the addition of up to eight cameras produced significant increases in detectability. However, for species detected at high frequencies, single cameras produced a season-long (i.e, the length of time over which cameras are deployed and actively monitored) detectability greater than 0.75. These results highlight the need for researchers to be critical about camera trap study designs based on their intended target species, as detectability for each focal species responded differently to array size and season length. We suggest that researchers a priori identify

  18. Camera trap arrays improve detection probability of wildlife: Investigating study design considerations using an empirical dataset.

    Directory of Open Access Journals (Sweden)

    Kelly M O'Connor

    Full Text Available Camera trapping is a standard tool in ecological research and wildlife conservation. Study designs, particularly for small-bodied or cryptic wildlife species often attempt to boost low detection probabilities by using non-random camera placement or baited cameras, which may bias data, or incorrectly estimate detection and occupancy. We investigated the ability of non-baited, multi-camera arrays to increase detection probabilities of wildlife. Study design components were evaluated for their influence on wildlife detectability by iteratively parsing an empirical dataset (1 by different sizes of camera arrays deployed (1-10 cameras, and (2 by total season length (1-365 days. Four species from our dataset that represented a range of body sizes and differing degrees of presumed detectability based on life history traits were investigated: white-tailed deer (Odocoileus virginianus, bobcat (Lynx rufus, raccoon (Procyon lotor, and Virginia opossum (Didelphis virginiana. For all species, increasing from a single camera to a multi-camera array significantly improved detection probability across the range of season lengths and number of study sites evaluated. The use of a two camera array increased survey detection an average of 80% (range 40-128% from the detection probability of a single camera across the four species. Species that were detected infrequently benefited most from a multiple-camera array, where the addition of up to eight cameras produced significant increases in detectability. However, for species detected at high frequencies, single cameras produced a season-long (i.e, the length of time over which cameras are deployed and actively monitored detectability greater than 0.75. These results highlight the need for researchers to be critical about camera trap study designs based on their intended target species, as detectability for each focal species responded differently to array size and season length. We suggest that researchers a priori

  19. Design of sparse Halbach magnet arrays for portable MRI using a genetic algorithm.

    Science.gov (United States)

    Cooley, Clarissa Zimmerman; Haskell, Melissa W; Cauley, Stephen F; Sappo, Charlotte; Lapierre, Cristen D; Ha, Christopher G; Stockmann, Jason P; Wald, Lawrence L

    2018-01-01

    Permanent magnet arrays offer several attributes attractive for the development of a low-cost portable MRI scanner for brain imaging. They offer the potential for a relatively lightweight, low to mid-field system with no cryogenics, a small fringe field, and no electrical power requirements or heat dissipation needs. The cylindrical Halbach array, however, requires external shimming or mechanical adjustments to produce B 0 fields with standard MRI homogeneity levels (e.g., 0.1 ppm over FOV), particularly when constrained or truncated geometries are needed, such as a head-only magnet where the magnet length is constrained by the shoulders. For portable scanners using rotation of the magnet for spatial encoding with generalized projections, the spatial pattern of the field is important since it acts as the encoding field. In either a static or rotating magnet, it will be important to be able to optimize the field pattern of cylindrical Halbach arrays in a way that retains construction simplicity. To achieve this, we present a method for designing an optimized cylindrical Halbach magnet using the genetic algorithm to achieve either homogeneity (for standard MRI applications) or a favorable spatial encoding field pattern (for rotational spatial encoding applications). We compare the chosen designs against a standard, fully populated sparse Halbach design, and evaluate optimized spatial encoding fields using point-spread-function and image simulations. We validate the calculations by comparing to the measured field of a constructed magnet. The experimentally implemented design produced fields in good agreement with the predicted fields, and the genetic algorithm was successful in improving the chosen metrics. For the uniform target field, an order of magnitude homogeneity improvement was achieved compared to the un-optimized, fully populated design. For the rotational encoding design the resolution uniformity is improved by 95% compared to a uniformly populated design.

  20. Design considerations for large detector arrays on submillimeter-wave telescopes

    Science.gov (United States)

    Stark, Antony A.

    2000-07-01

    The emerging technology of large (approximately 10,000 pixel) submillimeter-wave bolometer arrays presents a novel optical design problem -- how can such arrays be fed by diffraction- limited telescope optics where the primary mirror is less than 100,000 wavelengths in diameter? Standard Cassegrain designs for radiotelescope optics exhibit focal surface curvature so large that detectors cannot be placed more than 25 beam diameters from the central ray. The problem is worse for Ritchey-Chretien designs, because these minimize coma while increasing field curvature. Classical aberrations, including coma, are usually dominated by diffraction in submillimeter- wave single dish telescopes. The telescope designer must consider (1) diffraction, (2) aberration, (3) curvature of field, (4) cross-polarization, (5) internal reflections, (6) the effect of blockages, (7) means of beam chopping on- and off-source, (8) gravitational and thermal deformations of the primary mirror, (9) the physical mounting of large detector packages, and (10) the effect of gravity and (11) vibration on those detectors. Simultaneous optimization of these considerations in the case of large detector arrays leads to telescopes that differ considerably from standard radiotelescope designs. Offset optics provide flexibility for mounting detectors, while eliminating blockage and internal reflections. Aberrations and cross-polarization can be the same as on-axis designs having the same diameter and focal length. Trade-offs include the complication of primary mirror homology and an increase in overall cost. A dramatic increase in usable field of view can be achieved using shaped optics. Solutions having one to six mirrors will be discussed, including possible six-mirror design for the proposed South Pole 10 m telescope.

  1. Design for an IO block array in a tile-based FPGA

    International Nuclear Information System (INIS)

    Ding Guangxin; Chen Lingdou; Liu Zhongli

    2009-01-01

    A design for an IO block array in a tile-based FPGA is presented. Corresponding with the characteristics of the FPGA, each IO cell is composed of a signal path, local routing pool and configurable input/output buffers. Shared programmable registers in the signal path can be configured for the function of JTAG, without specific boundary scan registers/latches, saving layout area. The local routing pool increases the flexibility of routing and the routability of the whole FPGA. An auxiliary power supply is adopted to increase the performance of the IO buffers at different configured IO standards. The organization of the IO block array is described in an architecture description file, from which the array layout can be accomplished through use of an automated layout assembly tool. This design strategy facilitates the design of FPGAs with different capacities or architectures in an FPGA family series. The bond-out schemes of the same FPGA chip in different packages are also considered. The layout is based on SMIC 0.13 μm logic 1P8M salicide 1.2/2.5 V CMOS technology. Our performance is comparable with commercial SRAM-based FPGAs which use a similar process. (semiconductor integrated circuits)

  2. Design and array signal suggestion of array type pulsed eddy current probe for health monitoring of metal tubes

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Young Kil [Dept. of Electrical Engineering, Kunsan National University, Kunsan (Korea, Republic of)

    2015-10-15

    An array type probe for monitoring metal tubes is proposed in this paper which utilizes peak value and peak time of a pulsed eddy current(PEC) signal. The probe consists of an array of encircling coils along a tube and the outside of coils is shielded by ferrite to prevent source magnetic fields from directly affecting sensor signals since it is the magnetic fields produced by eddy currents that reflect the condition of metal tubes. The positions of both exciter and sensor coils are consecutively moved automatically so that manual scanning is not necessary. At one position of send-receive coils, peak value and peak time are extracted from a sensor PEC signal and these data are accumulated for all positions to form an array type peak value signal and an array type peak time signal. Numerical simulation was performed using the backward difference method in time and the finite element method for spatial analysis. Simulation results showed that peak value increases and the peak appears earlier as the defect depth or length increases. The proposed array signals are shown to be excellent in reflecting the defect location as well as variations of defect depth and length within the array probe.

  3. Co-Prime Frequency and Aperture Design for HF Surveillance, Wideband Radar Imaging, and Nonstationary Array Processing

    Science.gov (United States)

    2018-03-01

    to develop novel co-prime sampling and array design strategies that achieve high-resolution estimation of spectral power distributions and signal...by the array geometry and the frequency offset. We overcome this limitation by introducing a novel sparsity-based multi-target localization approach...estimation using a sparse uniform linear array with two CW signals of co-prime frequencies,” IEEE International Workshop on Computational Advances

  4. Innovative enclosure dome/observing aperture system design for the MROI Array Telescopes

    Science.gov (United States)

    Busatta, A.; Marchiori, G.; Mian, S.; Payne, I.; Pozzobon, M.

    2010-07-01

    The close-pack array of the MROI necessitated an original design for the Unit Telescope Enclosure (UTE) at Magdalena Ridge Observatory. The Magdalena Ridge Observatory Interferometer (MROI) is a project which comprises an array of up to ten (10) 1.4m diameter mirror telescopes arranged in a "Y" configuration. Each of these telescopes will be housed inside a Unit Telescope Enclosure (UTE) which are relocatable onto any of 28 stations. The most compact configuration includes all ten telescopes, several of which are at a relative distance of less than 8m center to center from each other. Since the minimum angle of the field of regard is 30° with respect to the horizon, it is difficult to prevent optical blockage caused by adjacent UTEs in this compact array. This paper presents the design constraints inherent in meeting the requirement for the close-pack array. An innovative design enclosure was created which incorporates an unique dome/observing aperture system. The description of this system focuses on how the field of regard requirement led to an unique and highly innovative concept that had to be able to operate in the harsh environmental conditions encountered at an altitude of 10,460ft (3,188m). Finally, we describe the wide use of composites materials and structures (e.g. glass/carbon fibres, sandwich panels etc.) on the aperture system which represents the only way to guarantee adequate thermal and environmental protection, compactness, structural stability and limited power consumption due to reduced mass.

  5. Note: The design of thin gap chamber simulation signal source based on field programmable gate array

    International Nuclear Information System (INIS)

    Hu, Kun; Wang, Xu; Li, Feng; Jin, Ge; Lu, Houbing; Liang, Futian

    2015-01-01

    The Thin Gap Chamber (TGC) is an important part of ATLAS detector and LHC accelerator. Targeting the feature of the output signal of TGC detector, we have designed a simulation signal source. The core of the design is based on field programmable gate array, randomly outputting 256-channel simulation signals. The signal is generated by true random number generator. The source of randomness originates from the timing jitter in ring oscillators. The experimental results show that the random number is uniform in histogram, and the whole system has high reliability

  6. Design and fabrication of a micro PZT cantilever array actuator for applications in fluidic systems

    DEFF Research Database (Denmark)

    Kim, H.; In, C.; Yoon, Gil Ho

    2005-01-01

    In this article, a micro cantilever array actuated by PZT films is designed and fabricated for micro fluidic systems. The design features for maximizing tip deflections and minimizing fluid leakage are described. The governing equation of the composite PZT cantilever is derived and the actuating......, dielectric constant, and dielectric loss. Tip deflections of 12 mu m at 5 V are measured, which agreed well with the predicted value. The 18 mu l/s leakage rate of air was observed at a pressure difference of 1000 Pa. Micro cooler is introduced, and its possible application to micro compressor is discussed....

  7. Optimized emission in nanorod arrays through quasi-aperiodic inverse design.

    Science.gov (United States)

    Anderson, P Duke; Povinelli, Michelle L

    2015-06-01

    We investigate a new class of quasi-aperiodic nanorod structures for the enhancement of incoherent light emission. We identify one optimized structure using an inverse design algorithm and the finite-difference time-domain method. We carry out emission calculations on both the optimized structure as well as a simple periodic array. The optimized structure achieves nearly perfect light extraction while maintaining a high spontaneous emission rate. Overall, the optimized structure can achieve a 20%-42% increase in external quantum efficiency relative to a simple periodic design, depending on material quality.

  8. Design and fabrication of a bidimentional microbolometer array for Terahertz detection characterized at different temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Orduna-Diaz, A [CIBA-Tlaxcala, IPN, Tlaxcala, Tlax.(Mexico); Castillo-DomInguez, E; Torres-Jacome, A; De la Hidalga-Wade, F J; Trevino-Palacios, C G, E-mail: abdu@inaoep.mx [Instituto Nacional de Astrofisica, Optica y Electronica, Apdo. Postal 51 y 216, Puebla, Pue. 72000 (Mexico)

    2011-01-01

    We present the design, micromachining and characterization of a bidimentional bolometer array for radiation detection in the 0.7-1.5 THz frequency range. The detector is based on a boron doped amorphous silicon film (a-Si-B:H). The film optimized for sensitivity enhancement was obtained using 500 sccm diborane flow with 95 nm thickness. The sensing layer was deposited using plasma enhanced chemical vapor deposition (PECVD) technique at low frequency on a 0.45 {mu}m thick silicon nitride membrane sustained by a micromachined frame in crystalline silicon. The design consists of four 5x5 bolometer arrays made by conventional lithography. The bolometer active area is 660 {mu}m x 420 {mu}m and the detector will operate as a focal plane array. The current-voltage characteristics present an ohmic behaviour; the temperature coefficient of resistance (TCR) was obtained by measuring the bolometer performance from room temperature down to liquid nitrogen temperature. The responsivity was measured under illumination from a black body radiating at 300, 500, 700, 900 and 1100 deg. C, obtaining a value of R =1.17 x 10{sup -2} A/W with a dark current of 4.43 x 10{sup -9} A

  9. Design and Fabrication of an Experimental Microheater Array Powder Sintering Printer

    Science.gov (United States)

    Holt, Nicholas; Zhou, Wenchao

    2018-03-01

    Microheater array powder sintering (MAPS) is a novel additive manufacturing process that uses an array of microheaters to selectively sinter powder particles. MAPS shows great promise as a new method of printing flexible electronics by enabling digital curing of conductive inks on a variety of substrates. For MAPS to work effectively, a microscale air gap needs to be maintained between the heater array and the conductive ink. In this article, we present an experimental MAPS printer with air gap control for printing conductive circuits. First, we discuss design aspects necessary to implement MAPS. An analysis is performed to validate that the design can maintain the desired air gap between the microheaters and the sintering layer, which consists of a silver nanoparticle ink. The printer is tested by printing conductive lines on a flexible plastic substrate with silver nanoparticle ink. Results show MAPS performs on par with or better than the existing fabrication methods for printed electronics in terms of both the print quality (conductivity of the printed line) and print speed, which shows MAPS' great promise as a competitive new method for digital production of printed electronics.

  10. Design and Development of the Space Technology 5 (ST5) Solar Arrays

    Science.gov (United States)

    Lyons, John; Fatemi, Navid; Gamica, Robert; Sharma, Surya; Senft, Donna; Maybery, Clay

    2005-01-01

    The National Aeronautics and Space Administration's (NASA's) Space Technology 5 (ST5) is designed to flight-test the concept of miniaturized 'small size" satellites and innovative technologies in Earth's magnetosphere. Three satellites will map the intensity and direction of the magnetic fields within the inner magnetosphere. Due to the small area available for the solar arrays, and to meet the mission power requirements, very high-efficiency multijunction solar cells were selected to power the spacecraft built by NASA Goddard Space Flight Center (GSFC). This was done in partnership with the Air Force Research Lab (AFRL) through the Dual-Use Science and Technology (DUS&T) program. Emcore's InGaP/lnGaAs/Ge Advanced triple-junction (ATJ) solar cells, exhibiting an average air mass zero (AMO) efficiency of 28.0% (one-sun, 28 C), were used to populate the arrays. Each spacecraft employs 8 identical solar panels (total area of about 0.3 square meters), with 15 large-area solar cells per panel. The requirement for power is to support on-orbit average load of 13.5 W at 8.4 V, with plus or minus 5% off pointing. The details of the solar array design, development and qualification considerations, as well as ground electrical performance & shadowing analysis results are presented.

  11. Direct Closed-Form Design of Finite Alphabet Constant Envelope Waveforms for Planar Array Beampatterns

    KAUST Repository

    Bouchoucha, Taha

    2015-05-01

    Multiple Input Multiple Output (MIMO) radar systems has attracted lately a lot of attention thanks to its advantage over the classical phased array radar systems. We site among these advantages the improvement of parametric identifiability, achievement of higher spatial resolution and design of complex beampatterns. In colocated multiple-input multiple-output radar systems, it is usually desirable to steer transmitted power in the region-of-interest in order to increase the Signal to Noise Ratio (SNR) and reduce any undesired signal and thus improve the detection process. This problem is also known as transmit beampattern design. To achieve this goal, conventional methods optimize the waveform covariance matrix, R, for the desired beampattern, which is then used to generate the actual transmitted waveforms. Both steps require constrained optimization. Most of the existing methods use iterative algorithms to solve these problems, therefore their computational complexity is very high which makes them hard to use in practice especially for real time radar applications. In this paper, we provide a closed-form solution to design the covariance matrix for a given beampattern in the three dimensional space using planar arrays, which is then used to derive a novel closed-form algorithm to directly design the finite-alphabet constant-envelope waveforms. The proposed algorithm exploits the two-dimensional discrete Fourier transform which is implemented using fast Fourier transform algorithm. Consequently, the computational complexity of the proposed beampattern solution is very low allowing it to be used for large arrays to change the beampattern in real time. We also show that the number of required snapshots in each waveform depends on the beampattern and that it is less than the total number of transmit antennas. In addition, we show that the proposed waveform design method can be used with non symmetric beampatterns. The performance of our proposed algorithm compares

  12. Synthesis of Gold Nanoparticles to Capture Lifelike Proteins: Application on the Multichannel Sensor Array Design

    Directory of Open Access Journals (Sweden)

    Yumin Leng

    2018-01-01

    Full Text Available The chemical elements of proteins are similar to that of DNA (e.g., C, H, O, and N, and DNA shows different knotted architectures. So we imagine that proteins may show a wealth of highly complex structures, especially when proteins interact with each other. The imagination was proved by synthesizing gold nanoparticles (GNPs to capture the lifelike protein structures. The optical responses (i.e., color of as-prepared GNPs are found to be characteristic to a given protein (or heavy metal ion. Based on the “three colors” principle of Thomas Young, we extracted the red, green, and blue (RGB alterations of as-synthesized GNPs to fabricate multichannel sensor arrays for proteins (or heavy metal ions discrimination. The designed multichannel sensor arrays demonstrate possibilities in semiquantitative analysis of multiple analytes (e.g., proteins and heavy metal ions. This work is believed to open new opportunities for GNPs-based label-free sensing.

  13. Design and Assembly of DNA Nano-Objects and 2D DNA Origami Arrays

    Science.gov (United States)

    Liu, Wenyan

    DNA, which plays a central role in biology as the carrier of genetic information, is also an excellent candidate for structural nanotechnology. Researches have proven that a variety of complicated DNA assemblies, such as objects, 2D & 3D crystals, and nanomechanical devices, can be fabricated through the combination of robust branched DNA motifs and sticky ends. This dissertation focuses on the design and construction of DNA nano--objects and 2D DNA origami arrays. In this dissertation, we first describe the formation of a triangular species that has four strands per edge, held together by PX interactions. We demonstrate by nondenaturing gel electrophoresis and by atomic force microscopy (AFM) that we can combine a partial triangle with other strands to form a robust four--stranded molecule. By combining them with a novel three--domain molecule, we also demonstrate by AFM that these triangles can be self--assembled into a linear array. Second, we demonstrate our attempts to design and self--assemble 2D DNA origami arrays using several different strategies. Specifically, we introduce the self--assembly of 2D DNA origami lattices using a symmetric cross--like design. This design strategy resulted in a well--ordered woven latticework array with edge dimensions of 2--3 mum. This size is likely to be large enough to connect bottom-up methods of patterning with top--down approaches. Third, we illustrate the design and construction of DNA nano--objects for exploring the substrate preferences of topoisomerase (topo) II. We designed and fabricated four double rhombus--like DNA molecules, each of which contains a different conformation of crossover in the middle, as possible substrates to establish the structural preferences for topo II. We characterized the formation of each substrate molecule by gel electrophoresis. Finally, we study the effect of M13 DNA knotting on the formation of the DNA origami tiles. We demonstrate by atomic force microscopy (AFM) that knotted M13

  14. Heavy Ion Transient Characterization of a Photobit Hardened-by-Design Active Pixel Sensor Array

    Science.gov (United States)

    Marshall, Paul W.; Byers, Wheaton B.; Conger, Christopher; Eid, El-Sayed; Gee, George; Jones, Michael R.; Marshall, Cheryl J.; Reed, Robert; Pickel, Jim; Kniffin, Scott

    2002-01-01

    This paper presents heavy ion data on the single event transient (SET) response of a Photobit active pixel sensor (APS) four quadrant test chip with different radiation tolerant designs in a standard 0.35 micron CMOS process. The physical design techniques of enclosed geometry and P-channel guard rings are used to design the four N-type active photodiode pixels as described in a previous paper. Argon transient measurements on the 256 x 256 chip array as a function of incident angle show a significant variation in the amount of charge collected as well as the charge spreading dependent on the pixel type. The results are correlated with processing and design information provided by Photobit. In addition, there is a large degree of statistical variability between individual ion strikes. No latch-up is observed up to an LET of 106 MeV/mg/sq cm.

  15. The Square Kilometre Array Science Data Processor. Preliminary compute platform design

    International Nuclear Information System (INIS)

    Broekema, P.C.; Nieuwpoort, R.V. van; Bal, H.E.

    2015-01-01

    The Square Kilometre Array is a next-generation radio-telescope, to be built in South Africa and Western Australia. It is currently in its detailed design phase, with procurement and construction scheduled to start in 2017. The SKA Science Data Processor is the high-performance computing element of the instrument, responsible for producing science-ready data. This is a major IT project, with the Science Data Processor expected to challenge the computing state-of-the art even in 2020. In this paper we introduce the preliminary Science Data Processor design and the principles that guide the design process, as well as the constraints to the design. We introduce a highly scalable and flexible system architecture capable of handling the SDP workload

  16. Design of readout drivers for ATLAS pixel detectors using field programmable gate arrays

    CERN Document Server

    Sivasubramaniyan, Sriram

    Microstrip detectors are an integral patt of high energy physics research . Special protocols are used to transmit the data from these detectors . To readout the data from such detectors specialized instrumentation have to be designed . To achieve this task, creative and innovative high speed algorithms were designed simulated and implemented in Field Programmable gate arrays, using CAD/CAE tools. The simulation results indicated that these algorithms would be able to perform all the required tasks quickly and efficiently. This thesis describes the design of data acquisition system called the Readout Drivers (ROD) . It focuses on the ROD data path for ATLAS Pixel detectors. The data path will be an integrated part of Readout Drivers setup to decode the data from the silicon micro strip detectors and pixel detectors. This research also includes the design of Readout Driver controller. This Module is used to control the operation of the ROD. This module is responsible for the operation of the Pixel decoders bas...

  17. Bi-Axial Solar Array Drive Mechanism: Design, Build and Environmental Testing

    Science.gov (United States)

    Scheidegger, Noemy; Ferris, Mark; Phillips, Nigel

    2014-01-01

    The development of the Bi-Axial Solar Array Drive Mechanism (BSADM) presented in this paper is a demonstration of SSTL's unique space manufacturing approach that enables performing rapid development cycles for cost-effective products that meet ever-challenging mission requirements: The BSADM is designed to orient a solar array wing towards the sun, using its first rotation axis to track the sun, and its second rotation axis to compensate for the satellite orbit and attitude changes needed for a successful payload operation. The tight development schedule, with manufacture of 7 Flight Models within 1.5 year after kick-off, is offset by the risk-reduction of using qualified key component-families from other proven SSTL mechanisms. This allowed focusing the BSADM design activities on the mechanism features that are unique to the BSADM, and having an Engineering Qualification Model (EQM) built 8 months after kick-off. The EQM is currently undergoing a full environmental qualification test campaign. This paper presents the BSADM design approach that enabled meeting such a challenging schedule, its design particularities, and the ongoing verification activities.

  18. Design, Fabrication, and Testing of Active Skin Antenna with 3D Printing Array Framework

    Directory of Open Access Journals (Sweden)

    Jinzhu Zhou

    2017-01-01

    Full Text Available An active skin antenna with structural load-bearing and electromagnetic functions is usually installed in the structural surface of mobile vehicles such as aircrafts, warships, and high-speed train. This paper presents the design, fabrication, and testing of a novel active skin antenna which consists of an encapsulation shell, antenna skin, and RF and beam control circuits. The antenna skin which consists of the facesheet, honeycomb, array framework, and microstrip antenna elements was designed by using Bayesian optimization, in order to improve the design efficiency. An active skin antenna prototype with 32 microstrip antenna elements was fabricated by using a hybrid manufacturing method. In this method, 3D printing technology was applied to fabricate the array framework, and the different layers were bonded to form the final antenna skin by using traditional composite process. Some experimental testing was conducted, and the testing results validate the feasibility the proposed antenna skin structure. The proposed design and fabrication technique is suitable for the development of conformal load-bearing antenna or smart skin antenna installed in the structural surface of aircraft, warships, and armored vehicles.

  19. Design and optimization of arrays of neodymium iron boron-based magnets for magnetic tweezers applications

    Energy Technology Data Exchange (ETDEWEB)

    Zacchia, Nicholas A.; Valentine, Megan T. [Department of Mechanical Engineering and Materials Research Laboratory, University of California, Santa Barbara, California 93106 (United States)

    2015-05-15

    We present the design methodology for arrays of neodymium iron boron (NdFeB)-based magnets for use in magnetic tweezers devices. Using finite element analysis (FEA), we optimized the geometry of the NdFeB magnet as well as the geometry of iron yokes designed to focus the magnetic fields toward the sample plane. Together, the magnets and yokes form a magnetic array which is the basis of the magnetic tweezers device. By systematically varying 15 distinct shape parameters, we determined those features that maximize the magnitude of the magnetic field gradient as well as the length scale over which the magnetic force operates. Additionally, we demonstrated that magnetic saturation of the yoke material leads to intrinsic limitations in any geometric design. Using this approach, we generated a compact and light-weight magnetic tweezers device that produces a high field gradient at the image plane in order to apply large forces to magnetic beads. We then fabricated the optimized yoke and validated the FEA by experimentally mapping the magnetic field of the device. The optimization data and iterative FEA approach outlined here will enable the streamlined design and construction of specialized instrumentation for force-sensitive microscopy.

  20. Design and optimization of arrays of neodymium iron boron-based magnets for magnetic tweezers applications.

    Science.gov (United States)

    Zacchia, Nicholas A; Valentine, Megan T

    2015-05-01

    We present the design methodology for arrays of neodymium iron boron (NdFeB)-based magnets for use in magnetic tweezers devices. Using finite element analysis (FEA), we optimized the geometry of the NdFeB magnet as well as the geometry of iron yokes designed to focus the magnetic fields toward the sample plane. Together, the magnets and yokes form a magnetic array which is the basis of the magnetic tweezers device. By systematically varying 15 distinct shape parameters, we determined those features that maximize the magnitude of the magnetic field gradient as well as the length scale over which the magnetic force operates. Additionally, we demonstrated that magnetic saturation of the yoke material leads to intrinsic limitations in any geometric design. Using this approach, we generated a compact and light-weight magnetic tweezers device that produces a high field gradient at the image plane in order to apply large forces to magnetic beads. We then fabricated the optimized yoke and validated the FEA by experimentally mapping the magnetic field of the device. The optimization data and iterative FEA approach outlined here will enable the streamlined design and construction of specialized instrumentation for force-sensitive microscopy.

  1. Design and optical analyses of an arrayed microfluidic tunable prism panel for enhancing solar energy collection

    International Nuclear Information System (INIS)

    Narasimhan, Vinayak; Jiang, Dongyue; Park, Sung-Yong

    2016-01-01

    Highlights: • We present an arrayed tunable prism panel enabling wide tracking and high solar concentration. • A microfluidic technology allows a low-cost, lightweight and precise solar tracking system. • Our prism panel enables high solar concentration up to 2032× factor. • Various liquid prism configurations (stacked prism arrays) and optical materials are considered. • Their impacts on solar beam steering, reflection losses and beam concentration are studied. - Abstract: We present the design and optical analyses of an arrayed microfluidic tunable prism panel that enables wide solar tracking and high solar concentration while minimizing energy loss. Each of the liquid prism modules is implemented by a microfluidic (i.e. non-mechanical) technology based on electrowetting for adaptive solar beam steering. Therefore the proposed platform offers a low-cost, lightweight and precise solar tracking system while obviating the need for bulky and heavy mechanical moving parts essentially required for a conventional motor-driven solar tracker. In this paper, various liquid prism configurations in terms of design (single, double, triple and quad-stacked prism arrays) as well as optical materials are considered and their impact on optical performance aspects such as solar beam steering, reflection losses and beam concentration is studied. Our system is able to achieve a wide solar tracking covering the whole-day movement of the Sun and a reflection loss below 4.4% with a Rayleigh’s film for a quad-stacked prism configuration. Furthermore, an arrayed prism panel is proposed to increase the aperture area and thus allows for the collection of large amounts of sunlight. Our simulation study based on the optical design software, ZEMAX, indicates that the prism panel is capable of high solar concentration up to 2032× factor even without conventional solar tracking devices. We also deal with dispersion characteristics of the materials and their corresponding effect on

  2. Design of UAVs-Based 3D Antenna Arrays for a Maximum Performance in Terms of Directivity and SLL

    Directory of Open Access Journals (Sweden)

    Jesus Garza

    2016-01-01

    Full Text Available This paper presents a design of UAVs-based 3D antenna arrays for a maximum performance in terms of directivity and side lobe level (SLL. This paper illustrates how to model the UAVs formation flight using 3D nonuniform antenna arrays. This design of 3D antenna arrays considers the optimization of the positions of the antenna elements to model the UAVs formation flight. In this case, a disk patch antenna is chosen to be used as element in each UAV. The disk patch antenna is formulated by the well-known cavity model. The synthesis process is carried out by the method of Differential Evolution for Multiobjective Optimization (DEMO. Furthermore, a comparison of the performance of 3D nonuniform antenna arrays is provided with respect to the most conventional arrays (circular, planar, linear, and the cubic for UAVs formation flight.

  3. Design, Fabrication, and Implementation of an Array-Type MEMS Piezoresistive Intelligent Pressure Sensor System

    Directory of Open Access Journals (Sweden)

    Jiahong Zhang

    2018-02-01

    Full Text Available To meet the radiosonde requirement of high sensitivity and linearity, this study designs and implements a monolithically integrated array-type piezoresistive intelligent pressure sensor system which is made up of two groups of four pressure sensors with the pressure range of 0–50 kPa and 0–100 kPa respectively. First, theoretical models and ANSYS (version 14.5, Canonsburg, PA, USA finite element method (FEM are adopted to optimize the parameters of array sensor structure. Combing with FEM stress distribution results, the size and material characteristics of the array-type sensor are determined according to the analysis of the sensitivity and the ratio of signal to noise (SNR. Based on the optimized parameters, the manufacture and packaging of array-type sensor chips are then realized by using the standard complementary metal-oxide-semiconductor (CMOS and microelectromechanical system (MEMS process. Furthermore, an intelligent acquisition and processing system for pressure and temperature signals is achieved. The S3C2440A microprocessor (Samsung, Seoul, Korea is regarded as the core part which can be applied to collect and process data. In particular, digital signal storage, display and transmission are realized by the application of a graphical user interface (GUI written in QT/E. Besides, for the sake of compensating the temperature drift and nonlinear error, the data fusion technique is proposed based on a wavelet neural network improved by genetic algorithm (GA-WNN for average measuring signal. The GA-WNN model is implemented in hardware by using a S3C2440A microprocessor. Finally, the results of calibration and test experiments achieved with the temperature ranges from −20 to 20 °C show that: (1 the nonlinear error and the sensitivity of the array-type pressure sensor are 8330 × 10−4 and 0.052 mV/V/kPa in the range of 0–50 kPa, respectively; (2 the nonlinear error and the sensitivity are 8129 × 10−4 and 0.020 mV/V/kPa in the

  4. Design and fabrication of two-dimensional semiconducting bolometer arrays for HAWC and SHARC-II

    Science.gov (United States)

    Voellmer, George M.; Allen, Christine A.; Amato, Michael J.; Babu, Sachidananda R.; Bartels, Arlin E.; Benford, Dominic J.; Derro, Rebecca J.; Dowell, C. D.; Harper, D. A.; Jhabvala, Murzy D.; Moseley, S. H.; Rennick, Timothy; Shirron, Peter J.; Smith, W. W.; Staguhn, Johannes G.

    2003-02-01

    The High resolution Airborne Wideband Camera (HAWC) and the Submillimeter High Angular Resolution Camera II (SHARC II) will use almost identical versions of an ion-implanted silicon bolometer array developed at the National Aeronautics and Space Administration's Goddard Space Flight Center (GSFC). The GSFC "Pop-Up" Detectors (PUD's) use a unique folding technique to enable a 12 × 32-element close-packed array of bolometers with a filling factor greater than 95 percent. A kinematic Kevlar suspension system isolates the 200 mK bolometers from the helium bath temperature, and GSFC - developed silicon bridge chips make electrical connection to the bolometers, while maintaining thermal isolation. The JFET preamps operate at 120 K. Providing good thermal heat sinking for these, and keeping their conduction and radiation from reaching the nearby bolometers, is one of the principal design challenges encountered. Another interesting challenge is the preparation of the silicon bolometers. They are manufactured in 32-element, planar rows using Micro Electro Mechanical Systems (MEMS) semiconductor etching techniques, and then cut and folded onto a ceramic bar. Optical alignment using specialized jigs ensures their uniformity and correct placement. The rows are then stacked to create the 12 × 32-element array. Engineering results from the first light run of SHARC II at the Caltech Submillimeter Observatory (CSO) are presented.

  5. Design of area array CCD image acquisition and display system based on FPGA

    Science.gov (United States)

    Li, Lei; Zhang, Ning; Li, Tianting; Pan, Yue; Dai, Yuming

    2014-09-01

    With the development of science and technology, CCD(Charge-coupled Device) has been widely applied in various fields and plays an important role in the modern sensing system, therefore researching a real-time image acquisition and display plan based on CCD device has great significance. This paper introduces an image data acquisition and display system of area array CCD based on FPGA. Several key technical challenges and problems of the system have also been analyzed and followed solutions put forward .The FPGA works as the core processing unit in the system that controls the integral time sequence .The ICX285AL area array CCD image sensor produced by SONY Corporation has been used in the system. The FPGA works to complete the driver of the area array CCD, then analog front end (AFE) processes the signal of the CCD image, including amplification, filtering, noise elimination, CDS correlation double sampling, etc. AD9945 produced by ADI Corporation to convert analog signal to digital signal. Developed Camera Link high-speed data transmission circuit, and completed the PC-end software design of the image acquisition, and realized the real-time display of images. The result through practical testing indicates that the system in the image acquisition and control is stable and reliable, and the indicators meet the actual project requirements.

  6. Design of coated standing nanowire array solar cell performing beyond the planar efficiency limits

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Yang; Ye, Qinghao; Shen, Wenzhong, E-mail: wzshen@sjtu.edu.cn [Institute of Solar Energy, and Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2016-05-28

    The single standing nanowire (SNW) solar cells have been proven to perform beyond the planar efficiency limits in both open-circuit voltage and internal quantum efficiency due to the built-in concentration and the shifting of the absorption front. However, the expandability of these nano-scale units to a macro-scale photovoltaic device remains unsolved. The main difficulty lies in the simultaneous preservation of an effective built-in concentration in each unit cell and a broadband high absorption capability of their array. Here, we have provided a detailed theoretical guideline for realizing a macro-scale solar cell that performs furthest beyond the planar limits. The key lies in a complementary design between the light-trapping of the single SNWs and that of the photonic crystal slab formed by the array. By tuning the hybrid HE modes of the SNWs through the thickness of a coaxial dielectric coating, the optimized coated SNW array can sustain an absorption rate over 97.5% for a period as large as 425 nm, which, together with the inherited carrier extraction advantage, leads to a cell efficiency increment of 30% over the planar limit. This work has demonstrated the viability of a large-size solar cell that performs beyond the planar limits.

  7. Mechanical design of SST-GATE, a dual-mirror telescope for the Cherenkov Telescope Array

    Science.gov (United States)

    Dournaux, Jean-Laurent; Huet, Jean-Michel; Amans, Jean-Philippe; Dumas, Delphine; Laporte, Philippe; Sol, Hélène; Blake, Simon

    2014-07-01

    The Cherenkov Telescope Array (CTA) project aims to create the next generation Very High Energy (VHE) gamma-ray telescope array. It will be devoted to the observation of gamma rays over a wide band of energy, from a few tens of GeV to more than 100 TeV. Two sites are foreseen to view the whole sky where about 100 telescopes, composed of three different classes, related to the specific energy region to be investigated, will be installed. Among these, the Small Size class of Telescopes, SSTs, are devoted to the highest energy region, to beyond 100 TeV. Due to the large number of SSTs, their unit cost is an important parameter. At the Observatoire de Paris, we have designed a prototype of a Small Size Telescope named SST-GATE, based on the dual-mirror Schwarzschild-Couder optical formula, which has never before been implemented in the design of a telescope. Over the last two years, we developed a mechanical design for SST-GATE from the optical and preliminary mechanical designs made by the University of Durham. The integration of this telescope is currently in progress. Since the early stages of mechanical design of SST-GATE, finite element method has been used employing shape and topology optimization techniques to help design several elements of the telescope. This allowed optimization of the mechanical stiffness/mass ratio, leading to a lightweight and less expensive mechanical structure. These techniques and the resulting mechanical design are detailed in this paper. We will also describe the finite element analyses carried out to calculate the mechanical deformations and the stresses in the structure under observing and survival conditions.

  8. Design and implementation of a low-cost multichannel seismic noise recorder for array measurements

    Science.gov (United States)

    Soler-Llorens, Juan Luis; Juan Giner-Caturla, Jose; Molina-Palacios, Sergio; Galiana-Merino, Juan Jose; Rosa-Herranz, Julio; Agea-Medina, Noelia

    2017-04-01

    Soil characterization is the starting point for seismic hazard studies. Currently, the methods based on ambient noise measurements are very used because they are non-invasive methods and relatively easy to implement in urban areas. Among these methods, the analysis of array measurements provides the dispersion curve and subsequently the shear-wave velocity profile associated to the site under study. In this case, we need several sensors recording simultaneously and a data acquisition system with one channel by sensor, what can become the complete equipment unaffordable for small research groups. In this work, we have designed and implemented a low-cost multichannel ambient noise recorder for array measurements. The complete system is based on Arduino, an open source electronic development platform, which allows recording 12 differential input channels simultaneously. Besides, it is complemented with a conditioning circuit that includes an anti-aliasing filter and a selectable gain between 0 and 40dB. The data acquisition is set up through a user-friendly graphical user interface. It is important to note that the electronic scheme as well as the programming code are open hardware and software, respectively, so it allows other researchers to suite the system to their particular requirements. The developed equipment has been tested at several sites around the province of Alicante (southeast of Spain), where the soil characteristics are well-known from previous studies. Array measurements have been taken and after that, the recorded data have been analysed using the frequency-wavenumber (f-k) and the extended spatial autocorrelation (ESAC) methods. The comparison of the obtained dispersion curves with the ones obtained in previous studies shows the suitability of the implemented low-cost system for array measurements.

  9. Design and fabrication of adjustable red-green-blue LED light arrays for plant research

    Directory of Open Access Journals (Sweden)

    Kenitz J Dustin

    2005-08-01

    Full Text Available Abstract Background Although specific light attributes, such as color and fluence rate, influence plant growth and development, researchers generally cannot control the fine spectral conditions of artificial plant-growth environments. Plant growth chambers are typically outfitted with fluorescent and/or incandescent fixtures that provide a general spectrum that is accommodating to the human eye and not necessarily supportive to plant development. Many studies over the last several decades, primarily in Arabidopsis thaliana, have clearly shown that variation in light quantity, quality and photoperiod can be manipulated to affect growth and control developmental transitions. Light emitting diodes (LEDs has been used for decades to test plant responses to narrow-bandwidth light. LEDs are particularly well suited for plant growth chambers, as they have an extraordinary life (about 100,000 hours, require little maintenance, and use negligible energy. These factors render LED-based light strategies particularly appropriate for space-biology as well as terrestrial applications. However, there is a need for a versatile and inexpensive LED array platform where individual wavebands can be specifically tuned to produce a series of light combinations consisting of various quantities and qualities of individual wavelengths. Two plans are presented in this report. Results In this technical report we describe the practical construction of tunable red-green-blue LED arrays to support research in plant growth and development. Two light fixture designs and corresponding circuitry are presented. The first is well suited for a laboratory environment for use in a finite area with small plants, such as Arabidopsis. The second is expandable and appropriate for growth chambers. The application of these arrays to early plant developmental studies has been validated with assays of hypocotyl growth inhibition/promotion and phototropic curvature in Arabidopsis seedlings

  10. Application of source biasing technique for energy efficient DECODER circuit design: memory array application

    Science.gov (United States)

    Gupta, Neha; Parihar, Priyanka; Neema, Vaibhav

    2018-04-01

    Researchers have proposed many circuit techniques to reduce leakage power dissipation in memory cells. If we want to reduce the overall power in the memory system, we have to work on the input circuitry of memory architecture i.e. row and column decoder. In this research work, low leakage power with a high speed row and column decoder for memory array application is designed and four new techniques are proposed. In this work, the comparison of cluster DECODER, body bias DECODER, source bias DECODER, and source coupling DECODER are designed and analyzed for memory array application. Simulation is performed for the comparative analysis of different DECODER design parameters at 180 nm GPDK technology file using the CADENCE tool. Simulation results show that the proposed source bias DECODER circuit technique decreases the leakage current by 99.92% and static energy by 99.92% at a supply voltage of 1.2 V. The proposed circuit also improves dynamic power dissipation by 5.69%, dynamic PDP/EDP 65.03% and delay 57.25% at 1.2 V supply voltage.

  11. VLSI design of an RSA encryption/decryption chip using systolic array based architecture

    Science.gov (United States)

    Sun, Chi-Chia; Lin, Bor-Shing; Jan, Gene Eu; Lin, Jheng-Yi

    2016-09-01

    This article presents the VLSI design of a configurable RSA public key cryptosystem supporting the 512-bit, 1024-bit and 2048-bit based on Montgomery algorithm achieving comparable clock cycles of current relevant works but with smaller die size. We use binary method for the modular exponentiation and adopt Montgomery algorithm for the modular multiplication to simplify computational complexity, which, together with the systolic array concept for electric circuit designs effectively, lower the die size. The main architecture of the chip consists of four functional blocks, namely input/output modules, registers module, arithmetic module and control module. We applied the concept of systolic array to design the RSA encryption/decryption chip by using VHDL hardware language and verified using the TSMC/CIC 0.35 m 1P4 M technology. The die area of the 2048-bit RSA chip without the DFT is 3.9 × 3.9 mm2 (4.58 × 4.58 mm2 with DFT). Its average baud rate can reach 10.84 kbps under a 100 MHz clock.

  12. Evaluation of a miniature microscope objective designed for fluorescence array microscopy detection of Mycobacterium tuberculosis.

    Science.gov (United States)

    McCall, Brian; Olsen, Randall J; Nelles, Nicole J; Williams, Dawn L; Jackson, Kevin; Richards-Kortum, Rebecca; Graviss, Edward A; Tkaczyk, Tomasz S

    2014-03-01

    A prototype miniature objective that was designed for a point-of-care diagnostic array microscope for detection of Mycobacterium tuberculosis and previously fabricated and presented in a proof of concept is evaluated for its effectiveness in detecting acid-fast bacteria. To evaluate the ability of the microscope to resolve submicron features and details in the image of acid-fast microorganisms stained with a fluorescent dye, and to evaluate the accuracy of clinical diagnoses made with digital images acquired with the objective. The lens prescription data for the microscope design are presented. A test platform is built by combining parts of a standard microscope, a prototype objective, and a digital single-lens reflex camera. Counts of acid-fast bacteria made with the prototype objective are compared to counts obtained with a standard microscope over matched fields of view. Two sets of 20 smears, positive and negative, are diagnosed by 2 pathologists as sputum smear positive or sputum smear negative, using both a standard clinical microscope and the prototype objective under evaluation. The results are compared to a reference diagnosis of the same sample. More bacteria are counted in matched fields of view in digital images taken with the prototype objective than with the standard clinical microscope. All diagnostic results are found to be highly concordant. An array microscope built with this miniature lens design will be able to detect M tuberculosis with high sensitivity and specificity.

  13. Tunable Absorption System based on magnetorheological elastomers and Halbach array: design and testing

    Energy Technology Data Exchange (ETDEWEB)

    Bocian, Mirosław; Kaleta, Jerzy; Lewandowski, Daniel, E-mail: daniel.lewandowski@pwr.edu.pl; Przybylski, Michał

    2017-08-01

    Highlights: • Construction of a Tunable Absorption System incorporating MRE has been done. • For system control by magnetic field a double circular Halbach array has been used. • Significant changes of the TSAs natural frequency and damping has been obtained. - Abstract: In this paper, the systematic design, construction and testing of a Tunable Absorption System (TAS) incorporating magnetorheological elastomer (MRE) has been investigated. The TAS has been designed for energy absorption and mitigation of vibratory motions from an impact excitation. The main advantage of the designed TAS is that it has the ability to change and adapt to working conditions. Tunability can be realised through a change in the magnetic field caused by the change of an internal arrangement of permanent magnets within a double dipolar circular Halbach array. To show the capabilities of the tested system, experiments based on an impulse excitation have been performed. Significant changes of the TASs natural frequency and damping characteristics have been obtained. By incorporating magnetic tunability within the TAS a significant qualitative and quantitative change in the devices mechanical properties and performance were obtained.

  14. Closed-form Solution to Directly Design FACE Waveforms for Beampatterns Using Planar Array

    KAUST Repository

    Bouchoucha, Taha; Ahmed, Sajid; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim

    2015-01-01

    In multiple-input multiple-output radar systems, it is usually desirable to steer transmitted power in the region-of-interest. To do this, conventional methods optimize the waveform covariance matrix, R, for the desired beampattern, which is then used to generate actual transmitted waveforms. Both steps require constrained optimization, therefore, use iterative algorithms. The main challenges encountered in the existing approaches are the computational complexity and the design of waveforms to use in practice. In this paper, we provide a closed-form solution to design covariance matrix for the given beampattern using the planar array, which is then used to derive a novel closed-form algorithm to directly design the finite-alphabet constant-envelope (FACE) waveforms. The proposed algorithm exploits the two-dimensional fast-Fourier-transform. The performance of our proposed algorithm is compared with existing methods that are based on semi-definite quadratic programming with the advantage of a considerably reduced complexity.

  15. Closed-form Solution to Directly Design FACE Waveforms for Beampatterns Using Planar Array

    KAUST Repository

    Bouchoucha, Taha

    2015-04-19

    In multiple-input multiple-output radar systems, it is usually desirable to steer transmitted power in the region-of-interest. To do this, conventional methods optimize the waveform covariance matrix, R, for the desired beampattern, which is then used to generate actual transmitted waveforms. Both steps require constrained optimization, therefore, use iterative algorithms. The main challenges encountered in the existing approaches are the computational complexity and the design of waveforms to use in practice. In this paper, we provide a closed-form solution to design covariance matrix for the given beampattern using the planar array, which is then used to derive a novel closed-form algorithm to directly design the finite-alphabet constant-envelope (FACE) waveforms. The proposed algorithm exploits the two-dimensional fast-Fourier-transform. The performance of our proposed algorithm is compared with existing methods that are based on semi-definite quadratic programming with the advantage of a considerably reduced complexity.

  16. Design of hybrid two-dimensional and three-dimensional nanostructured arrays for electronic and sensing applications

    Science.gov (United States)

    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 (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.

  17. Topology optimization for design of segmented permanent magnet arrays with ferromagnetic materials

    Science.gov (United States)

    Lee, Jaewook; Yoon, Minho; Nomura, Tsuyoshi; Dede, Ercan M.

    2018-03-01

    This paper presents multi-material topology optimization for the co-design of permanent magnet segments and iron material. Specifically, a co-design methodology is proposed to find an optimal border of permanent magnet segments, a pattern of magnetization directions, and an iron shape. A material interpolation scheme is proposed for material property representation among air, permanent magnet, and iron materials. In this scheme, the permanent magnet strength and permeability are controlled by density design variables, and permanent magnet magnetization directions are controlled by angle design variables. In addition, a scheme to penalize intermediate magnetization direction is proposed to achieve segmented permanent magnet arrays with discrete magnetization directions. In this scheme, permanent magnet strength is controlled depending on magnetization direction, and consequently the final permanent magnet design converges into permanent magnet segments having target discrete directions. To validate the effectiveness of the proposed approach, three design examples are provided. The examples include the design of a dipole Halbach cylinder, magnetic system with arbitrarily-shaped cavity, and multi-objective problem resembling a magnetic refrigeration device.

  18. Oligonucleotide aptamers against tyrosine kinase receptors: Prospect for anticancer applications.

    Science.gov (United States)

    Camorani, Simona; Crescenzi, Elvira; Fedele, Monica; Cerchia, Laura

    2018-04-01

    Transmembrane receptor tyrosine kinases (RTKs) play crucial roles in cancer cell proliferation, survival, migration and differentiation. Area of intense research is searching for effective anticancer therapies targeting these receptors and, to date, several monoclonal antibodies and small-molecule tyrosine kinase inhibitors have entered the clinic. However, some of these drugs show limited efficacy and give rise to acquired resistance. Emerging highly selective compounds for anticancer therapy are oligonucleotide aptamers that interact with their targets by recognizing a specific three-dimensional structure. Because of their nucleic acid nature, the rational design of advanced strategies to manipulate aptamers for both diagnostic and therapeutic applications is greatly simplified over antibodies. In this manuscript, we will provide a comprehensive overview of oligonucleotide aptamers as next generation strategies to efficiently target RTKs in human cancers. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Design of acoustic logging signal source of imitation based on field programmable gate array

    International Nuclear Information System (INIS)

    Zhang, K; Ju, X D; Lu, J Q; Men, B Y

    2014-01-01

    An acoustic logging signal source of imitation is designed and realized, based on the Field Programmable Gate Array (FPGA), to improve the efficiency of examining and repairing acoustic logging tools during research and field application, and to inspect and verify acoustic receiving circuits and corresponding algorithms. The design of this signal source contains hardware design and software design,and the hardware design uses an FPGA as the control core. Four signals are made first by reading the Random Access Memory (RAM) data which are inside the FPGA, then dealing with the data by digital to analog conversion, amplification, smoothing and so on. Software design uses VHDL, a kind of hardware description language, to program the FPGA. Experiments illustrate that the ratio of signal to noise for the signal source is high, the waveforms are stable, and also its functions of amplitude adjustment, frequency adjustment and delay adjustment are in accord with the characteristics of real acoustic logging waveforms. These adjustments can be used to imitate influences on sonic logging received waveforms caused by many kinds of factors such as spacing and span of acoustic tools, sonic speeds of different layers and fluids, and acoustic attenuations of different cementation planes. (paper)

  20. Design of acoustic logging signal source of imitation based on field programmable gate array

    Science.gov (United States)

    Zhang, K.; Ju, X. D.; Lu, J. Q.; Men, B. Y.

    2014-08-01

    An acoustic logging signal source of imitation is designed and realized, based on the Field Programmable Gate Array (FPGA), to improve the efficiency of examining and repairing acoustic logging tools during research and field application, and to inspect and verify acoustic receiving circuits and corresponding algorithms. The design of this signal source contains hardware design and software design,and the hardware design uses an FPGA as the control core. Four signals are made first by reading the Random Access Memory (RAM) data which are inside the FPGA, then dealing with the data by digital to analog conversion, amplification, smoothing and so on. Software design uses VHDL, a kind of hardware description language, to program the FPGA. Experiments illustrate that the ratio of signal to noise for the signal source is high, the waveforms are stable, and also its functions of amplitude adjustment, frequency adjustment and delay adjustment are in accord with the characteristics of real acoustic logging waveforms. These adjustments can be used to imitate influences on sonic logging received waveforms caused by many kinds of factors such as spacing and span of acoustic tools, sonic speeds of different layers and fluids, and acoustic attenuations of different cementation planes.

  1. Design and optimization of multi-class series-parallel linear electromagnetic array artificial muscle.

    Science.gov (United States)

    Li, Jing; Ji, Zhenyu; Shi, Xuetao; You, Fusheng; Fu, Feng; Liu, Ruigang; Xia, Junying; Wang, Nan; Bai, Jing; Wang, Zhanxi; Qin, Xiansheng; Dong, Xiuzhen

    2014-01-01

    Skeletal muscle exhibiting complex and excellent precision has evolved for millions of years. Skeletal muscle has better performance and simpler structure compared with existing driving modes. Artificial muscle may be designed by analyzing and imitating properties and structure of skeletal muscle based on bionics, which has been focused on by bionic researchers, and a structure mode of linear electromagnetic array artificial muscle has been designed in this paper. Half sarcomere is the minimum unit of artificial muscle and electromagnetic model has been built. The structural parameters of artificial half sarcomere actuator were optimized to achieve better movement performance. Experimental results show that artificial half sarcomere actuator possesses great motion performance such as high response speed, great acceleration, small weight and size, robustness, etc., which presents a promising application prospect of artificial half sarcomere actuator.

  2. Formulation Development and Evaluation of Hybrid Nanocarrier for Cancer Therapy: Taguchi Orthogonal Array Based Design

    Directory of Open Access Journals (Sweden)

    Rakesh K. Tekade

    2013-01-01

    Full Text Available Taguchi orthogonal array design is a statistical approach that helps to overcome limitations associated with time consuming full factorial experimental design. In this study, the Taguchi orthogonal array design was applied to establish the optimum conditions for bovine serum albumin (BSA nanocarrier (ANC preparation. Taguchi method with L9 type of robust orthogonal array design was adopted to optimize the experimental conditions. Three key dependent factors namely, BSA concentration (% w/v, volume of BSA solution to total ethanol ratio (v : v, and concentration of diluted ethanolic aqueous solution (% v/v, were studied at three levels 3%, 4%, and 5% w/v; 1 : 0.75, 1 : 0.90, and 1 : 1.05 v/v; 40%, 70%, and 100% v/v, respectively. The ethanolic aqueous solution was used to impart less harsh condition for desolvation and attain controlled nanoparticle formation. The interaction plot studies inferred the ethanolic aqueous solution concentration to be the most influential parameter that affects the particle size of nanoformulation. This method (BSA, 4% w/v; volume of BSA solution to total ethanol ratio, 1 : 0.90 v/v; concentration of diluted ethanolic solution, 70% v/v was able to successfully develop Gemcitabine (G loaded modified albumin nanocarrier (M-ANC-G of size 25.07±2.81 nm (ζ=-23.03±1.015 mV as against to 78.01±4.99 nm (ζ=-24.88±1.37 mV using conventional method albumin nanocarrier (C-ANC-G. Hybrid nanocarriers were generated by chitosan layering (solvent gelation technique of respective ANC to form C-HNC-G and M-HNC-G of sizes 125.29±5.62 nm (ζ=12.01±0.51 mV and 46.28±2.21 nm (ζ=15.05±0.39 mV, respectively. Zeta potential, entrapment, in vitro release, and pH-based stability studies were investigated and influence of formulation parameters are discussed. Cell-line-based cytotoxicity assay (A549 and H460 cells and cell internalization assay (H460 cell line were performed to assess the

  3. Driver-Array Based Flat-Panel Loudspeakers: Theoretical Background and Design Guidelines

    Science.gov (United States)

    Anderson, David Allan

    This thesis relates to the simulation and design of flat-panel loudspeakers using moving-coil driver elements. A brief history of the industry is given, including a collection of products and patents from 1925 until the present, an overview of research papers, and a discussion of current products available. The mechanics of bending flat panels are developed with respect to localized driving forces, both in the frequency domain and the time domain as an impulse response. These simulations are compared to measurements on prototype panels. Additional resonant elements influence the behavior of the system: an optional ported rear enclosure and the resonant characteristics of the drivers. The governing equations for these systems are derived and solutions are implemented using equivalent mechanical circuits and numerical methods. The idea of using driver arrays to independently actuate modes of the panel is discussed at length with respect to modal addressability, modal spillover, and experimental validation. The numerical approach to determining the optimal driver placement for a given set of modes is derived and experimentally validated. An investigation of the acoustic behavior of flat panel loudspeakers is presented, using mechanical simulation results to predict the acoustic radiation. The simulations are compared to measurements and found to accurately predict important mechanical and acoustical behaviors. It is demonstrated that a driver array, with the proper biasing, is capable of creating a flat panel loudspeaker which acts more like a piston than a "diffuse radiator" flat panel loudspeaker. The techniques of "Modal Crossover Networks" are introduced, which use multi-band filters to bias the driver array differently for different frequency bands, optimized for audio reproduction. The question of how many drivers are necessary for a modal crossover network is addressed and found to be dependent on the estimated quality factor (Q) of the panel material and edge

  4. Direct microcontact printing of oligonucleotides for biochip applications

    Directory of Open Access Journals (Sweden)

    Trévisiol E

    2005-07-01

    Full Text Available Abstract Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting

  5. Design Methodology of a Dual-Halbach Array Linear Actuator with Thermal-Electromagnetic Coupling.

    Science.gov (United States)

    Eckert, Paulo Roberto; Flores Filho, Aly Ferreira; Perondi, Eduardo; Ferri, Jeferson; Goltz, Evandro

    2016-03-11

    This paper proposes a design methodology for linear actuators, considering thermal and electromagnetic coupling with geometrical and temperature constraints, that maximizes force density and minimizes force ripple. The method allows defining an actuator for given specifications in a step-by-step way so that requirements are met and the temperature within the device is maintained under or equal to its maximum allowed for continuous operation. According to the proposed method, the electromagnetic and thermal models are built with quasi-static parametric finite element models. The methodology was successfully applied to the design of a linear cylindrical actuator with a dual quasi-Halbach array of permanent magnets and a moving-coil. The actuator can produce an axial force of 120 N and a stroke of 80 mm. The paper also presents a comparative analysis between results obtained considering only an electromagnetic model and the thermal-electromagnetic coupled model. This comparison shows that the final designs for both cases differ significantly, especially regarding its active volume and its electrical and magnetic loading. Although in this paper the methodology was employed to design a specific actuator, its structure can be used to design a wide range of linear devices if the parametric models are adjusted for each particular actuator.

  6. G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents.

    Science.gov (United States)

    Musumeci, Domenica; Riccardi, Claudia; Montesarchio, Daniela

    2015-09-22

    Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.

  7. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  8. Design of DSP-based high-power digital solar array simulator

    Science.gov (United States)

    Zhang, Yang; Liu, Zhilong; Tong, Weichao; Feng, Jian; Ji, Yibo

    2013-12-01

    To satisfy rigid performance specifications, a feedback control was presented for zoom optical lens plants. With the increasing of global energy consumption, research of the photovoltaic(PV) systems get more and more attention. Research of the digital high-power solar array simulator provides technical support for high-power grid-connected PV systems research.This paper introduces a design scheme of the high-power digital solar array simulator based on TMS320F28335. A DC-DC full-bridge topology was used in the system's main circuit. The switching frequency of IGBT is 25kHz.Maximum output voltage is 900V. Maximum output current is 20A. Simulator can be pre-stored solar panel IV curves.The curve is composed of 128 discrete points .When the system was running, the main circuit voltage and current values was feedback to the DSP by the voltage and current sensors in real-time. Through incremental PI,DSP control the simulator in the closed-loop control system. Experimental data show that Simulator output voltage and current follow a preset solar panels IV curve. In connection with the formation of high-power inverter, the system becomes gridconnected PV system. The inverter can find the simulator's maximum power point and the output power can be stabilized at the maximum power point (MPP).

  9. Functionalization and Self-Assembly of DNA Bidimensional Arrays

    Directory of Open Access Journals (Sweden)

    Ramon Eritja

    2011-09-01

    Full Text Available Oligonucleotides carrying amino, thiol groups, as well as fluorescein, c-myc peptide sequence and nanogold at internal positions were prepared and used for the assembly of bidimensional DNA arrays.

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

    Science.gov (United States)

    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.

  11. LINAC DESIGN FOR AN ARRAY OF SOFT X-RAY FREE ELECTRON LASERS

    International Nuclear Information System (INIS)

    Zholents, Alexander A.; Kur, E.; Penn, G.; Qiang, Ji; Venturini, M.; Wells, R. P.

    2008-01-01

    The design of the linac delivering electron bunches into ten independent soft x-ray free electron lasers (FELs) producing light at 1 nm and longer wavelengths is presented. The bunch repetition rate in the linac is 1 MHz and 100 kHz in each of ten FEL beam lines. Various issues regarding machine layout and lattice, bunch compression, collimation, and the beam switch yard are discussed. Particular attention is given to collective effects. A demanding goal is to preserve both a low beam slice emittance and low slice energy spread during acceleration, bunch compression and distribution of the electron bunches into the array of FEL beamlines. Detailed studies of the effect of the electron beam microbunching caused by longitudinal space-charge forces and coherent synchrotron radiation (CSR) have been carried out and their results are presented

  12. Reconfigurable phased antenna array for extending cubesat operations to Ka-band: Design and feasibility

    Science.gov (United States)

    Buttazzoni, G.; Comisso, M.; Cuttin, A.; Fragiacomo, M.; Vescovo, R.; Vincenti Gatti, R.

    2017-08-01

    Started as educational tools, CubeSats have immediately encountered the favor of the scientific community, subsequently becoming viable platforms for research and commercial applications. To ensure competitive data rates, some pioneers have started to explore the usage of the Ka-band beside the conventional amateur radio frequencies. In this context, this study proposes a phased antenna array design for Ka-band downlink operations consisting of 8×8 circularly polarized subarrays of microstrip patches filling one face of a single CubeSat unit. The conceived structure is developed to support 1.5 GHz bandwidth and dual-task missions, whose feasibility is verified by proper link budgets. The dual-task operations are enabled by a low-complexity phase-only control algorithm that provides pattern reconfigurability in order to satisfy both orbiting and intersatellite missions, while remaining adherent to the cost-effective CubeSat paradigm.

  13. Halbach array-based design and simulation of disc coreless permanen-magnet integrated starter generator

    Science.gov (United States)

    Li, Y. B.; Yang, Z. X.; Chen, W.; He, Q. Y.

    2017-11-01

    The functional performance, such as magnetic flux leakage, power density and efficiency, is related to the structural characteristics and design technique for the disc permanent magnet synchronous generators (PMSGs). Halbach array theory-based magnetic circuit structure is developed, and Maxwell3D simulation analysis approach of PMSG is proposed in this paper for integrated starter generator (ISG). The magnetization direction of adjacent permanent magnet is organized in difference of 45 degrees for focusing air gap side, and improving the performance of the generator. The magnetic field distribution and functional performance in load and/or unload conditions are simulated by Maxwell3D module. The proposed approach is verified by simulation analysis, the air gap flux density is 0.66T, and the phase voltage curve has the characteristics of a preferable sinusoidal wave and the voltage amplitude 335V can meet the design requirements while the disc coreless PMSG is operating at rated speed. And the developed magnetic circuit structure can be used for engineering design of the disc coreless PMSG to the integrated starter generator.

  14. Design of a Tritium-in-air-monitor using field programmable gate arrays

    International Nuclear Information System (INIS)

    McNelles, Phillip; Lu, Lixuan

    2015-01-01

    Field Programmable Gate Arrays (FPGAs) have recently garnered significant interest for certain applications within the nuclear field. Some applications of these devices include Instrumentation and Control (I and C) systems, pulse measurement systems, particle detectors and health physics purposes. In CANada Deuterium Uranium (CANDU) nuclear power plants, the use of heavy water (D2O) as the moderator leads to the increased production of Tritium, which poses a health risk and must be monitored by Tritium-In-Air Monitors (TAMs). Traditional TAMs are mostly designed using microprocessors. More recent studies show that FPGAs could be a potential alternative to implement the electronic logic used in radiation detectors, such as the TAM, more effectively. In this paper, an FPGA-based TAM is designed and constructed in a laboratory setting using an FPGA-based cRIO system. New functionalities, such as the detection of Carbon-14 and the addition of noble gas compensation are incorporated into a new FPGA-based TAM. Additionally, all of the standard functions included in the original microprocessor-based TAM, such as tritium detection, gamma compensation, pump and air flow control, and background and thermal drift corrections were also implemented. The effectiveness of the new design is demonstrated through simulations as well as laboratory testing on the prototype system. (author)

  15. Planar ESPAR Array Design with Nonsymmetrical Pattern by Means of Finite-Element Method, Domain Decomposition, and Spherical Wave Expansion

    Directory of Open Access Journals (Sweden)

    Jesús García

    2012-01-01

    Full Text Available The application of a 3D domain decomposition finite-element and spherical mode expansion for the design of planar ESPAR (electronically steerable passive array radiator made with probe-fed circular microstrip patches is presented in this work. A global generalized scattering matrix (GSM in terms of spherical modes is obtained analytically from the GSM of the isolated patches by using rotation and translation properties of spherical waves. The whole behaviour of the array is characterized including all the mutual coupling effects between its elements. This procedure has been firstly validated by analyzing an array of monopoles on a ground plane, and then it has been applied to synthesize a prescribed radiation pattern optimizing the reactive loads connected to the feeding ports of the array of circular patches by means of a genetic algorithm.

  16. Design and operation of a 2-D thin-film semiconductor neutron detector array for use as a beamport monitor

    International Nuclear Information System (INIS)

    Unruh, Troy C.; Bellinger, Steven L.; Huddleston, David E.; McNeil, Walter J.; Patterson, Eric; Sobering, Tim J.; McGregor, Douglas S.

    2009-01-01

    Silicon-based diodes coated with a thin film of neutron reactive materials have been shown to produce excellent low-efficiency neutron detectors. This work employs the same technology, but groups 25 equally sized and spaced diodes on a single 29 mm by 29 mm substrate. A 5x5 array was fabricated and coated with a thin film of 6 LiF for use as a low-efficiency neutron beam monitor. The 5x5 neutron detector array is coupled to an array of amplifiers, allowing the response to be interpreted using a LabVIEW FPGA. The 5x5 array has been characterized in a diffracted neutron beam. This work is a part of on-going research to develop various designs of high- and low-efficiency semiconductor neutron detectors.

  17. Design and characterization of a laterally mounted phased-array transducer breast-specific MRgHIFU device with integrated 11-channel receiver array.

    Science.gov (United States)

    Payne, A; Merrill, R; Minalga, E; Vyas, U; de Bever, J; Todd, N; Hadley, R; Dumont, E; Neumayer, L; Christensen, D; Roemer, R; Parker, D

    2012-03-01

    This work presents the design and preliminary evaluation of a new laterally mounted phased-array MRI-guided high-intensity focused ultrasound (MRgHIFU) system with an integrated 11-channel phased-array radio frequency (RF) coil intended for breast cancer treatment. The design goals for the system included the ability to treat the majority of tumor locations, to increase the MR image's signal-to-noise ratio (SNR) throughout the treatment volume and to provide adequate comfort for the patient. In order to treat the majority of the breast volume, the device was designed such that the treated breast is suspended in a 17-cm diameter treatment cylinder. A laterally shooting 1-MHz, 256-element phased-array ultrasound transducer with flexible positioning is mounted outside the treatment cylinder. This configuration achieves a reduced water volume to minimize RF coil loading effects, to position the coils closer to the breast for increased signal sensitivity, and to reduce the MR image noise associated with using water as the coupling fluid. This design uses an 11-channel phased-array RF coil that is placed on the outer surface of the cylinder surrounding the breast. Mechanical positioning of the transducer and electronic steering of the focal spot enable placement of the ultrasound focus at arbitrary locations throughout the suspended breast. The treatment platform allows the patient to lie prone in a face-down position. The system was tested for comfort with 18 normal volunteers and SNR capabilities in one normal volunteer and for heating accuracy and stability in homogeneous phantom and inhomogeneous ex vivo porcine tissue. There was a 61% increase in mean relative SNR achieved in a homogeneous phantom using the 11-channel RF coil when compared to using only a single-loop coil around the chest wall. The repeatability of the system's energy delivery in a single location was excellent, with less than 3% variability between repeated temperature measurements at the same

  18. Design techniques for a stable operation of cryogenic field-programmable gate arrays

    Science.gov (United States)

    Homulle, Harald; Visser, Stefan; Patra, Bishnu; Charbon, Edoardo

    2018-01-01

    In this paper, we show how a deep-submicron field-programmable gate array (FPGA) can be operated more stably at extremely low temperatures through special firmware design techniques. Stability at low temperatures is limited through long power supply wires and reduced performance of various printed circuit board components commonly employed at room temperature. Extensive characterization of these components shows that the majority of decoupling capacitor types and voltage regulators are not well behaved at cryogenic temperatures, asking for an ad hoc solution to stabilize the FPGA supply voltage, especially for sensitive applications. Therefore, we have designed a firmware that enforces a constant power consumption, so as to stabilize the supply voltage in the interior of the FPGA. The FPGA is powered with a supply at several meters distance, causing significant resistive voltage drop and thus fluctuations on the local supply voltage. To achieve the stabilization, the variation in digital logic speed, which directly corresponds to changes in supply voltage, is constantly measured and corrected for through a tunable oscillator farm, implemented on the FPGA. The impact of the stabilization technique is demonstrated together with a reconfigurable analog-to-digital converter (ADC), completely implemented in the FPGA fabric and operating at 15 K. The ADC performance can be improved by at most 1.5 bits (effective number of bits) thanks to the more stable supply voltage. The method is versatile and robust, enabling seamless porting to other FPGA families and configurations.

  19. Design and Development of an Array of Dielectric Suspended Membranes for Microhotplate Applications

    Directory of Open Access Journals (Sweden)

    Mahanth Prasad

    2014-05-01

    Full Text Available The paper presents the design, fabrication and characterization of an array of suspended dielectric suspended membranes for microhotplate applications. A single cell membrane (100 µm ´ 100 µm made of two different dielectric layers: SiO2 and Si3N4 separately, was designed and simulated using ANSYS 10.0. The simulation of stress generated in different dielectric membranes as a function of temperature is reported. The thickness of both layers was taken as 0.3 µm. The membranes of both SiO2 and Si3N4 dielectrics were fabricated on silicon substrate by bulk micromachining technique using TMAH solution. The buckling of the beam and breakage of membranes made of high-stress Si3N4 film are reported. The simulated results were verified by experiments. The membrane made of SiO2 layer was found to be more suitable in comparison to high-stress Si3N4 layer for microhotplate applications. The present approach provides high yield at low cost for fabrication of microhotplates for gas sensing applications.

  20. Study of the Carrier-Aided Thin Film Electrode Array Design for Cochlear Insertion

    Directory of Open Access Journals (Sweden)

    Yuchen Xu

    2018-04-01

    Full Text Available The micro-fabricated thin film electrode array (TFEA has been a promising design for cochlear implants (CIs because of its cost-effectiveness and fabrication precision. The latest polymer-based cochlear TFEAs have faced difficulties for cochlear insertion due to the lack of structural stiffness. To stiffen the TFEA, dissolvable stiffening materials, TFEAs with different structures, and TFEAs with commercial CIs as carriers have been invested. In this work, the concept of enhancing a Parylene TFEA with Kapton tape as a simpler carrier for cochlear insertion has been proved to be feasible. The bending stiffness of the Kapton-aided TFEA was characterized with an analytical model, a finite element model, and a cantilever bending experiment, respectively. While the Kapton tape increased the bending stiffness of the Parylene TFEA by 103 times, the 6-μm-thick TFEA with a similar Young’s modulus, as a polyimide, in turn significantly increased the bending stiffness of the 170-μm-thick Kapton carrier by 60%. This result indicated that even the TFEA is ultra-flexible and that its bending stiffness should not be neglected in the design or selection of its carrier.

  1. Array capabilities and future arrays

    International Nuclear Information System (INIS)

    Radford, D.

    1993-01-01

    Early results from the new third-generation instruments GAMMASPHERE and EUROGAM are confirming the expectation that such arrays will have a revolutionary effect on the field of high-spin nuclear structure. When completed, GAMMASHPERE will have a resolving power am order of magnitude greater that of the best second-generation arrays. When combined with other instruments such as particle-detector arrays and fragment mass analysers, the capabilites of the arrays for the study of more exotic nuclei will be further enhanced. In order to better understand the limitations of these instruments, and to design improved future detector systems, it is important to have some intelligible and reliable calculation for the relative resolving power of different instrument designs. The derivation of such a figure of merit will be briefly presented, and the relative sensitivities of arrays currently proposed or under construction presented. The design of TRIGAM, a new third-generation array proposed for Chalk River, will also be discussed. It is instructive to consider how far arrays of Compton-suppressed Ge detectors could be taken. For example, it will be shown that an idealised open-quote perfectclose quotes third-generation array of 1000 detectors has a sensitivity an order of magnitude higher again than that of GAMMASPHERE. Less conventional options for new arrays will also be explored

  2. Enzymatic Production of Monoclonal Stoichiometric Single-Stranded DNA Oligonucleotides

    Science.gov (United States)

    Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M.; Högberg, Björn

    2013-01-01

    Single-stranded oligonucleotides are important as research tools as probes for diagnostics and gene therapy. Today, production of oligonucleotides is done via solid-phase synthesis. However, the capabilities of current polymer chemistry are limited in comparison to what can be produced in biological systems. The errors in synthetic DNA increases with oligonucleotide length, and sequence diversity can often be a problem. Here, we present the Monoclonal Stoichiometric (MOSIC) method for enzymatic DNA oligonucleotide production. Using this method, we amplify oligonucleotides from clonal templates followed by digestion of a cutter-hairpin, resulting in pools of monoclonal oligonucleotides with precisely controlled relative stoichiometric ratios. We present data where MOSIC oligonucleotides, 14–378 nt long, were prepared either by in vitro rolling-circle amplification, or by amplification in Escherichia coli in the form of phagemid DNA. The formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides. PMID:23727986

  3. Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.

    Science.gov (United States)

    Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M; Högberg, Björn

    2013-07-01

    Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. Here we present the 'monoclonal stoichiometric' (MOSIC) method for enzyme-mediated production of DNA oligonucleotides. We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides.

  4. Millimeter-Wave Microstrip Antenna Array Design and an Adaptive Algorithm for Future 5G Wireless Communication Systems

    Directory of Open Access Journals (Sweden)

    Cheng-Nan Hu

    2016-01-01

    Full Text Available This paper presents a high gain millimeter-wave (mmW low-temperature cofired ceramic (LTCC microstrip antenna array with a compact, simple, and low-profile structure. Incorporating minimum mean square error (MMSE adaptive algorithms with the proposed 64-element microstrip antenna array, the numerical investigation reveals substantial improvements in interference reduction. A prototype is presented with a simple design for mass production. As an experiment, HFSS was used to simulate an antenna with a width of 1 mm and a length of 1.23 mm, resonating at 38 GHz. Two identical mmW LTCC microstrip antenna arrays were built for measurement, and the center element was excited. The results demonstrated a return loss better than 15 dB and a peak gain higher than 6.5 dBi at frequencies of interest, which verified the feasibility of the design concept.

  5. The Design, Implementation, and Performance of the Astro-H SXS Calorimeter Array and Anti-Coincidence Detector

    Science.gov (United States)

    Kilbourne, Caroline A.; Adams, Joseph S.; Brekosky, Regis P.; Chiao, Meng P.; Chervenak, James A.; Eckart, Megan E.; Figueroa-Feliciano, Enectali; Galeazzi, Masimilliano; Grein, Christoph; Jhabvala, Christine A.; hide

    2016-01-01

    The calorimeter array of the JAXA Astro-H (renamed Hitomi) Soft X-ray Spectrometer (SXS) was designed to provide unprecedented spectral resolution of spatially extended cosmic x-ray sources and of all cosmic x-ray sources in the Fe-K band around 6 keV, enabling essential plasma diagnostics. The SXS has a square array of 36 microcalorimeters at the focal plane. These calorimeters consist of ion-implanted silicon thermistors and HgTe thermalizing x-ray absorbers. These devices have demonstrated a resolution of better than 4.5 eV at 6 keV when operated at a heat-sink temperature of 50 mK. We will discuss the basic physical parameters of this array, including the array layout, thermal conductance of the link to the heat sink, resistance function, absorber details, and means of attaching the absorber to the thermistor-bearing element. We will also present the thermal characterization of the whole array, including thermal conductance and crosstalk measurements and the results of pulsing the frame temperature via alpha particles, heat pulses, and the environmental background. A silicon ionization detector is located behind the calorimeter array and serves to reject events due to cosmic rays. We will briefly describe this anti-coincidence detector and its performance.

  6. Assessment of High-Voltage Photovoltaic Technologies for the Design of a Direct Drive Hall Effect Thruster Solar Array

    Science.gov (United States)

    Mikellides, I. G.; Jongeward, G. A.; Schneider, T.; Carruth, M. R.; Peterson, T.; Kerslake, T. W.; Snyder, D.; Ferguson, D.; Hoskins, A.

    2004-01-01

    A three-year program to develop a Direct Drive Hall-Effect Thruster system (D2HET) begun in 2001 as part of the NASA Advanced Cross-Enterprise Technology Development initiative. The system, which is expected to reduce significantly the power processing, complexity, weight, and cost over conventional low-voltage systems, will employ solar arrays that operate at voltages higher than (or equal to) 300 V. The lessons learned from the development of the technology also promise to become a stepping-stone for the production of the next generation of power systems employing high voltage solar arrays. This paper summarizes the results from experiments conducted mainly at the NASA Marshal Space Flight Center with two main solar array technologies. The experiments focused on electron collection and arcing studies, when the solar cells operated at high voltages. The tests utilized small coupons representative of each solar array technology. A hollow cathode was used to emulate parts of the induced environment on the solar arrays, mostly the low-energy charge-exchange plasma (1012-1013 m-3 and 0.5-1 eV). Results and conclusions from modeling of electron collection are also summarized. The observations from the total effort are used to propose a preliminary, new solar array design for 2 kW and 30-40 kW class, deep space missions that may employ a single or a cluster of Hall- Effect thrusters.

  7. Design of Tunnel Magnetoresistive-Based Circular MFL Sensor Array for the Detection of Flaws in Steel Wire Rope

    Directory of Open Access Journals (Sweden)

    Liu Xiucheng

    2016-01-01

    Full Text Available Tunnel magnetoresistive (TMR devices have superior performances in weak magnetic field detection. In this study, TMR devices were first employed to form a circular magnetic flux leakage (MFL sensor for slight wire rope flaw detection. Two versions of this tailor-made circular TMR-based sensor array were presented for the inspection of wire ropes with the diameters of 14 mm and 40 mm, respectively. Helmholtz-like coils or a ferrite magnet-based magnetizer was selected to provide the proper magnetic field, in order to meet the technical requirements of the TMR devices. The coefficient of variance in the flaw detection performance of the sensor array elements was experimentally estimated at 4.05%. Both versions of the MFL sensor array were able to detect multiple single-broken wire flaws in the wire ropes. The accurate axial and circumferential positions of these broken wire flaws were estimated from the MFL scanning image results. In addition, the proposed TMR-based sensor array was applied to detect the MFL signal induced by slight surface wear defects. A mutual correlation analysis method was used to distinguish the signals caused by the lift-off fluctuation from the MFL scanning image results. The MFL sensor arrays presented in this study provide inspiration for the designing of tailor-made TMR-based circular sensor arrays for cylindrical ferromagnetic structural inspections.

  8. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2005-05-01

    Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

  9. Radio-marking and in vivo imagery of oligonucleotides

    International Nuclear Information System (INIS)

    Kuehnast, Bertrand

    2000-01-01

    This research thesis is part of activities aimed at the development of new molecules like oligonucleotides. Its first objective was the development and validation of a marking method with fluorine-18 of oligonucleotides for their in-vivo pharmacological assessment with positron emission tomography (PET). Further investigations addressed the use of iodine-125 for oligonucleotide marking purpose. This radio-marking, and in vivo and ex vivo imagery techniques are described, and their potential is highlighted for the pharmacological assessment of different oligonucleotides

  10. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Science.gov (United States)

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  11. Research on analytical model and design formulas of permanent magnetic bearings based on Halbach array with arbitrary segmented magnetized angle

    International Nuclear Information System (INIS)

    Wang, Nianxian; Wang, Dongxiong; Chen, Kuisheng; Wu, Huachun

    2016-01-01

    The bearing capacity of permanent magnetic bearings can be improved efficiently by using the Halbach array magnetization. However, the research on analytical model of Halbach array PMBs with arbitrary segmented magnetized angle has not been developed. The application of Halbach array PMBs has been limited by the absence of the analytical model and design formulas. In this research, the Halbach array PMBs with arbitrary segmented magnetized angle has been studied. The magnetization model of bearings is established. The magnetic field distribution model of the permanent magnet array is established by using the scalar magnetic potential model. On the basis of this, the bearing force model and the bearing stiffness model of the PMBs are established based on the virtual displacement method. The influence of the pair of magnetic rings in one cycle and the structure parameters of PMBs on the maximal bearing capacity and support stiffness characteristics are studied. The reference factors for the design process of PMBs have been given. Finally, the theoretical model and the conclusions are verified by the finite element analysis.

  12. Design of a Dry Dilution Refrigerator for MMC Gamma Detector Arrays

    Energy Technology Data Exchange (ETDEWEB)

    Friedrich, Stephan [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Boyd, Stephen [Univ. of New Mexico, Albuquerque, NM (United States); Cantor, Robin

    2017-04-03

    The goal of this LCP is to develop an ultra-high resolution gamma detector based on magnetic microcalorimeters (MMCs) for accurate non-destructive analysis (NDA) of nuclear materials. For highest energy resolution, we will introduce erbium-doped silver (Ag:Er) as a novel sensor material to replace current Au:Er sensors. The detector sensitivity will be increased by developing arrays of 32 Ag:Er pixels read out by 16 SQUID preamplifiers. MMC detectors require operating temperatures of ~15 mK and thus the use of a dilution refrigerator, and the desire for user-friendly operation without cryogenic liquids requires that this refrigerator use pulse-tube pre-cooling to ~4 K. For long-term reliability, we intend to re-design the heat switch that is needed to apply the magnetizing current to the Ag:Er sensor and that used to fail in earlier designs after months of operation. A cryogenic Compton veto will be installed to reduce the spectral background of the MMC, especially at low energies where ultra-high energy resolution is most important. The goals for FY16 were 1) to purchase a liquid-cryogen-free dilution refrigerator and adapt it for MMC operation, and 2) to fabricate Ag:Er-based MMC γ-detectors with improved performance and optimize their response. This report discusses the design of the instruments, and progress in MMC detector fabrication. Details of the MMC fabrication have been discussed in an April 2016 report to DOE.

  13. Progress on the design of a data push architecture for an array of optimized time tagging pixels

    International Nuclear Information System (INIS)

    Shapiro, S.; Cords, D.; Mani, S.; Holbrook, B.; Atlas, E.

    1993-06-01

    A pixel array has been proposed which features a completely data driven architecture. A pixel cell has been designed that has been optimized for this readout. It retains the features of preceding designs which allow low noise operation, time stamping, analog signal processing, XY address recording, ghost elimination and sparse data transmission. The pixel design eliminates a number of problems inherent in previous designs, by the use of sampled data techniques, destructive readout, and current mode output drivers. This architecture and pixel design is directed at applications such as a forward spectrometer at the SSC, an e + e - B factory at SLAC, and fixed target experiments at FNAL

  14. Designing an array for performing Near-field Acoustic Holography with a small number of p-u probes

    DEFF Research Database (Denmark)

    Fernandez Comesaña, Daniel; Wen, Junjie; Fernandez Grande, Efren

    2016-01-01

    , such approaches usually require that a large number of transducers is spatially distributed over the area of interest. This paper describes some practical considerations for the design and optimization of a compact sensor array for performing NAH with a small number of sound intensity p-u probes. Two sensor...

  15. Electronic Structures of LNA Phosphorothioate Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Henrik G. Bohr

    2017-09-01

    Full Text Available Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM calculations and chromatography experiments on locked nucleic acid (LNA phosphorothioate (PS oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules. Keywords: LNA phosphorothioate, DNA/LNA oligonucleotide, diastereoisomers, Hartree-Fock calculations, iso-potential surface, anion chromatograms

  16. Associating Oligonucleotides with Positively Charged Liposomes

    Czech Academy of Sciences Publication Activity Database

    Jurkiewicz, P.; Okruszek, A.; Hof, Martin; Langner, M.

    2003-01-01

    Roč. 8, č. 1 (2003), s. 77-84 ISSN 1425-8153 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : oligonucleotides * fluorescence correlation spectroscopy * DOTAP Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.455, year: 2003

  17. Triplex-forming ability of modified oligonucleotides

    DEFF Research Database (Denmark)

    Højland, Torben; Babu, Bolle Ravindra; Bryld, Torsten

    2007-01-01

    We present our studies on the ability of several different nucleotide analogs as triplex-forming oligonucleotides. The modifications tested include 4'-C-hydroxymethyl, LNA, 2'-amino-LNA and N2'-functionalized 2'-amino-LNA. Triplexes containing monomers of N2'-glycyl-functionalized 2'-amino-LNA ar...

  18. Bondwire array modeling for the design of hybrid high power amplifiers above C-band

    DEFF Research Database (Denmark)

    Hernández, Carlos Cilla; Jónasson, Sævar Þór; Hanberg, Jesper

    2012-01-01

    This paper presents a bondwire array model obtained using a software based on the finite elements method and validated up to 15 GHz by measurements over a purpose-build array structure. This work addresses the limits of the inductor-based bondwire model when used at frequencies above C-band to si...

  19. Binding of Dumbbell Oligonucleotides to MoMuLV Reverse Transcriptase: Inhibitory Properties of RNase H Activity

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    2010-01-01

    Full Text Available Dumbbell oligonucleotides with loops of various chemistry were synthesized. Incubation of dumbbell oligonucleotides containing phosphorothioate bonds or trimethylene phosphate linkages in loops with S1 nuclease did not result in significant cleavage under conditions which led to the degradation of dumbbell oligonucleotide containing phophodiester bonds in the loops. The binding of reverse transcriptase of Moloney Murine Leukemia Virus (MoMuLV was evaluated with all the five oligonucleotides. The protein binds to all the dumbbell oligonucleotides with similar affinity. The dissociation constants evaluated using PAGE band mobility shift assays were of the order of 10-7. The inhibitory properties of the retroviral RNase H activity was evaluated using 3H –UTP-labeled RNA:RNA-DNA hybrid. It was found that the best dumbbell oligonucleotide, inhibitor contained phosphorothioate residues in both the loops. Our value studies demonstrated that this particularly designed oligonucleotide displays an IC50 of 18 nM in its inhibition on the reverse transcriptase RNase H activity, a magnitude lower than that of first nucleotide reverse transcriptase of HIV-1, tenofovir, introduced by Gilead Science in the market.

  20. Thin-film sparse boundary array design for passive acoustic mapping during ultrasound therapy.

    Science.gov (United States)

    Coviello, Christian M; Kozick, Richard J; Hurrell, Andrew; Smith, Penny Probert; Coussios, Constantin-C

    2012-10-01

    A new 2-D hydrophone array for ultrasound therapy monitoring is presented, along with a novel algorithm for passive acoustic mapping using a sparse weighted aperture. The array is constructed using existing polyvinylidene fluoride (PVDF) ultrasound sensor technology, and is utilized for its broadband characteristics and its high receive sensitivity. For most 2-D arrays, high-resolution imagery is desired, which requires a large aperture at the cost of a large number of elements. The proposed array's geometry is sparse, with elements only on the boundary of the rectangular aperture. The missing information from the interior is filled in using linear imaging techniques. After receiving acoustic emissions during ultrasound therapy, this algorithm applies an apodization to the sparse aperture to limit side lobes and then reconstructs acoustic activity with high spatiotemporal resolution. Experiments show verification of the theoretical point spread function, and cavitation maps in agar phantoms correspond closely to predicted areas, showing the validity of the array and methodology.

  1. The high dynamic range pixel array detector (HDR-PAD): Concept and design

    Energy Technology Data Exchange (ETDEWEB)

    Shanks, Katherine S.; Philipp, Hugh T.; Weiss, Joel T.; Becker, Julian; Tate, Mark W. [Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853 (United States); Gruner, Sol M., E-mail: smg26@cornell.edu [Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853 (United States); Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853 (United States)

    2016-07-27

    Experiments at storage ring light sources as well as at next-generation light sources increasingly require detectors capable of high dynamic range operation, combining low-noise detection of single photons with large pixel well depth. XFEL sources in particular provide pulse intensities sufficiently high that a purely photon-counting approach is impractical. The High Dynamic Range Pixel Array Detector (HDR-PAD) project aims to provide a dynamic range extending from single-photon sensitivity to 10{sup 6} photons/pixel in a single XFEL pulse while maintaining the ability to tolerate a sustained flux of 10{sup 11} ph/s/pixel at a storage ring source. Achieving these goals involves the development of fast pixel front-end electronics as well as, in the XFEL case, leveraging the delayed charge collection due to plasma effects in the sensor. A first prototype of essential electronic components of the HDR-PAD readout ASIC, exploring different options for the pixel front-end, has been fabricated. Here, the HDR-PAD concept and preliminary design will be described.

  2. Design and analysis of a dual mode CMOS field programmable analog array

    International Nuclear Information System (INIS)

    Cheng Xiaoyan; Yang Haigang; Yin Tao; Wu Qisong; Zhang Hongfeng; Liu Fei

    2014-01-01

    This paper presents a novel field-programmable analog array (FPAA) architecture featuring a dual mode including discrete-time (DT) and continuous-time (CT) operation modes, along with a highly routable connection boxes (CBs) based interconnection lattice. The dual mode circuit for the FPAA is capable of achieving targeted optimal performance in different applications. The architecture utilizes routing switches in a CB not only for the signal interconnection purpose but also for control of the electrical charge transfer required in switched-capacitor circuits. This way, the performance of the circuit in either mode shall not be hampered with adding of programmability. The proposed FPAA is designed and implemented in a 0.18 μm standard CMOS process with a 3.3 V supply voltage. The result from post-layout simulation shows that a maximum bandwidth of 265 MHz through the interconnection network is achieved. The measured results from demonstrated examples show that the maximum signal bandwidth of up to 2 MHz in CT mode is obtained with the spurious free dynamic range of 54 dB, while the signal processing precision in DT mode reaches 96.4%. (semiconductor integrated circuits)

  3. Design and optimization of a high-efficiency array generator in the mid-IR with binary subwavelength grooves.

    Science.gov (United States)

    Bloom, Guillaume; Larat, Christian; Lallier, Eric; Lee-Bouhours, Mane-Si Laure; Loiseaux, Brigitte; Huignard, Jean-Pierre

    2011-02-10

    We have designed a high-efficiency array generator composed of subwavelength grooves etched in a GaAs substrate for operation at 4.5 μm. The method used combines rigorous coupled wave analysis with an optimization algorithm. The optimized beam splitter has both a high efficiency (∼96%) and a good intensity uniformity (∼0.2%). The fabrication error tolerances are numerically calculated, and it is shown that this subwavelength array generator could be fabricated with current electron beam writers and inductively coupled plasma etching. Finally, we studied the effect of a simple and realistic antireflection coating on the performance of the beam splitter.

  4. Intelligent Design of Metal Oxide Gas Sensor Arrays Using Reciprocal Kernel Support Vector Regression

    Science.gov (United States)

    Dougherty, Andrew W.

    Metal oxides are a staple of the sensor industry. The combination of their sensitivity to a number of gases, and the electrical nature of their sensing mechanism, make the particularly attractive in solid state devices. The high temperature stability of the ceramic material also make them ideal for detecting combustion byproducts where exhaust temperatures can be high. However, problems do exist with metal oxide sensors. They are not very selective as they all tend to be sensitive to a number of reduction and oxidation reactions on the oxide's surface. This makes sensors with large numbers of sensors interesting to study as a method for introducing orthogonality to the system. Also, the sensors tend to suffer from long term drift for a number of reasons. In this thesis I will develop a system for intelligently modeling metal oxide sensors and determining their suitability for use in large arrays designed to analyze exhaust gas streams. It will introduce prior knowledge of the metal oxide sensors' response mechanisms in order to produce a response function for each sensor from sparse training data. The system will use the same technique to model and remove any long term drift from the sensor response. It will also provide an efficient means for determining the orthogonality of the sensor to determine whether they are useful in gas sensing arrays. The system is based on least squares support vector regression using the reciprocal kernel. The reciprocal kernel is introduced along with a method of optimizing the free parameters of the reciprocal kernel support vector machine. The reciprocal kernel is shown to be simpler and to perform better than an earlier kernel, the modified reciprocal kernel. Least squares support vector regression is chosen as it uses all of the training points and an emphasis was placed throughout this research for extracting the maximum information from very sparse data. The reciprocal kernel is shown to be effective in modeling the sensor

  5. A Design of Wide Band and Wide Beam Cavity-Backed Slot Antenna Array with Slant Polarization

    Directory of Open Access Journals (Sweden)

    Huiying Qi

    2016-01-01

    Full Text Available Design of antenna array under the limitation of restricted size is a challenging problem. Cavity-backed slot antenna is widely used because of its advantages of small size, wide band, and wide beam. In this paper, a design of wide band and wide beam cavity-backed slot antenna array with the slant polarization is proposed. To obtain wide band and wide beam with limited size, the inverted microstrip-fed cavity-backed slot antenna (IMF-CBSA is adopted as the element of 1 × 4 antenna array. The slant polarized antennas and their feeding networks are adopted because of their simple structures. The performance of the proposed antenna array is verified by the simulations and experiments. The measured VSWR < 2 bandwidth is 55% at the center frequency 21.8 GHz, and the gain is larger than 12.2 dB. Experimental results demonstrate that the proposed design achieves wide band and beam with the size of 68 mm × 56 mm × 14.5 mm.

  6. A new DOI detector design using discrete crystal array with depth-dependent reflector patterns and single-ended readout

    International Nuclear Information System (INIS)

    Lee, Seung-Jae; Lee, Chaeyeong; Kang, Jihoon; Chung, Yong Hyun

    2017-01-01

    We developed a depth of interaction (DOI) positron emission tomography (PET) detector using depth-dependent reflector patterns in a discrete crystal array. Due to the different reflector patterns at depth, light distribution was changed relative to depth. As a preliminary experiment, we measured DOI detector module crystal identification performance. The crystal consisted of a 9×9 array of 2 mmx2 mmx20 mm lutetium-yttrium oxyorthosilicate (LYSO) crystals. The crystal array was optically coupled to a 64-channel position-sensitive photomultiplier tube with a 2 mmx2 mm anode size and an 18.1 mmx18.1 mm effective area. We obtained the flood image with an Anger-type calculation. DOI layers and 9×9 pixels were well distinguished in the obtained images. Preclinical PET scanners based on this detector design offer the prospect of high and uniform spatial resolution.

  7. A new DOI detector design using discrete crystal array with depth-dependent reflector patterns and single-ended readout

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung-Jae; Lee, Chaeyeong [Department of Radiological Science, Yonsei University, Wonju 26493 (Korea, Republic of); Kang, Jihoon, E-mail: ray.jihoon.kang@gmail.com [Department of Biomedical Engineering, Chonnam National University, 50 Daehak-ro, Yeosu, Jeonnam 59626 (Korea, Republic of); Chung, Yong Hyun, E-mail: ychung@yonsei.ac.kr [Department of Radiological Science, Yonsei University, Wonju 26493 (Korea, Republic of)

    2017-01-21

    We developed a depth of interaction (DOI) positron emission tomography (PET) detector using depth-dependent reflector patterns in a discrete crystal array. Due to the different reflector patterns at depth, light distribution was changed relative to depth. As a preliminary experiment, we measured DOI detector module crystal identification performance. The crystal consisted of a 9×9 array of 2 mmx2 mmx20 mm lutetium-yttrium oxyorthosilicate (LYSO) crystals. The crystal array was optically coupled to a 64-channel position-sensitive photomultiplier tube with a 2 mmx2 mm anode size and an 18.1 mmx18.1 mm effective area. We obtained the flood image with an Anger-type calculation. DOI layers and 9×9 pixels were well distinguished in the obtained images. Preclinical PET scanners based on this detector design offer the prospect of high and uniform spatial resolution.

  8. Design, testing, and economics of a 430 W sub p photovoltaic concentrator array for non grid-connected applications

    Science.gov (United States)

    Maish, A. B.; Rios, M., Jr.; Togami, H.

    A stand-alone 430 W/sub p/ photovoltaic (PV) concentrating system for low power, non grid-connected applications has been designed, fabricated, and tested at Sandia National Laboratories. The array consists of four passively cooled Fresnel lens concentrating modules on a newly developed polar axis tracking structure. Two axis tracking is provided using a self powered clock drive unit mounted on a single post foundation. Test results of tracking accuracy, array output power, parasitic power, performance in winds and array reliability are discussed. using a range of estimated production costs for small production volumes, the life-cycle energy costs have been calculated and compared to the equivalent energy costs of a 3 kW diesel electric generator set and of an equivalent flat panel PV system.

  9. Solar Powered Aircraft, Photovoltaic Array/Battery System Tabletop Demonstration: Design and Operation Manual

    Science.gov (United States)

    Colozza, Anthony J.; Scheiman, David A.; Bailey, Sheila (Technical Monitor)

    2000-01-01

    A system was constructed to demonstrate the power system operation of a solar powered aircraft. The system consists of a photovoltaic (PV) array, a charge controller, a battery, an electric motor and propeller. The system collects energy from the PV array and either utilizes this energy to operate an electric motor or stores it in a rechargeable battery for future use. The system has a control panel which displays the output of the array and battery as well as the total current going to the electric motor. The control panel also has a means for adjusting the output to the motor to control its speed. The entire system is regulated around 12 VDC.

  10. Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation

    Directory of Open Access Journals (Sweden)

    Roberta D'Agata

    2017-01-01

    Full Text Available Gold nanoparticles (AuNPs exhibit unique properties that can be modulated through a tailored surface functionalization, enabling their targeted use in biochemical sensing and medical diagnostics. In particular, streptavidin-modified AuNPs are increasingly used for biosensing purposes. We report here a study of AuNPs surface-functionalized with streptavidin-biotinylated oligonucleotide, focussing on the role played by the oligonucleotide probes in the stabilization/destabilization of the functionalized nanoparticle dispersion. The behaviour of the modified AuNP dispersion as a consequence of the competitive displacement of the biotinylated oligonucleotide has been investigated and the critical role of displaced oligonucletides in triggering the quasi one-dimensional aggregation of nanoparticles is demonstrated for the first time. The thorough understanding of the fundamental properties of bioconjugated AuNPs is of great importance for the design of highly sensitive and reliable functionalized AuNP-based assays.

  11. Optimal Design of Low-Density SNP Arrays for Genomic Prediction: Algorithm and Applications.

    Directory of Open Access Journals (Sweden)

    Xiao-Lin Wu

    Full Text Available Low-density (LD single nucleotide polymorphism (SNP arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for the optimal design of LD SNP chips. A multiple-objective, local optimization (MOLO algorithm was developed for design of optimal LD SNP chips that can be imputed accurately to medium-density (MD or high-density (HD SNP genotypes for genomic prediction. The objective function facilitates maximization of non-gap map length and system information for the SNP chip, and the latter is computed either as locus-averaged (LASE or haplotype-averaged Shannon entropy (HASE and adjusted for uniformity of the SNP distribution. HASE performed better than LASE with ≤1,000 SNPs, but required considerably more computing time. Nevertheless, the differences diminished when >5,000 SNPs were selected. Optimization was accomplished conditionally on the presence of SNPs that were obligated to each chromosome. The frame location of SNPs on a chip can be either uniform (evenly spaced or non-uniform. For the latter design, a tunable empirical Beta distribution was used to guide location distribution of frame SNPs such that both ends of each chromosome were enriched with SNPs. The SNP distribution on each chromosome was finalized through the objective function that was locally and empirically maximized. This MOLO algorithm was capable of selecting a set of approximately evenly-spaced and highly-informative SNPs, which in turn led to increased imputation accuracy compared with selection solely of evenly-spaced SNPs. Imputation accuracy increased with LD chip size, and imputation error rate was extremely low for chips with ≥3,000 SNPs. Assuming that genotyping or imputation error occurs at random, imputation error rate can be viewed as the upper limit for genomic prediction error. Our results show that about 25% of imputation error rate was propagated to genomic prediction in an Angus

  12. Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes.

    Science.gov (United States)

    Burggraf, S; Mayer, T; Amann, R; Schadhauser, S; Woese, C R; Stetter, K O

    1994-09-01

    Two 16S rRNA-targeted oligonucleotide probes were designed for the archaeal kingdoms Euryachaeota and Crenarchaeota. Probe specificities were evaluated by nonradioactive dot blot hybridization against selected reference organisms. The successful application of fluorescent-probe derivatives for whole-cell hybridization required organism-specific optimizations of fixation and hybridization conditions to assure probe penetration and morphological integrity of the cells. The probes allowed preliminary grouping of three new hyperthermophilic isolates. Together with other group-specific rRNA-targeted oligonucleotide probes, these probes will facilitate rapid in situ monitoring of the populations present in hydrothermal systems and support cultivation attempts.

  13. Compression and radiation of high-power short rf pulses. II. A novel antenna array design with combined compressor/radiator elements

    KAUST Repository

    Sirenko, Kostyantyn

    2011-01-01

    The paper discusses the radiation of compressed high power short RF pulses using two different types of antennas: (i) A simple monopole antenna and (ii) a novel array design, where each of the elements is constructed by combining a compressor and a radiator. The studies on the monopole antenna demonstrate the possibility of a high power short RF pulse\\'s efficient radiation even using simple antennas. The studies on the novel array design demonstrate that a reduced size array with lower pulse distortion and power decay can be constructed by assembling the array from elements each of which integrates a compressor and a radiator. This design idea can be used with any type of antenna array; in this work it is applied to a phased array.

  14. Design and implementation of Gm-APD array readout integrated circuit for infrared 3D imaging

    Science.gov (United States)

    Zheng, Li-xia; Yang, Jun-hao; Liu, Zhao; Dong, Huai-peng; Wu, Jin; Sun, Wei-feng

    2013-09-01

    A single-photon detecting array of readout integrated circuit (ROIC) capable of infrared 3D imaging by photon detection and time-of-flight measurement is presented in this paper. The InGaAs avalanche photon diodes (APD) dynamic biased under Geiger operation mode by gate controlled active quenching circuit (AQC) are used here. The time-of-flight is accurately measured by a high accurate time-to-digital converter (TDC) integrated in the ROIC. For 3D imaging, frame rate controlling technique is utilized to the pixel's detection, so that the APD related to each pixel should be controlled by individual AQC to sense and quench the avalanche current, providing a digital CMOS-compatible voltage pulse. After each first sense, the detector is reset to wait for next frame operation. We employ counters of a two-segmental coarse-fine architecture, where the coarse conversion is achieved by a 10-bit pseudo-random linear feedback shift register (LFSR) in each pixel and a 3-bit fine conversion is realized by a ring delay line shared by all pixels. The reference clock driving the LFSR counter can be generated within the ring delay line Oscillator or provided by an external clock source. The circuit is designed and implemented by CSMC 0.5μm standard CMOS technology and the total chip area is around 2mm×2mm for 8×8 format ROIC with 150μm pixel pitch. The simulation results indicate that the relative time resolution of the proposed ROIC can achieve less than 1ns, and the preliminary test results show that the circuit function is correct.

  15. Electrical crosstalk in front-illuminated photodiode array with different guard ring designs for medical CT applications

    International Nuclear Information System (INIS)

    Ji Fan; Juntunen, Mikko; Hietanen, Iiro

    2009-01-01

    This paper presents electrical crosstalk studies on front-illuminated photodiode arrays for medical computed tomography (CT) applications. Crosstalk is an important factor to the system noise and image quality. The electrical crosstalk depends on silicon substrate properties and photodiode structures. The photodiode samples employed in this paper are planar processed on high-resistivity n-type silicon substrate, resulting in a p+/n-/n+ diode structure. Two types of guard ring structures are designed and applied to the same geometry of two-dimensional photodiode arrays. One structure is an n guard ring in the gap area between pixels, and the other structure is an additional p+ guard ring around each pixel together with the n guard ring. A 10 μm light spot with wavelength of 525 nm is used to scan across the surface of the photodiode array in the electrical crosstalk measurements. The electrical currents of two neighbor pixels are measured and the results are compared between two guard ring designs. The design with the p+ guard ring structure gives better electrical crosstalk suppression. Moreover, the measurement results show much smaller influence on surrounding pixels with the p+ guard ring structure in the case of disconnected pixel. Besides the electrical crosstalk, the light sensitivity within the gap area is also discussed between two guard ring designs.

  16. Design a freeform microlens array module for any arbitrary-shape collimated beam shaping and color mixing

    Science.gov (United States)

    Chen, Enguo; Wu, Rengmao; Guo, Tailiang

    2014-06-01

    Collimated beam shaping with freeform surface usually employs a predefined mapping to tailor one or multiple freeform surfaces. Limitation on those designs is that the source, the freeform optics and the target are in fixed one-to-one correspondence with each other. To overcome this drawback, this paper presents a kind of freeform microlens array module integrated with an ultra-thin freeform microlens array and a condenser lens to reshape any arbitrary-shape collimated beam into a prescribed uniform rectangular illumination and achieve color mixing. The design theory is explicitly given, and some key issues are addressed. Several different application examples are given, and the target is obtained with high uniformity and energy efficiency. This freeform microlens array module, which shows better flexibility and practicality than the regular designs, can be used not only to reshape any arbitrary-shape collimated beam (or a collimated beam integrated with several sub-collimated beams), but also most importantly to achieve color mixing. With excellent optical performance and ultra-compact volume, this optical module together with the design theory can be further introduced into other applications and will have a huge market potential in the near future.

  17. A review of the design and clinical evaluation of the ShefStim array-based functional electrical stimulation system.

    Science.gov (United States)

    Kenney, Laurence P; Heller, Ben W; Barker, Anthony T; Reeves, Mark L; Healey, Jamie; Good, Timothy R; Cooper, Glen; Sha, Ning; Prenton, Sarah; Liu, Anmin; Howard, David

    2016-11-01

    Functional electrical stimulation has been shown to be a safe and effective means of correcting foot drop of central neurological origin. Current surface-based devices typically consist of a single channel stimulator, a sensor for determining gait phase and a cuff, within which is housed the anode and cathode. The cuff-mounted electrode design reduces the likelihood of large errors in electrode placement, but the user is still fully responsible for selecting the correct stimulation level each time the system is donned. Researchers have investigated different approaches to automating aspects of setup and/or use, including recent promising work based on iterative learning techniques. This paper reports on the design and clinical evaluation of an electrode array-based FES system for the correction of drop foot, ShefStim. The paper reviews the design process from proof of concept lab-based study, through modelling of the array geometry and interface layer to array search algorithm development. Finally, the paper summarises two clinical studies involving patients with drop foot. The results suggest that the ShefStim system with automated setup produces results which are comparable with clinician setup of conventional systems. Further, the final study demonstrated that patients can use the system without clinical supervision. When used unsupervised, setup time was 14min (9min for automated search plus 5min for donning the equipment), although this figure could be reduced significantly with relatively minor changes to the design. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

  18. Design of optical element combining Fresnel lens with microlens array for uniform light-emitting diode lighting.

    Science.gov (United States)

    Wang, Guangzhen; Wang, Lili; Li, Fuli; Kong, Depeng

    2012-09-01

    One kind of optical element combining Fresnel lens with microlens array is designed simply for LED lighting based on geometrical optics and nonimaging optics. This design method imposes no restriction on the source intensity pattern. The designed element has compact construction and can produce multiple shapes of illumination distribution. Taking square lighting as an example, tolerance analysis is carried out to determine tolerance limits for applying the element in the assembly process. This element can produce on-axis lighting and off-axis lighting.

  19. Splice-correcting oligonucleotides restore BTK function in X-linked agammaglobulinemia model

    DEFF Research Database (Denmark)

    Bestas, Burcu; Moreno, Pedro M D; Blomberg, K Emelie M

    2014-01-01

    , splice-correcting oligonucleotides (SCOs) targeting mutated BTK transcripts for treating XLA. Both the SCO structural design and chemical properties were optimized using 2'-O-methyl, locked nucleic acid, or phosphorodiamidate morpholino backbones. In order to have access to an animal model of XLA, we...

  20. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

    Science.gov (United States)

    Jin, Lian-Qun; Li, Jun-Wen; Wang, Sheng-Qi; Chao, Fu-Huan; Wang, Xin-Wei; Yuan, Zheng-Quan

    2005-01-01

    AIM: To detect the common intestinal pathogenic bacteria quickly and accurately. METHODS: A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays. RESULTS: One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified. CONCLUSION: Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost. PMID:16437687

  1. Interferometry with flexible point source array for measuring complex freeform surface and its design algorithm

    Science.gov (United States)

    Li, Jia; Shen, Hua; Zhu, Rihong; Gao, Jinming; Sun, Yue; Wang, Jinsong; Li, Bo

    2018-06-01

    The precision of the measurements of aspheric and freeform surfaces remains the primary factor restrict their manufacture and application. One effective means of measuring such surfaces involves using reference or probe beams with angle modulation, such as tilted-wave-interferometer (TWI). It is necessary to improve the measurement efficiency by obtaining the optimum point source array for different pieces before TWI measurements. For purpose of forming a point source array based on the gradients of different surfaces under test, we established a mathematical model describing the relationship between the point source array and the test surface. However, the optimal point sources are irregularly distributed. In order to achieve a flexible point source array according to the gradient of test surface, a novel interference setup using fiber array is proposed in which every point source can be independently controlled on and off. Simulations and the actual measurement examples of two different surfaces are given in this paper to verify the mathematical model. Finally, we performed an experiment of testing an off-axis ellipsoidal surface that proved the validity of the proposed interference system.

  2. Design, fabrication, and calibration of a cryogenic search-coil array for harmonic analysis of quadrupole magnets

    International Nuclear Information System (INIS)

    Green, M.I.; Barale, P.J.; Hassenzahl, W.V.; Nelson, D.H.; O'Neill, J.W.; Schafer, R.V.; Taylor, C.E.

    1987-09-01

    A cryogenic search-coil array has been fabricated at LBL for harmonic error analysis of SSC model quadrupoles. It consists of three triplets of coils; the center-coil triplet is 10 cm long, and the end coil triplets are 70 cm long. Design objectives are a high bucking ratio for the dipole and quadrupole signals and utility at cryogenic operating currents (∼6 kA) with sufficient sensitivity for use at room-temperature currents (∼10 A). the design and fabrication are described. Individual coils are mechanically measured to +-5 μm, and their magnetic areas measured to 0.05%. A computer program has been developed to predict the quadrupole and dipole bucking ratios from the mechanical and magnetic measurements. The calibration procedure and accuracy of the array are specified. Results of measurements of SSC model quadrupoles are presented. 1 ref., 4 figs

  3. Design of a Large-scale Three-dimensional Flexible Arrayed Tactile Sensor

    Directory of Open Access Journals (Sweden)

    Junxiang Ding

    2011-01-01

    Full Text Available This paper proposes a new type of large-scale three-dimensional flexible arrayed tactile sensor based on conductive rubber. It can be used to detect three-dimensional force information on the continuous surface of the sensor, which realizes a true skin type tactile sensor. The widely used method of liquid rubber injection molding (LIMS method is used for "the overall injection molding" sample preparation. The structure details of staggered nodes and a new decoupling algorithm of force analysis are given. Simulation results show that the sensor based on this structure can achieve flexible measurement of large-scale 3-D tactile sensor arrays.

  4. Optimal design of a double-sided linear motor with a multi-segmented trapezoidal magnet array for a high precision positioning system

    International Nuclear Information System (INIS)

    Lee, Moon G.; Gweon, Dae-Gab

    2004-01-01

    A comparative analysis is performed for linear motors adopting conventional and multi-segmented trapezoidal (MST) magnet arrays, respectively, for a high-precision positioning system. The proposed MST magnet array is a modified version of a Halbach magnet array. The MST array has trapezoidal magnets with variable shape and dimensions while the Halbach magnet array generally has a rectangular magnet with identical dimensions. We propose a new model that can describe the magnetic field resulting from the complex-shaped magnets. The model can be applied to both MST and conventional magnet arrays. Using the model, a design optimization of the two types of linear motors is performed and compared. The magnet array with trapezoidal magnets can produce more force than one with rectangular magnets when they are arrayed in a linear motor where there is a yoke with high permeability. After the optimization and comparison, we conclude that the linear motor with the MST magnet array can generate more actuating force per volume than the motor with the conventional array. In order to satisfy the requirements of next generation systems such as high resolution, high speed, and long stroke, the use of a linear motor with a MST array as an actuator in a high precision positioning system is recommended from the results obtained here

  5. Planar array stack design aided by rapid prototyping in development of air-breathing PEMFC

    Science.gov (United States)

    Chen, Chen-Yu; Lai, Wei-Hsiang; Weng, Biing-Jyh; Chuang, Huey-Jan; Hsieh, Ching-Yuan; Kung, Chien-Chih

    The polymer electrolyte membrane fuel cell (PEMFC) is one of the most important research topics in the new and clean energy area. The middle or high power PEMFCs can be applied to the transportation or the distributed power system. But for the small power application, it is needed to match the power requirement of the product generally. On the other hand, the direct methanol fuel cell (DMFC) is one of the most common type that researchers are interested in, but recently the miniature or the micro-PEMFCs attract more attention due to their advantages of high open circuit voltage and high power density. The objective of this study is to develop a new air-breathing planar array fuel cell stacked from 10 cells made by rapid prototyping technology which has potential for fast commercial design, low cost manufacturing, and even without converters/inverters for the system. In this paper, the main material of flow field plates is acrylonitrile-butadiene-styrene (ABS) which allows the fuel cell be mass-manufactured by plastic injection molding technology. The rapid prototyping technology is applied to construct the prototype and verify the practicability of the proposed stack design. A 10-cell air-breathing miniature PEMFC stack with a volume of 6 cm × 6 cm × 0.9 cm is developed and tested. Its segmented membrane electrode assembly (MEA) is designed with the active surface area of 1.3 cm × 1.3 cm in each individual MEA. The platinum loading at anode and cathode are 0.2 mg cm -2 and 0.4 mg cm -2, respectively. Results show that the peak power densities of the parallel connected and serial connected stack are 99 mW cm -2 at 0.425 V and 92 mW cm -2 at 4.25 V, respectively under the conditions of 70 °C relative saturated humidity (i.e., dew point temperature), ambient temperature and free convection air. Besides, the stack performance is increased under forced convection. If the cell surface air is blown by an electric fan, the peak power densities of parallel connected and

  6. Conceptual design of the early implementation of the NEutron Detector Array (NEDA) with AGATA

    Science.gov (United States)

    Hüyük, Tayfun; Di Nitto, Antonio; Jaworski, Grzegorz; Gadea, Andrés; Javier Valiente-Dobón, José; Nyberg, Johan; Palacz, Marcin; Söderström, Pär-Anders; Jose Aliaga-Varea, Ramon; de Angelis, Giacomo; Ataç, Ayşe; Collado, Javier; Domingo-Pardo, Cesar; Egea, Francisco Javier; Erduran, Nizamettin; Ertürk, Sefa; de France, Gilles; Gadea, Rafael; González, Vicente; Herrero-Bosch, Vicente; Kaşkaş, Ayşe; Modamio, Victor; Moszynski, Marek; Sanchis, Enrique; Triossi, Andrea; Wadsworth, Robert

    2016-03-01

    The NEutron Detector Array (NEDA) project aims at the construction of a new high-efficiency compact neutron detector array to be coupled with large γ-ray arrays such as AGATA. The application of NEDA ranges from its use as selective neutron multiplicity filter for fusion-evaporation reaction to a large solid angle neutron tagging device. In the present work, possible configurations for the NEDA coupled with the Neutron Wall for the early implementation with AGATA has been simulated, using Monte Carlo techniques, in order to evaluate their performance figures. The goal of this early NEDA implementation is to improve, with respect to previous instruments, efficiency and capability to select multiplicity for fusion-evaporation reaction channels in which 1, 2 or 3 neutrons are emitted. Each NEDA detector unit has the shape of a regular hexagonal prism with a volume of about 3.23l and it is filled with the EJ301 liquid scintillator, that presents good neutron- γ discrimination properties. The simulations have been performed using a fusion-evaporation event generator that has been validated with a set of experimental data obtained in the 58Ni + 56Fe reaction measured with the Neutron Wall detector array.

  7. Array Design: Literature Survey For A High-Resolution Imaging Sonal System. Part 1

    Science.gov (United States)

    1993-12-01

    radioastronomy or microwave arrays, or it may be elastic or acoustic (same as elastic but .-estricted to fields specified by a scalar quantity). There is...these are direction cosines (or sines) (see Ziomek 1985, or a radioastronomy book such as Perley et al. 1989). This 0 is because the Fourier

  8. Conceptual design of the early implementation of the NEutron Detector Array (NEDA) with AGATA

    Energy Technology Data Exchange (ETDEWEB)

    Hueyuek, Tayfun; Gadea, Andres; Domingo-Pardo, Cesar [Universidad de Valencia, Instituto de Fisica Corpuscular, CSIC, Paterna (Valencia) (Spain); Di Nitto, Antonio [Istituto Nazionale di Fisica Nucleare, Napoli (Italy); Johannes Gutenberg-Universitaet Mainz, Mainz (Germany); Jaworski, Grzegorz; Javier Valiente-Dobon, Jose; De Angelis, Giacomo; Modamio, Victor; Triossi, Andrea [Laboratori Nazionali di Legnaro, Istituto Nazionale di Fisica Nucleare, Legnaro (Italy); Nyberg, Johan [Uppsala University, Department of Physics and Astronomy, Uppsala (Sweden); Palacz, Marcin [University of Warsaw, Heavy Ion Laboratory, Warsaw (Poland); Soederstroem, Paer-Anders [RIKEN Nishina Center, Saitama (Japan); Aliaga-Varea, Ramon Jose [Universidad de Valencia, Instituto de Fisica Corpuscular, CSIC, Paterna (Valencia) (Spain); Universidad Politecnica de Valencia, I3M, Valencia (Spain); Atac, Ayse [Ankara University, Department of Physics, Faculty of Sciences, Ankara (Turkey); The Royal Institute of Technology, Stockholm (Sweden); Collado, Javier; Egea, Francisco Javier; Gonzalez, Vicente; Sanchis, Enrique [University of Valencia, Department of Electronic Engineering, Burjassot (Valencia) (Spain); Erduran, Nizamettin [Istanbul Sabahattin Zaim University, Faculty of Engineering and Natural Sciences, Istanbul (Turkey); Ertuerk, Sefa [University of Nigde, Department of Physics, Faculty of Science and Arts, Nigde (Turkey); France, Gilles de [CNRS/IN2P3, GANIL, CEA/DSAM, Caen (France); Gadea, Rafael; Herrero-Bosch, Vicente [Universidad Politecnica de Valencia, I3M, Valencia (Spain); Kaskas, Ayse [Ankara University, Department of Physics, Faculty of Sciences, Ankara (Turkey); Moszynski, Marek [National Centre for Nuclear Research, Otwock-Swierk (Poland); Wadsworth, Robert [University of York, Department of Physics, York (United Kingdom)

    2016-03-15

    The NEutron Detector Array (NEDA) project aims at the construction of a new high-efficiency compact neutron detector array to be coupled with large γ -ray arrays such as AGATA. The application of NEDA ranges from its use as selective neutron multiplicity filter for fusion-evaporation reaction to a large solid angle neutron tagging device. In the present work, possible configurations for the NEDA coupled with the Neutron Wall for the early implementation with AGATA has been simulated, using Monte Carlo techniques, in order to evaluate their performance figures. The goal of this early NEDA implementation is to improve, with respect to previous instruments, efficiency and capability to select multiplicity for fusion-evaporation reaction channels in which 1, 2 or 3 neutrons are emitted. Each NEDA detector unit has the shape of a regular hexagonal prism with a volume of about 3.23l and it is filled with the EJ301 liquid scintillator, that presents good neutron- γ discrimination properties. The simulations have been performed using a fusion-evaporation event generator that has been validated with a set of experimental data obtained in the {sup 58}Ni + {sup 56}Fe reaction measured with the Neutron Wall detector array. (orig.)

  9. Concept, Design, and Prototyping of XSAS: A High Power Extendable Solar Array for CubeSat Applications

    Science.gov (United States)

    Senatore, Patrick; Klesh, Andrew; Zurbuchen, Thomas H.; McKague, Darren; Cutler, James

    2010-01-01

    CubeSats have proven themselves as a reliable and cost-effective method to perform experiments in space, but they are highly constrained by their specifications and size. One such constraint is the average continuous power, about 5 W, which is available to the typical CubeSat. To improve this constraint, we have developed the eXtendable Solar Array System (XSAS), a deployable solar array prototype in a CubeSat package, which can provide an average 23 W of continuous power. The prototype served as a technology demonstrator for the high risk mechanisms needed to release, deploy, and control the solar array. Aside from this drastic power increase, it is in the integration of each mechanism, their application within the small CubeSat form-factor, and the inherent passive control benefit of the deployed geometry that make XSAS a novel design. In this paper, we discuss the requirements and design process for the XSAS system and mechanical prototype, and provide qualitative and quantitative results from numerical simulations and prototype tests. We also discuss future work, including an upcoming NASA zero-gravity flight campaign, to further improve on XSAS and prepare it for future launch opportunities.

  10. A comparative analysis of measles virus RNA by oligonucleotide fingerprinting

    International Nuclear Information System (INIS)

    Stephenson, J.R.; Meulen, V. ter

    1982-01-01

    Isolates from two cases of acute measles, one case of acute measles encephalitis and three patients with subacute sclerosing panencephalitis were compared. This comparison was based upon the electrophoretic analysis of T 1 oligonucleotides from single-stranded, full-length RNA isolated from cytoplasmic nucleocapsids. Although all viruses have oligonucleotides in common, each isolate generated a unique pattern of oligonucleotides. However, no group of oligonucleotides was observed which would allow differentiation between viruses isolated from acute infections and those isolated from CNS diseases; indicating that probably all measles viruses differ in their nucleotide sequence, regardless of origin. (Author)

  11. Design of photonic phased array switches using nano electromechanical systems on silicon-on-insulator integration platform

    Science.gov (United States)

    Hussein, Ali Abdulsattar

    This thesis presents an introduction to the design and simulation of a novel class of integrated photonic phased array switch elements. The main objective is to use nano-electromechanical (NEMS) based phase shifters of cascaded under-etched slot nanowires that are compact in size and require a small amount of power to operate them. The structure of the switch elements is organized such that it brings the phase shifting elements to the exterior sides of the photonic circuits. The transition slot couplers, used to interconnect the phase shifters, are designed to enable biasing one of the silicon beams of each phase shifter from an electrode located at the side of the phase shifter. The other silicon beam of each phase shifter is biased through the rest of the silicon structure of the switch element, which is taken as a ground. Phased array switch elements ranging from 2x2 up to 8x8 multiple-inputs/multiple-outputs (MIMO) are conveniently designed within reasonable footprints native to the current fabrication technologies. Chapter one presents the general layout of the various designs of the switch elements and demonstrates their novel features. This demonstration will show how waveguide disturbances in the interconnecting network from conventional switch elements can be avoided by adopting an innovative design. Some possible applications for the designed switch elements of different sizes and topologies are indicated throughout the chapter. Chapter two presents the design of the multimode interference (MMI) couplers used in the switch elements as splitters, combiners and waveguide crossovers. Simulation data and design methodologies for the multimode couplers of interest are detailed in this chapter. Chapter three presents the design and analysis of the NEMS-operated phase shifters. Both simulations and numerical analysis are utilized in the design of a 0°-180° capable NEMS-operated phase shifter. Additionally, the response of some of the designed photonic phased

  12. Design, development and evaluation of a resistor-based multiplexing circuit for a 20×20 SiPM array

    International Nuclear Information System (INIS)

    Wang, Zhonghai; Sun, Xishan; Lou, Kai; Meier, Joseph; Zhou, Rong; Yang, Chaowen; Zhu, Xiaorong; Shao, Yiping

    2016-01-01

    One technical challenge in developing a large-size scintillator detector with multiple Silicon Photomultiplier (SiPM) arrays is to read out a large number of detector output channels. To achieve this, different signal multiplexing circuits have been studied and applied with different performances and cost-effective tradeoffs. Resistor-based multiplexing circuits exhibit simplicity and signal integrity, but also present the disadvantage of timing shift among different channels. In this study, a resistor-based multiplexing circuit for a large-sized SiPM array readout was developed and evaluated by simulation and experimental studies. Similarly to a multiplexing circuit used for multi-anode PMT, grounding and branching resistors were connected to each SiPM output channel. The grounding resistor was used to simultaneously reduce the signal crosstalk among different channels and to improve timing performance. Both grounding and branching resistor values were optimized to maintain a balanced performance of the event energy, timing, and positioning. A multiplexing circuit was implemented on a compact PCB and applied for a flat-panel detector which consisted of a 32×32 LYSO scintillator crystals optically coupled to 5×5 SiPM arrays for a total 20×20 output channels. Test results showed excellent crystal identification for all 1024 LYSO crystals (each with 2×2×30 mm"3 size) with "2"2Na flood-source irradiation. The measured peak-to-valley ratio from typical crystal map profile is around 3:1 to 6.6:1, an average single crystal energy resolution of about 17.3%, and an average single crystal timing resolution of about 2 ns. Timing shift among different crystals, as reported in some other resistor-based multiplexing circuit designs, was not observed. In summary, we have designed and implemented a practical resistor-based multiplexing circuit that can be readily applied for reading out a large SiPM array with good detector performance.

  13. Design, development and evaluation of a resistor-based multiplexing circuit for a 20×20 SiPM array

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhonghai [College of Physical Science and Technology, Key Laboratory of Radiation Physics and Technology, Ministry of Education, Sichuan University, Chengdu (China); Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Tx (United States); Sun, Xishan [Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Tx (United States); Lou, Kai [Department of Electrical and Computer Engineering, Rice University, Houston, Tx (United States); Meier, Joseph [Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Tx (United States); Zhou, Rong; Yang, Chaowen [College of Physical Science and Technology, Key Laboratory of Radiation Physics and Technology, Ministry of Education, Sichuan University, Chengdu (China); Zhu, Xiaorong [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Tx (United States); Shao, Yiping [Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Tx (United States)

    2016-04-21

    One technical challenge in developing a large-size scintillator detector with multiple Silicon Photomultiplier (SiPM) arrays is to read out a large number of detector output channels. To achieve this, different signal multiplexing circuits have been studied and applied with different performances and cost-effective tradeoffs. Resistor-based multiplexing circuits exhibit simplicity and signal integrity, but also present the disadvantage of timing shift among different channels. In this study, a resistor-based multiplexing circuit for a large-sized SiPM array readout was developed and evaluated by simulation and experimental studies. Similarly to a multiplexing circuit used for multi-anode PMT, grounding and branching resistors were connected to each SiPM output channel. The grounding resistor was used to simultaneously reduce the signal crosstalk among different channels and to improve timing performance. Both grounding and branching resistor values were optimized to maintain a balanced performance of the event energy, timing, and positioning. A multiplexing circuit was implemented on a compact PCB and applied for a flat-panel detector which consisted of a 32×32 LYSO scintillator crystals optically coupled to 5×5 SiPM arrays for a total 20×20 output channels. Test results showed excellent crystal identification for all 1024 LYSO crystals (each with 2×2×30 mm{sup 3} size) with {sup 22}Na flood-source irradiation. The measured peak-to-valley ratio from typical crystal map profile is around 3:1 to 6.6:1, an average single crystal energy resolution of about 17.3%, and an average single crystal timing resolution of about 2 ns. Timing shift among different crystals, as reported in some other resistor-based multiplexing circuit designs, was not observed. In summary, we have designed and implemented a practical resistor-based multiplexing circuit that can be readily applied for reading out a large SiPM array with good detector performance.

  14. The Design and Analysis of Split Row-Column Addressing Array for 2-D Transducer

    Directory of Open Access Journals (Sweden)

    Xu Li

    2016-09-01

    Full Text Available For 3-D ultrasound imaging, the row-column addressing (RCA with 2N connections for an N × N 2-D array makes the fabrication and interconnection simpler than the fully addressing with N2 connections. However, RCA degrades the image quality because of defocusing in signal channel direction in the transmit event. To solve this problem, a split row-column addressing scheme (SRCA is proposed in this paper. Rather than connecting all the elements in the signal channel direction together, this scheme divides the elements in the signal channel direction into several disconnected blocks, thus enables focusing beam access in both signal channel and switch channel directions. Selecting an appropriate split scheme is the key for SRCA to maintaining a reasonable tradeoff between the image quality and the number of connections. Various split schemes for a 32 × 32 array are fully investigated with point spread function (PSF analysis and imaging simulation. The result shows the split scheme with five blocks (4, 6, 12, 6, and 4 elements of each block can provide similar image quality to fully addressing. The splitting schemes for different array sizes from 16 × 16 to 96 × 96 are also discussed.

  15. Array design considerations for exploitation of stable weakly dispersive modal pulses in the deep ocean

    Science.gov (United States)

    Udovydchenkov, Ilya A.

    2017-07-01

    Modal pulses are broadband contributions to an acoustic wave field with fixed mode number. Stable weakly dispersive modal pulses (SWDMPs) are special modal pulses that are characterized by weak dispersion and weak scattering-induced broadening and are thus suitable for communications applications. This paper investigates, using numerical simulations, receiver array requirements for recovering information carried by SWDMPs under various signal-to-noise ratio conditions without performing channel equalization. Two groups of weakly dispersive modal pulses are common in typical mid-latitude deep ocean environments: the lowest order modes (typically modes 1-3 at 75 Hz), and intermediate order modes whose waveguide invariant is near-zero (often around mode 20 at 75 Hz). Information loss is quantified by the bit error rate (BER) of a recovered binary phase-coded signal. With fixed receiver depths, low BERs (less than 1%) are achieved at ranges up to 400 km with three hydrophones for mode 1 with 90% probability and with 34 hydrophones for mode 20 with 80% probability. With optimal receiver depths, depending on propagation range, only a few, sometimes only two, hydrophones are often sufficient for low BERs, even with intermediate mode numbers. Full modal resolution is unnecessary to achieve low BERs. Thus, a flexible receiver array of autonomous vehicles can outperform a cabled array.

  16. Design of S-Band Phased Array Antenna with High Isolation Using Broadside Coupled Split Ring Resonator

    Directory of Open Access Journals (Sweden)

    Sungyoun Hwang

    2018-04-01

    Full Text Available In this paper, a method of designing a Vivaldi type phased array antenna (PAA which operates at S-band (2.8–3.3 GHz is presented. The presented antenna uses broadside coupled split ring resonators (BC-SRRs for high isolation, wide field of view, and good active S-parameter characteristics. As an example, we design a 1 × 8 array antenna with various BC-SRR structures using theory and EM simulations. The antenna is fabricated and measured to verify the design. With the BC-SRR implemented between the two radiating elements, the isolation is shown to be enhanced by 6 dB, up to 23 dB. The scan angle is shown to be within ±53° based on a −10 dB active reflection coefficient. The operation of the scan angle is possible within ±60° with a little larger reflection coefficient (−7 dB to −8 dB. The proposed design with BC-SRRs is expected to be useful for PAA applications.

  17. Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications.

    Science.gov (United States)

    Abe, Hiroshi; Kimura, Yasuaki

    2018-01-01

    Chemical ligation of oligonucleotides (ONs) is the key reaction for various ON-based technologies. We have tried to solve the problems of RNA interference (RNAi) technology by applying ON chemical ligation to RNAi. We designed a new RNAi system, called intracellular buildup RNAi (IBR-RNAi), where the RNA fragments are built up into active small-interference RNA (siRNA) in cells through a chemical ligation reaction. Using the phosphorothioate and iodoacetyl groups as reactive functional groups for the ligation, we achieved RNAi effects without inducing immune responses. Additionally, we developed a new chemical ligation for IBR-RNAi, which affords a more native-like structure in the ligated product. The new ligation method should be useful not only for IBR-RNAi but also for the chemical synthesis of biofunctional ONs.

  18. Design, development, manufacture, testing, and delivery of devices for connection of solar cell panel circuitry to flat conductor cable solar cell array harness

    Science.gov (United States)

    Dillard, P. A.; Waddington, D.

    1971-01-01

    The technology status and problem areas which exist for the application of flat conductor cabling to solar cell arrays are summarized. Details covering the design, connector manufacture, and prototype test results are also summarized.

  19. The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization

    Science.gov (United States)

    2013-01-01

    Background Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length – in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length. Results Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide. Conclusions Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative. PMID:23445545

  20. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  1. Design of a Weighted-Rotor Energy Harvester Based on Dynamic Analysis and Optimization of Circular Halbach Array Magnetic Disk

    Directory of Open Access Journals (Sweden)

    Yu-Jen Wang

    2015-03-01

    Full Text Available This paper proposes the design of a weighted-rotor energy harvester (WREH in which the oscillation is caused by the periodic change of the tangential component of gravity, to harvest kinetic energy from a rotating wheel. When a WREH is designed with a suitable characteristic length, the rotor’s natural frequency changes according to the wheel rotation speed and the rotor oscillates at a wide angle and high angular velocity to generate a large amount of power. The magnetic disk is designed according to an optimized circular Halbach array. The optimized circular Halbach array magnetic disk provides the largest induced EMF for different sector-angle ratios for the same magnetic disk volume. This study examined the output voltage and power by considering the constant and accelerating plate-rotation speeds, respectively. This paper discusses the effects of the angular acceleration speed of a rotating wheel corresponding to the dynamic behaviors of a weighted rotor. The average output power is 399 to 535 microwatts at plate-rotation speeds from 300 to 500 rpm, enabling the WREH to be a suitable power source for a tire-pressure monitoring system.

  2. A method to design high SNR nanoscale magnetic sensors using an array of tunnelling magneto-resistance (TMR) devices

    International Nuclear Information System (INIS)

    Gomez, P; Litvinov, D; Khizroev, S

    2007-01-01

    This paper presents a systematic method to design and calculate tunnelling magneto-resistance (TMR) sensors with high signal-to-noise ratio (SNR). The sensing module consists of four TMR devices arranged in a Wheatstone-bridge configuration. Closed-form equations were obtained to calculate TMR sensor current, array output voltage, magneto-resistance ratio, overall noise (thermal and shot) and SNR for a given bandwidth. Using this technique we were able to maximize the SNR by tuning the many parameters of the TMR devices. Typical SNR values are in excess of 45 dB

  3. Comparison of gene coverage of mouse oligonucleotide microarray platforms

    Directory of Open Access Journals (Sweden)

    Medrano Juan F

    2006-03-01

    Full Text Available Abstract Background The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. Results A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis: Affymetrix430 2.0 (75.6%, ABI Genome Survey (81.24%, Agilent (79.33%, Codelink (78.09%, Sentrix (90.47%; and four array-ready oligosets: Sigma (47.95%, Operon v.3 (69.89%, Operon v.4 (84.03%, and MEEBO (84.03%. The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. Conclusion The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here

  4. Design of a linear detector array unit for high energy x-ray helical computed tomography and linear scanner

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeong Tae; Park, Jong Hwan; Kim, Gi Yoon [Dept. of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon (Korea, Republic of); Kim, Dong Geun [Medical Imaging Department, ASTEL Inc., Seongnam (Korea, Republic of); Park, Shin Woong; Yi, Yun [Dept. of Electronics and Information Eng, Korea University, Seoul (Korea, Republic of); Kim, Hyun Duk [Research Center, Luvantix ADM Co., Ltd., Daejeon (Korea, Republic of)

    2016-11-15

    A linear detector array unit (LdAu) was proposed and designed for the high energy X-ray 2-d and 3-d imaging systems for industrial non-destructive test. Specially for 3-d imaging, a helical CT with a 15 MeV linear accelerator and a curved detector is proposed. the arc-shape detector can be formed by many LdAus all of which are arranged to face the focal spot when the source-to-detector distance is fixed depending on the application. An LdAu is composed of 10 modules and each module has 48 channels of CdWO{sub 4} (CWO) blocks and Si PIn photodiodes with 0.4 mm pitch. this modular design was made for easy manufacturing and maintenance. through the Monte carlo simulation, the CWO detector thickness of 17 mm was optimally determined. the silicon PIn photodiodes were designed as 48 channel arrays and fabricated with NTD (neutron transmutation doping) wafers of high resistivity and showed excellent leakage current properties below 1 nA at 10 V reverse bias. to minimize the low-voltage breakdown, the edges of the active layer and the guard ring were designed as a curved shape. the data acquisition system was also designed and fabricated as three independent functional boards; a sensor board, a capture board and a communication board to a Pc. this paper describes the design of the detectors (CWO blocks and Si PIn photodiodes) and the 3-board data acquisition system with their simulation results.

  5. The design of a focused ultrasound transducer array for the treatment of stroke: a simulation study

    International Nuclear Information System (INIS)

    Pajek, Daniel; Hynynen, Kullervo

    2012-01-01

    High intensity focused ultrasound (HIFU) is capable of mechanically disintegrating blood clots at high pressures. Safe thrombolysis may require frequencies higher than those currently utilized by transcranial HIFU. Since the attenuation and focal distortion of ultrasound in bone increases at higher frequencies, resulting focal pressures are diminished. This study investigated the feasibility of using transcranial HIFU for the non-invasive treatment of ischemic stroke. The use of large aperture, 1.1–1.5 MHz phased arrays in targeting four clinically relevant vessel locations was simulated. Resulting focal sizes decreased with frequency, producing a maximum –3 dB depth of field and lateral width of 2.0 and 1.2 mm, respectively. Mean focal gains above an order of magnitude were observed in three of four targets and transducer intensities required to achieve thrombolysis were determined. Required transducer element counts are about an order of magnitude higher than what currently exists and so, although technically feasible, new arrays would need to be developed to realize this as a treatment modality for stroke. (paper)

  6. Design and operation of a portable scanner for high performance microchip capillary array electrophoresis.

    Science.gov (United States)

    Scherer, James R; Liu, Peng; Mathies, Richard A

    2010-11-01

    We have developed a compact, laser-induced fluorescence detection scanner, the multichannel capillary array electrophoresis portable scanner (McCAEPs) as a platform for electrophoretic detection and control of high-throughput, integrated microfluidic devices for genetic and other analyses. The instrument contains a confocal optical system with a rotary objective for detecting four different fluorescence signals, a pneumatic system consisting of two pressure/vacuum pumps and 28 individual addressable solenoid valves for control of on-chip microvalves and micropumps, four Polymerase Chain Reaction (PCR) temperature control systems, and four high voltage power supplies for electrophoresis. The detection limit of the instrument is ~20 pM for on-chip capillary electrophoresis of fluorescein dyes. To demonstrate the system performance for forensic short tandem repeat (STR) analysis, two experiments were conducted: (i) electrophoretic separation and detection of STR samples on a 96-lane microfabricated capillary array electrophoresis microchip. Fully resolved PowerPlex(®) 16 STR profiles amplified from 1 ng of 9947A female standard DNA were successfully obtained; (ii) nine-plex STR amplification, sample injection, separation, and fluorescence detection of 100-copy 9948 male standard DNA in a single integrated PCR- capillary electrophoresis microchip. These results demonstrate that the McCAEPs can be used as a versatile control and detection instrument that operates integrated microfluidic devices for high-performance forensic human identification.

  7. TIA-1 RRM23 binding and recognition of target oligonucleotides.

    Science.gov (United States)

    Waris, Saboora; García-Mauriño, Sofía M; Sivakumaran, Andrew; Beckham, Simone A; Loughlin, Fionna E; Gorospe, Myriam; Díaz-Moreno, Irene; Wilce, Matthew C J; Wilce, Jacqueline A

    2017-05-05

    TIA-1 (T-cell restricted intracellular antigen-1) is an RNA-binding protein involved in splicing and translational repression. It mainly interacts with RNA via its second and third RNA recognition motifs (RRMs), with specificity for U-rich sequences directed by RRM2. It has recently been shown that RRM3 also contributes to binding, with preferential binding for C-rich sequences. Here we designed UC-rich and CU-rich 10-nt sequences for engagement of both RRM2 and RRM3 and demonstrated that the TIA-1 RRM23 construct preferentially binds the UC-rich RNA ligand (5΄-UUUUUACUCC-3΄). Interestingly, this binding depends on the presence of Lys274 that is C-terminal to RRM3 and binding to equivalent DNA sequences occurs with similar affinity. Small-angle X-ray scattering was used to demonstrate that, upon complex formation with target RNA or DNA, TIA-1 RRM23 adopts a compact structure, showing that both RRMs engage with the target 10-nt sequences to form the complex. We also report the crystal structure of TIA-1 RRM2 in complex with DNA to 2.3 Å resolution providing the first atomic resolution structure of any TIA protein RRM in complex with oligonucleotide. Together our data support a specific mode of TIA-1 RRM23 interaction with target oligonucleotides consistent with the role of TIA-1 in binding RNA to regulate gene expression. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Dissecting the hybridization of oligonucleotides to structured complementary sequences.

    Science.gov (United States)

    Peracchi, Alessio

    2016-06-01

    When oligonucleotides hybridize to long target molecules, the process is slowed by the secondary structure in the targets. The phenomenon has been analyzed in several previous studies, but many details remain poorly understood. I used a spectrofluorometric strategy, focusing on the formation/breaking of individual base pairs, to study the kinetics of association between a DNA hairpin and >20 complementary oligonucleotides ('antisenses'). Hybridization rates differed by over three orders of magnitude. Association was toehold-mediated, both for antisenses binding to the target's ends and for those designed to interact with the loop. Binding of these latter, besides being consistently slower, was affected to variable, non-uniform extents by the asymmetric loop structure. Divalent metal ions accelerated hybridization, more pronouncedly when nucleation occurred at the loop. Incorporation of locked nucleic acid (LNA) residues in the antisenses substantially improved the kinetics only when LNAs participated to the earliest hybridization steps. The effects of individual LNAs placed along the antisense indicated that the reaction transition state occurred after invading at least the first base pair of the stem. The experimental approach helps dissect hybridization reactions involving structured nucleic acids. Toehold-dependent, nucleation-invasion models appear fully appropriate for describing such reactions. Estimating the stability of nucleation complexes formed at internal toeholds is the major hurdle for the quantitative prediction of hybridization rates. While analyzing the mechanisms of a fundamental biochemical process (hybridization), this work also provides suggestions for the improvement of technologies that rely on such process. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

    Science.gov (United States)

    Geraldes, A; Difazio, S P; Slavov, G T; Ranjan, P; Muchero, W; Hannemann, J; Gunter, L E; Wymore, A M; Grassa, C J; Farzaneh, N; Porth, I; McKown, A D; Skyba, O; Li, E; Fujita, M; Klápště, J; Martin, J; Schackwitz, W; Pennacchio, C; Rokhsar, D; Friedmann, M C; Wasteneys, G O; Guy, R D; El-Kassaby, Y A; Mansfield, S D; Cronk, Q C B; Ehlting, J; Douglas, C J; Tuskan, G A

    2013-03-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids. © 2013 Blackwell Publishing Ltd.

  10. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA

    DEFF Research Database (Denmark)

    Moreno, Pedro M D; Geny, Sylvain; Pabon, Y Vladimir

    2013-01-01

    In spite of the many developments in synthetic oligonucleotide (ON) chemistry and design, invasion into double-stranded DNA (DSI) under physiological salt and pH conditions remains a challenge. In this work, we provide a new ON tool based on locked nucleic acids (LNAs), designed for strand invasi...

  11. Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

    DEFF Research Database (Denmark)

    Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte Stahl

    2016-01-01

    Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain ...

  12. Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells

    Directory of Open Access Journals (Sweden)

    Muyrers Joep PP

    2003-01-01

    Full Text Available Abstract Background The phage protein pairs, RecE/RecT from Rac or Redα/Redβ from λ, initiate efficient double strand break repair (DSBR in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined. Results Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redα but only requires a phage annealing protein (RecT or Redβ. Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein. Conclusion Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redα/Redβ.

  13. Application of high resolution SNP arrays in patients with congenital ...

    Indian Academy of Sciences (India)

    TING-YING LEI

    lent oligonucleotide-based array-CGH to determine the exact breakpoints in 14 patients with partial deletions of chromo- some 13q21.1-qter. They were able to refine the smallest deletion region linked to cleft lip/palate (13q31.3–13q33.1). Except for the arrays that measure DNA copy number differ- ences only, SNP arrays, ...

  14. Air shower array designed for cosmic ray variation measurements and high energy gamma ray astronomy

    Energy Technology Data Exchange (ETDEWEB)

    Morello, C; Navarra, G [Consiglio Nazionale delle Ricerche, Turin (Italy). Lab. di Cosmo-Geofisica

    1981-08-15

    We describe an array for performing measurements of counting rates and arrival directions of extensive air showers at primary energy E/sub 0/ approx. equal to 3 x 10/sup 9/ eV. The aim of the research is to study the time variations and the anisotropies of cosmic rays and the observable gamma ray sources in the high energy region. The installation, composed of four large area scintillation counters and completely controlled by a microcomputer system, operates at mountain altitude (3500 m a.s.l.). The preanalysis of data, stability tests and periodic calibrations are performed by on-line programs. The method for obtaining the required stability and the corrections on temperature and gain variations are also described.

  15. Design of an Acoustic Target Intrusion Detection System Based on Small-Aperture Microphone Array

    Science.gov (United States)

    Zu, Xingshui; Guo, Feng; Huang, Jingchang; Zhao, Qin; Liu, Huawei; Li, Baoqing; Yuan, Xiaobing

    2017-01-01

    Automated surveillance of remote locations in a wireless sensor network is dominated by the detection algorithm because actual intrusions in such locations are a rare event. Therefore, a detection method with low power consumption is crucial for persistent surveillance to ensure longevity of the sensor networks. A simple and effective two-stage algorithm composed of energy detector (ED) and delay detector (DD) with all its operations in time-domain using small-aperture microphone array (SAMA) is proposed. The algorithm analyzes the quite different velocities between wind noise and sound waves to improve the detection capability of ED in the surveillance area. Experiments in four different fields with three types of vehicles show that the algorithm is robust to wind noise and the probability of detection and false alarm are 96.67% and 2.857%, respectively. PMID:28273838

  16. Getting the Big Picture: Design Considerations for a ngVLA Short Spacing Array

    Science.gov (United States)

    Mason, Brian Scott; Cotton, William; Condon, James; Kepley, Amanda; Selina, Rob; Murphy, Eric Joseph

    2018-01-01

    The Next Generation VLA (ngVLA) aims to provide a revolutionary increase in cm-wavelength collecting area and sensitivity while at the same time providing excellent image fidelity for a broad spectrum of science cases. Likely ngVLA configurations currently envisioned provide sensitivity over a very wide range of spatial scales. The antenna diameter (notionally 18 meters) fundamentally limits the largest angular scales that can be reached. One simple and powerful way to image larger angular scales is to build a complementary interferometer comprising a smaller number of smaller-diameter dishes.We have investigated the requirements that such an array would need to meet in order to usefully scientifically complement the ngVLA; this poster presents the results of our investigation.

  17. Theory for optimal design of waveguiding light concentrators in photovoltaic microcell arrays.

    Science.gov (United States)

    Semichaevsky, Andrey V; Johnson, Harley T; Yoon, Jongseung; Nuzzo, Ralph G; Li, Lanfang; Rogers, John

    2011-06-10

    Efficiency of ultrathin flexible solar photovoltaic silicon microcell arrays can be significantly improved using nonimaging solar concentrators. A fluorophore is introduced to match the solar spectrum and the low-reflectivity wavelength range of Si, reduce the escape losses, and allow the nontracking operation. In this paper we optimize our solar concentrators using a luminescent/nonluminescent photon transport model. Key modeling results are compared quantitatively to experiments and are in good agreement with the latter. Our solar concentrator performance is not limited by the dye self-absorption. Bending deformations of the flexible solar collectors do not result in their indirect gain degradation compared to flat solar concentrators with the same projected area.

  18. Design and Implementation of Video Shot Detection on Field Programmable Gate Arrays

    Directory of Open Access Journals (Sweden)

    Jharna Majumdar

    2012-09-01

    Full Text Available Video has become an interactive medium of communication in everyday life. The sheer volume of video makes it extremely difficult to browse through and find the required data. Hence extraction of key frames from the video which represents the abstract of the entire video becomes necessary. The aim of the video shot detection is to find the position of the shot boundaries, so that key frames can be selected from each shot for subsequent processing such as video summarization, indexing etc. For most of the surveillance applications like video summery, face recognition etc., the hardware (real time implementation of these algorithms becomes necessary. Here in this paper we present the architecture for simultaneous accessing of consecutive frames, which are then used for the implementation of various Video Shot Detection algorithms. We also present the real time implementation of three video shot detection algorithms using the above mentioned architecture on FPGA (Field Programmable Gate Arrays.

  19. Improved Titanium Billet Inspection Sensitivity through Optimized Phased Array Design, Part II: Experimental Validation and Comparative Study with Multizone

    International Nuclear Information System (INIS)

    Hassan, W.; Vensel, F.; Knowles, B.; Lupien, V.

    2006-01-01

    The inspection of critical rotating components of aircraft engines has made important advances over the last decade. The development of Phased Array (PA) inspection capability for billet and forging materials used in the manufacturing of critical engine rotating components has been a priority for Honeywell Aerospace. The demonstration of improved PA inspection system sensitivity over what is currently used at the inspection houses is a critical step in the development of this technology and its introduction to the supply base as a production inspection. As described in Part I (in these proceedings), a new phased array transducer was designed and manufactured for optimal inspection of eight inch diameter Ti-6Al-4V billets. After confirming that the transducer was manufactured in accordance with the design specifications a validation study was conducted to assess the sensitivity improvement of the PAI over the current capability of Multi-zone (MZ) inspection. The results of this study confirm the significant (≅ 6 dB in FBH number sign sensitivity) improvement of the PAI sensitivity over that of MZI

  20. Design and Performance of the Multiplexed SQUID/TES Array at Ninety Gigahertz

    Science.gov (United States)

    Stanchfield, Sara; Ade, Peter; Aguirre, James; Brevik, Justus A.; Cho, Hsiao-Mei; Datta, Rahul; Devlin, Mark; Dicker, Simon R.; Dober, Bradley; Duff, Shannon M.; Egan, Dennis; Ford, Pam; Hilton, Gene; Hubmayr, Johannes; Irwin, Kent; Knowles, Kenda; Marganian, Paul; Mason, Brian Scott; Mates, John A. B.; McMahon, Jeff; Mello, Melinda; Mroczkowski, Tony; Romero, Charles; Sievers, Jonathon; Tucker, Carole; Vale, Leila R.; Vissers, Michael; White, Steven; Whitehead, Mark; Ullom, Joel; Young, Alexander

    2018-01-01

    We present the array performance and astronomical images from early science results from MUSTANG-2, a 90 GHz feedhorn-coupled, microwave SQUID-multiplexed TES bolometer array operating on the Robert C. Byrd Green Bank Telescope (GBT). MUSTANG-2 was installed on the GBT on December 2, 2016 and immediately began commissioning efforts, followed by science observations, which are expected to conclude June 2017. The feedhorn and waveguide-probe-coupled detector technology is a mature technology, which has been used on instrument including the South Pole Telescope, the Atacama Cosmology Telescope, and the Atacama B-mode Search telescope. The microwave SQUID readout system developed for MUSTANG-2 currently reads out 66 detectors with a single coaxial cable and will eventually allow thousands of detectors to be multiplexed. This microwave SQUID multiplexer combines the proven abilities of millimeterwave TES detectors with the multiplexing capabilities of KIDs with no degradation in noise performance of the detectors. Each multiplexing device is read out using warm electronics consisting of a commercially available ROACH board, a DAC/ADC card, and an Intermediate Frequency mixer circuit. The hardware was originally developed by the UC Berkeley Collaboration for Astronomy Signal Processing and Electronic Research (CASPER) group, whose primary goal is to develop scalable FPGA-based hardware with the flexibility to be used in a wide range of radio signal processing applications. MUSTANG-2 is the first on-sky instrument to use microwave SQUID multiplexing and is available as a shared-risk/PI instrument on the GBT. In MUSTANG-2's first season 7 separate proposals were awarded a total of 230 hours of telescope time.

  1. Regulation of Gene Expression with Double-Stranded Phosphorothioate Oligonucleotides

    Science.gov (United States)

    Bielinska, Anna; Shivdasani, Ramesh A.; Zhang, Liquan; Nabel, Gary J.

    1990-11-01

    Alteration of gene transcription by inhibition of specific transcriptional regulatory proteins is necessary for determining how these factors participate in cellular differentiation. The functions of these proteins can be antagonized by several methods, each with specific limitations. Inhibition of sequence-specific DNA-binding proteins was achieved with double-stranded (ds) phosphorothioate oligonucleotides that contained octamer or kappaB consensus sequences. The phosphorothioate oligonucleotides specifically bound either octamer transcription factor or nuclear factor (NF)-kappaB. The modified oligonucleotides accumulated in cells more effectively than standard ds oligonucleotides and modulated gene expression in a specific manner. Octamer-dependent activation of a reporter plasmid or NF-kappaB-dependent activation of the human immunodeficiency virus (HIV) enhancer was inhibited when the appropriate phosphorothioate oligonucleotide was added to a transiently transfected B cell line. Addition of phosphorothioate oligonucleotides that contained the octamer consensus to Jurkat T leukemia cells inhibited interleukin-2 (IL-2) secretion to a degree similar to that observed with a mutated octamer site in the IL-2 enhancer. The ds phosphorothioate oligonucleotides probably compete for binding of specific transcription factors and may provide anti-viral, immunosuppressive, or other therapeutic effects.

  2. Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery

    Directory of Open Access Journals (Sweden)

    Astrid Wachter

    2015-11-01

    Full Text Available Mastering the systematic analysis of tumor tissues on a large scale has long been a technical challenge for proteomics. In 2001, reverse phase protein arrays (RPPA were added to the repertoire of existing immunoassays, which, for the first time, allowed a profiling of minute amounts of tumor lysates even after microdissection. A characteristic feature of RPPA is its outstanding sample capacity permitting the analysis of thousands of samples in parallel as a routine task. Until today, the RPPA approach has matured to a robust and highly sensitive high-throughput platform, which is ideally suited for biomarker discovery. Concomitant with technical advancements, new bioinformatic tools were developed for data normalization and data analysis as outlined in detail in this review. Furthermore, biomarker signatures obtained by different RPPA screens were compared with another or with that obtained by other proteomic formats, if possible. Options for overcoming the downside of RPPA, which is the need to steadily validate new antibody batches, will be discussed. Finally, a debate on using RPPA to advance personalized medicine will conclude this article.

  3. Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes.

    OpenAIRE

    Burggraf, S; Mayer, T; Amann, R; Schadhauser, S; Woese, C R; Stetter, K O

    1994-01-01

    Two 16S rRNA-targeted oligonucleotide probes were designed for the archaeal kingdoms Euryachaeota and Crenarchaeota. Probe specificities were evaluated by nonradioactive dot blot hybridization against selected reference organisms. The successful application of fluorescent-probe derivatives for whole-cell hybridization required organism-specific optimizations of fixation and hybridization conditions to assure probe penetration and morphological integrity of the cells. The probes allowed prelim...

  4. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray

    DEFF Research Database (Denmark)

    Stolc, Viktor; Li, Lei; Wang, Xiangfeng

    2005-01-01

    As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map...... transcription of the japonica rice genome. In a pilot experiment to test this approach, one array representing the reverse strand of the last 11.2 Mb sequence of chromosome 10 was analyzed in detail based on a mathematical model developed in this study. Analysis of the array data detected 77% of the reference...... gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models...

  5. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

    Science.gov (United States)

    Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

    2015-01-01

    Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.

  6. The CHARA array adaptive optics I: common-path optical and mechanical design, and preliminary on-sky results

    Science.gov (United States)

    Che, Xiao; Sturmann, Laszlo; Monnier, John D.; ten Brummelaar, Theo A.; Sturmann, Judit; Ridgway, Stephen T.; Ireland, Michael J.; Turner, Nils H.; McAlister, Harold A.

    2014-07-01

    The CHARA array is an optical interferometer with six 1-meter diameter telescopes, providing baselines from 33 to 331 meters. With sub-milliarcsecond angular resolution, its versatile visible and near infrared combiners offer a unique angle of studying nearby stellar systems by spatially resolving their detailed structures. To improve the sensitivity and scientific throughput, the CHARA array was funded by NSF-ATI in 2011 to install adaptive optics (AO) systems on all six telescopes. The initial grant covers Phase I of the AO systems, which includes on-telescope Wavefront Sensors (WFS) and non-common-path (NCP) error correction. Meanwhile we are seeking funding for Phase II which will add large Deformable Mirrors on telescopes to close the full AO loop. The corrections of NCP error and static aberrations in the optical system beyond the WFS are described in the second paper of this series. This paper describes the design of the common-path optical system and the on-telescope WFS, and shows the on-sky commissioning results.

  7. Modern methods for the synthesis of peptide-oligonucleotide conjugates

    International Nuclear Information System (INIS)

    Zubin, Evgenii M; Oretskaya, Tat'yana S; Romanova, Elena A

    2002-01-01

    The published data on the methods of chemical solution and solid-phase synthesis of peptide-oligonucleotide conjugates are reviewed. The known methods are systematised and their advantages and disadvantages are considered. The approaches to the solution synthesis of peptide-oligonucleotide conjugates are systematised according to the type of chemical bonds between the fragments, whereas those to the solid-phase synthesis are classified according to the procedure used for the preparation of conjugates, viz., stepwise elongation of oligonucleotide and peptide chains on the same polymeric support or solid-phase condensation of two presynthesised fragments. The bibliography includes 141 references.

  8. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  9. Design, Construction, and Initial Test of High Spatial Resolution Thermometry Arrays for Detection of Surface Temperature Profiles on SRF Cavities in Super Fluid Helium

    Energy Technology Data Exchange (ETDEWEB)

    Ari Palczewski, Rongli Geng, Grigory Eremeev

    2011-07-01

    We designed and built two high resolution (0.6-0.55mm special resolution [1.1-1.2mm separation]) thermometry arrays prototypes out of the Allen Bradley 90-120 ohm 1/8 watt resistor to measure surface temperature profiles on SRF cavities. One array was designed to be physically flexible and conform to any location on a SRF cavity; the other was modeled after the common G-10/stycast 2850 thermometer and designed to fit on the equator of an ILC (Tesla 1.3GHz) SRF cavity. We will discuss the advantages and disadvantages of each array and their construction. In addition we will present a case study of the arrays performance on a real SRF cavity TB9NR001. TB9NR001 presented a unique opportunity to test the performance of each array as it contained a dual (4mm separation) cat eye defect which conventional methods such as OST (Oscillating Superleak second-sound Transducers) and full coverage thermometry mapping were unable to distinguish between. We will discuss the new arrays ability to distinguish between the two defects and their preheating performance.

  10. Optimal design method for magnetization directions of a permanent magnet array

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jae Seok [Center for Information Storage Device, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Yoo, Jeonghoon, E-mail: yoojh@yonsei.ac.k [School of Mechanical Engineering, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul 120-749 (Korea, Republic of)

    2010-08-15

    In many magnetic systems, the permanent magnet (PM) pattern has a great influence on their performance. This study proposes a systematic optimization method for designing discrete magnetization directions. While previous works have been mostly dependent on researchers' intuition, the developed method is systematic and can be applied to a two-dimensional PM-type eddy current brake model. The effectiveness of the method is confirmed, where the design's aim is to maximize the braking force on a moving conductor. The sensitivity analysis is accomplished by the adjoint variable method and the sequential linear programming is used as an optimizer. Several optimization results for various conditions through the proposed design method are compared to each other and the optimal magnet configuration for an eddy current brake is suggested.

  11. Programmable logic controller performance enhancement by field programmable gate array based design.

    Science.gov (United States)

    Patel, Dhruv; Bhatt, Jignesh; Trivedi, Sanjay

    2015-01-01

    PLC, the core element of modern automation systems, due to serial execution, exhibits limitations like slow speed and poor scan time. Improved PLC design using FPGA has been proposed based on parallel execution mechanism for enhancement of performance and flexibility. Modelsim as simulation platform and VHDL used to translate, integrate and implement the logic circuit in FPGA. Xilinx's Spartan kit for implementation-testing and VB has been used for GUI development. Salient merits of the design include cost-effectiveness, miniaturization, user-friendliness, simplicity, along with lower power consumption, smaller scan time and higher speed. Various functionalities and applications like typical PLC and industrial alarm annunciator have been developed and successfully tested. Results of simulation, design and implementation have been reported. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

  12. Objective assessment and design improvement of a staring, sparse transducer array by the spatial crosstalk matrix for 3D photoacoustic tomography.

    Directory of Open Access Journals (Sweden)

    Philip Wong

    Full Text Available Accurate reconstruction of 3D photoacoustic (PA images requires detection of photoacoustic signals from many angles. Several groups have adopted staring ultrasound arrays, but assessment of array performance has been limited. We previously reported on a method to calibrate a 3D PA tomography (PAT staring array system and analyze system performance using singular value decomposition (SVD. The developed SVD metric, however, was impractical for large system matrices, which are typical of 3D PAT problems. The present study consisted of two main objectives. The first objective aimed to introduce the crosstalk matrix concept to the field of PAT for system design. Figures-of-merit utilized in this study were root mean square error, peak signal-to-noise ratio, mean absolute error, and a three dimensional structural similarity index, which were derived between the normalized spatial crosstalk matrix and the identity matrix. The applicability of this approach for 3D PAT was validated by observing the response of the figures-of-merit in relation to well-understood PAT sampling characteristics (i.e. spatial and temporal sampling rate. The second objective aimed to utilize the figures-of-merit to characterize and improve the performance of a near-spherical staring array design. Transducer arrangement, array radius, and array angular coverage were the design parameters examined. We observed that the performance of a 129-element staring transducer array for 3D PAT could be improved by selection of optimal values of the design parameters. The results suggested that this formulation could be used to objectively characterize 3D PAT system performance and would enable the development of efficient strategies for system design optimization.

  13. Development of an Accelerated Test Design for Predicting the Service Life of the Solar Array at Mead, Nebraska

    Science.gov (United States)

    Gaines, G. B.; Thomas, R. E.; Noel, G. T.; Shilliday, T. S.; Wood, V. E.; Carmichael, D. C.

    1979-01-01

    An accelerated life test is described which was developed to predict the life of the 25 kW photovoltaic array installed near Mead, Nebraska. A quantitative model for accelerating testing using multiple environmental stresses was used to develop the test design. The model accounts for the effects of thermal stress by a relation of the Arrhenius form. This relation was then corrected for the effects of nonthermal environmental stresses, such as relative humidity, atmospheric pollutants, and ultraviolet radiation. The correction factors for the nonthermal stresses included temperature-dependent exponents to account for the effects of interactions between thermal and nonthermal stresses on the rate of degradation of power output. The test conditions, measurements, and data analyses for the accelerated tests are presented. Constant-temperature, cyclic-temperature, and UV types of tests are specified, incorporating selected levels of relative humidity and chemical contamination and an imposed forward-bias current and static electric field.

  14. Facile fabrication and configuration design of Co3O4 porous acicular nanorod arrays on Ni foam for supercapacitors.

    Science.gov (United States)

    Jiang, Tongtong; Yang, Siyu; Bai, Zhiman; Dai, Peng; Yu, Xinxin; Wu, Mingzai; Hu, Haibo

    2018-05-11

    The configuration of electrode materials is of great significance to the performance of supercapacitors (SCs) because of its direct effects on specific surface area and electron transfer path. Given this, herein, a series of Co3O4 hierarchical configurations composed of porous acicular nanorods are designedly synthesized on Ni foam with in-site self-organization method depending on the addition of NH4F. In the absence of NH4F, Co3O4 nanorods self-assemble into porous urchin-like structure (PULS), while the introduction of NH4F can induce the vertical growth of Co3O4 acicular nanorods, forming porous acicular nanorod arrays (PANRAs). By simply tuning the concentration of NH4F, the Co3O4 PANRAs with different specific surface area can be obtained. As expected, Co3O4 PANRAs electrode for SCs (using 1 mmol of NH4F) exhibits high specific capacitance (1486 F g-1 at 1 A g-1) and excellent cycling stability (98.8 % retention after 5000 continuous charge-discharge cycles), which are better than those of Co3O4 PULS electrode (658.2 F g-1 at 1 A g-1, 90.4 %). Corresponding solid-state symmetric SC achieves a high energy density of 48.63 Wh kg-1 at power density of 600 W kg-1. Such superior performance is attributed to fast charge-transfer kinetics, facile electron transport and ions diffusion rate resulting from porous array structure, indicating the importance of configuration design of electrode materials for high performance SCs. © 2018 IOP Publishing Ltd.

  15. The Bepicolombo Mercury Planetary Orbiter (MPO Solar Array Design, Major Developments and Qualification

    Directory of Open Access Journals (Sweden)

    Loehberg A.

    2017-01-01

    The MPO solar generator is composed of one wing consisting of three panels and provides an average power output up to 1800W during the nominal 1 Earth year mission around Mercury. The wing design is characterised by temperature reduction measures. The flight wing has already passed the majority of the environmental test program.

  16. Design of RS232-powered controller for switched parasitic array antenna

    CSIR Research Space (South Africa)

    Mofolo, MOR

    2013-09-01

    Full Text Available It is often convenient to power up peripheral devices directly from the host device interface, without a need for additional and/or external power supply. In this paper we present a design of the RS232-powered controller for electronically...

  17. Design and experimental validation of Unilateral Linear Halbach magnet arrays for single-sided magnetic resonance.

    Science.gov (United States)

    Bashyam, Ashvin; Li, Matthew; Cima, Michael J

    2018-07-01

    Single-sided NMR has the potential for broad utility and has found applications in healthcare, materials analysis, food quality assurance, and the oil and gas industry. These sensors require a remote, strong, uniform magnetic field to perform high sensitivity measurements. We demonstrate a new permanent magnet geometry, the Unilateral Linear Halbach, that combines design principles from "sweet-spot" and linear Halbach magnets to achieve this goal through more efficient use of magnetic flux. We perform sensitivity analysis using numerical simulations to produce a framework for Unilateral Linear Halbach design and assess tradeoffs between design parameters. Additionally, the use of hundreds of small, discrete magnets within the assembly allows for a tunable design, improved robustness to variability in magnetization strength, and increased safety during construction. Experimental validation using a prototype magnet shows close agreement with the simulated magnetic field. The Unilateral Linear Halbach magnet increases the sensitivity, portability, and versatility of single-sided NMR. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. A comparative design view for accurate control of servos using a field programmable gate array

    International Nuclear Information System (INIS)

    Tickle, A J; Harvey, P K; Smith, J S; Wu, F; Buckle, J R

    2009-01-01

    An embedded system is a special-purpose computer system designed to perform one or a few dedicated functions. Altera DSP Builder presents designers and users with an alternate approach when creating their systems by employing a blockset similar to that already used in Simulink. The application considered in this paper is the design of a Pulse Width Modulation (PWM) system for use in stereo vision. PWM can replace a digital-to-analogue converter to control audio speakers, LED intensity, motor speed, and servo position. Rather than the conventional HDL coding approach this Simulink approach provides an easy understanding platform to the PWM design. This paper includes a comparison between two approaches regarding resource usage and flexibility etc. Included is how DSP Builder manipulates an onboard clock signal, in order to create the control pulses to the 'raw' coding of a PWM generator in VHDL. Both methods were shown to a selection of people and their views on which version they would subsequently use in their relative fields is discussed.

  19. Sequence-dependent theory of oligonucleotide hybridization kinetics

    International Nuclear Information System (INIS)

    Marimuthu, Karthikeyan; Chakrabarti, Raj

    2014-01-01

    A theoretical approach to the prediction of the sequence and temperature-dependent rate constants for oligonucleotide hybridization reactions has been developed based on the theory of relaxation kinetics. One-sided and two-sided melting reaction mechanisms for oligonucleotide hybridization reactions have been considered, analyzed, modified, and compared to select a physically consistent as well as robust model for prediction of the relaxation times of DNA hybridization reactions that agrees with the experimental evidence. The temperature- and sequence-dependent parameters of the proposed model have been estimated using available experimental data. The relaxation time model that we developed has been combined with the nearest neighbor model of hybridization thermodynamics to estimate the temperature- and sequence-dependent rate constants of an oligonucleotide hybridization reaction. The model-predicted rate constants are compared to experimentally determined rate constants for the same oligonucleotide hybridization reactions. Finally, we consider a few important applications of kinetically controlled DNA hybridization reactions

  20. Oligonucleotide-based theranostic nanoparticles in cancer therapy

    Science.gov (United States)

    Shahbazi, Reza; Ozpolat, Bulent; Ulubayram, Kezban

    2016-01-01

    Theranostic approaches, combining the functionality of both therapy and imaging, have shown potential in cancer nanomedicine. Oligonucleotides such as small interfering RNA and microRNA, which are powerful therapeutic agents, have been effectively employed in theranostic systems against various cancers. Nanoparticles are used to deliver oligonucleotides into tumors by passive or active targeting while protecting the oligonucleotides from nucleases in the extracellular environment. The use of quantum dots, iron oxide nanoparticles and gold nanoparticles and tagging with contrast agents, like fluorescent dyes, optical or magnetic agents and various radioisotopes, has facilitated early detection of tumors and evaluation of therapeutic efficacy. In this article, we review the advantages of theranostic applications in cancer therapy and imaging, with special attention to oligonucleotide-based therapeutics. PMID:27102380

  1. Low concentration ratio solar array for low Earth orbit multi-100 kW application. Volume 1: Design, analysis and development tests

    Science.gov (United States)

    1983-01-01

    A preliminary design effort directed toward a low concentration ratio photovoltaic array system capable of delivering multihundred kilowatts (300 kW to 1000 kW range) in low earth orbit is described. The array system consists of two or more array modules each capable of delivering between 113 kW to 175 kW using silicon solar cells or gallium arsenide solar cells, respectively. The array module deployed area is 1320 square meters and consists of 4356 pyramidal concentrator elements. The module, when stowed in the Space Shuttle's payload bay, has a stowage volume of a cube with 3.24 meters on a side. The concentrator elements are sized for a geometric concentration ratio (GCR) of six with an aperture area of .25 sq. m. The structural analysis and design trades leading to the baseline design are discussed. It describes the configuration, as well as optical, thermal and electrical performance analyses that support the design and overall performance estimates for the array are described.

  2. SPAD array based TOF SoC design for unmanned vehicle

    Science.gov (United States)

    Pan, An; Xu, Yuan; Xie, Gang; Huang, Zhiyu; Zheng, Yanghao; Shi, Weiwei

    2018-03-01

    As for the requirement of unmanned-vehicle mobile Lidar system, this paper presents a SoC design based on pulsed TOF depth image sensor. This SoC has a detection range of 300m and detecting resolution of 1.5cm. Pixels are made of SPAD. Meanwhile, SoC adopts a structure of multi-pixel sharing TDC, which significantly reduces chip area and improve the fill factor of light-sensing surface area. SoC integrates a TCSPC module to achieve the functionality of receiving each photon, measuring photon flight time and processing depth information in one chip. The SOC is designed in the SMIC 0.13μm CIS CMOS technology

  3. A Parameterized Pattern-Error Objective for Large-Scale Phase-Only Array Pattern Design

    Science.gov (United States)

    2016-03-21

    of 1D heuristic design approaches can be found in [6–11]. Reference [12], which proposes separate beams on interlaced subarrays, represents a 2D...and is well suited for solving with efficient quasi-Newton methods. Although deliberately simple, the objective has several heuristic parameters for...with efficient quasi-Newton methods. Although deliberately simple, the objective has several heuristic parameters for flexibility and can be used to

  4. The flush-mounted rail Langmuir probe array designed for the Alcator C-Mod vertical target plate divertor

    Science.gov (United States)

    Kuang, A. Q.; Brunner, D.; LaBombard, B.; Leccacorvi, R.; Vieira, R.

    2018-04-01

    An array of flush-mounted and toroidally elongated Langmuir probes (henceforth called rail probes) have been specifically designed for the Alcator C-Mod's vertical target plate divertor and operated over multiple campaigns. The "flush" geometry enables the tungsten electrodes to survive high heat flux conditions in which traditional "proud" tungsten electrodes suffer damage from melting. The toroidally elongated rail-like geometry reduces the influence of sheath expansion, which is an important effect to consider in the design and interpretation of flush-mounted Langmuir probes. The new rail probes successfully operated during C-Mod's FY2015 and FY2016 experimental campaigns with no evidence of damage, despite being regularly subjected to heat flux densities parallel to the magnetic field exceeding ˜1 GW m-2 for short periods of time. A comparison between rail and proud probe data indicates that sheath expansion effects were successfully mitigated by the rail design, extending the use of these Langmuir probes to incident magnetic field line angles as low as 0.5°.

  5. Image processing system design for microcantilever-based optical readout infrared arrays

    Science.gov (United States)

    Tong, Qiang; Dong, Liquan; Zhao, Yuejin; Gong, Cheng; Liu, Xiaohua; Yu, Xiaomei; Yang, Lei; Liu, Weiyu

    2012-12-01

    Compared with the traditional infrared imaging technology, the new type of optical-readout uncooled infrared imaging technology based on MEMS has many advantages, such as low cost, small size, producing simple. In addition, the theory proves that the technology's high thermal detection sensitivity. So it has a very broad application prospects in the field of high performance infrared detection. The paper mainly focuses on an image capturing and processing system in the new type of optical-readout uncooled infrared imaging technology based on MEMS. The image capturing and processing system consists of software and hardware. We build our image processing core hardware platform based on TI's high performance DSP chip which is the TMS320DM642, and then design our image capturing board based on the MT9P031. MT9P031 is Micron's company high frame rate, low power consumption CMOS chip. Last we use Intel's company network transceiver devices-LXT971A to design the network output board. The software system is built on the real-time operating system DSP/BIOS. We design our video capture driver program based on TI's class-mini driver and network output program based on the NDK kit for image capturing and processing and transmitting. The experiment shows that the system has the advantages of high capturing resolution and fast processing speed. The speed of the network transmission is up to 100Mbps.

  6. Advances in Antisense Oligonucleotide Development for Target Identification, Validation, and as Novel Therapeutics

    Directory of Open Access Journals (Sweden)

    Moizza Mansoor

    2008-01-01

    Full Text Available Antisense oligonucleotides (As-ODNs are single stranded, synthetically prepared strands of deoxynucleotide sequences, usually 18–21 nucleotides in length, complementary to the mRNA sequence of the target gene. As-ODNs are able to selectively bind cognate mRNA sequences by sequence-specific hybridization. This results in cleavage or disablement of the mRNA and, thus, inhibits the expression of the target gene. The specificity of the As approach is based on the probability that, in the human genome, any sequence longer than a minimal number of nucleotides (nt, 13 for RNA and 17 for DNA, normally occurs only once. The potential applications of As-ODNs are numerous because mRNA is ubiquitous and is more accessible to manipulation than DNA. With the publication of the human genome sequence, it has become theoretically possible to inhibit mRNA of almost any gene by As-ODNs, in order to get a better understanding of gene function, investigate its role in disease pathology and to study novel therapeutic targets for the diseases caused by dysregulated gene expression. The conceptual simplicity, the availability of gene sequence information from the human genome, the inexpensive availability of synthetic oligonucleotides and the possibility of rational drug design makes As-ODNs powerful tools for target identification, validation and therapeutic intervention. In this review we discuss the latest developments in antisense oligonucleotide design, delivery, pharmacokinetics and potential side effects, as well as its uses in target identification and validation, and finally focus on the current developments of antisense oligonucleotides in therapeutic intervention in various diseases.

  7. Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel.

    Science.gov (United States)

    Tang, Weizhong; Zhou, Huafu; Li, Wei

    2015-01-01

    To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.

  8. Theory, Design, and Measurement of Novel Uniform Circular Antenna Arrays for Direction of Arrival Estimation

    Science.gov (United States)

    2015-01-01

    Queen in Right of Canada, as represented by the Minister of National Defence, 2015 c⃝ Sa Majesté la Reine (en droit du Canada), telle que réprésentée... publication in [1]. Sections 5 and 6 describe the design and fabrication of the three novel UCAs for DOA estimation and provide simulation results. Section...DoA resolution limits in MIMO channel sounding,” in 2004 IEEE International Symposium On Antennas and Propagation and USNC/URSI National Radio

  9. A one-step reaction for the rapid identification of Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti using oligonucleotide primers designed from the 16S-23S rRNA intergenic sequences.

    Science.gov (United States)

    Ferchichi, M; Valcheva, R; Prévost, H; Onno, B; Dousset, X

    2008-06-01

    Species-specific primers targeting the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR) were designed to rapidly discriminate between Lactobacillus mindensis, Lactobacillus panis, Lactobacillus paralimentarius, Lactobacillus pontis and Lactobacillus frumenti species recently isolated from French sourdough. The 16S-23S ISRs were amplified using primers 16S/p2 and 23S/p7, which anneal to positions 1388-1406 of the 16S rRNA gene and to positions 207-189 of the 23S rRNA gene respectively, Escherichia coli numbering (GenBank accession number V00331). Clone libraries of the resulting amplicons were constructed using a pCR2.1 TA cloning kit and sequenced. Species-specific primers were designed based on the sequences obtained and were used to amplify the 16S-23S ISR in the Lactobacillus species considered. For all of them, two PCR amplicons, designated as small ISR (S-ISR) and large ISR (L-ISR), were obtained. The L-ISR is composed of the corresponding S-ISR, interrupted by a sequence containing tRNA(Ile) and tRNA(Ala) genes. Based on these sequences, species-specific primers were designed and proved to identify accurately the species considered among 30 reference Lactobacillus species tested. Designed species-specific primers enable a rapid and accurate identification of L. mindensis, L. paralimentarius, L. panis, L. pontis and L. frumenti species among other lactobacilli. The proposed method provides a powerful and convenient means of rapidly identifying some sourdough lactobacilli, which could be of help in large starter culture surveys.

  10. INFLUENCE OF IONIZING IRRADIATION ON THE PARAMETERS OF ZN NANOTUBES ARRAYS FOR DESIGN OF FLEXIBLE ELECTRONICS ELEMENTS

    Directory of Open Access Journals (Sweden)

    D. B. Kadyrzhanov

    2018-01-01

    Full Text Available The aim of the study is establishing the possibility of using Zn nanotube arrays as a basis for design compact and lightweight elements of flexible electronics, including operating under influence of ionizing irradiation.The paper presents the results of the synthesis of Zn nanotubes obtained by electrochemical deposition in the pores of polymer matrices and the study of their structural and electrophysical properties after directional modification by ionizing radiation with different doses. Using the methods of scanning electron microscopy, X-ray diffraction and energy dispersive analysis, the structure of nanotubes having a polycrystalline structure and completely consisting of zinc was studied and it was demonstrated that irradiation with Ar8+ ions with a dose from 1 × 109 to 5 × 1011 ion/cm2 and energy 1.75 MeV/nucleon has an effect on the crystal structure of nanotubes.At high doses, localized highly defect zones arise, leading to a critical change in the structure and physical properties of the nanotubes, respectively. It is shown that the consequence of the modification of the crystal structure is a change in the electrical conductivity of nanotubes: at low doses the electrical conductivity increases, but when the threshold value is reached, it sharply decreases. The change in the crystal structure and the corresponding changes in the conductive properties of Zn nanotubes due to irradiation determine the mechanism of ionizing radiation influence on nanomaterials and determine the possibility of using Zn nanotubes arrays as a basis for creating compact and lightweight elements of flexible electronics.

  11. Design, fabrication and characterization of an arrayable all-polymer microfluidic valve employing highly magnetic rare-earth composite polymer

    International Nuclear Information System (INIS)

    Rahbar, Mona; Gray, Bonnie L; Shannon, Lesley

    2016-01-01

    We present a new magnetically actuated microfluidic valve that employs a highly magnetic composite polymer (M-CP) containing rare-earth hard-magnetic powder for its actuating element and for its valve seat. The M-CP offers much higher magnetization compared to the soft-magnetic, ferrite-based composite polymers typically used in microfluidic applications. Each valve consists of a permanently magnetized M-CP flap and valve seat mounted on a microfluidic channel system fabricated in poly(dimethylsiloxane) (PDMS). Each valve is actuated under a relatively small external magnetic field of 80 mT provided by a small permanent magnet mounted on a miniature linear actuator. The performance of the valve with different flap thicknesses is characterized. In addition, the effect of the magnetic valve seat on the valve’s performance is also characterized. It is experimentally shown that a valve with a 2.3 mm flap thickness, actuated under an 80 mT magnetic field, is capable of completely blocking liquid flow at a flow rate of 1 ml min −1 for pressures up to 9.65 kPa in microfluidic channels 200 μ m wide and 200 μ m deep. The valve can also be fabricated into an array for flow switching between multiple microfluidic channels under continuous flow conditions. The performance of arrays of valves for flow routing is demonstrated for flow rates up to 5 ml min −1 with larger microfluidic channels of up to 1 mm wide and 500 μ m deep. The design of the valves is compatible with other commonly used polymeric microfluidic components, as well as other components that use the same novel permanently magnetic composite polymer, such as our previously reported cilia-based mixing devices. (paper)

  12. Transition-Edge Sensor Pixel Parameter Design of the Microcalorimeter Array for the X-Ray Integral Field Unit on Athena

    Science.gov (United States)

    Smith, S. J.; Adams, J. S.; Bandler, S. R.; Betancourt-Martinez, G. L.; Chervenak, J. A.; Chiao, M. P.; Eckart, M. E.; Finkbeiner, F. M.; Kelley, R. L.; Kilbourne, C. A.; hide

    2016-01-01

    The focal plane of the X-ray integral field unit (X-IFU) for ESA's Athena X-ray observatory will consist of approximately 4000 transition edge sensor (TES) x-ray microcalorimeters optimized for the energy range of 0.2 to 12 kiloelectronvolts. The instrument will provide unprecedented spectral resolution of approximately 2.5 electronvolts at energies of up to 7 kiloelectronvolts and will accommodate photon fluxes of 1 milliCrab (90 counts per second) for point source observations. The baseline configuration is a uniform large pixel array (LPA) of 4.28 arcseconds pixels that is read out using frequency domain multiplexing (FDM). However, an alternative configuration under study incorporates an 18 by × 18 small pixel array (SPA) of 2 arcseconds pixels in the central approximately 36 arcseconds region. This hybrid array configuration could be designed to accommodate higher fluxes of up to 10 milliCrabs (900 counts per second) or alternately for improved spectral performance (less than 1.5 electronvolts) at low count-rates. In this paper we report on the TES pixel designs that are being optimized to meet these proposed LPA and SPA configurations. In particular we describe details of how important TES parameters are chosen to meet the specific mission criteria such as energy resolution, count-rate and quantum efficiency, and highlight performance trade-offs between designs. The basis of the pixel parameter selection is discussed in the context of existing TES arrays that are being developed for solar and x-ray astronomy applications. We describe the latest results on DC biased diagnostic arrays as well as large format kilo-pixel arrays and discuss the technical challenges associated with integrating different array types on to a single detector die.

  13. Transition-edge sensor pixel parameter design of the microcalorimeter array for the x-ray integral field unit on Athena

    Science.gov (United States)

    Smith, S. J.; Adams, J. S.; Bandler, S. R.; Betancourt-Martinez, G. L.; Chervenak, J. A.; Chiao, M. P.; Eckart, M. E.; Finkbeiner, F. M.; Kelley, R. L.; Kilbourne, C. A.; Miniussi, A. R.; Porter, F. S.; Sadleir, J. E.; Sakai, K.; Wakeham, N. A.; Wassell, E. J.; Yoon, W.; Bennett, D. A.; Doriese, W. B.; Fowler, J. W.; Hilton, G. C.; Morgan, K. M.; Pappas, C. G.; Reintsema, C. N.; Swetz, D. S.; Ullom, J. N.; Irwin, K. D.; Akamatsu, H.; Gottardi, L.; den Hartog, R.; Jackson, B. D.; van der Kuur, J.; Barret, D.; Peille, P.

    2016-07-01

    The focal plane of the X-ray integral field unit (X-IFU) for ESA's Athena X-ray observatory will consist of 4000 transition edge sensor (TES) x-ray microcalorimeters optimized for the energy range of 0.2 to 12 keV. The instrument will provide unprecedented spectral resolution of 2.5 eV at energies of up to 7 keV and will accommodate photon fluxes of 1 mCrab (90 cps) for point source observations. The baseline configuration is a uniform large pixel array (LPA) of 4.28" pixels that is read out using frequency domain multiplexing (FDM). However, an alternative configuration under study incorporates an 18 × 18 small pixel array (SPA) of 2" pixels in the central 36" region. This hybrid array configuration could be designed to accommodate higher fluxes of up to 10 mCrab (900 cps) or alternately for improved spectral performance (< 1.5 eV) at low count-rates. In this paper we report on the TES pixel designs that are being optimized to meet these proposed LPA and SPA configurations. In particular we describe details of how important TES parameters are chosen to meet the specific mission criteria such as energy resolution, count-rate and quantum efficiency, and highlight performance trade-offs between designs. The basis of the pixel parameter selection is discussed in the context of existing TES arrays that are being developed for solar and x-ray astronomy applications. We describe the latest results on DC biased diagnostic arrays as well as large format kilo-pixel arrays and discuss the technical challenges associated with integrating different array types on to a single detector die.

  14. Optimal Design of MPPT Controllers for Grid Connected Photovoltaic Array System

    Science.gov (United States)

    Ebrahim, M. A.; AbdelHadi, H. A.; Mahmoud, H. M.; Saied, E. M.; Salama, M. M.

    2016-10-01

    Integrating photovoltaic (PV) plants into electric power system exhibits challenges to power system dynamic performance. These challenges stem primarily from the natural characteristics of PV plants, which differ in some respects from the conventional plants. The most significant challenge is how to extract and regulate the maximum power from the sun. This paper presents the optimal design for the most commonly used Maximum Power Point Tracking (MPPT) techniques based on Proportional Integral tuned by Particle Swarm Optimization (PI-PSO). These suggested techniques are, (1) the incremental conductance, (2) perturb and observe, (3) fractional short circuit current and (4) fractional open circuit voltage techniques. This research work provides a comprehensive comparative study with the energy availability ratio from photovoltaic panels. The simulation results proved that the proposed controllers have an impressive tracking response. The system dynamic performance improved greatly using the proposed controllers.

  15. Design of a muon tomography system with a plastic scintillator and wavelength-shifting fiber arrays

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Woo Jin; Kim, Hyun-Il; An, Su Jung; Lee, Chae Young [Department of Radiological Science, College of Health Science, Yonsei University, Wonju 220-710 (Korea, Republic of); Baek, Cheol-Ha [Department of Radiological Science, Dongseo University, Busan 617-716 (Korea, Republic of); Chung, Yong Hyun, E-mail: ychung@yonsei.ac.kr [Department of Radiological Science, College of Health Science, Yonsei University, Wonju 220-710 (Korea, Republic of)

    2013-12-21

    Recently, monitoring nuclear materials to avoid nuclear terrorism has become an important area of national security. It can be difficult to detect gamma rays from nuclear material because they are easily shielded by shielding material. Muon tomography using multiple -Coulomb scattering derived from muons can be utilized to detect special nuclear materials (SNMs) such as uranium-235 and plutonium-239. We designed a muon tomography system composed of four detector modules. The incident and scattered muon tracks can be calculated by two top and two bottom detectors, respectively. 3D tomographic images are obtained by extracting the crossing points of muon tracks with a point-of-closest-approach algorithm. The purpose of this study was to optimize the muon tomography system using Monte Carlo simulation code. The effects of the geometric parameters of the muon tomography system on material Z-discrimination capability were simulated and evaluated.

  16. A new method for the design of slot antenna arrays: Theory and experiment

    KAUST Repository

    Clauzier, Sebastien

    2016-04-10

    The present paper proposes and validates a new general design methodology that can be used to automatically find proper positions and orientations of waveguide-based radiating slots capable of realizing any given radiation beam profile. The new technique combines basic radiation theory and waveguide propagation theory in a novel analytical model that allows the prediction of the radiation characteristics of generic slots without the need to perform full-wave numerical solution. The analytical model is then used to implement a low-cost objective function within a global optimization scheme (here genetic algorithm.) The algorithm is then deployed to find optimum positions and orientations of clusters of radiating slots cut into the waveguide surface such that any desired beam pattern can be obtained. The method is verified using both full-wave numerical solution and experiment.

  17. Pharmacokinetics on a microscale: visualizing Cy5-labeled oligonucleotide release from poly(n-butylcyanoacrylate nanocapsules in cells

    Directory of Open Access Journals (Sweden)

    Tomcin S

    2014-11-01

    Full Text Available Stephanie Tomcin,1 Grit Baier,1 Katharina Landfester,1 Volker Mailänder1,21Max Planck Institute for Polymer Research, 2University Medical Center of the Johannes Gutenberg University, III Medical Clinic, Mainz, GermanyAbstract: For successful design of a nanoparticulate drug delivery system, the fate of the carrier and cargo need to be followed. In this work, we fluorescently labeled poly(n-butylcyanoacrylate (PBCA nanocapsules as a shell and separately an oligonucleotide (20 mer as a payload. The nanocapsules were formed by interfacial anionic polymerization on aqueous droplets generated by an inverse miniemulsion process. After uptake, the PBCA capsules were shown to be round-shaped, endosomal structures and the payload was successfully released. Cy5-labeled oligonucleotides accumulated at the mitochondrial membrane due to a combination of the high mitochondrial membrane potential and the specific molecular structure of Cy5. The specificity of this accumulation at the mitochondria was shown as the uncoupler dinitrophenol rapidly diminished the accumulation of the Cy5-labeled oligonucleotide. Importantly, a fluorescence resonance energy transfer investigation showed that the dye-labeled cargo (Cy3/Cy5-labeled oligonucleotides reached its target site without degradation during escape from an endosomal compartment to the cytoplasm. The time course of accumulation of fluorescent signals at the mitochondria was determined by evaluating the colocalization of Cy5-labeled oligonucleotides and mitochondrial markers for up to 48 hours. As oligonucleotides are an ideal model system for small interfering RNA PBCA nanocapsules demonstrate to be a versatile delivery platform for small interfering RNA to treat a variety of diseases.Keywords: drug delivery, mitochondria, miniemulsion, colocalization

  18. Design and study of a coplanar grid array CdZnTe detector for improved spatial resolution

    International Nuclear Information System (INIS)

    Ma, Yuedong; Xiao, Shali; Yang, Guoqiang; Zhang, Liuqiang

    2014-01-01

    Coplanar grid (CPG) CdZnTe detectors have been used as gamma-ray spectrometers for years. Comparing with pixelated CdZnTe detectors, CPG CdZnTe detectors have either no or poor spatial resolution, which directly limits its use in imaging applications. To address the issue, a 2×2 CPG array CdZnTe detector with dimensions of 7×7×5 mm 3 was fabricated. Each of the CPG pairs in the detector was moderately shrunk in size and precisely designed to improve the spatial resolution while maintaining good energy resolution, considering the charge loss at the surface between the strips of each CPG pairs. Preliminary measurements were demonstrated at an energy resolution of 2.7–3.9% for the four CPG pairs using 662 keV gamma rays and with a spatial resolution of 3.3 mm, which is the best spatial resolution ever achieved for CPG CdZnTe detectors. The results reveal that the CPG CdZnTe detector can also be applied to imaging applications at a substantially higher spatial resolution. - Highlights: • A novel structure of coplanar grid CdZnTe detector was designed to evaluate the possibility of applying the detector to gamma-ray imaging applications. • The best spatial resolution of coplanar grid CdZnTe detectors ever reported has been achieved, along with good spectroscopic performance. • Depth correction of the energy spectra using a new algorithm is presented

  19. Design of a bovine low-density SNP array optimized for imputation.

    Directory of Open Access Journals (Sweden)

    Didier Boichard

    Full Text Available The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.

  20. Design of collimating and rearrangement systems of laser diode array beam

    Science.gov (United States)

    Gao, Runmei; Fang, Tao; Fu, Rulian; Yao, Jianquan

    2015-10-01

    To improve the laser diode output beam quality, micro-cylindrical lens and the step-type lens combination are designed. The former is used to collimate beam in fast-axis direction, while the latter plays a role in the slow-axis of splitting and the rearrangement. The micro-column semi-elliptical lens is made with the drops of spherical zoom lensin electric field and with the help of the material properties of light-cured production, which can reduce the reflection of the front surface and total reflection loss of the after. The divergence angle in the fast axis is compressed to roughly the same as that in the slow-axis direction; Stepped lens splits compressed long strip beam in the slow axis, with parallelogram style of level equidistant and rearrange in the fast axis direction. The spot in the slow axis gets smaller and the spot becomes larger in the fast axis. At last divergence angle and the beam spot achieve balanced in the fast axis and slow axis, optical parameters BPP integrates approximate the same, and beam quality can be improved.

  1. Field Programmable Gate Array Based Parallel Strapdown Algorithm Design for Strapdown Inertial Navigation Systems

    Directory of Open Access Journals (Sweden)

    Long-Hua Ma

    2011-08-01

    Full Text Available A new generalized optimum strapdown algorithm with coning and sculling compensation is presented, in which the position, velocity and attitude updating operations are carried out based on the single-speed structure in which all computations are executed at a single updating rate that is sufficiently high to accurately account for high frequency angular rate and acceleration rectification effects. Different from existing algorithms, the updating rates of the coning and sculling compensations are unrelated with the number of the gyro incremental angle samples and the number of the accelerometer incremental velocity samples. When the output sampling rate of inertial sensors remains constant, this algorithm allows increasing the updating rate of the coning and sculling compensation, yet with more numbers of gyro incremental angle and accelerometer incremental velocity in order to improve the accuracy of system. Then, in order to implement the new strapdown algorithm in a single FPGA chip, the parallelization of the algorithm is designed and its computational complexity is analyzed. The performance of the proposed parallel strapdown algorithm is tested on the Xilinx ISE 12.3 software platform and the FPGA device XC6VLX550T hardware platform on the basis of some fighter data. It is shown that this parallel strapdown algorithm on the FPGA platform can greatly decrease the execution time of algorithm to meet the real-time and high precision requirements of system on the high dynamic environment, relative to the existing implemented on the DSP platform.

  2. Ultrasensitive Detection of Ebola Virus Oligonucleotide Based on Upconversion Nanoprobe/Nanoporous Membrane System.

    Science.gov (United States)

    Tsang, Ming-Kiu; Ye, WeiWei; Wang, Guojing; Li, Jingming; Yang, Mo; Hao, Jianhua

    2016-01-26

    Ebola outbreaks are currently of great concern, and therefore, development of effective diagnosis methods is urgently needed. The key for lethal virus detection is high sensitivity, since early-stage detection of virus may increase the probability of survival. Here, we propose a luminescence scheme of assay consisting of BaGdF5:Yb/Er upconversion nanoparticles (UCNPs) conjugated with oligonucleotide probe and gold nanoparticles (AuNPs) linked with target Ebola virus oligonucleotide. As a proof of concept, a homogeneous assay was fabricated and tested, yielding a detection limit at picomolar level. The luminescence resonance energy transfer is ascribed to the spectral overlapping of upconversion luminescence and the absorption characteristics of AuNPs. Moreover, we anchored the UCNPs and AuNPs on a nanoporous alumina (NAAO) membrane to form a heterogeneous assay. Importantly, the detection limit was greatly improved, exhibiting a remarkable value at the femtomolar level. The enhancement is attributed to the increased light-matter interaction throughout the nanopore walls of the NAAO membrane. The specificity test suggested that the nanoprobes were specific to Ebola virus oligonucleotides. The strategy combining UCNPs, AuNPs, and NAAO membrane provides new insight into low-cost, rapid, and ultrasensitive detection of different diseases. Furthermore, we explored the feasibility of clinical application by using inactivated Ebola virus samples. The detection results showed great potential of our heterogeneous design for practical application.

  3. Antineoplastic Effect of Decoy Oligonucleotide Derived from MGMT Enhancer

    Science.gov (United States)

    Refael, Miri; Zrihan, Daniel; Siegal, Tali; Lavon, Iris

    2014-01-01

    Silencing of O(6)-methylguanine-DNA-methyltransferase (MGMT) in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1) within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA) modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN). Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy. PMID:25460932

  4. Antineoplastic effect of decoy oligonucleotide derived from MGMT enhancer.

    Directory of Open Access Journals (Sweden)

    Tamar Canello

    Full Text Available Silencing of O(6-methylguanine-DNA-methyltransferase (MGMT in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1 within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN. Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy.

  5. Effect of oligonucleotide primers in determining viral variability within hosts

    Directory of Open Access Journals (Sweden)

    Moya Andrés

    2004-12-01

    Full Text Available Abstract Background Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. Results To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient. Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. Conclusions Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.

  6. Effect of oligonucleotide primers in determining viral variability within hosts.

    Science.gov (United States)

    Bracho, Maria Alma; García-Robles, Inmaculada; Jiménez, Nuria; Torres-Puente, Manuela; Moya, Andrés; González-Candelas, Fernando

    2004-12-09

    Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR) based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV) populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient). Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.

  7. Respirable antisense oligonucleotides: a new drug class for respiratory disease

    Directory of Open Access Journals (Sweden)

    Tanaka Makoto

    2000-12-01

    Full Text Available Abstract Respirable antisense oligonucleotides (RASONs, which attenuate specific disease-associated mRNAs, represent a new class of respiratory therapeutics with considerable potential. RASONs overcome previous obstacles that have impeded the development of antisense therapeutics targeting diseases in other organ systems. RASONs are delivered directly to the target tissue via inhalation; their uptake seems to be enhanced by cationic properties inherent in pulmonary surfactant, and, because of the markedly different target properties of mRNA and proteins, they can have very long durations of effect compared with traditional drugs targeting the protein of the same gene. RASONs contain chemical modifications that decrease their degradation by cellular nucleases. However, total insensitivity to nucleases is probably not an optimal design criterion for RASONs, because moderate nuclease sensitivity can prevent their systemic delivery, decreasing the potential for systemic toxicity. EPI-2010 is a 21-mer phosphorothioate RASON that attenuates bronchoconstriction, inflammation and surfactant depletion in preclinical models of human asthma, has a duration of effect of seven days, and seems to undergo minimal systemic delivery.

  8. Recent advances in antisense oligonucleotide therapy in genetic neuromuscular diseases

    Directory of Open Access Journals (Sweden)

    Ashok Verma

    2018-01-01

    Full Text Available Genetic neuromuscular diseases are caused by defective expression of nuclear or mitochondrial genes. Mutant genes may reduce expression of wild-type proteins, and strategies to activate expression of the wild-type proteins might provide therapeutic benefits. Also, a toxic mutant protein may cause cell death, and strategies that reduce mutant gene expression may provide therapeutic benefit. Synthetic antisense oligonucleotide (ASO can recognize cellular RNA and control gene expression. In recent years, advances in ASO chemistry, creation of designer ASO molecules to enhance their safety and target delivery, and scientific controlled clinical trials to ascertain their therapeutic safety and efficacy have led to an era of plausible application of ASO technology to treat currently incurable neuromuscular diseases. Over the past 1 year, for the first time, the United States Food and Drug Administration has approved two ASO therapies in genetic neuromuscular diseases. This overview summarizes the recent advances in ASO technology, evolution and use of synthetic ASOs as a therapeutic platform, and the mechanism of ASO action by exon-skipping in Duchenne muscular dystrophy and exon-inclusion in spinal muscular atrophy, with comments on their advantages and limitations.

  9. Defibrotide: An Oligonucleotide for Sinusoidal Obstruction Syndrome.

    Science.gov (United States)

    Aziz, May T; Kakadiya, Payal P; Kush, Samantha M; Weigel, Kylie; Lowe, Denise K

    2018-02-01

    To review the efficacy and safety of defibrotide as well as its pharmacology, mechanism of action, pharmacokinetics (PK), drug-drug interactions, dosing, cost considerations, and place in therapy. A PubMed search was performed through August 2017 using the terms defibrotide, oligonucleotide, hepatic veno-occlusive disease (VOD), sinusoidal obstruction syndrome (SOS), and hematopoietic cell transplantation (HCT). Other data sources were from references of identified studies, review articles, and conference abstracts plus manufacturer product labeling and website, the Food and Drug Administration website, and clinicaltrials.gov. English-language trials that examined defibrotide's pharmacodynamics, mechanism, PK, efficacy, safety, dosing, and cost-effectiveness were included. Trials have confirmed the safety and efficacy of defibrotide for treatment of VOD/SOS in adult and pediatric HCT patients, with complete response rates and day +100 overall survival rates ranging from 25.5% to 76% and 35% to 64%, respectively. The British Committee for Standards in Haematology/British Society for Blood and Marrow Transplantation Guidelines recommend defibrotide prophylaxis in pediatric and adult HCT patients with risk factors for VOD/SOS; however, its prophylactic use in the United States is controversial. Although there are efficacy data to support this strategy, cost-effectiveness data have not shown it to be cost-effective. Defibrotide has manageable toxicities, with low rates of grade 3 to 4 adverse effects. Defibrotide is the first medication approved in the United States for the treatment of adults and children with hepatic VOD/SOS, with renal or pulmonary dysfunction following HCT. Data evaluating defibrotide for VOD/SOS prevention are conflicting and have not shown cost-effectiveness.

  10. Biominetic High Density Lipoproteins for the Delivery of Therapeutic Oligonucleotides

    Science.gov (United States)

    Tripathy, Sushant

    Advances in nanotechnology have brought about novel inorganic and hybrid nanoparticles with unique physico-chemical properties that make them suitable for a broad range of applications---from nano-circuitry to drug delivery. A significant part of those advancements have led to ground-breaking discoveries that have changed the approaches to formulation of therapeutics against diseases, such as cancer. Now-a-days the focus does not lie solely on finding a candidate small-molecule therapeutic with minimal adverse effects, but researchers are looking up to nanoparticles to improve biodistribution and biocompatibility profile of clinically proven therapeutics. The plethora of conjugation chemistries offered by currently extant inorganic nanoparticles have, in recent years, led to great leaps in the field of biomimicry---a modality that promises high biocompatibility. Further, in the pursuit of highly specific therapeutic molecules, researchers have turned to silencing oligonucleotides and some have already brought together the strengths of nanoparticles and silencing oligonucleotides in search of an efficacious therapy for cancer with minimal adverse effects. This dissertation work focuses on such a biomimetic platform---a gold nanoparticle based high density lipoprotein biomimetic (HDL NP), for the delivery of therapeutic oligonucleotides. The first chapter of this body of work introduces the molecular target of the silencing oligonucleotides---VEGFR2, and its role in the progression of solid tumor cancers. The background information also covers important aspects of natural high density lipoproteins (HDL), especially their innate capacity to bind and deliver exogenous and endogenous silencing oligonucleotides to tissues that express their high affinity receptor SRB1. We subsequently describe the synthesis of the biomimetic HDL NP and its oligonucleotide conjugates, and establish their biocompatibility. Further on, experimental data demonstrate the efficacy of silencing

  11. Compression and radiation of high-power short rf pulses. II. A novel antenna array design with combined compressor/radiator elements

    KAUST Repository

    Sirenko, Kostyantyn; Pazynin, Vadim L.; Sirenko, Yu K.; Bagci, Hakan

    2011-01-01

    The paper discusses the radiation of compressed high power short RF pulses using two different types of antennas: (i) A simple monopole antenna and (ii) a novel array design, where each of the elements is constructed by combining a compressor and a

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

    Science.gov (United States)

    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.

  13. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

    DEFF Research Database (Denmark)

    Li, Yun R.; van Setten, Jessica; Verma, Shefali S.

    2015-01-01

    genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples...

  14. Design and implementation of a reconfigurable mixed-signal SoC based on field programmable analog arrays

    Science.gov (United States)

    Liu, Lintao; Gao, Yuhan; Deng, Jun

    2017-11-01

    This work presents a reconfigurable mixed-signal system-on-chip (SoC), which integrates switched-capacitor-based field programmable analog arrays (FPAA), analog-to-digital converter (ADC), digital-to-analog converter, digital down converter , digital up converter, 32-bit reduced instruction-set computer central processing unit (CPU) and other digital IPs on a single chip with 0.18 μm CMOS technology. The FPAA intellectual property could be reconfigured as different function circuits, such as gain amplifier, divider, sine generator, and so on. This single-chip integrated mixed-signal system is a complete modern signal processing system, occupying a die area of 7 × 8 mm 2 and consuming 719 mW with a clock frequency of 150 MHz for CPU and 200 MHz for ADC/DAC. This SoC chip can help customers to shorten design cycles, save board area, reduce the system power consumption and depress the system integration risk, which would afford a big prospect of application for wireless communication. Project supported by the National High Technology and Development Program of China (No. 2012AA012303).

  15. Optimization of supercritical fluid extraction and HPLC identification of wedelolactone from Wedelia calendulacea by orthogonal array design.

    Science.gov (United States)

    Patil, Ajit A; Sachin, Bhusari S; Wakte, Pravin S; Shinde, Devanand B

    2014-11-01

    The purpose of this work is to provide a complete study of the influence of operational parameters of the supercritical carbon dioxide assisted extraction (SC CO2E) on yield of wedelolactone from Wedelia calendulacea Less., and to find an optimal combination of factors that maximize the wedelolactone yield. In order to determine the optimal combination of the four factors viz. operating pressure, temperature, modifier concentration and extraction time, a Taguchi experimental design approach was used: four variables (three levels) in L9 orthogonal array. Wedelolactone content was determined using validated HPLC methodology. Optimum extraction conditions were found to be as follows: extraction pressure, 25 MPa; temperature, 40 °C; modifier concentration, 10% and extraction time, 90 min. Optimum extraction conditions demonstrated wedelolactone yield of 8.01 ± 0.34 mg/100 g W. calendulacea Less. Pressure, temperature and time showed significant (p yield. The supercritical carbon dioxide extraction showed higher selectivity than the conventional Soxhlet assisted extraction method.

  16. Optimization of supercritical fluid extraction and HPLC identification of wedelolactone from Wedelia calendulacea by orthogonal array design

    Directory of Open Access Journals (Sweden)

    Ajit A. Patil

    2014-11-01

    Full Text Available The purpose of this work is to provide a complete study of the influence of operational parameters of the supercritical carbon dioxide assisted extraction (SC CO2E on yield of wedelolactone from Wedelia calendulacea Less., and to find an optimal combination of factors that maximize the wedelolactone yield. In order to determine the optimal combination of the four factors viz. operating pressure, temperature, modifier concentration and extraction time, a Taguchi experimental design approach was used: four variables (three levels in L9 orthogonal array. Wedelolactone content was determined using validated HPLC methodology. Optimum extraction conditions were found to be as follows: extraction pressure, 25 MPa; temperature, 40 °C; modifier concentration, 10% and extraction time, 90 min. Optimum extraction conditions demonstrated wedelolactone yield of 8.01 ± 0.34 mg/100 g W. calendulacea Less. Pressure, temperature and time showed significant (p < 0.05 effect on the wedelolactone yield. The supercritical carbon dioxide extraction showed higher selectivity than the conventional Soxhlet assisted extraction method.

  17. Conceptual design and optimization of a plastic scintillator array for 2D tomography using a compact D-D fast neutron generator.

    Science.gov (United States)

    Adams, Robert; Zboray, Robert; Cortesi, Marco; Prasser, Horst-Michael

    2014-04-01

    A conceptual design optimization of a fast neutron tomography system was performed. The system is based on a compact deuterium-deuterium fast neutron generator and an arc-shaped array of individual neutron detectors. The array functions as a position sensitive one-dimensional detector allowing tomographic reconstruction of a two-dimensional cross section of an object up to 10 cm across. Each individual detector is to be optically isolated and consists of a plastic scintillator and a Silicon Photomultiplier for measuring light produced by recoil protons. A deterministic geometry-based model and a series of Monte Carlo simulations were used to optimize the design geometry parameters affecting the reconstructed image resolution. From this, it is expected that with an array of 100 detectors a reconstructed image resolution of ~1.5mm can be obtained. Other simulations were performed in order to optimize the scintillator depth (length along the neutron path) such that the best ratio of direct to scattered neutron counts is achieved. This resulted in a depth of 6-8 cm and an expected detection efficiency of 33-37%. Based on current operational capabilities of a prototype neutron generator being developed at the Paul Scherrer Institute, planned implementation of this detector array design should allow reconstructed tomograms to be obtained with exposure times on the order of a few hours. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Design of a rectenna system for GSM-900 band using novel broadside 2 × 1 array antenna

    Directory of Open Access Journals (Sweden)

    Manish Singh

    2017-05-01

    Full Text Available In this study, a rectenna operating at the GSM-900 frequency band has been fabricated and tested. This rectenna composed of a 2 × 1 T-shaped monopole array antenna and an energy processing circuit. In order to reduce the gap between adjacent antenna elements in the array structure, the proposed array antenna uses a ground stub. Compared with other array antennas, the proposed array antenna with the ground stub reduces the size up to 50% without affecting the gain and bandwidth. An antenna prototype is fabricated and experimentally tested. The measured antenna's gain and bandwidth are 3.2 and 152 MHz, respectively, hence showing its suitability for radio-frequency (RF energy harvesting application. For this to be feasible, the developed array antenna is matched with the rectifier at GSM-900 using a single stub matching network. The measured result demonstrates that the proposed rectifier circuit offers the conversion efficiency of 21.2 and 63.6% for an input power of −20 and 0 dBm, respectively. Finally, the rectifier performance is attested experimentally with the developed array antenna. The rectenna's measured RF-to-dc conversion efficiency was found to be 60% at the far-field distance from the transmitting antenna.

  19. Detection of genomic deletions in rice using oligonucleotide microarrays

    Directory of Open Access Journals (Sweden)

    Bordeos Alicia

    2009-03-01

    Full Text Available Abstract Background The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL. However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. Results We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/. Conclusion We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a

  20. High performance architecture design for large scale fibre-optic sensor arrays using distributed EDFAs and hybrid TDM/DWDM

    Science.gov (United States)

    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.

  1. A Two-dimensional Sixteen Channel Transmit/Receive Coil Array for Cardiac MRI at 7.0 Tesla: Design, Evaluation and Application

    Science.gov (United States)

    Thalhammer, Christof; Renz, Wolfgang; Winter, Lukas; Hezel, Fabian; Rieger, Jan; Pfeiffer, Harald; Graessl, Andreas; Seifert, Frank; Hoffmann, Werner; von Knobelsdorff-Brenkenhoff, Florian; Tkachenko, Valeriy; Schulz-Menger, Jeanette; Kellman, Peter; Niendorf, Thoralf

    2012-01-01

    Purpose To design, evaluate and apply a two-dimensional 16 channel transmit/receive coil array tailored for cardiac MRI at 7.0 Tesla. Material and Methods The cardiac coil array consists of 2 sections each using 8 elements arranged in a 2 × 4 array. RF safety was validated by SAR simulations. Cardiac imaging was performed using 2D CINE FLASH imaging, T2* mapping and fat-water separation imaging. The characteristics of the coil array were analyzed including parallel imaging performance, left ventricular chamber quantification and overall image quality. Results RF characteristics were found to be appropriate for all subjects included in the study. The SAR values derived from the simulations fall well in the limits of legal guidelines. The baseline SNR advantage at 7.0 T was put to use to acquire 2D CINE images of the heart with a very high spatial resolution of (1 × 1 × 4) mm3. The proposed coil array supports 1D acceleration factors of up to R=4 without impairing image quality significantly. Conclusions The 16 channel TX/RX coil has the capability to acquire high contrast and high spatial resolution images of the heart at 7.0 Tesla. PMID:22706727

  2. An investigation of signal performance enhancements achieved through innovative pixel design across several generations of indirect detection, active matrix, flat-panel arrays

    International Nuclear Information System (INIS)

    Antonuk, Larry E.; Zhao Qihua; El-Mohri, Youcef; Du Hong; Wang Yi; Street, Robert A.; Ho, Jackson; Weisfield, Richard; Yao, William

    2009-01-01

    Active matrix flat-panel imager (AMFPI) technology is being employed for an increasing variety of imaging applications. An important element in the adoption of this technology has been significant ongoing improvements in optical signal collection achieved through innovations in indirect detection array pixel design. Such improvements have a particularly beneficial effect on performance in applications involving low exposures and/or high spatial frequencies, where detective quantum efficiency is strongly reduced due to the relatively high level of additive electronic noise compared to signal levels of AMFPI devices. In this article, an examination of various signal properties, as determined through measurements and calculations related to novel array designs, is reported in the context of the evolution of AMFPI pixel design. For these studies, dark, optical, and radiation signal measurements were performed on prototype imagers incorporating a variety of increasingly sophisticated array designs, with pixel pitches ranging from 75 to 127 μm. For each design, detailed measurements of fundamental pixel-level properties conducted under radiographic and fluoroscopic operating conditions are reported and the results are compared. A series of 127 μm pitch arrays employing discrete photodiodes culminated in a novel design providing an optical fill factor of ∼80% (thereby assuring improved x-ray sensitivity), and demonstrating low dark current, very low charge trapping and charge release, and a large range of linear signal response. In two of the designs having 75 and 90 μm pitches, a novel continuous photodiode structure was found to provide fill factors that approach the theoretical maximum of 100%. Both sets of novel designs achieved large fill factors by employing architectures in which some, or all of the photodiode structure was elevated above the plane of the pixel addressing transistor. Generally, enhancement of the fill factor in either discrete or continuous

  3. Oligonucleotide Therapy for Obstructive and Restrictive Respiratory Diseases

    Directory of Open Access Journals (Sweden)

    Wupeng Liao

    2017-01-01

    Full Text Available Inhaled oligonucleotide is an emerging therapeutic modality for various common respiratory diseases, including obstructive airway diseases like asthma and chronic obstructive pulmonary disease (COPD and restrictive airway diseases like idiopathic pulmonary fibrosis (IPF. The advantage of direct accessibility for oligonucleotide molecules to the lung target sites, bypassing systemic administration, makes this therapeutic approach promising with minimized potential systemic side effects. Asthma, COPD, and IPF are common chronic respiratory diseases, characterized by persistent airway inflammation and dysregulated tissue repair and remodeling, although each individual disease has its unique etiology. Corticosteroids have been widely prescribed for the treatment of asthma, COPD, and IPF. However, the effectiveness of corticosteroids as an anti-inflammatory drug is limited by steroid resistance in severe asthma, the majority of COPD cases, and pulmonary fibrosis. There is an urgent medical need to develop target-specific drugs for the treatment of these respiratory conditions. Oligonucleotide therapies, including antisense oligonucleotide (ASO, small interfering RNA (siRNA, and microRNA (miRNA are now being evaluated both pre-clinically and clinically as potential therapeutics. The mechanisms of action of ASO and siRNA are highly target mRNA specific, ultimately leading to target protein knockdown. miRNA has both biomarker and therapeutic values, and its knockdown by a miRNA antagonist (antagomir has a broader but potentially more non-specific biological outcome. This review will compile the current findings of oligonucleotide therapeutic targets, verified in various respiratory disease models and in clinical trials, and evaluate different chemical modification approaches to improve the stability and potency of oligonucleotides for the treatment of respiratory diseases.

  4. Versatile functionalization of nanoelectrodes by oligonucleotides via pyrrole electrochemistry.

    Science.gov (United States)

    Descamps, Emeline; Nguyen, Khoa; Bouchain-Gautier, Christelle; Filoramo, Arianna; Goux-Capes, Laurence; Goffman, Marcello; Bourgoin, Jean-Philippe; Mailley, Pascal; Livache, Thierry

    2010-11-15

    Surface modification at the nanometer scale is a challenge for the future of molecular electronics. In particular, the precise anchoring and electrical addressing of biological scaffolds such as complex DNA nanonetworks is of importance for generating bio-directed assemblies of nano-objects for nanocircuit purposes. Herein, we consider the individual modification of nanoelectrodes with different oligonucleotide sequences by an electrochemically driven co-polymerization process of pyrrole and modified oligonucleotide sequences bearing pyrrole monomers. We demonstrate that this one-step technique presents the advantages of simplicity, localization of surface modification, mechanical, biological and chemical stability of the coatings, and high lateral resolution.

  5. Multi-frequency response from a designed array of micromechanical cantilevers fabricated using a focused ion beam

    International Nuclear Information System (INIS)

    Ghatnekar-Nilsson, S; Graham, J; Hull, R; Montelius, L

    2006-01-01

    We demonstrate arrays of cantilevers with different lengths, fabricated by focused ion beam milling. The arrays of oscillators generate a spectrum of different resonant frequencies, where each frequency correlates to the corresponding individual cantilever. The frequency response from all the cantilevers is collected from a single measurement under the same environment and conditions for the entire array. The mass response of the system generated the same Δf/f 0 for the cantilevers, within 0.1% accuracy. We denote the method MFSAC: multi-frequency signal analysis from an array of cantilevers. The simultaneous detection of several frequencies in one spectrum has great benefits in mass sensor applications, offering the possibility for true label-free detection

  6. Design of a QA method to characterize submillimeter-sized PBS beam properties using a 2D ionization chamber array

    Science.gov (United States)

    Lin, Yuting; Bentefour, Hassan; Flanz, Jacob; Kooy, Hanne; Clasie, Benjamin

    2018-05-01

    Pencil beam scanning (PBS) periodic quality assurance (QA) programs ensure the beam delivered to patients is within technical specifications. Two critical specifications for PBS delivery are the beam width and position. The aim of this study is to investigate whether a 2D ionization chamber array, such as the MatriXX detector (IBA Dosimetry, Schwarzenbruck, Germany), can be used to characterize submillimeter-sized PBS beam properties. The motivation is to use standard equipment, which may have pixel spacing coarser than the pencil beam size, and simplify QA workflow. The MatriXX pixels are cylindrical in shape with 4.5 mm diameter and are spaced 7.62 mm from center to center. Two major effects limit the ability of using the MatriXX to measure the spot position and width accurately. The first effect is that too few pixels sample the Gaussian shaped pencil beam profile and the second effect is volume averaging of the Gaussian profile over the pixel sensitive volumes. We designed a method that overcomes both limitations and hence enables the use of the MatriXX to characterize sub-millimeter-sized PBS beam properties. This method uses a cross-like irradiation pattern that is designed to increase the number of sampling data points and a modified Gaussian fitting technique to correct for volume averaging effects. Detector signals were calculated in this study and random noise and setup errors were added to simulate measured data. With the techniques developed in this work, the MatriXX detector can be used to characterize the position and width of sub-millimeter, σ  =  0.7 mm, sized pencil beams with uncertainty better than 3% relative to σ. With the irradiation only covering 60% of the MatriXX, the position and width of σ  =  0.9 mm sized pencil beams can be determined with uncertainty better than 3% relative to σ. If one were to not use a cross-like irradiation pattern, then the position and width of σ  =  3.6 mm sized pencil beams

  7. Factor XI Antisense Oligonucleotide for Prevention of Venous Thrombosis

    NARCIS (Netherlands)

    Büller, Harry R.; Bethune, Claudette; Bhanot, Sanjay; Gailani, David; Monia, Brett P.; Raskob, Gary E.; Segers, Annelise; Verhamme, Peter; Weitz, Jeffrey I.; Weitz, Jeffrey; Prins, Martin; Beenen, Ludo; Otten, Hans-Martin; Roos, Yvo; Slagboom, Ton; Vandenbriele, Christophe; Vanassche, Thomas; Dani, Vidhi; Schulz, Dan; Shapiro, Cara; Kwoh, Katherine; Jung, Bill; Gawinek-Samelczak, Agata; Kaemmer, Christina; Angelov, S.; Stavrev, V.; Kinov, P.; Dessouki, E.; Abuzgaya, F.; Baurovskis, A.; Peredistijs, A.; Petronis, S.; Danilyak, V.; Driagin, V.; Kuropatkin, G.; Parfeev, S.; Safronov, A.; Ankin, M.; Korzh, M.; Olinichenko, G.; Polivoda, A.; Shevchenko, V.; Sulyma, V.

    2015-01-01

    Background Experimental data indicate that reducing factor XI levels attenuates thrombosis without causing bleeding, but the role of factor XI in the prevention of postoperative venous thrombosis in humans is unknown. FXI-ASO (ISIS 416858) is a second-generation antisense oligonucleotide that

  8. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence

    DEFF Research Database (Denmark)

    Taskova, Maria; Uhd, Jesper; Miotke, Laura

    2017-01-01

    opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA...

  9. Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles

    DEFF Research Database (Denmark)

    Cogoi, S; Jakobsen, U; Pedersen, E B

    2016-01-01

    KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription fa...

  10. Effects of Atelocollagen Formulation Containing Oligonucleotide on Endothelial Permeability

    Directory of Open Access Journals (Sweden)

    Koji Hanai

    2012-01-01

    Full Text Available Atelocollagen is a major animal protein that is used as a highly biocompatible biomaterial. To date, atelocollagen has been used as an effective drug delivery technology to sustain the release of antitumor proteins and to enhance the antitumor activity of oligonucleotides in in vivo models. However, the biological effects of this technology are not fully understood. In the present study, we investigated the effects of atelocollagen on endothelial paracellular barrier function. An atelocollagen formulation containing oligonucleotides specifically increased the permeability of two types of endothelial cells, and the change was dependent on the molecular size, structure of the oligonucleotides used and the concentrations of the oligonucleotide and atelocollagen in the formulation. An immunohistochemical examination revealed that the formulation had effects on the cellular skeleton and intercellular structure although it did not affect the expression of adherens junction or tight junction proteins. These changes were induced through p38 MAP kinase signaling. It is important to elucidate the biological functions of atelocollagen in order to be able to exploit its drug delivery properties.

  11. Design and performance of large-pixel-size high-fill-fraction TES arrays for future X-ray astrophysics missions

    International Nuclear Information System (INIS)

    Figueroa-Feliciano, E.; Bandler, S.R.; Chervenak, J.; Finkbeiner, F.; Iyomoto, N.; Kelley, R.L.; Kilbourne, C.A.; Porter, F.S.; Saab, T.; Sadleir, J.; White, J.

    2006-01-01

    We have designed, modeled, fabricated and tested a 600μm high-fill-fraction microcalorimeter array that will be a good match to the requirements of future X-ray missions. Our devices use transition-edge sensors coupled to overhanging bismuth/copper absorbers to produce arrays with 97% or higher fill fraction. An extensive modeling effort was undertaken in order to accommodate large pixel sizes (500-1000μm) and maintain the best energy resolution possible. The finite thermalization time of the large absorber and the associated position dependence of the pulse shape on absorption position constrain the time constants of the system given a desired energy-resolution performance. We show the results of our analysis and our new pixel design, consisting of a novel TES-on-the-side architecture which creates a controllable TES-absorber conductance

  12. Reliability of mechanical and phased-array designs for serial intravascular ultrasound examinations--animal and clinical studies in stented and non-stented coronary arteries.

    Science.gov (United States)

    Tardif, J C; Bertrand, O F; Mongrain, R; Lespérance, J; Grégoire, J; Paiement, P; Bonan, R

    2000-10-01

    Both mechanical and multi-element intravascular ultrasound designs have potential advantages and limitations that may impact on their value for clinical and research purposes. Determination of the reproducibility of measurements is critical before a given system can be used in studies such as regression of atherosclerosis trials. We performed serial intravascular ultrasound imaging with catheters using mechanical and phased-array designs in stented and non-stented coronary arteries in dogs and in patients. Both systems correlated well for areas (r > or = 0.90, p or = 0.84. p mechanical designs for measurements of area (mean difference in dogs and in patients: -0.24 and 0.96 mm2, p mechanical system (r > or = 0.96 for all measurements). The differences in absolute and relative variability between the mechanical and phased-array designs, both for reanalysis of same frames and serial pullbacks, were very small. Although multi-element and mechanical intravascular ultrasound designs are not strictly interchangeable, their similar reproducibility and the small differences in measurements demonstrate that both designs are acceptable alternatives for trials of regression of atherosclerosis. Determination of the variability for serial pullbacks of both designs was also important to assess the statistical power of such trials.

  13. DNA-Catalytically Active Gold Nanoparticle Conjugates-Based Colorimetric Multidimensional Sensor Array for Protein Discrimination.

    Science.gov (United States)

    Wei, Xiangcong; Chen, Zhengbo; Tan, Lulu; Lou, Tianhong; Zhao, Yan

    2017-01-03

    A series of single-strand oligonucleotides functionalized catalytically active gold nanoparticle (AuNPs) as nonspecific receptors have been designed to build a protein sensing array. We take advantage of the correlation between the catalytic activity and the exposed surface area of AuNPs, i.e., DNA-proteins interactions mask the surface area of AuNPs, leading to poor catalytic performance of AuNPs. As the number of DNA-bound proteins increases, the surfaces of AuNPs become more masked; thus, the time of 4- nitrophenol/NaBH 4 reaction for color change (yellow → colorless) of the solution increases. Taking advantage of three nonspecific SH-labeled DNA sequences (A15, C15, and T15) as array sensing elements and the color-change time (CCT) of the solution as signal readout, colorimetric response patterns can be obtained on the array and identified via linear discriminant analysis (LDA). Eleven proteins have been completely distinguished with 100% accuracy with the naked eye at the 30 nM level. Remarkably, two similar proteins (bovine serum albumin and human serum albumin), two different proteins (bovine serum albumin and concanavalin) at the same concentration, and the mixtures of the two proteins with different molar ratios have been discriminated with 100%. The practicability of this sensor array is further validated by high accuracy (100%) identification of 11 proteins in human serum samples.

  14. Design of Vivaldi antenna array with end-fire beam steering function for 5G mobile terminals

    DEFF Research Database (Denmark)

    Ojaroudiparchin, Naser; Shen, Ming; Pedersen, Gert F.

    2015-01-01

    to form a linear phased array in the edge region (top-side) on a mobile phone PCB. The simulated results show that the antenna has the reflection coefficient (S11) less than -10 dB in the frequency range of 27.4 to 28.6 GHz. The proposed phased array antenna has good gain, efficiency, and 3D beam steering...... characteristics in the entire operation band, which makes it suitable for millimeter-wave 5G communications. In addition, the performance of the antenna in the vicinity of user’s hand has been investigated in this study....

  15. Peptide array-based interaction assay of solid-bound peptides and anchorage-dependant cells and its effectiveness in cell-adhesive peptide design.

    Science.gov (United States)

    Kato, Ryuji; Kaga, Chiaki; Kunimatsu, Mitoshi; Kobayashi, Takeshi; Honda, Hiroyuki

    2006-06-01

    Peptide array, the designable peptide library covalently synthesized on cellulose support, was applied to assay peptide-cell interaction, between solid-bound peptides and anchorage-dependant cells, to study objective peptide design. As a model case, cell-adhesive peptides that could enhance cell growth as tissue engineering scaffold material, was studied. On the peptide array, the relative cell-adhesion ratio of NIH/3T3 cells was 2.5-fold higher on the RGDS (Arg-Gly-Asp-Ser) peptide spot as compared to the spot with no peptide, thus indicating integrin-mediated peptide-cell interaction. Such strong cell adhesion mediated by the RGDS peptide was easily disrupted by single residue substitution on the peptide array, thus indicating that the sequence recognition accuracy of cells was strictly conserved in our optimized scheme. The observed cellular morphological extension with active actin stress-fiber on the RGD motif-containing peptide supported our strategy that peptide array-based interaction assay of solid-bound peptide and anchorage-dependant cells (PIASPAC) could provide quantitative data on biological peptide-cell interaction. The analysis of 180 peptides obtained from fibronectin type III domain (no. 1447-1629) yielded 18 novel cell-adhesive peptides without the RGD motif. Taken together with the novel candidates, representative rules of ineffective amino acid usage were obtained from non-effective candidate sequences for the effective designing of cell-adhesive peptides. On comparing the amino acid usage of the top 20 and last 20 peptides from the 180 peptides, the following four brief design rules were indicated: (i) Arg or Lys of positively charged amino acids (except His) could enhance cell adhesion, (ii) small hydrophilic amino acids are favored in cell-adhesion peptides, (iii) negatively charged amino acids and small amino acids (except Gly) could reduce cell adhesion, and (iv) Cys and Met could be excluded from the sequence combination since they have

  16. Antisense Oligonucleotides Promote Exon Inclusion and Correct the Common c.-32-13T>G GAA Splicing Variant in Pompe Disease

    Directory of Open Access Journals (Sweden)

    Erik van der Wal

    2017-06-01

    Full Text Available The most common variant causing Pompe disease is c.-32-13T>G (IVS1 in the acid α-glucosidase (GAA gene, which weakens the splice acceptor of GAA exon 2 and induces partial and complete exon 2 skipping. It also allows a low level of leaky wild-type splicing, leading to a childhood/adult phenotype. We hypothesized that cis-acting splicing motifs may exist that could be blocked using antisense oligonucleotides (AONs to promote exon inclusion. To test this, a screen was performed in patient-derived primary fibroblasts using a tiling array of U7 small nuclear RNA (snRNA-based AONs. This resulted in the identification of a splicing regulatory element in GAA intron 1. We designed phosphorodiamidate morpholino oligomer-based AONs to this element, and these promoted exon 2 inclusion and enhanced GAA enzyme activity to levels above the disease threshold. These results indicate that the common IVS1 GAA splicing variant in Pompe disease is subject to negative regulation, and inhibition of a splicing regulatory element using AONs is able to restore canonical GAA splicing and endogenous GAA enzyme activity.

  17. Novel ring resonator-based integrated photonic beamformer for broadband phased array receive antennas - part 1: design and performance analysis

    NARCIS (Netherlands)

    Meijerink, Arjan; Roeloffzen, C.G.H.; Meijerink, Roland; Zhuang, L.; Marpaung, D.A.I.; Bentum, Marinus Jan; Burla, M.; Verpoorte, Jaco; Jorna, Pieter; Huizinga, Adriaan; van Etten, Wim

    2010-01-01

    A novel optical beamformer concept is introduced that can be used for seamless control of the reception angle in broadband wireless receivers employing a large phased array antenna (PAA). The core of this beamformer is an optical beamforming network (OBFN), using ring resonator-based broadband

  18. Rational Design of QCM-D Virtual Sensor Arrays Based on Film Thickness, Viscoelasticity, and Harmonics for Vapor Discrimination.

    Science.gov (United States)

    Speller, Nicholas C; Siraj, Noureen; Regmi, Bishnu P; Marzoughi, Hassan; Neal, Courtney; Warner, Isiah M

    2015-01-01

    Herein, we demonstrate an alternative strategy for creating QCM-based sensor arrays by use of a single sensor to provide multiple responses per analyte. The sensor, which simulates a virtual sensor array (VSA), was developed by depositing a thin film of ionic liquid, either 1-octyl-3-methylimidazolium bromide ([OMIm][Br]) or 1-octyl-3-methylimidazolium thiocyanate ([OMIm][SCN]), onto the surface of a QCM-D transducer. The sensor was exposed to 18 different organic vapors (alcohols, hydrocarbons, chlorohydrocarbons, nitriles) belonging to the same or different homologous series. The resulting frequency shifts (Δf) were measured at multiple harmonics and evaluated using principal component analysis (PCA) and discriminant analysis (DA) which revealed that analytes can be classified with extremely high accuracy. In almost all cases, the accuracy for identification of a member of the same class, that is, intraclass discrimination, was 100% as determined by use of quadratic discriminant analysis (QDA). Impressively, some VSAs allowed classification of all 18 analytes tested with nearly 100% accuracy. Such results underscore the importance of utilizing lesser exploited properties that influence signal transduction. Overall, these results demonstrate excellent potential of the virtual sensor array strategy for detection and discrimination of vapor phase analytes utilizing the QCM. To the best of our knowledge, this is the first report on QCM VSAs, as well as an experimental sensor array, that is based primarily on viscoelasticity, film thickness, and harmonics.

  19. Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs

    Directory of Open Access Journals (Sweden)

    Lanfranchi Gerolamo

    2002-10-01

    Full Text Available Abstract Background We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 EST clusters from a non-normalized subtracted muscle EST sequencing project (28,074 EST sequences. This set included 369 novel EST clusters showing no match to previously characterized proteins in any database. Each probe set was designed to contain 20–32 25 mer oligonucleotides (10–16 paired perfect match and mismatch probe pairs per gene, with each probe evaluated for hybridization kinetics (Tm and similarity to other sequences. The 120,000 oligonucleotides were synthesized by photolithography and light-activated chemistry on each microarray. Results Hybridization of human muscle cRNAs to this MuscleChip (33 samples showed a correlation of 0.6 between the number of ESTs sequenced in each cluster and hybridization intensity. Out of 369 novel EST clusters not showing any similarity to previously characterized proteins, we focused on 250 EST clusters that were represented by robust probe sets on the MuscleChip fulfilling all stringent rules. 102 (41% were found to be consistently "present" by analysis of hybridization to human muscle RNA, of which 40 ESTs (39% could be genome anchored to potential transcription units in the human genome sequence. 19 ESTs of the 40 ESTs were furthermore computer-predicted as exons by one or more than three gene identification algorithms. Conclusion Our analysis found 40 transcriptionally validated, genome-anchored novel EST clusters to be expressed in human muscle. As most of these ESTs were low copy clusters (duplex and triplex in the original 28,000 EST project, the identification of these as significantly expressed is a robust validation of the transcript units that permits subsequent focus on the novel proteins encoded by these genes.

  20. Ultrasensitive electrochemical biosensor based on the oligonucleotide self-assembled monolayer-mediated immunosensing interface

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Dengyou; Luo, Qimei [Science College of Hunan Agricultural University, Changsha 410128 (China); Deng, Fawen [The Fourth Hospital of Chansha, Changsha 410006 (China); Li, Zhen [Science College of Hunan Agricultural University, Changsha 410128 (China); Li, Benxiang, E-mail: 172170960@qq.com [Science College of Hunan Agricultural University, Changsha 410128 (China); Shen, Zhifa, E-mail: shenzhifa@wmu.edu.cn [Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035 (China)

    2017-06-08

    Highly sensitive and selective quantitation of a variety of proteins over a wide concentration range is highly desirable for increased accuracy of biomarker detection or for multidisease diagnostics. In the present contribution, using human immunoglobulin G (HIgG) as the model target protein, an electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer-mediated (OSAM) sensing interface. For this immunosensor, the “signal-on” signaling mechanism and enzymatic signal amplification effect were integrated into one sensing architecture. Moreover, the thiolated flexible single-stranded DNAs immobilized onto gold electrode surface not only performs the wobbling motion to facilitate the electron transfer between the electrode surface and biosensing layer but also fundamentally prohibiting the direct interaction of proteins with gold substrate. Thus, the electrochemical signal could be efficiently enhanced and the unspecific adsorption or cross-reaction might be eliminated. As a result, utilizing the newly-proposed immunosensor, the HIgG can be detected down to 0.5 ng/mL, and the high detection specificity is offered. The successful design of OSAM and the highly desirable detection capability of new immunosensor are expected to provide a perspective for fabricating new robust immunosensing platform and for promising potential of oligonucleotide probe in biological research and biomedical diagnosis. - Highlights: • An electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer (OASM). • OASM severs as a flexible monolayer to promote electron transfer and prohibits the direct interaction of proteins with gold substrate. • The electrochemical signal is efficiently enhanced and the unspecific adsorption or cross-reaction is eliminated. • Target protein can be detected down to 0.5 ng/mL, and the high detection specificity can be obtained.

  1. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation

    Science.gov (United States)

    Panpradist, Nuttada; Beck, Ingrid A.; Chung, Michael H.; Kiarie, James N.; Frenkel, Lisa M.; Lutz, Barry R.

    2016-01-01

    Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories. PMID:26751207

  2. Antisense Oligonucleotides Internally Labeled with Peptides Show Improved Target Recognition and Stability to Enzymatic Degradation

    DEFF Research Database (Denmark)

    Taskova, Maria; Madsen, Charlotte S.; Jensen, Knud J.

    2017-01-01

    Specific target binding and stability in diverse biological media is of crucial importance for applications of synthetic oligonucleotides as diagnostic and therapeutic tools. So far, these issues have been addressed by chemical modification of oligonucleotides and by conjugation with a peptide, m...... and makes internally labeled POCs an exciting object of study, i.e., showing high target specificity and simultaneous stability in biological media.......Specific target binding and stability in diverse biological media is of crucial importance for applications of synthetic oligonucleotides as diagnostic and therapeutic tools. So far, these issues have been addressed by chemical modification of oligonucleotides and by conjugation with a peptide......, most often at the terminal position of the oligonucleotide. Herein, we for the first time systematically investigate the influence of internally attached short peptides on the properties of antisense oligonucleotides. We report the synthesis and internal double labeling of 21-mer oligonucleotides...

  3. Static magnetic field reduced exogenous oligonucleotide uptake by spermatozoa using magnetic nanoparticle gene delivery system

    Science.gov (United States)

    Katebi, Samira; Esmaeili, Abolghasem; Ghaedi, Kamran

    2016-03-01

    Spermatozoa could introduce exogenous oligonucleotides of interest to the oocyte. The most important reason of low efficiency of sperm mediated gene transfer (SMGT) is low uptake of exogenous DNA by spermatozoa. The aim of this study was to evaluate the effects of static magnetic field on exogenous oligonucleotide uptake of spermatozoa using magnetofection method. Magnetic nanoparticles (MNPs) associated with the labeled oligonucleotides were used to increase the efficiency of exogenous oligonucleotide uptake by rooster spermatozoa. We used high-field/high-gradient magnet (NdFeB) to enhance and accelerate exogenous DNA sedimentation at the spermatozoa surface. Flow cytometry analysis was performed to measure viability and percentage of exogenous oligonucleotide uptake by sperm. Flow cytometry analysis showed a significant increase in exogenous oligonucleotide uptake by rooster spermatozoa (Prooster spermatozoa; however unlike others studies, static magnetic field, was not only ineffective to enhance exogenous oligonucleotide uptake by rooster spermatozoa but also led to reduction in efficiency of magnetic nanoparticles in gene transfer.

  4. Timed arrays wideband and time varying antenna arrays

    CERN Document Server

    Haupt, Randy L

    2015-01-01

    Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

  5. Design of patient-specific focused ultrasound arrays for non-invasive brain therapy with increased trans-skull transmission and steering range

    Science.gov (United States)

    Hughes, Alec; Hynynen, Kullervo

    2017-09-01

    The use of a phased array of ultrasound transducer elements to sonicate through the skull has opened the way for new treatments and the delivery of therapeutics beyond the blood-brain barrier. The limited steering range of current clinical devices, particularly at higher frequencies, limits the regions of the brain that are considered treatable by ultrasound. A new array design is introduced that allows for high levels of beam steering and increased transmission throughout the brain. These improvements are achieved using concave transducers normal to the outer-skull surface in a patient-specific configuration to target within the skull, so that the far-field of each beam is within the brain. It is shown that by using pulsed ultrasound waves timed to arrive in-phase at the desired target, sufficient levels of acoustic energy are delivered for blood-brain barrier opening throughout the brain.

  6. Correlation test to assess low-level processing of high-density oligonucleotide microarray data

    Directory of Open Access Journals (Sweden)

    Bergh Jonas

    2005-03-01

    Full Text Available Abstract Background There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data. Results We analyzed coregulation between genes in order to detect insufficient normalization between arrays, where coregulation is measured in terms of statistical correlation. In a large collection of genes, a random pair of genes should have on average zero correlation, hence allowing a correlation test. For all data sets that we evaluated, and the three most commonly used low-level processing procedures including MAS5, RMA and MBEI, the housekeeping-gene normalization failed the test. For a real clinical data set, RMA and MBEI showed significant correlation for absent genes. We also found that a second round of normalization on the probe set level improved normalization significantly throughout. Conclusion Previous evaluation of low-level processing in the literature has been limited to artificial spike-in and mixture data sets. In the absence of a known gold-standard, the correlation criterion allows us to assess the appropriateness of low-level processing of a specific data set and the success of normalization for subsets of genes.

  7. A new oligonucleotide microarray for detection of pathogenic and non-pathogenic Legionella spp.

    Directory of Open Access Journals (Sweden)

    Boyang Cao

    Full Text Available Legionella pneumophila has been recognized as the major cause of legionellosis since the discovery of the deadly disease. Legionella spp. other than L. pneumophila were later found to be responsible to many non-pneumophila infections. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this report, we have sequenced the 16S-23S rRNA gene internal transcribed spacer (ITS of 10 Legionella species and subspecies, including L. anisa, L. bozemanii, L. dumoffii, L. fairfieldensis, L. gormanii, L. jordanis, L. maceachernii, L. micdadei, L. pneumophila subspp. fraseri and L. pneumophila subspp. pasculleii, and developed a rapid oligonucleotide microarray detection technique accordingly to identify 12 most common Legionella spp., which consist of 11 pathogenic species of L. anisa, L. bozemanii, L. dumoffii, L. gormanii, L. jordanis, L. longbeachae, L. maceachernii, L. micdadei, and L. pneumophila (including subspp. pneumophila, subspp. fraseri, and subspp. pasculleii and one non-pathogenic species, L. fairfieldensis. Twenty-nine probes that reproducibly detected multiple Legionella species with high specificity were included in the array. A total of 52 strains, including 30 target pathogens and 22 non-target bacteria, were used to verify the oligonucleotide microarray assay. The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven samples of air conditioner-condensed water with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. The phylogenetic study based on the ITS has also revealed that the non-pathogenic L. fairfieldensis is the closest to L. pneumophila than the nine other pathogenic Legionella spp.

  8. A New Oligonucleotide Microarray for Detection of Pathogenic and Non-Pathogenic Legionella spp.

    Science.gov (United States)

    Cao, Boyang; Liu, Xiangqian; Yu, Xiang; Chen, Min; Feng, Lu; Wang, Lei

    2014-01-01

    Legionella pneumophila has been recognized as the major cause of legionellosis since the discovery of the deadly disease. Legionella spp. other than L. pneumophila were later found to be responsible to many non-pneumophila infections. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this report, we have sequenced the 16S-23S rRNA gene internal transcribed spacer (ITS) of 10 Legionella species and subspecies, including L. anisa, L. bozemanii, L. dumoffii, L. fairfieldensis, L. gormanii, L. jordanis, L. maceachernii, L. micdadei, L. pneumophila subspp. fraseri and L. pneumophila subspp. pasculleii, and developed a rapid oligonucleotide microarray detection technique accordingly to identify 12 most common Legionella spp., which consist of 11 pathogenic species of L. anisa, L. bozemanii, L. dumoffii, L. gormanii, L. jordanis, L. longbeachae, L. maceachernii, L. micdadei, and L. pneumophila (including subspp. pneumophila, subspp. fraseri, and subspp. pasculleii) and one non-pathogenic species, L. fairfieldensis. Twenty-nine probes that reproducibly detected multiple Legionella species with high specificity were included in the array. A total of 52 strains, including 30 target pathogens and 22 non-target bacteria, were used to verify the oligonucleotide microarray assay. The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven samples of air conditioner-condensed water with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. The phylogenetic study based on the ITS has also revealed that the non-pathogenic L. fairfieldensis is the closest to L. pneumophila than the nine other pathogenic Legionella spp. PMID:25469776

  9. Software design and code generation for the engineering graphical user interface of the ASTRI SST-2M prototype for the Cherenkov Telescope Array

    Science.gov (United States)

    Tanci, Claudio; Tosti, Gino; Antolini, Elisa; Gambini, Giorgio F.; Bruno, Pietro; Canestrari, Rodolfo; Conforti, Vito; Lombardi, Saverio; Russo, Federico; Sangiorgi, Pierluca; Scuderi, Salvatore

    2016-08-01

    ASTRI is an on-going project developed in the framework of the Cherenkov Telescope Array (CTA). An end- to-end prototype of a dual-mirror small-size telescope (SST-2M) has been installed at the INAF observing station on Mt. Etna, Italy. The next step is the development of the ASTRI mini-array composed of nine ASTRI SST-2M telescopes proposed to be installed at the CTA southern site. The ASTRI mini-array is a collaborative and international effort carried on by Italy, Brazil and South-Africa and led by the Italian National Institute of Astrophysics, INAF. To control the ASTRI telescopes, a specific ASTRI Mini-Array Software System (MASS) was designed using a scalable and distributed architecture to monitor all the hardware devices for the telescopes. Using code generation we built automatically from the ASTRI Interface Control Documents a set of communication libraries and extensive Graphical User Interfaces that provide full access to the capabilities offered by the telescope hardware subsystems for testing and maintenance. Leveraging these generated libraries and components we then implemented a human designed, integrated, Engineering GUI for MASS to perform the verification of the whole prototype and test shared services such as the alarms, configurations, control systems, and scientific on-line outcomes. In our experience the use of code generation dramatically reduced the amount of effort in development, integration and testing of the more basic software components and resulted in a fast software release life cycle. This approach could be valuable for the whole CTA project, characterized by a large diversity of hardware components.

  10. Co-Prime Frequency and Aperture Design for HF Surveillance, Wideband Radar Imaging, and Nonstationary Array Processing

    Science.gov (United States)

    2018-03-10

    circuit boards. A computational electromagnetics software package, FEKO [24], is used to model the antenna arrays, and the RMIM [12] is used to...Symposium on Intelligent Signal Processing and Communications Systems, Chengdu, China, 2010. [24] FEKO Suite 6.3, EM Software & Systems- S.A. (Pty) Ltd...including suggestions for reducing the burden, to Department of Defense, Washington Headquarters Services , Directorate for Information Operations and

  11. Array-based techniques for fingerprinting medicinal herbs

    Directory of Open Access Journals (Sweden)

    Xue Charlie

    2011-05-01

    Full Text Available Abstract Poor quality control of medicinal herbs has led to instances of toxicity, poisoning and even deaths. The fundamental step in quality control of herbal medicine is accurate identification of herbs. Array-based techniques have recently been adapted to authenticate or identify herbal plants. This article reviews the current array-based techniques, eg oligonucleotides microarrays, gene-based probe microarrays, Suppression Subtractive Hybridization (SSH-based arrays, Diversity Array Technology (DArT and Subtracted Diversity Array (SDA. We further compare these techniques according to important parameters such as markers, polymorphism rates, restriction enzymes and sample type. The applicability of the array-based methods for fingerprinting depends on the availability of genomics and genetics of the species to be fingerprinted. For the species with few genome sequence information but high polymorphism rates, SDA techniques are particularly recommended because they require less labour and lower material cost.

  12. Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments

    Science.gov (United States)

    Jourdren, Laurent; Duclos, Aurélie; Brion, Christian; Portnoy, Thomas; Mathis, Hugues; Margeot, Antoine; Le Crom, Stéphane

    2010-01-01

    Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/. PMID:20176570

  13. Design, simulation and characterization of a MEMS inertia switch with flexible CNTs/Cu composite array layer between electrodes for prolonging contact time

    International Nuclear Information System (INIS)

    Wang, Yang; Yang, Zhuoqing; Xu, Qiu; Chen, Wenguo; Ding, Guifu; Zhao, Xiaolin

    2015-01-01

    This paper reports an inertia switch with a flexible carbon nanotubes/copper (CNTs/Cu) composite array layer between movable and fixed electrodes, which achieves a longer contact time compared to the traditional design using rigid-to-rigid impact between electrodes. The CNTs/Cu layer is fabricated using the composite electroplating method, and the whole device is completed by multi-layer metal electroplating based on the micro-electro-mechanical systems (MEMS) process. The dynamic responses of the designed inertia switch and the contact impact between a single CNT and a fixed electrode/another CNT have both been simulated by the ANSYS finite-element-method (FEM). It is shown that the contact time of the designed inertia switch is about 100 µs under the applied 80 g half-sine-shaped acceleration in the sensing direction. Finally, the fabricated MEMS inertia switch with the flexible CNTs/Cu composite array layer between electrodes has been evaluated by a dropping hammer system. The test contact time is about112 µs, which has a good agreement with the simulation and is much longer than that of the traditional design. (paper)

  14. Thermoplastic polymers surfaces for Dip-Pen Nanolithography of oligonucleotides

    International Nuclear Information System (INIS)

    Suriano, Raffaella; Biella, Serena; Cesura, Federico; Levi, Marinella; Turri, Stefano

    2013-01-01

    Different thermoplastic polymers were spin-coated to prepare smooth surfaces for the direct deposition of end-group modified oligonucleotides by Dip-Pen Nanolithography. A study of the diffusion process was done in order to investigate the dependence of calibration coefficient and quality of deposited features on environmental parameters (temperature, relative humidity) and ink's molecular weight and functionality. The optimization of the process parameters led to the realization of high quality and density nanoarrays on plastics.

  15. Thermoplastic polymers surfaces for Dip-Pen Nanolithography of oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Suriano, Raffaella [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Biella, Serena, E-mail: serena.biella@polimi.it [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Cesura, Federico; Levi, Marinella; Turri, Stefano [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2013-05-15

    Different thermoplastic polymers were spin-coated to prepare smooth surfaces for the direct deposition of end-group modified oligonucleotides by Dip-Pen Nanolithography. A study of the diffusion process was done in order to investigate the dependence of calibration coefficient and quality of deposited features on environmental parameters (temperature, relative humidity) and ink's molecular weight and functionality. The optimization of the process parameters led to the realization of high quality and density nanoarrays on plastics.

  16. THERAPEUTIC ANTISENSE OLIGONUCLEOTIDES AGAINST CANCER: HURDLING TO THE CLINIC

    Directory of Open Access Journals (Sweden)

    Pedro Miguel Duarte Moreno

    2014-10-01

    Full Text Available Under clinical development since the early 90’s and with two successfully approved drugs (Fomivirsen and Mipomersen, oligonucleotide-based therapeutics have not yet delivered a clinical drug to the market in the cancer field. Whilst many pre-clinical data has been generated, a lack of understanding still exists on how to efficiently tackle all the different challenges presented for cancer targeting in a clinical setting. Namely, effective drug vectorization, careful choice of target gene or synergistic multi-gene targeting are surely decisive, while caution must be exerted to avoid potential toxic, often misleading off-target-effects. Here a brief overview will be given on the nucleic acid chemistry advances that established oligonucleotide technologies as a promising therapeutic alternative and ongoing cancer related clinical trials. Special attention will be given towards a perspective on the hurdles encountered specifically in the cancer field by this class of therapeutic oligonucleotides and a view on possible avenues for success is presented, with particular focus on the contribution from nanotechnology to the field.

  17. Peroxide-mediated desulfurization of phosphorothioate oligonucleotides and its prevention.

    Science.gov (United States)

    Krotz, Achim H; Mehta, Rahul C; Hardee, Gregory E

    2005-02-01

    Desulfurization at the internucleotide phosphorothioate linkage of antisense oligonucleotides (ASOs) in dermatological formulations has been investigated using strong ion exchange chromatography and mass spectroscopy. The formation of phosphate diester linkages appeared to arise from a reaction between the phosphorothioate oligonucleotide and a potent oxidizing agent. Screening of excipients used in the formulation indicated that the cause of desulfurization was related to the presence of polyethylene glycol-derived nonionic surfactants MYRJ 52 or BRIJ 58. Autoxidation of the polyethylene glycol chain is suggested as the probable origin for the observed incompatibility. The ability of various antioxidants to prevent oxidative degradation of ASO-1 in simple test systems and in oil-in-water emulsions is described. It is found that in test systems both lipophilic and hydrophilic antioxidants are effective. However, in cream formulation (oil-in-water emulsions) of ASO-1 the addition of hydrophilic antioxidants L-cysteine or DL-alpha-lipoic acid has been shown to be superior in protecting the oligonucleotide from desulfurization upon storage. Copyright 2004 Wiley-Liss, Inc.

  18. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model.

    Science.gov (United States)

    Moreira, Bernardo G; You, Yong; Owczarzy, Richard

    2015-03-01

    Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications. Copyright © 2015. Published by Elsevier B.V.

  19. Antiproliferation effects of an androgen receptor triple-helix forming oligonucleotide on prostate cancer cells

    International Nuclear Information System (INIS)

    Zhang Yong; Chen Weizhen; Xie Yao; Gao Jinhui

    2005-01-01

    Objective: To provide experimental basis for antigene radiation therapy through exploring the effects of antigene strategy on androgen receptor (AR) expression and proliferation of prostate cancer cells. Methods: The triple-helix forming oligonucleotide (TFO) targeting 2447-2461nt of AR cDNA was designed and transfected LNCaP prostate cancer cells with liposome. 24-72 h after transfection, the cellular proliferation was detected by 3 H-thymidine (TdR) incorporation test, the expression of AR gene was examined by reverse transcription-polymerase chain reaction (RT-PCR) and expression of AR protein was performed by radioligand binding assay. The results of TFO were compared with antisense oligonucleotide (ASON). Results: At all time points, the AR expression levels in TFO group were markedly lower than that of ASON group (P<0.05). The inhibitory rate of TFO for cellular proliferation was significantly higher than that of ASON (P<0.05). Conclusion: The TFO was a potent inhibitor for AR expression and cell proliferation of LNCaP cells , and could be used in antigene radiotherapy. (authors)

  20. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.

  1. Efficacy and Safety Profile of Tricyclo-DNA Antisense Oligonucleotides in Duchenne Muscular Dystrophy Mouse Model

    Directory of Open Access Journals (Sweden)

    Karima Relizani

    2017-09-01

    Full Text Available Antisense oligonucleotides (AONs hold promise for therapeutic splice-switching correction in many genetic diseases. However, despite advances in AON chemistry and design, systemic use of AONs is limited due to poor tissue uptake and sufficient therapeutic efficacy is still difficult to achieve. A novel class of AONs made of tricyclo-DNA (tcDNA is considered very promising for the treatment of Duchenne muscular dystrophy (DMD, a neuromuscular disease typically caused by frameshifting deletions or nonsense mutations in the gene-encoding dystrophin and characterized by progressive muscle weakness, cardiomyopathy, and respiratory failure in addition to cognitive impairment. Herein, we report the efficacy and toxicology profile of a 13-mer tcDNA in mdx mice. We show that systemic delivery of 13-mer tcDNA allows restoration of dystrophin in skeletal muscles and to a lower extent in the brain, leading to muscle function improvement and correction of behavioral features linked to the emotional/cognitive deficiency. More importantly, tcDNA treatment was generally limited to minimal glomerular changes and few cell necroses in proximal tubules, with only slight variation in serum and urinary kidney toxicity biomarker levels. These results demonstrate an encouraging safety profile for tcDNA, albeit typical of phosphorothiate AONs, and confirm its therapeutic potential for the systemic treatment of DMD patients. Keywords: antisense oligonucleotides, Duchenne muscular dystrophy, preclinical, splice switching, tcDNA-AONs

  2. Static magnetic field reduced exogenous oligonucleotide uptake by spermatozoa using magnetic nanoparticle gene delivery system

    International Nuclear Information System (INIS)

    Katebi, Samira; Esmaeili, Abolghasem; Ghaedi, Kamran

    2016-01-01

    Spermatozoa could introduce exogenous oligonucleotides of interest to the oocyte. The most important reason of low efficiency of sperm mediated gene transfer (SMGT) is low uptake of exogenous DNA by spermatozoa. The aim of this study was to evaluate the effects of static magnetic field on exogenous oligonucleotide uptake of spermatozoa using magnetofection method. Magnetic nanoparticles (MNPs) associated with the labeled oligonucleotides were used to increase the efficiency of exogenous oligonucleotide uptake by rooster spermatozoa. We used high-field/high-gradient magnet (NdFeB) to enhance and accelerate exogenous DNA sedimentation at the spermatozoa surface. Flow cytometry analysis was performed to measure viability and percentage of exogenous oligonucleotide uptake by sperm. Flow cytometry analysis showed a significant increase in exogenous oligonucleotide uptake by rooster spermatozoa (P<0.001) when spermatozoa were incubated in exogenous oligonucleotide solution and MNPs. However, by applying static magnetic field during magnetofection method, a significant decrease in exogenous oligonucleotide uptake was observed (P<0.05). Findings of this study showed that MNPs were effective to increase exogenous oligonucleotide uptake by rooster spermatozoa; however unlike others studies, static magnetic field, was not only ineffective to enhance exogenous oligonucleotide uptake by rooster spermatozoa but also led to reduction in efficiency of magnetic nanoparticles in gene transfer. - Highlights: • Core/shell type Iron oxide nanoparticles were used as a novel and efficient method. • This method increases exogenous DNA uptake by rooster spermatozoa. • Static magnetic field decreased DNA uptake by rooster spermatozoa.

  3. Static magnetic field reduced exogenous oligonucleotide uptake by spermatozoa using magnetic nanoparticle gene delivery system

    Energy Technology Data Exchange (ETDEWEB)

    Katebi, Samira; Esmaeili, Abolghasem, E-mail: aesmaeili@sci.ui.ac.ir; Ghaedi, Kamran

    2016-03-15

    Spermatozoa could introduce exogenous oligonucleotides of interest to the oocyte. The most important reason of low efficiency of sperm mediated gene transfer (SMGT) is low uptake of exogenous DNA by spermatozoa. The aim of this study was to evaluate the effects of static magnetic field on exogenous oligonucleotide uptake of spermatozoa using magnetofection method. Magnetic nanoparticles (MNPs) associated with the labeled oligonucleotides were used to increase the efficiency of exogenous oligonucleotide uptake by rooster spermatozoa. We used high-field/high-gradient magnet (NdFeB) to enhance and accelerate exogenous DNA sedimentation at the spermatozoa surface. Flow cytometry analysis was performed to measure viability and percentage of exogenous oligonucleotide uptake by sperm. Flow cytometry analysis showed a significant increase in exogenous oligonucleotide uptake by rooster spermatozoa (P<0.001) when spermatozoa were incubated in exogenous oligonucleotide solution and MNPs. However, by applying static magnetic field during magnetofection method, a significant decrease in exogenous oligonucleotide uptake was observed (P<0.05). Findings of this study showed that MNPs were effective to increase exogenous oligonucleotide uptake by rooster spermatozoa; however unlike others studies, static magnetic field, was not only ineffective to enhance exogenous oligonucleotide uptake by rooster spermatozoa but also led to reduction in efficiency of magnetic nanoparticles in gene transfer. - Highlights: • Core/shell type Iron oxide nanoparticles were used as a novel and efficient method. • This method increases exogenous DNA uptake by rooster spermatozoa. • Static magnetic field decreased DNA uptake by rooster spermatozoa.

  4. β-galactosidase Production by Aspergillus niger ATCC 9142 Using Inexpensive Substrates in Solid-State Fermentation: Optimization by Orthogonal Arrays Design.

    Science.gov (United States)

    Kazemi, Samaneh; Khayati, Gholam; Faezi-Ghasemi, Mohammad

    2016-01-01

    Enzymatic hydrolysis of lactose is one of the most important biotechnological processes in the food industry, which is accomplished by enzyme β-galactosidase (β-gal, β-D-galactoside galactohydrolase, EC 3.2.1.23), trivial called lactase. Orthogonal arrays design is an appropriate option for the optimization of biotechnological processes for the production of microbial enzymes. Design of experimental (DOE) methodology using Taguchi orthogonal array (OA) was employed to screen the most significant levels of parameters, including the solid substrates (wheat straw, rice straw, and peanut pod), the carbon/nitrogen (C/N) ratios, the incubation time, and the inducer. The level of β-gal production was measured by a photometric enzyme activity assay using the artificial substrate ortho-Nitrophenyl-β-D-galactopyranoside. The results showed that C/N ratio (0.2% [w/v], incubation time (144 hour), and solid substrate (wheat straw) were the best conditions determined by the design of experiments using the Taguchi approach. Our finding showed that the use of rice straw and peanut pod, as solid-state substrates, led to 2.041-folds increase in the production of the enzyme, as compared to rice straw. In addition, the presence of an inducer did not have any significant impact on the enzyme production levels.

  5. Design and Analysis of Printed Yagi-Uda Antenna and Two-Element Array for WLAN Applications

    Directory of Open Access Journals (Sweden)

    Cai Run-Nan

    2012-01-01

    Full Text Available A printed director antenna with compact structure is proposed. The antenna is fed by a balanced microstrip-slotline and makes good use of space to reduce feeding network area and the size of antenna. According to the simulation results of CST MICROWAVE STUDIO software, broadband characteristics and directional radiation properties of the antenna are explained. The operating bandwidth is 1.8 GHz–3.5 GHz with reflection coefficient less than −10 dB. Antenna gain in band can achieve 4.5–6.8 dBi, and the overall size of antenna is smaller than 0.34λ0×0.58λ0. Then the antenna is developed to a two-element antenna array, working frequency and relative bandwidth of which are 2.15–2.87 GHz and 28.7%, respectively. Compared with antenna unit, the gain of the antenna array has increased by 2 dB. Thus the proposed antenna has characteristics of compact structure, relatively small size, and wideband, and it can be widely used in PCS/UMTS/WLAN/ WiMAX fields.

  6. Salivary gland carcinosarcoma: oligonucleotide array CGH reveals similar genomic profiles in epithelial and mesenchymal components

    NARCIS (Netherlands)

    Vékony, H.; Leemans, C.R.; Ylstra, B.; Meijer, G.A.; van der Waal, I.; Bloemena, E.

    2009-01-01

    In this study, we present a case of parotid gland de novo carcinosarcoma. Salivary gland carcinosarcoma (or true malignant mixed tumor) is a rare biphasic neoplasm, composed of both malignant epithelial and malignant mesenchymal components. It is yet unclear whether these two phenotypes occur by

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

    Science.gov (United States)

    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.

  8. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam

    2016-10-09

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  9. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

    2016-01-01

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  10. Versatile, modular 3D microelectrode arrays for neuronal ensemble recordings: from design to fabrication, assembly, and functional validation in non-human primates

    Science.gov (United States)

    Barz, F.; Livi, A.; Lanzilotto, M.; Maranesi, M.; Bonini, L.; Paul, O.; Ruther, P.

    2017-06-01

    Objective. Application-specific designs of electrode arrays offer an improved effectiveness for providing access to targeted brain regions in neuroscientific research and brain machine interfaces. The simultaneous and stable recording of neuronal ensembles is the main goal in the design of advanced neural interfaces. Here, we describe the development and assembly of highly customizable 3D microelectrode arrays and demonstrate their recording performance in chronic applications in non-human primates. Approach. System assembly relies on a microfabricated stacking component that is combined with Michigan-style silicon-based electrode arrays interfacing highly flexible polyimide cables. Based on the novel stacking component, the lead time for implementing prototypes with altered electrode pitches is minimal. Once the fabrication and assembly accuracy of the stacked probes have been characterized, their recording performance is assessed during in vivo chronic experiments in awake rhesus macaques (Macaca mulatta) trained to execute reaching-grasping motor tasks. Main results. Using a single set of fabrication tools, we implemented three variants of the stacking component for electrode distances of 250, 300 and 350 µm in the stacking direction. We assembled neural probes with up to 96 channels and an electrode density of 98 electrodes mm-2. Furthermore, we demonstrate that the shank alignment is accurate to a few µm at an angular alignment better than 1°. Three 64-channel probes were chronically implanted in two monkeys providing single-unit activity on more than 60% of all channels and excellent recording stability. Histological tissue sections, obtained 52 d after implantation from one of the monkeys, showed minimal tissue damage, in accordance with the high quality and stability of the recorded neural activity. Significance. The versatility of our fabrication and assembly approach should significantly support the development of ideal interface geometries for a broad

  11. Oligonucleotide assisted light-emitting Alq3 microrods: energy transfer effect with fluorescent dyes.

    Science.gov (United States)

    Cui, Chunzhi; Park, Dong Hyuk; Kim, Jeongyong; Joo, Jinsoo; Ahn, Dong June

    2013-06-14

    Oligonucleotide assisted tri(8-hydroxyquinoline) aluminium (Alq3) microrods were prepared for the first time. When hybridized with oligonucleotide labeled by Cy3 fluorescent dye, a significant photoluminescence variation of the Alq3 microrods was observed due to Förster resonance energy transfer, unlike when Cy5-oligonucleotide was used. Versatile nucleotide manipulation would open up wider applications of Alq3-based materials, based on this fundamental observation.

  12. Transcriptional landscape estimation from tiling array data using a model of signal shift and drift

    DEFF Research Database (Denmark)

    Rasmussen, Simon; Jarmer, Hanne Østergaard; Nicolas, P

    2009-01-01

    MOTIVATION: High-density oligonucleotide tiling array technology holds the promise of a better description of the complexity and the dynamics of transcriptional landscapes. In organisms such as bacteria and yeasts, transcription can be measured on a genome-wide scale with a resolution >25 bp...

  13. Fluid Micro-Reservoirs Array Design with Auto-Pressure Regulation for High-Speed 3D Printers

    Directory of Open Access Journals (Sweden)

    Moshe Einat

    2016-11-01

    Full Text Available Three dimensional (3D printing technology is rapidly evolving such that printing speed is now a crucial factor in technological developments and future applications. For printing heads based on the inkjet concept, the number of nozzles on the print head is a limiting factor of printing speed. This paper offers a method to practically increase the number of nozzles unlimitedly, and thus to dramatically ramp up printing speed. Fluid reservoirs are used in inkjet print heads to supply fluid through a manifold to the jetting chambers. The pressure in the reservoir’s outlet is important and influences device performance. Many efforts have been made to regulate pressure inside the fluid reservoirs so as to obtain a constant pressure in the chambers. When the number of nozzles is increased too much, the regulation of uniform pressure among all the nozzles becomes too complicated. In this paper, a different approach is taken. The reservoir is divided into an array of many micro-reservoirs. Each micro-reservoir supports one or a few chambers, and has a unique structure with auto-pressure regulation, where the outlet pressure is independent of the fluid level. The regulation is based on auto-compensation of the gravity force and a capillary force having the same dependence on the fluid level; this feature is obtained by adding a wedge in the reservoir with a unique shape. When the fluid level drops, the gravitational force and the capillary force decrease with it, but at similar rates. Terms for the force balance are derived and, consequently, a constant pressure in the fluid micro-reservoir segment is obtained automatically, with each segment being autonomous. This micro reservoir array is suggested for the enlargement of an inkjet print head and the achievement of high-speed 3D printing.

  14. Design of a 5-MA 100-ns linear-transformer-driver accelerator for wire array Z-pinch experiments

    Science.gov (United States)

    Zhou, Lin; Li, Zhenghong; Wang, Zhen; Liang, Chuan; Li, Mingjia; Qi, Jianmin; Chu, Yanyun

    2016-03-01

    The linear-transformer-driver (LTD) is a recently developed pulsed-power technology that shows great promise for a number of applications. These include a Z -pinch-driven fission-fusion-hybrid reactor that is being developed by the Chinese Academy of Engineering Physics. In support of the reactor development effort, we are planning to build an LTD-based accelerator that is optimized for driving wire-array Z -pinch loads. The accelerator comprises six modules in parallel, each of which has eight series 0.8-MA LTD cavities in a voltage-adder configuration. Vacuum transmission lines are used from the interior of the adder to the central vacuum chamber where the load is placed. Thus the traditional stack-flashover problem is eliminated. The machine is 3.2 m tall and 12 m in outer diameter including supports. A prototype cavity was built and tested for more than 6000 shots intermittently at a repetition rate of 0.1 Hz. A novel trigger, in which only one input trigger pulse is needed by utilizing an internal trigger brick, was developed and successfully verified in these shots. A full circuit modeling was conducted for the accelerator. The simulation result shows that a current pulse rising to 5.2 MA in 91 ns (10%-90%) can be delivered to the wire-array load, which is 1.5 cm in height, 1.2 cm in initial radius, and 1 mg in mass. The maximum implosion velocity of the load is 32 cm /μ s when compressed to 0.1 of the initial radius. The maximum kinetic energy is 78 kJ, which is 11.7% of the electric energy stored in the capacitors. This accelerator is supposed to enable a radiation energy efficiency of 20%-30%, providing a high efficient facility for research on the fast Z pinch and technologies for repetition-rate-operated accelerators.

  15. SNP Arrays

    Directory of Open Access Journals (Sweden)

    Jari Louhelainen

    2016-10-01

    Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

  16. Fabrication of micro-channel arrays on thin metallic sheet using internal fluid pressure: Investigations on size effects and development of design guidelines

    Energy Technology Data Exchange (ETDEWEB)

    Mahabunphachai, Sasawat [NSF I/UCR Center for Precision Forming, Department of Mechanical Engineering, Virginia Commonwealth University, Richmond, VA 23284 (United States); Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Koc, Muammer [NSF I/UCR Center for Precision Forming, Department of Mechanical Engineering, Virginia Commonwealth University, Richmond, VA 23284 (United States)

    2008-01-03

    Micro-feature (channel, protrusion, cavity, etc.) arrays on large area-thin metallic sheet alloys are increasingly needed for compact and integrated heat/mass transfer applications (such as fuel cells and fuel processors) that require high temperature resistance, corrosion resistance, good electrical/thermal conductivity, etc. The performance of these micro-feature arrays mainly affects the volume flow velocity of the reactants inside the arrays which directly controls the rate of convection mass/heat transport. The key factors that affect the flow velocity include channel size and shape, flow field pattern, flow path length, fluid pressure, etc. In this study, we investigated these micro-feature arrays from the manufacturability perspective since it is also an important factor to be considered in the design process. Internal fluid pressure (hydroforming) technique is investigated in this study with the specific goals to, first, understand if the so-called ''size effects'' (grain vs. feature size) are effective on the manufacturability of thin metallic sheet into micro-channels, and second, to establish design guidelines for the micro-channel hydroforming technique for robust mass production conditions. Thin stainless steel 304 blanks of 0.051 mm thick with three different grain sizes of 9.3, 10.6, and 17.0 {mu}m were used in hydroforming experiments to form micro-channels with the dimensions between 0.46-1.33 and 0.15-0.98 mm in width and height, respectively. Based on the experimental results, the effect of the grain size on the channel formability was found to be insignificant for the grain size range used in this study. On the other hand, the effect of the channel (feature) size was shown to dominate the overall formability. In addition, FE models of the process were developed and validated with the experimental results, then used to conduct a parametric study to establish micro-channel design guidelines. The results from the parametric

  17. Design concepts for the Cherenkov Telescope Array CTA: an advanced facility for ground-based high-energy gamma-ray astronomy

    International Nuclear Information System (INIS)

    Allekotte, I.; Arnaldi, H.; Asorey, H.; Gomez Berisso, M.; Sofo Haro, M.; Cillis, A.; Rovero, A.C.; Supanitsky, A.D.; Actis, M.; Antico, F.; Bottani, A.; Ochoa, I.; Ringegni, P.; Vallejo, G.; De La Vega, G.; Etchegoyen, A.; Videla, M.; Gonzalez, F.; Pallota, J.; Quel, E.; Ristori, P.; Romero, G.E.; Suarez, A.; Papyan, G.; Pogosyan, L.; Sahakian, V.; Bissaldi, E.; Egberts, K.; Reimer, A.; Reimer, O.; Shellard, R.C.; Santos, E.M.; De Gouveia Dal Pino, E.M.; Kowal, G.; De Souza, V.; Todero Peixoto, C.J.; Maneva, G.; Temnikov, P.; Vankov, H.; Golev, V.; Ovcharov, E.; Bonev, T.; Dimitrov, D.; Hrupec, D.; Nedbal, D.; Rob, L.; Sillanpaa, A.; Takalo, L.; Beckmann, V.; Benallou, M.; Boutonnet, C.; Corlier, M.; Courty, B.; Djannati-Atai, A.; Dufour, C.; Gabici, S.; Guglielmi, L.; Olivetto, C.; Pita, S.; Punch, M.; Selmane, S.; Terrier, R.; Yoffo, B.; Brun, P.; Carton, P.H.; Cazaux, S.; Corpace, O.; Delagnes, E.; Disset, G.; Durand, D.; Glicenstein, J.F.; Guilloux, F.; Kosack, K.; Medina, C.; Micolon, P.; Mirabel, F.; Moulin, E.; Peyaud, B.; Reymond, J.M.; Veyssiere, C.

    2011-01-01

    Ground-based gamma-ray astronomy has had a major breakthrough with the impressive results obtained using systems of imaging atmospheric Cherenkov telescopes. Ground-based gamma-ray astronomy has a huge potential in astrophysics, particle physics and cosmology. CTA is an international initiative to build the next generation instrument, with a factor of 5-10 improvement in sensitivity in the 100 GeV-10 TeV range and the extension to energies well below 100 GeV and above 100 TeV. CTA will consist of two arrays (one in the north, one in the south) for full sky coverage and will be operated as open observatory. The design of CTA is based on currently available technology. This document reports on the status and presents the major design concepts of CTA. (authors)

  18. Chemically modified oligonucleotides with efficient RNase H response

    DEFF Research Database (Denmark)

    Vester, Birte; Boel, Anne Marie; Lobedanz, Sune

    2008-01-01

    Ten different chemically modified nucleosides were incorporated into short DNA strands (chimeric oligonucleotides ON3-ON12 and ON15-ON24) and then tested for their capacity to mediate RNAse H cleavage of the complementary RNA strand. The modifications were placed at two central positions directly...... in the RNase H cleaving region. The RNA strand of duplexes with ON3, ON5 and ON12 were cleaved more efficiently than the RNA strand of the DNA:RNA control duplex. There seems to be no correlation between the thermal stability between the duplexes and RNase H cleavage....

  19. Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry.

    OpenAIRE

    Jensen, O N; Kulkarni, S; Aldrich, J V; Barofsky, D F

    1996-01-01

    Two peptide-oligothymidylic acids, prepared by joining an 11 residue synthetic peptide containing one internal carboxyl group (Asp side chain) to amino-linker-5'pdT6 and amino-linker-5'pdT10 oligonucleotides, were analyzed by matrix-assisted laser desorption/ionization (MALDI) on a linear time-of-flight mass spectrometer and by electrospray ionization (ESI) on a triple-quadrupole system. These synthetic compounds model peptide-nucleic acid heteroconjugates encountered in antisense research an...

  20. PCR amplification on microarrays of gel immobilized oligonucleotides

    Science.gov (United States)

    Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

    2003-11-04

    The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

  1. electrode array

    African Journals Online (AJOL)

    PROF EKWUEME

    A geoelectric investigation employing vertical electrical soundings (VES) using the Ajayi - Makinde Two-Electrode array and the ... arrangements used in electrical D.C. resistivity survey. These include ..... Refraction Tomography to Study the.

  2. Design of a 5-MA 100-ns linear-transformer-driver accelerator for wire array Z-pinch experiments

    Directory of Open Access Journals (Sweden)

    Zhou Lin

    2016-03-01

    Full Text Available The linear-transformer-driver (LTD is a recently developed pulsed-power technology that shows great promise for a number of applications. These include a Z-pinch-driven fission-fusion-hybrid reactor that is being developed by the Chinese Academy of Engineering Physics. In support of the reactor development effort, we are planning to build an LTD-based accelerator that is optimized for driving wire-array Z-pinch loads. The accelerator comprises six modules in parallel, each of which has eight series 0.8-MA LTD cavities in a voltage-adder configuration. Vacuum transmission lines are used from the interior of the adder to the central vacuum chamber where the load is placed. Thus the traditional stack-flashover problem is eliminated. The machine is 3.2 m tall and 12 m in outer diameter including supports. A prototype cavity was built and tested for more than 6000 shots intermittently at a repetition rate of 0.1 Hz. A novel trigger, in which only one input trigger pulse is needed by utilizing an internal trigger brick, was developed and successfully verified in these shots. A full circuit modeling was conducted for the accelerator. The simulation result shows that a current pulse rising to 5.2 MA in 91 ns (10%–90% can be delivered to the wire-array load, which is 1.5 cm in height, 1.2 cm in initial radius, and 1 mg in mass. The maximum implosion velocity of the load is 32  cm/μs when compressed to 0.1 of the initial radius. The maximum kinetic energy is 78 kJ, which is 11.7% of the electric energy stored in the capacitors. This accelerator is supposed to enable a radiation energy efficiency of 20%–30%, providing a high efficient facility for research on the fast Z pinch and technologies for repetition-rate-operated accelerators.

  3. Design of Arrangement of Solar Array and Energy Storage in Solar Photovoltaic Generation%光伏阵列及储能的布置设计

    Institute of Scientific and Technical Information of China (English)

    韩学栋; 王海华

    2015-01-01

    Facing energy and environmental pressure, solar which is a kind natural renewable clean energy has become the focus of world development and utilization. This paper describes the optimal choice of the best dip angle of the solar array, deducing the layout spacing theoretical formula when the battery array in the horizontal plane and on the roof with a slope. Also, the paper describes the formula of the calculating components in series and parallel arrays of photovoltaic cells and storage cells in series and parallel. This paper provides some theoretical support to the design of the photovoltaic power generation system.%在能源和环境的双重压力下,太阳能这一清洁可再生的自然能源成为世界各国开发利用的重点。本文介绍了太阳能电池阵列最佳倾角的优化选择,推导了电池阵列在水平面以及带有一定坡度的屋面上进行布置时前后间距的理论计算公式,介绍了光伏电池阵列中组件的串并联以及储能蓄电池的串并联计算公式。上述工作对太阳能光伏发电系统的设计提供了一定的理论支撑。

  4. Synthesis and Structural Characterization of 2'-Fluoro-α-L-RNA-Modified Oligonucleotides

    DEFF Research Database (Denmark)

    Bundgaard Jensen, Troels; Pasternak, Anna; Stahl Madsen, Andreas

    2011-01-01

    with the smallest destabilization towards RNA. Thermodynamic data show that the duplex formation with 2'-fluoro-α-L-RNA nucleotides is enthalpically disfavored but entropically favored. 2'-Fluoro-α-L-RNA nucleotides exhibit very good base pairing specificity following Watson-Crick rules. The 2'-fluoro......-α-L-RNA monomer was designed as a monocyclic mimic of the bicyclic α-L-LNA, and molecular modeling showed that this indeed is the case as the 2'-fluoro monomer adopts a C3'-endo/C2'-exo sugar pucker. Molecular modeling of modified duplexes show that the 2'-fluoro-α-L-RNA nucleotides partake in Watson-Crick base......We describe the synthesis and binding properties of oligonucleotides that contain one or more 2'-fluoro-α-L-RNA thymine monomer(s). Incorporation of 2'-fluoro-α-L-RNA thymine into oligodeoxynucleotides decreased thermal binding stability slightly upon hybridization with complementary DNA and RNA...

  5. An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2002-03-01

    Full Text Available Abstract Background The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However, it shows also great promise for other small organisms that are taxonomically difficult to tract. Results We have devised here an algorithm that aims to find the optimal probes for any given set of sequences. The program requires only a crude alignment of these sequences as input and is optimized for performance to deal also with very large datasets. The algorithm is designed such that the position of mismatches in the probes influences the selection and makes provision of single nucleotide outloops. Program implementations are available for Linux and Windows.

  6. Design of Smart Ion-Selective Electrode Arrays Based on Source Separation through Nonlinear Independent Component Analysis

    Directory of Open Access Journals (Sweden)

    Duarte L.T.

    2014-03-01

    Full Text Available The development of chemical sensor arrays based on Blind Source Separation (BSS provides a promising solution to overcome the interference problem associated with Ion-Selective Electrodes (ISE. The main motivation behind this new approach is to ease the time-demanding calibration stage. While the first works on this problem only considered the case in which the ions under analysis have equal valences, the present work aims at developing a BSS technique that works when the ions have different charges. In this situation, the resulting mixing model belongs to a particular class of nonlinear systems that have never been studied in the BSS literature. In order to tackle this sort of mixing process, we adopted a recurrent network as separating system. Moreover, concerning the BSS learning strategy, we develop a mutual information minimization approach based on the notion of the differential of the mutual information. The method works requires a batch operation, and, thus, can be used to perform off-line analysis. The validity of our approach is supported by experiments where the mixing model parameters were extracted from actual data.

  7. Design and reliability analysis of high-speed and continuous data recording system based on disk array

    Science.gov (United States)

    Jiang, Changlong; Ma, Cheng; He, Ning; Zhang, Xugang; Wang, Chongyang; Jia, Huibo

    2002-12-01

    In many real-time fields the sustained high-speed data recording system is required. This paper proposes a high-speed and sustained data recording system based on the complex-RAID 3+0. The system consists of Array Controller Module (ACM), String Controller Module (SCM) and Main Controller Module (MCM). ACM implemented by an FPGA chip is used to split the high-speed incoming data stream into several lower-speed streams and generate one parity code stream synchronously. It also can inversely recover the original data stream while reading. SCMs record lower-speed streams from the ACM into the SCSI disk drivers. In the SCM, the dual-page buffer technology is adopted to implement speed-matching function and satisfy the need of sustainable recording. MCM monitors the whole system, controls ACM and SCMs to realize the data stripping, reconstruction, and recovery functions. The method of how to determine the system scale is presented. At the end, two new ways Floating Parity Group (FPG) and full 2D-Parity Group (full 2D-PG) are proposed to improve the system reliability and compared with the Traditional Parity Group (TPG). This recording system can be used conveniently in many areas of data recording, storing, playback and remote backup with its high-reliability.

  8. Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays

    DEFF Research Database (Denmark)

    Petersen, J.; Poulsen, Lena; Petronis, S.

    2008-01-01

    is called a multi-thermal array washer (MTAW), and it has eight individually controlled heating zones, each of which corresponds to the location of a subarray on a slide. Allele-specific oligonucleotide probes for nine mutations in the beta-globin gene were spotted in eight identical subarrays at positions......DNA microarrays are generally operated at a single condition, which severely limits the freedom of designing probes for allele-specific hybridization assays. Here, we demonstrate a fluidic device for multi-stringency posthybridization washing of microarrays on microscope slides. This device...

  9. Microneedle Array Design Determines the Induction of Protective Memory CD8+ T Cell Responses Induced by a Recombinant Live Malaria Vaccine in Mice

    Science.gov (United States)

    Carey, John B.; Pearson, Frances E.; Vrdoljak, Anto; McGrath, Marie G.; Crean, Abina M.; Walsh, Patrick T.; Doody, Timothy; O'Mahony, Conor; Hill, Adrian V. S.; Moore, Anne C.

    2011-01-01

    Background Vaccine delivery into the skin has received renewed interest due to ease of access to the immune system and microvasculature, however the stratum corneum (SC), must be breached for successful vaccination. This has been achieved by removing the SC by abrasion or scarification or by delivering the vaccine intradermally (ID) with traditional needle-and-syringes or with long microneedle devices. Microneedle patch-based transdermal vaccine studies have predominantly focused on antibody induction by inactivated or subunit vaccines. Here, our principal aim is to determine if the design of a microneedle patch affects the CD8+ T cell responses to a malaria antigen induced by a live vaccine. Methodology and Findings Recombinant modified vaccinia virus Ankara (MVA) expressing a malaria antigen was percutaneously administered to mice using a range of silicon microneedle patches, termed ImmuPatch, that differed in microneedle height, density, patch area and total pore volume. We demonstrate that microneedle arrays that have small total pore volumes induce a significantly greater proportion of central memory T cells that vigorously expand to secondary immunization. Microneedle-mediated vaccine priming induced significantly greater T cell immunity post-boost and equivalent protection against malaria challenge compared to ID vaccination. Notably, unlike ID administration, ImmuPatch-mediated vaccination did not induce inflammatory responses at the site of immunization or in draining lymph nodes. Conclusions/Significance This study demonstrates that the design of microneedle patches significantly influences the magnitude and memory of vaccine-induced CD8+ T cell responses and can be optimised for the induction of desired immune responses. Furthermore, ImmuPatch-mediated delivery may be of benefit to reducing unwanted vaccine reactogenicity. In addition to the advantages of low cost and lack of pain, the development of optimised microneedle array designs for the induction

  10. Microneedle array design determines the induction of protective memory CD8+ T cell responses induced by a recombinant live malaria vaccine in mice.

    Directory of Open Access Journals (Sweden)

    John B Carey

    Full Text Available Vaccine delivery into the skin has received renewed interest due to ease of access to the immune system and microvasculature, however the stratum corneum (SC, must be breached for successful vaccination. This has been achieved by removing the SC by abrasion or scarification or by delivering the vaccine intradermally (ID with traditional needle-and-syringes or with long microneedle devices. Microneedle patch-based transdermal vaccine studies have predominantly focused on antibody induction by inactivated or subunit vaccines. Here, our principal aim is to determine if the design of a microneedle patch affects the CD8(+ T cell responses to a malaria antigen induced by a live vaccine.Recombinant modified vaccinia virus Ankara (MVA expressing a malaria antigen was percutaneously administered to mice using a range of silicon microneedle patches, termed ImmuPatch, that differed in microneedle height, density, patch area and total pore volume. We demonstrate that microneedle arrays that have small total pore volumes induce a significantly greater proportion of central memory T cells that vigorously expand to secondary immunization. Microneedle-mediated vaccine priming induced significantly greater T cell immunity post-boost and equivalent protection against malaria challenge compared to ID vaccination. Notably, unlike ID administration, ImmuPatch-mediated vaccination did not induce inflammatory responses at the site of immunization or in draining lymph nodes.This study demonstrates that the design of microneedle patches significantly influences the magnitude and memory of vaccine-induced CD8(+ T cell responses and can be optimised for the induction of desired immune responses. Furthermore, ImmuPatch-mediated delivery may be of benefit to reducing unwanted vaccine reactogenicity. In addition to the advantages of low cost and lack of pain, the development of optimised microneedle array designs for the induction of T cell responses by live vaccines aids

  11. A Nonlinear Model for Designing Herschel-Quincke Waveguide Arrays to Attenuate Shock Waves from Transonic Turbofan Engines, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Techsburg is teaming with the Vibration and Acoustics Laboratory of Virginia Tech to propose a non-linear analytical tool for designing Herschel-Quincke (HQ)...

  12. Oligonucleotide Aptamers: New Tools for Targeted Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Hongguang Sun

    2014-01-01

    Full Text Available Aptamers are a class of small nucleic acid ligands that are composed of RNA or single-stranded DNA oligonucleotides and have high specificity and affinity for their targets. Similar to antibodies, aptamers interact with their targets by recognizing a specific three-dimensional structure and are thus termed “chemical antibodies.” In contrast to protein antibodies, aptamers offer unique chemical and biological characteristics based on their oligonucleotide properties. Hence, they are more suitable for the development of novel clinical applications. Aptamer technology has been widely investigated in various biomedical fields for biomarker discovery, in vitro diagnosis, in vivo imaging, and targeted therapy. This review will discuss the potential applications of aptamer technology as a new tool for targeted cancer therapy with emphasis on the development of aptamers that are able to specifically target cell surface biomarkers. Additionally, we will describe several approaches for the use of aptamers in targeted therapeutics, including aptamer-drug conjugation, aptamer-nanoparticle conjugation, aptamer-mediated targeted gene therapy, aptamer-mediated immunotherapy, and aptamer-mediated biotherapy.

  13. The use of oligonucleotide probes for meningococcal serotype characterization

    Directory of Open Access Journals (Sweden)

    SACCHI Claudio Tavares

    1998-01-01

    Full Text Available In the present study we examine the potential use of oligonucleotide probes to characterize Neisseria meningitidis serotypes without the use of monoclonal antibodies (MAbs. Antigenic diversity on PorB protein forms the bases of serotyping method. However, the current panel of MAbs underestimated, by at least 50% the PorB variability, presumably because reagents for several PorB variable regions (VRs are lacking, or because a number of VR variants are not recognized by serotype-defining MAbs12. We analyzed the use of oligonucleotide probes to characterize serotype 10 and serotype 19 of N. meningitidis. The porB gene sequence for the prototype strain of serotype 10 was determined, aligned with 7 other porB sequences from different serotypes, and analysis of individual VRs were performed. The results of DNA probes 21U (VR1-A and 615U (VR3-B used against 72 N. meningitidis strains confirm that VR1 type A and VR3 type B encode epitopes for serotype-defined MAbs 19 and 10, respectively. The use of probes for characterizing serotypes possible can type 100% of the PorB VR diversity. It is a simple and rapid method specially useful for analysis of large number of samples.

  14. Differentiation of the seven major lyssavirus species by oligonucleotide microarray.

    Science.gov (United States)

    Xi, Jin; Guo, Huancheng; Feng, Ye; Xu, Yunbin; Shao, Mingfu; Su, Nan; Wan, Jiayu; Li, Jiping; Tu, Changchun

    2012-03-01

    An oligonucleotide microarray, LyssaChip, has been developed and verified as a highly specific diagnostic tool for differentiation of the 7 major lyssavirus species. As with conventional typing microarray methods, the LyssaChip relies on sequence differences in the 371-nucleotide region coding for the nucleoprotein. This region was amplified using nested reverse transcription-PCR primers that bind to the 7 major lyssaviruses. The LyssaChip includes 57 pairs of species typing and corresponding control oligonucleotide probes (oligoprobes) immobilized on glass slides, and it can analyze 12 samples on a single slide within 8 h. Analysis of 111 clinical brain specimens (65 from animals with suspected rabies submitted to the laboratory and 46 of butchered dog brain tissues collected from restaurants) showed that the chip method was 100% sensitive and highly consistent with the "gold standard," a fluorescent antibody test (FAT). The chip method could detect rabies virus in highly decayed brain tissues, whereas the FAT did not, and therefore the chip test may be more applicable to highly decayed brain tissues than the FAT. LyssaChip may provide a convenient and inexpensive alternative for diagnosis and differentiation of rabies and rabies-related diseases.

  15. SKALA, a log-periodic array antenna for the SKA-low instrument: design, simulations, tests and system considerations

    Science.gov (United States)

    de Lera Acedo, E.; Razavi-Ghods, N.; Troop, N.; Drought, N.; Faulkner, A. J.

    2015-10-01

    The very demanding requirements of the SKA-low instrument call for a challenging antenna design capable of delivering excellent performance in radiation patterns, impedance matching, polarization purity, cost, longevity, etc. This paper is devoted to the development (design and test of the first prototypes) of an active ultra-wideband antenna element for the low-frequency instrument of the SKA radio telescope. The antenna element and differential low noise amplifier described here were originally designed to cover the former SKA-low band (70-450 MHz) but it is now aimed to cover the re-defined SKA-low band (50-350 MHz) and furthermore the antenna is capable of performing up to 650 MHz with the current design. The design is focused on maximum sensitivity in a wide field of view (+/- 45° from zenith) and low cross-polarization ratios. Furthermore, the size and cost of the element has to be kept to a minimum as millions of these antennas will need to be deployed for the full SKA in very compact configurations. The primary focus of this paper is therefore to discuss various design implications for the SKA-low telescope.

  16. Genetic Algorithm Design And Testing of a Random Element 3-D 2.4 Ghz Phased Array Transmit Antenna Constructed of Commercial Rf Microchips

    National Research Council Canada - National Science Library

    Esswein, Lance

    2003-01-01

    ..., development and evaluation of a test-bed array. The test-bed array was constructed of commercially available components, including a unique and innovative application of a quadrature modulator microchip used in commercial communications applications...

  17. Membrane-Assisted Growth of DNA Origami Nanostructure Arrays

    Science.gov (United States)

    2015-01-01

    Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors—a three-layered rectangular block and a Y-shaped DNA structure—to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes. PMID:25734977

  18. Membrane-assisted growth of DNA origami nanostructure arrays.

    Science.gov (United States)

    Kocabey, Samet; Kempter, Susanne; List, Jonathan; Xing, Yongzheng; Bae, Wooli; Schiffels, Daniel; Shih, William M; Simmel, Friedrich C; Liedl, Tim

    2015-01-01

    Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors--a three-layered rectangular block and a Y-shaped DNA structure--to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

  19. Synthesis of 3'-, or 5'-, or internal methacrylamido-modified oligonucleotides

    Science.gov (United States)

    Golova, Julia B.; Chernov, Boris K.

    2010-04-27

    New modifiers were synthesized for incorporation of a methacrylic function in 3'-, 5'- and internal positions of oligonucleotides during solid phase synthesis. A modifier was used for synthesis of 5'-methacrylated oligonucleotides for preparation of microarrays by a co-polymerization method.

  20. Design of a high-gain laser diode-array pumped Nd:YAG alternating precessive slab amplifier (APS amplifier)

    Science.gov (United States)

    Coyle, D. B.

    1991-01-01

    In the design of space-qualifiable laser systems for ranging and altimetry, such as NASA's Geodynamic Laser Ranging System (GLRS), the transmitter must be kept small, powerful yet efficient, and must consist of as few components as possible. A novel preamplifier design is examined which requires no external beam steering optics, yielding a compact component with simple alignment procedures. The gains achieved are comparable to multipass zigzag amplifiers using two or more sets of external optics for extra passes through the amplifying medium.

  1. Final report on the scientific and engineering design of a soft X-ray diode array diagnostic system for JET (KJ 1)

    International Nuclear Information System (INIS)

    Fahrbach, H.U.; Goss, H.; Harmeyer, E.; Schramm, G.

    1982-07-01

    This report describes the Soft-X-Ray Diode Array Diagnostic System for JET. It was designed by the IPP under an Article 14 contract for Phase I. The diagnostics will be capable of measuring the Soft-X-ray emission from H and D plasmas in JET with high resolution in space and time. Two slot-hole cameras with 150 detectors viewing the same toroidal cross-section of the plasma are foreseen. Thin beryllium and aluminium filters in the line of sight of the detectors allow simultaneous measurements within different limits of the X-ray spectrum. Heavy shielding against neutron and gamma radiation is provided in order to reduce radiation induced signals and to increase detector lifetimes. The signals of 100 detectors can be simultaneously sampled with a sampling rate variable up to 250 KHz and stored in 12 bit memories of about 20 Kwords size. (orig.)

  2. Nucleobase-modified antisense oligonucleotides containing 5-(phenyltriazol)-2′-deoxyuridine nucleotides induce exon-skipping

    DEFF Research Database (Denmark)

    Le, Bao T.; Hornum, Mick; Sharma, Pawan K.

    2017-01-01

    Chemically-modified antisense oligonucleotide-mediated exon-skipping has been validated as a therapeutic strategy for tackling several disease pathologies, particularly duchenne muscular dystrophy. To date, only sugar-modified and internucleotide linkage-modified oligonucleotide chemistries have...

  3. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon].

    Science.gov (United States)

    Dmitrienko, E V; Pyshnaia, I A; Pyshnyĭ, D V

    2010-01-01

    The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

  4. Oral tongue cancer gene expression profiling: Identification of novel potential prognosticators by oligonucleotide microarray analysis

    International Nuclear Information System (INIS)

    Estilo, Cherry L; Boyle, Jay O; Kraus, Dennis H; Patel, Snehal; Shaha, Ashok R; Wong, Richard J; Huryn, Joseph M; Shah, Jatin P; Singh, Bhuvanesh; O-charoenrat, Pornchai; Talbot, Simon; Socci, Nicholas D; Carlson, Diane L; Ghossein, Ronald; Williams, Tijaana; Yonekawa, Yoshihiro; Ramanathan, Yegnanarayana

    2009-01-01

    The present study is aimed at identifying potential candidate genes as prognostic markers in human oral tongue squamous cell carcinoma (SCC) by large scale gene expression profiling. The gene expression profile of patients (n=37) with oral tongue SCC were analyzed using Affymetrix HG-U95Av2 high-density oligonucleotide arrays. Patients (n=20) from which there were available tumor and matched normal mucosa were grouped into stage (early vs. late) and nodal disease (node positive vs. node negative) subgroups and genes differentially expressed in tumor vs. normal and between the subgroups were identified. Three genes, GLUT3, HSAL2, and PACE4, were selected for their potential biological significance in a larger cohort of 49 patients via quantitative real-time RT-PCR. Hierarchical clustering analyses failed to show significant segregation of patients. In patients (n=20) with available tumor and matched normal mucosa, 77 genes were found to be differentially expressed (P< 0.05) in the tongue tumor samples compared to their matched normal controls. Among the 45 over-expressed genes, MMP-1 encoding interstitial collagenase showed the highest level of increase (average: 34.18 folds). Using the criterion of two-fold or greater as overexpression, 30.6%, 24.5% and 26.5% of patients showed high levels of GLUT3, HSAL2 and PACE4, respectively. Univariate analyses demonstrated that GLUT3 over-expression correlated with depth of invasion (P<0.0001), tumor size (P=0.024), pathological stage (P=0.009) and recurrence (P=0.038). HSAL2 was positively associated with depth of invasion (P=0.015) and advanced T stage (P=0.047). In survival studies, only GLUT3 showed a prognostic value with disease-free (P=0.049), relapse-free (P=0.002) and overall survival (P=0.003). PACE4 mRNA expression failed to show correlation with any of the relevant parameters. The characterization of genes identified to be significant predictors of prognosis by oligonucleotide microarray and further validation by

  5. Filter arrays

    Science.gov (United States)

    Page, Ralph H.; Doty, Patrick F.

    2017-08-01

    The various technologies presented herein relate to a tiled filter array that can be used in connection with performance of spatial sampling of optical signals. The filter array comprises filter tiles, wherein a first plurality of filter tiles are formed from a first material, the first material being configured such that only photons having wavelengths in a first wavelength band pass therethrough. A second plurality of filter tiles is formed from a second material, the second material being configured such that only photons having wavelengths in a second wavelength band pass therethrough. The first plurality of filter tiles and the second plurality of filter tiles can be interspersed to form the filter array comprising an alternating arrangement of first filter tiles and second filter tiles.

  6. Cascading Constrained 2-D Arrays using Periodic Merging Arrays

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Laursen, Torben Vaarby

    2003-01-01

    We consider a method for designing 2-D constrained codes by cascading finite width arrays using predefined finite width periodic merging arrays. This provides a constructive lower bound on the capacity of the 2-D constrained code. Examples include symmetric RLL and density constrained codes...

  7. Design verification enhancement of field programmable gate array-based safety-critical I&C system of nuclear power plant

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Ibrahim [Department of Nuclear Engineering, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104 (Korea, Republic of); Jung, Jaecheon, E-mail: jcjung@kings.ac.kr [Department of Nuclear Power Plant Engineering, KEPCO International Nuclear Graduate School, 658-91 Haemaji-ro, Seosang-myeon, Ulju-gun, Ulsan 45014 (Korea, Republic of); Heo, Gyunyoung [Department of Nuclear Engineering, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104 (Korea, Republic of)

    2017-06-15

    Highlights: • An enhanced, systematic and integrated design verification approach is proposed for V&V of FPGA-based I&C system of NPP. • RPS bistable fixed setpoint trip algorithm is designed, analyzed, verified and discussed using the proposed approaches. • The application of integrated verification approach simultaneously verified the entire design modules. • The applicability of the proposed V&V facilitated the design verification processes. - Abstract: Safety-critical instrumentation and control (I&C) system in nuclear power plant (NPP) implemented on programmable logic controllers (PLCs) plays a vital role in safe operation of the plant. The challenges such as fast obsolescence, the vulnerability to cyber-attack, and other related issues of software systems have currently led to the consideration of field programmable gate arrays (FPGAs) as an alternative to PLCs because of their advantages and hardware related benefits. However, safety analysis for FPGA-based I&C systems, and verification and validation (V&V) assessments still remain important issues to be resolved, which are now become a global research point of interests. In this work, we proposed a systematic design and verification strategies from start to ready-to-use in form of model-based approaches for FPGA-based reactor protection system (RPS) that can lead to the enhancement of the design verification and validation processes. The proposed methodology stages are requirement analysis, enhanced functional flow block diagram (EFFBD) models, finite state machine with data path (FSMD) models, hardware description language (HDL) code development, and design verifications. The design verification stage includes unit test – Very high speed integrated circuit Hardware Description Language (VHDL) test and modified condition decision coverage (MC/DC) test, module test – MATLAB/Simulink Co-simulation test, and integration test – FPGA hardware test beds. To prove the adequacy of the proposed

  8. Design verification enhancement of field programmable gate array-based safety-critical I&C system of nuclear power plant

    International Nuclear Information System (INIS)

    Ahmed, Ibrahim; Jung, Jaecheon; Heo, Gyunyoung

    2017-01-01

    Highlights: • An enhanced, systematic and integrated design verification approach is proposed for V&V of FPGA-based I&C system of NPP. • RPS bistable fixed setpoint trip algorithm is designed, analyzed, verified and discussed using the proposed approaches. • The application of integrated verification approach simultaneously verified the entire design modules. • The applicability of the proposed V&V facilitated the design verification processes. - Abstract: Safety-critical instrumentation and control (I&C) system in nuclear power plant (NPP) implemented on programmable logic controllers (PLCs) plays a vital role in safe operation of the plant. The challenges such as fast obsolescence, the vulnerability to cyber-attack, and other related issues of software systems have currently led to the consideration of field programmable gate arrays (FPGAs) as an alternative to PLCs because of their advantages and hardware related benefits. However, safety analysis for FPGA-based I&C systems, and verification and validation (V&V) assessments still remain important issues to be resolved, which are now become a global research point of interests. In this work, we proposed a systematic design and verification strategies from start to ready-to-use in form of model-based approaches for FPGA-based reactor protection system (RPS) that can lead to the enhancement of the design verification and validation processes. The proposed methodology stages are requirement analysis, enhanced functional flow block diagram (EFFBD) models, finite state machine with data path (FSMD) models, hardware description language (HDL) code development, and design verifications. The design verification stage includes unit test – Very high speed integrated circuit Hardware Description Language (VHDL) test and modified condition decision coverage (MC/DC) test, module test – MATLAB/Simulink Co-simulation test, and integration test – FPGA hardware test beds. To prove the adequacy of the proposed

  9. Mechanism of inhibition of HIV-1 integrase by G-tetrad-forming oligonucleotides in Vitro.

    Science.gov (United States)

    Jing, N; Marchand, C; Liu, J; Mitra, R; Hogan, M E; Pommier, Y

    2000-07-14

    The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.

  10. Microbial Diagnostic Array Workstation (MDAW: a web server for diagnostic array data storage, sharing and analysis

    Directory of Open Access Journals (Sweden)

    Chang Yung-Fu

    2008-09-01

    Full Text Available Abstract Background Microarrays are becoming a very popular tool for microbial detection and diagnostics. Although these diagnostic arrays are much simpler when compared to the traditional transcriptome arrays, due to the high throughput nature of the arrays, the data analysis requirements still form a bottle neck for the widespread use of these diagnostic arrays. Hence we developed a new online data sharing and analysis environment customised for diagnostic arrays. Methods Microbial Diagnostic Array Workstation (MDAW is a database driven application designed in MS Access and front end designed in ASP.NET. Conclusion MDAW is a new resource that is customised for the data analysis requirements for microbial diagnostic arrays.

  11. Oligonucleotides with 1,4-dioxane-based nucleotide monomers

    DEFF Research Database (Denmark)

    Madsen, Andreas S; Wengel, Jesper

    2012-01-01

    An epimeric mixture of H-phosphonates 5R and 5S has been synthesized in three steps from known secouridine 1. Separation of the epimers has been accomplished by RP-HPLC, allowing full characterization and incorporation of monomers X and Y into 9-mer oligonucleotides using H-phosphonates building...... blocks 5R and 5S, respectively. A single incorporation of either monomer X or monomer Y in the central position of a DNA 9-mer results in decreased thermal affinity toward both DNA and RNA complements (ΔT(m) = -3.5 °C/-3.5 °C for monomer X and ΔT(m) = -11.0 °C/-6.5 °C for monomer Y). CD measurements do...

  12. The Spectral Properties and Photostability of DNA, RNA and Oligonucleotides

    International Nuclear Information System (INIS)

    Kudrya, V.Yu.; Yashchuk, V.M.

    2012-01-01

    The present work discusses the results of comparative investigations of the optical absorption, luminescence, and photostability of the biomacromolecules (DNA, RNA), as well as synthetic poly- and oligonucleotides. The separate nucleotides in DNA and RNA are examined as almost independent absorbing centers. It is confirmed that the main triplet excitons traps responsible for the DNA phosphorescence emission are AT-complexes in DNA. In contrast to DNA, the main triplet excitons traps in RNA are adenosine bases. These bases are the most photostable against UV-irradiation as compared with all other nucleotides in both DNA and RNA. The fact of the photostability of adenosine bases and the AT-complex provides the existence of the DNA/RNA self-protection mechanisms against a damage caused by UV-irradiation. It is found the deoxyribonucleotides are more photostable than the corresponding ribonucleotides. So, the results presented here show that DNA is more photostable than RNA.

  13. Electrical manipulation of oligonucleotides grafted to charged surfaces.

    Science.gov (United States)

    Rant, Ulrich; Arinaga, Kenji; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard; Tornow, Marc

    2006-09-21

    The electrical manipulation of short DNA molecules on surfaces offers novel functionalities with fascinating possibilities in the field of bio-interfaces. Here we present systematic investigations of the electrical interactions which govern the structure of oligonucleotides on charged gold surfaces. Successively, we address influences of the applied field strength, the role of DC electrode potentials, in particular for polycrystalline surfaces, as well as screening effects of the surrounding electrolyte solution. Data obtained for single and double stranded DNA exhibit differences which can be attributed to the dissimilar flexibility of the different molecular conformations. A comparison of the experimental results with a basic model shows how the alignment of the molecules adjusts according to a balance between electrically induced ordering and stochastic thermal motions. The presented conclusions are expected to be of general relevance for the behaviour of polyelectrolytes exposed to localized electric fields at interfaces.

  14. Stereospecificity of oligonucleotide interactions revisited: no evidence for heterochiral hybridization and ribozyme/DNAzyme activity.

    Directory of Open Access Journals (Sweden)

    Kai Hoehlig

    Full Text Available A major challenge for the application of RNA- or DNA-oligonucleotides in biotechnology and molecular medicine is their susceptibility to abundant nucleases. One intriguing possibility to tackle this problem is the use of mirror-image (l-oligonucleotides. For aptamers, this concept has successfully been applied to even develop therapeutic agents, so-called Spiegelmers. However, for technologies depending on RNA/RNA or RNA/DNA hybridization, like antisense or RNA interference, it has not been possible to use mirror-image oligonucleotides because Watson-Crick base pairing of complementary strands is (thought to be stereospecific. Many scientists consider this a general principle if not a dogma. A recent publication proposing heterochiral Watson-Crick base pairing and sequence-specific hydrolysis of natural RNA by mirror-image ribozymes or DNAzymes (and vice versa prompted us to systematically revisit the stereospecificity of oligonucleotides hybridization and catalytic activity. Using hyperchromicity measurements we demonstrate that hybridization only occurs among homochiral anti-parallel complementary oligonucleotide strands. As expected, achiral PNA hybridizes to RNA and DNA irrespective of their chirality. In functional assays we could not confirm an alleged heterochiral hydrolytic activity of ribozymes or DNAzymes. Our results confirm a strict stereospecificity of oligonucleotide hybridization and clearly argue against the possibility to use mirror-image oligonucleotides for gene silencing or antisense applications.

  15. Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Xiaolong Wang

    Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

  16. Design and construction of hierarchical TiO2 nanorod arrays by combining layer-by-layer and hydrothermal crystallization techniques for electrochromic application

    Science.gov (United States)

    Chen, Yongbo; Li, Xiaomin; Bi, Zhijie; He, Xiaoli; Li, Guanjie; Xu, Xiaoke; Gao, Xiangdong

    2018-05-01

    The hierarchical TiO2 (H-TiO2) nanorod arrays (NRAs) composed of single-crystalline nanorods and nanocrystals were finely designed and successfully constructed for electrochromic (EC) application. By combining layer-by-layer (LBL) method and hydrothermal crystallization technique, the superfine nanocrystals (5-7 nm), which can provide abundant active sites and facilitate ion insertion/extraction during EC reactions, were uniformly and conformally assembled on the surface of single-crystalline TiO2 (SC-TiO2) NRAs. The as-formed H-TiO2 NRAs integrate the advantages of one-dimensional NRAs with fast kinetics and superfine nanocrystals with high ion capacity, showing highly enhanced EC performance. Large optical contrast (40.3%), shorter coloring/bleaching time (22/4 s), high coloration efficiency (11.2 cm2 C-1), and excellent cycling stability can be achieved in H-TiO2 NRAs, superior to the pristine SC-TiO2 NRAs and nanocrystalline TiO2 films. This work provides a feasible and well-designed strategy to explore high-performance materials for EC application.

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

    Science.gov (United States)

    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.

  18. mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models for In Silico Evaluation of Oligonucleotide Probes for Fluorescence In Situ Hybridization▿ †

    OpenAIRE

    Yilmaz, L. Safak; Parnerkar, Shreyas; Noguera, Daniel R.

    2010-01-01

    Mathematical models of RNA-targeted fluorescence in situ hybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.

  19. mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.

    Science.gov (United States)

    Yilmaz, L Safak; Parnerkar, Shreyas; Noguera, Daniel R

    2011-02-01

    Mathematical models of RNA-targeted fluorescence in situ hybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.

  20. Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis.

    Science.gov (United States)

    Kalendar, Ruslan; Tselykh, Timofey V; Khassenov, Bekbolat; Ramanculov, Erlan M

    2017-01-01

    This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP). It also contains a built-in program to design oligonucleotide sets both for long sequence assembly by ligase chain reaction and for design of amplicons that tile across a region(s) of interest. The software calculates the melting temperature for the standard and degenerate oligonucleotides including locked nucleic acid (LNA) and other modifications. It also provides analyses for a set of primers with the prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity as well as a primer dilution and resuspension calculator. The program consists of various bioinformatical tools for analysis of sequences with the GC or AT skew, CG% and GA% content, and the purine-pyrimidine skew. It also analyzes the linguistic sequence complexity and performs generation of random DNA sequence as well as restriction endonucleases analysis. The program allows to find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It performs efficient and complete detection of various repeat types with visual display. The FastPCR software allows the sequence file batch processing that is essential for automation. The program is available for download at http://primerdigital.com/fastpcr.html , and its online version is located at http://primerdigital.com/tools/pcr.html .

  1. Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes

    OpenAIRE

    Schwiertz, Andreas; Le Blay, Gwenaelle; Blaut, Michael

    2000-01-01

    Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none...

  2. Tomographic array

    International Nuclear Information System (INIS)

    1976-01-01

    The configuration of a tomographic array in which the object can rotate about its axis is described. The X-ray detector is a cylindrical screen perpendicular to the axis of rotation. The X-ray source has a line-shaped focus coinciding with the axis of rotation. The beam is fan-shaped with one side of this fan lying along the axis of rotation. The detector screen is placed inside an X-ray image multiplier tube

  3. Tomographic array

    International Nuclear Information System (INIS)

    1976-01-01

    A tomographic array with the following characteristics is described. An X-ray screen serving as detector is placed before a photomultiplier tube which itself is placed in front of a television camera connected to a set of image processors. The detector is concave towards the source and is replacable. Different images of the object are obtained simultaneously. Optical fibers and lenses are used for transmission within the system

  4. The Big Optical Array

    International Nuclear Information System (INIS)

    Mozurkewich, D.; Johnston, K.J.; Simon, R.S.

    1990-01-01

    This paper describes the design and the capabilities of the Naval Research Laboratory Big Optical Array (BOA), an interferometric optical array for high-resolution imaging of stars, stellar systems, and other celestial objects. There are four important differences between the BOA design and the design of Mark III Optical Interferometer on Mount Wilson (California). These include a long passive delay line which will be used in BOA to do most of the delay compensation, so that the fast delay line will have a very short travel; the beam combination in BOA will be done in triplets, to allow measurement of closure phase; the same light will be used for both star and fringe tracking; and the fringe tracker will use several wavelength channels

  5. Synthetic Method for Oligonucleotide Block by Using Alkyl-Chain-Soluble Support.

    Science.gov (United States)

    Matsuno, Yuki; Shoji, Takao; Kim, Shokaku; Chiba, Kazuhiro

    2016-02-19

    A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal nucleosides was developed. The Z-ACSS allowed for the preparation of fully protected deoxyribo- and ribo-oligonucleotides without chromatographic purification and released dimer- to tetramer-size oligonucleotide blocks via hydrogenation using a Pd/C catalyst without significant loss or migration of protective groups such as 5'-end 4,4'-dimethoxtrityl, 2-cyanoethyl on internucleotide bonds, or 2'-TBS.

  6. Solid-phase synthesis of 2{sup '}-O-methoxyethyl oligonucleotides using dimeric phosphoramidate blocks

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Gi Weon; Kang, Yong Han [Dept. of Applied Chemistry, Hanyang University, Ansan (Korea, Republic of)

    2016-11-15

    This research focused on the method of using dimeric phosphoramidite blocks to synthesize oligonucleotides for development as oligonucleotide drugs. A 16-mer oligonucleotide with the randomly selected sequence of C*C*T*C*G*C *T*C*T*C*G*C*C* C*G*C was synthesized using CC, GC, and TC dimers, a combination of monomers and dimers, or only monomers as building blocks. Using dimer blocks in this synthetic method provided a significant decrease in critical impurities that had similar properties to the main product, which was confirmed by LC-MS and HPLC analysis.

  7. Dielectric properties of DNA oligonucleotides on the surface of silicon nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Bagraev, N. T., E-mail: bagraev@mail.ioffe.ru [St. Petersburg Polytechnic University (Russian Federation); Chernev, A. L. [Russian Academy of Sciences, St. Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation); Klyachkin, L. E. [St. Petersburg Polytechnic University (Russian Federation); Malyarenko, A. M. [Russian Academy of Sciences, Ioffe Physical–Technical Institute (Russian Federation); Emel’yanov, A. K.; Dubina, M. V. [Russian Academy of Sciences, St. Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation)

    2016-10-15

    Planar silicon nanostructures that are formed as a very narrow silicon quantum well confined by δ barriers heavily doped with boron are used to study the dielectric properties of DNA oligonucleotides deposited onto the surface of the nanostructures. The capacitance characteristics of the silicon nanostructures with oligonucleotides deposited onto their surface are determined by recording the local tunneling current–voltage characteristics by means of scanning tunneling microscopy. The results show the possibility of identifying the local dielectric properties of DNA oligonucleotide segments consisting of repeating G–C pairs. These properties apparently give grounds to correlate the segments with polymer molecules exhibiting the properties of multiferroics.

  8. Design and operation of a high-heat flux, flush-mounted ‘rail’ Langmuir probe array on Alcator C-Mod

    Directory of Open Access Journals (Sweden)

    A.Q. Kuang

    2017-08-01

    Full Text Available A poloidal array of toroidally-extended, flush-mounted ‘rail’ Langmuir probes was recently installed on Alcator C-Mod's vertical target plate divertor. The aim was to investigate if a Langmuir probe array could be designed to survive reactor-level heat fluxes and have the ability to make measurements that could be reliably interpreted under reactor-level plasma densities, neutral densities and magnetic fields. Langmuir probes are typically built to have incident field-line angles >10° to avoid interpretation issues associated with sheath expansion. However, at the high parallel heat fluxes experienced in reactor-relevant conditions such a probe would quickly overheat and melt. To mitigate both the issues of extreme heat flux and sheath expansion, each probe was designed to be flush with the divertor surface, toroidally-extended and field-aligned, giving it a ‘rail’ geometry. The flush mounted probes have proven to be exceptionally robust surviving the 2015–2016 campaign – a first for a C-Mod probe system. Examination of the probe current-voltage (I-V characteristics reveals that they are immune to sheath expansion at incident field angles down to ∼0.5°. Comparison of the flush probes to traditional proud probes shows that both measure the same electron pressure across the divertor plate. However, there are significant and systematic differences in the density, temperature and floating potential. This suggests that there is important physics, perhaps unique to conditions in a vertical-target plate divertor with small field-line attack angles, that affects the I-V characteristics and is not currently included in probe data analyses. Finally, the probe response is examined in the ‘death-ray’ regime, just near detachment. Previous work using proud probes has suggested that the ‘death-ray’ is an artefact of the probe bias. However, on flush mounted probes the ‘death-ray’ manifests itself under different conditions, which

  9. Comparative analysis of human conjunctival and corneal epithelial gene expression with oligonucleotide microarrays.

    Science.gov (United States)

    Turner, Helen C; Budak, Murat T; Akinci, M A Murat; Wolosin, J Mario

    2007-05-01

    To determine global mRNA expression levels in corneal and conjunctival epithelia and identify transcripts that exhibit preferential tissue expression. cDNA samples derived from human conjunctival and corneal epithelia were hybridized in three independent experiments to a commercial oligonucleotide array representing more than 22,000 transcripts. The resultant signal intensities and microarray software transcript present/absent calls were used in conjunction with the local pooled error (LPE) statistical method to identify transcripts that are preferentially or exclusively expressed in one of the two tissues at significant levels (expression >1% of the beta-actin level). EASE (Expression Analysis Systematic Explorer software) was used to identify biological systems comparatively overrepresented in either epithelium. Immuno-, and cytohistochemistry was performed to validate or expand on selected results of interest. The analysis identified 332 preferential and 93 exclusive significant corneal epithelial transcripts. The corresponding numbers of conjunctival epithelium transcripts were 592 and 211, respectively. The overrepresented biological processes in the cornea were related to cell adhesion and oxiredox equilibria and cytoprotection activities. In the conjunctiva, the biological processes that were most prominent were related to innate immunity and melanogenesis. Immunohistochemistry for antigen-presenting cells and melanocytes was consistent with these gene signatures. The transcript comparison identified a substantial number of genes that have either not been identified previously or are not known to be highly expressed in these two epithelia, including testican-1, ECM1, formin, CRTAC1, and NQO1 in the cornea and, in the conjunctiva, sPLA(2)-IIA, lipocalin 2, IGFBP3, multiple MCH class II proteins, and the Na-Pi cotransporter type IIb. Comparative gene expression profiling leads to the identification of many biological processes and previously unknown genes that

  10. Maximum gain of Yagi-Uda arrays

    DEFF Research Database (Denmark)

    Bojsen, J.H.; Schjær-Jacobsen, Hans; Nilsson, E.

    1971-01-01

    Numerical optimisation techniques have been used to find the maximum gain of some specific parasitic arrays. The gain of an array of infinitely thin, equispaced dipoles loaded with arbitrary reactances has been optimised. The results show that standard travelling-wave design methods are not optimum....... Yagi–Uda arrays with equal and unequal spacing have also been optimised with experimental verification....

  11. Microneedle array electrode for human EEG recording.

    NARCIS (Netherlands)

    Lüttge, Regina; van Nieuwkasteele-Bystrova, Svetlana Nikolajevna; van Putten, Michel Johannes Antonius Maria; Vander Sloten, Jos; Verdonck, Pascal; Nyssen, Marc; Haueisen, Jens

    2009-01-01

    Microneedle array electrodes for EEG significantly reduce the mounting time, particularly by circumvention of the need for skin preparation by scrubbing. We designed a new replication process for numerous types of microneedle arrays. Here, polymer microneedle array electrodes with 64 microneedles,

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

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract 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

  13. Design of a phased array for the generation of adaptive radiation force along a path surrounding a breast lesion for dynamic ultrasound elastography imaging.

    Science.gov (United States)

    Ekeom, Didace; Hadj Henni, Anis; Cloutier, Guy

    2013-03-01

    This work demonstrates, with numerical simulations, the potential of an octagonal probe for the generation of radiation forces in a set of points following a path surrounding a breast lesion in the context of dynamic ultrasound elastography imaging. Because of the in-going wave adaptive focusing strategy, the proposed method is adapted to induce shear wave fronts to interact optimally with complex lesions. Transducer elements were based on 1-3 piezocomposite material. Three-dimensional simulations combining the finite element method and boundary element method with periodic boundary conditions in the elevation direction were used to predict acoustic wave radiation in a targeted region of interest. The coupling factor of the piezocomposite material and the radiated power of the transducer were optimized. The transducer's electrical impedance was targeted to 50 Ω. The probe was simulated by assembling the designed transducer elements to build an octagonal phased-array with 256 elements on each edge (for a total of 2048 elements). The central frequency is 4.54 MHz; simulated transducer elements are able to deliver enough power and can generate the radiation force with a relatively low level of voltage excitation. Using dynamic transmitter beamforming techniques, the radiation force along a path and resulting acoustic pattern in the breast were simulated assuming a linear isotropic medium. Magnitude and orientation of the acoustic intensity (radiation force) at any point of a generation path could be controlled for the case of an example representing a heterogeneous medium with an embedded soft mechanical inclusion.

  14. Evaluation of fluorine-18-labeled alkylating agents as potential synthons for the labeling of oligonucleotides

    NARCIS (Netherlands)

    de Vries, EFJ; Vroegh, J; Elsinga, PH; Vaalburg, W

    Six fluorine-18-labeled alkylating agents were selected as potentially suitable synthons for the labeling of antisense oligonucleotides. The selected synthons were evaluated in a model reaction with the monomer adenosine 5'-O-thiomonophosphate. Of these synthons,

  15. Novel approaches to study low-energy electron-induced damage to DNA oligonucleotides

    International Nuclear Information System (INIS)

    Rackwitz, Jenny; Bald, Ilko; Ranković, Miloš Lj; Milosavljević, Aleksandar R

    2015-01-01

    The novel approach of DNA origami structures as templates for precise quantification of various well- defined oligonucleotides provides the opportunity to determine the sensitivity of complex DNA sequences towards low-energy electrons. (paper)

  16. Functionalization of PVC membrane with ss oligonucleotides for a potentiometric biosensor.

    Science.gov (United States)

    Shishkanova, T V; Volf, R; Krondak, M; Král, V

    2007-05-15

    A novel application of a single stranded (ss) oligonucleotide as an active component of polymeric membrane in an ion-selective electrode (ISE) is described. The original oligonucleotides, oligo(dA)(15), modified by cholesterol, triphenylmethyl and hexadecyl derivatives, were immobilized into poly(vinyl chloride) (PVC) membrane using extraction protocol. In parallel, the adsorption protocol was used to immobilize unmodified oligo(dA)(15) on the PVC membrane based on tridodecylmethyammonium chloride (TDDMA(+)Cl(-)). Immobilization of ss oligonucleotide probe through spacer was more effective for the potentiometric detection of the hybridization between complementary oligonucleotides. It was found that cholesterol-oligo(dA)(15) modified membranes were sensitive toward complementary oligo(dT)(15) in the concentration range 2-80 nM at pH 7. An explanation for the detection mechanism is proposed.

  17. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection.

    Science.gov (United States)

    Jung, Il Young; Lee, Eun Hee; Suh, Ah Young; Lee, Seung Jin; Lee, Hyukjin

    2016-04-01

    Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.

  18. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  19. Rapid Induction of Protective Immunity Against Biothreat Agents Using CPG-Based Oligonucleotides

    National Research Council Canada - National Science Library

    Klinman, Dennis

    2003-01-01

    This research project examines the ability of synthetic oligonucleotides (ODN) containing immunostimulatory "CpG motifs' to trigger the innate immune system, thereby improving the host's ability to survive infection by biowarfare agents...

  20. Efficient assessment of modified nucleoside stability under conditions of automated oligonucleotide synthesis: characterization of the oxidation and oxidative desulfurization of 2-thiouridine.

    Science.gov (United States)

    Sochacka, E

    2001-01-01

    In order to efficiently assess the chemical stability of modified nucleosides to the reagents and conditions of automated oligonucleotide synthesis, we designed, developed and tested a scheme in which the modified nucleoside, directly attached to a solid support, is exposed to the cyclic chemistry of the instrument. Stability of 2-thiouridine against different oxidizers was investigated. Tertbutyl hydroperoxide (1 M) in anhydrous acetonitrile was a more effective oxidizer for the incorporation of 2-thiouridine into oligonucleotide chains than the same oxidizer in methylene chloride. Carbon tetrachloride/water in the presence of a basic catalyst was superior in maintaining the thiocarbonyl function, but its utility for RNA synthesis has yet to be fully tested, whereas 2-phenylsulfonyloxaziridine was a very efficient reagent for oxidative desulfurization of 2-thiouridine.

  1. Large scale biomimetic membrane arrays

    DEFF Research Database (Denmark)

    Hansen, Jesper Søndergaard; Perry, Mark; Vogel, Jörg

    2009-01-01

    To establish planar biomimetic membranes across large scale partition aperture arrays, we created a disposable single-use horizontal chamber design that supports combined optical-electrical measurements. Functional lipid bilayers could easily and efficiently be established across CO2 laser micro......-structured 8 x 8 aperture partition arrays with average aperture diameters of 301 +/- 5 mu m. We addressed the electro-physical properties of the lipid bilayers established across the micro-structured scaffold arrays by controllable reconstitution of biotechnological and physiological relevant membrane...... peptides and proteins. Next, we tested the scalability of the biomimetic membrane design by establishing lipid bilayers in rectangular 24 x 24 and hexagonal 24 x 27 aperture arrays, respectively. The results presented show that the design is suitable for further developments of sensitive biosensor assays...

  2. Structural Determinants of Photoreactivity of Triplex Forming Oligonucleotides Conjugated to Psoralens

    Science.gov (United States)

    Krishnan, Rajagopal; Oh, Dennis H.

    2010-01-01

    Triplex-forming oligonucleotides (TFOs) with both DNA and 2′-O-methyl RNA backbones can direct psoralen photoadducts to specific DNA sequences. However, the functional consequences of these differing structures on psoralen photoreactivity are unknown. We designed TFO sequences with DNA and 2′-O-methyl RNA backbones conjugated to psoralen by 2-carbon linkers and examined their ability to bind and target damage to model DNA duplexes corresponding to sequences within the human HPRT gene. While TFO binding affinity was not dramatically affected by the type of backbone, psoralen photoreactivity was completely abrogated by the 2′-O-methyl RNA backbone. Photoreactivity was restored when the psoralen was conjugated to the RNA TFO via a 6-carbon linker. In contrast to the B-form DNA of triplexes formed by DNA TFOs, the CD spectra of triplexes formed with 2′-O-methyl RNA TFOs exhibited features of A-form DNA. These results indicate that 2′-O-methyl RNA TFOs induce a partial B-to-A transition in their target DNA sequences which may impair the photoreactivity of a conjugated psoralen and suggest that optimal design of TFOs to target DNA damage may require a balance between binding ability and drug reactivity. PMID:20725628

  3. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

    Science.gov (United States)

    Kupriushkin, M S; Pyshnyĭ, D V

    2012-01-01

    Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

  4. Oligonucleotide Length-Dependent Formation of Virus-Like Particles.

    Science.gov (United States)

    Maassen, Stan J; de Ruiter, Mark V; Lindhoud, Saskia; Cornelissen, Jeroen J L M

    2018-05-23

    Understanding the assembly pathway of viruses can contribute to creating monodisperse virus-based materials. In this study, the cowpea chlorotic mottle virus (CCMV) is used to determine the interactions between the capsid proteins of viruses and their cargo. The assembly of the capsid proteins in the presence of different lengths of short, single-stranded (ss) DNA is studied at neutral pH, at which the protein-protein interactions are weak. Chromatography, electrophoresis, microscopy, and light scattering data show that the assembly efficiency and speed of the particles increase with increasing length of oligonucleotides. The minimal length required for assembly under the conditions used herein is 14 nucleotides. Assembly of particles containing such short strands of ssDNA can take almost a month. This slow assembly process enabled the study of intermediate states, which confirmed a low cooperative assembly for CCMV and allowed for further expansion of current assembly theories. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Selective Covalent Conjugation of Phosphorothioate DNA Oligonucleotides with Streptavidin

    Directory of Open Access Journals (Sweden)

    Christof M. Niemeyer

    2011-08-01

    Full Text Available Protein-DNA conjugates have found numerous applications in the field of diagnostics and nanobiotechnology, however, their intrinsic susceptibility to DNA degradation by nucleases represents a major obstacle for many applications. We here report the selective covalent conjugation of the protein streptavidin (STV with phosphorothioate oligonucleotides (psDNA containing a terminal alkylthiolgroup as the chemically addressable linking unit, using a heterobifunctional NHS-/maleimide crosslinker. The psDNA-STV conjugates were synthesized in about 10% isolated yields. We demonstrate that the terminal alkylthiol group selectively reacts with the maleimide while the backbone sulfur atoms are not engaged in chemical conjugation. The novel psDNA-STV conjugates retain their binding capabilities for both biotinylated macromolecules and the complementary nucleic acid. Moreover, the psDNA-STV conjugate retained its binding capacity for complementary oligomers even after a nuclease digestion step, which effectively degrades deoxyribonucleotide oligomers and thus the binding capability of regular DNA-STV conjugates. The psDNA-STV therefore hold particular promise for applications e.g. in proteome research and novel biosensing devices, where interfering endogenous nucleic acids need to be removed from analytes by nuclease digestion.

  6. Characterization of adjacent breast tumors using oligonucleotide microarrays

    International Nuclear Information System (INIS)

    Unger, Meredith A; Rishi, Mazhar; Clemmer, Virginia B; Hartman, Jennifer L; Keiper, Elizabeth A; Greshock, Joel D; Chodosh, Lewis A; Liebman, Michael N; Weber, Barbara L

    2001-01-01

    Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles. Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip ® (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite ® 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN ® 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics. The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710. Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making

  7. Advancements of antisense oligonucleotides in treatment of breast cancer

    Institute of Scientific and Technical Information of China (English)

    YANGShuan-Ping; SONGSan-Tai; 等

    2003-01-01

    Breast cancer is one kind of multi-gene related malignancy.Overexpression of some oncogenes such as HER-2(c-erbB-2,Neu),bcl-2/bcl-xL,protein kinase A(PKA),and transferrin receptor gene(TfR gene),etc significantly affect the prognosis of breast cancer.It was shown that specific suppression of the overexpressed genes above resulted in the improvement of the therapy of breast cancer.Antisense interference.one of useful tools for inhibiting the overexpression of specific oncogenes,was involved in the therapy of breast cancer in recent years. Data indicated that antisense oligonucleotides(ON)could inhibit specially the expression of the target genes on mRNA or protein levels in most of cases;some ON candidates showed encouraging therapeutic effects in vitro and in vivo on breast cancer cell lines or xenografts.Furthermore,the combination use of the antisense ON and normal chemotherapeutic agents indicated synergistic antitumor effects,which was probably the best utilization of antisense ON in the treatment of breast cancer.

  8. Methods for the preparation of protein-oligonucleotide-lipid constructs.

    Science.gov (United States)

    Takasaki, Jennifer; Raney, Sameersingh G; Chikh, Ghania; Sekirov, Laura; Brodsky, Irina; Tam, Ying; Ansell, Steven M

    2006-01-01

    A mixture of ionizable cationic lipids, steric barrier lipids, and colipids is used to encapsulate oligonucleotide DNA in lipidic particles called SALP. This material is under development as an adjuvant for vaccines. Previously we have shown that coupling the antigen directly to the surface of SALP can lead to enhanced immunological responses in vivo. Two different methods for preparing ovalbumin-SALP were assessed in this work. Originally the conjugates were prepared by treating SALP containing a maleimide-derivatized lipid with thiolated ovalbumin, a method we refer to as active coupling. This reaction was found to be difficult to control and generally resulted in low coupling efficiencies. The issues relating to this approach were characterized. We have recently developed alternative techniques based on first coupling ovalbumin to a micelle and then incubating the resultant product with SALP, methods we refer to as passive coupling. We have shown that this method allows accurate control of the levels of protein associated SALP and does not suffer from surface saturation effects seen with the active coupling method that places maximum limits on the amount of protein that can be coupled to the SALP surface. The products from the passive coupling protocol are shown to have activity comparable to those derived from the active coupling protocol in investigations of in vivo immune responses.

  9. The use of oligonucleotide aptamers in cancer therapy

    Directory of Open Access Journals (Sweden)

    Adrian Odrzywolski

    2016-05-01

    Full Text Available Aptamers are a new class of molecules which originated in the 1990s. They are usually RNA or DNA oligonucleotides, the length of which ranges between 20 and 80 nt. They are produced using the SELEX method that allows one to obtain aptamers that bind to virtually any molecule of interest, providing a high specificity. Aptamers are an alternative to antibodies because on the one hand, their sensitivity is at a similar or sometimes even higher level, while on the other hand they do not show immunogenicity, and may be synthesized in vitro. To date, a broad range of different applications of aptamers has been described: as components of biosensors, or use in various laboratory techniques, such as microarrays or chromatography. One of the most important is the use of aptamers in medicine, especially in the fight against cancer. They can be used both for diagnosis and for the eradication of cancers – particularly through the delivery of drugs. Currently, most transport-related research is devoted to the delivery of chemotherapeutic drugs, such as doxorubicin. This was used in research on liver cancer cells, prostate, and acute lymphoblastic leukemia blast cells. Another possibility is to use aptamers to deliver siRNAs. In this way inhibition of the quality control process of the mRNA in tumor cells is possible. An aptamer complex with the drug allows for direct delivery of the active substance in a particular cell type, substantially eliminating the non-specific effect of the drug.

  10. Syntheses of prodrug-type phosphotriester oligonucleotides responsive to intracellular reducing environment for improvement of cell membrane permeability and nuclease resistance.

    Science.gov (United States)

    Hayashi, Junsuke; Samezawa, Yusuke; Ochi, Yosuke; Wada, Shun-Ichi; Urata, Hidehito

    2017-07-15

    We synthesized prodrug-type phosphotriester (PTE) oligonucleotides containing the six-membered cyclic disulfide moiety by using phosphoramidite chemistry. Prodrug-type oligonucleotides named "Reducing-Environment-Dependent Uncatalyzed Chemical Transforming (REDUCT) PTE oligonucleotides" were converted into natural oligonucleotides under cytosol-mimetic reductive condition. Furthermore, the REDUCT PTE oligonucleotides were robust to nuclease digestion and exhibited good cell membrane permeability. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. In vitro transcription in the presence of DNA oligonucleotides can generate strong anomalous initiation sites.

    Science.gov (United States)

    Chow, C W; Clark, M P; Rinaldo, J E; Chalkley, R

    1996-03-01

    In the present study, we have explored an unexpected observation in transcription initiation that is mediated by single-stranded oligonucleotides. Initially, our goal was to understand the function of different upstream regulatory elements/initiation sites in the rat xanthine dehydrogenase/oxidase (XDH/XO) promoter. We performed in vitro transcription with HeLa nuclear extracts in the presence of different double-stranded oligonucleotides against upstream elements as competitors. A new and unusual transcription initiation site was detected by primer extension. This new initiation site maps to the downstream region of the corresponding competitor. Subsequent analyses have indicated that the induction of a new transcription initiation site is anomalous which is due to the presence of a small amount of single-stranded oligonucleotide in the competitor. We found that this anomalous initiation site is insensitive to the orientation of the promoter and requires only a small amount of single-stranded oligonucleotide (< 2-fold molar excess relative to template). We surmise that a complementary interaction between the single-stranded oligonucleotide and transiently denatured promoter template may be responsible for this sequence-specific transcription initiation artifact. To study the regulation of transcription initiation by in vitro transcription approaches, we propose that one should probe the effect of removing transacting factors by adding an excess of a cognate oligonucleotide which does not bear exact sequence identity to the template.

  12. Digital electrostatic acoustic transducer array

    KAUST Repository

    Carreno, Armando Arpys Arevalo

    2016-12-19

    In this paper we present the fabrication and characterization of an array of electrostatic acoustic transducers. The array is micromachined on a silicon wafer using standard micro-machining techniques. Each array contains 2n electrostatic transducer membranes, where “n” is the bit number. Every element of the array has a hexagonal membrane shape structure, which is separated from the substrate by 3µm air gap. The membrane is made out 5µm thick polyimide layer that has a bottom gold electrode on the substrate and a gold top electrode on top of the membrane (250nm). The wafer layout design was diced in nine chips with different array configurations, with variation of the membrane dimensions. The device was tested with 90 V giving and sound output level as high as 35dB, while actuating all the elements at the same time.

  13. Digital electrostatic acoustic transducer array

    KAUST Repository

    Carreno, Armando Arpys Arevalo; Castro, David; Conchouso Gonzalez, David; Kosel, Jü rgen; Foulds, Ian G.

    2016-01-01

    In this paper we present the fabrication and characterization of an array of electrostatic acoustic transducers. The array is micromachined on a silicon wafer using standard micro-machining techniques. Each array contains 2n electrostatic transducer membranes, where “n” is the bit number. Every element of the array has a hexagonal membrane shape structure, which is separated from the substrate by 3µm air gap. The membrane is made out 5µm thick polyimide layer that has a bottom gold electrode on the substrate and a gold top electrode on top of the membrane (250nm). The wafer layout design was diced in nine chips with different array configurations, with variation of the membrane dimensions. The device was tested with 90 V giving and sound output level as high as 35dB, while actuating all the elements at the same time.

  14. Processes for design, construction and utilisation of arrays of light-emitting diodes and light-emitting diode-coupled optical fibres for multi-site brain light delivery.

    Science.gov (United States)

    Bernstein, Jacob G; Allen, Brian D; Guerra, Alexander A; Boyden, Edward S

    2015-05-01

    Optogenetics enables light to be used to control the activity of genetically targeted cells in the living brain. Optical fibers can be used to deliver light to deep targets, and LEDs can be spatially arranged to enable patterned light delivery. In combination, arrays of LED-coupled optical fibers can enable patterned light delivery to deep targets in the brain. Here we describe the process flow for making LED arrays and LED-coupled optical fiber arrays, explaining key optical, electrical, thermal, and mechanical design principles to enable the manufacturing, assembly, and testing of such multi-site targetable optical devices. We also explore accessory strategies such as surgical automation approaches as well as innovations to enable low-noise concurrent electrophysiology.

  15. Synthesis, hybridization characteristics, and fluorescence properties of oligonucleotides modified with nucleobase-functionalized locked nucleic acid adenosine and cytidine monomers.

    Science.gov (United States)

    Kaura, Mamta; Kumar, Pawan; Hrdlicka, Patrick J

    2014-07-03

    Conformationally restricted nucleotides such as locked nucleic acid (LNA) are very popular as affinity-, specificity-, and stability-enhancing modifications in oligonucleotide chemistry to produce probes for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. Considerable efforts have been devoted in recent years to optimize the biophysical properties of LNA through additional modification of the sugar skeleton. We recently introduced C5-functionalization of LNA uridines as an alternative and synthetically more straightforward approach to improve the biophysical properties of LNA. In the present work, we set out to test the generality of this concept by studying the characteristics of oligonucleotides modified with four different C5-functionalized LNA cytidine and C8-functionalized LNA adenosine monomers. The results strongly suggest that C5-functionalization of LNA pyrimidines is indeed a viable approach for improving the binding affinity, target specificity, and/or enzymatic stability of LNA-modified ONs, whereas C8-functionalization of LNA adenosines is detrimental to binding affinity and specificity. These insights will impact the future design of conformationally restricted nucleotides for nucleic acid targeting applications.

  16. A statistical method for predicting splice variants between two groups of samples using GeneChip® expression array data

    Directory of Open Access Journals (Sweden)

    Olson James M

    2006-04-01

    Full Text Available Abstract Background Alternative splicing of pre-messenger RNA results in RNA variants with combinations of selected exons. It is one of the essential biological functions and regulatory components in higher eukaryotic cells. Some of these variants are detectable with the Affymetrix GeneChip® that uses multiple oligonucleotide probes (i.e. probe set, since the target sequences for the multiple probes are adjacent within each gene. Hybridization intensity from a probe correlates with abundance of the corresponding transcript. Although the multiple-probe feature in the current GeneChip® was designed to assess expression values of individual genes, it also measures transcriptional abundance for a sub-region of a gene sequence. This additional capacity motivated us to develop a method to predict alternative splicing, taking advance of extensive repositories of GeneChip® gene expression array data. Results We developed a two-step approach to predict alternative splicing from GeneChip® data. First, we clustered the probes from a probe set into pseudo-exons based on similarity of probe intensities and physical adjacency. A pseudo-exon is defined as a sequence in the gene within which multiple probes have comparable probe intensity values. Second, for each pseudo-exon, we assessed the statistical significance of the difference in probe intensity between two groups of samples. Differentially expressed pseudo-exons are predicted to be alternatively spliced. We applied our method to empirical data generated from GeneChip® Hu6800 arrays, which include 7129 probe sets and twenty probes per probe set. The dataset consists of sixty-nine medulloblastoma (27 metastatic and 42 non-metastatic samples and four cerebellum samples as normal controls. We predicted that 577 genes would be alternatively spliced when we compared normal cerebellum samples to medulloblastomas, and predicted that thirteen genes would be alternatively spliced when we compared metastatic

  17. Functional oligonucleotide recognition nanomodules for electrochemical DNA biosensors

    OpenAIRE

    Campàs i Homs, Mònica

    2002-01-01

    El objetivo de esta tesis ha sido diseñar, caracterizar y optimizar un array de sensores de ADN electroquímico. Para el estudio de la inmovilización de las sondas de oligonucleótidos y la detección de la hibridación se realizaron experimentos preliminares con un sistema simplificado. Dicho sistema demostró que las monocapas auto-ensambladas (SAMs) en superficies de oro eran apropiadas como método de inmovilización. Debido al rápido desarrollo de los sensores de ADN hacia los arrays de ADN, se...

  18. Fundamentals of ultrasonic phased arrays

    CERN Document Server

    Schmerr, Lester W

    2014-01-01

    This book describes in detail the physical and mathematical foundations of ultrasonic phased array measurements.?The book uses linear systems theory to develop a comprehensive model of the signals and images that can be formed with phased arrays. Engineers working in the field of ultrasonic nondestructive evaluation (NDE) will find in this approach a wealth of information on how to design, optimize and interpret ultrasonic inspections with phased arrays. The fundamentals and models described in the book will also be of significant interest to other fields, including the medical ultrasound and

  19. Antitumor effects of radioiodinated antisense oligonucleotide mediated by VIP receptor

    International Nuclear Information System (INIS)

    Ou Xiaohong; Tan Tianzhi; Li Yunchun; Kuang Anren

    2004-01-01

    Purpose: we had constructed a targeting delivery system based on intestinal peptide (VIP) for antisense oligonucleotide (ASON) transfer into VIP receptor-positive cells in previous study. The aims of present studies are to observe the antitumor effect of VIP-131I-ASON in HT29 human colon adenocarcinoma xenografts. Methods: A 15-met phosphorothioate ASON, which was complementary to the translation start region of the C-myc oncogene mRNA, was labeled with 131I and the labelled compound was linked to the VIP bound covalently 'to a polylysine chain so as to deliver oligonucleotide into tumor cells. Distribution experiments for evaluating the radiolabeled antisense complexe uptake in tumor tissue were performed in BALB/c nude mice bearing with HT29 tumor xenografts. Nude mice beating HT29 tumor xenografts were adminstered VIP-131I-ASON (3.7,7.4 MBq) or 131I-ASON (3.7 MBq), 131I labeled control sense and nosense DNA (3.7 MBq), or saline. Antitumor effects were assessed using endpoints of tumor growth delay. C-myc-encoded protein expression of tumor was measured by immunocytohistochemical staining. Results: Distribution experiment performed with athymic mice bearing human colon tumor xenografts revealed maximal accumulation of conjugated ASON in the tumor tissue 2 h after administration and significantly higher than that in nude mice injected unconjngated ASON [(5.89±1.03)%ID/g and(1.56±0.31)%ID/g, respectively; t=7.7954 P<0.001]. The radioratio of tumor to muscle was peaked 4h after administration. VIP-131I-ASON exhibited strong antitumor effects against HT29 xenografts, decreasing their growth rate 7-fold compare with that in saline-treated mice(tumor growth delay, 25.4±0.89 day). The antitumor effects of unconjugated 131I-ASON were much less profound than VIP-131I-ASON (tumor growth delay, 3.2±1.3 and 25.4±0.89 day, respectively; q=51.4126 P<0.01). Sense, nosense control ON with VIP carder caused no therapeutic effect. There was no progressive weight loss or

  20. Photovoltaic array: Power conditioner interface characteristics

    Science.gov (United States)

    Gonzalez, C. C.; Hill, G. M.; Ross, R. G., Jr.

    1982-01-01

    The electrical output (power, current, and voltage) of flat plate solar arrays changes constantly, due primarily to changes in cell temperature and irradiance level. As a result, array loads such as dc-to-ac power conditioners must be capable of accommodating widely varying input levels while maintaining operation at or near the maximum power point of the array. The array operating characteristics and extreme output limits necessary for the systematic design of array load interfaces under a wide variety of climatic conditions are studied. A number of interface parameters are examined, including optimum operating voltage, voltage energy, maximum power and current limits, and maximum open circuit voltage. The effect of array degradation and I-V curve fill factor or the array power conditioner interface is also discussed. Results are presented as normalized ratios of power conditioner parameters to array parameters, making the results universally applicable to a wide variety of system sizes, sites, and operating modes.