Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

PubMed

Sewer, Alain; Gubian, Sylvain; Kogel, Ulrike; Veljkovic, Emilija; Han, Wanjiang; Hengstermann, Arnd; Peitsch, Manuel C; Hoeng, Julia

2014-05-17

High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression

PubMed Central

2014-01-01

Background High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Results Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the “common reference design” and processed as “pseudo-single-channel”. They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription–polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Conclusions Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository. PMID:24886675

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

PubMed Central

Laubinger, Sascha; Zeller, Georg; Henz, Stefan R; Sachsenberg, Timo; Widmer, Christian K; Naouar, Naïra; Vuylsteke, Marnik; Schölkopf, Bernhard; Rätsch, Gunnar; Weigel, Detlef

2008-01-01

Gene expression maps for model organisms, including Arabidopsis thaliana, have typically been created using gene-centric expression arrays. Here, we describe a comprehensive expression atlas, Arabidopsis thaliana Tiling Array Express (At-TAX), which is based on whole-genome tiling arrays. We demonstrate that tiling arrays are accurate tools for gene expression analysis and identified more than 1,000 unannotated transcribed regions. Visualizations of gene expression estimates, transcribed regions, and tiling probe measurements are accessible online at the At-TAX homepage. PMID:18613972

Analysis of microRNA and gene expression profiling in triazole fungicide-treated HepG2 cell line.

PubMed

An, Yu Ri; Kim, Seung Jun; Oh, Moon-Ju; Kim, Hyun-Mi; Shim, Il-Seob; Kim, Pil-Je; Choi, Kyunghee; Hwang, Seung Yong

2013-01-07

MicroRNA (miRNA) plays an important role in various diseases and in cellular and molecular responses to toxicants. In the present study, we investigated differential expression of miRNAs in response to three triazole fungicides (myclobutanil, propiconazole, and triadimefon). The human hepatoma cell line (HepG2) was treated with the above triazoles for 3 h or 48 h. miRNA-based microarray experiments were carried out using the Agilent human miRNA v13 array. At early exposure (3h), six miRNAs were differentially expressed and at late exposure (48 h), three miRNAs were significantly expressed. Overall, this study provides an array of potential biomarkers for the above triazole fungicides. Furthermore, these miRNAs induced by triazoles could be the foundation for the development of a miRNA-based toxic biomarker library that can predict environmental toxicity. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Course 10: Three Lectures on Biological Networks

NASA Astrophysics Data System (ADS)

Magnasco, M. O.

1 Enzymatic networks. Proofreading knots: How DNA topoisomerases disentangle DNA 1.1 Length scales and energy scales 1.2 DNA topology 1.3 Topoisomerases 1.4 Knots and supercoils 1.5 Topological equilibrium 1.6 Can topoisomerases recognize topology? 1.7 Proposal: Kinetic proofreading 1.8 How to do it twice 1.9 The care and proofreading of knots 1.10 Suppression of supercoils 1.11 Problems and outlook 1.12 Disquisition 2 Gene expression networks. Methods for analysis of DNA chip experiments 2.1 The regulation of gene expression 2.2 Gene expression arrays 2.3 Analysis of array data 2.4 Some simplifying assumptions 2.5 Probeset analysis 2.6 Discussion 3 Neural and gene expression networks: Song-induced gene expression in the canary brain 3.1 The study of songbirds 3.2 Canary song 3.3 ZENK 3.4 The blush 3.5 Histological analysis 3.6 Natural vs. artificial 3.7 The Blush II: gAP 3.8 Meditation

BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments

PubMed Central

2012-01-01

Background It is known from recent studies that more than 90% of human multi-exon genes are subject to Alternative Splicing (AS), a key molecular mechanism in which multiple transcripts may be generated from a single gene. It is widely recognized that a breakdown in AS mechanisms plays an important role in cellular differentiation and pathologies. Polymerase Chain Reactions, microarrays and sequencing technologies have been applied to the study of transcript diversity arising from alternative expression. Last generation Affymetrix GeneChip Human Exon 1.0 ST Arrays offer a more detailed view of the gene expression profile providing information on the AS patterns. The exon array technology, with more than five million data points, can detect approximately one million exons, and it allows performing analyses at both gene and exon level. In this paper we describe BEAT, an integrated user-friendly bioinformatics framework to store, analyze and visualize exon arrays datasets. It combines a data warehouse approach with some rigorous statistical methods for assessing the AS of genes involved in diseases. Meta statistics are proposed as a novel approach to explore the analysis results. BEAT is available at http://beat.ba.itb.cnr.it. Results BEAT is a web tool which allows uploading and analyzing exon array datasets using standard statistical methods and an easy-to-use graphical web front-end. BEAT has been tested on a dataset with 173 samples and tuned using new datasets of exon array experiments from 28 colorectal cancer and 26 renal cell cancer samples produced at the Medical Genetics Unit of IRCCS Casa Sollievo della Sofferenza. To highlight all possible AS events, alternative names, accession Ids, Gene Ontology terms and biochemical pathways annotations are integrated with exon and gene level expression plots. The user can customize the results choosing custom thresholds for the statistical parameters and exploiting the available clinical data of the samples for a multivariate AS analysis. Conclusions Despite exon array chips being widely used for transcriptomics studies, there is a lack of analysis tools offering advanced statistical features and requiring no programming knowledge. BEAT provides a user-friendly platform for a comprehensive study of AS events in human diseases, displaying the analysis results with easily interpretable and interactive tables and graphics. PMID:22536968

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.

PubMed

Chitturi, Neelima; Balagannavar, Govindkumar; Chandrashekar, Darshan S; Abinaya, Sadashivam; Srini, Vasan S; Acharya, Kshitish K

2013-12-27

Standard 3' Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentially expressed genes, but not their alternatively spliced transcript forms. No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this. We report a web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. The tool has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition). About 4000 gene expression datasets were downloaded from a public repository. 'Good probes' with complete coverage and identity to latest reference transcript sequences were first identified. Using them, 'Transcript specific probe-clusters' were derived for each platform and used to identify expression status of possible transcripts. The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers. It can identify, in the tissues and conditions of interest, about 40% of known transcripts as 'transcribed', 'not-detected' or 'differentially regulated'. Corresponding additional information for probes, genes, transcripts and proteins can be viewed too. We identified the expression of transcripts in a specific clinical condition and validated a few of these transcripts by experiments (using reverse transcription followed by polymerase chain reaction). The experimental observations indicated higher agreements with the web server results, than contradictions. The tool is accessible at http://resource.ibab.ac.in/TIPMaP. The newly developed online tool forms a reliable means for identification of alternatively spliced transcript-isoforms that may be differentially expressed in various tissues, cell types or physiological conditions. Thus, by making better use of existing data, TIPMaP avoids the dependence on precious tissue-samples, in experiments with a goal to establish expression profiles of alternative splice forms--at least in some cases.

DSSTox chemical-index files for exposure-related ...

EPA Pesticide Factsheets

The Distributed Structure-Searchable Toxicity (DSSTox) ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus (GEO) Series (based on data extracted on September 20, 2008). ARYEXP and GEOGSE contain 887 and 1064 unique chemical substances mapped to 1835 and 2381 chemical exposure-related experiment accession IDs, respectively. The standardized files allow one to assess, compare and search the chemical content in each resource, in the context of the larger DSSTox toxicology data network, as well as across large public cheminformatics resources such as PubChem (http://pubchem.ncbi.nlm.nih.gov). The Distributed Structure-Searchable Toxicity (DSSTox) ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus (GEO) Series (based on data extracted on September 20, 2008). ARYEXP and GEOGSE contain 887 and 1064 unique chemical substances mapped to 1835 and 2381 chemical exposure-related experiment accession IDs, respectively. The standardized files allow one to assess, compare and search the chemical content in each resource, in the context of the larger DSSTox toxicology data network, as well as across large public cheminformatics resourc

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

PubMed Central

2011-01-01

Background Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications. Results ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms. Conclusions ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor. PMID:21548938

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties

PubMed Central

2012-01-01

Background For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described. Results From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties. Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissues to understand the genetic make-up of the Cd accumulation. Conclusions An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment. PMID:23190529

In situ synthesis of protein arrays.

PubMed

He, Mingyue; Stoevesandt, Oda; Taussig, Michael J

2008-02-01

In situ or on-chip protein array methods use cell free expression systems to produce proteins directly onto an immobilising surface from co-distributed or pre-arrayed DNA or RNA, enabling protein arrays to be created on demand. These methods address three issues in protein array technology: (i) efficient protein expression and availability, (ii) functional protein immobilisation and purification in a single step and (iii) protein on-chip stability over time. By simultaneously expressing and immobilising many proteins in parallel on the chip surface, the laborious and often costly processes of DNA cloning, expression and separate protein purification are avoided. Recently employed methods reviewed are PISA (protein in situ array) and NAPPA (nucleic acid programmable protein array) from DNA and puromycin-mediated immobilisation from mRNA.

Role of NF-Kappa B Signaling in X-Box Binding Protein 1 (XBP1)-Mediated Antiestrogen Resistance in Breast Cancer

DTIC Science & Technology

2013-10-01

experiments, a statistically significant data is not yet available. Additional experiments are needed for us to be able to draw   conclu comb Figure...well-defined stress pathways, UPR and autophagy, are involved breast involution regulation. Using published gene expression array datasets from...performed involution time-course experiments using both low-dose drug interventions and an autophagy-related gene 7 (ATG7) deletion mouse model

Analysis of gene expression on anodic porous alumina microarrays

PubMed Central

Nicolini, Claudio; Singh, Manjul; Spera, Rosanna; Felli, Lamberto

2013-01-01

This paper investigates the application of anodic porous alumina as an advancement on chip laboratory for gene expressions. The surface was prepared by a suitable electrolytic process to obtain a regular distribution of deep micrometric holes and printed bypen robot tips under standard conditions. The gene expression within the Nucleic Acid Programmable Protein Array (NAPPA) is realized in a confined environment of 16 spots, containing circular DNA plasmids expressed using rabbit reticulocyte lysate. Authors demonstrated the usefulness of APA in withholding the protein expression by detecting with a CCD microscope the photoluminescence signal emitted from the complex secondary antibody anchored to Cy3 and confined in the pores. Friction experiments proved the mechanical resistance under external stresses by the robot tip pens printing. So far, no attempts have been made to directly compare APA with any other surface/substrate; the rationale for pursuing APA as a potential surface coating is that it provides advantages over the simple functionalization of a glass slide, overcoming concerns about printing and its ability to generate viable arrays. PMID:23783000

Tissue Gene Expression Analysis Using Arrayed Normalized cDNA Libraries

PubMed Central

Eickhoff, Holger; Schuchhardt, Johannes; Ivanov, Igor; Meier-Ewert, Sebastian; O'Brien, John; Malik, Arif; Tandon, Neeraj; Wolski, Eryk-Witold; Rohlfs, Elke; Nyarsik, Lajos; Reinhardt, Richard; Nietfeld, Wilfried; Lehrach, Hans

2000-01-01

We have used oligonucleotide-fingerprinting data on 60,000 cDNA clones from two different mouse embryonic stages to establish a normalized cDNA clone set. The normalized set of 5,376 clones represents different clusters and therefore, in almost all cases, different genes. The inserts of the cDNA clones were amplified by PCR and spotted on glass slides. The resulting arrays were hybridized with mRNA probes prepared from six different adult mouse tissues. Expression profiles were analyzed by hierarchical clustering techniques. We have chosen radioactive detection because it combines robustness with sensitivity and allows the comparison of multiple normalized experiments. Sensitive detection combined with highly effective clustering algorithms allowed the identification of tissue-specific expression profiles and the detection of genes specifically expressed in the tissues investigated. The obtained results are publicly available (http://www.rzpd.de) and can be used by other researchers as a digital expression reference. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AL360374–AL36537.] PMID:10958641

Power enhancement via multivariate outlier testing with gene expression arrays.

PubMed

Asare, Adam L; Gao, Zhong; Carey, Vincent J; Wang, Richard; Seyfert-Margolis, Vicki

2009-01-01

As the use of microarrays in human studies continues to increase, stringent quality assurance is necessary to ensure accurate experimental interpretation. We present a formal approach for microarray quality assessment that is based on dimension reduction of established measures of signal and noise components of expression followed by parametric multivariate outlier testing. We applied our approach to several data resources. First, as a negative control, we found that the Affymetrix and Illumina contributions to MAQC data were free from outliers at a nominal outlier flagging rate of alpha=0.01. Second, we created a tunable framework for artificially corrupting intensity data from the Affymetrix Latin Square spike-in experiment to allow investigation of sensitivity and specificity of quality assurance (QA) criteria. Third, we applied the procedure to 507 Affymetrix microarray GeneChips processed with RNA from human peripheral blood samples. We show that exclusion of arrays by this approach substantially increases inferential power, or the ability to detect differential expression, in large clinical studies. http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.html and http://bioconductor.org/packages/2.3/bioc/html/affyContam.html affyContam (credentials: readonly/readonly)

Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays.

PubMed

Goldstein, Darlene R

2006-10-01

Studies of gene expression using high-density short oligonucleotide arrays have become a standard in a variety of biological contexts. Of the expression measures that have been proposed to quantify expression in these arrays, multi-chip-based measures have been shown to perform well. As gene expression studies increase in size, however, utilizing multi-chip expression measures is more challenging in terms of computing memory requirements and time. A strategic alternative to exact multi-chip quantification on a full large chip set is to approximate expression values based on subsets of chips. This paper introduces an extrapolation method, Extrapolation Averaging (EA), and a resampling method, Partition Resampling (PR), to approximate expression in large studies. An examination of properties indicates that subset-based methods can perform well compared with exact expression quantification. The focus is on short oligonucleotide chips, but the same ideas apply equally well to any array type for which expression is quantified using an entire set of arrays, rather than for only a single array at a time. Software implementing Partition Resampling and Extrapolation Averaging is under development as an R package for the BioConductor project.

Optimised 'on demand' protein arraying from DNA by cell free expression with the 'DNA to Protein Array' (DAPA) technology.

PubMed

Schmidt, Ronny; Cook, Elizabeth A; Kastelic, Damjana; Taussig, Michael J; Stoevesandt, Oda

2013-08-02

We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an increased amount of detected protein and an optimised spot morphology on the resulting protein array compared to the previously published protocol. The specificity of protein capture was improved using a tag-specific capture antibody on a protein repellent surface coating. The conditions for protein expression were optimised to yield the maximum amount of protein or the best detection results using specific monoclonal antibodies or a scaffold binder against the expressed targets. The optimised DAPA system was able to increase by threefold the expression of a representative model protein while conserving recognition by a specific antibody. The amount of expressed protein in DAPA was comparable to those of classically spotted protein arrays. Reaction conditions can be tailored to suit the application of interest. DAPA represents a cost effective, easy and convenient way of producing protein arrays on demand. The reported work is expected to facilitate the application of DAPA for personalized medicine and screening purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Development of Perceptual Expertise in Emotion Recognition

ERIC Educational Resources Information Center

Pollak, Seth D.; Messner, Michael; Kistler, Doris J.; Cohn, Jeffrey F.

2009-01-01

How do children's early social experiences influence their perception of emotion-specific information communicated by the face? To examine this question, we tested a group of abused children who had been exposed to extremely high levels of parental anger expression and physical threat. Children were presented with arrays of stimuli that depicted…

Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress.

PubMed

Williams-Devane, ClarLynda R; Wolf, Maritja A; Richard, Ann M

2009-06-01

A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate and aggregate such information by chemical, and broad data coverage within chemical, genomics, and toxicological information domains. This capability also depends on common genomics standards, protocol description, and functional linkages of diverse public Internet data resources. We present a survey of public genomics resources from these vantage points and conclude that, despite progress in many areas, the current state of the majority of public microarray databases is inadequate for supporting these objectives, particularly with regard to chemical indexing. To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus. Automated scripts and extensive manual review were employed to transform free-text experiment descriptions into a standardized, chemically indexed inventory of experiments in both resources. These files, which include top-level summary annotations, allow for identification of current chemical-associated experimental content, as well as chemical-exposure-related (or "Treatment") content of greatest potential value to toxicogenomics investigation. With these chemical-index files, it is possible for the first time to assess the breadth and overlap of chemical study space represented in these databases, and to begin to assess the sufficiency of data with shared protocols for chemical similarity inferences. Chemical indexing of public genomics databases is a first important step toward integrating chemical, toxicological and genomics data into predictive toxicology.

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

PubMed

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

2011-01-01

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

Three gangliogliomas: results of GTG-banding, SKY, genome-wide high resolution SNP-array, gene expression and review of the literature.

PubMed

Xu, Li-Xin; Holland, Heidrun; Kirsten, Holger; Ahnert, Peter; Krupp, Wolfgang; Bauer, Manfred; Schober, Ralf; Mueller, Wolf; Fritzsch, Dominik; Meixensberger, Jürgen; Koschny, Ronald

2015-04-01

According to the World Health Organization gangliogliomas are classified as well-differentiated and slowly growing neuroepithelial tumors, composed of neoplastic mature ganglion and glial cells. It is the most frequent tumor entity observed in patients with long-term epilepsy. Comprehensive cytogenetic and molecular cytogenetic data including high-resolution genomic profiling (single nucleotide polymorphism (SNP)-array) of gangliogliomas are scarce but necessary for a better oncological understanding of this tumor entity. For a detailed characterization at the single cell and cell population levels, we analyzed genomic alterations of three gangliogliomas using trypsin-Giemsa banding (GTG-banding) and by spectral karyotyping (SKY) in combination with SNP-array and gene expression array experiments. By GTG and SKY, we could confirm frequently detected chromosomal aberrations (losses within chromosomes 10, 13 and 22; gains within chromosomes 5, 7, 8 and 12), and identify so far unknown genetic aberrations like the unbalanced non-reciprocal translocation t(1;18)(q21;q21). Interestingly, we report on the second so far detected ganglioglioma with ring chromosome 1. Analyses of SNP-array data from two of the tumors and respective germline DNA (peripheral blood) identified few small gains and losses and a number of copy-neutral regions with loss of heterozygosity (LOH) in germline and in tumor tissue. In comparison to germline DNA, tumor tissues did not show substantial regions with significant loss or gain or with newly developed LOH. Gene expression analyses of tumor-specific genes revealed similarities in the profile of the analyzed samples regarding different relevant pathways. Taken together, we describe overlapping but also distinct and novel genetic aberrations of three gangliogliomas. © 2014 Japanese Society of Neuropathology.

Arabidopsis gene expression patterns are altered during spaceflight

NASA Astrophysics Data System (ADS)

Paul, Anna-Lisa; Popp, Michael P.; Gurley, William B.; Guy, Charles; Norwood, Kelly L.; Ferl, Robert J.

The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments results in differential gene expression. A 5-day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β-Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on gene expression patterns initially by using the Adh/GUS transgene to address specifically the possibility that spaceflight induces a hypoxic stress response (Paul, A.L., Daugherty, C.J., Bihn, E.A., Chapman, D.K., Norwood, K.L., Ferl, R.J., 2001. Transgene expression patterns indicate that spaceflight affects stress signal perception and transduction in arabidopsis, Plant Physiol. 126, 613-621). As a follow-on to the reporter gene analysis, we report here the evaluation of genome-wide patterns of native gene expression within Arabidopsis shoots utilizing the Agilent DNA array of 21,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes was further characterized with quantitative Real-Time RT PCR (ABI - Taqman®). Comparison of the patterns of expression for arrays probed with RNA isolated from plants exposed to spaceflight compared to RNA isolated from ground control plants revealed 182 genes that were differentially expressed in response to the spaceflight mission by more than 4-fold, and of those only 50 genes were expressed at levels chosen to support a conservative change call. None of the genes that are hallmarks of hypoxic stress were induced to this level. However, genes related to heat shock were dramatically induced - but in a pattern and under growth conditions that are not easily explained by elevated temperatures. These gene expression data are discussed in light of current models for plant responses to the spaceflight environment and with regard to potential future spaceflight experiment opportunities.

Expression profiling of microRNAs in human bone tissue from postmenopausal women.

PubMed

De-Ugarte, Laura; Serra-Vinardell, Jenny; Nonell, Lara; Balcells, Susana; Arnal, Magdalena; Nogues, Xavier; Mellibovsky, Leonardo; Grinberg, Daniel; Diez-Perez, Adolfo; Garcia-Giralt, Natalia

2018-01-01

Bone tissue is composed of several cell types, which express their own microRNAs (miRNAs) that will play a role in cell function. The set of total miRNAs expressed in all cell types configures the specific signature of the bone tissue in one physiological condition. The aim of this study was to explore the miRNA expression profile of bone tissue from postmenopausal women. Tissue was obtained from trabecular bone and was analyzed in fresh conditions (n = 6). Primary osteoblasts were also obtained from trabecular bone (n = 4) and human osteoclasts were obtained from monocyte precursors after in vitro differentiation (n = 5). MicroRNA expression profiling was obtained for each sample by microarray and a global miRNA analysis was performed combining the data acquired in all the microarray experiments. From the 641 miRNAs detected in bone tissue samples, 346 (54%) were present in osteoblasts and/or osteoclasts. The other 46% were not identified in any of the bone cells analyzed. Intersection of osteoblast and osteoclast arrays identified 101 miRNAs shared by both cell types, which accounts for 30-40% of miRNAs detected in these cells. In osteoblasts, 266 miRNAs were detected, of which 243 (91%) were also present in the total bone array, representing 38% of all bone miRNAs. In osteoclasts, 340 miRNAs were detected, of which 196 (58%) were also present in the bone tissue array, representing 31% of all miRNAs detected in total bone. These analyses provide an overview of miRNAs expressed in bone tissue, broadening our knowledge in the microRNA field.

Automated, Miniaturized Instrument for Measuring Gene Expression in Space

NASA Technical Reports Server (NTRS)

Pohorille, A.; Peyvan, K.; Danley, D.; Ricco, A. J.

2010-01-01

To facilitate astrobiological studies on the survival and adaptation of microorganisms and mixed microbial cultures to space environment, we have been developing a fully automated, miniaturized system for measuring their gene expression on small spacecraft. This low-cost, multi-purpose instrument represents a major scientific and technological advancement in our ability to study the impact of the space environment on biological systems by providing data on cellular metabolism and regulation orders of magnitude richer than what is currently available. The system supports growth of the organism, lyse it to release the expressed RNA, label the RNA, read the expression levels of a large number of genes by microarray analysis of labeled RNA and transmit the measurements to Earth. To measure gene expression we use microarray technology developed by CombiMatrix, which is based on electrochemical reactions on arrays of electrodes on a semiconductor substrate. Since the electrical integrity of the microarray remains intact after probe synthesis, the circuitry can be employed to sense nucleic acid binding at each electrode. CombiMatrix arrays can be sectored to allow multiple samples per chip. In addition, a single array can be used for several assays. The array has been integrated into an automated microfluidic cartridge that uses flexible reagent blisters and pinch pumping to move liquid reagents between chambers. The proposed instrument will help to understand adaptation of terrestrial life to conditions beyond the planet of origin, identify deleterious effects of the space environment, develop effective countermeasures against these effects, and test our ability to sustain and grow in space organisms that can be used for life support and in situ resource utilization during long-duration space exploration. The instrument is suitable for small satellite platforms, which provide frequent, low cost access to space. It can be also used on any other platform in space, including the ISS. It can be replicated and used with only small modifications in multiple biological experiments with a broad range of goals in mind.

Automated, Miniaturized Instrument for Measuring Gene Expression in Space

NASA Astrophysics Data System (ADS)

Pohorille, Andrew; Danley, David; Payvan, Kia; Ricco, Antonio

To facilitate astrobiological studies on the survival and adaptation of microorganisms and mixed microbial cultures to space environment, we have been developing a fully automated, minia-turized system for measuring their gene expression on small spacecraft. This low-cost, multi-purpose instrument represents a major scientific and technological advancement in our ability to study the impact of the space environment on biological systems by providing data on cel-lular metabolism and regulation orders of magnitude richer than what is currently available. The system supports growth of the organism, lyse it to release the expressed RNA, label the RNA, read the expression levels of a large number of genes by microarray analysis of labeled RNA and transmit the measurements to Earth. To measure gene expression we use microarray technology developed by CombiMatrix, which is based on electrochemical reactions on arrays of electrodes on a semiconductor substrate. Since the electrical integrity of the microarray re-mains intact after probe synthesis, the circuitry can be employed to sense nucleic acid binding at each electrode. CombiMatrix arrays can be sectored to allow multiple samples per chip. In addition, a single array can be used for several assays. The array has been integrated into an automated microfluidic cartridge that uses flexible reagent blisters and pinch pumping to move liquid reagents between chambers. The proposed instrument will help to understand adaptation of terrestrial life to conditions be-yond the planet of origin, identify deleterious effects of the space environment, develop effective countermeasures against these effects, and test our ability to sustain and grow in space organ-isms that can be used for life support and in situ resource utilization during long-duration space exploration. The instrument is suitable for small satellite platforms, which provide frequent, low cost access to space. It can be also used on any other platform in space, including the ISS. It can be replicated and used with only small modifications in multiple biological experiments with a broad range of goals in mind.

Gene expression patterns in rainbow trout, Oncorhynchus mykiss, exposed to a suite of model toxicants

PubMed Central

Hook, Sharon E.; Skillman, Ann D.; Small, Jack A.; Schultz, Irvin R.

2008-01-01

The increased availability and use of DNA microarrays has allowed the characterization of gene expression patterns associated with exposure to different toxicants. An important question is whether toxicant induced changes in gene expression in fish are sufficiently diverse to allow for identification of specific modes of action and/or specific contaminants. In theory, each class of toxicant may generate a gene expression profile unique to its mode of toxic action. In this study, isogenic (cloned) rainbow trout Oncorhynchus mykiss were exposed to sublethal levels of a series of model toxicants with varying modes of action, including ethynylestradiol (xeno-estrogen), 2,2,4,4′-tetrabromodiphenyl ether (BDE-47, thyroid active), diquat (oxidant stressor), chromium VI, and benzo[a]pyrene (BaP) for a period of 1–3 weeks. An additional experiment measured trenbolone (anabolic steroid; model androgen) induced gene expression changes in sexually mature female trout. Following exposure, fish were euthanized, livers removed and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNA’s. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up- and downregulated genes, as well as to determine gene clustering patterns that can be used as “expression signatures”. The results indicate each toxicant exposure caused between 64 and 222 genes to be significantly altered in expression. Most genes exhibiting altered expression responded to only one of the toxicants and relatively few were co-expressed in multiple treatments. For example, BaP and Diquat, both of which exert toxicity via oxidative stress, upregulated 28 of the same genes, of over 100 genes altered by either treatment. Other genes associated with steroidogenesis, p450 and estrogen responsive genes appear to be useful for selectively identifying toxicant mode of action in fish, suggesting a link between gene expression profile and mode of toxicity. Our array results showed good agreement with quantitative real time polymerase chain reaction (qRT PCR), which demonstrates that the arrays are an accurate measure of gene expression. The specificity of the gene expression profile in response to a model toxicant, the link between genes with altered expression and mode of toxic action, and the consistency between array and qRT PCR results all suggest that cDNA microarrays have the potential to screen environmental contaminants for biomarkers and mode of toxic action. PMID:16488489

Gene expression patterns in rainbow trout, Oncorhynchus mykiss, exposed to a suite of model toxicants.

PubMed

Hook, Sharon E; Skillman, Ann D; Small, Jack A; Schultz, Irvin R

2006-05-25

The increased availability and use of DNA microarrays has allowed the characterization of gene expression patterns associated with exposure to different toxicants. An important question is whether toxicant induced changes in gene expression in fish are sufficiently diverse to allow for identification of specific modes of action and/or specific contaminants. In theory, each class of toxicant may generate a gene expression profile unique to its mode of toxic action. In this study, isogenic (cloned) rainbow trout Oncorhynchus mykiss were exposed to sublethal levels of a series of model toxicants with varying modes of action, including ethynylestradiol (xeno-estrogen), 2,2,4,4'-tetrabromodiphenyl ether (BDE-47, thyroid active), diquat (oxidant stressor), chromium VI, and benzo[a]pyrene (BaP) for a period of 1-3 weeks. An additional experiment measured trenbolone (anabolic steroid; model androgen) induced gene expression changes in sexually mature female trout. Following exposure, fish were euthanized, livers removed and RNA extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNA's. The slides were scanned to measure abundance of a given transcript in each sample relative to controls. Data were analyzed via Genespring (Silicon Genetics) to identify a list of up- and downregulated genes, as well as to determine gene clustering patterns that can be used as "expression signatures". The results indicate each toxicant exposure caused between 64 and 222 genes to be significantly altered in expression. Most genes exhibiting altered expression responded to only one of the toxicants and relatively few were co-expressed in multiple treatments. For example, BaP and Diquat, both of which exert toxicity via oxidative stress, upregulated 28 of the same genes, of over 100 genes altered by either treatment. Other genes associated with steroidogenesis, p450 and estrogen responsive genes appear to be useful for selectively identifying toxicant mode of action in fish, suggesting a link between gene expression profile and mode of toxicity. Our array results showed good agreement with quantitative real time polymerase chain reaction (qRT PCR), which demonstrates that the arrays are an accurate measure of gene expression. The specificity of the gene expression profile in response to a model toxicant, the link between genes with altered expression and mode of toxic action, and the consistency between array and qRT PCR results all suggest that cDNA microarrays have the potential to screen environmental contaminants for biomarkers and mode of toxic action.

Detection of doublecortin domain-containing 2 (DCDC2), a new candidate tumor suppressor gene of hepatocellular carcinoma, by triple combination array analysis

PubMed Central

2013-01-01

Background To detect genes correlated with hepatocellular carcinoma (HCC), we developed a triple combination array consisting of methylation array, gene expression array and single nucleotide polymorphism (SNP) array analysis. Methods A surgical specimen obtained from a 68-year-old female HCC patient was analyzed by triple combination array, which identified doublecortin domain-containing 2 (DCDC2) as a candidate tumor suppressor gene of HCC. Subsequently, samples from 48 HCC patients were evaluated for their DCDC2 methylation and expression status using methylation specific PCR (MSP) and semi-quantitative reverse transcriptase (RT) PCR, respectively. Then, we investigated the relationship between clinicopathological factors and methylation status of DCDC2. Results DCDC2 was revealed to be hypermethylated (methylation value 0.846, range 0–1.0) in cancer tissue, compared with adjacent normal tissue (0.212) by methylation array in the 68-year-old female patient. Expression array showed decreased expression of DCDC2 in cancerous tissue. SNP array showed that the copy number of chromosome 6p22.1, in which DCDC2 resides, was normal. MSP revealed hypermethylation of the promoter region of DCDC2 in 41 of the tumor samples. DCDC2 expression was significantly decreased in the cases with methylation (P = 0.048). Furthermore, the methylated cases revealed worse prognosis for overall survival than unmethylated cases (P = 0.048). Conclusions The present study indicates that triple combination array is an effective method to detect novel genes related to HCC. We propose that DCDC2 is a tumor suppressor gene of HCC. PMID:24034596

Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression.

PubMed

Li, Shuyu; Li, Yiqun Helen; Wei, Tao; Su, Eric Wen; Duffin, Kevin; Liao, Birong

2006-10-25

The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repository through different technology platforms. However, exploitations of these rich data sources remain limited in part due to issues of technology standardization. Our objective is to test the data comparability between SAGE and microarray technologies, through examining the expression pattern of genes under normal physiological states across variety of tissues. There are 42-54% of genes showing significant correlations in tissue expression patterns between SAGE and GeneChip, with 30-40% of genes whose expression patterns are positively correlated and 10-15% of genes whose expression patterns are negatively correlated at a statistically significant level (p = 0.05). Our analysis suggests that the discrepancy on the expression patterns derived from technology platforms is not likely from the heterogeneity of tissues used in these technologies, or other spurious correlations resulting from microarray probe design, abundance of genes, or gene function. The discrepancy can be partially explained by errors in the original assignment of SAGE tags to genes due to the evolution of sequence databases. In addition, sequence analysis has indicated that many SAGE tags and Affymetrix array probe sets are mapped to different splice variants or different sequence regions although they represent the same gene, which also contributes to the observed discrepancies between SAGE and array expression data. To our knowledge, this is the first report attempting to mine gene expression patterns across tissues using public data from different technology platforms. Unlike previous similar studies that only demonstrated the discrepancies between the two gene expression platforms, we carried out in-depth analysis to further investigate the cause for such discrepancies. Our study shows that the exploitation of rich public expression resource requires extensive knowledge about the technologies, and experiment. Informatic methodologies for better interoperability among platforms still remain a gap. One of the areas that can be improved practically is the accurate sequence mapping of SAGE tags and array probes to full-length genes.

Pre-amplification in the context of high-throughput qPCR gene expression experiment.

PubMed

Korenková, Vlasta; Scott, Justin; Novosadová, Vendula; Jindřichová, Marie; Langerová, Lucie; Švec, David; Šídová, Monika; Sjöback, Robert

2015-03-11

With the introduction of the first high-throughput qPCR instrument on the market it became possible to perform thousands of reactions in a single run compared to the previous hundreds. In the high-throughput reaction, only limited volumes of highly concentrated cDNA or DNA samples can be added. This necessity can be solved by pre-amplification, which became a part of the high-throughput experimental workflow. Here, we focused our attention on the limits of the specific target pre-amplification reaction and propose the optimal, general setup for gene expression experiment using BioMark instrument (Fluidigm). For evaluating different pre-amplification factors following conditions were combined: four human blood samples from healthy donors and five transcripts having high to low expression levels; each cDNA sample was pre-amplified at four cycles (15, 18, 21, and 24) and five concentrations (equivalent to 0.078 ng, 0.32 ng, 1.25 ng, 5 ng, and 20 ng of total RNA). Factors identified as critical for a success of cDNA pre-amplification were cycle of pre-amplification, total RNA concentration, and type of gene. The selected pre-amplification reactions were further tested for optimal Cq distribution in a BioMark Array. The following concentrations combined with pre-amplification cycles were optimal for good quality samples: 20 ng of total RNA with 15 cycles of pre-amplification, 20x and 40x diluted; and 5 ng and 20 ng of total RNA with 18 cycles of pre-amplification, both 20x and 40x diluted. We set up upper limits for the bulk gene expression experiment using gene expression Dynamic Array and provided an easy-to-obtain tool for measuring of pre-amplification success. We also showed that variability of the pre-amplification, introduced into the experimental workflow of reverse transcription-qPCR, is lower than variability caused by the reverse transcription step.

Gravitational wave searches with pulsar timing arrays: Cancellation of clock and ephemeris noises

NASA Astrophysics Data System (ADS)

Tinto, Massimo

2018-04-01

We propose a data processing technique to cancel monopole and dipole noise sources (such as clock and ephemeris noises, respectively) in pulsar timing array searches for gravitational radiation. These noises are the dominant sources of correlated timing fluctuations in the lower-part (≈10-9-10-8 Hz ) of the gravitational wave band accessible by pulsar timing experiments. After deriving the expressions that reconstruct these noises from the timing data, we estimate the gravitational wave sensitivity of our proposed processing technique to single-source signals to be at least one order of magnitude higher than that achievable by directly processing the timing data from an equal-size array. Since arrays can generate pairs of clock and ephemeris-free timing combinations that are no longer affected by correlated noises, we implement with them the cross-correlation statistic to search for an isotropic stochastic gravitational wave background. We find the resulting optimal signal-to-noise ratio to be more than one order of magnitude larger than that obtainable by correlating pairs of timing data from arrays of equal size.

Characterization of transformation related genes in oral cancer cells.

PubMed

Chang, D D; Park, N H; Denny, C T; Nelson, S F; Pe, M

1998-04-16

A cDNA representational difference analysis (cDNA-RDA) and an arrayed filter technique were used to characterize transformation-related genes in oral cancer. From an initial comparison of normal oral epithelial cells and a human papilloma virus (HPV)-immortalized oral epithelial cell line, we obtained 384 differentially expressed gene fragments and arrayed them on a filter. Two hundred and twelve redundant clones were identified by three rounds of back hybridization. Sequence analysis of the remaining clones revealed 99 unique clones corresponding to 69 genes. The expression of these transformation related gene fragments in three nontumorigenic HPV-immortalized oral epithelial cell lines and three oral cancer cell lines were simultaneously monitored using a cDNA array hybridization. Although there was a considerable cell line-to-cell line variability in the expression of these clones, a reliable prediction of their expression could be made from the cDNA array hybridization. Our study demonstrates the utility of combining cDNA-RDA and arrayed filters in high-throughput gene expression difference analysis. The differentially expressed genes identified in this study should be informative in studying oral epithelial cell carcinogenesis.

Specific roles for the Ccr4-Not complex subunits in expression of the genome

PubMed Central

Azzouz, Nowel; Panasenko, Olesya O.; Deluen, Cécile; Hsieh, Julien; Theiler, Grégory; Collart, Martine A.

2009-01-01

In this work we used micro-array experiments to determine the role of each nonessential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast Saccharomyces cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene deregulation were observed upon deletion of any given subunit, revealing the specificity of each subunit's function. Consistently, the purification of the Ccr4-Not complex through Caf40p by tandem affinity purification from wild-type cells or cells lacking individual subunits of the Ccr4-Not complex revealed that each subunit had a particular impact on complex integrity. Furthermore, the micro-arrays revealed that the role of each subunit was specific to the growth conditions. From the study of only two different growth conditions, revealing an impact of the Ccr4-Not complex on more than 85% of all studied genes, we can infer that the Ccr4-Not complex is important for expression of most of the yeast genome. PMID:19155328

Asymmetric van der Waals Forces Drive Orientation of Compositionally Anisotropic Nanocylinders within Smectic Arrays: Experiment and Simulation

PubMed Central

Smith, Benjamin D.; Fichthorn, Kristen A.; Kirby, David J.; Quimby, Lisa M.; Triplett, Derek A.; González, Pedro; Hernández, Darimar; Keating, Christine D.

2014-01-01

Understanding how micro- and nanoparticles interact is important for achieving bottom-up assembly of desired structures. Here, we examine the self-assembly of two-component, compositionally asymmetric nanocylinders that sediment from solution onto a solid surface. These particles spontaneously formed smectic arrays. Within the rows of an array, nanocylinders tended to assemble such that neighboring particles had the same orientation of their segments. As a probe of interparticle interactions, we classified nanocylinder alignments by measuring the segment orientations of many sets of neighboring particles. Monte Carlo simulations incorporating an exact expression for the van der Waals (vdW) energy indicate that differences in the vdW interactions, even when small, are the key factor in producing observed segment alignment. These results point to asymmetrical vdW interactions as a potentially powerful means of controlling orientation in multicomponent cylinder arrays, and suggest that designing for these interactions could yield new ways to control self-assembly. PMID:24308771

A bio-inspired structural health monitoring system based on ambient vibration

NASA Astrophysics Data System (ADS)

Lin, Tzu-Kang; Kiremidjian, Anne; Lei, Chi-Yang

2010-11-01

A structural health monitoring (SHM) system based on naïve Bayesian (NB) damage classification and DNA-like expression data was developed in this research. Adapted from the deoxyribonucleic acid (DNA) array concept in molecular biology, the proposed structural health monitoring system is constructed utilizing a double-tier regression process to extract the expression array from the structural time history recorded during external excitations. The extracted array is symbolized as the various genes of the structure from the viewpoint of molecular biology and reflects the possible damage conditions prevalent in the structure. A scaled down, six-story steel building mounted on the shaking table of the National Center for Research on Earthquake Engineering (NCREE) was used as the benchmark. The structural response at different damage levels and locations under ambient vibration was collected to support the database for the proposed SHM system. To improve the precision of detection in practical applications, the system was enhanced by an optimization process using the likelihood selection method. The obtained array representing the DNA array of the health condition of the structure was first evaluated and ranked. A total of 12 groups of expression arrays were regenerated from a combination of four damage conditions. To keep the length of the array unchanged, the best 16 coefficients from every expression array were selected to form the optimized SHM system. Test results from the ambient vibrations showed that the detection accuracy of the structural damage could be greatly enhanced by the optimized expression array, when compared to the original system. Practical verification also demonstrated that a rapid and reliable result could be given by the final system within 1 min. The proposed system implements the idea of transplanting the DNA array concept from molecular biology into the field of SHM.

Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots

PubMed Central

Scholma, Jetse; Fuhler, Gwenny M.; Joore, Jos; Hulsman, Marc; Schivo, Stefano; List, Alan F.; Reinders, Marcel J. T.; Peppelenbosch, Maikel P.; Post, Janine N.

2016-01-01

Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. PMID:27225531

THE USE OF GENE ARRAYS TO DETERMINE TEMPORAL GENE INDUCTION IN SHEEPSHEAD MINNOWS EXPOSED TO E2

EPA Science Inventory

Gene arrays provide a means to study differential gene expression in fish exposed to environmental estrogens by providing a "snapshot" of the genes expressed at a given time. Such array data may also uncover previously unknown biochemical pathways affected by estrogenic compounds...

NCBI GEO: mining millions of expression profiles--database and tools.

PubMed

Barrett, Tanya; Suzek, Tugba O; Troup, Dennis B; Wilhite, Stephen E; Ngau, Wing-Chi; Ledoux, Pierre; Rudnev, Dmitry; Lash, Alex E; Fujibuchi, Wataru; Edgar, Ron

2005-01-01

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30,000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

Fully moderated T-statistic for small sample size gene expression arrays.

PubMed

Yu, Lianbo; Gulati, Parul; Fernandez, Soledad; Pennell, Michael; Kirschner, Lawrence; Jarjoura, David

2011-09-15

Gene expression microarray experiments with few replications lead to great variability in estimates of gene variances. Several Bayesian methods have been developed to reduce this variability and to increase power. Thus far, moderated t methods assumed a constant coefficient of variation (CV) for the gene variances. We provide evidence against this assumption, and extend the method by allowing the CV to vary with gene expression. Our CV varying method, which we refer to as the fully moderated t-statistic, was compared to three other methods (ordinary t, and two moderated t predecessors). A simulation study and a familiar spike-in data set were used to assess the performance of the testing methods. The results showed that our CV varying method had higher power than the other three methods, identified a greater number of true positives in spike-in data, fit simulated data under varying assumptions very well, and in a real data set better identified higher expressing genes that were consistent with functional pathways associated with the experiments.

Interaction between scene-based and array-based contextual cueing.

PubMed

Rosenbaum, Gail M; Jiang, Yuhong V

2013-07-01

Contextual cueing refers to the cueing of spatial attention by repeated spatial context. Previous studies have demonstrated distinctive properties of contextual cueing by background scenes and by an array of search items. Whereas scene-based contextual cueing reflects explicit learning of the scene-target association, array-based contextual cueing is supported primarily by implicit learning. In this study, we investigated the interaction between scene-based and array-based contextual cueing. Participants searched for a target that was predicted by both the background scene and the locations of distractor items. We tested three possible patterns of interaction: (1) The scene and the array could be learned independently, in which case cueing should be expressed even when only one cue was preserved; (2) the scene and array could be learned jointly, in which case cueing should occur only when both cues were preserved; (3) overshadowing might occur, in which case learning of the stronger cue should preclude learning of the weaker cue. In several experiments, we manipulated the nature of the contextual cues present during training and testing. We also tested explicit awareness of scenes, scene-target associations, and arrays. The results supported the overshadowing account: Specifically, scene-based contextual cueing precluded array-based contextual cueing when both were predictive of the location of a search target. We suggest that explicit, endogenous cues dominate over implicit cues in guiding spatial attention.

A facial expression of pax: Assessing children's "recognition" of emotion from faces.

PubMed

Nelson, Nicole L; Russell, James A

2016-01-01

In a classic study, children were shown an array of facial expressions and asked to choose the person who expressed a specific emotion. Children were later asked to name the emotion in the face with any label they wanted. Subsequent research often relied on the same two tasks--choice from array and free labeling--to support the conclusion that children recognize basic emotions from facial expressions. Here five studies (N=120, 2- to 10-year-olds) showed that these two tasks produce illusory recognition; a novel nonsense facial expression was included in the array. Children "recognized" a nonsense emotion (pax or tolen) and two familiar emotions (fear and jealousy) from the same nonsense face. Children likely used a process of elimination; they paired the unknown facial expression with a label given in the choice-from-array task and, after just two trials, freely labeled the new facial expression with the new label. These data indicate that past studies using this method may have overestimated children's expression knowledge. Copyright © 2015 Elsevier Inc. All rights reserved.

Detecting novel genes with sparse arrays

PubMed Central

Haiminen, Niina; Smit, Bart; Rautio, Jari; Vitikainen, Marika; Wiebe, Marilyn; Martinez, Diego; Chee, Christine; Kunkel, Joe; Sanchez, Charles; Nelson, Mary Anne; Pakula, Tiina; Saloheimo, Markku; Penttilä, Merja; Kivioja, Teemu

2014-01-01

Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions. We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9 Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25mer microarray oligonucleotide probe was used for every 100 b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties. PMID:20691772

Golden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes.

PubMed

Vad-Nielsen, Johan; Lin, Lin; Bolund, Lars; Nielsen, Anders Lade; Luo, Yonglun

2016-11-01

The engineered CRISPR/Cas9 technology has developed as the most efficient and broadly used genome editing tool. However, simultaneously targeting multiple genes (or genomic loci) in the same individual cells using CRISPR/Cas9 remain one technical challenge. In this article, we have developed a Golden Gate Assembly method for the generation of CRISPR gRNA expression arrays, thus enabling simultaneous gene targeting. Using this method, the generation of CRISPR gRNA expression array can be accomplished in 2 weeks, and contains up to 30 gRNA expression cassettes. We demonstrated in the study that simultaneously targeting 10 genomic loci or simultaneously inhibition of multiple endogenous genes could be achieved using the multiplexed gRNA expression array vector in human cells. The complete set of plasmids is available through the non-profit plasmid repository Addgene.

Simple method for assembly of CRISPR synergistic activation mediator gRNA expression array.

PubMed

Vad-Nielsen, Johan; Nielsen, Anders Lade; Luo, Yonglun

2018-05-20

When studying complex interconnected regulatory networks, effective methods for simultaneously manipulating multiple genes expression are paramount. Previously, we have developed a simple method for generation of an all-in-one CRISPR gRNA expression array. We here present a Golden Gate Assembly-based system of synergistic activation mediator (SAM) compatible CRISPR/dCas9 gRNA expression array for the simultaneous activation of multiple genes. Using this system, we demonstrated the simultaneous activation of the transcription factors, TWIST, SNAIL, SLUG, and ZEB1 a human breast cancer cell line. Copyright © 2018 Elsevier B.V. All rights reserved.

Streamwise evolution of statistical events and the triple correlation in a model wind turbine array

NASA Astrophysics Data System (ADS)

Viestenz, Kyle; Cal, Raúl Bayoán

2013-11-01

Hot-wire anemometry data, obtained from a wind tunnel experiment containing a 3 × 3 wind turbine array, are used to conditionally average the Reynolds stresses. Nine profiles at the centerline behind the array are analyzed to characterize the turbulent velocity statistics of the wake flow. Quadrant analysis yields statistical events occurring in the wake of the wind farm, where quadrants 2 and 4 produce ejections and sweeps, respectively. A balance between these quadrants is expressed via the ΔSo parameter, which attains a maximum value at the bottom tip and changes sign near the top tip of the rotor. These are then associated to the triple correlation term present in the turbulent kinetic energy equation of the fluctuations. The development of these various quantities is assessed in light of wake remediation, energy transport and possess significance in closure models. National Science Foundation: ECCS-1032647.

Analysis of differential gene expression by bead-based fiber-optic array in nonfunctioning pituitary adenomas.

PubMed

Jiang, Z; Gui, S; Zhang, Y

2011-05-01

Nonfunctioning pituitary adenomas (NFPAs) are relatively common, accounting for 30% of all pituitary adenomas; however, their pathogenesis remains enigmatic. To explore the possible pathogenesis of NFPAs, we used fiber-optic BeadArray to examine gene expression in 5 NFPAs compared with 3 normal pituitaries. 4 differentially expressed genes were chosen randomly for validation by reverse transcriptase-real time quantitative polymerase chain reaction (RT-qPCR). We then analyzed the differentially expressed gene profile with Kyoto Encyclopedia of Genes and Genomes (KEGG). The array analysis indentified significant increases in the expression of 1,402 genes and 383 expressed sequence tags (ESTs), and decreases in 1,697 genes and 113 ESTs in the NFPAs. Bioinformatic and pathway analysis showed that the genes HIGD1B, FAM5C, PMAIP1 and the pathway cell-cycle regulation may play an important role in tumorigenesis and progression of NFPAs. Our data suggest fiber-optic BeadArray combined with pathway analysis of differential gene expression profile appears to be a valid approach for investigating the pathogenesis of tumors. © Georg Thieme Verlag KG Stuttgart · New York.

Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium.

PubMed

Die, Jose V; Baldwin, Ransom L; Rowland, Lisa J; Li, Robert; Oh, Sunghee; Li, Congjun; Connor, Erin E; Ranilla, Maria-Jose

2017-01-01

The rumen is lined on the luminal side by a stratified squamous epithelium that is responsible for not only absorption, but also transport, extensive short-chain fatty acid (SCFA) metabolism and protection. Butyrate has been demonstrated to initiate the differentiation of the tissue following introduction of solid feed to the weaning neonate as well as affecting the metabolism of other nutrients and absorption of nutrients in in vitro experiments. The objective of the present study was to validate expression stability of eight putative reference genes bovine rumen, considering the intrinsic heterogeneity of bovine rumen with regard to different luminal characteristics due to direct infusion of butyrate to double the intra-ruminal content of the rumen liquor. Our focus was on identifying stable reference genes which are suitable to normalize real-time RT-qPCR experiments from rumen samples collected from clinical assays, irrespective of localization within the organ and the across physiological state. The most stably expressed genes included: ACTB, UXT, DBNDD2, RPS9, DDX54 and HMBS. Their high stability values suggest these reference genes will facilitate better evaluation of variation of across an array of conditions including: localization within the rumen, differences among cattle fed an array of rations, as well as response to development in the weaning animal. Moreover, we anticipate these reference genes may be useful for expression studies in other ruminants.

STUDIES OF NORMAL GENE EXPRESSION IN THE RAT NASAL EPITHELIUM USNG CDNA ARRAY TECHNOLOGY

EPA Science Inventory

Studies of Normal Gene Expression in the Rat Nasal Epithelium Using cDNA Array

The nasal epithelium is an important target site for chemically-induced toxicity and carcinogenicity .Gene expression data are being used increasingly for studies of such conditions. In or...

A universal reference sample derived from clone vector for improved detection of differential gene expression

PubMed Central

Khan, Rishi L; Gonye, Gregory E; Gao, Guang; Schwaber, James S

2006-01-01

Background Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing signals to be undetectable. In addition, undetectable spots represent a large problem for two-color microarray designs and most arrays contain at least 40% undetectable spots even when labeled with reference samples such as Stratagene's Universal Reference RNAs™. Results We introduce a novel universal reference sample that produces strong signal for all spots on the array, increasing the average fraction of detectable spots to 97%. Maximizing detectable spots on the reference image channel also decreases the variability of microarray data allowing for reliable detection of smaller differential gene expression changes. The reference sample is derived from sequence contained in the parental EST clone vector pT7T3D-Pac and is called vector RNA (vRNA). We show that vRNA can also be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This reference sample can be made inexpensively in large quantities as a renewable resource that is consistent across experiments. Conclusion Results of this study show that vRNA provides a useful universal reference that yields high signal for almost all spots on a microarray, reduces variation and allows for comparisons between experiments and laboratories. Further, it can be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This type of reference allows for detection of small changes in differential expression while reference designs in general allow for large-scale multivariate experimental designs. vRNA in combination with reference designs enable systems biology microarray experiments of small physiologically relevant changes. PMID:16677381

Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology

PubMed Central

Ding, Liang-Hao; Xie, Yang; Park, Seongmi; Xiao, Guanghua; Story, Michael D.

2008-01-01

Despite the tremendous growth of microarray usage in scientific studies, there is a lack of standards for background correction methodologies, especially in single-color microarray platforms. Traditional background subtraction methods often generate negative signals and thus cause large amounts of data loss. Hence, some researchers prefer to avoid background corrections, which typically result in the underestimation of differential expression. Here, by utilizing nonspecific negative control features integrated into Illumina whole genome expression arrays, we have developed a method of model-based background correction for BeadArrays (MBCB). We compared the MBCB with a method adapted from the Affymetrix robust multi-array analysis algorithm and with no background subtraction, using a mouse acute myeloid leukemia (AML) dataset. We demonstrated that differential expression ratios obtained by using the MBCB had the best correlation with quantitative RT–PCR. MBCB also achieved better sensitivity in detecting differentially expressed genes with biological significance. For example, we demonstrated that the differential regulation of Tnfr2, Ikk and NF-kappaB, the death receptor pathway, in the AML samples, could only be detected by using data after MBCB implementation. We conclude that MBCB is a robust background correction method that will lead to more precise determination of gene expression and better biological interpretation of Illumina BeadArray data. PMID:18450815

Arabidopsis gene expression patterns during spaceflight

NASA Astrophysics Data System (ADS)

Paul, A.-L.; Ferl, R. J.

The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments resulted in the differential expression of hundreds of genes. A 5 day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β -Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on two fronts. First, expression patterns visualized with the Adh/GUS transgene were used to address specifically the possibility that spaceflight induces a hypoxic stress response, and to assess whether any spaceflight response was similar to control terrestrial hypoxia-induced gene expression patterns. (Paul et al., Plant Physiol. 2001, 126:613). Second, genome-wide patterns of native gene expression were evaluated utilizing the Affymetrix ATH1 GeneChip? array of 8,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes identified with the arrays was further characterized with quantitative Real-Time RT PCR (ABI - TaqmanTM). Comparison of the patterns of expression for arrays of hybridized with RNA isolated from plants exposed to spaceflight compared to the control arrays revealed hundreds of genes that were differentially expressed in response to spaceflight, yet most genes that are hallmarks of hypoxic stress were unaffected. These results will be discussed in light of current models for plant responses to the spaceflight environment, and with regard to potential future flight opportunities.

A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.

PubMed

Pozhitkov, Alex E; Noble, Peter A; Bryk, Jarosław; Tautz, Diethard

2014-01-01

Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations.

Using mummichog (Fundulus heteroclitus) arrays to monitor the effectiveness of remediation at a superfund site in Charleston, South Carolina, U.S.A.

PubMed

Roling, Jonathan A; Bain, Lisa J; Gardea-Torresdey, Jorge; Key, Peter B; Baldwin, William S

2007-06-01

We previously developed a cDNA array for mummichogs (Fundulus heteroclitus), an estuarine minnow, that is targeted for identifying differentially expressed genes from exposure to polycyclic aromatic hydrocarbons and several metals, including chromium. A chromium-contaminated Superfund site at Shipyard Creek in Charleston, South Carolina, USA, is undergoing remediation, providing us a unique opportunity to study the utility of arrays for monitoring the effectiveness of site remediation. Mummichogs were captured in Shipyard Creek in Charleston prior to remediation (2000) and after remediation began (2003 and 2005). Simultaneously, mummichogs were collected from a reference site at the Winyah Bay National Estuarine Research Reserve (NERR) in Georgetown, South Carolina, USA. The hepatic gene expression pattern of fish captured at Shipyard Creek in 2000 showed wide differences from the fish captured at NERR in 2000. Interestingly, as remediation progressed the gene expression pattern of mummichogs captured at Shipyard Creek became increasingly similar to those captured at NERR. The arrays acted as multidimensional biomarkers as the number of differentially expressed genes dropped from 22 in 2000 to four in 2003, and the magnitude of differential expression dropped from 3.2-fold in 2000 to no gene demonstrating a difference over 1.5-fold in 2003. Furthermore, the arrays indicated changes in the bioavailability of chromium caused by hydraulic dredging in the summer of 2005. This research is, to our knowledge, the first report using arrays as biomarkers for a weight-of-evidence hazard assessment and demonstrates that arrays can be used as multidimensional biomarkers to monitor site mitigation because the gene expression profile is associated with chromium bioavailability and body burden.

Dynamic gene expression response to altered gravity in human T cells.

PubMed

Thiel, Cora S; Hauschild, Swantje; Huge, Andreas; Tauber, Svantje; Lauber, Beatrice A; Polzer, Jennifer; Paulsen, Katrin; Lier, Hartwin; Engelmann, Frank; Schmitz, Burkhard; Schütte, Andreas; Layer, Liliana E; Ullrich, Oliver

2017-07-12

We investigated the dynamics of immediate and initial gene expression response to different gravitational environments in human Jurkat T lymphocytic cells and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. We used the Affymetrix GeneChip® Human Transcriptome Array 2.0 containing 44,699 protein coding genes and 22,829 non-protein coding genes and performed the experiments during a parabolic flight and a suborbital ballistic rocket mission to cross-validate gravity-regulated gene expression through independent research platforms and different sets of control experiments to exclude other factors than alteration of gravity. We found that gene expression in human T cells rapidly responded to altered gravity in the time frame of 20 s and 5 min. The initial response to microgravity involved mostly regulatory RNAs. We identified three gravity-regulated genes which could be cross-validated in both completely independent experiment missions: ATP6V1A/D, a vacuolar H + -ATPase (V-ATPase) responsible for acidification during bone resorption, IGHD3-3/IGHD3-10, diversity genes of the immunoglobulin heavy-chain locus participating in V(D)J recombination, and LINC00837, a long intergenic non-protein coding RNA. Due to the extensive and rapid alteration of gene expression associated with regulatory RNAs, we conclude that human cells are equipped with a robust and efficient adaptation potential when challenged with altered gravitational environments.

Dimensionality of Data Matrices with Applications to Gene Expression Profiles

ERIC Educational Resources Information Center

Feng, Xingdong

2009-01-01

Probe-level microarray data are usually stored in matrices. Take a given probe set (gene), for example, each row of the matrix corresponds to an array, and each column corresponds to a probe. Often, people summarize each array by the gene expression level. Is one number sufficient to summarize a whole probe set for a specific gene in an array?…

Bioinformatic analysis of primary endothelial cell gene array data illustrated by the analysis of transcriptome changes in endothelial cells exposed to VEGF-A and PlGF.

PubMed

Schoenfeld, Jonathan; Lessan, Khashayar; Johnson, Nicola A; Charnock-Jones, D Stephen; Evans, Amanda; Vourvouhaki, Ekaterini; Scott, Laurie; Stephens, Richard; Freeman, Tom C; Saidi, Samir A; Tom, Brian; Weston, Gareth C; Rogers, Peter; Smith, Stephen K; Print, Cristin G

2004-01-01

We recently published a review in this journal describing the design, hybridisation and basic data processing required to use gene arrays to investigate vascular biology (Evans et al. Angiogenesis 2003; 6: 93-104). Here, we build on this review by describing a set of powerful and robust methods for the analysis and interpretation of gene array data derived from primary vascular cell cultures. First, we describe the evaluation of transcriptome heterogeneity between primary cultures derived from different individuals, and estimation of the false discovery rate introduced by this heterogeneity and by experimental noise. Then, we discuss the appropriate use of Bayesian t-tests, clustering and independent component analysis to mine the data. We illustrate these principles by analysis of a previously unpublished set of gene array data in which human umbilical vein endothelial cells (HUVEC) cultured in either rich or low-serum media were exposed to vascular endothelial growth factor (VEGF)-A165 or placental growth factor (PlGF)-1(131). We have used Affymetrix U95A gene arrays to map the effects of these factors on the HUVEC transcriptome. These experiments followed a paired design and were biologically replicated three times. In addition, one experiment was repeated using serial analysis of gene expression (SAGE). In contrast to some previous studies, we found that VEGF-A and PlGF consistently regulated only small, non-overlapping and culture media-dependant sets of HUVEC transcripts, despite causing significant cell biological changes.

Cable Crosstalk Suppression with Two-Wire Voltage Feedback Method for Resistive Sensor Array

PubMed Central

Wu, Jianfeng; He, Shangshang; Li, Jianqing; Song, Aiguo

2016-01-01

Using a long, flexible test cable connected with a one-wire voltage feedback circuit, a resistive tactile sensor in a shared row-column fashion exhibited flexibility in robotic operations but suffered from crosstalk caused by the connected cable due to its wire resistances and its contacted resistances. Firstly, we designed a new non-scanned driving-electrode (VF-NSDE) circuit using two wires for every row line and every column line to reduce the crosstalk caused by the connected cables in the circuit. Then, an equivalent resistance expression of the element being tested (EBT) for the two-wire VF-NSDE circuit was analytically derived. Following this, the one-wire VF-NSDE circuit and the two-wire VF-NSDE circuit were evaluated by simulation experiments. Finally, positive features of the proposed method were verified with the experiments of a two-wire VF-NSDE prototype circuit. The experiment results show that the two-wire VF-NSDE circuit can greatly reduce the crosstalk error caused by the cables in the 2-D networked resistive sensor array. PMID:26907279

Glycan array data management at Consortium for Functional Glycomics.

PubMed

Venkataraman, Maha; Sasisekharan, Ram; Raman, Rahul

2015-01-01

Glycomics or the study of structure-function relationships of complex glycans has reshaped post-genomics biology. Glycans mediate fundamental biological functions via their specific interactions with a variety of proteins. Recognizing the importance of glycomics, large-scale research initiatives such as the Consortium for Functional Glycomics (CFG) were established to address these challenges. Over the past decade, the Consortium for Functional Glycomics (CFG) has generated novel reagents and technologies for glycomics analyses, which in turn have led to generation of diverse datasets. These datasets have contributed to understanding glycan diversity and structure-function relationships at molecular (glycan-protein interactions), cellular (gene expression and glycan analysis), and whole organism (mouse phenotyping) levels. Among these analyses and datasets, screening of glycan-protein interactions on glycan array platforms has gained much prominence and has contributed to cross-disciplinary realization of the importance of glycomics in areas such as immunology, infectious diseases, cancer biomarkers, etc. This manuscript outlines methodologies for capturing data from glycan array experiments and online tools to access and visualize glycan array data implemented at the CFG.

Identification of the collagen type 1 alpha 1 gene (COL1A1) as a candidate survival-related factor associated with hepatocellular carcinoma

PubMed Central

2014-01-01

Background Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related death especially among Asian and African populations. It is urgent that we identify carcinogenesis-related genes to establish an innovative treatment strategy for this disease. Methods Triple-combination array analysis was performed using one pair each of HCC and noncancerous liver samples from a 68-year-old woman. This analysis consists of expression array, single nucleotide polymorphism array and methylation array. The gene encoding collagen type 1 alpha 1 (COL1A1) was identified and verified using HCC cell lines and 48 tissues from patients with primary HCC. Results Expression array revealed that COL1A1 gene expression was markedly decreased in tumor tissues (log2 ratio –1.1). The single nucleotide polymorphism array showed no chromosomal deletion in the locus of COL1A1. Importantly, the methylation value in the tumor tissue was higher (0.557) than that of the adjacent liver tissue (0.008). We verified that expression of this gene was suppressed by promoter methylation. Reactivation of COL1A1 expression by 5-aza-2′-deoxycytidine treatment was seen in HCC cell lines, and sequence analysis identified methylated CpG sites in the COL1A1 promoter region. Among 48 pairs of surgical specimens, 13 (27.1%) showed decreased COL1A1 mRNA expression in tumor sites. Among these 13 cases, 10 had promoter methylation at the tumor site. The log-rank test indicated that mRNA down-regulated tumors were significantly correlated with a poor overall survival rate (P = 0.013). Conclusions Triple-combination array analysis successfully identified COL1A1 as a candidate survival-related gene in HCCs. Epigenetic down-regulation of COL1A1 mRNA expression might have a role as a prognostic biomarker of HCC. PMID:24552139

An alternative method to amplify RNA without loss of signal conservation for expression analysis with a proteinase DNA microarray in the ArrayTube format.

PubMed

Schüler, Susann; Wenz, Ingrid; Wiederanders, B; Slickers, P; Ehricht, R

2006-06-12

Recent developments in DNA microarray technology led to a variety of open and closed devices and systems including high and low density microarrays for high-throughput screening applications as well as microarrays of lower density for specific diagnostic purposes. Beside predefined microarrays for specific applications manufacturers offer the production of custom-designed microarrays adapted to customers' wishes. Array based assays demand complex procedures including several steps for sample preparation (RNA extraction, amplification and sample labelling), hybridization and detection, thus leading to a high variability between several approaches and resulting in the necessity of extensive standardization and normalization procedures. In the present work a custom designed human proteinase DNA microarray of lower density in ArrayTube format was established. This highly economic open platform only requires standard laboratory equipment and allows the study of the molecular regulation of cell behaviour by proteinases. We established a procedure for sample preparation and hybridization and verified the array based gene expression profile by quantitative real-time PCR (QRT-PCR). Moreover, we compared the results with the well established Affymetrix microarray. By application of standard labelling procedures with e.g. Klenow fragment exo-, single primer amplification (SPA) or In Vitro Transcription (IVT) we noticed a loss of signal conservation for some genes. To overcome this problem we developed a protocol in accordance with the SPA protocol, in which we included target specific primers designed individually for each spotted oligomer. Here we present a complete array based assay in which only the specific transcripts of interest are amplified in parallel and in a linear manner. The array represents a proof of principle which can be adapted to other species as well. As the designed protocol for amplifying mRNA starts from as little as 100 ng total RNA, it presents an alternative method for detecting even low expressed genes by microarray experiments in a highly reproducible and sensitive manner. Preservation of signal integrity is demonstrated out by QRT-PCR measurements. The little amounts of total RNA necessary for the analyses make this method applicable for investigations with limited material as in clinical samples from, for example, organ or tumour biopsies. Those are arguments in favour of the high potential of our assay compared to established procedures for amplification within the field of diagnostic expression profiling. Nevertheless, the screening character of microarray data must be mentioned, and independent methods should verify the results.

Impedance of curved rectangular spiral coils around a conductive cylinder

NASA Astrophysics Data System (ADS)

Burke, S. K.; Ditchburn, R. J.; Theodoulidis, T. P.

2008-07-01

Eddy-current induction due to a thin conformable coil wrapped around a long conductive cylinder is examined using a second-order vector potential formalism. Compact closed-form expressions are derived for the self- and mutual impedances of curved rectangular spiral coils (i) in free space and (ii) when wrapped around the surface of the cylindrical rod. The validity of these expressions was tested against the results of a systematic series of experiments using a cylindrical Al-alloy rod and conformable coils manufactured using flexible printed-circuit-board technology. The theoretical expressions were in very good agreement with the experimental measurements. The significance of the results for eddy-current nondestructive inspection using flexible coils and flexible coil arrays is discussed.

Talbot effect of quasi-periodic grating.

PubMed

Zhang, Chong; Zhang, Wei; Li, Furui; Wang, Junhong; Teng, Shuyun

2013-07-20

Theoretic and experimental studies of the Talbot effect of quasi-periodic gratings are performed in this paper. The diffractions of periodic and quasi-periodic square aperture arrays in Fresnel fields are analyzed according to the scalar diffraction theory. The expressions of the diffraction intensities of two types of quasi-periodic gratings are deduced. Talbot images of the quasi-periodic gratings are predicted to appear at multiple certain distances. The quasi-periodic square aperture arrays are produced with the aid of a liquid crystal light modulator, and the self-images of the quasi-periodic gratings are measured successfully in the experiment. This study indicates that even a structure in short-range disorder may take on the self-imaging effect in a Fresnel field.

Pulsars Probe the Low-Frequency Gravitational Sky: Pulsar Timing Arrays Basics and Recent Results

NASA Astrophysics Data System (ADS)

Tiburzi, Caterina

2018-03-01

Pulsar Timing Array experiments exploit the clock-like behaviour of an array of millisecond pulsars, with the goal of detecting low-frequency gravitational waves. Pulsar Timing Array experiments have been in operation over the last decade, led by groups in Europe, Australia, and North America. These experiments use the most sensitive radio telescopes in the world, extremely precise pulsar timing models and sophisticated detection algorithms to increase the sensitivity of Pulsar Timing Arrays. No detection of gravitational waves has been made to date with this technique, but Pulsar Timing Array upper limits already contributed to rule out some models of galaxy formation. Moreover, a new generation of radio telescopes, such as the Five hundred metre Aperture Spherical Telescope and, in particular, the Square Kilometre Array, will offer a significant improvement to the Pulsar Timing Array sensitivity. In this article, we review the basic concepts of Pulsar Timing Array experiments, and discuss the latest results from the established Pulsar Timing Array collaborations.

Analysis of differential gene expression by bead-based fiber-optic array in growth-hormone-secreting pituitary adenomas.

PubMed

Jiang, Zhiquan; Gui, Songbo; Zhang, Yazhuo

2010-09-01

Growth-hormone-secreting pituitary adenomas (GHomas) account for approximately 20% of all pituitary neoplasms. However, the pathogenesis of GHomas remains to be elucidated. To explore the possible pathogenesis of GHomas, we used bead-based fiber-optic arrays to examine the gene expression in five GHomas and compared them to three healthy pituitaries. Four differentially expressed genes were chosen randomly for validation by quantitative real-time reverse transcription-polymerase chain reaction. We then performed pathway analysis on the identified differentially expressed genes using the Kyoto Encyclopedia of Genes and Genomes. Array analysis showed significant increases in the expression of 353 genes and 206 expressed sequence tags (ESTs) and decreases in 565 genes and 29 ESTs. Bioinformatic analysis showed that the genes HIGD1B, HOXB2, ANGPT2, HPGD and BTG2 may play an important role in the tumorigenesis and progression of GHomas. Pathway analysis showed that the wingless-type signaling pathway and extracellular-matrix receptor interactions may play a key role in the tumorigenesis and progression of GHomas. Our data suggested that there are numerous aberrantly expressed genes and pathways involved in the pathogenesis of GHomas. Bead-based fiber-optic arrays combined with pathway analysis of differentially expressed genes appear to be a valid method for investigating the pathogenesis of tumors.

Analysis of differential gene expression by bead-based fiber-optic array in growth-hormone-secreting pituitary adenomas

PubMed Central

JIANG, ZHIQUAN; GUI, SONGBO; ZHANG, YAZHUO

2010-01-01

Growth-hormone-secreting pituitary adenomas (GHomas) account for approximately 20% of all pituitary neoplasms. However, the pathogenesis of GHomas remains to be elucidated. To explore the possible pathogenesis of GHomas, we used bead-based fiber-optic arrays to examine the gene expression in five GHomas and compared them to three healthy pituitaries. Four differentially expressed genes were chosen randomly for validation by quantitative real-time reverse transcription-polymerase chain reaction. We then performed pathway analysis on the identified differentially expressed genes using the Kyoto Encyclopedia of Genes and Genomes. Array analysis showed significant increases in the expression of 353 genes and 206 expressed sequence tags (ESTs) and decreases in 565 genes and 29 ESTs. Bioinformatic analysis showed that the genes HIGD1B, HOXB2, ANGPT2, HPGD and BTG2 may play an important role in the tumorigenesis and progression of GHomas. Pathway analysis showed that the wingless-type signaling pathway and extracellular-matrix receptor interactions may play a key role in the tumorigenesis and progression of GHomas. Our data suggested that there are numerous aberrantly expressed genes and pathways involved in the pathogenesis of GHomas. Bead-based fiber-optic arrays combined with pathway analysis of differentially expressed genes appear to be a valid method for investigating the pathogenesis of tumors. PMID:22993617

Identification of Mouse Serum miRNA Endogenous References by Global Gene Expression Profiles

PubMed Central

Mi, Qing-Sheng; Weiland, Matthew; Qi, Rui-Qun; Gao, Xing-Hua; Poisson, Laila M.; Zhou, Li

2012-01-01

MicroRNAs (miRNAs) are recently discovered small non-coding RNAs and can serve as serum biomarkers for disease diagnosis and prognoses. Lack of reliable serum miRNA endogenous references for normalization in miRNA gene expression makes single miRNA assays inaccurate. Using TaqMan® real-time PCR miRNA arrays with a global gene expression normalization strategy, we have analyzed serum miRNA expression profiles of 20 female mice of NOD/ShiLtJ (n = 8), NOR/LtJ (n = 6), and C57BL/6J (n = 6) at different ages and disease conditions. We identified five miRNAs, miR-146a, miR-16, miR-195, miR-30e and miR-744, to be stably expressed in all strains, which could serve as mouse serum miRNA endogenous references for single assay experiments. PMID:22348064

Digital detection of multiple minority mutants and expression levels of multiple colorectal cancer-related genes using digital-PCR coupled with bead-array.

PubMed

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed "multiplex ligation-dependent probe amplification-digital amplification coupled with hydrogel bead-array" (MLPA-DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA-DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA-DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC.

Development of multitissue microfluidic dynamic array for assessing changes in gene expression associated with channel catfish appetite, growth, metabolism, and intestinal health

USDA-ARS?s Scientific Manuscript database

Large-scale, gene expression methods allow for high throughput analysis of physiological pathways at a fraction of the cost of individual gene expression analysis. Systems, such as the Fluidigm quantitative PCR array described here, can provide powerful assessments of the effects of diet, environme...

Normalization of High Dimensional Genomics Data Where the Distribution of the Altered Variables Is Skewed

PubMed Central

Landfors, Mattias; Philip, Philge; Rydén, Patrik; Stenberg, Per

2011-01-01

Genome-wide analysis of gene expression or protein binding patterns using different array or sequencing based technologies is now routinely performed to compare different populations, such as treatment and reference groups. It is often necessary to normalize the data obtained to remove technical variation introduced in the course of conducting experimental work, but standard normalization techniques are not capable of eliminating technical bias in cases where the distribution of the truly altered variables is skewed, i.e. when a large fraction of the variables are either positively or negatively affected by the treatment. However, several experiments are likely to generate such skewed distributions, including ChIP-chip experiments for the study of chromatin, gene expression experiments for the study of apoptosis, and SNP-studies of copy number variation in normal and tumour tissues. A preliminary study using spike-in array data established that the capacity of an experiment to identify altered variables and generate unbiased estimates of the fold change decreases as the fraction of altered variables and the skewness increases. We propose the following work-flow for analyzing high-dimensional experiments with regions of altered variables: (1) Pre-process raw data using one of the standard normalization techniques. (2) Investigate if the distribution of the altered variables is skewed. (3) If the distribution is not believed to be skewed, no additional normalization is needed. Otherwise, re-normalize the data using a novel HMM-assisted normalization procedure. (4) Perform downstream analysis. Here, ChIP-chip data and simulated data were used to evaluate the performance of the work-flow. It was found that skewed distributions can be detected by using the novel DSE-test (Detection of Skewed Experiments). Furthermore, applying the HMM-assisted normalization to experiments where the distribution of the truly altered variables is skewed results in considerably higher sensitivity and lower bias than can be attained using standard and invariant normalization methods. PMID:22132175

Mobile phone radiation causes changes in gene and protein expression in human endothelial cell lines and the response seems to be genome- and proteome-dependent.

PubMed

Nylund, Reetta; Leszczynski, Dariusz

2006-09-01

We have examined in vitro cell response to mobile phone radiation (900 MHz GSM signal) using two variants of human endothelial cell line: EA.hy926 and EA.hy926v1. Gene expression changes were examined in three experiments using cDNA Expression Arrays and protein expression changes were examined in ten experiments using 2-DE and PDQuest software. Obtained results show that gene and protein expression were altered, in both examined cell lines, in response to one hour mobile phone radiation exposure at an average specific absorption rate of 2.8 W/kg. However, the same genes and proteins were differently affected by the exposure in each of the cell lines. This suggests that the cell response to mobile phone radiation might be genome- and proteome-dependent. Therefore, it is likely that different types of cells and from different species might respond differently to mobile phone radiation or might have different sensitivity to this weak stimulus. Our findings might also explain, at least in part, the origin of discrepancies in replication studies between different laboratories.

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

PubMed Central

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

2002-01-01

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

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

PubMed Central

2009-01-01

Background Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear. Results We have performed a comprehensive sensitivity analysis of microarray breast cancer classification under the two types of feature variability mentioned above. We used data from six state of the art preprocessing methods, using a compendium consisting of eight diferent datasets, involving 1131 hybridizations, containing data from both one and two-color array technology. For a wide range of classifiers, we performed a joint study on performance, concordance and stability. In the stability analysis we explicitly tested classifiers for their noise tolerance by using perturbed expression profiles that are based on uncertainty information directly related to the preprocessing methods. Our results indicate that signature composition is strongly influenced by feature variability, even if the array platform and the stratification of patient samples are identical. In addition, we show that there is often a high level of discordance between individual class assignments for signatures constructed on data coming from different preprocessing schemes, even if the actual signature composition is identical. Conclusion Feature variability can have a strong impact on breast cancer signature composition, as well as the classification of individual patient samples. We therefore strongly recommend that feature variability is considered in analyzing data from microarray breast cancer expression profiling experiments. PMID:19941644

Choosing the Right Tool for the Job: RNAi, TALEN or CRISPR

PubMed Central

Boettcher, Michael; McManus, Michael T.

2015-01-01

The most widely used approach for defining a genes’ function is to reduce or completely disrupt its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to disrupt gene expression in many organisms. However, new biotechnological tools - specifically CRISPR-based technologies - have become available and are squeezing out RNAi dominance in mammalian cell studies. These seemingly competing technologies leave research investigators with the question: ‘Which technology should I use in my experiment?’ This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools. PMID:26000843

The atmospheric transparency of Telescope Array experiment from LIDAR

NASA Astrophysics Data System (ADS)

Tomida, T.

2011-09-01

UV fluorescence light generated by an air shower is scattered and lost along the path of transmission to the telescope. The main scattering processes are Rayleigh scattering by molecules and scattering by aerosols in an atmosphere. In the Telescope Array Experiment, we make use of LIDAR (LIght Detection And Ranging), which observes the back-scattered light of laser. The LIDAR system is operated before the beginning and after the end of an FD observation, twice a night. The typical transparency of aerosols on clear night is obtained two years observation from September, 2007. The extinction coefficient of aerosols (αAS) at ground level are 0.040-0.013+0.036 km-1. The dependence of typical aerosols on height above ground level (1450 m a.s.l.) can be express by two exponential components as following: αAS(h) = 0.021 exp(-h/0.2)+0.019 exp(-h/1.9). The atmospheric transparency measured with the LIDAR system in TA site is discussed in this paper.

Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

PubMed Central

Janssen, Bart J; Thodey, Kate; Schaffer, Robert J; Alba, Rob; Balakrishnan, Lena; Bishop, Rebecca; Bowen, Judith H; Crowhurst, Ross N; Gleave, Andrew P; Ledger, Susan; McArtney, Steve; Pichler, Franz B; Snowden, Kimberley C; Ward, Shayna

2008-01-01

Background Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45–55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple. Results Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes. Conclusion Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development. PMID:18279528

Global gene expression analysis of apple fruit development from the floral bud to ripe fruit.

PubMed

Janssen, Bart J; Thodey, Kate; Schaffer, Robert J; Alba, Rob; Balakrishnan, Lena; Bishop, Rebecca; Bowen, Judith H; Crowhurst, Ross N; Gleave, Andrew P; Ledger, Susan; McArtney, Steve; Pichler, Franz B; Snowden, Kimberley C; Ward, Shayna

2008-02-17

Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45-55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple. Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes. Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.

Plasma chamber testing of advanced photovoltaic solar array coupons

NASA Technical Reports Server (NTRS)

Hillard, G. Barry

1994-01-01

The solar array module plasma interactions experiment is a space shuttle experiment designed to investigate and quantify the high voltage plasma interactions. One of the objectives of the experiment is to test the performance of the Advanced Photovoltaic Solar Array (APSA). The material properties of array blanket are also studied as electric insulators for APSA arrays in high voltage conditions. Three twelve cell prototype coupons of silicon cells were constructed and tested in a space simulation chamber.

Array data extractor (ADE): a LabVIEW program to extract and merge gene array data.

PubMed

Kurtenbach, Stefan; Kurtenbach, Sarah; Zoidl, Georg

2013-12-01

Large data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists. Here, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets. Although existing software allows for complex data analyses, the LabVIEW based program presented here, "Array Data Extractor (ADE)", provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge.

The Photovoltaic Array Space Power plus Diagnostics (PASP Plus) Flight Experiment

NASA Technical Reports Server (NTRS)

Piszczor, Michael F.; Curtis, Henry B.; Guidice, Donald A.; Severance, Paul S.

1992-01-01

An overview of the Photovoltaic Array Space Power Plus Diagnostics (PASP Plus) flight experiment is presented in outline and graphic form. The goal of the experiment is to test a variety of photovoltaic cell and array technologies under various space environmental conditions. Experiment objectives, flight hardware, experiment control and diagnostic instrumentation, and illuminated thermal vacuum testing are addressed.

NORMAL NASAL GENE EXPRESSION LEVELS USING CDNA ARRAY TECHNOLOGY

EPA Science Inventory

Normal Nasal Gene Expression Levels Using cDNA Array Technology.

The nasal epithelium is a target site for chemically-induced toxicity and carcinogenicity. To detect and analyze genetic events which contribute to nasal tumor development, we first defined the gene expressi...

GENE EXPRESSION PATTERNS ASSOCIATED WITH INFERTILITY IN HUMAN AND RODENT MODELS

EPA Science Inventory

Modern genomic technologies such as DNA arrays provide the means to investigate molecular interactions at an unprecedented level, and arrays have been used to carry out gene expression profiling as a means of identifying candidate genes involved in molecular mechanisms underlying...

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

PubMed

Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; Seo, Young-Su; Shultz, Michael; Ouyang, Shu; Yuan, Qiaoping; Frank, Bryan C; Ly, Eugene; Zheng, Li; Jia, Yi; Hsia, An-Ping; An, Kyungsook; Chou, Hui-Hsien; Rocke, David; Lee, Geun Cheol; Schnable, Patrick S; An, Gynheung; Buell, C Robin; Ronald, Pamela C

2008-10-06

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

Mothers' pupillary responses to infant facial expressions.

PubMed

Yrttiaho, Santeri; Niehaus, Dana; Thomas, Eileen; Leppänen, Jukka M

2017-02-06

Human parental care relies heavily on the ability to monitor and respond to a child's affective states. The current study examined pupil diameter as a potential physiological index of mothers' affective response to infant facial expressions. Pupillary time-series were measured from 86 mothers of young infants in response to an array of photographic infant faces falling into four emotive categories based on valence (positive vs. negative) and arousal (mild vs. strong). Pupil dilation was highly sensitive to the valence of facial expressions, being larger for negative vs. positive facial expressions. A separate control experiment with luminance-matched non-face stimuli indicated that the valence effect was specific to facial expressions and cannot be explained by luminance confounds. Pupil response was not sensitive to the arousal level of facial expressions. The results show the feasibility of using pupil diameter as a marker of mothers' affective responses to ecologically valid infant stimuli and point to a particularly prompt maternal response to infant distress cues.

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile

PubMed Central

Boudry, Pierre; Semenova, Ekaterina; Monot, Marc; Datsenko, Kirill A.; Lopatina, Anna; Sekulovic, Ognjen; Ospina-Bedoya, Maicol; Fortier, Louis-Charles; Severinov, Konstantin; Dupuy, Bruno

2015-01-01

ABSTRACT Clostridium difficile is the cause of most frequently occurring nosocomial diarrhea worldwide. As an enteropathogen, C. difficile must be exposed to multiple exogenous genetic elements in bacteriophage-rich gut communities. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems allow bacteria to adapt to foreign genetic invaders. Our recent data revealed active expression and processing of CRISPR RNAs from multiple type I-B CRISPR arrays in C. difficile reference strain 630. Here, we demonstrate active expression of CRISPR arrays in strain R20291, an epidemic C. difficile strain. Through genome sequencing and host range analysis of several new C. difficile phages and plasmid conjugation experiments, we provide evidence of defensive function of the CRISPR-Cas system in both C. difficile strains. We further demonstrate that C. difficile Cas proteins are capable of interference in a heterologous host, Escherichia coli. These data set the stage for mechanistic and physiological analyses of CRISPR-Cas-mediated interactions of important global human pathogen with its genetic parasites. PMID:26330515

A random variance model for detection of differential gene expression in small microarray experiments.

PubMed

Wright, George W; Simon, Richard M

2003-12-12

Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true. We propose a model by which the within gene variances are drawn from an inverse gamma distribution, whose parameters are estimated across all genes. This results in a test statistic that is a minor variation of those used in standard linear models. We demonstrate that the model assumptions are valid on experimental data, and that the model has more power than standard tests to pick up large changes in expression, while not increasing the rate of false positives. This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf

Modeling and analysis of a novel planar eddy current damper

NASA Astrophysics Data System (ADS)

Zhang, He; Kou, Baoquan; Jin, Yinxi; Zhang, Lu; Zhang, Hailin; Li, Liyi

2014-05-01

In this paper, a novel 2-DOF permanent magnet planar eddy current damper is proposed, of which the stator is made of a copper plate and the mover is composed of two orthogonal 1-D permanent magnet arrays with a double sided structure. The main objective of the planar eddy current damper is to provide two orthogonal damping forces for dynamic systems like the 2-DOF high precision positioning system. Firstly, the basic structure and the operating principle of the planar damper are introduced. Secondly, the analytical model of the planar damper is established where the magnetic flux density distribution of the permanent magnet arrays is obtained by using the equivalent magnetic charge method and the image method. Then, the analytical expressions of the damping force and damping coefficient are derived. Lastly, to verify the analytical model, the finite element method (FEM) is adopted for calculating the flux density and a planar damper prototype is manufactured and thoroughly tested. The results from FEM and experiments are in good agreement with the ones from the analytical expressions indicating that the analytical model is reasonable and correct.

Visual short-term memory for sequential arrays.

PubMed

Kumar, Arjun; Jiang, Yuhong

2005-04-01

The capacity of visual short-term memory (VSTM) for a single visual display has been investigated in past research, but VSTM for multiple sequential arrays has been explored only recently. In this study, we investigate the capacity of VSTM across two sequential arrays separated by a variable stimulus onset asynchrony (SOA). VSTM for spatial locations (Experiment 1), colors (Experiments 2-4), orientations (Experiments 3 and 4), and conjunction of color and orientation (Experiment 4) were tested, with the SOA across the two sequential arrays varying from 100 to 1,500 msec. We find that VSTM for the trailing array is much better than VSTM for the leading array, but when averaged across the two arrays VSTM has a constant capacity independent of the SOA. We suggest that multiple displays compete for retention in VSTM and that separating information into two temporally discrete groups does not enhance the overall capacity of VSTM.

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

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

A database for the analysis of immunity genes in Drosophila: PADMA database.

PubMed

Lee, Mark J; Mondal, Ariful; Small, Chiyedza; Paddibhatla, Indira; Kawaguchi, Akira; Govind, Shubha

2011-01-01

While microarray experiments generate voluminous data, discerning trends that support an existing or alternative paradigm is challenging. To synergize hypothesis building and testing, we designed the Pathogen Associated Drosophila MicroArray (PADMA) database for easy retrieval and comparison of microarray results from immunity-related experiments (www.padmadatabase.org). PADMA also allows biologists to upload their microarray-results and compare it with datasets housed within PADMA. We tested PADMA using a preliminary dataset from Ganaspis xanthopoda-infected fly larvae, and uncovered unexpected trends in gene expression, reshaping our hypothesis. Thus, the PADMA database will be a useful resource to fly researchers to evaluate, revise, and refine hypotheses.

Gene expression of cell surface antigens in the early phase of murine influenza pneumonia determined by a cDNA expression array technique.

PubMed

Sakai, Shinya; Mantani, Naoki; Kogure, Toshiaki; Ochiai, Hiroshi; Shimada, Yutaka; Terasawa, Katsutoshi

2002-12-01

Influenza virus is a worldwide health problem with significant economic consequences. To study the gene expression pattern induced by influenza virus infection, it is useful to reveal the pathogenesis of influenza virus infection; but this has not been well examined, especially in vivo study. To assess the influence of influenza virus infection on gene expression in mice, mRNA levels in the lung and tracheal tissue 48 h after infection were investigated by cDNA array analysis. Four-week-old outbred, specific pathogen free strain, ICR female mice were infected by intra-nasal inoculation of a virus solution under ether anesthesia. The mice were sacrificed 48 h after infection and the tracheas and lungs were removed. To determine gene expression, the membrane-based microtechnique with an Atlas cDNA expression array (mouse 1.2 array II) was performed in accordance with the manual provided. We focused on the expression of 46 mRNAs for cell surface antigens. Of these 46 mRNAs that we examined, four (CD1d2 antigen, CD39 antigen-like 1, CD39 antigen-like 3, CD68 antigen) were up-regulated and one (CD36 antigen) was down-regulated. Although further studies are required, these data suggest that these molecules play an important role in influenza virus infection, especially the phase before specific immunity.

Closed-Form Evaluation of Mutual Coupling in a Planar Array of Circular Apertures

NASA Technical Reports Server (NTRS)

Bailey, M. C.

1996-01-01

The integral expression for the mutual admittance between circular apertures in a planar array is evaluated in closed form. Very good accuracy is realized when compared with values that were obtained by numerical integration. Utilization of this closed-form expression, for all element pairs that are separated by more than one element spacing, yields extremely accurate results and significantly reduces the computation time that is required to analyze the performance of a large electronically scanning antenna array.

Array data extractor (ADE): a LabVIEW program to extract and merge gene array data

PubMed Central

2013-01-01

Background Large data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists. Findings Here, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets. Conclusions Although existing software allows for complex data analyses, the LabVIEW based program presented here, “Array Data Extractor (ADE)”, provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge. PMID:24289243

Modulation of intestinal gene expression by dietary zinc status: Effectiveness of cDNA arrays for expression profiling of a single nutrient deficiency

PubMed Central

Blanchard, Raymond K.; Moore, J. Bernadette; Green, Calvert L.; Cousins, Robert J.

2001-01-01

Mammalian nutritional status affects the homeostatic balance of multiple physiological processes and their associated gene expression. Although DNA array analysis can monitor large numbers of genes, there are no reports of expression profiling of a micronutrient deficiency in an intact animal system. In this report, we have tested the feasibility of using cDNA arrays to compare the global changes in expression of genes of known function that occur in the early stages of rodent zinc deficiency. The gene-modulating effects of this deficiency were demonstrated by real-time quantitative PCR measurements of altered mRNA levels for metallothionein 1, zinc transporter 2, and uroguanylin, all of which have been previously documented as zinc-regulated genes. As a result of the low level of inherent noise within this model system and application of a recently reported statistical tool for statistical analysis of microarrays [Tusher, V.G., Tibshirani, R. & Chu, G. (2001) Proc. Natl. Acad. Sci. USA 98, 5116–5121], we demonstrate the ability to reproducibly identify the modest changes in mRNA abundance produced by this single micronutrient deficiency. Among the genes identified by this array profile are intestinal genes that influence signaling pathways, growth, transcription, redox, and energy utilization. Additionally, the influence of dietary zinc supply on the expression of some of these genes was confirmed by real-time quantitative PCR. Overall, these data support the effectiveness of cDNA array expression profiling to investigate the pleiotropic effects of specific nutrients and may provide an approach to establishing markers for assessment of nutritional status. PMID:11717422

Design, modelling and preliminary characterisation of microneedle-based electrodes for tissue electroporation in vivo

NASA Astrophysics Data System (ADS)

O'Mahony, Conor; Houlihan, Ruth; Grygoryev, Konstantin; Ning, Zhenfei; Williams, John; Moore, Tom

2016-10-01

We analysed the use of microneedle-based electrodes to enhance electroporation of mouse testis with DNA vectors for production of transgenic mice. Different microneedle formats were developed and tested, and we ultimately used electrodes based on arrays of 500 μm tall microneedles. In a series of experiments involving injection of a DNA vector expressing Green Fluorescent Protein (GFP) and electroporation using microneedle electrodes and a commercially available voltage supply, we compared the performance of flat and microneedle electrodes by measuring GFP expression at various timepoints after electroporation. Our main finding, supported by both experimental and simulated data, is that needles significantly enhanced electroporation of testis.

Uniform and nonuniform V-shaped planar arrays for 2-D direction-of-arrival estimation

NASA Astrophysics Data System (ADS)

Filik, T.; Tuncer, T. E.

2009-10-01

In this paper, isotropic and directional uniform and nonuniform V-shaped arrays are considered for azimuth and elevation direction-of-arrival (DOA) angle estimation simultaneously. It is shown that the uniform isotropic V-shaped arrays (UI V arrays) have no angle coupling between the azimuth and elevation DOA. The design of the UI V arrays is investigated, and closed form expressions are presented for the parameters of the UI V arrays and nonuniform V arrays. These expressions allow one to find the isotropic V angle for different array types. The DOA performance of the UI V array is compared with the uniform circular array (UCA) for correlated signals and in case of mutual coupling between array elements. The modeling error for the sensor positions is also investigated. It is shown that V array and circular array have similar robustness for the position errors while the performance of UI V array is better than the UCA for correlated source signals and when there is mutual coupling. Nonuniform V-shaped isotropic arrays are investigated which allow good DOA performance with limited number of sensors. Furthermore, a new design method for the directional V-shaped arrays is proposed. This method is based on the Cramer-Rao Bound for joint estimation where the angle coupling effect between the azimuth and elevation DOA angles is taken into account. The design method finds an optimum angle between the linear subarrays of the V array. The proposed method can be used to obtain directional arrays with significantly better DOA performance.

Concept Definition Study for In-Space Structural Characterization of a Lightweight Solar Array

NASA Technical Reports Server (NTRS)

Woods-Vedeler, Jessica A.; Pappa, Richard S.; Jones, Thomas W.; Spellman, Regina; Scott, Willis; Mockensturm, Eric M.; Liddle, Donn; Oshel, Ed; Snyder, Michael

2002-01-01

A Concept Definition Study (CDS) was conducted to develop a proposed "Lightweight High-Voltage Stretched-Lens Concentrator Solar Array Experiment" under NASA's New Millennium Program Space Technology-6 (NMP ST-6) activity. As part of a multi-organizational team, NASA Langley Research Center's role in this proposed experiment was to lead Structural Characterization of the solar array during the flight experiment. In support of this role, NASA LaRC participated in the CDS to de.ne an experiment for static, dynamic, and deployment characterization of the array. In this study, NASA LaRC traded state-of-the-art measurement approaches appropriate for an in-space, STS-based flight experiment, provided initial analysis and testing of the lightweight solar array and lens elements, performed a lighting and photogrammetric simulation in conjunction with JSC, and produced an experiment concept definition to meet structural characterization requirements.

Suboptimal evolutionary novel environments promote singular altered gravity responses of transcriptome during Drosophila metamorphosis

PubMed Central

2013-01-01

Background Previous experiments have shown that the reduced gravity aboard the International Space Station (ISS) causes important alterations in Drosophila gene expression. These changes were shown to be intimately linked to environmental space-flight related constraints. Results Here, we use an array of different techniques for ground-based simulation of microgravity effects to assess the effect of suboptimal environmental conditions on the gene expression of Drosophila in reduced gravity. A global and integrative analysis, using “gene expression dynamics inspector” (GEDI) self-organizing maps, reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices. Although the genes that are affected are different in each simulation technique, we find that the same gene ontology groups, including at least one large multigene family related with behavior, stress response or organogenesis, are over represented in each case. Conclusions These results suggest that the transcriptome as a whole can be finely tuned to gravity force. In optimum environmental conditions, the alteration of gravity has only mild effects on gene expression but when environmental conditions are far from optimal, the gene expression must be tuned greatly and effects become more robust, probably linked to the lack of experience of organisms exposed to evolutionary novel environments such as a gravitational free one. PMID:23806134

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

PubMed Central

Holloway, Andrew J; Oshlack, Alicia; Diyagama, Dileepa S; Bowtell, David DL; Smyth, Gordon K

2006-01-01

Background Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. Results A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression levels. The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model. The methodology is used to compare three data extraction algorithms for the Affymetrix platforms, demonstrating poor performance for the commonly used proprietary algorithm relative to the other algorithms. For probes which can be matched across platforms, the cross-platform variability is decomposed into within-platform and between-platform components, showing that platform disagreement is almost entirely systematic rather than due to measurement variability. Conclusion The results demonstrate good precision and sensitivity for all the platforms, but highlight the need for improved probe annotation. They quantify the extent to which cross-platform measures can be expected to be less accurate than within-platform comparisons for predicting disease progression or outcome. PMID:17118209

Emerging Use of Gene Expression Microarrays in Plant Physiology

DOE PAGES

Wullschleger, Stan D.; Difazio, Stephen P.

2003-01-01

Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology weremore » selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.« less

Defining Genomic Changes in Triple-Negative Breast Cancer in Women of African Descent

DTIC Science & Technology

2012-06-01

Triple negative breast cancer • Ethnic disparities • Breast cancer amongst African Americans and Africans • Gene expression profiling • Array... negative cases seen in both African and African - American breast cancer cases. Gene Expression Array Studies The 31 triple negative Kijabe... African - American Adjacent Normal Breast Tissue PI: Pegram &

THE USE OF GENE ARRAYS TO MEASURE CHANGES IN GENE EXPRESSION PATTERNS IN FISH EXPOSED TO COMPOUNDS THAT MIMIC ESTROGEN

EPA Science Inventory

We have developed estrogen-sensitive gene arrays to measure changes in gene expression in sheepshead minnows and largemouth bass exposed to anthropogenic chemicals that mimic estrogen. The in vivo exposures, which realize the full physiological response in fish, result in changes...

DEVELOPMENT OF A 950-GENE DNA ARRAY FOR EXAMINING GENE EXPRESSION PATTERNS IN MOUSE TESTIS

EPA Science Inventory

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

Rockett JC, Christopher Luft J, Brian Garges J, Krawetz SA, Hughes MR, Hee Kirn K, Oudes AJ, Dix DJ.

Reproductive Toxicology Division, National Health and Environmental Effec...

Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method).

PubMed

He, M; Taussig, M J

2001-08-01

We describe a format for production of protein arrays termed 'protein in situ array' (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced by PCR using primers designed from information in DNA databases. Coupled transcription and translation is carried out on a surface to which the tagged protein adheres as soon as it is synthesised. Because proteins generated by cell-free synthesis are usually soluble and functional, this method can overcome problems of insolubility or degradation associated with bacterial expression of recombinant proteins. Moreover, the use of PCR-generated DNA enables rapid production of proteins or domains based on genome information alone and will be particularly useful where cloned material is not available. Here we show that human single-chain antibody fragments (three domain, V(H)/K form) and an enzyme (luciferase) can be functionally arrayed by the PISA method.

Toward a Public Toxicogenomics Capability for Supporting ...

EPA Pesticide Factsheets

A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate and aggregate such information by chemical, and broad data coverage within chemical, genomics, and toxicological information domains. This capability also depends on common genomics standards, protocol description, and functional linkages of diverse public Internet data resources. We present a survey of public genomics resources from these vantage points and conclude that, despite progress in many areas, the current state of the majority of public microarray databases is inadequate for supporting these objectives, particularly with regard to chemical indexing. To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus. Automated scripts and extensive manual review were employed to transform free-text experiment descriptions into a standardized, chemically indexed inventory of experiments in both resources. These files, which include top-level summary annotations, allow for identification of current chemical-associated experimental content, as well as chemical-exposure–related (or

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

NASA Technical Reports Server (NTRS)

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;

Mechanical designs and development of TES bolometer detector arrays for the Advanced ACTPol experiment

NASA Astrophysics Data System (ADS)

Ward, Jonathan T.; Austermann, Jason; Beall, James A.; Choi, Steve K.; Crowley, Kevin T.; Devlin, Mark J.; Duff, Shannon M.; Gallardo, Patricio A.; Henderson, Shawn W.; Ho, Shuay-Pwu Patty; Hilton, Gene; Hubmayr, Johannes; Khavari, Niloufar; Klein, Jeffrey; Koopman, Brian J.; Li, Dale; McMahon, Jeffrey; Mumby, Grace; Nati, Federico; Niemack, Michael D.; Page, Lyman A.; Salatino, Maria; Schillaci, Alessandro; Schmitt, Benjamin L.; Simon, Sara M.; Staggs, Suzanne T.; Thornton, Robert; Ullom, Joel N.; Vavagiakis, Eve M.; Wollack, Edward J.

2016-07-01

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 profile 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 modified to incorporate the new AdvACT instruments. Therefore, we discuss the integration of all AdvACT arrays with pre-existing ACTPol infrastructure.

A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis.

PubMed

Yasuike, Motoshige; Fujiwara, Atushi; Nakamura, Yoji; Iwasaki, Yuki; Nishiki, Issei; Sugaya, Takuma; Shimizu, Akio; Sano, Motohiko; Kobayashi, Takanori; Ototake, Mitsuru

2016-02-01

Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna. Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

The arcing rate for a High Voltage Solar Array - Theory, experiment and predictions

NASA Technical Reports Server (NTRS)

Hastings, Daniel E.; Cho, Mengu; Kuninaka, Hitoshi

1992-01-01

All solar arrays have biased surfaces which can be exposed to the space environment. It has been observed that when the array bias is less than a few hundred volts negative then the exposed conductive surfaces may undergo arcing in the space plasma. A theory for arcing is developed on these high voltage solar arrays which ascribes the arcing to electric field runaway at the interface of the plasma, conductor and solar cell dielectric. Experiments were conducted in the laboratory for the High Voltage Solar Array (HVSA) experiment which will fly on the Japanese Space Flyer Unit (SFU) in 1994. The theory was compared in detail to the experiment and shown to give a reasonable explanation for the data. The combined theory and ground experiments were then used to develop predictions for the SFU flight.

Arcing rates for High Voltage Solar Arrays - Theory, experiment, and predictions

NASA Technical Reports Server (NTRS)

Hastings, Daniel E.; Cho, Mengu; Kuninaka, Hitoshi

1992-01-01

All solar arrays have biased surfaces that can be exposed to the space environment. It has been observed that when the array bias is less than a few hundred volts negative, then the exposed conductive surfaces may undergo arcing in the space plasma. A theory for arcing is developed on these high voltage solar arrays that ascribes the arcing to electric field runaway at the interface of the plasma, conductor, and solar cell dielectric. Experiments were conducted in the laboratory for the High Voltage Solar Array experiment that will fly on the Japanese Space Flyer Unit (SFU) in 1994. The theory was compared in detail with the experiment and shown to give a reasonable explanation for the data. The combined theory and ground experiments were then used to develop predictions for the SFU flight.

The TGF-beta-Pseudoreceptor BAMBI is strongly expressed in COPD lungs and regulated by nontypeable Haemophilus influenzae

PubMed Central

2010-01-01

Background Nontypeable Haemophilus influenzae (NTHI) may play a role as an infectious trigger in the pathogenesis of chronic obstructive pulmonary disease (COPD). Few data are available regarding the influence of acute and persistent infection on tissue remodelling and repair factors such as transforming growth factor (TGF)-β. Methods NTHI infection in lung tissues obtained from COPD patients and controls was studied in vivo and using an in vitro model. Infection experiments were performed with two different clinical isolates. Detection of NTHI was done using in situ hybridization (ISH) in unstimulated and in in vitro infected lung tissue. For characterization of TGF-β signaling molecules a transcriptome array was performed. Expression of the TGF-pseudoreceptor BMP and Activin Membrane-bound Inhibitor (BAMBI) was analyzed using immunohistochemistry (IHC), ISH and PCR. CXC chemokine ligand (CXCL)-8, tumor necrosis factor (TNF)-α and TGF-β expression were evaluated in lung tissue and cell culture using ELISA. Results In 38% of COPD patients infection with NTHI was detected in vivo in contrast to 0% of controls (p < 0.05). Transcriptome arrays showed no significant changes of TGF-β receptors 1 and 2 and Smad-3 expression, whereas a strong expression of BAMBI with upregulation after in vitro infection of COPD lung tissue was demonstrated. BAMBI was expressed ubiquitously on alveolar macrophages (AM) and to a lesser degree on alveolar epithelial cells (AEC). Measurement of cytokine concentrations in lung tissue supernatants revealed a decreased expression of TGF-β (p < 0.05) in combination with a strong proinflammatory response (p < 0.01). Conclusions We show for the first time the expression of the TGF pseudoreceptor BAMBI in the human lung, which is upregulated in response to NTHI infection in COPD lung tissue in vivo and in vitro. The combination of NTHI-mediated induction of proinflammatory cytokines and inhibition of TGF-β expression may influence inflammation induced tissue remodeling. PMID:20513241

The TGF-beta-pseudoreceptor BAMBI is strongly expressed in COPD lungs and regulated by nontypeable Haemophilus influenzae.

PubMed

Drömann, Daniel; Rupp, Jan; Rohmann, Kristina; Osbahr, Sinia; Ulmer, Artur J; Marwitz, Sebastian; Röschmann, Kristina; Abdullah, Mahdi; Schultz, Holger; Vollmer, Ekkehard; Zabel, Peter; Dalhoff, Klaus; Goldmann, Torsten

2010-05-31

Nontypeable Haemophilus influenzae (NTHI) may play a role as an infectious trigger in the pathogenesis of chronic obstructive pulmonary disease (COPD). Few data are available regarding the influence of acute and persistent infection on tissue remodelling and repair factors such as transforming growth factor (TGF)-beta. NTHI infection in lung tissues obtained from COPD patients and controls was studied in vivo and using an in vitro model. Infection experiments were performed with two different clinical isolates. Detection of NTHI was done using in situ hybridization (ISH) in unstimulated and in in vitro infected lung tissue. For characterization of TGF-beta signaling molecules a transcriptome array was performed. Expression of the TGF-pseudoreceptor BMP and Activin Membrane-bound Inhibitor (BAMBI) was analyzed using immunohistochemistry (IHC), ISH and PCR. CXC chemokine ligand (CXCL)-8, tumor necrosis factor (TNF)-alpha and TGF-beta expression were evaluated in lung tissue and cell culture using ELISA. In 38% of COPD patients infection with NTHI was detected in vivo in contrast to 0% of controls (p < 0.05). Transcriptome arrays showed no significant changes of TGF-beta receptors 1 and 2 and Smad-3 expression, whereas a strong expression of BAMBI with upregulation after in vitro infection of COPD lung tissue was demonstrated. BAMBI was expressed ubiquitously on alveolar macrophages (AM) and to a lesser degree on alveolar epithelial cells (AEC). Measurement of cytokine concentrations in lung tissue supernatants revealed a decreased expression of TGF-beta (p < 0.05) in combination with a strong proinflammatory response (p < 0.01). We show for the first time the expression of the TGF pseudoreceptor BAMBI in the human lung, which is upregulated in response to NTHI infection in COPD lung tissue in vivo and in vitro. The combination of NTHI-mediated induction of proinflammatory cytokines and inhibition of TGF-beta expression may influence inflammation induced tissue remodeling.

Sound Source Localization Using Non-Conformal Surface Sound Field Transformation Based on Spherical Harmonic Wave Decomposition

PubMed Central

Zhang, Lanyue; Ding, Dandan; Yang, Desen; Wang, Jia; Shi, Jie

2017-01-01

Spherical microphone arrays have been paid increasing attention for their ability to locate a sound source with arbitrary incident angle in three-dimensional space. Low-frequency sound sources are usually located by using spherical near-field acoustic holography. The reconstruction surface and holography surface are conformal surfaces in the conventional sound field transformation based on generalized Fourier transform. When the sound source is on the cylindrical surface, it is difficult to locate by using spherical surface conformal transform. The non-conformal sound field transformation by making a transfer matrix based on spherical harmonic wave decomposition is proposed in this paper, which can achieve the transformation of a spherical surface into a cylindrical surface by using spherical array data. The theoretical expressions of the proposed method are deduced, and the performance of the method is simulated. Moreover, the experiment of sound source localization by using a spherical array with randomly and uniformly distributed elements is carried out. Results show that the non-conformal surface sound field transformation from a spherical surface to a cylindrical surface is realized by using the proposed method. The localization deviation is around 0.01 m, and the resolution is around 0.3 m. The application of the spherical array is extended, and the localization ability of the spherical array is improved. PMID:28489065

Pupil geometry and pupil re-imaging in telescope arrays

NASA Technical Reports Server (NTRS)

Traub, Wesley A.

1990-01-01

This paper considers the issues of lateral and longitudinal pupil geometry in ground-based telescope arrays, such as IOTA. In particular, it is considered whether or not pupil re-imaging is required before beam combination. By considering the paths of rays through the system, an expression is derived for the optical path errors in the combined wavefront as a function of array dimensions, telescope magnification factor, viewing angle, and field-of-view. By examining this expression for the two cases of pupil-plane and image-plane combination, operational limits can be found for any array. As a particular example, it is shown that for IOTA no pupil re-imaging optics will be needed.

Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography

PubMed Central

Weiler, Nicholas C; Collman, Forrest; Vogelstein, Joshua T; Burns, Randal; Smith, Stephen J

2014-01-01

A major question in neuroscience is how diverse subsets of synaptic connections in neural circuits are affected by experience dependent plasticity to form the basis for behavioral learning and memory. Differences in protein expression patterns at individual synapses could constitute a key to understanding both synaptic diversity and the effects of plasticity at different synapse populations. Our approach to this question leverages the immunohistochemical multiplexing capability of array tomography (ATomo) and the columnar organization of mouse barrel cortex to create a dataset comprising high resolution volumetric images of spared and deprived cortical whisker barrels stained for over a dozen synaptic molecules each. These dataset has been made available through the Open Connectome Project for interactive online viewing, and may also be downloaded for offline analysis using web, Matlab, and other interfaces. PMID:25977797

Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography.

PubMed

Weiler, Nicholas C; Collman, Forrest; Vogelstein, Joshua T; Burns, Randal; Smith, Stephen J

2014-01-01

A major question in neuroscience is how diverse subsets of synaptic connections in neural circuits are affected by experience dependent plasticity to form the basis for behavioral learning and memory. Differences in protein expression patterns at individual synapses could constitute a key to understanding both synaptic diversity and the effects of plasticity at different synapse populations. Our approach to this question leverages the immunohistochemical multiplexing capability of array tomography (ATomo) and the columnar organization of mouse barrel cortex to create a dataset comprising high resolution volumetric images of spared and deprived cortical whisker barrels stained for over a dozen synaptic molecules each. These dataset has been made available through the Open Connectome Project for interactive online viewing, and may also be downloaded for offline analysis using web, Matlab, and other interfaces.

Two years of on-orbit gallium arsenide performance from the LIPS solar cell panel experiment

NASA Technical Reports Server (NTRS)

Francis, R. W.; Betz, F. E.

1985-01-01

The LIPS on-orbit performance of the gallium arsenide panel experiment was analyzed from flight operation telemetry data. Algorithms were developed to calculate the daily maximum power and associated solar array parameters by two independent methods. The first technique utilizes a least mean square polynomial fit to the power curve obtained with intensity and temperature corrected currents and voltages; whereas, the second incorporates an empirical expression for fill factor based on an open circuit voltage and the calculated series resistance. Maximum power, fill factor, open circuit voltage, short circuit current and series resistance of the solar cell array are examined as a function of flight time. Trends are analyzed with respect to possible mechanisms which may affect successive periods of output power during 2 years of flight operation. Degradation factors responsible for the on-orbit performance characteristics of gallium arsenide are discussed in relation to the calculated solar cell parameters. Performance trends and the potential degradation mechanisms are correlated with existing laboratory and flight data on both gallium arsenide and silicon solar cells for similar environments.

Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

PubMed Central

2011-01-01

Background Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this architecture. However general understanding of how this process is achieved remains ambiguous. The mantle is a conserved organ involved in shell formation throughout molluscs. Specifically the mantle is thought to be responsible for secreting the protein component of the shell. This study employs molecular approaches to determine the spatial expression of genes within the mantle tissue to further the elucidation of the shell biomineralization. Results A microarray platform was custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from mantle tissue. This microarray was used to analyze the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and analyzed for differential gene expression with PmaxArray 1.0. Over 2000 ESTs were determined to be differentially expressed among the tissue sections, identifying five major expression regions. In situ hybridization validated and further localized the expression for a subset of these ESTs. Comparative sequence similarity analysis of these ESTs revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell related genes. Conclusions This investigation has mapped the spatial distribution for over 2000 ESTs present on PmaxArray 1.0 with reference to specific locations of the mantle. Expression profile clusters have indicated at least five unique functioning zones in the mantle. Three of these zones are likely involved in shell related activities including formation of nacre, periostracum and calcitic prismatic microstructure. A number of novel and known transcripts have been identified from these clusters. The development of PmaxArray 1.0, and the spatial map of its ESTs expression in the mantle has begun characterizing the molecular mechanisms linking the organics and inorganics of the molluscan shell. PMID:21936921

DNA ARRAYS TO MONITOR GENE EXPRESSION IN RAT BLOOD AND UTERUS FOLLOWING 17-BETA-ESTRADIOL EXPOSURE: BIOMONITORING ENVIRONMENTAL EFFECTS USING SURROGATE TISSUES

EPA Science Inventory

DNA arrays to monitor gene expression in rat blood and uterus following 17-b-estradiol exposure - biomonitoring environmental effects using surrogate tissues
John C. Rockett, Robert J. Kavlock, Christy R. Lambright, Louise G. Parks, Judith E. Schmid, Vickie S. Wilson, Carmen W...

ANALYSIS OF CHANGES IN GENE EXPRESSION PATTERNS IN FISH EXPOSED TO NATURAL PHARMACEUTICAL AND ENVIRONMENTAL ESTROGENS USING GENE ARRAYS.

EPA Science Inventory

Denslow, N.D., P. Larkin, T.L. Sabo-Attwood, J. Kocerha, K.J. Kroll, M.J. Hemmer and L.C. Folmar. 2004. Analysis of Changes in Gene Expression Patterns in Fish Exposed to Natural, Pharmaceutical and Environmental Estrogens Using Gene Arrays (Abstract). Mar. Environ. Res. 58(2-5):...

Profiling differential gene expression of corals along a transect of waters adjacent to the Bermuda municipal dump.

PubMed

Morgan, Michael B; Edge, Sara E; Snell, Terry W

2005-01-01

A coral cDNA array containing 32 genes was used to examine the gene expression profiles of coral populations located at four sites that varied with distance from a semi-submerged municipal dump in Castle Harbour, Bermuda (previously identified as a point source of anthropogenic stressors). Genes on the array represent transcripts induced under controlled laboratory conditions to a variety of stressors both natural (temperature, sediment, salinity, darkness) and xenobiotic (heavy metals, pesticides, PAH) in origin. The gene expression profiles produced revealed information about the types of stressors. Consistent with other studies undertaken in Castle Harbour, the coral cDNA array detected responses to heavy metals, sedimentation, as well as oxidative stress.

Dose-response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol.

PubMed

Hook, Sharon E; Skillman, Ann D; Small, Jack A; Schultz, Irvin R

2006-07-01

Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss,were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as "expression signatures". Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that different doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose.

Analysis of MMIC arrays for use in the ACTS Aero Experiment

NASA Technical Reports Server (NTRS)

Zimmerman, M.; Lee, R.; Rho, E.; Zaman, Z.

1993-01-01

The Aero Experiment is designed to demonstrate communication from an aircraft to an Earth terminal via the ACTS. This paper describes the link budget and antenna requirements for a 4.8 kbps full-duplex voice link at Ka-Band frequencies. Three arrays, one transmit array developed by TI and two receive arrays developed by GE and Boeing, were analyzed. The predicted performance characteristics of these arrays are presented and discussed in the paper.

The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

PubMed Central

2011-01-01

Background Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. Conclusion We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research. PMID:21208403

The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits.

PubMed

Privat, Isabelle; Bardil, Amélie; Gomez, Aureliano Bombarely; Severac, Dany; Dantec, Christelle; Fuentes, Ivanna; Mueller, Lukas; Joët, Thierry; Pot, David; Foucrier, Séverine; Dussert, Stéphane; Leroy, Thierry; Journot, Laurent; de Kochko, Alexandre; Campa, Claudine; Combes, Marie-Christine; Lashermes, Philippe; Bertrand, Benoit

2011-01-05

Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.

Plasma-mediated transfection of RPE

NASA Astrophysics Data System (ADS)

Palanker, D.; Chalberg, T.; Vankov, A.; Huie, P.; Molnar, F. E.; Butterwick, A.; Calos, M.; Marmor, M.; Blumenkranz, M. S.

2006-02-01

A major obstacle in applying gene therapy to clinical practice is the lack of efficient and safe gene delivery techniques. Viral delivery has encountered a number of serious problems including immunological reactions and malignancy. Non-viral delivery methods (liposomes, sonoporation and electroporation) have either low efficiency in-vivo or produce severe collateral damage to ocular tissues. We discovered that tensile stress greatly increases the susceptibility of cellular membranes to electroporation. For synchronous application of electric field and mechanical stress, both are generated by the electric discharge itself. A pressure wave is produced by rapid vaporization of the medium. To prevent termination of electric current by the vapor cavity it is ionized thus restoring its electric conductivity. For in-vivo experiments with rabbits a plasmid DNA was injected into the subretinal space, and RPE was treated trans-sclerally with an array of microelectodes placed outside the eye. Application of 250-300V and 100-200 μs biphasic pulses via a microelectrode array resulted in efficient transfection of RPE without visible damage to the retina. Gene expression was quantified and monitored using bioluminescence (luciferase) and fluorescence (GFP) imaging. Transfection efficiency of RPE with this new technique exceeded that of standard electroporation by a factor 10,000. Safe and effective non-viral DNA delivery to the mammalian retina may help to materialize the enormous potential of the ocular gene therapy. Future experiments will focus on continued characterization of the safety and efficacy of this method and evaluation of long-term transgene expression in the presence of phiC31 integrase.

Time Reversal Mirrors and Cross Correlation Functions in Acoustic Wave Propagation

NASA Astrophysics Data System (ADS)

Fishman, Louis; Jonsson, B. Lars G.; de Hoop, Maarten V.

2009-03-01

In time reversal acoustics (TRA), a signal is recorded by an array of transducers, time reversed, and then retransmitted into the configuration. The retransmitted signal propagates back through the same medium and retrofocuses on the source that generated the signal. If the transducer array is a single, planar (flat) surface, then this configuration is referred to as a planar, one-sided, time reversal mirror (TRM). In signal processing, for example, in active-source seismic interferometry, the measurement of the wave field at two distinct receivers, generated by a common source, is considered. Cross correlating these two observations and integrating the result over the sources yield the cross correlation function (CCF). Adopting the TRM experiments as the basic starting point and identifying the kinematically correct correspondences, it is established that the associated CCF signal processing constructions follow in a specific, infinite recording time limit. This perspective also provides for a natural rationale for selecting the Green's function components in the TRM and CCF expressions. For a planar, one-sided, TRM experiment and the corresponding CCF signal processing construction, in a three-dimensional homogeneous medium, the exact expressions are explicitly calculated, and the connecting limiting relationship verified. Finally, the TRM and CCF results are understood in terms of the underlying, governing, two-way wave equation, its corresponding time reversal invariance (TRI) symmetry, and the absence of TRI symmetry in the associated one-way wave equations, highlighting the role played by the evanescent modal contributions.

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer

NASA Astrophysics Data System (ADS)

Petersson, Linn; Berthet Duroure, Nathalie; Auger, Angèle; Dexlin-Mellby, Linda; Borrebaeck, Carl AK; Ait Ikhlef, Ali; Wingren, Christer

2014-07-01

Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm-2) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, BioplumeTM—consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels—to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced—based on miniaturized spot features (78.5 um2, Ø 10 μm) at a 7-125-times increased spot density (250 000 spots cm-2), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined.

Channel capacity of an array system for Gaussian channels with applications to combining and noise cancellation

NASA Technical Reports Server (NTRS)

Cheung, K. M.; Vilnrotter, V.

1996-01-01

A closed-form expression for the capacity of an array of correlated Gaussian channels is derived. It is shown that when signal and noise are independent, the array of observables can be replaced with a single observable without diminishing the capacity of the array channel. Examples are provided to illustrate the dependence of channel capacity on noise correlation for two- and three-channel arrays.

Channel Capacity of an Array System for Gaussian Channels With Applications to Combining and Noise Cancellation

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Vilnrotter, V.

1996-01-01

A closed-form expression for the capacity of an array of correlated Gaussian channels is derived. It is shown that when signal and noise are independent, the array of observables can be replaced with a single observable without diminishing the capacity of the array channel. Examples are provided to illustrate the dependence of channel capacity on noise correlation for two- and three-channel arrays.

University of Texas Southwestern Medical Center: Functional Signature Ontology Tool: Triplicate Measurements of Reporter Gene Expression in Response to Individual Genetic and Chemical Perturbations in HCT116 Cells | Office of Cancer Genomics

Cancer.gov

The goal of this project is to use an eight-gene expression profile to define functional signatures for small molecules and natural products with heretofore undefined mechanism of action. Two genes in the eight gene set are used as internal controls and do not vary across gene expression array data collected from the public domain. The remaining six genes are found to vary independently across a large collection of publically available gene expression array datasets.  Read the abstract

SEPARABLE FACTOR ANALYSIS WITH APPLICATIONS TO MORTALITY DATA

PubMed Central

Fosdick, Bailey K.; Hoff, Peter D.

2014-01-01

Human mortality data sets can be expressed as multiway data arrays, the dimensions of which correspond to categories by which mortality rates are reported, such as age, sex, country and year. Regression models for such data typically assume an independent error distribution or an error model that allows for dependence along at most one or two dimensions of the data array. However, failing to account for other dependencies can lead to inefficient estimates of regression parameters, inaccurate standard errors and poor predictions. An alternative to assuming independent errors is to allow for dependence along each dimension of the array using a separable covariance model. However, the number of parameters in this model increases rapidly with the dimensions of the array and, for many arrays, maximum likelihood estimates of the covariance parameters do not exist. In this paper, we propose a submodel of the separable covariance model that estimates the covariance matrix for each dimension as having factor analytic structure. This model can be viewed as an extension of factor analysis to array-valued data, as it uses a factor model to estimate the covariance along each dimension of the array. We discuss properties of this model as they relate to ordinary factor analysis, describe maximum likelihood and Bayesian estimation methods, and provide a likelihood ratio testing procedure for selecting the factor model ranks. We apply this methodology to the analysis of data from the Human Mortality Database, and show in a cross-validation experiment how it outperforms simpler methods. Additionally, we use this model to impute mortality rates for countries that have no mortality data for several years. Unlike other approaches, our methodology is able to estimate similarities between the mortality rates of countries, time periods and sexes, and use this information to assist with the imputations. PMID:25489353

Quantitative comparison of microarray experiments with published leukemia related gene expression signatures.

PubMed

Klein, Hans-Ulrich; Ruckert, Christian; Kohlmann, Alexander; Bullinger, Lars; Thiede, Christian; Haferlach, Torsten; Dugas, Martin

2009-12-15

Multiple gene expression signatures derived from microarray experiments have been published in the field of leukemia research. A comparison of these signatures with results from new experiments is useful for verification as well as for interpretation of the results obtained. Currently, the percentage of overlapping genes is frequently used to compare published gene signatures against a signature derived from a new experiment. However, it has been shown that the percentage of overlapping genes is of limited use for comparing two experiments due to the variability of gene signatures caused by different array platforms or assay-specific influencing parameters. Here, we present a robust approach for a systematic and quantitative comparison of published gene expression signatures with an exemplary query dataset. A database storing 138 leukemia-related published gene signatures was designed. Each gene signature was manually annotated with terms according to a leukemia-specific taxonomy. Two analysis steps are implemented to compare a new microarray dataset with the results from previous experiments stored and curated in the database. First, the global test method is applied to assess gene signatures and to constitute a ranking among them. In a subsequent analysis step, the focus is shifted from single gene signatures to chromosomal aberrations or molecular mutations as modeled in the taxonomy. Potentially interesting disease characteristics are detected based on the ranking of gene signatures associated with these aberrations stored in the database. Two example analyses are presented. An implementation of the approach is freely available as web-based application. The presented approach helps researchers to systematically integrate the knowledge derived from numerous microarray experiments into the analysis of a new dataset. By means of example leukemia datasets we demonstrate that this approach detects related experiments as well as related molecular mutations and may help to interpret new microarray data.

Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight.

PubMed

Johnson, Christina M; Subramanian, Aswati; Pattathil, Sivakumar; Correll, Melanie J; Kiss, John Z

2017-08-21

Plants will play an important role in the future of space exploration as part of bioregenerative life support. Thus, it is important to understand the effects of microgravity and spaceflight on gene expression in plant development. We analyzed the transcriptome of Arabidopsis thaliana using the Biological Research in Canisters (BRIC) hardware during Space Shuttle mission STS-131. The bioinformatics methods used included RMA (robust multi-array average), MAS5 (Microarray Suite 5.0), and PLIER (probe logarithmic intensity error estimation). Glycome profiling was used to analyze cell wall composition in the samples. In addition, our results were compared to those of two other groups using the same hardware on the same mission (BRIC-16). In our BRIC-16 experiments, we noted expression changes in genes involved in hypoxia and heat shock responses, DNA repair, and cell wall structure between spaceflight samples compared to the ground controls. In addition, glycome profiling supported our expression analyses in that there was a difference in cell wall components between ground control and spaceflight-grown plants. Comparing our studies to those of the other BRIC-16 experiments demonstrated that, even with the same hardware and similar biological materials, differences in results in gene expression were found among these spaceflight experiments. A common theme from our BRIC-16 space experiments and those of the other two groups was the downregulation of water stress response genes in spaceflight. In addition, all three studies found differential regulation of genes associated with cell wall remodeling and stress responses between spaceflight-grown and ground control plants. © 2017 Botanical Society of America.

Ka-band MMIC arrays for ACTS Aero Terminal Experiment

NASA Technical Reports Server (NTRS)

Raquet, C.; Zakrajsek, R.; Lee, R.; Turtle, J.

1992-01-01

An antenna system consisting of three experimental Ka-band active arrays using GaAs MMIC devices at each radiating element for electronic beam steering and distributed power amplification is presented. The MMIC arrays are to be demonstrated in the ACTS Aeronautical Terminal Experiment, planned for early 1994. The experiment is outlined, with emphasis on a description of the antenna system. Attention is given to the way in which proof-of-concept MMIC arrays featuring three different state-of-the-art approaches to Ka-band MMIC insertion are being incorporated into an experimental aircraft terminal for the demonstration of an aircraft-to-satellite link, providing a basis for follow-on MMIC array development.

Large Aperture Acoustic Arrays in Support of Reverberation Studies

DTIC Science & Technology

1990-04-01

Acoustic Reverberation Special Research Program (SRP). Approach We propose the development of several acoustic arrays in preparation for a FY92 experiment...hydrophone array to measure the directional spectrum of seafloor scattered wavefields. Approach As part of the ONT-sponsored, 1987 SVLA experiment, we...scattered energy. Approach Two methods will be described by which vertical and horizontal acoustic arrays can be deployed together for making bottom

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

PubMed

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

2009-07-31

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

Solar array experiments on the SPHINX satellite. [Space Plasma High voltage INteraction eXperiment satellite

NASA Technical Reports Server (NTRS)

Stevens, N. J.

1974-01-01

The Space Plasma, High Voltage Interaction Experiment (SPHINX) is the name given to an auxiliary payload satellite scheduled to be launched in January 1974. The principal experiments carried on this satellite are specifically designed to obtain the engineering data on the interaction of high voltage systems with the space plasma. The classes of experiments are solar array segments, insulators, insulators with pin holes and conductors. The satellite is also carrying experiments to obtain flight data on three new solar array configurations: the edge illuminated-multijunction cells, the teflon encased cells, and the violet cells.

Solar array experiments on the Sphinx satellite

NASA Technical Reports Server (NTRS)

Stevens, N. J.

1973-01-01

The Space Plasma, High Voltage Interaction Experiment (SPHINX) is the name given to an auxiliary payload satellite scheduled to be launched in January 1974. The principal experiments carried on this satellite are specifically designed to obtain the engineering data on the interaction of high voltage systems with the space plasma. The classes of experiments are solar array segments, insulators, insulators with pin holes and conductors. The satellite is also carrying experiments to obtain flight data on three new solar array configurations; the edge illuminated-multijunction cells, the Teflon encased cells and the violet cells.

Digital Detection of Multiple Minority Mutants and Expression Levels of Multiple Colorectal Cancer-Related Genes Using Digital-PCR Coupled with Bead-Array

PubMed Central

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed “multiplex ligation-dependent probe amplification–digital amplification coupled with hydrogel bead-array” (MLPA–DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA–DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA–DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC. PMID:25880764

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

PubMed

Knowles, David W; Biggin, Mark D

2013-01-01

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

Study of cross-shaped ultrasonic array sensor applied to partial discharge location in transformer oil.

PubMed

Li, Jisheng; Xin, Xiaohu; Luo, Yongfen; Ji, Haiying; Li, Yanming; Deng, Junbo

2013-11-01

A conformal combined sensor is designed and it is used in Partial Discharge (PD) location experiments in transformer oil. The sensor includes a cross-shaped ultrasonic phased array of 13 elements and an ultra-high-frequency (UHF) electromagnetic rectangle array of 2 × 2 elements. Virtual expansion with high order cumulants, the ultrasonic array can achieve the effect of array with 61 elements. This greatly improves the aperture and direction sharpness of original array and reduces the cost of follow-up hardware. With the cross-shaped ultrasonic array, the results of PD location experiments are precise and the maximum error of the direction of arrival (DOA) is less than 5°.

Linear model for fast background subtraction in oligonucleotide microarrays.

PubMed

Kroll, K Myriam; Barkema, Gerard T; Carlon, Enrico

2009-11-16

One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects: 1) Correlated intensities between neighboring features in the chip and 2) sequence-dependent affinities for non-specific hybridization fitted by an extended nearest-neighbor model. The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.

Small space station electrical power system design concepts

NASA Technical Reports Server (NTRS)

Jones, G. M.; Mercer, L. N.

1976-01-01

A small manned facility, i.e., a small space station, placed in earth orbit by the Shuttle transportation system would be a viable, cost effective addition to the basic Shuttle system to provide many opportunities for R&D programs, particularly in the area of earth applications. The small space station would have many similarities with Skylab. This paper presents design concepts for an electrical power system (EPS) for the small space station based on Skylab experience, in-house work at Marshall Space Flight Center, SEPS (Solar Electric Propulsion Stage) solar array development studies, and other studies sponsored by MSFC. The proposed EPS would be a solar array/secondary battery system. Design concepts expressed are based on maximizing system efficiency and five year operational reliability. Cost, weight, volume, and complexity considerations are inherent in the concepts presented. A small space station EPS based on these concepts would be highly efficient, reliable, and relatively inexpensive.

Impact of LDEF photovoltaic experiment findings upon spacecraft solar array design and development requirements

NASA Technical Reports Server (NTRS)

Young, Leighton E.

1993-01-01

Photovoltaic cells (solar cells) and other solar array materials were flown in a variety of locations on the Long Duration Exposure Facility (LDEF). With respect to the predicted leading edge, solar array experiments were located at 0 degrees (row 9), 30 degrees (row 8) and 180 degrees (row 3). Postflight estimates of location of the experiments with respect to the velocity vector add 8.1 degrees to these values. Experiments were also located on the Earth end of the LDEF longitudinal axis. Types and magnitudes of detrimental effects differ between the locations with some commonality. Postflight evaluation of the solar array experiments reveal that some components/materials are very resistant to the environment to which they were exposed while others need protection, modification, or replacement. Interaction of materials with atomic oxygen (AO), as an area of major importance, was dramatically demonstrated by LDEF results. Information gained from the LDEF flight allows array developers to set new requirements for on-going and future technology and flight component development.

Performance of the Broadband Golay 3x6 Array Associated with the 2016 IRIS Community Wavefields Experiment

NASA Astrophysics Data System (ADS)

Bolarinwa, O. J.; Langston, C. A.; Sweet, J. R.; Anderson, K. R.; Woodward, R.

2017-12-01

A 6 km aperture regional array in the Golay 3x6 configuration was fielded as part of the IRIS Community Wavefields Experiment near Enid, Oklahoma from June 26 through November 12, 2016. The array consisted of 18 broadband CMG-3T seismometers deployed using a PASSCAL insulated vault design and RT130 data recorders. The Golay geometry is unusual in that it features 6 tripartite arrays in an open arrangement. Spacing and orientation of each tripartite array is such that the array uniformly samples the wavefield in space as determined from the co-array diagram even though the interior of the array configuration contains no seismic stations. The short wavelength performance of this array requires a high degree of phase correlation across its entire aperture, a characteristic that has been difficult to achieve for other regional array designs because of velocity heterogeneity in the earth. Located within an area of high regional seismicity, the IRIS experiment offered an opportunity to examine the slowness-frequency performance of a real-world Golay 3x6 array that was subject to constraints on land usage during deployment. Individual tripartite arrays fit well within a land survey quarter section but it proved difficult to match the ideal spacing between each subarray because of permitting problems. Nevertheless, these unavoidable geometry perturbations caused only minor changes to the theoretical array response. More surprisingly, observations of high frequency regional P and S phases show very high correlation over the array aperture that gives rise to precise array responses that are close to theoretical. Both the array geometry and relatively homogeneous structure under the array produces an exceptional facility that can be used for high-resolution studies of regional seismic waves.

Skylab experiment performance evaluation manual. Appendix S: Experiment T027 contamination measurement sample array (MSFC)

NASA Technical Reports Server (NTRS)

Tonetti, B. B.

1973-01-01

Analyses for Experiment T027, Contamination Measurement Sample Array (MSFC), to be used for evaluating the performance of the Skylab corrollary experiments under preflight, inflight, and post-flight conditions are presented. Experiment contingency plan workaround procedure and malfunction analyses are presented in order to assist in making the experiment operationally successful.

Estrogen regulation of uterine genes in vivo detected by complementary DNA array.

PubMed

Andrade, P M; Silva, I D C G; Borra, R C; de Lima, G R; Baracat, E C

2002-05-01

In the present study, our aim was to identify differentially expressed genes involved in estrogen actions at the endometrium level in rats. Thirty adult rats were ovariectomized four days prior to drug administration for 48 days. Rats were divided in 2 groups: I, control and II, conjugated equine estrogens (CCE). Total RNA was isolated from uterus, and differential expression was analyzed by array technology and RT-PCR. A total of 32 candidate genes were shown to be upregulated or downregulated in groups I or II. Among them, differential expression was already confirmed by RT-PCR for IGFBP5, S12, c-kit, and VEGF, genes whose expression was up regulated during CCE therapy, and casein kinase II and serine kinase expression was the same level in both groups. We have demonstrated that cDNA array represents a powerful approach to identify key molecules in the estrogens therapy. A number of the candidates reported here should provide new markers that may contribute to the detection of target estrogen receptor. This information may also aid the development of new approaches to therapeutic intervention.

Dual-task interference in visual working memory: A limitation in storage capacity but not in encoding or retrieval

PubMed Central

Fougnie, Daryl; Marois, René

2009-01-01

The concurrent maintenance of two visual working memory (VWM) arrays can lead to profound interference. It is unclear, however, whether these costs arise from limitations in VWM storage capacity (Fougnie & Marois, 2006), or from interference between the storage of one visual array and encoding or retrieval of another visual array (Cowan & Morey, 2007). Here, we show that encoding a VWM array does not interfere with maintenance of another VWM array unless the two displays exceed maintenance capacity (Experiments 1 and 2). Moreover, manipulating the extent to which encoding and maintenance can interfere with one another had no discernable effect on dual-task performance (Experiment 2). Finally, maintenance of a VWM array was not affected by retrieval of information from another VWM array (Experiment 3). Taken together, these findings demonstrate that dual-task interference between two concurrent VWM tasks is due to a capacity-limited store that is independent from encoding and retrieval processes. PMID:19933566

Radiation characteristics of Al wire arrays on Z*

NASA Astrophysics Data System (ADS)

Coverdale, C. A.; Ampleford, D. J.; Jones, B.; Cuneo, M. E.; Hansen, S.; Jennings, C. A.; Moore, N.; Jones, S. C.; Deeney, C.

2011-10-01

Analysis of mixed material nested wire array experiments at Z have shown that the inner wire array dominates the hottest regions of the stagnated z pinch. In those experiments, substantial free-bound continuum radiation was observed when Al was fielded on the inner wire array. Experiments with Al (5% Mg) on both wire arrays have also been fielded, with variations in the free-bound continuum observed. These variations appear to be tied to the initial mass and diameter of the wire array. The results presented here will investigate the trends in the measured emission (Al and Mg K-shell and free-bound continuum) and will compare the measured output to more recent Al wire array experimental results on the refurbished Z accelerator. *Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. +current address: NNSA/DOE Headquarters, Washington D.C.

University of Texas Southwestern Medical Center (UTSW): Functional Signature Ontology Tool: Triplicate Measurements of Reporter Gene Expression in Response to Individual Genetic and Chemical Perturbations in HCT116 Cells | Office of Cancer Genomics

Cancer.gov

The goal of this project is to use an eight-gene expression profile to define functional signatures for small molecules and natural products with heretofore undefined mechanism of action. Two genes in the eight gene set are used as internal controls and do not vary across gene expression array data collected from the public domain. The remaining six genes are found to vary independently across a large collection of publically available gene expression array datasets.  Read the abstract

Dose–response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol

PubMed Central

Hook, Sharon E.; Skillman, Ann D.; Small, Jack A.; Schultz, Irvin R.

2008-01-01

Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss, were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as “expression signatures”. Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that diffierent doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose. PMID:16725192

An EDMD mutation in C. elegans lamin blocks muscle-specific gene relocation and compromises muscle integrity.

PubMed

Mattout, Anna; Pike, Brietta L; Towbin, Benjamin D; Bank, Erin M; Gonzalez-Sandoval, Adriana; Stadler, Michael B; Meister, Peter; Gruenbaum, Yosef; Gasser, Susan M

2011-10-11

In worms, as in other organisms, many tissue-specific promoters are sequestered at the nuclear periphery when repressed and shift inward when activated. It has remained unresolved, however, whether the association of facultative heterochromatin with the nuclear periphery, or its release, has functional relevance for cell or tissue integrity. Using ablation of the unique lamin gene in C. elegans, we show that lamin is necessary for the perinuclear positioning of heterochromatin. We then express at low levels in otherwise wild-type worms a lamin carrying a point mutation, Y59C, which in humans is linked to an autosomal-dominant form of Emery-Dreifuss muscular dystrophy. Using embryos and differentiated tissues, we track the subnuclear position of integrated heterochromatic arrays and their expression. In LMN-1 Y59C-expressing worms, we see abnormal retention at the nuclear envelope of a gene array bearing a muscle-specific promoter. This correlates with impaired activation of the array-borne myo-3 promoter and altered expression of a number of muscle-specific genes. However, an equivalent array carrying the intestine-specific pha-4 promoter is expressed normally and shifts inward when activated in gut cells of LMN-1 Y59C worms. Remarkably, adult LMN-1 Y59C animals have selectively perturbed body muscle ultrastructure and reduced muscle function. Lamin helps sequester heterochromatin at the nuclear envelope, and wild-type lamin permits promoter release following tissue-specific activation. A disease-linked point mutation in lamin impairs muscle-specific reorganization of a heterochromatic array during tissue-specific promoter activation in a dominant manner. This dominance and the correlated muscle dysfunction in LMN-1 Y59C worms phenocopies Emery-Dreifuss muscular dystrophy. Copyright © 2011 Elsevier Ltd. All rights reserved.

MicroRNA array normalization: an evaluation using a randomized dataset as the benchmark.

PubMed

Qin, Li-Xuan; Zhou, Qin

2014-01-01

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays.

MicroRNA Array Normalization: An Evaluation Using a Randomized Dataset as the Benchmark

PubMed Central

Qin, Li-Xuan; Zhou, Qin

2014-01-01

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays. PMID:24905456

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

PubMed Central

Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

2005-01-01

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 . PMID:15910681

The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.

PubMed

Quinn, Michael C J; Wilson, Daniel J; Young, Fiona; Dempsey, Adam A; Arcand, Suzanna L; Birch, Ashley H; Wojnarowicz, Paulina M; Provencher, Diane; Mes-Masson, Anne-Marie; Englert, David; Tonin, Patricia N

2009-07-06

As gene expression signatures may serve as biomarkers, there is a need to develop technologies based on mRNA expression patterns that are adaptable for translational research. Xceed Molecular has recently developed a Ziplex technology, that can assay for gene expression of a discrete number of genes as a focused array. The present study has evaluated the reproducibility of the Ziplex system as applied to ovarian cancer research of genes shown to exhibit distinct expression profiles initially assessed by Affymetrix GeneChip analyses. The new chemiluminescence-based Ziplex gene expression array technology was evaluated for the expression of 93 genes selected based on their Affymetrix GeneChip profiles as applied to ovarian cancer research. Probe design was based on the Affymetrix target sequence that favors the 3' UTR of transcripts in order to maximize reproducibility across platforms. Gene expression analysis was performed using the Ziplex Automated Workstation. Statistical analyses were performed to evaluate reproducibility of both the magnitude of expression and differences between normal and tumor samples by correlation analyses, fold change differences and statistical significance testing. Expressions of 82 of 93 (88.2%) genes were highly correlated (p < 0.01) in a comparison of the two platforms. Overall, 75 of 93 (80.6%) genes exhibited consistent results in normal versus tumor tissue comparisons for both platforms (p < 0.001). The fold change differences were concordant for 87 of 93 (94%) genes, where there was agreement between the platforms regarding statistical significance for 71 (76%) of 87 genes. There was a strong agreement between the two platforms as shown by comparisons of log2 fold differences of gene expression between tumor versus normal samples (R = 0.93) and by Bland-Altman analysis, where greater than 90% of expression values fell within the 95% limits of agreement. Overall concordance of gene expression patterns based on correlations, statistical significance between tumor and normal ovary data, and fold changes was consistent between the Ziplex and Affymetrix platforms. The reproducibility and ease-of-use of the technology suggests that the Ziplex array is a suitable platform for translational research.

Methods for processing microarray data.

PubMed

Ares, Manuel

2014-02-01

Quality control must be maintained at every step of a microarray experiment, from RNA isolation through statistical evaluation. Here we provide suggestions for analyzing microarray data. Because the utility of the results depends directly on the design of the experiment, the first critical step is to ensure that the experiment can be properly analyzed and interpreted. What is the biological question? What is the best way to perform the experiment? How many replicates will be required to obtain the desired statistical resolution? Next, the samples must be prepared, pass quality controls for integrity and representation, and be hybridized and scanned. Also, slides with defects, missing data, high background, or weak signal must be rejected. Data from individual slides must be normalized and combined so that the data are as free of systematic bias as possible. The third phase is to apply statistical filters and tests to the data to determine genes (1) expressed above background, (2) whose expression level changes in different samples, and (3) whose RNA-processing patterns or protein associations change. Next, a subset of the data should be validated by an alternative method, such as reverse transcription-polymerase chain reaction (RT-PCR). Provided that this endorses the general conclusions of the array analysis, gene sets whose expression, splicing, polyadenylation, protein binding, etc. change in different samples can be classified with respect to function, sequence motif properties, as well as other categories to extract hypotheses for their biological roles and regulatory logic.

Multiplexed chemiluminescent assays in ArrayPlates for high-throughput measurement of gene expression

NASA Astrophysics Data System (ADS)

Martel, Ralph R.; Rounseville, Matthew P.; Botros, Ihab W.; Seligmann, Bruce E.

2002-06-01

Multiplexed Molecular Profiling (MMP) assays for drug discovery are performed in ArrayPlates. ArrayPlates are 96- well microtiter plates that contain a 16-element array at the bottom of each well. Each element within an array measures one analyte in a sample. A CCD imager records the quantitative chemiluminescent readout of all 1,536 elements in a 96-well plate simultaneously. Since array elements are reagent modifiable by the end-user, ArrayPlates can be adapted to a broad range of nucleic acid- and protein-based assays. Such multiplexed assays are rapidly established, flexible, robust, automation-friendly and cost-effective. Nucleic acid assays in ArrayPlates can detect DNA and RNA, including SNPs and ESTs. A multiplexed mRNA assay to measure the expression of 16 genes is described. The assay combines a homogeneous nuclease protection assay with subsequent probe immobilization to the array by means of a sandwich hybridization followed with chemiluminescent detection. This assay was used to examine cells grown and treated in microplates and avoided cloning, transfection, RNA insolation, reverse transcription, amplification and fluorochrome labeling. Standard deviations for the measurement of 16 genes ranged from 3 percent to 13 percent in samples of 30,000 cells. Such ArrayPlates transcription assays are useful in drug discovery and development for target validation, screening, lead optimization, metabolism and toxicity profiling. Chemiluminescent detection provides ArrayPlates assays with high signal-to-noise readout and simplifies imager requirements. Imaging a 2D surface that contains arrays simplifies lens requirements relative to imaging columns of liquid in microtiter plate wells. The Omix imager for ArrayPlates is described.

Apollo lunar surface experiments package

NASA Technical Reports Server (NTRS)

1972-01-01

Developments in the ALSEP program are reported. A summary of the status for the total ALSEP program is included. Other areas discussed include: (1) status of Apollo 16 (array D) and Apollo 17 (array E), (2) lunar seismic profiling experiment, (3) lunar ejecta and meteorites experiment, and (4) lunar mass spectrometer experiments.

Aesthetic engagements: "being" in everyday life with advanced cancer.

PubMed

la Cour, Karen; Hansen, Helle Ploug

2012-03-01

Living with advanced cancer can present an overwhelming challenge. It may impact the everyday life of the individual with respect to an array of psychological, physical, social, and existential issues. We focus on ways in which people with advanced cancer experience and use their engagement in daily activities when confronting nearing death. Through a phenomenological analysis based on Heidegger's thinking, we illuminate the complexities of "being toward death" and the human striving for authentic being through engagement in daily living. The main findings demonstrate how sensory experiences support being through an appreciation of everyday aesthetics. Furthermore, the making of material things was identified as a means to express the value of self and others in relation to the involved individual's past, present, and future.

Lectin array and glycogene expression analyses of ovarian cancer cell line A2780 and its cisplatin-resistant derivate cell line A2780-cp.

PubMed

Zhao, Ran; Qin, Wenjun; Qin, Ruihuan; Han, Jing; Li, Can; Wang, Yisheng; Xu, Congjian

2017-01-01

Ovarian cancer is one of the most lethal gynecological malignancies, in which platinum resistance is a common cause of its relapse and death. Glycosylation has been reported to be involved in drug resistance, and glycomic analyses of ovarian cancer may improve our understanding of the mechanisms underlying cancer cell drug resistance and provide potential biomarkers and therapeutic targets. The serous ovarian cancer cell line A2780 and its platinum-resistant counterpart A2780-cp were used in this study. We performed a lectin array analysis to compare the glycosylation patterns of the two cell lines, a gene expression array was employed to probe the differences in glycogenes. Furthermore, the results were verified by lectin blots. A2780-cp cell exhibited stronger intensities of Lens culinaris (LCA) Canavalia ensiformis (ConA), and Lycopersicon esculentum (LEL) and weaker intensities of Sambucus nigra (SNA) lectins. The gene expression array analysis revealed increased expression of Fut8, B3gnt4, B3gnt5, B4galt2 and decreased expression of Fut1 and ST6GalNAc 6 expression were evident in the A2780-cp cells. The lectin blot confirmed the differences in LCA, ConA, SNA and LEL between the A2780 and A2780-cp cells. The combination of the lectin and gene expression analyses showed that the levels of core fucosylation and poly-LacNAc were increased in the A2780-cp cells and the levels of Fuc α1-2(gal β1-4) GlcNAc and α2-6-linked sialic structures were decreased in the A2780-cp cells. These glycans represent potential biomarkers and might be involved in the mechanism of drug resistance in ovarian cancer.

Optimal expression evaluation for data parallel architectures

NASA Technical Reports Server (NTRS)

Gilbert, John R.; Schreiber, Robert

1990-01-01

A data parallel machine represents an array or other composite data structure by allocating one processor (at least conceptually) per data item. A pointwise operation can be performed between two such arrays in unit time, provided their corresponding elements are allocated in the same processors. If the arrays are not aligned in this fashion, the cost of moving one or both of them is part of the cost of the operation. The choice of where to perform the operation then affects this cost. If an expression with several operands is to be evaluated, there may be many choices of where to perform the intermediate operations. An efficient algorithm is given to find the minimum-cost way to evaluate an expression, for several different data parallel architectures. This algorithm applies to any architecture in which the metric describing the cost of moving an array is robust. This encompasses most of the common data parallel communication architectures, including meshes of arbitrary dimension and hypercubes. Remarks are made on several variations of the problem, some of which are solved and some of which remain open.

Integrated residential photovoltaic array development

NASA Astrophysics Data System (ADS)

Shepard, N. F., Jr.

1981-12-01

An advanced, universally-mountable, integrated residential photovoltaic array concept was defined based upon an in-depth formulation and evaluation of three candidate approaches which were synthesized from existing or proposed residential array concepts. The impact of module circuitry and process sequence is considered and technology gaps and performance drivers associated with residential photovoltaic array concepts are identified. The actual learning experience gained from the comparison of the problem areas of the hexagonal shingle design with the rectangular module design led to what is considered an advanced array concept. Building the laboratory mockup provided actual experience and the opportunity to uncover additional technology gaps.

Integrated residential photovoltaic array development

NASA Technical Reports Server (NTRS)

Shepard, N. F., Jr.

1981-01-01

An advanced, universally-mountable, integrated residential photovoltaic array concept was defined based upon an in-depth formulation and evaluation of three candidate approaches which were synthesized from existing or proposed residential array concepts. The impact of module circuitry and process sequence is considered and technology gaps and performance drivers associated with residential photovoltaic array concepts are identified. The actual learning experience gained from the comparison of the problem areas of the hexagonal shingle design with the rectangular module design led to what is considered an advanced array concept. Building the laboratory mockup provided actual experience and the opportunity to uncover additional technology gaps.

Analytic solution of field distribution and demagnetization function of ideal hollow cylindrical field source

NASA Astrophysics Data System (ADS)

Xu, Xiaonong; Lu, Dingwei; Xu, Xibin; Yu, Yang; Gu, Min

2017-09-01

The Halbach type hollow cylindrical permanent magnet array (HCPMA) is a volume compact and energy conserved field source, which have attracted intense interests in many practical applications. Here, using the complex variable integration method based on the Biot-Savart Law (including current distributions inside the body and on the surfaces of magnet), we derive analytical field solutions to an ideal multipole HCPMA in entire space including the interior of magnet. The analytic field expression inside the array material is used to construct an analytic demagnetization function, with which we can explain the origin of demagnetization phenomena in HCPMA by taking into account an ideal magnetic hysteresis loop with finite coercivity. These analytical field expressions and demagnetization functions provide deeper insight into the nature of such permanent magnet array systems and offer guidance in designing optimized array system.

Qualitative assessment of gene expression in affymetrix genechip arrays

NASA Astrophysics Data System (ADS)

Nagarajan, Radhakrishnan; Upreti, Meenakshi

2007-01-01

Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array and in turn govern the gene expression. In the present study, we make several interesting observations. We show that there is considerable correlation between the probe intensities across the array which defy the independence assumption. While the mechanism behind such correlations is unclear, we show that scaling behavior and the profiles of perfect match (PM) as well as mismatch (MM) probes are similar and immune-to-background subtraction. We believe that the observed correlations are possibly an outcome of inherent non-stationarities or patchiness in the array devoid of biological significance. This is demonstrated by inspecting their scaling behavior and profiles of the PM and MM probe intensities obtained from publicly available Genechip arrays from three eukaryotic genomes, namely: Drosophila melanogaster (fruit fly), Homo sapiens (humans) and Mus musculus (house mouse) across distinct biological paradigms and across laboratories, with and without background subtraction. The fluctuation functions were estimated using detrended fluctuation analysis (DFA) with fourth-order polynomial detrending. The results presented in this study provide new insights into correlation signatures of PM and MM probe intensities and suggests the choice of DFA as a tool for qualitative assessment of Affymetrix Genechip microarrays prior to their analysis. A more detailed investigation is necessary in order to understand the source of these correlations.

Integrated Microfluidic Devices for Automated Microarray-Based Gene Expression and Genotyping Analysis

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Lodes, Mike; Fuji, H. Sho; Danley, David; McShea, Andrew

Microarray assays typically involve multistage sample processing and fluidic handling, which are generally labor-intensive and time-consuming. Automation of these processes would improve robustness, reduce run-to-run and operator-to-operator variation, and reduce costs. In this chapter, a fully integrated and self-contained microfluidic biochip device that has been developed to automate the fluidic handling steps for microarray-based gene expression or genotyping analysis is presented. The device consists of a semiconductor-based CustomArray® chip with 12,000 features and a microfluidic cartridge. The CustomArray was manufactured using a semiconductor-based in situ synthesis technology. The micro-fluidic cartridge consists of microfluidic pumps, mixers, valves, fluid channels, and reagent storage chambers. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated in the cartridge to provide pumping of liquid solutions. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross-talk of the stored reagents. Gene expression study of the human leukemia cell line (K562) and genotyping detection and sequencing of influenza A subtypes have been demonstrated using this integrated biochip platform. For gene expression assays, the microfluidic CustomArray device detected sample RNAs with a concentration as low as 0.375 pM. Detection was quantitative over more than three orders of magnitude. Experiment also showed that chip-to-chip variability was low indicating that the integrated microfluidic devices eliminate manual fluidic handling steps that can be a significant source of variability in genomic analysis. The genotyping results showed that the device identified influenza A hemagglutinin and neuraminidase subtypes and sequenced portions of both genes, demonstrating the potential of integrated microfluidic and microarray technology for multiple virus detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps and allows microarray-based DNA analysis in a rapid and automated fashion.

Validation Report for the EO-1 Lightweight Flexible Solar Array Experiment

NASA Technical Reports Server (NTRS)

Carpenter, Bernie; Lyons, John; Day, John (Technical Monitor)

2001-01-01

The controlled deployment of the Lightweight Flexible Solar Array (LFSA) experiment using the shape memory alloy release and deployment system has been demonstrated. Work remains to be done in increasing the efficiency of Copper Indium Diselinide (CIS) terminations to the flexible harness that carries current from the array to the I-V measurement electronics.

A 4-channel 3 Tesla phased array receive coil for awake rhesus monkey fMRI and diffusion MRI experiments.

PubMed

Khachaturian, Mark Haig

2010-01-01

Awake monkey fMRI and diffusion MRI combined with conventional neuroscience techniques has the potential to study the structural and functional neural network. The majority of monkey fMRI and diffusion MRI experiments are performed with single coils which suffer from severe EPI distortions which limit resolution. By constructing phased array coils for monkey MRI studies, gains in SNR and anatomical accuracy (i.e., reduction of EPI distortions) can be achieved using parallel imaging. The major challenges associated with constructing phased array coils for monkeys are the variation in head size and space constraints. Here, we apply phased array technology to a 4-channel phased array coil capable of improving the resolution and image quality of full brain awake monkey fMRI and diffusion MRI experiments. The phased array coil is that can adapt to different rhesus monkey head sizes (ages 4-8) and fits in the limited space provided by monkey stereotactic equipment and provides SNR gains in primary visual cortex and anatomical accuracy in conjunction with parallel imaging and improves resolution in fMRI experiments by a factor of 2 (1.25 mm to 1.0 mm isotropic) and diffusion MRI experiments by a factor of 4 (1.5 mm to 0.9 mm isotropic).

A 4-channel 3 Tesla phased array receive coil for awake rhesus monkey fMRI and diffusion MRI experiments

PubMed Central

Khachaturian, Mark Haig

2010-01-01

Awake monkey fMRI and diffusion MRI combined with conventional neuroscience techniques has the potential to study the structural and functional neural network. The majority of monkey fMRI and diffusion MRI experiments are performed with single coils which suffer from severe EPI distortions which limit resolution. By constructing phased array coils for monkey MRI studies, gains in SNR and anatomical accuracy (i.e., reduction of EPI distortions) can be achieved using parallel imaging. The major challenges associated with constructing phased array coils for monkeys are the variation in head size and space constraints. Here, we apply phased array technology to a 4-channel phased array coil capable of improving the resolution and image quality of full brain awake monkey fMRI and diffusion MRI experiments. The phased array coil is that can adapt to different rhesus monkey head sizes (ages 4–8) and fits in the limited space provided by monkey stereotactic equipment and provides SNR gains in primary visual cortex and anatomical accuracy in conjunction with parallel imaging and improves resolution in fMRI experiments by a factor of 2 (1.25 mm to 1.0 mm isotropic) and diffusion MRI experiments by a factor of 4 (1.5 mm to 0.9 mm isotropic). PMID:21243106

The Extensive Air Shower Experiment Kascade-Grande

NASA Astrophysics Data System (ADS)

Kang, Donghwa; Apel, W. D.; Arteaga, J. C.; Badea, F.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Brüggemann, M.; Buchholz, P.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuhrmann, D.; Ghia, P. L.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huege, T.; Isar, P. G.; Kampert, K.-H.; Kickelbick, D.; Klages, H. O.; Kolotaev, Y.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Navarra, G.; Nehls, S.; Oehlschläger, J.; Ostapchenko, S.; Over, S.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schatz, G.; Schieler, H.; Schröder, F.; Sima, O.; Stümpert, M.; Toma, G.; Trinchero, G. C.; Ulrich, H.; van Buren, J.; Walkowiak, W.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

The extensive air shower experiment KASCADE-Grande (KArlsruhe Shower Core and Array DEtector and Grande array) is located on site of the Forschungszentrum Karlsruhe in Germany. The original KASCADE experiment consisted of a densely packed scintillator array with unshielded and shielded detectors for the measurement of the electromagnetic and muonic shower component independently, as well as muon tracking devices and a hadron calorimeter. The Grande array as an extension of KASCADE consists of 37 scintillation detector stations covering an area of 700×700 m2. The main goal for the combined measurements of KASCADE and Grande is the investigation of the energy spectrum and composition of primary cosmic rays in the energy range of 1016 to 1018 eV. In this paper an overview of the KASCADE-Grande experiment and recent results will be presented.

The MSX1 homeobox transcription factor is a downstream target of PHOX2B and activates the Delta-Notch pathway in neuroblastoma

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

Revet, Ingrid; Huizenga, Gerda; Chan, Alvin

Neuroblastoma is an embryonal tumour of the peripheral sympathetic nervous system (SNS). One of the master regulator genes for peripheral SNS differentiation, the homeobox transcription factor PHOX2B, is mutated in familiar and sporadic neuroblastomas. Here we report that inducible expression of PHOX2B in the neuroblastoma cell line SJNB-8 down-regulates MSX1, a homeobox gene important for embryonic neural crest development. Inducible expression of MSX1 in SJNB-8 caused inhibition of both cell proliferation and colony formation in soft agar. Affymetrix micro-array and Northern blot analysis demonstrated that MSX1 strongly up-regulated the Delta-Notch pathway genes DLK1, NOTCH3, and HEY1. In addition, the proneuralmore » gene NEUROD1 was down-regulated. Western blot analysis showed that MSX1 induction caused cleavage of the NOTCH3 protein to its activated form, further confirming activation of the Delta-Notch pathway. These experiments describe for the first time regulation of the Delta-Notch pathway by MSX1, and connect these genes to the PHOX2B oncogene, indicative of a role in neuroblastoma biology. Affymetrix micro-array analysis of a neuroblastic tumour series consisting of neuroblastomas and the more benign ganglioneuromas showed that MSX1, NOTCH3 and HEY1 are more highly expressed in ganglioneuromas. This suggests a block in differentiation of these tumours at distinct developmental stages or lineages.« less

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

PubMed

Memon, Farhat N; Owen, Anne M; Sanchez-Graillet, Olivia; Upton, Graham J G; Harrison, Andrew P

2010-01-15

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays.

Characterization of Settled Atmospheric Dust by the DART Experiment

NASA Technical Reports Server (NTRS)

Landis, Geoffrey A.; Jenkins, Phillip P.; Baraona, Cosmo

1999-01-01

The DART ("Dust Accumulation and Removal Test") package is an experiment which will fly as part of the MIP experiment on the Mars-2001 Surveyor Lander. Dust deposition could be a significant problem for photovoltaic array operation for long duration emissions on the surface of Mars. Measurements made by Pathfinder showed 0.3% loss of solar array performance per day due to dust obscuration. The DART experiment is designed to quantify dust deposition from the Mars atmosphere, measure the properties of settled dust, measure the effect of dust deposition on the array performance, and test several methods of mitigating the effect of settled dust on a solar array. Although the purpose of DART (along with its sister experiment, MATE) is to gather information critical to the design of future power systems on the surface of Mars, the dust characterization instrumentation on DART will also provide significant scientific data on the properties of settled atmospheric dust.

In-Space Structural Validation Plan for a Stretched-Lens Solar Array Flight Experiment

NASA Technical Reports Server (NTRS)

Pappa, Richard S.; Woods-Vedeler, Jessica A.; Jones, Thomas W.

2001-01-01

This paper summarizes in-space structural validation plans for a proposed Space Shuttle-based flight experiment. The test article is an innovative, lightweight solar array concept that uses pop-up, refractive stretched-lens concentrators to achieve a power/mass density of at least 175 W/kg, which is more than three times greater than current capabilities. The flight experiment will validate this new technology to retire the risk associated with its first use in space. The experiment includes structural diagnostic instrumentation to measure the deployment dynamics, static shape, and modes of vibration of the 8-meter-long solar array and several of its lenses. These data will be obtained by photogrammetry using the Shuttle payload-bay video cameras and miniature video cameras on the array. Six accelerometers are also included in the experiment to measure base excitations and small-amplitude tip motions.

Synthetic resistivity calculations for the canonical depth-to-bedrock problem: A critical examination of the thin interbed problem and electrical equivalence theories

NASA Astrophysics Data System (ADS)

Weiss, C. J.; Knight, R.

2009-05-01

One of the key factors in the sensible inference of subsurface geologic properties from both field and laboratory experiments is the ability to quantify the linkages between the inherently fine-scale structures, such as bedding planes and fracture sets, and their macroscopic expression through geophysical interrogation. Central to this idea is the concept of a "minimal sampling volume" over which a given geophysical method responds to an effective medium property whose value is dictated by the geometry and distribution of sub- volume heterogeneities as well as the experiment design. In this contribution we explore the concept of effective resistivity volumes for the canonical depth-to-bedrock problem subject to industry-standard DC resistivity survey designs. Four models representing a sedimentary overburden and flat bedrock interface were analyzed through numerical experiments of six different resistivity arrays. In each of the four models, the sedimentary overburden consists of a thinly interbedded resistive and conductive laminations, with equivalent volume-averaged resistivity but differing lamination thickness, geometry, and layering sequence. The numerical experiments show striking differences in the apparent resistivity pseudo-sections which belie the volume-averaged equivalence of the models. These models constitute the synthetic data set offered for inversion in this Back to Basics Resistivity Modeling session and offer the promise to further our understanding of how the sampling volume, as affected by survey design, can be constrained by joint-array inversion of resistivity data.

A Meta-Analysis of Multiple Matched Copy Number and Transcriptomics Data Sets for Inferring Gene Regulatory Relationships

PubMed Central

Newton, Richard; Wernisch, Lorenz

2014-01-01

Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments. PMID:25148247

Solar array flight dynamic experiment

NASA Technical Reports Server (NTRS)

Schock, R. W.

1986-01-01

The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on space shuttle flight STS-31D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

Solar array flight dynamic experiment

NASA Technical Reports Server (NTRS)

Schock, Richard W.

1986-01-01

The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on Space Shuttle flight STS-31D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

Solar array flight dynamic experiment

NASA Technical Reports Server (NTRS)

Schock, Richard W.

1987-01-01

The purpose of the Solar Array Flight Dynamic Experiment (SAFDE) is to demonstrate the feasibility of on-orbit measurement and ground processing of large space structures' dynamic characteristics. Test definition or verification provides the dynamic characteristic accuracy required for control systems use. An illumination/measurement system was developed to fly on space shuttle flight STS-41D. The system was designed to dynamically evaluate a large solar array called the Solar Array Flight Experiment (SAFE) that had been scheduled for this flight. The SAFDE system consisted of a set of laser diode illuminators, retroreflective targets, an intelligent star tracker receiver and the associated equipment to power, condition, and record the results. In six tests on STS-41D, data was successfully acquired from 18 retroreflector targets and ground processed, post flight, to define the solar array's dynamic characteristic. The flight experiment proved the viability of on-orbit test definition of large space structures dynamic characteristics. Future large space structures controllability should be greatly enhanced by this capability.

Breadboard linear array scan imager using LSI solid-state technology

NASA Technical Reports Server (NTRS)

Tracy, R. A.; Brennan, J. A.; Frankel, D. G.; Noll, R. E.

1976-01-01

The performance of large scale integration photodiode arrays in a linear array scan (pushbroom) breadboard was evaluated for application to multispectral remote sensing of the earth's resources. The technical approach, implementation, and test results of the program are described. Several self scanned linear array visible photodetector focal plane arrays were fabricated and evaluated in an optical bench configuration. A 1728-detector array operating in four bands (0.5 - 1.1 micrometer) was evaluated for noise, spectral response, dynamic range, crosstalk, MTF, noise equivalent irradiance, linearity, and image quality. Other results include image artifact data, temporal characteristics, radiometric accuracy, calibration experience, chip alignment, and array fabrication experience. Special studies and experimentation were included in long array fabrication and real-time image processing for low-cost ground stations, including the use of computer image processing. High quality images were produced and all objectives of the program were attained.

Response Surface Model Building Using Orthogonal Arrays for Computer Experiments

NASA Technical Reports Server (NTRS)

Unal, Resit; Braun, Robert D.; Moore, Arlene A.; Lepsch, Roger A.

1997-01-01

This study investigates response surface methods for computer experiments and discusses some of the approaches available. Orthogonal arrays constructed for computer experiments are studied and an example application to a technology selection and optimization study for a reusable launch vehicle is presented.

Apollo lunar surface experiments package. Apollo 17 ALSEP (array E) familiarization course handout

NASA Technical Reports Server (NTRS)

1972-01-01

The familiarization course for the Apollo 17 ALSEP (ARRAY E) is presented. The subjects discussed are: (1) power and data subsystems, (2) lunar surface gravimeter, (3) lunar mass spectrometer, (4) lunar seismic profiling experiment, and (5) heat flow experiment.

STS-74/MIR Photogrammetric Appendage Structural Dynamics Experiment Preliminary Data Analysis

NASA Technical Reports Server (NTRS)

Gilbert, Michael G.; Welch, Sharon S.; Pappa, Richard S.; Demeo, Martha E.

1997-01-01

The Photogrammetric Appendage Structural Dynamics Experiment was designed, developed, and flown to demonstrate and prove measurement of the structural vibration response of a Russian Space Station Mir solar array using photogrammetric methods. The experiment flew on the STS-74 Space Shuttle mission to Mir in November 1995 and obtained video imagery of solar array structural response to various excitation events. The video imagery has been digitized and triangulated to obtain response time history data at discrete points on the solar array. This data has been further processed using the Eigensystem Realization Algorithm modal identification technique to determine the natural vibration frequencies, damping, and mode shapes of the solar array. The results demonstrate that photogrammetric measurement of articulating, nonoptically targeted, flexible solar arrays and appendages is a viable, low-cost measurement option for the International Space Station.

Spatiotemporal dynamics of oscillatory cellular patterns in three-dimensional directional solidification.

PubMed

Bergeon, N; Tourret, D; Chen, L; Debierre, J-M; Guérin, R; Ramirez, A; Billia, B; Karma, A; Trivedi, R

2013-05-31

We report results of directional solidification experiments conducted on board the International Space Station and quantitative phase-field modeling of those experiments. The experiments image for the first time in situ the spatially extended dynamics of three-dimensional cellular array patterns formed under microgravity conditions where fluid flow is suppressed. Experiments and phase-field simulations reveal the existence of oscillatory breathing modes with time periods of several 10's of minutes. Oscillating cells are usually noncoherent due to array disorder, with the exception of small areas where the array structure is regular and stable.

Two-pass imputation algorithm for missing value estimation in gene expression time series.

PubMed

Tsiporkova, Elena; Boeva, Veselka

2007-10-01

Gene expression microarray experiments frequently generate datasets with multiple values missing. However, most of the analysis, mining, and classification methods for gene expression data require a complete matrix of gene array values. Therefore, the accurate estimation of missing values in such datasets has been recognized as an important issue, and several imputation algorithms have already been proposed to the biological community. Most of these approaches, however, are not particularly suitable for time series expression profiles. In view of this, we propose a novel imputation algorithm, which is specially suited for the estimation of missing values in gene expression time series data. The algorithm utilizes Dynamic Time Warping (DTW) distance in order to measure the similarity between time expression profiles, and subsequently selects for each gene expression profile with missing values a dedicated set of candidate profiles for estimation. Three different DTW-based imputation (DTWimpute) algorithms have been considered: position-wise, neighborhood-wise, and two-pass imputation. These have initially been prototyped in Perl, and their accuracy has been evaluated on yeast expression time series data using several different parameter settings. The experiments have shown that the two-pass algorithm consistently outperforms, in particular for datasets with a higher level of missing entries, the neighborhood-wise and the position-wise algorithms. The performance of the two-pass DTWimpute algorithm has further been benchmarked against the weighted K-Nearest Neighbors algorithm, which is widely used in the biological community; the former algorithm has appeared superior to the latter one. Motivated by these findings, indicating clearly the added value of the DTW techniques for missing value estimation in time series data, we have built an optimized C++ implementation of the two-pass DTWimpute algorithm. The software also provides for a choice between three different initial rough imputation methods.

Environmental stress alters genes expression and induces ovule abortion: reactive oxygen species appear as ovules commit to abort.

PubMed

Sun, Kelian; Cui, Yuehua; Hauser, Bernard A

2005-11-01

Environmental stress dramatically reduces plant reproduction. Previous results showed that placing roots in 200 mM NaCl for 12 h caused 90% of the developing Arabidopsis ovules to abort (Sun et al. in Plant Physiol 135:2358-2367, 2004). To discover the molecular responses that occur during ovule abortion, gene expression was monitored using Affymetrix 24k genome arrays. Transcript levels were measured in pistils that were stressed for 6, 12, 18, and 24 h, then compared with the levels in healthy pistils. Over the course of this experiment, a total of 535 salt-responsive genes were identified. Cluster analysis showed that differentially expressed genes exhibited reproducible changes in expression. The expression of 65 transcription factors, some of which are known to be involved in stress responses, were modulated during ovule abortion. In flowers, salt stress led to a 30-fold increase in Na+ ions and modest, but significant, decreases in the accumulation of other ions. The expression of cation exchangers and ion transporters were induced, presumably to reestablish ion homeostasis following salt stress. Genes that encode enzymes that detoxify reactive oxygen species (ROS), including ascorbate peroxidase and peroxidase, were downregulated after ovules committed to abort. These changes in gene expression coincided with the synthesis of ROS in female gametophytes. One day after salt stress, ROS spread from the gametophytes to the maternal chalaza and integuments. In addition, genes encoding proteins that regulate ethylene responses, including ethylene biosynthesis, ethylene signal transduction and ethylene-responsive transcription factors, were upregulated after stress. Hypotheses are proposed on the basis of this expression analysis, which will be evaluated further in future experiments.

The PIX-2 experiment: An overview

NASA Astrophysics Data System (ADS)

Purvis, C. K.

1985-03-01

The second Plasma Interactions Experiment (PIX-2) was launched in January 1983 as a piggyback on the second stage of the Delta launch vehicle that carried IRAS into orbit. Placed in a 870 km circular polar orbit, it returned 18 hrs of data on the plasma current collection and arcing behavior of solar arrays biased to +/-1000 V in steps. The four 500 sq cm solar array segments were biased singly and in combinations. In addition to the array segments PIX-2 carried a Sun sensor, a Langmuir probe to measure electron currents, and a hot-wire filament electron emitter to control vehicle potential during positive array bias sequences. The PIX-2 experiment is reviewed from program and operational perspectives.

Isolated Reporter Bacteria in Supramolecular Hydrogel Microwell Arrays

PubMed Central

2017-01-01

The combination of supramolecular hydrogels formed by low molecular weight gelator self-assembly via noncovalent interactions within a scaffold derived from polyethylene glycol (PEG) affords an interesting approach to immobilize fully functional, isolated reporter bacteria in novel microwell arrays. The PEG-based scaffold serves as a stabilizing element and provides physical support for the self-assembly of the C2-phenyl-derived gelator on the micrometer scale. Supramolecular hydrogel microwell arrays with various shapes and sizes were used to isolate single or small numbers of Escherichia coli TOP10 pTetR-LasR-pLuxR-GFP. In the presence of the autoinducer N-(3-oxododecanoyl) homoserine lactone, the entrapped E. coli in the hydrogel microwell arrays showed an increased GFP expression. The shape and size of microwell arrays did not influence the fluorescence intensity and the projected size of the bacteria markedly, while the population density of seeded bacteria affected the number of bacteria expressing GFP per well. The hydrogel microwell arrays can be further used to investigate quorum sensing, reflecting communication in inter- and intraspecies bacterial communities for biology applications in the field of biosensors. In the future, these self-assembled hydrogel microwell arrays can also be used as a substrate to detect bacteria via secreted autoinducers. PMID:28486805

Isolated Reporter Bacteria in Supramolecular Hydrogel Microwell Arrays.

PubMed

Li, Ping; Dou, Xiaoqiu; Feng, Chuanliang; Müller, Mareike; Chang, Matthew Wook; Frettlöh, Martin; Schönherr, Holger

2017-08-08

The combination of supramolecular hydrogels formed by low molecular weight gelator self-assembly via noncovalent interactions within a scaffold derived from polyethylene glycol (PEG) affords an interesting approach to immobilize fully functional, isolated reporter bacteria in novel microwell arrays. The PEG-based scaffold serves as a stabilizing element and provides physical support for the self-assembly of the C 2 -phenyl-derived gelator on the micrometer scale. Supramolecular hydrogel microwell arrays with various shapes and sizes were used to isolate single or small numbers of Escherichia coli TOP10 pTetR-LasR-pLuxR-GFP. In the presence of the autoinducer N-(3-oxododecanoyl) homoserine lactone, the entrapped E. coli in the hydrogel microwell arrays showed an increased GFP expression. The shape and size of microwell arrays did not influence the fluorescence intensity and the projected size of the bacteria markedly, while the population density of seeded bacteria affected the number of bacteria expressing GFP per well. The hydrogel microwell arrays can be further used to investigate quorum sensing, reflecting communication in inter- and intraspecies bacterial communities for biology applications in the field of biosensors. In the future, these self-assembled hydrogel microwell arrays can also be used as a substrate to detect bacteria via secreted autoinducers.

LUNASKA experiments using the Australia Telescope Compact Array to search for ultrahigh energy neutrinos and develop technology for the lunar Cherenkov technique

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

James, C. W.; Protheroe, R. J.; Ekers, R. D.

2010-02-15

We describe the design, performance, sensitivity and results of our recent experiments using the Australia Telescope Compact Array (ATCA) for lunar Cherenkov observations with a very wide (600 MHz) bandwidth and nanosecond timing, including a limit on an isotropic neutrino flux. We also make a first estimate of the effects of small-scale surface roughness on the effective experimental aperture, finding that contrary to expectations, such roughness will act to increase the detectability of near-surface events over the neutrino energy-range at which our experiment is most sensitive (though distortions to the time-domain pulse profile may make identification more difficult). The aimmore » of our 'Lunar UHE Neutrino Astrophysics using the Square Kilometre Array' (LUNASKA) project is to develop the lunar Cherenkov technique of using terrestrial radio telescope arrays for ultrahigh energy (UHE) cosmic ray (CR) and neutrino detection, and, in particular, to prepare for using the Square Kilometre Array (SKA) and its path-finders such as the Australian SKA Pathfinder (ASKAP) and the Low Frequency Array (LOFAR) for lunar Cherenkov experiments.« less

Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle

PubMed Central

2011-01-01

Background Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species is essential to the production of high quality meat products. For example, consumer demand for lean, inexpensive meat products has driven the turkey industry to unprecedented production through intensive genetic selection. However, achievements of increased body weight and muscle mass have been countered by an increased incidence of myopathies and meat quality defects. In a previous study, we developed and validated a turkey skeletal muscle-specific microarray as a tool for functional genomics studies. The goals of the current study were to utilize this microarray to elucidate functional pathways of genes responsible for key events in turkey skeletal muscle development and to compare differences in gene expression between two genetic lines of turkeys. To achieve these goals, skeletal muscle samples were collected at three critical stages in muscle development: 18d embryo (hyperplasia), 1d post-hatch (shift from myoblast-mediated growth to satellite cell-modulated growth by hypertrophy), and 16wk (market age) from two genetic lines: a randombred control line (RBC2) maintained without selection pressure, and a line (F) selected from the RBC2 line for increased 16wk body weight. Array hybridizations were performed in two experiments: Experiment 1 directly compared the developmental stages within genetic line, while Experiment 2 directly compared the two lines within each developmental stage. Results A total of 3474 genes were differentially expressed (false discovery rate; FDR < 0.001) by overall effect of development, while 16 genes were differentially expressed (FDR < 0.10) by overall effect of genetic line. Ingenuity Pathways Analysis was used to group annotated genes into networks, functions, and canonical pathways. The expression of 28 genes involved in extracellular matrix regulation, cell death/apoptosis, and calcium signaling/muscle function, as well as genes with miscellaneous function was confirmed by qPCR. Conclusions The current study identified gene pathways and uncovered novel genes important in turkey muscle growth and development. Future experiments will focus further on several of these candidate genes and the expression and mechanism of action of their protein products. PMID:21385442

Gene expression profile of mouse prostate tumors reveals dysregulations in major biological processes and identifies potential murine targets for preclinical development of human prostate cancer therapy.

PubMed

Haram, Kerstyn M; Peltier, Heidi J; Lu, Bin; Bhasin, Manoj; Otu, Hasan H; Choy, Bob; Regan, Meredith; Libermann, Towia A; Latham, Gary J; Sanda, Martin G; Arredouani, Mohamed S

2008-10-01

Translation of preclinical studies into effective human cancer therapy is hampered by the lack of defined molecular expression patterns in mouse models that correspond to the human counterpart. We sought to generate an open source TRAMP mouse microarray dataset and to use this array to identify differentially expressed genes from human prostate cancer (PCa) that have concordant expression in TRAMP tumors, and thereby represent lead targets for preclinical therapy development. We performed microarrays on total RNA extracted and amplified from eight TRAMP tumors and nine normal prostates. A subset of differentially expressed genes was validated by QRT-PCR. Differentially expressed TRAMP genes were analyzed for concordant expression in publicly available human prostate array datasets and a subset of resulting genes was analyzed by QRT-PCR. Cross-referencing differentially expressed TRAMP genes to public human prostate array datasets revealed 66 genes with concordant expression in mouse and human PCa; 56 between metastases and normal and 10 between primary tumor and normal tissues. Of these 10 genes, two, Sox4 and Tubb2a, were validated by QRT-PCR. Our analysis also revealed various dysregulations in major biologic pathways in the TRAMP prostates. We report a TRAMP microarray dataset of which a gene subset was validated by QRT-PCR with expression patterns consistent with previous gene-specific TRAMP studies. Concordance analysis between TRAMP and human PCa associated genes supports the utility of the model and suggests several novel molecular targets for preclinical therapy.

Impact of S100A8 expression on kidney cancer progression and molecular docking studies for kidney cancer therapeutics.

PubMed

Mirza, Zeenat; Schulten, Hans-Juergen; Farsi, Hasan Ma; Al-Maghrabi, Jaudah A; Gari, Mamdooh A; Chaudhary, Adeel Ga; Abuzenadah, Adel M; Al-Qahtani, Mohammed H; Karim, Sajjad

2014-04-01

The proinflammatory protein S100A8, which is expressed in myeloid cells under physiological conditions, is strongly expressed in human cancer tissues. Its role in tumor cell differentiation and tumor progression is largely unclear and virtually unstudied in kidney cancer. In the present study, we investigated whether S100A8 could be a potential anticancer drug target and therapeutic biomarker for kidney cancer, and the underlying molecular mechanisms by exploiting its interaction profile with drugs. Microarray-based transcriptomics experiments using Affymetrix HuGene 1.0 ST arrays were applied to renal cell carcinoma specimens from Saudi patients for identification of significant genes associated with kidney cancer. In addition, we retrieved selected expression data from the National Center for Biotechnology Information Gene Expression Omnibus database for comparative analysis and confirmation of S100A8 expression. Ingenuity Pathway Analysis (IPA) was used to elucidate significant molecular networks and pathways associated with kidney cancer. The probable polar and non-polar interactions of possible S100A8 inhibitors (aspirin, celecoxib, dexamethasone and diclofenac) were examined by performing molecular docking and binding free energy calculations. Detailed analysis of bound structures and their binding free energies was carried out for S100A8, its known partner (S100A9), and S100A8-S100A9 complex (calprotectin). In our microarray experiments, we identified 1,335 significantly differentially expressed genes, including S100A8, in kidney cancer using a cut-off of p<0.05 and fold-change of 2. Functional analysis of kidney cancer-associated genes showed overexpression of genes involved in cell-cycle progression, DNA repair, cell death, tumor morphology and tissue development. Pathway analysis showed significant disruption of pathways of atherosclerosis signaling, liver X receptor/retinoid X receptor (LXR/RXR) activation, notch signaling, and interleukin-12 (IL-12) signaling. We identified S100A8 as a prospective biomarker for kidney cancer and in silico analysis showed that aspirin, celecoxib, dexamethasone and diclofenac binds to S100A8 and may inhibit downstream signaling in kidney cancer. The present study provides an initial overview of differentially expressed genes in kidney cancer of Saudi Arabian patients using whole-transcript, high-density expression arrays. Our analysis suggests distinct transcriptomic signatures, with significantly high levels of S100A8, and underlying molecular mechanisms contributing to kidney cancer progression. Our docking-based findings shed insight into S100A8 protein as an attractive anticancer target for therapeutic intervention in kidney cancer. To our knowledge, this is the first structure-based docking study for the selected protein targets using the chosen ligands.

Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments.

PubMed

Munkácsy, Gyöngyi; Sztupinszki, Zsófia; Herman, Péter; Bán, Bence; Pénzváltó, Zsófia; Szarvas, Nóra; Győrffy, Balázs

2016-09-27

No independent cross-validation of success rate for studies utilizing small interfering RNA (siRNA) for gene silencing has been completed before. To assess the influence of experimental parameters like cell line, transfection technique, validation method, and type of control, we have to validate these in a large set of studies. We utilized gene chip data published for siRNA experiments to assess success rate and to compare methods used in these experiments. We searched NCBI GEO for samples with whole transcriptome analysis before and after gene silencing and evaluated the efficiency for the target and off-target genes using the array-based expression data. Wilcoxon signed-rank test was used to assess silencing efficacy and Kruskal-Wallis tests and Spearman rank correlation were used to evaluate study parameters. All together 1,643 samples representing 429 experiments published in 207 studies were evaluated. The fold change (FC) of down-regulation of the target gene was above 0.7 in 18.5% and was above 0.5 in 38.7% of experiments. Silencing efficiency was lowest in MCF7 and highest in SW480 cells (FC = 0.59 and FC = 0.30, respectively, P = 9.3E-06). Studies utilizing Western blot for validation performed better than those with quantitative polymerase chain reaction (qPCR) or microarray (FC = 0.43, FC = 0.47, and FC = 0.55, respectively, P = 2.8E-04). There was no correlation between type of control, transfection method, publication year, and silencing efficiency. Although gene silencing is a robust feature successfully cross-validated in the majority of experiments, efficiency remained insufficient in a significant proportion of studies. Selection of cell line model and validation method had the highest influence on silencing proficiency.

Molecular characterization of immortalized normal and dysplastic oral cell lines.

PubMed

Dickman, Christopher T D; Towle, Rebecca; Saini, Rajan; Garnis, Cathie

2015-05-01

Cell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make-up of these systems is critical for understanding the disease biology modeled. Six immortalized normal, one immortalized dysplasia, one self-immortalized dysplasia, and two primary normal cell lines derived from oral tissues were analyzed for DNA copy number changes and changes in both mRNA and miRNA expression using SMRT-v.2 genome-wide tiling comparative genomic hybridization arrays, Agilent Whole Genome 4x44k expression arrays, and Exiqon V2.M-RT-PCR microRNA Human panels. DNA copy number alterations were detected in both normal and dysplastic immortalized cell lines-as well as in the single non-immortalized dysplastic cell line. These lines were found to have changes in expression of genes related to cell cycle control as well as alterations in miRNAs that are deregulated in clinical oral squamous cell carcinoma tissues. Immortal lines-whether normal or dysplastic-had increased disruption in expression relative to primary lines. All data are available as a public resource. Molecular profiling experiments have identified DNA, mRNA, and miRNA alterations for a panel of normal and dysplastic oral tissue cell lines. These data are a valuable resource to those modeling diseases of the oral mucosa, and give insight into the selection of model cell lines and the interpretation of data from those lines. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Experimental investigations of ablation stream interaction dynamics in tungsten wire arrays: Interpenetration, magnetic field advection, and ion deflection

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

Swadling, G. F.; Lebedev, S. V.; Hall, G. N.

2016-05-01

Experiments have been carried out to investigate the collisional dynamics of ablation streams produced by cylindrical wire array z-pinches. A combination of laser interferometric imaging, Thomson scattering, and Faraday rotation imaging has been used to make a range of measurements of the temporal evolution of various plasma and flow parameters. Our paper presents a summary of previously published data, drawing together a range of different measurements in order to give an overview of the key results. The paper focuses mainly on the results of experiments with tungsten wire arrays. Early interferometric imaging measurements are reviewed, then more recent Thomson scatteringmore » measurements are discussed; these measurements provided the first direct evidence of ablation stream interpenetration in a wire array experiment. Combining the data from these experiments gives a view of the temporal evolution of the tungsten stream collisional dynamics. In the final part of the paper, we present new experimental measurements made using an imaging Faraday rotation diagnostic. Our experiments investigated the structure of magnetic fields near the array axis directly; the presence of a magnetic field has previously been inferred based on Thomson scattering measurements of ion deflection near the array axis. Although the Thomson and Faraday measurements are not in full quantitative agreement, the Faraday data do qualitatively supports the conjecture that the observed deflections are induced by a static toroidal magnetic field, which has been advected to the array axis by the ablation streams. It is likely that detailed modeling will be needed in order to fully understand the dynamics observed in the experiment.« less

Experimental investigations of ablation stream interaction dynamics in tungsten wire arrays: Interpenetration, magnetic field advection, and ion deflection

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

Swadling, G. F.; Lebedev, S. V.; Hall, G. N.

2016-05-15

Experiments have been carried out to investigate the collisional dynamics of ablation streams produced by cylindrical wire array z-pinches. A combination of laser interferometric imaging, Thomson scattering, and Faraday rotation imaging has been used to make a range of measurements of the temporal evolution of various plasma and flow parameters. This paper presents a summary of previously published data, drawing together a range of different measurements in order to give an overview of the key results. The paper focuses mainly on the results of experiments with tungsten wire arrays. Early interferometric imaging measurements are reviewed, then more recent Thomson scatteringmore » measurements are discussed; these measurements provided the first direct evidence of ablation stream interpenetration in a wire array experiment. Combining the data from these experiments gives a view of the temporal evolution of the tungsten stream collisional dynamics. In the final part of the paper, we present new experimental measurements made using an imaging Faraday rotation diagnostic. These experiments investigated the structure of magnetic fields near the array axis directly; the presence of a magnetic field has previously been inferred based on Thomson scattering measurements of ion deflection near the array axis. Although the Thomson and Faraday measurements are not in full quantitative agreement, the Faraday data do qualitatively supports the conjecture that the observed deflections are induced by a static toroidal magnetic field, which has been advected to the array axis by the ablation streams. It is likely that detailed modeling will be needed in order to fully understand the dynamics observed in the experiment.« less

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

PubMed

Khan, Haseeb Ahmad

2005-01-28

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

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle

PubMed Central

Ron, Micha; Israeli, Galit; Seroussi, Eyal; Weller, Joel I; Gregg, Jeffrey P; Shani, Moshe; Medrano, Juan F

2007-01-01

Background Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN) determination. Results We hybridized Affymetrix microarray (MG-U74v2), containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL) that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2) were over expressed in the target organ. Thus, cgQTL can be used to determine priority of candidate genes for QTN analysis based on differential expression in the target organ. PMID:17584498

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

PubMed Central

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

2008-01-01

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

Functional Heterologous Protein Expression by Genetically Engineered Probiotic Yeast Saccharomyces boulardii

PubMed Central

Hudson, Lauren E.; Fasken, Milo B.; McDermott, Courtney D.; McBride, Shonna M.; Kuiper, Emily G.; Guiliano, David B.; Corbett, Anita H.; Lamb, Tracey J.

2014-01-01

Recent studies have suggested the potential of probiotic organisms to be adapted for the synthesis and delivery of oral therapeutics. The probiotic yeast Saccharomyces boulardii would be especially well suited for this purpose due to its ability, in contrast to probiotic prokaryotes, to perform eukaryotic post translational modifications. This probiotic yeast thus has the potential to express a broad array of therapeutic proteins. Currently, however, use of wild type (WT) S. boulardii relies on antibiotic resistance for the selection of transformed yeast. Here we report the creation of auxotrophic mutant strains of S. boulardii that can be selected without antibiotics and demonstrate that these yeast can express functional recombinant protein even when recovered from gastrointestinal immune tissues in mice. A UV mutagenesis approach was employed to generate three uracil auxotrophic S. boulardii mutants that show a low rate of reversion to wild type growth. These mutants can express recombinant protein and are resistant in vitro to low pH, bile acid salts, and anaerobic conditions. Critically, oral gavage experiments using C57BL/6 mice demonstrate that mutant S. boulardii survive and are taken up into gastrointestinal immune tissues on a similar level as WT S. boulardii. Mutant yeast recovered from gastrointestinal immune tissues furthermore retain expression of functional recombinant protein. These data show that auxotrophic mutant S. boulardii can safely express recombinant protein without antibiotic selection and can deliver recombinant protein to gastrointestinal immune tissues. These auxotrophic mutants of S. boulardii pave the way for future experiments to test the ability of S. boulardii to deliver therapeutics and mediate protection against gastrointestinal disorders. PMID:25391025

Functional heterologous protein expression by genetically engineered probiotic yeast Saccharomyces boulardii.

PubMed

Hudson, Lauren E; Fasken, Milo B; McDermott, Courtney D; McBride, Shonna M; Kuiper, Emily G; Guiliano, David B; Corbett, Anita H; Lamb, Tracey J

2014-01-01

Recent studies have suggested the potential of probiotic organisms to be adapted for the synthesis and delivery of oral therapeutics. The probiotic yeast Saccharomyces boulardii would be especially well suited for this purpose due to its ability, in contrast to probiotic prokaryotes, to perform eukaryotic post translational modifications. This probiotic yeast thus has the potential to express a broad array of therapeutic proteins. Currently, however, use of wild type (WT) S. boulardii relies on antibiotic resistance for the selection of transformed yeast. Here we report the creation of auxotrophic mutant strains of S. boulardii that can be selected without antibiotics and demonstrate that these yeast can express functional recombinant protein even when recovered from gastrointestinal immune tissues in mice. A UV mutagenesis approach was employed to generate three uracil auxotrophic S. boulardii mutants that show a low rate of reversion to wild type growth. These mutants can express recombinant protein and are resistant in vitro to low pH, bile acid salts, and anaerobic conditions. Critically, oral gavage experiments using C57BL/6 mice demonstrate that mutant S. boulardii survive and are taken up into gastrointestinal immune tissues on a similar level as WT S. boulardii. Mutant yeast recovered from gastrointestinal immune tissues furthermore retain expression of functional recombinant protein. These data show that auxotrophic mutant S. boulardii can safely express recombinant protein without antibiotic selection and can deliver recombinant protein to gastrointestinal immune tissues. These auxotrophic mutants of S. boulardii pave the way for future experiments to test the ability of S. boulardii to deliver therapeutics and mediate protection against gastrointestinal disorders.

From MAD to SAD: The Italian experience for the low-frequency aperture array of SKA1-LOW

NASA Astrophysics Data System (ADS)

Bolli, P.; Pupillo, G.; Virone, G.; Farooqui, M. Z.; Lingua, A.; Mattana, A.; Monari, J.; Murgia, M.; Naldi, G.; Paonessa, F.; Perini, F.; Pluchino, S.; Rusticelli, S.; Schiaffino, M.; Schillirò, F.; Tartarini, G.; Tibaldi, A.

2016-03-01

This paper describes two small aperture array demonstrators called Medicina and Sardinia Array Demonstrators (MAD and SAD, respectively). The objectives of these instruments are to acquire experience and test new technologies for a possible application to the low-frequency aperture array of the low-frequency telescope of the Square Kilometer Array phase 1 (SKA1-LOW). The MAD experience was concluded in 2014, and it turned out to be an important test bench for implementing calibration techniques based on an artificial source mounted in an aerial vehicle. SAD is based on 128 dual-polarized Vivaldi antennas and is 1 order of magnitude larger than MAD. The architecture and the station size of SAD, which is along the construction phase, are more similar to those under evaluation for SKA1-LOW, and therefore, SAD is expected to provide useful hints for SKA1-LOW.

HES1, a target of Notch signaling, is elevated in canine osteosarcoma, but reduced in the most aggressive tumors.

PubMed

Dailey, Deanna D; Anfinsen, Kristin P; Pfaff, Liza E; Ehrhart, E J; Charles, J Brad; Bønsdorff, Tina B; Thamm, Douglas H; Powers, Barbara E; Jonasdottir, Thora J; Duval, Dawn L

2013-07-01

Hairy and enhancer of split 1 (HES1), a basic helix-loop-helix transcriptional repressor, is a downstream target of Notch signaling. Notch signaling and HES1 expression have been linked to growth and survival in a variety of human cancer types and have been associated with increased metastasis and invasiveness in human osteosarcoma cell lines. Osteosarcoma (OSA) is an aggressive cancer demonstrating both high metastatic rate and chemotherapeutic resistance. The current study examined expression of Notch signaling mediators in primary canine OSA tumors and canine and human osteosarcoma cell lines to assess their role in OSA development and progression. Reverse transcriptase - quantitative PCR (RT-qPCR) was utilized to quantify HES1, HEY1, NOTCH1 and NOTCH2 gene expression in matched tumor and normal metaphyseal bone samples taken from dogs treated for appendicular OSA at the Colorado State University Veterinary Teaching Hospital. Gene expression was also assessed in tumors from dogs with a disease free interval (DFI) of <100 days compared to those with a DFI > 300 days following treatment with surgical amputation followed by standard chemotherapy. Immunohistochemistry was performed to confirm expression of HES1. Data from RT-qPCR and immunohistochemical (IHC) experiments were analyzed using REST2009 software and survival analysis based on IHC expression employed the Kaplan-Meier method and log rank analysis. Unbiased clustered images were generated from gene array analysis data for Notch/HES1 associated genes. Gene array analysis of Notch/HES1 associated genes suggested alterations in the Notch signaling pathway may contribute to the development of canine OSA. HES1 mRNA expression was elevated in tumor samples relative to normal bone, but decreased in tumor samples from dogs with a DFI < 100 days relative to those with a DFI > 300 days. NOTCH2 and HEY1 mRNA expression was also elevated in tumors relative to normal bone, but was not differentially expressed between the DFI tumor groups. Survival analysis confirmed an association between decreased HES1 immunosignal and shorter DFI. Our findings suggest that activation of Notch signaling occurs and may contribute to the development of canine OSA. However, association of low HES1 expression and shorter DFI suggests that mechanisms that do not alter HES1 expression may drive the most aggressive tumors.

Comparative expression profiling of Nicotiana benthamiana leaves systemically infected with three fruit tree viruses.

PubMed

Dardick, Christopher

2007-08-01

Plant viruses cause a wide array of disease symptoms and cytopathic effects. Although some of these changes are virus specific, many appear to be common even among diverse viruses. Currently, little is known about the underlying molecular determinants. To identify gene expression changes that are concomitant with virus symptoms, we performed comparative expression profiling experiments on Nicotiana benthamiana leaves infected with one of three different fruit tree viruses that produce distinct symptoms: Plum pox potyvirus (PPV; leaf distortion and mosaic), Tomato ringspot nepovirus (ToRSV; tissue necrosis and general chlorosis), and Prunus necrotic ringspot ilarvirus (PNRSV; subtle chlorotic mottling). The numbers of statistically significant genes identified were consistent with the severity of the observed symptoms: 1,082 (ToRSV), 744 (PPV), and 89 (PNRSV). In all, 56% of the gene expression changes found in PPV-infected leaves also were altered by ToRSV, 87% of which changed in the same direction. Both PPV- and ToRSV-infected leaves showed widespread repression of genes associated with plastid functions. PPV uniquely induced the expression of large numbers of cytosolic ribosomal genes whereas ToRSV repressed the expression of plastidic ribosomal genes. How these and other observed expression changes might be associated with symptom development are discussed.

Current status of the expanded GRAPES collaboration experiment at Ooty in India

NASA Astrophysics Data System (ADS)

Gupta, S.K.; Anita, H.M.; Iyer, A.; Jagadeesan, P.; Jain, A.; Karthikeyan, S.; Manoharan, P.K.; Mohanty, P.K.; Nayak, P.K.; Rao, B.S.; Ravindran, K.C.; Tanaka, H.; Tonwar, S.C.; Ogio, S.; Okuda, T.; Oshima, A.; Shimizu, N.; Yoshikoshi, T.; Badruddin; Hasan, R.; Ahmad, Shakeel; Mishra, A.P.; Shrivastava, P.K.; Koul, R.; Shah, G.N.; Mir, T.A.; Mufti, S.; Raha, S.; Ghosh, S.; Joarder, P.; Saha, S.; Boruah, K.; Datta, P.; Boruah, P.K.; Baruah, A.G.; Baishya, R.; Saikia, J.; Banerjee, D.; Subramanian, P.; Bhadra, A.; Kumar, S.; Agarwal, R.; Dubey, S.K.; Bhattacharjee, P.

GRAPES-3 experiment employs a high-density array of scintillators and a large area tracking muon telescope. The GRAPES collaboration is being expanded with addition of several major facilities. These include a Cerenkov telescope and low frequency dipole array for the measurement of shower energy. Addition of several modules of muon telescopes to cover a larger area, expansion of the scintillator array with greater separation between detectors. Installation of a neutron monitor is also planned. The current status of the experiment would be summarized.

Construction and application of a bovine immune-endocrine cDNA microarray.

PubMed

Tao, Wenjing; Mallard, Bonnie; Karrow, Niel; Bridle, Byram

2004-09-01

A variety of commercial DNA arrays specific for humans and rodents are widely available; however, microarrays containing well-characterized genes to study pathway-specific gene expression are not as accessible for domestic animals, such as cattle, sheep and pigs. Therefore, a small-scale application-targeted bovine immune-endocrine cDNA array was developed to evaluate genetic pathways involved in the immune-endocrine axis of cattle during periods of altered homeostasis provoked by physiological or environmental stressors, such as infection, vaccination or disease. For this purpose, 167 cDNA sequences corresponding to immune, endocrine and inflammatory response genes were collected and categorized. Positive controls included 5 housekeeping genes (glyceraldehydes-3-phosphate dehydrogenase, hypoxanthine phosphoribosyltransferase, ribosomal protein L19, beta-actin, beta2-microglobulin) and bovine genomic DNA. Negative controls were a bacterial gene (Rhodococcus equi 17-kDa virulence-associated protein) and a partial sequence of the plasmid pACYC177. In addition, RNA extracted from un-stimulated, as well as superantigen (Staphylococcus aureus enterotoxin-A, S. aureus Cowan Pansorbin Cells) and mitogen-stimulated (LPS, ConA) bovine blood leukocytes was mixed, reverse transcribed and PCR amplified using gene-specific primers. The endocrine-associated genes were amplified from cDNA derived from un-stimulated bovine hypothalamus, pituitary, adrenal and thyroid gland tissues. The array was constructed in 4 repeating grids of 180 duplicated spots by coupling the PCR amplified 213-630 bp gene fragments onto poly-l-lysine coated glass slides. The bovine immune-endocrine arrays were standardized and preliminary gene expression profiles generated using Cy3 and Cy5 labelled cDNA from un-stimulated and ConA (5 microg/ml) stimulated PBMC of 4 healthy Holstein cows (2-4 replicate arrays/cow) in a time course study. Mononuclear cell-derived cytokine and chemokine (IL-2, IL-1alpha, TNFalpha, IFN-gamma, TGFbeta-1, MCP-1, MCP-2 and MIP-3alpha) mRNA exhibited a repeatable and consistently low expression in un-stimulated cells and at least a two-fold increased expression following 6 and 24 h ConA stimulation as compared to 0 h un-stimulated controls. In contrast, expression of antigen presenting molecules, MHC-DR, MHC-DQ and MHC-DY, were consistently at least two-fold lower following 6 and 24 h ConA stimulation. The only endocrine gene with differential expression following ConA stimulation was prolactin. Additionally, due to the high level of genetic homology between ovine, swine and bovine genes, RNA similarly acquired from sheep and pigs was evaluated and similar gene expression patterns were noted. These data demonstrate that this application-targeted array containing a set of well characterized genes can be used to determine the relative gene expression corresponding to immune-endocrine responses of cattle and related species, sheep and pigs.

Photovoltaic array space power plus diagnostics experiment

NASA Technical Reports Server (NTRS)

Guidice, Donald A.

1990-01-01

The objective of the Photovoltaic Array Space Power Plus Diagnostics (PASP Plus) experiment is to measure the effects of the interaction of the low- to mid-altitude space environment on the performance of a diverse set of small solar-cell arrays (planar and concentrator, representative of present and future military technologies) under differing conditions of velocity-vector orientation and simulated (by biasing) high-voltage operation. Solar arrays to be tested include Si and GaAs planar arrays and several types of GaAs concentrator arrays. Diagnostics (a Langmuir probe and a pressure gauge) and a transient pulse monitor (to measure radiated and conducted EMI during arcing) will be used to determine the impact of the environment on array operation to help verify various interactions models. Results from a successful PASP Plus flight will furnish answers to important interactions questions and provide inputs for design and test standards for photovoltaic space-power subsystems.

High density diffusion-free nanowell arrays.

PubMed

Takulapalli, Bharath R; Qiu, Ji; Magee, D Mitchell; Kahn, Peter; Brunner, Al; Barker, Kristi; Means, Steven; Miersch, Shane; Bian, Xiaofang; Mendoza, Alex; Festa, Fernanda; Syal, Karan; Park, Jin G; LaBaer, Joshua; Wiktor, Peter

2012-08-03

Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA) is a robust in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced interspot spacing. To address this limitation, we have developed an innovative platform using photolithographically etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8000 nanowell arrays. This is the highest density of individual proteins in nanovessels demonstrated on a single slide. We further present proof of principle results on ultrahigh density protein arrays capable of up to 24000 nanowells on a single slide.

Noninvasive Ultrasound Transdermal Insulin Delivery and Glucose Monitoring Using a Low-Profile Cymbal Array

NASA Astrophysics Data System (ADS)

Park, E.-J.; Luis, J.; Meyer, R. J.; Pishko, M. V.; Smith, N. B.

2006-05-01

Recent studies have shown that ultrasound mediated transdermal drug delivery offers promising results for noninvasive drug administration. The purpose of this study was to demonstrate ultrasonic transdermal insulin delivery and in vivo sensing glucose with a novel, low-profile ultrasound array based on the cymbal transducer. As a practical device, the array composed of circular cymbal transducers was thin (< 7mm) and weighed less than 22g. Using this array on hyperglycemic rats, our previous experiments demonstrated that blood glucose would decrease by 296.7 mg/dL from 60 minutes of ultrasound exposure. With a similar intensity, our goal was to evaluate the feasibility of insulin delivery with large animals (rabbits and pigs) and noninvasively determine the glucose level of hyperglycemic rats with the array system. Ultrasound was exposed for 60 minutes at Isptp=100 mW/cm2. With the same procedure, a preliminary experiment of large animal was performed on a pig (12 kg) at Isptp=50 mW/cm2. For the control experiments in insulin delivery, the blood glucose level varied little from the initial baseline. However, for the ultrasound and insulin exposure experiment, the glucose level was found to decrease by 132.6 mg/dL in 60 minutes and continued to decrease by 208.1 mg/dL in 90 minutes. From the preliminary pig experiment, the blood glucose level decreased by 120 mg/dL in 90 minutes. To noninvasively determine the glucose level, ultrasound exposure experiments with an electrochemical glucose biosensor were performed on hyperglycemic rats. After 20 minutes ultrasound exposure, the biosensor was placed at the exposure area to determine the concentration of glucose diffused through the skin. The glucose level of rats determined by the biosensor was 408 mg/dL which was very similar to the results of conventional glucose meter reading 396.7 mg/dL. Recently, a rectangular cymbal transducer was developed to obtain a larger sonication area without an increase in array size. Preliminary experiments were performed on hyperglycemic rabbits to evaluate the new transducer design. The results showed that the rectangular array has enhanced performance compared to the circular array. All results of ultrasound application indicate the feasibility of using a low-cost, light-weight cymbal array for enhanced noninvasive transdermal insulin delivery and glucose monitoring.

Fundamental formulae for wave-energy conversion

PubMed Central

Falnes, Johannes; Kurniawan, Adi

2015-01-01

The time-average wave power that is absorbed from an incident wave by means of a wave-energy conversion (WEC) unit, or by an array of WEC units—i.e. oscillating immersed bodies and/or oscillating water columns (OWCs)—may be mathematically expressed in terms of the WEC units' complex oscillation amplitudes, or in terms of the generated outgoing (diffracted plus radiated) waves, or alternatively, in terms of the radiated waves alone. Following recent controversy, the corresponding three optional expressions are derived, compared and discussed in this paper. They all provide the correct time-average absorbed power. However, only the first-mentioned expression is applicable to quantify the instantaneous absorbed wave power and the associated reactive power. In this connection, new formulae are derived that relate the ‘added-mass’ matrix, as well as a couple of additional reactive radiation-parameter matrices, to the difference between kinetic energy and potential energy in the water surrounding the immersed oscillating WEC array. Further, a complex collective oscillation amplitude is introduced, which makes it possible to derive, by a very simple algebraic method, various simple expressions for the maximum time-average wave power that may be absorbed by the WEC array. The real-valued time-average absorbed power is illustrated as an axisymmetric paraboloid defined on the complex collective-amplitude plane. This is a simple illustration of the so-called ‘fundamental theorem for wave power’. Finally, the paper also presents a new derivation that extends a recently published result on the direction-average maximum absorbed wave power to cases where the WEC array's radiation damping matrix may be singular and where the WEC array may contain OWCs in addition to oscillating bodies. PMID:26064612

Fundamental formulae for wave-energy conversion.

PubMed

Falnes, Johannes; Kurniawan, Adi

2015-03-01

The time-average wave power that is absorbed from an incident wave by means of a wave-energy conversion (WEC) unit, or by an array of WEC units-i.e. oscillating immersed bodies and/or oscillating water columns (OWCs)-may be mathematically expressed in terms of the WEC units' complex oscillation amplitudes, or in terms of the generated outgoing (diffracted plus radiated) waves, or alternatively, in terms of the radiated waves alone. Following recent controversy, the corresponding three optional expressions are derived, compared and discussed in this paper. They all provide the correct time-average absorbed power. However, only the first-mentioned expression is applicable to quantify the instantaneous absorbed wave power and the associated reactive power. In this connection, new formulae are derived that relate the 'added-mass' matrix, as well as a couple of additional reactive radiation-parameter matrices, to the difference between kinetic energy and potential energy in the water surrounding the immersed oscillating WEC array. Further, a complex collective oscillation amplitude is introduced, which makes it possible to derive, by a very simple algebraic method, various simple expressions for the maximum time-average wave power that may be absorbed by the WEC array. The real-valued time-average absorbed power is illustrated as an axisymmetric paraboloid defined on the complex collective-amplitude plane. This is a simple illustration of the so-called 'fundamental theorem for wave power'. Finally, the paper also presents a new derivation that extends a recently published result on the direction-average maximum absorbed wave power to cases where the WEC array's radiation damping matrix may be singular and where the WEC array may contain OWCs in addition to oscillating bodies.

Single-cell analysis of Daxx and ATRX-dependent transcriptional repression

PubMed Central

Newhart, Alyshia; Rafalska-Metcalf, Ilona U.; Yang, Tian; Negorev, Dmitri G.; Janicki, Susan M.

2012-01-01

Summary Histone H3.3 is a constitutively expressed H3 variant implicated in the epigenetic inheritance of chromatin structures. Recently, the PML-nuclear body (PML-NB)/Nuclear Domain 10 (ND10) proteins, Daxx and ATRX, were found to regulate replication-independent histone H3.3 chromatin assembly at telomeres and pericentric heterochromatin. As it is not completely understood how PML-NBs/ND10s regulate transcription and resistance to viral infection, we have used a CMV-promoter-regulated inducible transgene array, at which Daxx and ATRX are enriched, to delineate the mechanisms through which they regulate transcription. When integrated into HeLa cells, which express both Daxx and ATRX, the array is refractory to activation. However, transcription can be induced when ICP0, the HSV-1 E3 ubiquitin ligase required to reverse latency, is expressed. As ATRX and Daxx are depleted from the activated array in ICP0-expressing HeLa cells, this suggests that they are required to maintain a repressed chromatin environment. As histone H3.3 is strongly recruited to the ICP0-activated array but does not co-localize with the DNA, this also suggests that chromatin assembly is blocked during activation. The conclusion that the Daxx and ATRX pathway is required for transcriptional repression and chromatin assembly at this site is further supported by the finding that an array integrated into the ATRX-negative U2OS cell line can be robustly activated and that histone H3.3 is similarly recruited and unincorporated into the chromatin. Therefore, this study has important implications for understanding gene silencing, viral latency and PML-NB/ND10 function. PMID:22976303

Investigating radial wire array Z pinches as a compact x-ray source on the Saturn generator

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

Ampleford, David J.; Bland, S. N.; Jennings, Christopher A.

2015-08-27

Radial wire array z pinches, where wires are positioned radially outward from a central cathode to a concentric anode, can act as a compact bright x-ray source that could potentially be used to drive a hohlraum. Experiments were performed on the 7-MA Saturn generator using radial wire arrays. These experiments studied a number of potential risks in scaling radial wire arrays up from the 1-MA level, where they have been shown to be a promising compact X-ray source. Data indicates that at 7 MA, radial wire arrays can radiate ~9 TW with 10-ns full-width at half-maximum from a compact pinch.

The application of DNA microarrays in gene expression analysis.

PubMed

van Hal, N L; Vorst, O; van Houwelingen, A M; Kok, E J; Peijnenburg, A; Aharoni, A; van Tunen, A J; Keijer, J

2000-03-31

DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed how DNA microarrays can be applied in the working fields of: safety, functionality and health of food and gene discovery and pathway engineering in plants.

Molecular Profiles for Lung Cancer Pathogenesis and Detection in US Veterans

DTIC Science & Technology

2011-10-01

expression data was analyzed using the BRB-ArrayTools v .4.1.0 developed by Dr. Richard Simon and the BRB-ArrayTools Development Team and then normalized...14. Spira A, Beane J, Shah V , et al. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A 2004;101...10143-10148 15. Spira A, Beane JE, Shah V , et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer

Microreactor Array Device

NASA Astrophysics Data System (ADS)

Wiktor, Peter; Brunner, Al; Kahn, Peter; Qiu, Ji; Magee, Mitch; Bian, Xiaofang; Karthikeyan, Kailash; Labaer, Joshua

2015-03-01

We report a device to fill an array of small chemical reaction chambers (microreactors) with reagent and then seal them using pressurized viscous liquid acting through a flexible membrane. The device enables multiple, independent chemical reactions involving free floating intermediate molecules without interference from neighboring reactions or external environments. The device is validated by protein expressed in situ directly from DNA in a microarray of ~10,000 spots with no diffusion during three hours incubation. Using the device to probe for an autoantibody cancer biomarker in blood serum sample gave five times higher signal to background ratio compared to standard protein microarray expressed on a flat microscope slide. Physical design principles to effectively fill the array of microreactors with reagent and experimental results of alternate methods for sealing the microreactors are presented.

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform.

PubMed

Salehi, Reza; Tsoi, Stephen C M; Colazo, Marcos G; Ambrose, Divakar J; Robert, Claude; Dyck, Michael K

2017-01-30

Early embryonic loss is a large contributor to infertility in cattle. Moreover, bovine becomes an interesting model to study human preimplantation embryo development due to their similar developmental process. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. Microarray technology allows quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. One of the main decisions that have to be made when planning a microarray experiment is whether to use a one- or two-color approach. Two-color design increases technical replication, minimizes variability, improves sensitivity and accuracy as well as allows having loop designs, defining the common reference samples. Although microarray is a powerful biological tool, there are potential pitfalls that can attenuate its power. Hence, in this technical paper we demonstrate an optimized protocol for RNA extraction, amplification, labeling, hybridization of the labeled amplified RNA to the array, array scanning and data analysis using the two-color analysis strategy.

Three dimensional measurement with an electrically tunable focused plenoptic camera

NASA Astrophysics Data System (ADS)

Lei, Yu; Tong, Qing; Xin, Zhaowei; Wei, Dong; Zhang, Xinyu; Liao, Jing; Wang, Haiwei; Xie, Changsheng

2017-03-01

A liquid crystal microlens array (LCMLA) with an arrayed microhole pattern electrode based on nematic liquid crystal materials using a fabrication method including traditional UV-photolithography and wet etching is presented. Its focusing performance is measured under different voltage signals applied between the electrodes of the LCMLA. The experimental outcome shows that the focal length of the LCMLA can be tuned easily by only changing the root mean square value of the voltage signal applied. The developed LCMLA is further integrated with a main lens and an imaging sensor to construct a LCMLA-based focused plenoptic camera (LCFPC) prototype. The focused range of the LCFPC can be shifted electrically along the optical axis of the imaging system. The principles and methods for acquiring several key parameters such as three dimensional (3D) depth, positioning, and motion expression are given. The depth resolution is discussed in detail. Experiments are carried out to obtain the static and dynamic 3D information of objects chosen.

Three dimensional measurement with an electrically tunable focused plenoptic camera.

PubMed

Lei, Yu; Tong, Qing; Xin, Zhaowei; Wei, Dong; Zhang, Xinyu; Liao, Jing; Wang, Haiwei; Xie, Changsheng

2017-03-01

A liquid crystal microlens array (LCMLA) with an arrayed microhole pattern electrode based on nematic liquid crystal materials using a fabrication method including traditional UV-photolithography and wet etching is presented. Its focusing performance is measured under different voltage signals applied between the electrodes of the LCMLA. The experimental outcome shows that the focal length of the LCMLA can be tuned easily by only changing the root mean square value of the voltage signal applied. The developed LCMLA is further integrated with a main lens and an imaging sensor to construct a LCMLA-based focused plenoptic camera (LCFPC) prototype. The focused range of the LCFPC can be shifted electrically along the optical axis of the imaging system. The principles and methods for acquiring several key parameters such as three dimensional (3D) depth, positioning, and motion expression are given. The depth resolution is discussed in detail. Experiments are carried out to obtain the static and dynamic 3D information of objects chosen.

Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics

DOE PAGES

Geng, Tao; Bredeweg, Erin L.; Szymanski, Craig J.; ...

2015-11-04

Here, interrogating polarized growth is technologically challenging due to extensive cellular branching and uncontrollable environmental conditions in conventional assays. Here we present a robust and high-performance microfluidic system that enables observations of polarized growth with enhanced temporal and spatial control over prolonged periods. The system has built-in tunability and versatility to accommodate a variety of science applications requiring precisely controlled environments. Using the model filamentous fungus, Neurospora crassa, this microfluidic system enabled direct visualization and analysis of cellular heterogeneity in a clonal fungal cell population, nuclear distribution and dynamics at the subhyphal level, and quantitative dynamics of gene expression withmore » single hyphal compartment resolution in response to carbon source starvation and exchange experiments. Although the microfluidic device is demonstrated on filamentous fungi, our technology is immediately extensible to a wide array of other biosystems that exhibit similar polarized cell growth with applications ranging from bioenergy production to human health.« less

High-throughput multiplex HLA-typing by ligase detection reaction (LDR) and universal array (UA) approach.

PubMed

Consolandi, Clarissa

2009-01-01

One major goal of genetic research is to understand the role of genetic variation in living systems. In humans, by far the most common type of such variation involves differences in single DNA nucleotides, and is thus termed single nucleotide polymorphism (SNP). The need for improvement in throughput and reliability of traditional techniques makes it necessary to develop new technologies. Thus the past few years have witnessed an extraordinary surge of interest in DNA microarray technology. This new technology offers the first great hope for providing a systematic way to explore the genome. It permits a very rapid analysis of thousands genes for the purpose of gene discovery, sequencing, mapping, expression, and polymorphism detection. We generated a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. In particular, we set up a universal array approach in combination with a PCR-LDR (polymerase chain reaction-ligation detection reaction) strategy for allele identification in the HLA gene.

Dimension-based attention in visual short-term memory.

PubMed

Pilling, Michael; Barrett, Doug J K

2016-07-01

We investigated how dimension-based attention influences visual short-term memory (VSTM). This was done through examining the effects of cueing a feature dimension in two perceptual comparison tasks (change detection and sameness detection). In both tasks, a memory array and a test array consisting of a number of colored shapes were presented successively, interleaved by a blank interstimulus interval (ISI). In Experiment 1 (change detection), the critical event was a feature change in one item across the memory and test arrays. In Experiment 2 (sameness detection), the critical event was the absence of a feature change in one item across the two arrays. Auditory cues indicated the feature dimension (color or shape) of the critical event with 80 % validity; the cues were presented either prior to the memory array, during the ISI, or simultaneously with the test array. In Experiment 1, the cue validity influenced sensitivity only when the cue was given at the earliest position; in Experiment 2, the cue validity influenced sensitivity at all three cue positions. We attributed the greater effectiveness of top-down guidance by cues in the sameness detection task to the more active nature of the comparison process required to detect sameness events (Hyun, Woodman, Vogel, Hollingworth, & Luck, Journal of Experimental Psychology: Human Perception and Performance, 35; 1140-1160, 2009).

Torsional Buckling Tests of a Simulated Solar Array

NASA Technical Reports Server (NTRS)

Thornton, E. A.

1996-01-01

Spacecraft solar arrays are typically large structures supported by long, thin deployable booms. As such, they may be particularly susceptible to abnormal structural behavior induced by mechanical and thermal loading. One example is the Hubble Space Telescope solar arrays which consist of two split tubes fit one inside the other called BiSTEMs. The original solar arrays on the Hubble Space Telescope were found to be severely twisted following deployment and later telemetry data showed the arrays were vibrating during daylight to night and night to daylight transition. The solar array twist however can force the BiSTEM booms to change in cross-section and cause tile solar arrays to react unpredictably to future loading. The solar arrays were redesigned to correct for tile vibration, however, upon redeployment they again twisted. To assess the influence of boom cross-sectional configuration, experiments were conducted on two types of booms, (1)booms with closed cross-sections, and (2) booms with open cross-sections. Both models were subjected to compressive loading and imposed tip deflections. An existing analytical model by Chung and Thornton was used to define the individual load ranges for each model solar array configuration. The load range for the model solar array using closed cross-section booms was 0-120 Newtons and 0-160 Newtons for the model solar array using open cross-section booms. The results indicate the model solar array with closed cross-section booms buckled only in flexure. However, the results of the experiment with open cross-section booms indicate the model solar array buckled only in torsion and with imposed tip deflections the cross section can degrade by rotation of the inner relative to the outer STEM. For tile Hubble Space Telescope solar arrays the results of these experiments indicate the twisting resulted from the initial mechanical loading of the open cross-section booms.

Engineering sciences area and module performance and failure analysis area

NASA Technical Reports Server (NTRS)

Ross, R. G., Jr.; Runkle, L. D.

1982-01-01

Photovoltaic-array/power-conditioner interface studies are updated. An experiment conducted to evaluate different operating-point strategies, such as constant voltage and pilot cells, and to determine array energy losses when the array is operated off the maximum power points is described. Initial results over a test period of three and a half weeks showed a 2% energy loss when the array is operated at a fixed voltage. Degraded-array studies conducted at NE RES that used a range of simulated common types of degraded I-V curves are reviewed. The instrumentation installed at the JPL field-test site to obtain the irradiance data was described. Experiments using an optical filter to adjust the spectral irradiance of the large-area pulsed solar simulator (LAPSS) to AM1.5 are described. Residential-array research activity is reviewed. Voltage isolation test results are described. Experiments performed on one type of module to determine the relationship between leakage current and temperature are reviewed. An encapsulated-cell testing approach is explained. The test program, data reduction methods, and initial results of long-duration module testing are described.

ARRAYS OF BOTTLES OF PLUTONIUM NITRATE SOLUTION

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

Margaret A. Marshall

2012-09-01

In October and November of 1981 thirteen approaches-to-critical were performed on a remote split table machine (RSTM) in the Critical Mass Laboratory of Pacific Northwest Laboratory (PNL) in Richland, Washington using planar arrays of polyethylene bottles filled with plutonium (Pu) nitrate solution. Arrays of up to sixteen bottles were used to measure the critical number of bottles and critical array spacing with a tight fitting Plexiglas® reflector on all sides of the arrays except the top. Some experiments used Plexiglas shells fitted around each bottles to determine the effect of moderation on criticality. Each bottle contained approximately 2.4 L ofmore » Pu(NO3)4 solution with a Pu content of 105 g Pu/L and a free acid molarity H+ of 5.1. The plutonium was of low 240Pu (2.9 wt.%) content. These experiments were sponsored by Rockwell Hanford Operations because of the lack of experimental data on the criticality of arrays of bottles of Pu solution such as might be found in storage and handling at the Purex Facility at Hanford. The results of these experiments were used “to provide benchmark data to validate calculational codes used in criticality safety assessments of [the] plant configurations” (Ref. 1). Data for this evaluation were collected from the published report (Ref. 1), the approach to critical logbook, the experimenter’s logbook, and communication with the primary experimenter, B. Michael Durst. Of the 13 experiments preformed 10 were evaluated. One of the experiments was not evaluated because it had been thrown out by the experimenter, one was not evaluated because it was a repeat of another experiment and the third was not evaluated because it reported the critical number of bottles as being greater than 25. Seven of the thirteen evaluated experiments were determined to be acceptable benchmark experiments. A similar experiment using uranyl nitrate was benchmarked as U233-SOL-THERM-014.« less

Transcriptome Profiling of Lotus japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with that of Nodulation

PubMed Central

Deguchi, Yuichi; Banba, Mari; Shimoda, Yoshikazu; Chechetka, Svetlana A.; Suzuri, Ryota; Okusako, Yasuhiro; Ooki, Yasuhiro; Toyokura, Koichi; Suzuki, Akihiro; Uchiumi, Toshiki; Higashi, Shiro; Abe, Mikiko; Kouchi, Hiroshi; Izui, Katsura; Hata, Shingo

2007-01-01

Abstract To better understand the molecular responses of plants to arbuscular mycorrhizal (AM) fungi, we analyzed the differential gene expression patterns of Lotus japonicus, a model legume, with the aid of a large-scale cDNA macroarray. Experiments were carried out considering the effects of contaminating microorganisms in the soil inoculants. When the colonization by AM fungi, i.e. Glomus mosseae and Gigaspora margarita, was well established, four cysteine protease genes were induced. In situ hybridization revealed that these cysteine protease genes were specifically expressed in arbuscule-containing inner cortical cells of AM roots. On the other hand, phenylpropanoid biosynthesis-related genes for phenylalanine ammonia-lyase (PAL), chalcone synthase, etc. were repressed in the later stage, although they were moderately up-regulated on the initial association with the AM fungus. Real-time RT–PCR experiments supported the array experiments. To further confirm the characteristic expression, a PAL promoter was fused with a reporter gene and introduced into L. japonicus, and then the transformants were grown with a commercial inoculum of G. mosseae. The reporter activity was augmented throughout the roots due to the presence of contaminating microorganisms in the inoculum. Interestingly, G. mosseae only colonized where the reporter activity was low. Comparison of the transcriptome profiles of AM roots and nitrogen-fixing root nodules formed with Mesorhizobium loti indicated that the PAL genes and other phenylpropanoid biosynthesis-related genes were similarly repressed in the two organs. PMID:17634281

Characterization of MicroRNA Expression Profiles and Identification of Potential Biomarkers in Leprosy.

PubMed

Jorge, Karina T O S; Souza, Renan P; Assis, Marieta T A; Araújo, Marcelo G; Locati, Massimo; Jesus, Amélia M R; Dias Baptista, Ida M F; Lima, Cristiano X; Teixeira, Antônio L; Teixeira, Mauro M; Soriani, Frederico M

2017-05-01

Leprosy is an important cause of disability in the developing world. Early diagnosis is essential to allow for cure and to interrupt transmission of this infection. MicroRNAs (miRNAs) are important factors for host-pathogen interaction and they have been identified as biomarkers for various infectious diseases. The expression profile of 377 microRNAs were analyzed by TaqMan low-density array (TLDA) in skin lesions of tuberculoid and lepromatous leprosy patients as well as skin specimens from healthy controls. In a second step, 16 microRNAs were selected for validation experiments with reverse transcription-quantitative PCR (qRT-PCR) in skin samples from new individuals. Principal-component analysis followed by logistic regression model and receiver operating characteristic (ROC) curve analyses were performed to evaluate the diagnostic potential of selected miRNAs. Four patterns of differential expression were identified in the TLDA experiment, suggesting a diagnostic potential of miRNAs in leprosy. After validation experiments, a combination of four miRNAs (miR-101, miR-196b, miR-27b, and miR-29c) was revealed as able to discriminate between healthy control and leprosy patients with 80% sensitivity and 91% specificity. This set of miRNAs was also able to discriminate between lepromatous and tuberculoid patients with a sensitivity of 83% and 80% specificity. In this work, it was possible to identify a set of miRNAs with good diagnostic potential for leprosy. Copyright © 2017 American Society for Microbiology.

Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array

PubMed Central

Wong, Yick Ching; Kwong, Qi Bin; Lee, Heng Leng; Ong, Chuang Kee; Mayes, Sean; Chew, Fook Tim; Appleton, David R.; Kulaveerasingam, Harikrishna

2014-01-01

Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r2 = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield. PMID:27600348

Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array.

PubMed

Wong, Yick Ching; Kwong, Qi Bin; Lee, Heng Leng; Ong, Chuang Kee; Mayes, Sean; Chew, Fook Tim; Appleton, David R; Kulaveerasingam, Harikrishna

2014-11-13

Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r² = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r² = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.

Radiation Exposure Alters Expression of Metabolic Enzyme Genes In Mice

NASA Technical Reports Server (NTRS)

Wotring, Virginia E.; Mangala, L. S.; Zhang, Y.; Wu, H.

2010-01-01

Most pharmaceuticals are metabolized by the liver. The health of the liver, especially the rate of its metabolic enzymes, determines the concentration of circulating drugs as well as the duration of their efficacy. Because of the importance of the liver in drug metabolism it is important to understand the effects of spaceflight on the enzymes of the liver. Exposure to cosmic radiation is one aspect of spaceflight that can be modeled in ground experiments. This study is an effort to examine the effects of adaptive mechanisms that may be triggered by early exposure to low radiation doses. Using procedures approved by the JSC Animal Care & Use Committee, C57 male mice were exposed to Cs-137 in groups: controls, low dose (50 mGy), high dose (6Gy) and a fourth group that received both radiation doses separated by 24 hours. Animals were anesthetized and sacrificed 4 hours after their last radiation exposure. Livers were removed immediately and flash-frozen in liquid nitrogen. Tissue was homogenized, RNA extracted and purified (Absolutely RNA, Agilent). Quality of RNA samples was evaluated (Agilent Bioanalyzer 2100). Complementary DNA was prepared from high-quality RNA samples, and used to run RT-qPCR screening arrays for DNA Repair and Drug Metabolism (SuperArray, SABiosciences/Qiagen; BioRad Cfx96 qPCR System). Of 91 drug metabolism genes examined, expression of 7 was altered by at least one treatment condition. Genes that had elevated expression include those that metabolize promethazine and steroids (4-8-fold), many that reduce oxidation products, and one that reduces heavy metal exposure (greater than 200-fold). Of the 91 DNA repair and general metabolism genes examined, expression of 14 was altered by at least one treatment condition. These gene expression changes are likely homeostatic and could lead to development of new radioprotective countermeasures.

The energy spectrum of ultra-high-energy cosmic rays measured by the Telescope Array FADC fluorescence detectors in monocular mode

NASA Astrophysics Data System (ADS)

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

2013-08-01

We present a measurement of the energy spectrum of ultra-high-energy cosmic rays performed by the Telescope Array experiment using monocular observations from its two new FADC-based fluorescence detectors. After a short description of the experiment, we describe the data analysis and event reconstruction procedures. Since the aperture of the experiment must be calculated by Monte Carlo simulation, we describe this calculation and the comparisons of simulated and real data used to verify the validity of the aperture calculation. Finally, we present the energy spectrum calculated from the merged monocular data sets of the two FADC-based detectors, and also the combination of this merged spectrum with an independent, previously published monocular spectrum measurement performed by Telescope Array's third fluorescence detector [T. Abu-Zayyad et al., The energy spectrum of Telescope Array's middle drum detector and the direct comparison to the high resolution fly's eye experiment, Astroparticle Physics 39 (2012) 109-119, http://dx.doi.org/10.1016/j.astropartphys.2012.05.012, Available from: ]. This combined spectrum corroborates the recently published Telescope Array surface detector spectrum [T. Abu-Zayyad, et al., The cosmic-ray energy spectrum observed with the surface detector of the Telescope Array experiment, ApJ 768 (2013) L1, http://dx.doi.org/10.1088/2041-8205/768/1/L1, Available from: ] with independent systematic uncertainties.

The FDA's Experience with Emerging Genomics Technologies-Past, Present, and Future.

PubMed

Xu, Joshua; Thakkar, Shraddha; Gong, Binsheng; Tong, Weida

2016-07-01

The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented a novel data submission program, Voluntary Genomics Data Submission (VGDS), and also to engage the stakeholders. As part of the endeavor, for the past 10 years, the FDA has led an international consortium of regulatory agencies, academia, pharmaceutical companies, and genomics platform providers, which was named MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation. Three projects have been completed so far assessing these genomics technologies: gene expression microarrays, whole genome genotyping arrays, and whole transcriptome sequencing (i.e., RNA-seq). The resultant studies provide the basic parameters for fit-for-purpose application of these new data streams in regulatory environments, and the solutions have been made available to the public through peer-reviewed publications. The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing. Using reference samples with built-in controls, SEQC studies have demonstrated that relative gene expression can be measured accurately and reliably across laboratories and RNA-seq platforms. Besides prediction performance comparable to microarrays in clinical settings and safety assessments, RNA-seq is shown to have better sensitivity for low expression and reveal novel transcriptomic features. Future effort of MAQC will be focused on quality control of whole genome sequencing and targeted sequencing.

The FDA’s Experience with Emerging Genomics Technologies—Past, Present, and Future

PubMed Central

Xu, Joshua; Thakkar, Shraddha; Gong, Binsheng; Tong, Weida

2016-01-01

The rapid advancement of emerging genomics technologies and their application for assessing safety and efficacy of FDA-regulated products require a high standard of reliability and robustness supporting regulatory decision-making in the FDA. To facilitate the regulatory application, the FDA implemented a novel data submission program, Voluntary Genomics Data Submission (VGDS), and also to engage the stakeholders. As part of the endeavor, for the past 10 years, the FDA has led an international consortium of regulatory agencies, academia, pharmaceutical companies, and genomics platform providers, which was named MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation. Three projects have been completed so far assessing these genomics technologies: gene expression microarrays, whole genome genotyping arrays, and whole transcriptome sequencing (i.e., RNA-seq). The resultant studies provide the basic parameters for fit-for-purpose application of these new data streams in regulatory environments, and the solutions have been made available to the public through peer-reviewed publications. The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing. Using reference samples with built-in controls, SEQC studies have demonstrated that relative gene expression can be measured accurately and reliably across laboratories and RNA-seq platforms. Besides prediction performance comparable to microarrays in clinical settings and safety assessments, RNA-seq is shown to have better sensitivity for low expression and reveal novel transcriptomic features. Future effort of MAQC will be focused on quality control of whole genome sequencing and targeted sequencing. PMID:27116022

Hopping transport through an array of Luttinger liquid stubs

NASA Astrophysics Data System (ADS)

Chudnovskiy, A. L.

2004-01-01

We consider a thermally activated transport across and array of parallel one-dimensional quantum wires of finite length (quantum stubs). The disorder enters as a random tunneling between the nearest-neighbor stubs as well as a random shift of the bottom of the energy band in each stub. Whereas one-particle wave functions are localized across the array, the plasmons are delocalized, which affects the variable-range hopping. A perturbative analytical expression for the low-temperature resistance across the array is obtained for a particular choice of plasmon dispersion.

Helicopter noise experiments in an urban environment

DOT National Transportation Integrated Search

1974-08-01

In two series of helicopter noise experiments, soundpressurelevel recordings were made on the ground while a helicopter flew over (i) an array of microphones placed in an open field, and (ii) a similar array placed in the center of a city stree...

Experimental and numerical research of synthetic jet array

NASA Astrophysics Data System (ADS)

Dančová, Petra; Novosád, Jan; Vít, Tomáš; Trávníček, Zdeněk

2016-03-01

This paper describes the additional research of the synthetic jet array in a channel flow and continues the paper of authors Dančová, Trávníček and Vít, [1]. Numerical simulations support the experiments from [1] and the influence of the new slope of the synthetic jet orifices is studied here. This research will be used for preparation of the experiments with inclined orifices of the synthetic jet array.

Cell-Based Odorant Sensor Array for Odor Discrimination Based on Insect Odorant Receptors.

PubMed

Termtanasombat, Maneerat; Mitsuno, Hidefumi; Misawa, Nobuo; Yamahira, Shinya; Sakurai, Takeshi; Yamaguchi, Satoshi; Nagamune, Teruyuki; Kanzaki, Ryohei

2016-07-01

The olfactory system of living organisms can accurately discriminate numerous odors by recognizing the pattern of activation of several odorant receptors (ORs). Thus, development of an odorant sensor array based on multiple ORs presents the possibility of mimicking biological odor discrimination mechanisms. Recently, we developed novel odorant sensor elements with high sensitivity and selectivity based on insect OR-expressing Sf21 cells that respond to target odorants by displaying increased fluorescence intensity. Here we introduce the development of an odorant sensor array composed of several Sf21 cell lines expressing different ORs. In this study, an array pattern of four cell lines expressing Or13a, Or56a, BmOR1, and BmOR3 was successfully created using a patterned polydimethylsiloxane film template and cell-immobilizing reagents, termed biocompatible anchor for membrane (BAM). We demonstrated that BAM could create a clear pattern of Sf21 sensor cells without impacting their odorant-sensing performance. Our sensor array showed odorant-specific response patterns toward both odorant mixtures and single odorant stimuli, allowing us to visualize the presence of 1-octen-3-ol, geosmin, bombykol, and bombykal as an increased fluorescence intensity in the region of Or13a, Or56a, BmOR1, and BmOR3 cell lines, respectively. Therefore, we successfully developed a new methodology for creating a cell-based odorant sensor array that enables us to discriminate multiple target odorants. Our method might be expanded into the development of an odorant sensor capable of detecting a large range of environmental odorants that might become a promising tool used in various applications including the study of insect semiochemicals and food contamination.

ArraySolver: an algorithm for colour-coded graphical display and Wilcoxon signed-rank statistics for comparing microarray gene expression data.

PubMed

Khan, Haseeb Ahmad

2004-01-01

The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann-Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n < or = 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform.

ArraySolver: An Algorithm for Colour-Coded Graphical Display and Wilcoxon Signed-Rank Statistics for Comparing Microarray Gene Expression Data

PubMed Central

2004-01-01

The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann–Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n ≤ 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform. PMID:18629036

Gene expression analysis of pancreatic cell lines reveals genes overexpressed in pancreatic cancer.

PubMed

Alldinger, Ingo; Dittert, Dag; Peiper, Matthias; Fusco, Alberto; Chiappetta, Gennaro; Staub, Eike; Lohr, Matthias; Jesnowski, Ralf; Baretton, Gustavo; Ockert, Detlef; Saeger, Hans-Detlev; Grützmann, Robert; Pilarsky, Christian

2005-01-01

Pancreatic cancer is one of the leading causes of cancer-related death. Using DNA gene expression analysis based on a custom made Affymetrix cancer array, we investigated the expression pattern of both primary and established pancreatic carcinoma cell lines. We analyzed the gene expression of 5 established pancreatic cancer cell lines (AsPC-1, BxPC-3, Capan-1, Capan-2 and HPAF II) and 5 primary isolates, 1 of them derived from benign pancreatic duct cells. Out of 1,540 genes which were expressed in at least 3 experiments, we found 122 genes upregulated and 18 downregulated in tumor cell lines compared to benign cells with a fold change >3. Several of the upregulated genes (like Prefoldin 5, ADAM9 and E-cadherin) have been associated with pancreatic cancer before. The other differentially regulated genes, however, play a so far unknown role in the course of human pancreatic carcinoma. By means of immunohistochemistry we could show that thymosin beta-10 (TMSB10), upregulated in tumor cell lines, is expressed in human pancreatic carcinoma, but not in non-neoplastic pancreatic tissue, suggesting a role for TMSB10 in the carcinogenesis of pancreatic carcinoma. Using gene expression profiling of pancreatic cell lines we were able to identify genes differentially expressed in pancreatic adenocarcinoma, which might contribute to pancreatic cancer development. Copyright 2005 S. Karger AG, Basel.

Nucleic acid programmable protein array a just-in-time multiplexed protein expression and purification platform.

PubMed

Qiu, Ji; LaBaer, Joshua

2011-01-01

Systematic study of proteins requires the availability of thousands of proteins in functional format. However, traditional recombinant protein expression and purification methods have many drawbacks for such study at the proteome level. We have developed an innovative in situ protein expression and capture system, namely NAPPA (nucleic acid programmable protein array), where C-terminal tagged proteins are expressed using an in vitro expression system and efficiently captured/purified by antitag antibodies coprinted at each spot. The NAPPA technology presented in this chapter enable researchers to produce and display fresh proteins just in time in a multiplexed high-throughput fashion and utilize them for various downstream biochemical researches of interest. This platform could revolutionize the field of functional proteomics with it ability to produce thousands of spatially separated proteins in high density with narrow dynamic rand of protein concentrations, reproducibly and functionally. Copyright © 2011 Elsevier Inc. All rights reserved.

Servo scanning 3D micro EDM for array micro cavities using on-machine fabricated tool electrodes

NASA Astrophysics Data System (ADS)

Tong, Hao; Li, Yong; Zhang, Long

2018-02-01

Array micro cavities are useful in many fields including in micro molds, optical devices, biochips and so on. Array servo scanning micro electro discharge machining (EDM), using array micro electrodes with simple cross-sectional shape, has the advantage of machining complex 3D micro cavities in batches. In this paper, the machining errors caused by offline-fabricated array micro electrodes are analyzed in particular, and then a machining process of array servo scanning micro EDM is proposed by using on-machine fabricated array micro electrodes. The array micro electrodes are fabricated on-machine by combined procedures including wire electro discharge grinding, array reverse copying and electrode end trimming. Nine-array tool electrodes with Φ80 µm diameter and 600 µm length are obtained. Furthermore, the proposed process is verified by several machining experiments for achieving nine-array hexagonal micro cavities with top side length of 300 µm, bottom side length of 150 µm, and depth of 112 µm or 120 µm. In the experiments, a chip hump accumulates on the electrode tips like the built-up edge in mechanical machining under the conditions of brass workpieces, copper electrodes and the dielectric of deionized water. The accumulated hump can be avoided by replacing the water dielectric by an oil dielectric.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

ADGO: analysis of differentially expressed gene sets using composite GO annotation.

PubMed

Nam, Dougu; Kim, Sang-Bae; Kim, Seon-Kyu; Yang, Sungjin; Kim, Seon-Young; Chu, In-Sun

2006-09-15

Genes are typically expressed in modular manners in biological processes. Recent studies reflect such features in analyzing gene expression patterns by directly scoring gene sets. Gene annotations have been used to define the gene sets, which have served to reveal specific biological themes from expression data. However, current annotations have limited analytical power, because they are classified by single categories providing only unary information for the gene sets. Here we propose a method for discovering composite biological themes from expression data. We intersected two annotated gene sets from different categories of Gene Ontology (GO). We then scored the expression changes of all the single and intersected sets. In this way, we were able to uncover, for example, a gene set with the molecular function F and the cellular component C that showed significant expression change, while the changes in individual gene sets were not significant. We provided an exemplary analysis for HIV-1 immune response. In addition, we tested the method on 20 public datasets where we found many 'filtered' composite terms the number of which reached approximately 34% (a strong criterion, 5% significance) of the number of significant unary terms on average. By using composite annotation, we can derive new and improved information about disease and biological processes from expression data. We provide a web application (ADGO: http://array.kobic.re.kr/ADGO) for the analysis of differentially expressed gene sets with composite GO annotations. The user can analyze Affymetrix and dual channel array (spotted cDNA and spotted oligo microarray) data for four species: human, mouse, rat and yeast. chu@kribb.re.kr http://array.kobic.re.kr/ADGO.

Single atom array to form a Rydberg ring

NASA Astrophysics Data System (ADS)

Zhan, Mingsheng; Xu, Peng; He, Xiaodong; Liu, Min; Wang, Jin

2012-02-01

Single atom arrays are ideal quantum systems for studying few-body quantum simulation and quantum computation [1]. Towards realizing a fully controllable array we did a lot of experimental efforts, which include rotating single atoms in a ring optical lattice generated by a spatial light modulator [2], high efficient loading of two atoms into a microscopic optical trap by dynamically reshaping the trap with a spatial light modulator [3], and trapping a single atom in a blue detuned optical bottle beam trap [4]. Recently, we succeeded in trapping up to 6 atoms in a ring optical lattice with one atom in each site. Further laser cooling the array and manipulation of the inner states will provide chance to form Ryberg rings for quantum simulation. [4pt] [1] M. Saffman et al., Rev. Mod. Phys. 82, 2313 (2010)[0pt] [2] X.D. He et al., Opt. Express 17, 21014 (2009)[0pt] [3] X.D. He et al., Opt. Express 18, 13586 (2010)[0pt] [4] P. Xu et al., Opt. Lett. 35, 2164 (2010)

Building biochips: a protein production pipeline

NASA Astrophysics Data System (ADS)

de Carvalho-Kavanagh, Marianne G. S.; Albala, Joanna S.

2004-06-01

Protein arrays are emerging as a practical format in which to study proteins in high-throughput using many of the same techniques as that of the DNA microarray. The key advantage to array-based methods for protein study is the potential for parallel analysis of thousands of samples in an automated, high-throughput fashion. Building protein arrays capable of this analysis capacity requires a robust expression and purification system capable of generating hundreds to thousands of purified recombinant proteins. We have developed a method to utilize LLNL-I.M.A.G.E. cDNAs to generate recombinant protein libraries using a baculovirus-insect cell expression system. We have used this strategy to produce proteins for analysis of protein/DNA and protein/protein interactions using protein microarrays in order to understand the complex interactions of proteins involved in homologous recombination and DNA repair. Using protein array techniques, a novel interaction between the DNA repair protein, Rad51B, and histones has been identified.

Transdermal Delivery of siRNA through Microneedle Array

NASA Astrophysics Data System (ADS)

Deng, Yan; Chen, Jiao; Zhao, Yi; Yan, Xiaohui; Zhang, Li; Choy, Kwongwai; Hu, Jun; Sant, Himanshu J.; Gale, Bruce K.; Tang, Tao

2016-02-01

Successful development of siRNA therapies has significant potential for the treatment of skin conditions (alopecia, allergic skin diseases, hyperpigmentation, psoriasis, skin cancer, pachyonychia congenital) caused by aberrant gene expression. Although hypodermic needles can be used to effectively deliver siRNA through the stratum corneum, the major challenge is that this approach is painful and the effects are restricted to the injection site. Microneedle arrays may represent a better way to deliver siRNAs across the stratum corneum. In this study, we evaluated for the first time the ability of the solid silicon microneedle array for punching holes to deliver cholesterol-modified housekeeping gene (Gapdh) siRNA to the mouse ear skin. Treating the ear with microneedles showed permeation of siRNA in the skin and could reduce Gapdh gene expression up to 66% in the skin without accumulation in the major organs. The results showed that microneedle arrays could effectively deliver siRNA to relevant regions of the skin noninvasively.

Expression of stress/defense-related genes in barley grown under space environment

NASA Astrophysics Data System (ADS)

Sugimoto, Manabu; Shagimardanova, Elena; Gusev, Oleg; Bingham, Gail; Levinskikh, Margarita; Sychev, Vladimir

Plants are exposed to the extreme environment in space, especially space radiation is suspected to induce oxidative stress by generating high-energy free radicals and microgravity would enhance the effect of space radiation, however, current understandings of plant growth and responses on this synergistic effect of radiation and microgravity is limited to a few experiments. In this study, expression of stress/defense-related genes in barley grown under space environment was analyzed by RT-PCR and DNA microarray experiments to understand plant responses and adaptation to space environment and to develop the space stress-tolerant plants. The seeds of barley, Hordeum vulgare L. cv. Haruna nijo, kept in the international space station (ISS) over 4 months, were germinated after 3 days of irrigation in LADA plant growth chamber onboard Russian segment of ISS and the final germination ratio was over 90 %. The height of plants was about 50 to 60 cm and flag leaf has been opened after 26 days of irrigation under 24 hr lighting, showing the similar growth to ground-grown barley. Expression levels of stress/defense-related genes in space-grown barley were compared to those in ground-grown barley by semi-quantitative RT-PCR. In 17 stress/defense-related genes that are up-regulated by oxidative stress or other abiotic stress, only catalase, pathogenesis-related protein 13, chalcone synthase, and phenylalanine ammonia-lyase genes were increased in space-grown barley. DNA microarrya analysis with the GeneChip Barley Genome Array showed the similar expression profiles of the stress/defense-related genes to those by RT-PCR experiment, suggesting that the barley germinated and grown in LADA onboard ISS is not damaged by space environment, especially oxidative stress induced by space radiation and microgravity.

Powerful inhibition of in-vivo growth of experimental hepatic cancers by bombesin/gastrin-releasing peptide antagonist RC-3940-II.

PubMed

Szepeshazi, Karoly; Schally, Andrew V; Rick, Ferenc G; Block, Norman L; Vidaurre, Irving; Halmos, Gabor; Szalontay, Luca

2012-10-01

Hepatic carcinoma is a major health problem worldwide. Its incidence is increasing in Western countries and there is currently no effective systemic therapy against it. Targeted treatment modalities developed in the past few years have provided very limited success. Development of new treatment strategies is therefore essential. We investigated the effects of bombesin/gastrin-releasing peptide (BN/GRP) antagonist RC-3940-II on experimental human liver cancers in nude mice. SK-Hep-1 and Hep-G2 cancers transplanted subcutaneously into nude mice were treated daily with 10 or 20 µg of RC-3940-II. Tumor growth was monitored for 50-184 days in five experiments. Tumor gene expression was analyzed with PCR array and protein expression by immunoblotting. Characteristics of BN/GRP receptors in the tumors were analyzed by binding assays. Effects of RC-3940-II on cell proliferation were investigated in vitro. RC-3940-II inhibited the growth of SK-Hep-1 cancers in nude mice by 65-98%, with total regression in 9 of 36 tumors in three experiments. The BN/GRP antagonist inhibited the growth of Hep-G2 cancers as well by 73-82% in two experiments, being effective even on originally large tumors. Gene expression analysis showed an increase in several angiogenesis inhibitors and decrease in proangiogenic genes after RC-3940-II treatment. Receptor assays demonstrated high-affinity binding sites for BN/GRP in both tumor lines. BN/GRP antagonist RC-3940-II powerfully inhibits growth of SK-Hep-1 and Hep-G2 cancers in nude mice. Its effect may be linked to changes in expression of those cancer genes important in angiogenesis, invasion, and metastasis. RC-3940-II may be considered for further investigations in treatment of liver cancers.

Space experiment "Rad Gene"-report 1; p53-Dependent gene expression in human cultured cells exposed to space environment

NASA Astrophysics Data System (ADS)

Takahashi, Akihisa; Ohnishi, Takeo; Suzuki, Hiromi; Omori, Katsunori; Seki, Masaya; Hashizume, Toko; Shimazu, Toru; Ishioka, Noriaki

The space environment contains two major biologically significant influences: space radiations and microgravity. A p53 tumor suppressor protein plays a role as a guardian of the genome through the activity of p53-centered signal transduction pathways. The aim of this study was to clarify the biological effects of space radiations, microgravity and a space environment on the gene and protein expression of p53-dependent regulated genes. Space experiments were performed with two human cultured lymphoblastoid cell lines: one cells line (TSCE5) bears a wild-type p53 gene status, and another cells line (WTK1) bears a mutated p53 gene status. Un-der one gravity or microgravity condition, the cells were grown in the cell biology experimental facility (CBEF) of the International Space Station (ISS) for 8 days without experiencing the stress during launching and landing because the cells were frozen during these periods. Ground control samples also were cultured for 8 days in the CBEF on the ground during the same periods as space flight. Gene and protein expression was analyzed by using DNA chip (a 44k whole human genome microarray, Agilent Technologies Inc.) and protein chip (PanoramaTM Ab MicroArray, Sigma-Aldrich Co.), respectively. In addition, we analyzed the gene expression in cultured cells after space flight during 133 days with frozen condition. We report the results and discussion from the viewpoint of the functions of the up-regulated and down-regulated genes after an exposure to space radiations and/or microgravity. The initial goal of this space experiment was completely achieved. It is expected that data from this type of work will be helpful in designing physical protection from the deleterious effects of space radiations during long term stays in space.

MicroRNA Expression Profiling to Identify and Validate Reference Genes for the Relative Quantification of microRNA in Rectal Cancer.

PubMed

Eriksen, Anne Haahr Mellergaard; Andersen, Rikke Fredslund; Pallisgaard, Niels; Sørensen, Flemming Brandt; Jakobsen, Anders; Hansen, Torben Frøstrup

2016-01-01

MicroRNAs (miRNAs) play important roles in regulating biological processes at the post-transcriptional level. Deregulation of miRNAs has been observed in cancer, and miRNAs are being investigated as potential biomarkers regarding diagnosis, prognosis and prediction in cancer management. Real-time quantitative polymerase chain reaction (RT-qPCR) is commonly used, when measuring miRNA expression. Appropriate normalisation of RT-qPCR data is important to ensure reliable results. The aim of the present study was to identify stably expressed miRNAs applicable as normaliser candidates in future studies of miRNA expression in rectal cancer. We performed high-throughput miRNA profiling (OpenArray®) on ten pairs of laser micro-dissected rectal cancer tissue and adjacent stroma. A global mean expression normalisation strategy was applied to identify the most stably expressed miRNAs for subsequent validation. In the first validation experiment, a panel of miRNAs were analysed on 25 pairs of micro dissected rectal cancer tissue and adjacent stroma. Subsequently, the same miRNAs were analysed in 28 pairs of rectal cancer tissue and normal rectal mucosa. From the miRNA profiling experiment, miR-645, miR-193a-5p, miR-27a and let-7g were identified as stably expressed, both in malignant and stromal tissue. In addition, NormFinder confirmed high expression stability for the four miRNAs. In the RT-qPCR based validation experiments, no significant difference between tumour and stroma/normal rectal mucosa was detected for the mean of the normaliser candidates miR-27a, miR-193a-5p and let-7g (first validation P = 0.801, second validation P = 0.321). MiR-645 was excluded from the data analysis, because it was undetected in 35 of 50 samples (first validation) and in 24 of 56 samples (second validation), respectively. Significant difference in expression level of RNU6B was observed between tumour and adjacent stromal (first validation), and between tumour and normal rectal mucosa (second validation). We recommend the mean expression of miR-27a, miR-193a-5p and let-7g as normalisation factor, when performing miRNA expression analyses by RT-qPCR on rectal cancer tissue.

Microreactor Array Device

PubMed Central

Wiktor, Peter; Brunner, Al; Kahn, Peter; Qiu, Ji; Magee, Mitch; Bian, Xiaofang; Karthikeyan, Kailash; LaBaer, Joshua

2015-01-01

We report a device to fill an array of small chemical reaction chambers (microreactors) with reagent and then seal them using pressurized viscous liquid acting through a flexible membrane. The device enables multiple, independent chemical reactions involving free floating intermediate molecules without interference from neighboring reactions or external environments. The device is validated by protein expressed in situ directly from DNA in a microarray of ~10,000 spots with no diffusion during three hours incubation. Using the device to probe for an autoantibody cancer biomarker in blood serum sample gave five times higher signal to background ratio compared to standard protein microarray expressed on a flat microscope slide. Physical design principles to effectively fill the array of microreactors with reagent and experimental results of alternate methods for sealing the microreactors are presented. PMID:25736721

Sometimes area counts more than number.

PubMed

Hurewitz, Felicia; Gelman, Rochel; Schnitzer, Brian

2006-12-19

Using an interference paradigm, we show across three experiments that adults' order judgments of numbers, sizes, or combined area of dots in pairs of arrays occur spontaneously and automatically, but at different speeds and levels of accuracy. Experiment 1 used circles whose sizes varied between but not within arrays. Variation in circle size interfered with judgments of which array had more circles. Experiment 2 used displays in which circle size varied within and between arrays. Between-array differences in the amount of "circle stuff" (area occupied by circles) interfered with judgments of number. Experiment 3 examined whether variation in number also interferes with judgments of area. Interference between discrete and continuous stimulus dimensions occurred in both directions, although it was stronger from the continuous to the discrete than vice versa. These results bear on interpretations of studies with infants and preschoolers wherein subjects respond on the basis of continuous quantity rather than discrete quantity. In light of our results with adults, these findings do not license the conclusion that young children cannot represent discrete quantity. Absent data on attentional hierarchies and speed of processing, it is premature to conclude that infant and child quantity processes are fundamentally different from that of adults.

Status of the MARE experiment in Milan

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

Ferri, E.; Arnaboldi, C.; Ceruti, G.

2009-12-16

An international collaboration has grown around the project of Microcalorimeter Arrays for a Rhenium Experiment (MARE) for a direct and calorimetric measurement of the electron antineutrino mass with sub-electronvolt sensitivity.MARE is divided into two phases. The first phase (MARE-1) consists of two independent experiments using the presently available detector technology to reach a sensitivity of m{sub v}{<=}2eV/c{sup 2}. The goal of the second phase (MARE-2) is to achieve a sub-electronvolt sensitivity on the neutrino mass.The Milan MARE-1 experiment is based on arrays of silicon implanted microcalorimeters, produced by NASA/GSFC, with dielectric silver perrhenate absorbers, AgReO{sub 4}. We present here themore » status of MARE-1 in Milan which is starting data taking with 2 arrays (72 detectors). In this configuration a sensitivity of about 5 eV can be achieved in two years. We describe in details the experimental setup which is designed to host up to 8 arrays (288 detectors). With 8 arrays, two years of measurement would improve the sensitivity to about 3 eV. This talk reports on the activity of the group for the MARE project in Milan.« less

An IBM PC-based math model for space station solar array simulation

NASA Technical Reports Server (NTRS)

Emanuel, E. M.

1986-01-01

This report discusses and documents the design, development, and verification of a microcomputer-based solar cell math model for simulating the Space Station's solar array Initial Operational Capability (IOC) reference configuration. The array model is developed utilizing a linear solar cell dc math model requiring only five input parameters: short circuit current, open circuit voltage, maximum power voltage, maximum power current, and orbit inclination. The accuracy of this model is investigated using actual solar array on orbit electrical data derived from the Solar Array Flight Experiment/Dynamic Augmentation Experiment (SAFE/DAE), conducted during the STS-41D mission. This simulator provides real-time simulated performance data during the steady state portion of the Space Station orbit (i.e., array fully exposed to sunlight). Eclipse to sunlight transients and shadowing effects are not included in the analysis, but are discussed briefly. Integrating the Solar Array Simulator (SAS) into the Power Management and Distribution (PMAD) subsystem is also discussed.

The hyperion particle-γ detector array

DOE PAGES

Hughes, R. O.; Burke, J. T.; Casperson, R. J.; ...

2017-03-08

Hyperion is a new high-efficiency charged-particle γ-ray detector array which consists of a segmented silicon telescope for charged-particle detection and up to fourteen high-purity germanium clover detectors for the detection of coincident γ rays. The array will be used in nuclear physics measurements and Stockpile Stewardship studies and replaces the STARLiTeR array. In conclusion, this article discusses the features of the array and presents data collected with the array in the commissioning experiment.

Measurement of high-voltage and radiation-damage limitations to advanced solar array performance

NASA Technical Reports Server (NTRS)

Guidice, D. A.; Severance, P. S.; Keinhardt, K. C.

1991-01-01

A description is given of the reconfigured Photovoltaic Array Space Power (PASP) Plus experiment: its objectives, solar-array complement, and diagnostic sensors. Results from a successful spaceflight will lead to a better understanding of high-voltage and radiation-damage limitations in the operation of new-technology solar arrays.

Design of a Synthetic Aperture Array to Support Experiments in Active Control of Scattering

DTIC Science & Technology

1990-06-01

becomes necessary to validate the theory and test the control system algorithms . While experiments in open water would be most like the anticipated...mathematical development of the beamforming algorithms used as well as an estimate of their applicability to the specifics of beamforming in a reverberant...Chebyshev array have been proposed. The method used in ARRAY, a nested product algorithm , proposed by Bresler [21] is recommended by Pozar [19] and

Intensity modulation of HF heater-induced plasma lines

NASA Technical Reports Server (NTRS)

Kuo, S. P.; Lee, M. C.

1990-01-01

The Arecibo HF heater is normally composed of two separate sets of antenna array, transmitting waves vertically at the same frequency and polarization. However, when these two sets of antenna array radiate at slightly different frequencies, the intensities of HF heater-induced plasma lines (HFPLs) can be drastically modulated. In recent Duncan et al.'s (1989) experiments the 100 percent intensity modulation of HFPLs was seen to persist even when the secondary set of antenna array radiated at a few percent of the power transmitted by the primary set of antenna array. An explanation is offered, and it is shown that there exists a minimum power, Pmin, and if the secondary set of antenna array radiates at a power lower than Pmin, the 100-percent intensity modulation of HFPLs will not be observed. The functional dependence of Pmin on the difference frequency of the two sets of antenna array is also predicted for future experiments to corroborate.

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

PubMed Central

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

2005-01-01

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

Use of microfasteners to produce damage tolerant composite structures

PubMed Central

Hallett, Stephen R.

2016-01-01

The paper concerns the mechanical performance of continuous fibre/thermosetting polymer matrix composites reinforced in the through-thickness direction with fibrous or metallic rods or threads in order to mitigate against low delamination resistance. Specific illustrations of the effects of microfasteners in reducing delamination crack growth are made for Z-pinned and tufted composites. Response to loading in such ‘structured materials’ is subject to multiple parameters defining their in-plane and out-of-plane properties. Single microfastener mechanical tests are well suited to establish the crack bridging laws under a range of loading modes, from simple delamination crack opening to shear, and provide the basis for predicting the corresponding response of microfastener arrays, within a given material environment. The fundamental experiments on microfasteners can be used to derive analytical expressions to describe the crack bridging behaviour in a general sense, to cover all possible loadings. These expressions can be built into cohesive element constitutive laws in a finite-element framework for modelling the effects of microfastener arrays on the out-of-plane mechanical response of reinforced structural elements, including the effects of known manufacturing imperfections. Such predictive behaviour can then be used to assess structural integrity under complex loading, as part of the component design process. This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’. PMID:27242299

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

NASA Technical Reports Server (NTRS)

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

The Square Kilometre Array Epoch of Reionisation and Cosmic Dawn Experiment

NASA Astrophysics Data System (ADS)

Trott, Cathryn M.

2018-05-01

The Square Kilometre Array (SKA) Epoch of Reionisation and Cosmic Dawn (EoR/CD) experiments aim to explore the growth of structure and production of ionising radiation in the first billion years of the Universe. Here I describe the experiments planned for the future low-frequency components of the Observatory, and work underway to define, design and execute these programs.

SigReannot-mart: a query environment for expression microarray probe re-annotations.

PubMed

Moreews, François; Rauffet, Gaelle; Dehais, Patrice; Klopp, Christophe

2011-01-01

Expression microarrays are commonly used to study transcriptomes. Most of the arrays are now based on oligo-nucleotide probes. Probe design being a tedious task, it often takes place once at the beginning of the project. The oligo set is then used for several years. During this time period, the knowledge gathered by the community on the genome and the transcriptome increases and gets more precise. Therefore re-annotating the set is essential to supply the biologists with up-to-date annotations. SigReannot-mart is a query environment populated with regularly updated annotations for different oligo sets. It stores the results of the SigReannot pipeline that has mainly been used on farm and aquaculture species. It permits easy extraction in different formats using filters. It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

Advances in Mixed Signal Processing for Regional and Teleseismic Arrays

DTIC Science & Technology

2006-08-15

1: Mixture of signals from two earthquakes from south of Africa and the Philippines observed at USAEDS long-period seismic array in Korea. Correct...window where the detector will miss valid signals . 2 Approaches to detecting signals on arrays all focus on the basic model that expresses the observed...possible use in detecting infrasound signals . The approach is based on orthogonal- ity properties of the eigen vectors of the spectral matrix under a

Detecting Spatial Patterns in Biological Array Experiments

PubMed Central

ROOT, DAVID E.; KELLEY, BRIAN P.; STOCKWELL, BRENT R.

2005-01-01

Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments arranged in a spatial array. It is often difficult to ensure that uniform experimental conditions are present throughout the entire array, and as a result, one often observes systematic spatially correlated errors, especially when array experiments are performed using robots. Here, the authors apply techniques based on the discrete Fourier transform to identify and quantify spatially correlated errors superimposed on a spatially random background. They demonstrate that these techniques are effective in identifying common spatially systematic errors in high-throughput 384-well microplate assay data. In addition, the authors employ a statistical test to allow for automatic detection of such errors. Software tools for using this approach are provided. PMID:14567791

Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays* | Office of Cancer Genomics

Cancer.gov

Cancer cell lines are major model systems for mechanistic investigation and drug development. However, protein expression data linked to high-quality DNA, RNA, and drug-screening data have not been available across a large number of cancer cell lines. Using reverse-phase protein arrays, we measured expression levels of ∼230 key cancer-related proteins in >650 independent cell lines, many of which have publically available genomic, transcriptomic, and drug-screening data.

High Density Diffusion-Free Nanowell Arrays

PubMed Central

Takulapalli, Bharath R; Qiu, Ji; Magee, D. Mitchell; Kahn, Peter; Brunner, Al; Barker, Kristi; Means, Steven; Miersch, Shane; Bian, Xiaofang; Mendoza, Alex; Festa, Fernanda; Syal, Karan; Park, Jin; LaBaer, Joshua; Wiktor, Peter

2012-01-01

Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA), is a robust, in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced inter-spot spacing. To address this limitation, we have developed an innovative platform using photolithographically-etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8,000 nanowell arrays. This is the highest density of individual proteins in nano-vessels demonstrated on a single slide. We further present proof of principle results on ultra-high density protein arrays capable of up to 24,000 nanowells on a single slide. PMID:22742968

Muon Detector R&D in Telescope Array Experiment

NASA Astrophysics Data System (ADS)

Nonaka, T.; Takamura, M.; Honda, K.; Matthews, J. N.; Ogio, S.; Sakurai, N.; Sagawa, H.; Stokes, B. T.; Tsujimoto, M.; Yashiro, K.

The Telescope Array (TA) experiment, located in the western desert of Utah, U.S.A., at 39.38° north and 112.9° west, is collecting data of ultra high energy cosmic rays in the energy range 1018-1020 eV. The experiment has a Surface Detector (SD) array surrounded by three Fluorescence Detector (FD) stations to enable simultaneous detection of shower particles and fluorescence photons generated by the extensive air shower. Measurement of shower particles at the ground level, with different absorber thickness, enables a more detailed studies of the experiment's energy scale and of hadron interaction models. In this report, we present a design and the first observation result of a surface muon detector using lead plates and concrete as absorbers.

A FADC-Based Data Acquisition System for the KASCADE-Grande Experiment

NASA Astrophysics Data System (ADS)

Walkowiak, W.; Antoni, T.; Apel, W. D.; Badea, F.; Bekk, K.; Bercuci, A.; Bertaina, M.; Blumer, H.; Bozdog, H.; Brancus, I. M.; Bruggemann, M.; Buchholz, P.; Buttner, C.; Chiavassa, A.; Daumiller, K.; Dipierro, F.; Doll, P.; Engel, R.; Engler, J.; Febler, F.; Ghia, P. L.; Gils, H. J.; Glasstetter, R.; Haungs, A.; Heck, D.; Horandel, J. R.; Kampert, K.-H.; Klages, H. O.; Kolotaev, Y.; Maier, G.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Muller, M.; Navarra, G.; Obenland, R.; Oehlschlager, J.; Ostapchenko, S.; Over, S.; Petcu, M.; Plewnia, S.; Rebel, H.; Risse, A.; Roth, M.; Schieler, H.; Scholz, J.; Stumpert, M.; Thouw, T.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Valchierotti, S.; Vanburen, J.; Weindl, A.; Wochele, J.; Zabierowski, J.; Zagromski, S.; Zimmermann, D.

2006-02-01

We present the design and first test results of a new FADC-based data acquisition (DAQ) system for the Grande array of the KASCADE-Grande experiment. The original KASCADE experiment at the Forschungszentrum Karlsruhe, Germany, has been extended by 37 detector stations of the former EAS-TOP experiment (Grande array)to provide sensitivity to energies of primary particles from the cosmos of up to $10^{18}$ eV. The new FADC-based DAQ system will improve the quality of the data taken by the Grande array by digitizing the scintillator signals with a 250 MHz sampling rate. events per second. Two Grande stations have been equipped with the FADC-based data acquisition system and first data are shown.

Computer modeling of high-voltage solar array experiment using the NASCAP/LEO (NASA Charging Analyzer Program/Low Earth Orbit) computer code

NASA Astrophysics Data System (ADS)

Reichl, Karl O., Jr.

1987-06-01

The relationship between the Interactions Measurement Payload for Shuttle (IMPS) flight experiment and the low Earth orbit plasma environment is discussed. Two interactions (parasitic current loss and electrostatic discharge on the array) may be detrimental to mission effectiveness. They result from the spacecraft's electrical potentials floating relative to plasma ground to achieve a charge flow equilibrium into the spacecraft. The floating potentials were driven by external biases applied to a solar array module of the Photovoltaic Array Space Power (PASP) experiment aboard the IMPS test pallet. The modeling was performed using the NASA Charging Analyzer Program/Low Earth Orbit (NASCAP/LEO) computer code which calculates the potentials and current collection of high-voltage objects in low Earth orbit. Models are developed by specifying the spacecraft, environment, and orbital parameters. Eight IMPS models were developed by varying the array's bias voltage and altering its orientation relative to its motion. The code modeled a typical low Earth equatorial orbit. NASCAP/LEO calculated a wide variety of possible floating potential and current collection scenarios. These varied directly with both the array bias voltage and with the vehicle's orbital orientation.

Altered retinal microRNA expression profiles in early diabetic retinopathy: an in silico analysis.

PubMed

Xiong, Fen; Du, Xinhua; Hu, Jianyan; Li, Tingting; Du, Shanshan; Wu, Qiang

2014-07-01

MicroRNAs (miRNAs) - as negative regulators of target genes - are associated with various human diseases, but their precise role(s) in diabetic retinopathy (DR) remains to be elucidated. The aim of this study was to elucidate the involvement of miRNAs in early DR using in silico analysis to explore their gene expression patterns. We used the streptozotocin (STZ)-induced diabetic rat to investigate the roles of miRNAs in early DR. Retinal miRNA expression profiles from diabetic versus healthy control rats were examined by miRNA array analysis. Based on several bioinformatic systems, specifically, gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we identified signatures of the potential pathological processes, gene functions, and signaling pathways that are influenced by dysregulated miRNAs. We used quantitative real-time polymerase chain reaction (qRT-PCR) to validate six (i.e. those with significant changes in expression levels) of the 17 miRNAs that were detected in the miRNA array. We also describe the significant role of the miRNA-gene network, which is based on the interactions between miRNAs and target genes. GO analysis of the 17 miRNAs detected in the miRNA array analysis revealed the most prevalent miRNAs to be those related to biological processes, olfactory bulb development and axonogenesis. These miRNAs also exert significant influence on additional pathways, including the mitogen-activated protein and calcium signaling pathways. Six of the seventeen miRNAs were chosen for qRT-PCR validation. With the exception of a slight difference in miRNA-350, our results are in close agreement with the differential expressions detected by array analysis. This study, which describes miRNA expression during the early developmental phases of DR, revealed extensive miRNA interactions. Based on both their target genes and signaling pathways, we suggest that miRNAs perform critical regulatory functions during the early stages of DR evolution.

Differential expression of extracellular matrix constituents and cell adhesion molecules between malignant pleural mesothelioma and mesothelial hyperplasia.

PubMed

Alì, Greta; Borrelli, Nicla; Riccardo, Giannini; Proietti, Agnese; Pelliccioni, Serena; Niccoli, Cristina; Boldrini, Laura; Lucchi, Marco; Mussi, Alfredo; Fontanini, Gabriella

2013-11-01

Malignant pleural mesothelioma (MPM) is a highly aggressive neoplasm associated with asbestos exposure. Currently, the molecular mechanisms that induce MPM development are still unknown. The purpose of this study was to identify new molecular biomarkers for mesothelial carcinogenesis. We analyzed a panel of 84 genes involved in extracellular matrix remodeling and cell adhesion by polymerase chain reaction (PCR) array in 15 samples of epithelioid mesothelioma and 10 samples of reactive mesothelial hyperplasia (MH; 3 of 25 samples were inadequate for mRNA analysis). To validate the differentially expressed genes identified by PCR array, we analyzed 27 more samples by immunohistochemistry, in addition to the 25 samples already studied. Twenty-five genes were differentially expressed in MPM and MH by PCR array. Of these we studied matrix metalloproteinase 7 (MMP7), MMP14, CD44, and integrin, alpha3 expression by immunohistochemistry in 26 epithelioid MPM and 26 MH samples from the entire series of 52 cases. We observed higher MMP14 and integrin, alpha3 expression in MPM samples compared with MH samples (p = 0.000002 and p = 0.000002, respectively). Conversely, CD44 expression was low in most (57.7%) mesothelioma samples but only in 11.5% of the MH samples (p = 0.0013). As regards MMP7, we did not observe differential expression between MH and MPM samples. We have extensively studied genes involved in cell adhesion and extracellular matrix remodeling in MPM and MH samples, gaining new insight into the pathophysiology of mesothelioma. Moreover, our data suggest that these factors could be potential biomarkers for MPM.

Transcription-dependent radial distribution of TCF7L2 regulated genes in chromosome territories.

PubMed

Torabi, Keyvan; Wangsa, Darawalee; Ponsa, Immaculada; Brown, Markus; Bosch, Anna; Vila-Casadesús, Maria; Karpova, Tatiana S; Calvo, Maria; Castells, Antoni; Miró, Rosa; Ried, Thomas; Camps, Jordi

2017-10-01

Human chromosomes occupy distinct territories in the interphase nucleus. Such chromosome territories (CTs) are positioned according to gene density. Gene-rich CTs are generally located in the center of the nucleus, while gene-poor CTs are positioned more towards the nuclear periphery. However, the association between gene expression levels and the radial positioning of genes within the CT is still under debate. In the present study, we performed three-dimensional fluorescence in situ hybridization experiments in the colorectal cancer cell lines DLD-1 and LoVo using whole chromosome painting probes for chromosomes 8 and 11 and BAC clones targeting four genes with different expression levels assessed by gene expression arrays and RT-PCR. Our results confirmed that the two over-expressed genes, MYC on chromosome 8 and CCND1 on chromosome 11, are located significantly further away from the center of the CT compared to under-expressed genes on the same chromosomes, i.e., DLC1 and SCN3B. When CCND1 expression was reduced after silencing the major transcription factor of the WNT/β-catenin signaling pathway, TCF7L2, the gene was repositioned and mostly detected in the interior of the CT. Thus, we suggest a non-random distribution in which over-expressed genes are located more towards the periphery of the respective CTs.

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

Curto, Sergio; Taj-Eldin, Mohammed; Fairchild, Dillon

Purpose: The relationship between microwave ablation system operating frequency and ablation performance is not currently well understood. The objective of this study was to comparatively assess the differences in microwave ablation at 915 MHz and 2.45 GHz. Methods: Analytical expressions for electromagnetic radiation from point sources were used to compare power deposition at the two frequencies of interest. A 3D electromagnetic-thermal bioheat transfer solver was implemented with the finite element method to characterize power deposition and thermal ablation with asymmetrical insulated dipole antennas (single-antenna and dual-antenna synchronous arrays). Simulation results were validated against experiments in ex vivo tissue. Results: Theoretical,more » computational, and experimental results indicated greater power deposition and larger diameter ablation zones when using a single insulated microwave antenna at 2.45 GHz; experimentally, 32 ± 4.1 mm and 36.3 ± 1.0 mm for 5 and 10 min, respectively, at 2.45 GHz, compared to 24 ± 1.7 mm and 29.5 ± 0.6 mm at 915 MHz, with 30 W forward power at the antenna input port. In experiments, faster heating was observed at locations 5 mm (0.91 vs 0.49 °C/s) and 10 mm (0.28 vs 0.15 °C/s) from the antenna operating at 2.45 GHz. Larger ablation zones were observed with dual-antenna arrays at 2.45 GHz; however, the differences were less pronounced than for single antennas. Conclusions: Single- and dual-antenna arrays systems operating at 2.45 GHz yield larger ablation zone due to greater power deposition in proximity to the antenna, as well as greater role of thermal conduction.« less

The drift chamber array at the external target facility in HIRFL-CSR

NASA Astrophysics Data System (ADS)

Sun, Y. Z.; Sun, Z. Y.; Wang, S. T.; Duan, L. M.; Sun, Y.; Yan, D.; Tang, S. W.; Yang, H. R.; Lu, C. G.; Ma, P.; Yu, Y. H.; Zhang, X. H.; Yue, K.; Fang, F.; Su, H.

2018-06-01

A drift chamber array at the External Target Facility in HIRFL-CSR has been constructed for three-dimensional particle tracking in high-energy radioactive ion beam experiments. The design, readout, track reconstruction program and calibration procedures for the detector are described. The drift chamber array was tested in a 311 AMeV 40Ar beam experiment. The detector performance based on the measurements of the beam test is presented. A spatial resolution of 230 μm is achieved.

Automated array assembly

NASA Technical Reports Server (NTRS)

Williams, B. F.

1976-01-01

Manufacturing techniques are evaluated using expenses based on experience and studying basic cost factors for each step to evaluate expenses from a first-principles point of view. A formal cost accounting procedure is developed which is used throughout the study for cost comparisons. The first test of this procedure is a comparison of its predicted costs for array module manufacturing with costs from a study which is based on experience factors. A manufacturing cost estimate for array modules of $10/W is based on present-day manufacturing techniques, expenses, and materials costs.

Results from the Telescope Array Experiment

NASA Astrophysics Data System (ADS)

Jui, Charles C. H.; Telescope Array Collaboration

2016-04-01

The Telescope Array (TA) is the largest ultrahigh energy cosmic ray detector in the northern hemisphere. The experiment consists of three fluorescence stations viewing the air space over a surface array of 507 scintillation counters deployed over 700 square kilometers. TA has been in operation since 2008. The most recent results from TA, including that of composition studies and search for arrival direction anisotropy, will be presented. We will also report on the progress of the new TA low energy extension (TALE).

The protein expression landscape of mitosis and meiosis in diploid budding yeast.

PubMed

Becker, Emmanuelle; Com, Emmanuelle; Lavigne, Régis; Guilleux, Marie-Hélène; Evrard, Bertrand; Pineau, Charles; Primig, Michael

2017-03-06

Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome ofmajor phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of the proteome when cells switch from mitotic growth to meiotic development. We report a quantitative protein profiling analysis of yeast cell division and differentiation based on mass spectrometry. Information about protein levels was integrated with strand-specific tiling array expression data. We identified a total of 2366 proteins in at least one condition, including 175 proteins showing a statistically significant>5-fold change across the sample set, and 136 proteins detectable in sporulating but not respiring cells. We correlate protein expression patterns with biological processes and molecular function by Gene Ontology term enrichment, chemoprofiling, transcription interference and the formation of double stranded RNAs by overlapping sense/antisense transcripts. Our work provides initial quantitative insight into protein expression in diploid respiring and differentiating yeast cells. Critically, it associates developmentally regulated induction of antisense long noncoding RNAs and double stranded RNAs with fluctuating protein concentrations during growth and development. This integrated genomics analysis helps better understand how the transcriptome and the proteome correlate in diploid yeast cells undergoing mitotic growth in the presence of acetate (respiration) versus meiotic differentiation (Meiosis I and II). The study (i) provides quantitative expression data for 2366 proteins and their cognate mRNAs in at least one sample, (ii) shows strongly fluctuating protein levels during growth and differentiation for 175 cases, and (iii) identifies 136 proteins absent in mitotic but present in meiotic yeast cells. We have integrated protein profiling data using mass spectrometry with tiling array RNA profiling data and information on double-stranded RNAs (dsRNAs) by overlapping sense/antisense transcripts from an RNA-Sequencing experiment. This work therefore provides quantitative insight into protein expression during cell division and development and associates changing protein levels with developmental stage specific induction of antisense transcripts and the formation of dsRNAs. Copyright © 2017 Elsevier B.V. All rights reserved.

TEMPORAL GENE INDUCTION PATTERNS IN SHEEPSHEAD MINNOWS EXPOSED TO 17-ESTRADIOL

EPA Science Inventory

Gene arrays provide a powerful method to examine changes in gene expression in fish due to chemical exposures in the environment. In this study, we expanded an existing gene array for sheepshead minnows (Cyprinodon variegatus) (SHM) and used it to examine temporal changes in gene...

Big data analytics workflow management for eScience

NASA Astrophysics Data System (ADS)

Fiore, Sandro; D'Anca, Alessandro; Palazzo, Cosimo; Elia, Donatello; Mariello, Andrea; Nassisi, Paola; Aloisio, Giovanni

2015-04-01

In many domains such as climate and astrophysics, scientific data is often n-dimensional and requires tools that support specialized data types and primitives if it is to be properly stored, accessed, analysed and visualized. Currently, scientific data analytics relies on domain-specific software and libraries providing a huge set of operators and functionalities. However, most of these software fail at large scale since they: (i) are desktop based, rely on local computing capabilities and need the data locally; (ii) cannot benefit from available multicore/parallel machines since they are based on sequential codes; (iii) do not provide declarative languages to express scientific data analysis tasks, and (iv) do not provide newer or more scalable storage models to better support the data multidimensionality. Additionally, most of them: (v) are domain-specific, which also means they support a limited set of data formats, and (vi) do not provide a workflow support, to enable the construction, execution and monitoring of more complex "experiments". The Ophidia project aims at facing most of the challenges highlighted above by providing a big data analytics framework for eScience. Ophidia provides several parallel operators to manipulate large datasets. Some relevant examples include: (i) data sub-setting (slicing and dicing), (ii) data aggregation, (iii) array-based primitives (the same operator applies to all the implemented UDF extensions), (iv) data cube duplication, (v) data cube pivoting, (vi) NetCDF-import and export. Metadata operators are available too. Additionally, the Ophidia framework provides array-based primitives to perform data sub-setting, data aggregation (i.e. max, min, avg), array concatenation, algebraic expressions and predicate evaluation on large arrays of scientific data. Bit-oriented plugins have also been implemented to manage binary data cubes. Defining processing chains and workflows with tens, hundreds of data analytics operators is the real challenge in many practical scientific use cases. This talk will specifically address the main needs, requirements and challenges regarding data analytics workflow management applied to large scientific datasets. Three real use cases concerning analytics workflows for sea situational awareness, fire danger prevention, climate change and biodiversity will be discussed in detail.

Recognition Time for Letters and Nonletters: Effects of Serial Position, Array Size, and Processing Order.

ERIC Educational Resources Information Center

Mason, Mildred

1982-01-01

Three experiments report additional evidence that it is a mistake to account for all interletter effects solely in terms of sensory variables. These experiments attest to the importance of structural variables such as retina location, array size, and ordinal position. (Author/PN)

PCR array analysis of gene expression profiles in chronic active Epstein-Barr virus infection.

PubMed

Murakami, Masanao; Hashida, Yumiko; Imajoh, Masayuki; Maeda, Akihiko; Kamioka, Mikio; Senda, Yasutaka; Sato, Tetsuya; Fujieda, Mikiya; Wakiguchi, Hiroshi; Daibata, Masanori

2014-07-01

To determine the host cellular gene expression profiles in chronic active Epstein-Barr virus infection (CAEBV), peripheral blood samples were obtained from three patients with CAEBV and investigated using a PCR array analysis that focused on T-cell/B-cell activation. We identified six genes with expression levels that were tenfold higher in CAEBV patients compared with those in healthy controls. These results were verified by quantitative reverse transcription-PCR. We identified four highly upregulated genes, i.e., IL-10, IL-2, IFNGR1, and INHBA. These genes may be involved in inflammatory responses and cell proliferation, and they may contribute to the development and progression of CAEBV. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

MORPHOLOGIC ANALYSIS CORRELATES WITH GENE EXPRESSION CHANGES IN CULTURED F344 RAT MESOTHELIAL CELLS

EPA Science Inventory

The gene expression pattern of mesothelial cells in vitro was determined after 4 or 12 h exposure to the rat mesothelial, kidney and thyroid carcinogen, and oxidative stressor potassium bromate (KBr03). Gene expression changes observed using cDNA arrays indicated oxidative stres...

HES1, a target of Notch signaling, is elevated in canine osteosarcoma, but reduced in the most aggressive tumors

PubMed Central

2013-01-01

Background Hairy and enhancer of split 1 (HES1), a basic helix-loop-helix transcriptional repressor, is a downstream target of Notch signaling. Notch signaling and HES1 expression have been linked to growth and survival in a variety of human cancer types and have been associated with increased metastasis and invasiveness in human osteosarcoma cell lines. Osteosarcoma (OSA) is an aggressive cancer demonstrating both high metastatic rate and chemotherapeutic resistance. The current study examined expression of Notch signaling mediators in primary canine OSA tumors and canine and human osteosarcoma cell lines to assess their role in OSA development and progression. Results Reverse transcriptase - quantitative PCR (RT-qPCR) was utilized to quantify HES1, HEY1, NOTCH1 and NOTCH2 gene expression in matched tumor and normal metaphyseal bone samples taken from dogs treated for appendicular OSA at the Colorado State University Veterinary Teaching Hospital. Gene expression was also assessed in tumors from dogs with a disease free interval (DFI) of <100 days compared to those with a DFI > 300 days following treatment with surgical amputation followed by standard chemotherapy. Immunohistochemistry was performed to confirm expression of HES1. Data from RT-qPCR and immunohistochemical (IHC) experiments were analyzed using REST2009 software and survival analysis based on IHC expression employed the Kaplan-Meier method and log rank analysis. Unbiased clustered images were generated from gene array analysis data for Notch/HES1 associated genes. Gene array analysis of Notch/HES1 associated genes suggested alterations in the Notch signaling pathway may contribute to the development of canine OSA. HES1 mRNA expression was elevated in tumor samples relative to normal bone, but decreased in tumor samples from dogs with a DFI < 100 days relative to those with a DFI > 300 days. NOTCH2 and HEY1 mRNA expression was also elevated in tumors relative to normal bone, but was not differentially expressed between the DFI tumor groups. Survival analysis confirmed an association between decreased HES1 immunosignal and shorter DFI. Conclusions Our findings suggest that activation of Notch signaling occurs and may contribute to the development of canine OSA. However, association of low HES1 expression and shorter DFI suggests that mechanisms that do not alter HES1 expression may drive the most aggressive tumors. PMID:23816051

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

Hughes, R. O.; Burke, J. T.; Casperson, R. J.

Hyperion is a new high-efficiency charged-particle γ-ray detector array which consists of a segmented silicon telescope for charged-particle detection and up to fourteen high-purity germanium clover detectors for the detection of coincident γ rays. The array will be used in nuclear physics measurements and Stockpile Stewardship studies and replaces the STARLiTeR array. In conclusion, this article discusses the features of the array and presents data collected with the array in the commissioning experiment.

Design and Fabrication of Aspheric Microlens Array for Optical Read-Only-Memory Card System

NASA Astrophysics Data System (ADS)

Kim, Hongmin; Jeong, Gibong; Kim, Young‑Joo; Kang, Shinill

2006-08-01

An optical head based on the Talbot effect with an aspheric microlens array for an optical read-only-memory (ROM) card system was designed and fabricated. The mathematical expression for the wavefield diffracted by a periodic microlens array showed that the amplitude distribution at the Talbot plane from the focal plane of the microlens array was identically equal to that at the focal plane. To use a reflow microlens array as a master pattern of an ultraviolet-imprinted (UV-imprinted) microlens array, the reflow microlens was defined as having an aspheric shape. To obtain optical probes with good optical qualities, a microlens array with the minimum spherical aberration was designed by ray tracing. The reflow condition was optimized to realize the master pattern of a microlens with a designed aspheric shape. The intensity distribution of the optical probes at the Talbot plane from the focal plane showed a diffraction-limited shape.

Investigation on transmission and reflection characteristics of plasma array to 6 GHz high-power microwave

NASA Astrophysics Data System (ADS)

Yang, Liu; Yang, Zhongcun; Wan, Jianing; Liu, Hao

2016-10-01

For the safety of electronic equipment, a double-layer barrier of cylindrical plasma array was designed, and its protective performance to high-power microwave (HPM) were analyzed and the protective performance experiment was conducted. Combining the density distribution characteristic of the discharge plasma, the shielding effectiveness of the double-layer plasma on 6GHz HPM pulse was studied. The experiment results indicate that the protective effectiveness of two layers plasma array is better than that of one layer. Two layers plasma array can make the peak electric field of transmission waveform less than interference threshold of electronic equipment to achieve better protection effectiveness. Transmission attenuation of one layer and two layers plasma array to HPM can reach -6.6066dB and -24.9357dB. The results also show that for the existence of multiple reflection, even the plasma electron density is not high enough, it can realize a strong attenuation. The experiment results in this paper are of great significance in protecting against HPM and electromagnetic pulse.

SEP solar array Shuttle flight experiment

NASA Technical Reports Server (NTRS)

Elms, R. V., Jr.; Young, L. E.; Hill, H. C.

1981-01-01

An experiment to verify the operational performance of a full-scale Solar Electric Propulsion (SEP) solar array is described. Scheduled to fly on the Shuttle in 1983, the array will be deployed from the bay for ten orbits, with dynamic excitation to test the structural integrity being furnished by the Orbiter verniers; thermal, electrical, and sun orientation characteristics will be monitored, in addition to safety, reliability, and cost effective performance. The blanket, with aluminum and glass as solar cell mass simulators, is 4 by 32 m, with panels (each 0.38 by 4 m) hinged together; two live Si cell panels will be included. The panels are bonded to stiffened graphite-epoxy ribs and are storable in a box in the bay. The wing support structure is detailed, noting the option of releasing the wing into space by use of the Remote Manipulator System if the wing cannot be refolded. Procedures and equipment for monitoring the array behavior are outlined, and comprise both analog data and TV recording for later playback and analysis. The array wing experiment will also aid in developing measurement techniques for large structure dynamics in space.

Convergence of shock waves generated by underwater electrical explosion of cylindrical wire arrays between different boundary geometries

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

Yanuka, D.; Zinowits, H. E.; Krasik, Ya. E.

The results of experiments and numerical simulations of a shock wave propagating between either conical or parabolic bounding walls are presented. The shock wave was generated by a microsecond timescale underwater electrical explosion of a cylindrical wire array supplied by a current pulse having an amplitude of ∼230 kA and a rise time of ∼1 μs. It is shown that with the same energy density deposition into the exploding wire array, the shock wave converges faster between parabolic walls, and as a result, the pressure in the vicinity of convergence is ∼2.3 times higher than in the case of conical walls. Themore » results obtained are compared to those of earlier experiments [Antonov et al., Appl. Phys. Lett. 102, 124104 (2013)] with explosions of spherical wire arrays. It is shown that at a distance of ∼400 μm from the implosion origin the pressure obtained in the current experiments is higher than for the case of spherical wire arrays.« less

Automated analysis of siRNA screens of cells infected by hepatitis C and dengue viruses based on immunofluorescence microscopy images

NASA Astrophysics Data System (ADS)

Matula, Petr; Kumar, Anil; Wörz, Ilka; Harder, Nathalie; Erfle, Holger; Bartenschlager, Ralf; Eils, Roland; Rohr, Karl

2008-03-01

We present an image analysis approach as part of a high-throughput microscopy siRNA-based screening system using cell arrays for the identification of cellular genes involved in hepatitis C and dengue virus replication. Our approach comprises: cell nucleus segmentation, quantification of virus replication level in the neighborhood of segmented cell nuclei, localization of regions with transfected cells, cell classification by infection status, and quality assessment of an experiment and single images. In particular, we propose a novel approach for the localization of regions of transfected cells within cell array images, which combines model-based circle fitting and grid fitting. By this scheme we integrate information from single cell array images and knowledge from the complete cell arrays. The approach is fully automatic and has been successfully applied to a large number of cell array images from screening experiments. The experimental results show a good agreement with the expected behaviour of positive as well as negative controls and encourage the application to screens from further high-throughput experiments.

Increased expression of proenkephalin and prodynorphin mRNAs in the nucleus accumbens of compulsive methamphetamine taking rats.

PubMed

Cadet, Jean Lud; Krasnova, Irina N; Walther, Donna; Brannock, Christie; Ladenheim, Bruce; McCoy, Michael T; Collector, Daniel; Torres, Oscar V; Terry, Ndeah; Jayanthi, Subramaniam

2016-11-14

Addiction is associated with neuroadaptive changes in the brain. In the present paper, we used a model of methamphetamine self-administration during which we used footshocks to divide rats into animals that continue to press a lever to get methamphetamine (shock-resistant) and those that significantly reduce pressing the lever (shock-sensitive) despite the shocks. We trained male Sprague-Dawley rats to self-administer methamphetamine (0.1 mg/kg/infusion) for 9 hours daily for 20 days. Control group self-administered saline. Subsequently, methamphetamine self-administration rats were punished by mild electric footshocks for 10 days with gradual increases in shock intensity. Two hours after stopping behavioral experiments, we euthanized rats and isolated nucleus accumbens (NAc) samples. Affymetrix Array experiments revealed 24 differentially expressed genes between the shock-resistant and shock-sensitive rats, with 15 up- and 9 downregulated transcripts. Ingenuity pathway analysis showed that these transcripts belong to classes of genes involved in nervous system function, behavior, and disorders of the basal ganglia. These genes included prodynorphin (PDYN) and proenkephalin (PENK), among others. Because PDYN and PENK are expressed in dopamine D1- and D2-containing NAc neurons, respectively, these findings suggest that mechanisms, which impact both cell types may play a role in the regulation of compulsive methamphetamine taking by rats.

Microgravity Induction of TRAIL Expression in Preosteoclast Cells Enhances Osteoclast Differentiation

NASA Astrophysics Data System (ADS)

Sambandam, Yuvaraj; Baird, Kelsey L.; Stroebel, Maxwell; Kowal, Emily; Balasubramanian, Sundaravadivel; Reddy, Sakamuri V.

2016-05-01

Evidence indicates that astronauts experience significant bone loss in space. We previously showed that simulated microgravity (μXg) using the NASA developed rotary cell culture system (RCCS) enhanced bone resorbing osteoclast (OCL) differentiation. However, the mechanism by which μXg increases OCL formation is unclear. RANK/RANKL signaling pathway is critical for OCL differentiation. Tumor necrosis factor-related apoptosis inducing ligand (TRAIL) has been shown to increase osteoclastogenesis. We hypothesize that TRAIL may play an important role in μXg enhanced OCL differentiation. In this study, we identified by RT profiler PCR array screening that μXg induces high levels of TRAIL expression in murine preosteoclast cells in the absence of RANKL stimulation compared to ground based (Xg) cultures. We further identified that μXg elevated the adaptor protein TRAF-6 and fusion genes OC-STAMP and DC-STAMP expression in preosteoclast cells. Interestingly, neutralizing antibody against TRAIL significantly reduced μXg induced OCL formation. We further identified that over-expression of pTRAIL in RAW 264.7 cells enhanced OCL differentiation. These results indicate that TRAIL signaling plays an important role in the μXg increased OCL differentiation. Therefore, inhibition of TRAIL expression could be an effective countermeasure for μXg induced bone loss.

Preliminary Results from the Flight of the Solar Array Module Plasma Interactions Experiment (SAMPIE)

NASA Technical Reports Server (NTRS)

Ferguson, Dale C.; Hillard, G. Barry

1994-01-01

SAMPIE, the Solar Array Module Plasma Interactions Experiment, flew in the Space Shuttle Columbia payload bay as part of the OAST-2 mission on STS-62, March, 1994. SAMPIE biased samples of solar arrays and space power materials to varying potentials with respect to the surrounding space plasma, and recorded the plasma currents collected and the arcs which occurred, along with a set of plasma diagnostics data. A large set of high quality data was obtained on the behavior of solar arrays and space power materials in the space environment. This paper is the first report on the data SAMPIE telemetered to the ground during the mission. It will be seen that the flight data promise to help determine arcing thresholds, snapover potentials and floating potentials for arrays and spacecraft in LEO.

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments

PubMed Central

Zheng, Jie; Stoyanovich, Julia; Manduchi, Elisabetta; Liu, Junmin; Stoeckert, Christian J.

2011-01-01

The ever-increasing scale of biological data sets, particularly those arising in the context of high-throughput technologies, requires the development of rich data exploration tools. In this article, we present AnnotCompute, an information discovery platform for repositories of functional genomics experiments such as ArrayExpress. Our system leverages semantic annotations of functional genomics experiments with controlled vocabulary and ontology terms, such as those from the MGED Ontology, to compute conceptual dissimilarities between pairs of experiments. These dissimilarities are then used to support two types of exploratory analysis—clustering and query-by-example. We show that our proposed dissimilarity measures correspond to a user's intuition about conceptual dissimilarity, and can be used to support effective query-by-example. We also evaluate the quality of clustering based on these measures. While AnnotCompute can support a richer data exploration experience, its effectiveness is limited in some cases, due to the quality of available annotations. Nonetheless, tools such as AnnotCompute may provide an incentive for richer annotations of experiments. Code is available for download at http://www.cbil.upenn.edu/downloads/AnnotCompute. Database URL: http://www.cbil.upenn.edu/annotCompute/ PMID:22190598

Validation of MCNP: SPERT-D and BORAX-V fuel

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

Crawford, C.; Palmer, B.

1992-11-01

This report discusses critical experiments involving SPERT-D{sup 1,2} fuel elements and BORAX-V{sup 3-8} fuel which have been modeled and calculations performed with MCNP. MCNP is a Monte Carlo based transport code. For this study continuous-energy nuclear data from the ENDF/B-V cross section library was used. The SPERT-D experiments consisted of various arrays of fuel elements moderated and reflected with either water or a uranyl nitrate solution. Some SPERT-D experiments used cadmium as a fixed neutron poison, while others were poisoned with various concentrations of boron in the moderating/reflecting solution. ne BORAX-V experiments were arrays of either boiling fuel rod assembliesmore » or superheater assemblies, both types of arrays were moderated and reflected with water. In one boiling fuel experiment, two fuel rods were replaced with borated stainless steel poison rods.« less

Validation of MCNP: SPERT-D and BORAX-V fuel

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

Crawford, C.; Palmer, B.

1992-11-01

This report discusses critical experiments involving SPERT-D[sup 1,2] fuel elements and BORAX-V[sup 3-8] fuel which have been modeled and calculations performed with MCNP. MCNP is a Monte Carlo based transport code. For this study continuous-energy nuclear data from the ENDF/B-V cross section library was used. The SPERT-D experiments consisted of various arrays of fuel elements moderated and reflected with either water or a uranyl nitrate solution. Some SPERT-D experiments used cadmium as a fixed neutron poison, while others were poisoned with various concentrations of boron in the moderating/reflecting solution. ne BORAX-V experiments were arrays of either boiling fuel rod assembliesmore » or superheater assemblies, both types of arrays were moderated and reflected with water. In one boiling fuel experiment, two fuel rods were replaced with borated stainless steel poison rods.« less

Study of large adaptive arrays for space technology applications

NASA Technical Reports Server (NTRS)

Berkowitz, R. S.; Steinberg, B.; Powers, E.; Lim, T.

1977-01-01

The research in large adaptive antenna arrays for space technology applications is reported. Specifically two tasks were considered. The first was a system design study for accurate determination of the positions and the frequencies of sources radiating from the earth's surface that could be used for the rapid location of people or vehicles in distress. This system design study led to a nonrigid array about 8 km in size with means for locating the array element positions, receiving signals from the earth and determining the source locations and frequencies of the transmitting sources. It is concluded that this system design is feasible, and satisfies the desired objectives. The second task was an experiment to determine the largest earthbound array which could simulate a spaceborne experiment. It was determined that an 800 ft array would perform indistinguishably in both locations and it is estimated that one several times larger also would serve satisfactorily. In addition the power density spectrum of the phase difference fluctuations across a large array was measured. It was found that the spectrum falls off approximately as f to the minus 5/2 power.

How Many Peripheral Solder Joints in a Surface Mounted Design Experience Inelastic Strains?

NASA Astrophysics Data System (ADS)

Suhir, E.; Yi, S.; Ghaffarian, R.

2017-03-01

It has been established that it is the peripheral solder joints that are the most vulnerable in the ball-grid-array (BGA) and column-grid-array (CGA) designs and most often fail. As far as the long-term reliability of a soldered microelectronics assembly as a whole is concerned, it makes a difference, if just one or more peripheral joints experience inelastic strains. It is clear that the low cycle fatigue lifetime of the solder system is inversely proportional to the number of joints that simultaneously experience inelastic strains. A simple and physically meaningful analytical expression (formula) is obtained for the prediction, at the design stage, of the number of such joints, if any, for the given effective thermal expansion (contraction) mismatch of the package and PCB; materials and geometrical characteristics of the package/PCB assembly; package size; and, of course, the level of the yield stress in the solder material. The suggested formula can be used to determine if the inelastic strains in the solder material could be avoided by the proper selection of the above characteristics and, if not, how many peripheral joints are expected to simultaneously experience inelastic strains. The general concept is illustrated by a numerical example carried out for a typical BGA package. The suggested analytical model (formula) is applicable to any soldered microelectronics assembly. The roles of other important factors, such as, e.g., solder material anisotropy, grain size, and their random orientation within a joint, are viewed in this analysis as less important factors than the level of the interfacial stress. The roles of these factors will be accounted for in future work and considered, in addition to the location of the joint, in a more complicated, more sophisticated, and more comprehensive reliability/fatigue model.

FPGA-accelerated algorithm for the regular expression matching system

NASA Astrophysics Data System (ADS)

Russek, P.; Wiatr, K.

2015-01-01

This article describes an algorithm to support a regular expressions matching system. The goal was to achieve an attractive performance system with low energy consumption. The basic idea of the algorithm comes from a concept of the Bloom filter. It starts from the extraction of static sub-strings for strings of regular expressions. The algorithm is devised to gain from its decomposition into parts which are intended to be executed by custom hardware and the central processing unit (CPU). The pipelined custom processor architecture is proposed and a software algorithm explained accordingly. The software part of the algorithm was coded in C and runs on a processor from the ARM family. The hardware architecture was described in VHDL and implemented in field programmable gate array (FPGA). The performance results and required resources of the above experiments are given. An example of target application for the presented solution is computer and network security systems. The idea was tested on nearly 100,000 body-based viruses from the ClamAV virus database. The solution is intended for the emerging technology of clusters of low-energy computing nodes.

Quantitative Magnetic Separation of Particles and Cells using Gradient Magnetic Ratcheting

PubMed Central

Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

2016-01-01

Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting (MACS), are robust but perform coarse, qualitative separations based on surface antigen expression. We report a quantitative magnetic separation technology using high-force magnetic ratcheting over arrays of magnetically soft micro-pillars with gradient spacing, and use the system to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micro-pillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic-field. Particles with higher IOC separate and equilibrate along the miro-pillar array at larger pitches. We develop a semi-analytical model that predicts behavior for particles and cells. Using the system, LNCaP cells were separated based on the bound quantity of 1μm anti-EpCAM particles as a metric for expression. The ratcheting cytometry system was able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof of concept, EpCAM-labeled cells from patient blood were isolated with 74% purity, demonstrating potential towards a quantitative magnetic separation instrument. PMID:26890496

Use of planar array electrophysiology for the development of robust ion channel cell lines.

PubMed

Clare, Jeffrey J; Chen, Mao Xiang; Downie, David L; Trezise, Derek J; Powell, Andrew J

2009-01-01

The tractability of ion channels as drug targets has been significantly improved by the advent of planar array electrophysiology platforms which have dramatically increased the capacity for electrophysiological profiling of lead series compounds. However, the data quality and through-put obtained with these platforms is critically dependent on the robustness of the expression reagent being used. The generation of high quality, recombinant cell lines is therefore a key step in the early phase of ion channel drug discovery and this can present significant challenges due to the diversity and organisational complexity of many channel types. This article focuses on several complex and difficult to express ion channels and illustrates how improved stable cell lines can be obtained by integration of planar array electrophysiology systems into the cell line generation process per se. By embedding this approach at multiple stages (e.g., during development of the expression strategy, during screening and validation of clonal lines, and during characterisation of the final cell line), the cycle time and success rate in obtaining robust expression of complex multi-subunit channels can be significantly improved. We also review how recent advances in this technology (e.g., population patch clamp) have further widened the versatility and applicability of this approach.

Adaptive multibeam phased array design for a Spacelab experiment

NASA Technical Reports Server (NTRS)

Noji, T. T.; Fass, S.; Fuoco, A. M.; Wang, C. D.

1977-01-01

The parametric tradeoff analyses and design for an Adaptive Multibeam Phased Array (AMPA) for a Spacelab experiment are described. This AMPA Experiment System was designed with particular emphasis to maximize channel capacity and minimize implementation and cost impacts for future austere maritime and aeronautical users, operating with a low gain hemispherical coverage antenna element, low effective radiated power, and low antenna gain-to-system noise temperature ratio.

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

PubMed

Canver, Matthew C; Haeussler, Maximilian; Bauer, Daniel E; Orkin, Stuart H; Sanjana, Neville E; Shalem, Ophir; Yuan, Guo-Cheng; Zhang, Feng; Concordet, Jean-Paul; Pinello, Luca

2018-05-01

CRISPR (clustered regularly interspaced short palindromic repeats) genome-editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep-sequencing data resulting from genome-editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments. Here, we present a protocol that describes in detail both the computational and benchtop implementation of an arrayed and/or pooled CRISPR genome-editing experiment. This protocol provides instructions for sgRNA design with CRISPOR (computational tool for the design, evaluation, and cloning of sgRNA sequences), experimental implementation, and analysis of the resulting high-throughput sequencing data with CRISPResso (computational tool for analysis of genome-editing outcomes from deep-sequencing data). This protocol allows for design and execution of arrayed and pooled CRISPR experiments in 4-5 weeks by non-experts, as well as computational data analysis that can be performed in 1-2 d by both computational and noncomputational biologists alike using web-based and/or command-line versions.

Comparison of NMDA and AMPA Channel Expression and Function between Embryonic and Adult Neurons Utilizing Microelectrode Array Systems.

PubMed

Edwards, Darin; Sommerhage, Frank; Berry, Bonnie; Nummer, Hanna; Raquet, Martina; Clymer, Brad; Stancescu, Maria; Hickman, James J

2017-12-11

Microelectrode arrays (MEAs) are innovative tools used to perform electrophysiological experiments for the study of electrical activity and connectivity in populations of neurons from dissociated cultures. Reliance upon neurons derived from embryonic tissue is a common limitation of neuronal/MEA hybrid systems and perhaps of neuroscience research in general, and the use of adult neurons could model fully functional in vivo parameters more closely. Spontaneous network activity was concurrently recorded from both embryonic and adult rat neurons cultured on MEAs for up to 10 weeks in vitro to characterize the synaptic connections between cell types. The cultures were exposed to synaptic transmission antagonists against NMDA and AMPA channels, which revealed significantly different receptor profiles of adult and embryonic networks in vitro. In addition, both embryonic and adult neurons were evaluated for NMDA and AMPA channel subunit expression over five weeks in vitro. The results established that neurons derived from embryonic tissue did not express mature synaptic channels for several weeks in vitro under defined conditions. Consequently, the embryonic response to synaptic antagonists was significantly different than that of neurons derived from adult tissue sources. These results are especially significant because most studies reported with embryonic hippocampal neurons do not begin at two to four weeks in culture. In addition, the utilization of MEAs in lieu of patch-clamp electrophysiology avoided a large-scale, labor-intensive study. These results establish the utility of this unique hybrid system derived from adult hippocampal tissue in combination with MEAs and offer a more appropriate representation of in vivo function for drug discovery. It has application for neuronal development and regeneration as well as for investigations into neurodegenerative disease, traumatic brain injury, and stroke.

Revisiting the Cramér Rao Lower Bound for Elastography: Predicting the Performance of Axial, Lateral and Polar Strain Elastograms.

PubMed

Verma, Prashant; Doyley, Marvin M

2017-09-01

We derived the Cramér Rao lower bound for 2-D estimators employed in quasi-static elastography. To illustrate the theory, we modeled the 2-D point spread function as a sinc-modulated sine pulse in the axial direction and as a sinc function in the lateral direction. We compared theoretical predictions of the variance incurred in displacements and strains when quasi-static elastography was performed under varying conditions (different scanning methods, different configuration of conventional linear array imaging and different-size kernels) with those measured from simulated or experimentally acquired data. We performed studies to illustrate the application of the derived expressions when performing vascular elastography with plane wave and compounded plane wave imaging. Standard deviations in lateral displacements were an order higher than those in axial. Additionally, the derived expressions predicted that peak performance should occur when 2% strain is applied, the same order of magnitude as observed in simulations (1%) and experiments (1%-2%). We assessed how different configurations of conventional linear array imaging (number of active reception and transmission elements) influenced the quality of axial and lateral strain elastograms. The theoretical expressions predicted that 2-D echo tracking should be performed with wide kernels, but the length of the kernels should be selected using knowledge of the magnitude of the applied strain: specifically, longer kernels for small strains (<5%) and shorter kernels for larger strains. Although the general trends of theoretical predictions and experimental observations were similar, biases incurred during beamforming and subsample displacement estimation produced noticeable differences. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Orienting attention to locations in internal representations.

PubMed

Griffin, Ivan C; Nobre, Anna C

2003-11-15

Three experiments investigated whether it is possible to orient selective spatial attention to internal representations held in working memory in a similar fashion to orienting to perceptual stimuli. In the first experiment, subjects were either cued to orient to a spatial location before a stimulus array was presented (pre-cue), cued to orient to a spatial location in working memory after the array was presented (retro-cue), or given no cueing information (neutral cue). The stimulus array consisted of four differently colored crosses, one in each quadrant. At the end of a trial, a colored cross (probe) was presented centrally, and subjects responded according to whether it had occurred in the array. There were equivalent patterns of behavioral costs and benefits of cueing for both pre-cues and retro-cues. A follow-up experiment used a peripheral probe stimulus requiring a decision about whether its color matched that of the item presented at the same location in the array. Replication of the behavioral costs and benefits of pre-cues and retro-cues in this experiment ruled out changes in response criteria as the only explanation for the effects. The third experiment used event-related potentials (ERPs) to compare the neural processes involved in orienting attention to a spatial location in an external versus an internal spatial representation. In this task, subjects responded according to whether a central probe stimulus occurred at the cued location in the array. There were both similarities and differences between ERPs to spatial cues toward a perception versus an internal spatial representation. Lateralized early posterior and later frontal negativities were observed for both pre- and retro-cues. Retro-cues also showed additional neural processes to be involved in orienting to an internal representation, including early effects over frontal electrodes.

Investigating the Trade-Off Between Power Generation and Environmental Impact of Tidal-Turbine Arrays Using Array Layout Optimisation and Habitat Sustainability Modelling.

NASA Astrophysics Data System (ADS)

du Feu, R. J.; Funke, S. W.; Kramer, S. C.; Hill, J.; Piggott, M. D.

2016-12-01

The installation of tidal turbines into the ocean will inevitably affect the environment around them. However, due to the relative infancy of this sector the extent and severity of such effects is unknown. The layout of an array of turbines is an important factor in determining not only the array's final yield but also how it will influence regional hydrodynamics. This in turn could affect, for example, sediment transportation or habitat suitability. The two potentially competing objectives of extracting energy from the tidal current, and of limiting any environmental impact consequent to influencing that current, are investigated here. This relationship is posed as a multi-objective optimisation problem. OpenTidalFarm, an array layout optimisation tool, and MaxEnt, habitat sustainability modelling software, are used to evaluate scenarios off the coast of the UK. MaxEnt is used to estimate the likelihood of finding a species in a given location based upon environmental input data and presence data of the species. Environmental features which are known to impact habitat, specifically those affected by the presence of an array, such as bed shear stress, are chosen as inputs. MaxEnt then uses a maximum-entropy modelling approach to estimate population distribution across the modelled area. OpenTidalFarm is used to maximise the power generated by an array, or multiple arrays, through adjusting the position and number of turbines within them. It uses a 2D shallow water model with turbine arrays represented as adjustable friction fields. It has the capability to also optimise for user created functionals that can be expressed mathematically. This work uses two functionals; power extracted by the array, and the suitability of habitat as predicted by MaxEnt. A gradient-based local optimisation is used to adjust the array layout at each iteration. This work presents arrays that are optimised for both yield and the viability of habitat for chosen species. In each scenario studied, a range of array formations is found expressing varying preferences for either functional. Further analyses then allow for the identification of trade-offs between the two key societal objectives of energy production and conservation. This in turn produces information valuable to stakeholders and policymakers when making decisions on array design.

The word disgust may refer to more than one emotion.

PubMed

Yoder, Anne M; Widen, Sherri C; Russell, James A

2016-04-01

Contrary to a common presupposition, the word disgust may refer to more than one emotion. From an array of 3 facial expressions (produced in our lab), participants (N = 44) in Study 1 selected the one that best matched 11 types of emotion-eliciting events: anger, sadness, and 9 types of disgust (7 types of physical disgust plus moral disgust and simply feeling ill). From an array of 4 facial expressions (two from Matsumoto & Ekman, 1988; two produced in lab), participants (N = 120) in Study 2 selected the one that best matched 14 types of disgust-eliciting events (8 physical and 6 moral). In both studies, the modal facial expression for physical disgust was the "sick face" developed by Widen, Pochedly, Pieloch, and Russell (2013), which shows someone about to vomit. The modal facial expression for the moral violations was the standard disgust face or, when available, an anger face. If facial expression is a constituent of an emotion, physical disgust and moral disgust are separate emotions. (c) 2016 APA, all rights reserved).

MILSTAR's flexible substrate solar array: Lessons learned, addendum

NASA Technical Reports Server (NTRS)

Gibb, John

1990-01-01

MILSTAR's Flexible Substrate Solar Array (FSSA) is an evolutionary development of the lightweight, flexible substrate design pioneered at Lockheed during the seventies. Many of the features of the design are related to the Solar Array Flight Experiment (SAFE), flown on STS-41D in 1984. FSSA development has created a substantial technology base for future flexible substrate solar arrays such as the array for the Space Station Freedom. Lessons learned during the development of the FSSA can and should be applied to the Freedom array and other future flexible substrate designs.

Propagation of a phase-locked circular dark hollow beams array in a turbulent atmosphere

NASA Astrophysics Data System (ADS)

Zhou, Pu; Wang, Xiaolin; Ma, Yanxing; Ma, Haotong; Xu, Xiaojun; Liu, Zejin

2010-10-01

The propagation of phase-locked circular dark hollow beams array in a turbulent atmosphere is studied. An analytical expression for the average intensity distribution at the receiving plane is obtained based on the extended Huygens-Fresnel principle. The effects of turbulence, dark parameter and beam order of the beams array on the intensity pattern are studied and analyzed. It is found that the intensity pattern of the phase-locked circular dark hollow beams array will evolve from a multiple-spot-pattern into a Gaussian beam spot under the isotropic influence of the turbulence. The intensity pattern of beam array with a larger dark parameter and beam order evolves into the Gaussian-shape faster with increasing propagation distance.

Selective deposition and self-assembly of triblock copolymers into matrix arrays for membrane protein production.

PubMed

Andreasson-Ochsner, Mirjam; Fu, Zhikang; May, Sylvia; Xiu, Low Ying; Nallani, Madhavan; Sinner, Eva-Kathrin

2012-01-31

To improve the stability of cell membrane mimics, there has been growing interest in the use of block copolymers. Here, we present an easy approach to create an array of planar polymeric matrices capable of hosting membrane proteins. The array of polymeric matrices was formed by the selective deposition of triblock copolymers onto an array of hydrophilic islands situated within a hydrophobic background. The thickness of these matrices corresponds to the length of a single polymer chain. These polymeric matrices were used to host cell-free expressed membrane proteins, and offers a prototype from which a membrane protein array can be created for diagnostics or drug discovery purposes. © 2011 American Chemical Society

A linear refractive photovoltaic concentrator solar array flight experiment

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

Jones, P.A.; Murphy, D.M.; Piszczor, M.F.

1995-12-31

Concentrator arrays deliver a number of generic benefits for space including high array efficiency, protection from space radiation effects, and minimized plasma interactions. The line focus concentrator concept delivers two added advantages: (1) low-cost mass production of the lens material and, (2) relaxation of precise array tracking requirements to only a single axis. New array designs emphasize lightweight, high stiffness, stow-ability and ease of manufacture and assembly. The linear refractive concentrator can be designed to provide an essentially flat response over a wide range of longitudinal pointing errors for satellites having only single-axis tracking capability. In this paper the authorsmore » address the current status of the SCARLET linear concentrator program with special emphasis on hardware development of an array-level linear refractive concentrator flight experiment. An aggressive, 6-month development and flight validation program, sponsored by the Ballistic Missile Defense Organization (BMDO) and NASA Lewis Research Center, will quantify and verify SCARLET benefits with in-orbit performance measurements.« less

Adaptive antenna arrays for weak interfering signals. [in satellite communication

NASA Technical Reports Server (NTRS)

Gupta, I. J.; Ksienski, A. A.

1986-01-01

It is shown that conventional adaptive arrays are unable to suppress weak interfering signals. To overcome this problem, the feedback loops controlling the array weights were modified, reducing the noise level by reducing the correlation between the noise components of the two inputs to the loop correlator. Various techniques to decorrelate these noise components are discussed. An expression is derived for the amount of noise decorrelation required to achieve a specified interference suppression. The results are of interest in connection with satellite communications.

Target-based coherent beam combining of an optical phased array fed by a broadband laser source

NASA Astrophysics Data System (ADS)

Hyde, Milo W., IV; McCrae, Jack E.; Tyler, Glenn A.

2017-11-01

The target-based phasing of an optical phased array (OPA) fed by a broadband master oscillator laser source is investigated. The specific scenario examined here considers an OPA phasing through atmospheric turbulence on a rough curved object. An analytical expression for the detected or received intensity is derived. Gleaned from this expression are the conditions under which target-based phasing is possible. A detailed OPA wave optics simulation is performed to validate the theoretical findings. Key aspects of the simulation set-up as well as the results are thoroughly discussed.

Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

USDA-ARS?s Scientific Manuscript database

A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification o...

Micro-Expression Recognition Using Color Spaces.

PubMed

Wang, Su-Jing; Yan, Wen-Jing; Li, Xiaobai; Zhao, Guoying; Zhou, Chun-Guang; Fu, Xiaolan; Yang, Minghao; Tao, Jianhua

2015-12-01

Micro-expressions are brief involuntary facial expressions that reveal genuine emotions and, thus, help detect lies. Because of their many promising applications, they have attracted the attention of researchers from various fields. Recent research reveals that two perceptual color spaces (CIELab and CIELuv) provide useful information for expression recognition. This paper is an extended version of our International Conference on Pattern Recognition paper, in which we propose a novel color space model, tensor independent color space (TICS), to help recognize micro-expressions. In this paper, we further show that CIELab and CIELuv are also helpful in recognizing micro-expressions, and we indicate why these three color spaces achieve better performance. A micro-expression color video clip is treated as a fourth-order tensor, i.e., a four-dimension array. The first two dimensions are the spatial information, the third is the temporal information, and the fourth is the color information. We transform the fourth dimension from RGB into TICS, in which the color components are as independent as possible. The combination of dynamic texture and independent color components achieves a higher accuracy than does that of RGB. In addition, we define a set of regions of interests (ROIs) based on the facial action coding system and calculated the dynamic texture histograms for each ROI. Experiments are conducted on two micro-expression databases, CASME and CASME 2, and the results show that the performances for TICS, CIELab, and CIELuv are better than those for RGB or gray.

Compressed Symmetric Nested Arrays and Their Application for Direction-of-Arrival Estimation of Near-Field Sources.

PubMed

Li, Shuang; Xie, Dongfeng

2016-11-17

In this paper, a new sensor array geometry, called a compressed symmetric nested array (CSNA), is designed to increase the degrees of freedom in the near field. As its name suggests, a CSNA is constructed by getting rid of some elements from two identical nested arrays. The closed form expressions are also presented for the sensor locations and the largest degrees of freedom obtainable as a function of the total number of sensors. Furthermore, a novel DOA estimation method is proposed by utilizing the CSNA in the near field. By employing this new array geometry, our method can identify more sources than sensors. Compared with other existing methods, the proposed method achieves higher resolution because of increased array aperture. Simulation results are demonstrated to verify the effectiveness of the proposed method.

Status On Multi-microsecond Prepulse Technique On Sphinx Machine Going From Nested To Single Wire Array For 800 ns Implosion Time Z-pinch

NASA Astrophysics Data System (ADS)

Maury, P.; Calamy, H.; Grunenwald, J.; Lassalle, F.; Zucchini, F.; Loyen, A.; Georges, A.; Morell, A.; Bedoch, J. P.

2009-01-01

The Sphinx machine[1] is a 6 MA, 1 μS driver based on the LTD technology, used for Z-pinch experiments. Important improvements of Sphinx radiation output were recently obtained using a multi-microsecond current prepulse[2]. Total power per unit of length is multiplied by a factor of 6 and FWHM divided by a factor of 2.5. Early breakdown of the wires during the prepulse phase dramatically changes the ablation phase leading to an improvement of axial homogeneity of both the implosion and the final radiating column. As a consequence, the cathode bubble observed on classical shots is definitively removed. The implosion is then centered and zippering effect is reduced, leading to simultaneous x-ray emission of the whole length. A great reproducibility is obtained. Nested arrays were used before to mitigate the Rayleigh-Taylor instabilities during the implosion phase. Further experiments with pre-pulse technique are described here were inner array was removed. The goal of these experiments was to see if long prepulse could give stable enough implosion with single array and at the same time increase the η parameter by reducing the mass of the load. Experimental results of single wire array loads of typical dimension 5 cm in height with implosion time between 700 and 900 ns and diameter varying between 80 and 140 mm are given. Parameters of the loads were varying in term of radius and number of wires. Comparisons with nested wire array loads are done and trends are proposed. Characteristics of both the implosion and the final radiating column are shown. 2D MHD numerical simulations of single wire array become easier as there is no interaction between outer and inner array anymore. A systematic study was done using injection mass model to benchmark simulation with experiments.

MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation

PubMed Central

Zubakov, Dmitry; Boersma, Anton W. M.; Choi, Ying; van Kuijk, Patricia F.; Wiemer, Erik A. C.

2010-01-01

MicroRNAs (miRNAs) are non-protein coding molecules with important regulatory functions; many have tissue-specific expression patterns. Their very small size in principle makes them less prone to degradation processes, unlike messenger RNAs (mRNAs), which were previously proposed as molecular tools for forensic body fluid identification. To identify suitable miRNA markers for forensic body fluid identification, we first screened total RNA samples derived from saliva, semen, vaginal secretion, and venous and menstrual blood for the expression of 718 human miRNAs using a microarray platform. All body fluids could be easily distinguished from each other on the basis of complete array-based miRNA expression profiles. Results from quantitative reverse transcription PCR (RT-PCR; TaqMan) assays for microarray candidate markers confirmed strong over-expression in the targeting body fluid of several miRNAs for venous blood and several others for semen. However, no candidate markers from array experiments for other body fluids such as saliva, vaginal secretion, or menstrual blood could be confirmed by RT-PCR. Time-wise degradation of venous blood and semen stains for at least 1 year under lab conditions did not significantly affect the detection sensitivity of the identified miRNA markers. The detection limit of the TaqMan assays tested for selected venous blood and semen miRNA markers required only subpicogram amounts of total RNA per single RT-PCR test, which is considerably less than usually needed for reliable mRNA RT-PCR detection. We therefore propose the application of several stable miRNA markers for the forensic identification of blood stains and several others for semen stain identification, using commercially available TaqMan assays. Additional work remains necessary in search for suitable miRNA markers for other forensically relevant body fluids. Electronic supplementary material The online version of this article (doi:10.1007/s00414-009-0402-3) contains supplementary material, which is available to authorized users. PMID:20145944

Patterning nanowire and micro-nanoparticle array on micropillar-structured surface: Experiment and modeling.

PubMed

Lin, Chung Hsun; Guan, Jingjiao; Chau, Shiu Wu; Chen, Shia Chung; Lee, L James

2010-08-04

DNA molecules in a solution can be immobilized and stretched into a highly ordered array on a solid surface containing micropillars by molecular combing technique. However, the mechanism of this process is not well understood. In this study, we demonstrated the generation of DNA nanostrand array with linear, zigzag, and fork-zigzag patterns and the microfluidic processes are modeled based on a deforming body-fitted grid approach. The simulation results provide insights for explaining the stretching, immobilizing, and patterning of DNA molecules observed in the experiments.

Modal processing for acoustic communications in shallow water experiment.

PubMed

Morozov, Andrey K; Preisig, James C; Papp, Joseph

2008-09-01

Acoustical array data from the Shallow Water Acoustics experiment was processed to show the feasibility of broadband mode decomposition as a preprocessing method to reduce the effective channel delay spread and concentrate received signal energy in a small number of independent channels. The data were collected by a vertical array designed at the Woods Hole Oceanographic Institution. Phase-shift Keying (PSK) m-sequence modulated signals with different carrier frequencies were transmitted at a distance 19.2 km from the array. Even during a strong internal waves activity a low bit error rate was achieved.

Microtubule reorganization in tobacco BY-2 cells stably expressing GFP-MBD

NASA Technical Reports Server (NTRS)

Granger, C. L.; Cyr, R. J.

2000-01-01

Microtubule organization plays an important role in plant morphogenesis; however, little is known about how microtubule arrays transit from one organized state to another. The use of a genetically incorporated fluorescent marker would allow long-term observation of microtubule behavior in living cells. Here, we have characterized a Nicotiana tabacum L. cv. Bright Yellow 2 (BY-2) cell line that had been stably transformed with a gfp-mbd construct previously demonstrated to label microtubules (J. Marc et al., 1998, Plant Cell 10: 1927-1939). Fluorescence levels were low, but interphase and mitotic microtubule arrays, as well as the transitions between these arrays, could be observed in individual gfp-mbd-transformed cells. By comparing several attributes of transformed and untransformed cells it was concluded that the transgenic cells are not adversely affected by low-level expression of the transgene and that these cells will serve as a useful and accurate model system for observing microtubule reorganization in vivo. Indeed, some initial observations were made that are consistent with the involvement of motor proteins in the transition between the spindle and phragmoplast arrays. Our observations also support the role of the perinuclear region in nucleating microtubules at the end of cell division with a progressive shift of these microtubules and/or nucleating activity to the cortex to form the interphase cortical array.

GCaMP expression in retinal ganglion cells characterized using a low-cost fundus imaging system

NASA Astrophysics Data System (ADS)

Chang, Yao-Chuan; Walston, Steven T.; Chow, Robert H.; Weiland, James D.

2017-10-01

Objective. Virus-transduced, intracellular-calcium indicators are effective reporters of neural activity, offering the advantage of cell-specific labeling. Due to the existence of an optimal time window for the expression of calcium indicators, a suitable tool for tracking GECI expression in vivo following transduction is highly desirable. Approach. We developed a noninvasive imaging approach based on a custom-modified, low-cost fundus viewing system that allowed us to monitor and characterize in vivo bright-field and fluorescence images of the mouse retina. AAV2-CAG-GCaMP6f was injected into a mouse eye. The fundus imaging system was used to measure fluorescence at several time points post injection. At defined time points, we prepared wholemount retina mounted on a transparent multielectrode array and used calcium imaging to evaluate the responsiveness of retinal ganglion cells (RGCs) to external electrical stimulation. Main results. The noninvasive fundus imaging system clearly resolves individual (RGCs and axons. RGC fluorescence intensity and the number of observable fluorescent cells show a similar rising trend from week 1 to week 3 after viral injection, indicating a consistent increase of GCaMP6f expression. Analysis of the in vivo fluorescence intensity trend and in vitro neurophysiological responsiveness shows that the slope of intensity versus days post injection can be used to estimate the optimal time for calcium imaging of RGCs in response to external electrical stimulation. Significance. The proposed fundus imaging system enables high-resolution digital fundus imaging in the mouse eye, based on off-the-shelf components. The long-term tracking experiment with in vitro calcium imaging validation demonstrates the system can serve as a powerful tool monitoring the level of genetically-encoded calcium indicator expression, further determining the optimal time window for following experiment.

Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.

PubMed

Ling, Zhi-Qiang; Wang, Yi; Mukaisho, Kenichi; Hattori, Takanori; Tatsuta, Takeshi; Ge, Ming-Hua; Jin, Li; Mao, Wei-Min; Sugihara, Hiroyuki

2010-06-01

Tests of differentially expressed genes (DEGs) from microarray experiments are based on the null hypothesis that genes that are irrelevant to the phenotype/stimulus are expressed equally in the target and control samples. However, this strict hypothesis is not always true, as there can be several transcriptomic background differences between target and control samples, including different cell/tissue types, different cell cycle stages and different biological donors. These differences lead to increased false positives, which have little biological/medical significance. In this article, we propose a statistical framework to identify DEGs between target and control samples from expression microarray data allowing transcriptomic background differences between these samples by introducing a modified null hypothesis that the gene expression background difference is normally distributed. We use an iterative procedure to perform robust estimation of the null hypothesis and identify DEGs as outliers. We evaluated our method using our own triplicate microarray experiment, followed by validations with reverse transcription-polymerase chain reaction (RT-PCR) and on the MicroArray Quality Control dataset. The evaluations suggest that our technique (i) results in less false positive and false negative results, as measured by the degree of agreement with RT-PCR of the same samples, (ii) can be applied to different microarray platforms and results in better reproducibility as measured by the degree of DEG identification concordance both intra- and inter-platforms and (iii) can be applied efficiently with only a few microarray replicates. Based on these evaluations, we propose that this method not only identifies more reliable and biologically/medically significant DEG, but also reduces the power-cost tradeoff problem in the microarray field. Source code and binaries freely available for download at http://comonca.org.cn/fdca/resources/softwares/deg.zip.

A novel interaction of PAK4 with PPARγ to regulate Nox1 and radiation-induced epithelial-to-mesenchymal transition in glioma.

PubMed

Kesanakurti, D; Maddirela, D; Banasavadi-Siddegowda, Y K; Lai, T-H; Qamri, Z; Jacob, N K; Sampath, D; Mohanam, S; Kaur, B; Puduvalli, V K

2017-09-14

Tumor recurrence in glioblastoma (GBM) is, in part, attributed to increased epithelial-to-mesenchymal transition (EMT) and enhanced tumor cell dissemination in adjacent brain parenchyma after ionizing radiation (IR). EMT is associated with aggressive behavior, increased stem-like characteristics and treatment resistance in malignancies; however, the underlying signaling mechanisms that regulate EMT are poorly understood. We identified grade-dependent p21-activated kinases 4 (PAK4) upregulation in gliomas and further determined its role in mesenchymal transition and radioresistance. IR treatment significantly elevated expression and nuclear localization of PAK4 in correlation with induction of reactive oxygen species (ROS) and mesenchymal transition in GBM cells. Stable PAK4 overexpression promoted mesenchymal transition by elevating EMT marker expression in these cells. Of note, transcription factor-DNA-binding arrays and chromatin immunoprecipitation experiments identified the formation of a novel nuclear PAK4/PPARγ complex which was recruited to the promoter of Nox1, a peroxisome proliferator-activated receptor gamma (PPARγ) target gene. In addition, IR further elevated PAK4/PPARγ complex co-recruitment to Nox1 promoter, and increased Nox1 expression and ROS levels associated with mesenchymal transition in these cells. Conversely, specific PAK4 downregulation decreased PPARγ-mediated Nox1 expression and suppressed EMT in IR-treated cells. In vivo orthotopic tumor experiments showed inhibition of growth and suppression of IR-induced PPARγ and Nox1 expression by PAK4 downregulation in tumors. Our results provide the first evidence of a novel role for PAK4 in IR-induced EMT and suggest potential therapeutic efficacy of targeting PAK4 to overcome radioresistance in gliomas.

Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome.

PubMed

Tothill, Richard W; Tinker, Anna V; George, Joshy; Brown, Robert; Fox, Stephen B; Lade, Stephen; Johnson, Daryl S; Trivett, Melanie K; Etemadmoghadam, Dariush; Locandro, Bianca; Traficante, Nadia; Fereday, Sian; Hung, Jillian A; Chiew, Yoke-Eng; Haviv, Izhak; Gertig, Dorota; DeFazio, Anna; Bowtell, David D L

2008-08-15

The study aim to identify novel molecular subtypes of ovarian cancer by gene expression profiling with linkage to clinical and pathologic features. Microarray gene expression profiling was done on 285 serous and endometrioid tumors of the ovary, peritoneum, and fallopian tube. K-means clustering was applied to identify robust molecular subtypes. Statistical analysis identified differentially expressed genes, pathways, and gene ontologies. Laser capture microdissection, pathology review, and immunohistochemistry validated the array-based findings. Patient survival within k-means groups was evaluated using Cox proportional hazards models. Class prediction validated k-means groups in an independent dataset. A semisupervised survival analysis of the array data was used to compare against unsupervised clustering results. Optimal clustering of array data identified six molecular subtypes. Two subtypes represented predominantly serous low malignant potential and low-grade endometrioid subtypes, respectively. The remaining four subtypes represented higher grade and advanced stage cancers of serous and endometrioid morphology. A novel subtype of high-grade serous cancers reflected a mesenchymal cell type, characterized by overexpression of N-cadherin and P-cadherin and low expression of differentiation markers, including CA125 and MUC1. A poor prognosis subtype was defined by a reactive stroma gene expression signature, correlating with extensive desmoplasia in such samples. A similar poor prognosis signature could be found using a semisupervised analysis. Each subtype displayed distinct levels and patterns of immune cell infiltration. Class prediction identified similar subtypes in an independent ovarian dataset with similar prognostic trends. Gene expression profiling identified molecular subtypes of ovarian cancer of biological and clinical importance.

Molecular pathology of acute kidney injury in a choline-deficient model and fish oil protective effect.

PubMed

Denninghoff, Valeria; Ossani, Georgina; Uceda, Ana; Rugnone, Matias; Fernández, Elmer; Fresno, Cristóbal; González, German; Díaz, Maria Luisa; Avagnina, Alejandra; Elsner, Boris; Monserrat, Alberto

2014-04-01

The aim of this work was to investigate the potential protective effects of fish oil on the basis of kidney transcriptomic data on a nutritional experimental model. Male weanling Wistar rats were divided into four groups and fed choline-deficient (CD) and choline-supplemented (CS) diets with vegetable oil (VO) and menhaden oil (MO): CSVO, CDVO, CSMO and CDMO. Animals were killed after receiving the diets for 6 days. Total RNA was purified from the right kidney and hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array. Differentially expressed genes were analyzed. All CSVO, CSMO and CDMO rats showed no renal alterations, while all CDVO rats showed renal cortical necrosis. A thorough analysis of the differential expression between groups CSMO and CDMO was carried out. There were no differential genes for p < 0.01. The analysis of the differential expression between groups CSVO and CSMO revealed 32 genes, 11 were over-expressed and 21 were under-expressed in CSMO rats. This work was part of a large set of experiments and was used in a hypothesis-generating manner. The comprehensive analysis of genetic expression allowed confirming that menhaden oil has a protective effect on this nutritional experimental model and identifying 32 genes that could be responsible for that protection, including Gstp1. These results reveal that gene changes could play a role in renal injury.

Gene expression profiling of single cells on large-scale oligonucleotide arrays

PubMed Central

Hartmann, Claudia H.; Klein, Christoph A.

2006-01-01

Over the last decade, important insights into the regulation of cellular responses to various stimuli were gained by global gene expression analyses of cell populations. More recently, specific cell functions and underlying regulatory networks of rare cells isolated from their natural environment moved to the center of attention. However, low cell numbers still hinder gene expression profiling of rare ex vivo material in biomedical research. Therefore, we developed a robust method for gene expression profiling of single cells on high-density oligonucleotide arrays with excellent coverage of low abundance transcripts. The protocol was extensively tested with freshly isolated single cells of very low mRNA content including single epithelial, mature and immature dendritic cells and hematopoietic stem cells. Quantitative PCR confirmed that the PCR-based global amplification method did not change the relative ratios of transcript abundance and unsupervised hierarchical cluster analysis revealed that the histogenetic origin of an individual cell is correctly reflected by the gene expression profile. Moreover, the gene expression data from dendritic cells demonstrate that cellular differentiation and pathway activation can be monitored in individual cells. PMID:17071717

TOXICOGENOMICS AND HUMAN DISEASE RISK ASSESSMENT

EPA Science Inventory

Toxicogenomics and Human Disease Risk Assessment.

Complete sequencing of human and other genomes, availability of large-scale gene
expression arrays with ever-increasing numbers of genes displayed, and steady
improvements in protein expression technology can hav...

Cryogenic Design of the Setup for MARE-1 in Milan

NASA Astrophysics Data System (ADS)

Schaeffer, D.; Arnaboldi, C.; Ceruti, G.; Ferri, E.; Kilbourne, C.; Kraft-Bermuth, S.; Margesin, B.; McCammon, D.; Monfardini, A.; Nucciotti, A.; Pessina, G.; Previtali, E.; Sisti, M.

2008-05-01

A large worldwide collaboration is growing around the project of Micro-calorimeter Arrays for a Rhenium Experiment (MARE) for a direct calorimetric measurement of the neutrino mass. To validate the use of cryogenic detectors by checking the presence of unexpected systematic errors, two first experiments are planned using the available techniques composed of arrays of 300 detectors to measure 1010 events in a reasonable time of 3 years (step MARE-1) to reach a sensitivity on the neutrino mass of ˜2 eV/c2. Our experiment in Milan is based on compensated doped silicon implanted thermistor arrays made in NASA/GSFC and on AgReO4 crystals. We present here the design of the cryogenic system that integrates all the requirements for such experiment (electronics for high impedances, low parasitic capacitances, low micro-phonic noise).

Stacked, Filtered Multi-Channel X-Ray Diode Array

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

MacNeil, Lawrence P.; Dutra, Eric C.; Raphaelian, Mark

2015-08-01

This system meets the need for a low-cost, robust X-ray diode array to use for experiments in hostile environments on multiple platforms, and for experiments utilizing forces that may destroy the diode(s). Since these uses require a small size with a minimal single line-of-sight, a parallel array often cannot be used. So a stacked, filtered multi-channel X-ray diode array was developed that was called the MiniXRD. The design was modeled, built, and tested at National Security Technologies, LLC (NSTec) Livermore Operations (LO) to determine fundamental characteristics. Then, several different systems were fielded as ancillary “ridealong” diagnostics at several national facilitiesmore » to allow us to iteratively improve the design and usability. Presented here are design considerations and experimental results. This filtered diode array is currently at Technical Readiness Level (TRL) 6.« less

Preliminary results from the flight of the Solar Array Module Plasma Interactions Experiment (SAMPIE)

NASA Technical Reports Server (NTRS)

Ferguson, Dale C.; Hillard, G. Barry

1994-01-01

SAMPIE, the Solar Array Module Plasma Interactions Experiment, flew in the Space Shuttle Columbia payload bay as part of the Office of Aeronautics and Space Technology-2 (OAST-2) mission on STS-62, March, 1994. SAMPIE biased samples of solar arrays and space power materials to varying potentials with respect to the surrounding space plasma, and recorded the plasma currents collected and the arcs which occurred, along with a set of plasma diagnostics data. A large set of high quality data was obtained on the behavior of solar arrays and space power materials in the space environment. This paper is the first report on the data SAMPIE telemetered to the ground during the mission. It will be seen that the flight data promise to help determine arcing thresholds, snapover potentials, and floating potentials for arrays and spacecraft in LEO.

Design of a dual sensor probe array for internal field measurement in Versatile Experiment Spherical Torusa)

NASA Astrophysics Data System (ADS)

Jeong-hun, Yang; Chung, Kyoung-Jae; An, YoungHwa; Jung, Bong Ki; Jo, Jong Gab; Hwang, Y. S.

2012-10-01

A dual sensor probe array is designed and constructed for internal magnetic field measurement at Versatile Experiment Spherical Torus (VEST) at the Seoul National University. Simultaneous use of Hall sensors and chip inductors allows cross-calibration among the measurements and compensation for each other's weaknesses while their small sizes are expected to cause only mild plasma perturbations. Calibration of the dual sensor probe array, using a Helmholtz coil, shows good sensitivity for the magnetic field measurement of the VEST. Prior to Ohmic start-up, the magnetic field structure inside the vacuum chamber is measured by using the calibrated probe array. The dual sensor probe array is expected to be useful in analyzing the temporal magnetic field structure change during the magnetic reconnection and in reconstruction of the current profile during the discharge of the VEST device.

Vortex motion and dynamical states in Josephson arrays

NASA Astrophysics Data System (ADS)

Trias, Enrique

Underdamped Josephson junction arrays are used as model systems to study novel nonlinear effects. A combination of experiments, numerical simulations, and analytical analysis is used to probe different nonlinear behavior such as intrinsic localized modes, resonances in fully frustrated arrays, Meissner-like states, and vortex ratchets. Circuit models of Josephson networks are also developed, and applied to the design and measurement of parallel array oscillators. Ladder arrays have been used for an experimental study of intrinsic localized modes, or discrete breathers. Measurements of breather stability indicate that the maximum allowable bias current is proportional to the array depinning current while the minimum current is related to a junction retrapping mechanism. This retrapping instability usually leads to the formation of multi-site breathers. Collisions between the two nonlinear excitations in ladder arrays, discrete breathers and vortices, have also been numerically investigated. Discrete breathers act as pinning centers to vortex motion and the collisions can be modeled by an energy barrier activation process. When vortices are thermally induced over this barrier, a two-site breather is created. Experiments also reveal remarkable similarities among the do current-voltage characteristics of several kinds of square and triangular arrays, where two resonant voltages are observed. Simulations indicate that at full frustration a dynamical checkerboard state underlies these similarities. For such a traveling solution, the governing equations of the arrays are reduced to three coupled pendulum equations that have two characteristic resonant frequencies. Finally, a kink ratchet potential has been designed using a parallel array of Josephson junctions with alternating cell inductances and junctions areas. Experiments show that the depinning current depends on the direction of the applied current. Other properties of the depinning current versus applied field, such as a long period and a lack of reflection symmetry, have been observed and explained analytically. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139- 4307. Ph. 617-253-5668; Fax 617-253-1690.)

Measurement of Fluctuations in the Tilt of Arctic Ice at the Cearex Oceanography Camp: Experiment Review, Data Catalog and Preliminary Results

DTIC Science & Technology

1989-09-01

enables a study of the internal wave field simultaneously using tiltmeters , strainmeters, and oceanographic sensors . It offers the chance to determine...Williams, personal communication]. Their sensors include a bubble level tiltmeter installed near the instrument hut, as well as a triangular array of...Plan Three sensor arrays are deployed near each other, as shown in Figure 2.3: our tiltmeter array, the SPRI strainmeter array, and the array of moored

Status of the NOAO evaluation of the Hughes 20x64 Si:As impurity band conduction array. [for ground and space-based astronomy

NASA Technical Reports Server (NTRS)

Fowler, A. M.; Joyce, R. R.

1990-01-01

The Hughes 20 x 64 Si:As impurity band conduction arrays designed for ground-based and spaceborne astronomy observations is described together with experiments performed at NOAO to test these arrays. Special attention is given to the design and the characteristics of the test system and to the test methods. The initial tests on two columns of one array indicate that the array is easy to operate and performed satisfactorily.

Serine, Glycine and One-carbon Metabolism in Colorectal Cancer Cell in Heterogeneous Microenvironment

NASA Astrophysics Data System (ADS)

Lin, Ke-Chih; Austin, Robert; Ducker, Greg; Sturm, James; Sturm, James

The up-regulation of serine metabolism associated with one-carbon metabolism has been identified to support cellular biosynthesis and redox maintenance of tumors. The consistently over-expressed one-carbon genes have been targeted for potential drug development. To investigate the biological function of specific enzymes, we had genetic engineered HCT116 cell lines, methylenetetrahydrofolate dehydrogenase (MTHFD) and phosphoglycerate dehydrogenase (PHGDH) deleted cell lines, growing in the artificial microhabitats array with serine and glycine gradient across. The impact of depletion of serine and the blocking of biosynthesis pathway will be shown in terms of cell morphology, proliferation rate, and cell motility. The evolution dynamic and migration rate can also be tracked throughout the experiments.

Ultra-sparse dielectric nanowire grids as wideband reflectors and polarizers.

PubMed

Yoon, Jae Woong; Lee, Kyu Jin; Magnusson, Robert

2015-11-02

Engaging both theory and experiment, we investigate resonant photonic lattices in which the duty cycle tends to zero. Corresponding dielectric nanowire grids are mostly empty space if operated as membranes in vacuum or air. These grids are shown to be effective wideband reflectors with impressive polarizing properties. We provide computed results predicting nearly complete reflection and attendant polarization extinction in multiple spectral regions. Experimental results with Si nanowire arrays with 10% duty cycle show ~200-nm-wide band of high reflection for one polarization state and free transmission for the orthogonal state. These results agree quantitatively with theoretical predictions. It is fundamentally extremely significant that the wideband spectral expressions presented can be generated in these minimal systems.

Studies of encapsulant materials for terrestrial solar-cell arrays

NASA Technical Reports Server (NTRS)

Carmichael, D. C. (Compiler)

1975-01-01

Study 1 of this contract is entitled ""Evaluation of World Experience and Properties of Materials for Encapsulation of Terrestrial Solar-Cell Arrays.'' The approach of this study is to review and analyze world experience and to compile data on properties of encapsulants for photovoltaic cells and for related applications. The objective of the effort is to recommend candidate materials and processes for encapsulating terrestrial photovoltaic arrays at low cost for a service life greater than 20 years. The objectives of Study 2, ""Definition of Encapsulant Service Environments and Test Conditions,'' are to develop the climatic/environmental data required to define the frequency and duration of detrimental environmental conditions in a 20-year array lifetime and to develop a corresponding test schedule for encapsulant systems.

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

NASA Technical Reports Server (NTRS)

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.;

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

NASA Astrophysics Data System (ADS)

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.

Highlights from the Telescope Array Experiment

NASA Astrophysics Data System (ADS)

Sagawa, H.

2014-10-01

The Telescope Array (TA) is the largest experiment in the Northern Hemisphere currently studying the origin and nature of ultra-high-energy cosmic rays above ˜1018 eV by measuring their energy spectrum, mass composition, and arrival directions. It is located in the western desert of central Utah, USA. The TA detector consists of a surface array of 507 scintillation counters, deployed on a square grid of 1.2-km spacing that covers approximately 700 km2, and 38 fluorescence telescopes located at three sites looking over the surface array. The TA commenced hybrid observation with both sets of detectors in 2008. Here, we present recent results from these 5 years of data and outline our ongoing and near future plans.

Imaging with hypertelescopes: a simple modal approach

NASA Astrophysics Data System (ADS)

Aime, C.

2008-05-01

Aims: We give a simple analysis of imaging with hypertelescopes, a technique proposed by Labeyrie to produce snapshot images using arrays of telescopes. The approach is modal: we describe the transformations induced by the densification onto a sinusoidal decomposition of the focal image instead of the usual point spread function approach. Methods: We first express the image formed at the focus of a diluted array of apertures as the product R_0(α) X_F(α) of the diffraction pattern of the elementary apertures R_0(α) by the object-dependent interference term X_F(α) between all apertures. The interference term, which can be written in the form of a Fourier Series for an extremely diluted array, produces replications of the object, which makes observing the image difficult. We express the focal image after the densification using the approach of Tallon and Tallon-Bosc. Results: The result is very simple for an extremely diluted array. We show that the focal image in a periscopic densification of the array can be written as R_0(α) X_F(α/γ), where γ is the factor of densification. There is a dilatation of the interference term while the diffraction term is unchanged. After de-zooming, the image can be written as γ2 X_F(α)R_0(γ α), an expression which clearly indicates that the final image corresponds to the center of the Fizeau image intensified by γ2. The imaging limitations of hypertelescopes are therefore those of the original configuration. The effect of the suppression of image replications is illustrated in a numerical simulation for a fully redundant configuration and a non-redundant one.

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

PubMed

Vathipadiekal, Vinod; Wang, Victoria; Wei, Wei; Waldron, Levi; Drapkin, Ronny; Gillette, Michael; Skates, Steven; Birrer, Michael

2015-11-01

To generate a comprehensive "Secretome" of proteins potentially found in the blood and derive a virtual Affymetrix array. To validate the utility of this database for the discovery of novel serum-based biomarkers using ovarian cancer transcriptomic data. The secretome was constructed by aggregating the data from databases of known secreted proteins, transmembrane or membrane proteins, signal peptides, G-protein coupled receptors, or proteins existing in the extracellular region, and the virtual array was generated by mapping them to Affymetrix probeset identifiers. Whole-genome microarray data from ovarian cancer, normal ovarian surface epithelium, and fallopian tube epithelium were used to identify transcripts upregulated in ovarian cancer. We established the secretome from eight public databases and a virtual array consisting of 16,521 Affymetrix U133 Plus 2.0 probesets. Using ovarian cancer transcriptomic data, we identified candidate blood-based biomarkers for ovarian cancer and performed bioinformatic validation by demonstrating rediscovery of known biomarkers including CA125 and HE4. Two novel top biomarkers (FGF18 and GPR172A) were validated in serum samples from an independent patient cohort. We present the secretome, comprising the most comprehensive resource available for protein products that are potentially found in the blood. The associated virtual array can be used to translate gene-expression data into cancer biomarker discovery. A list of blood-based biomarkers for ovarian cancer detection is reported and includes CA125 and HE4. FGF18 and GPR172A were identified and validated by ELISA as being differentially expressed in the serum of ovarian cancer patients compared with controls. ©2015 American Association for Cancer Research.

Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer.

PubMed

Kündig, Pascale; Giesen, Charlotte; Jackson, Hartland; Bodenmiller, Bernd; Papassotirolopus, Bärbel; Freiberger, Sandra Nicole; Aquino, Catharine; Opitz, Lennart; Varga, Zsuzsanna

2018-05-08

Intra-tumoral heterogeneity has been recently addressed in different types of cancer, including breast cancer. A concept describing the origin of intra-tumoral heterogeneity is the cancer stem-cell hypothesis, proposing the existence of cancer stem cells that can self-renew limitlessly and therefore lead to tumor progression. Clonal evolution in accumulated single cell genomic alterations is a further possible explanation in carcinogenesis. In this study, we addressed the question whether intra-tumoral heterogeneity can be reliably detected in tissue-micro-arrays in breast cancer by comparing expression levels of conventional predictive/prognostic tumor markers, tumor progression markers and stem cell markers between central and peripheral tumor areas. We analyzed immunohistochemical expression and/or gene amplification status of conventional prognostic tumor markers (ER, PR, HER2, CK5/6), tumor progression markers (PTEN, PIK3CA, p53, Ki-67) and stem cell markers (mTOR, SOX2, SOX9, SOX10, SLUG, CD44, CD24, TWIST) in 372 tissue-micro-array samples from 72 breast cancer patients. Expression levels were compared between central and peripheral tumor tissue areas and were correlated to histopathological grading. 15 selected cases additionally underwent RNA sequencing for transcriptome analysis. No significant difference in any of the analyzed between central and peripheral tumor areas was seen with any of the analyzed methods/or results that showed difference. Except mTOR, PIK3CA and SOX9 (nuclear) protein expression, all markers correlated significantly (p < 0.05) with histopathological grading both in central and peripheral areas. Our results suggest that intra-tumoral heterogeneity of stem-cell and tumor-progression markers cannot be reliably addressed in tissue-micro-array samples in breast cancer. However, most markers correlated strongly with histopathological grading confirming prognostic information as expression profiles were independent on the site of the biopsy was taken.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients.

PubMed

Schlick, Bettina; Massoner, Petra; Lueking, Angelika; Charoentong, Pornpimol; Blattner, Mirjam; Schaefer, Georg; Marquart, Klaus; Theek, Carmen; Amersdorfer, Peter; Zielinski, Dirk; Kirchner, Matthias; Trajanoski, Zlatko; Rubin, Mark A; Müllner, Stefan; Schulz-Knappe, Peter; Klocker, Helmut

2016-01-01

Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens. Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology. Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076). We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation.

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients

PubMed Central

Schlick, Bettina; Massoner, Petra; Lueking, Angelika; Charoentong, Pornpimol; Blattner, Mirjam; Schaefer, Georg; Marquart, Klaus; Theek, Carmen; Amersdorfer, Peter; Zielinski, Dirk; Kirchner, Matthias; Trajanoski, Zlatko; Rubin, Mark A.; Müllner, Stefan; Schulz-Knappe, Peter; Klocker, Helmut

2016-01-01

Background Chronic inflammation is frequently observed on histological analysis of malignant and non-malignant prostate specimens. It is a suspected supporting factor for prostate diseases and their progression and a main cause of false positive PSA tests in cancer screening. We hypothesized that inflammation induces autoantibodies, which may be useful biomarkers. We aimed to identify and validate prostate inflammation associated serum autoantibodies in prostate cancer patients and evaluate the expression of corresponding autoantigens. Methods Radical prostatectomy specimens of prostate cancer patients (N = 70) were classified into high and low inflammation groups according to the amount of tissue infiltrating lymphocytes. The corresponding pre-surgery blood serum samples were scrutinized for autoantibodies using a low-density protein array. Selected autoantigens were identified in prostate tissue and their expression pattern analyzed by immunohistochemistry and qPCR. The identified autoantibody profile was cross-checked in an independent sample set (N = 63) using the Luminex-bead protein array technology. Results Protein array screening identified 165 autoantibodies differentially abundant in the serum of high compared to low inflammation patients. The expression pattern of three corresponding antigens were established in benign and cancer tissue by immunohistochemistry and qPCR: SPAST (Spastin), STX18 (Syntaxin 18) and SPOP (speckle-type POZ protein). Of these, SPAST was significantly increased in prostate tissue with high inflammation. All three autoantigens were differentially expressed in primary and/or castration resistant prostate tumors when analyzed in an inflammation-independent tissue microarray. Cross-validation of the inflammation autoantibody profile on an independent sample set using a Luminex-bead protein array, retrieved 51 of the significantly discriminating autoantibodies. Three autoantibodies were significantly upregulated in both screens, MUT, RAB11B and CSRP2 (p>0.05), two, SPOP and ZNF671, close to statistical significance (p = 0.051 and 0.076). Conclusions We provide evidence of an inflammation-specific autoantibody profile and confirm the expression of corresponding autoantigens in prostate tissue. This supports evaluation of autoantibodies as non-invasive markers for prostate inflammation. PMID:26863016

Compression dynamics of quasi-spherical wire arrays with different linear mass profiles

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

Mitrofanov, K. N., E-mail: mitrofan@triniti.ru; Aleksandrov, V. V.; Gritsuk, A. N.

Results of experimental studies of the implosion of quasi-spherical wire (or metalized fiber) arrays are presented. The goal of the experiments was to achieve synchronous three-dimensional compression of the plasma produced in different regions of a quasi-spherical array into its geometrical center. To search for optimal synchronization conditions, quasi-spherical arrays with different initial profiles of the linear mass were used. The following dependences of the linear mass on the poloidal angle were used: m{sub l}(θ) ∝ sin{sup –1}θ and m{sub l}(θ) ∝ sin{sup –2}θ. The compression dynamics of such arrays was compared with that of quasi-spherical arrays without linear massmore » profiling, m{sub l}(θ) = const. To verify the experimental data, the spatiotemporal dynamics of plasma compression in quasi-spherical arrays was studied using various diagnostics. The experiments on three-dimensional implosion of quasi-spherical arrays made it possible to study how the frozen-in magnetic field of the discharge current penetrates into the array. By measuring the magnetic field in the plasma of a quasi-spherical array, information is obtained on the processes of plasma production and formation of plasma flows from the wire/fiber regions with and without an additionally deposited mass. It is found that penetration of the magnetic flux depends on the initial linear mass profile m{sub l}(θ) of the quasi-spherical array. From space-resolved spectral measurements and frame imaging of plasma X-ray emission, information is obtained on the dimensions and shape of the X-ray source formed during the implosion of a quasi-spherical array. The intensity of this source is estimated and compared with that of the Z-pinch formed during the implosion of a cylindrical array.« less

Attention Capture by Faces

ERIC Educational Resources Information Center

Langton, Stephen R. H.; Law, Anna S.; Burton, A. Mike; Schweinberger, Stefan R.

2008-01-01

We report three experiments that investigate whether faces are capable of capturing attention when in competition with other non-face objects. In Experiment 1a participants took longer to decide that an array of objects contained a butterfly target when a face appeared as one of the distracting items than when the face did not appear in the array.…

Progress of the Dust Accumulation and Removal Technology Experiment (DART) for the Mars 2001 Lander

NASA Technical Reports Server (NTRS)

Jenkins, Phillip; Landis, Geoffrey A.; Wilt, David; Krasowski, Michael; Greer, Lawrence; Baraona, Cosmo; Scheiman, David

2005-01-01

Dust deposition could be a significant problem for photovoltaic array operation for long duration missions on the surface of Mars. Measurements made by Pathfinder showed 0.3 percent loss of solar array performance per day due to dust obscuration. We have designed an experiment package, "DART", which is part of the Mars ISPP Precursor (MIP) package, to fly on the Mars-2001 Surveyor Lander. This mission, to launch in April 2001, will arrive on Mars in January 2002. The DART experiment is designed to quantify dust deposition from the Mars atmosphere, measure the properties of settled dust, measure the effect of dust deposition on array performance, and test several methods of clearing dust from solar cells.

The MGED Ontology: a resource for semantics-based description of microarray experiments.

PubMed

Whetzel, Patricia L; Parkinson, Helen; Causton, Helen C; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Game, Laurence; Heiskanen, Mervi; Morrison, Norman; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; White, Joseph; Stoeckert, Christian J

2006-04-01

The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Stoeckrt@pcbi.upenn.edu Supplementary data are available at Bioinformatics online.

Integrated Array/Metadata Analytics

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Baumann, Peter

2015-04-01

Data comes in various forms and types, and integration usually presents a problem that is often simply ignored and solved with ad-hoc solutions. Multidimensional arrays are an ubiquitous data type, that we find at the core of virtually all science and engineering domains, as sensor, model, image, statistics data. Naturally, arrays are richly described by and intertwined with additional metadata (alphanumeric relational data, XML, JSON, etc). Database systems, however, a fundamental building block of what we call "Big Data", lack adequate support for modelling and expressing these array data/metadata relationships. Array analytics is hence quite primitive or non-existent at all in modern relational DBMS. Recognizing this, we extended SQL with a new SQL/MDA part seamlessly integrating multidimensional array analytics into the standard database query language. We demonstrate the benefits of SQL/MDA with real-world examples executed in ASQLDB, an open-source mediator system based on HSQLDB and rasdaman, that already implements SQL/MDA.

SAMPIE Measurements of the Space Station Plasma Current Analyzed

NASA Technical Reports Server (NTRS)

1996-01-01

In March of 1994, STS-62 carried the NASA Lewis Research Center's Solar Array Module Plasma Interactions Experiment (SAMPIE) into orbit, where it investigated the plasma current collected and the arcs from solar arrays and other space power materials immersed in the low-Earth-orbit space plasma. One of the important experiments conducted was the plasma current collected by a four-cell coupon sample of solar array cells for the international space station. The importance of this experiment dates back to the 1990 and 1991 meetings of the Space Station Electrical Grounding Tiger Team. The Tiger Team determined that unless the electrical potentials on the space station structure were actively controlled via a plasma contactor, the space station structure would arc into the plasma at a rate that would destroy the thermal properties of its surface coatings in only a few years of operation. The space station plasma contactor will control its potentials by emitting electrons into the surrounding low-Earth-orbit plasma at the same rate that they are collected by the solar arrays. Thus, the level at which the space station solar arrays can collect current is very important in verifying that the plasma contactor design can do its job.

A new three-dimensional nonscanning laser imaging system based on the illumination pattern of a point-light-source array

NASA Astrophysics Data System (ADS)

Xia, Wenze; Ma, Yayun; Han, Shaokun; Wang, Yulin; Liu, Fei; Zhai, Yu

2018-06-01

One of the most important goals of research on three-dimensional nonscanning laser imaging systems is the improvement of the illumination system. In this paper, a new three-dimensional nonscanning laser imaging system based on the illumination pattern of a point-light-source array is proposed. This array is obtained using a fiber array connected to a laser array with each unit laser having independent control circuits. This system uses a point-to-point imaging process, which is realized using the exact corresponding optical relationship between the point-light-source array and a linear-mode avalanche photodiode array detector. The complete working process of this system is explained in detail, and the mathematical model of this system containing four equations is established. A simulated contrast experiment and two real contrast experiments which use the simplified setup without a laser array are performed. The final results demonstrate that unlike a conventional three-dimensional nonscanning laser imaging system, the proposed system meets all the requirements of an eligible illumination system. Finally, the imaging performance of this system is analyzed under defocusing situations, and analytical results show that the system has good defocusing robustness and can be easily adjusted in real applications.

Crosstalk analyse of DFB fiber laser hydrophone array based on time division multiplexing

NASA Astrophysics Data System (ADS)

Li, Yu; Huang, Junbin; Gu, Hongcan; Tang, Bo; Wu, Jing

2014-12-01

In this paper, the crosstalk of a time division multiplexed (TDM) system of distributed feedback (DFB) fiber laser (FL)hydrophones based on optical switch using Phase Generated Carrier (PGC) method was quantitatively analyzed. After mathematical deduction, the relationship among crosstalk, multiplexing scale and extinction ratio of optical switch was given. The simulation results show that to realize a TDM system of DFB fiber laser hydrophones with crosstalk lower than -40dB, the average extinction ratio should be higher than 24.78dB for a 4- channel system, while higher than 28.45dB for an 8- channel system. Two experiments to analyze the array crosstalk to a certain channel in an 8- channel array were conducted in this paper. Firstly, by testing the powers of leak laser to a certain channel from others, the array crosstalk to this channel was obtained according to the equation mathematically deduced in this paper. The result shows the array crosstalk to a certain channel of the 8-channel array was -7.6dB. An experiment of underwater acoustic detection was carried out finally to get the real array crosstalk to this certain channel, and the experimental result shows that the array crosstalk to this channel is -8.8dB, which is close to the calculated result.

Generation of ultra-fast cumulative water jets by sub-microsecond underwater electrical explosion of conical wire arrays

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

Shafer, D.; Gurovich, V. Tz.; Gleizer, S.

The results of experiments with underwater electrical explosion of modified conical arrays of copper and aluminum wires are presented. A pulsed generator producing a 550 kA-amplitude current with a 400 ns rise time was used in the explosion of the arrays. The array explosion generates water flows converging at the axis of the cone. This flow generates a fast-moving water jet with a velocity exceeding 1.8 × 10{sup 5 }cm/s, which was observed being ejected from the surface of the water covering the array. The positions of the water jet were measured by multiple-exposure fast framing imaging. In experiments, the apex angle of the array,more » the thickness of the water layer above the arrays, or the material of the wires was altered, which changed the resulting velocities and shapes of the emitted jets. A model that considers the converging stationary flow of a slightly compressible fluid is suggested. The velocities and shapes of the jets obtained by this model agree well with the experimentally measured jet velocities.« less

Interference within the focus of attention: working memory tasks reflect more than temporary maintenance.

PubMed

Shipstead, Zach; Engle, Randall W

2013-01-01

One approach to understanding working memory (WM) holds that individual differences in WM capacity arise from the amount of information a person can store in WM over short periods of time. This view is especially prevalent in WM research conducted with the visual arrays task. Within this tradition, many researchers have concluded that the average person can maintain approximately 4 items in WM. The present study challenges this interpretation by demonstrating that performance on the visual arrays task is subject to time-related factors that are associated with retrieval from long-term memory. Experiment 1 demonstrates that memory for an array does not decay as a product of absolute time, which is consistent with both maintenance- and retrieval-based explanations of visual arrays performance. Experiment 2 introduced a manipulation of temporal discriminability by varying the relative spacing of trials in time. We found that memory for a target array was significantly influenced by its temporal compression with, or isolation from, a preceding trial. Subsequent experiments extend these effects to sub-capacity set sizes and demonstrate that changes in the size of k are meaningful to prediction of performance on other measures of WM capacity as well as general fluid intelligence. We conclude that performance on the visual arrays task does not reflect a multi-item storage system but instead measures a person's ability to accurately retrieve information in the face of proactive interference.

A Mid-Latitude Skywave Propagation Experiment: Overview and Results

NASA Astrophysics Data System (ADS)

Munton, D. C.; Calfas, R. S.; Gaussiran, T., II; Rainwater, D.; Flesichmann, A. M.; Schofield, J. R.

2016-12-01

We will describe a mid-latitude HF skywave propagation experiment conducted during 19-27 January, 2014. There were two primary goals to the experiment. First, we wanted to build an understanding of the impact that medium scale traveling ionospheric disturbances have on the angles of arrival of the HF signals. The second goal was to provide a diverse data set that could serve as a baseline for propagation model development and evaluation. We structured individual tests during the experiment to increase the knowledge of temporal and spatial length scales of various ionospheric features. The experiment was conducted during both day and night periods and spanned a wide range of ionospheric states. We conducted the experiment at White Sands Missile Range, New Mexico and in the surrounding area. As part of the experiment, we deployed a number of active HF transmitters, and an array of dipole antennas to provide angle of arrival measurements. We also deployed a smaller array of more novel compact electro-magnetic vector sensors (EMVSs). Other instrumentation specific to the remote sensing of the ionosphere included digisondes, GNSS receivers, beacon satellite receivers, and optical instruments. We will provide a complete description of the experiment configuration and the data products.Finally, we will provide a discussion of experimental results, focusing on ionospheric conditions during the angle-of-arrival determinations, and the impact ionospheric disturbances can have on these measurements. We use the angle-of-arrival determinations to estimate TID properties, including velocity and direction.This research is based upon work supported in part by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), via US Navy Contract N00024-07-D-6200. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of ODNI, IARPA, US Navy, or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation thereon.

Gingival transcriptome patterns during induction and resolution of experimental gingivitis in humans.

PubMed

Offenbacher, Steven; Barros, Silvana P; Paquette, David W; Winston, J Leslie; Biesbrock, Aaron R; Thomason, Ryan G; Gibb, Roger D; Fulmer, Andy W; Tiesman, Jay P; Juhlin, Kenton D; Wang, Shuo L; Reichling, Tim D; Chen, Ker-Sang; Ho, Begonia

2009-12-01

To our knowledge, changes in the patterns of whole-transcriptome gene expression that occur during the induction and resolution of experimental gingivitis in humans were not previously explored using bioinformatic tools. Gingival biopsy samples collected from 14 subjects during a 28-day stent-induced experimental gingivitis model, followed by treatment, and resolution at days 28 through 35 were analyzed using gene-expression arrays. Biopsy samples were collected at different sites within each subject at baseline (day 0), at the peak of gingivitis (day 28), and at resolution (day 35) and processed using whole-transcriptome gene-expression arrays. Gene-expression data were analyzed to identify biologic themes and pathways associated with changes in gene-expression profiles that occur during the induction and resolution of experimental gingivitis using bioinformatic tools. During disease induction and resolution, the dominant expression pathway was the immune response, with 131 immune response genes significantly up- or downregulated during induction, during resolution, or during both at P <0.05. During induction, there was significant transient increase in the expression of inflammatory and oxidative stress mediators, including interleukin (IL)-1 alpha (IL1A), IL-1 beta (IL1B), IL8, RANTES, colony stimulating factor 3 (CSF3), and superoxide dismutase 2 (SOD2), and a decreased expression of IP10, interferon inducible T-cell alpha chemoattractant (ITAC), matrix metalloproteinase 10 (MMP10), and beta 4 defensin (DEFB4). These genes reversed expression patterns upon resolution in parallel with the reversal of gingival inflammation. A relatively small subset (11.9%) of the immune response genes analyzed by array was transiently activated in response to biofilm overgrowth, suggesting a degree of specificity in the transcriptome-expression response. The fact that this same subset demonstrates a reversal in expression patterns during clinical resolution implicates these genes as being critical for maintaining tissue homeostasis at the biofilm-gingival interface. In addition to the immune response pathway as the dominant response theme, new candidate genes and pathways were identified as being selectively modulated in experimental gingivitis, including neural processes, epithelial defenses, angiogenesis, and wound healing.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

PubMed

Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

2016-01-01

Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools. © 2016 Elsevier Inc. All rights reserved.

Scintillation and bit error rate analysis of a phase-locked partially coherent flat-topped array laser beam in oceanic turbulence.

PubMed

Yousefi, Masoud; Kashani, Fatemeh Dabbagh; Golmohammady, Shole; Mashal, Ahmad

2017-12-01

In this paper, the performance of underwater wireless optical communication (UWOC) links, which is made up of the partially coherent flat-topped (PCFT) array laser beam, has been investigated in detail. Providing high power, array laser beams are employed to increase the range of UWOC links. For characterization of the effects of oceanic turbulence on the propagation behavior of the considered beam, using the extended Huygens-Fresnel principle, an analytical expression for cross-spectral density matrix elements and a semi-analytical one for fourth-order statistical moment have been derived. Then, based on these expressions, the on-axis scintillation index of the mentioned beam propagating through weak oceanic turbulence has been calculated. Furthermore, in order to quantify the performance of the UWOC link, the average bit error rate (BER) has also been evaluated. The effects of some source factors and turbulent ocean parameters on the propagation behavior of the scintillation index and the BER have been studied in detail. The results of this investigation indicate that in comparison with the Gaussian array beam, when the source size of beamlets is larger than the first Fresnel zone, the PCFT array laser beam with the higher flatness order is found to have a lower scintillation index and hence lower BER. Specifically, in the sense of scintillation index reduction, using the PCFT array laser beams has a considerable benefit in comparison with the single PCFT or Gaussian laser beams and also Gaussian array beams. All the simulation results of this paper have been shown by graphs and they have been analyzed in detail.

Identifying equivalent sound sources from aeroacoustic simulations using a numerical phased array

NASA Astrophysics Data System (ADS)

Pignier, Nicolas J.; O'Reilly, Ciarán J.; Boij, Susann

2017-04-01

An application of phased array methods to numerical data is presented, aimed at identifying equivalent flow sound sources from aeroacoustic simulations. Based on phased array data extracted from compressible flow simulations, sound source strengths are computed on a set of points in the source region using phased array techniques assuming monopole propagation. Two phased array techniques are used to compute the source strengths: an approach using a Moore-Penrose pseudo-inverse and a beamforming approach using dual linear programming (dual-LP) deconvolution. The first approach gives a model of correlated sources for the acoustic field generated from the flow expressed in a matrix of cross- and auto-power spectral values, whereas the second approach results in a model of uncorrelated sources expressed in a vector of auto-power spectral values. The accuracy of the equivalent source model is estimated by computing the acoustic spectrum at a far-field observer. The approach is tested first on an analytical case with known point sources. It is then applied to the example of the flow around a submerged air inlet. The far-field spectra obtained from the source models for two different flow conditions are in good agreement with the spectra obtained with a Ffowcs Williams-Hawkings integral, showing the accuracy of the source model from the observer's standpoint. Various configurations for the phased array and for the sources are used. The dual-LP beamforming approach shows better robustness to changes in the number of probes and sources than the pseudo-inverse approach. The good results obtained with this simulation case demonstrate the potential of the phased array approach as a modelling tool for aeroacoustic simulations.

Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins

NASA Astrophysics Data System (ADS)

Wnęk, M.; Górzny, M. Ł.; Ward, M. B.; Wälti, C.; Davies, A. G.; Brydson, R.; Evans, S. D.; Stockley, P. G.

2013-01-01

The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating.

Classification of Genes and Putative Biomarker Identification Using Distribution Metrics on Expression Profiles

PubMed Central

Huang, Hung-Chung; Jupiter, Daniel; VanBuren, Vincent

2010-01-01

Background Identification of genes with switch-like properties will facilitate discovery of regulatory mechanisms that underlie these properties, and will provide knowledge for the appropriate application of Boolean networks in gene regulatory models. As switch-like behavior is likely associated with tissue-specific expression, these gene products are expected to be plausible candidates as tissue-specific biomarkers. Methodology/Principal Findings In a systematic classification of genes and search for biomarkers, gene expression profiles (GEPs) of more than 16,000 genes from 2,145 mouse array samples were analyzed. Four distribution metrics (mean, standard deviation, kurtosis and skewness) were used to classify GEPs into four categories: predominantly-off, predominantly-on, graded (rheostatic), and switch-like genes. The arrays under study were also grouped and examined by tissue type. For example, arrays were categorized as ‘brain group’ and ‘non-brain group’; the Kolmogorov-Smirnov distance and Pearson correlation coefficient were then used to compare GEPs between brain and non-brain for each gene. We were thus able to identify tissue-specific biomarker candidate genes. Conclusions/Significance The methodology employed here may be used to facilitate disease-specific biomarker discovery. PMID:20140228

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

PubMed

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Harnessing Gene Conversion in Chicken B Cells to Create a Human Antibody Sequence Repertoire

PubMed Central

Schusser, Benjamin; Yi, Henry; Collarini, Ellen J.; Izquierdo, Shelley Mettler; Harriman, William D.; Etches, Robert J.; Leighton, Philip A.

2013-01-01

Transgenic chickens expressing human sequence antibodies would be a powerful tool to access human targets and epitopes that have been intractable in mammalian hosts because of tolerance to conserved proteins. To foster the development of the chicken platform, it is beneficial to validate transgene constructs using a rapid, cell culture-based method prior to generating fully transgenic birds. We describe a method for the expression of human immunoglobulin variable regions in the chicken DT40 B cell line and the further diversification of these genes by gene conversion. Chicken VL and VH loci were knocked out in DT40 cells and replaced with human VK and VH genes. To achieve gene conversion of human genes in chicken B cells, synthetic human pseudogene arrays were inserted upstream of the functional human VK and VH regions. Proper expression of chimeric IgM comprised of human variable regions and chicken constant regions is shown. Most importantly, sequencing of DT40 genetic variants confirmed that the human pseudogene arrays contributed to the generation of diversity through gene conversion at both the Igl and Igh loci. These data show that engineered pseudogene arrays produce a diverse pool of human antibody sequences in chicken B cells, and suggest that these constructs will express a functional repertoire of chimeric antibodies in transgenic chickens. PMID:24278246

Quantitative Magnetic Separation of Particles and Cells Using Gradient Magnetic Ratcheting.

PubMed

Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

2016-04-13

Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting, are robust but perform coarse, qualitative separations based on surface antigen expression. A quantitative magnetic separation technology is reported using high-force magnetic ratcheting over arrays of magnetically soft micropillars with gradient spacing, and the system is used to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micropillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic field. Particles with higher IOC separate and equilibrate along the miropillar array at larger pitches. A semi-analytical model is developed that predicts behavior for particles and cells. Using the system, LNCaP cells are separated based on the bound quantity of 1 μm anti-epithelial cell adhesion molecule (EpCAM) particles as a metric for expression. The ratcheting cytometry system is able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof-of-concept, EpCAM-labeled cells from patient blood are isolated with 74% purity, demonstrating potential toward a quantitative magnetic separation instrument. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Upgrade of the Mirnov probe arrays on the J-TEXT tokamak.

PubMed

Guo, Daojing; Hu, Qiming; Li, Da; Shen, Chengshuo; Wang, Nengchao; Huang, Zhuo; Huang, Mingxiang; Ding, Yonghua; Xu, Guo; Yu, Qingquan; Tang, Yuejin; Zhuang, Ge

2017-12-01

The magnetic diagnostic of Mirnov probe arrays has been upgraded on the J-TEXT tokamak to measure the magnetohydrodynamic instabilities with higher spatial resolution and better amplitude-frequency characteristics. The upgraded Mirnov probe array contains one poloidal array with 48 probe modules and two toroidal arrays with 25 probe modules. Each probe module contains two probes which measure both the poloidal and the radial magnetic fields (B p and B r ). To ensure that the Mirnov probe possess better amplitude-frequency characteristics, a novel kind of Mirnov probe made of low temperature co-fired ceramics is utilized. The parameters and frequency response of the probe are measured and can meet the experiment requirement. The new Mirnov arrays have been normally applied for a round of experiments, including the observation of tearing modes and their coupling as well as high frequency magnetic perturbation due to the Alfvén eigenmode. In order to extract useful information from raw signals, visualization processing methods based on singular value decomposition and cross-power spectrum are applied to decompose the coupled modes and to determine the mode number.

Upgrade of the Mirnov probe arrays on the J-TEXT tokamak

NASA Astrophysics Data System (ADS)

Guo, Daojing; Hu, Qiming; Li, Da; Shen, Chengshuo; Wang, Nengchao; Huang, Zhuo; Huang, Mingxiang; Ding, Yonghua; Xu, Guo; Yu, Qingquan; Tang, Yuejin; Zhuang, Ge

2017-12-01

The magnetic diagnostic of Mirnov probe arrays has been upgraded on the J-TEXT tokamak to measure the magnetohydrodynamic instabilities with higher spatial resolution and better amplitude-frequency characteristics. The upgraded Mirnov probe array contains one poloidal array with 48 probe modules and two toroidal arrays with 25 probe modules. Each probe module contains two probes which measure both the poloidal and the radial magnetic fields (Bp and Br). To ensure that the Mirnov probe possess better amplitude-frequency characteristics, a novel kind of Mirnov probe made of low temperature co-fired ceramics is utilized. The parameters and frequency response of the probe are measured and can meet the experiment requirement. The new Mirnov arrays have been normally applied for a round of experiments, including the observation of tearing modes and their coupling as well as high frequency magnetic perturbation due to the Alfvén eigenmode. In order to extract useful information from raw signals, visualization processing methods based on singular value decomposition and cross-power spectrum are applied to decompose the coupled modes and to determine the mode number.

PASP Plus: An experiment to measure space-environment effects on photovoltaic power subsystems

NASA Technical Reports Server (NTRS)

Guidice, Donald A.

1992-01-01

The Photovoltaic Array Space Power Plus Diagnostic experiment (PASP Plus) was accepted as part of the APEX Mission payload aboard a Pegastar satellite to be orbited by a Pegasus launch vehicle in late 1992. The mission's elliptical orbit will allow us to investigate both space plasma and space radiation effects. PASP Plus will have eleven types of solar arrays and a full complement of environmental and interactions diagnostic sensors. Measurements of space-plasma interactions on the various solar arrays will be made at large negative voltages (to investigate arcing parameters) and at large positive voltages (to investigate leakage currents) by biasing the arrays to various levels up to -500 and +500 volts. The long-term deterioration in solar array performance caused by exposure to space radiation will also be investigated; radiation dosage will be measured by an electron/proton dosimeter included in the environmental sensor complement. Experimental results from PASP Plus will help establish cause-and-effect relationships and lead to improved design guidelines and test standards for new-technology solar arrays.

PAPER: The Precision Array To Probe The Epoch Of Reionization

NASA Astrophysics Data System (ADS)

Backer, Donald C.; Parsons, A.; Bradley, R.; Parashare, C.; Gugliucci, N.; Mastrantonio, E.; Herne, D.; Lynch, M.; Wright, M.; Werhimer, D.; Carilli, C.; Datta, A.; Aguirre, J.

2007-12-01

The Precision Array to Probe the Epoch of Reionization (PAPER) is an experiment that is being designed to detect the faint HI signal from the epoch of reionization. Our instrumentation goals include: the design and building of dipole elements that are optimized for operation from 120-190 MHz with a clean beam response; amplifiers and receivers with good impedance match and overall flat gain response over a large bandpass; and an FPGA correlator capable of producing full Stokes products for the array. The array is being built and evaluated in stages at the Green Bank Observatory in West Virginia with deployment of the full instrument in Western Australia. We present results from an eight-station deployment in Green Bank and four-station deployment in Western Australia, including phase and amplitude calibration, RFI mitigation and removal, full sky maps, and wide-field snapshot imaging. We have discovered new ways to improve our system's stability and sensitivity from these early experiments, and are applying these concepts to a 16-element array in Green Bank in early 2008 and a 32-element array in Western Australia later in 2008.

3D MHD Simulations of Radial Wire Array Z-pinches

NASA Astrophysics Data System (ADS)

Niasse, N.; Chittenden, J. P.; Bland, S. N.; Suzuki-Vidal, F. A.; Hall, G. N.; Lebedev, S. V.; Calamy, H.; Zucchini, F.; Lassalle, F.; Bedoch, J. P.

2009-01-01

Recent experiments carried out on the MAGPIE (1 MA, 250 ns), OEDIPE (730 kA, 1.5 μs) and SPHINX (4 MA, 700 ns)[1] facilities have shown the relatively high level of scalability of the Radial Wire Array Z-pinches. These configurations where the wires stretch radially outwards from a central cathode offer numerous advantages over standard cylindrical arrays. In particular, imploding in a very stable and compact way, they seem suitable for coupling to small scale hohlraums. Making use of the 3D resistive magneto-hydrodynamic code GORGON[2] developed at Imperial College, the dynamic of the radial wire arrays is investigated. Influence of the cathode hotspots and wires angle on the x-ray emissions is also discussed. Comparison with experiments is offered to validate the numerical studies.

Neutron Capture Experiments Using the DANCE Array at Los Alamos

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

Dashdorj, D.; MonAme Scientific Research Center, Ulaanbaatar; Mitchell, G. E.

2009-03-31

The Detector for Advanced Neutron Capture Experiments (DANCE) is designed for neutron capture measurements on very small and/or radioactive targets. The DANCE array of 160 BaF{sub 2} scintillation detectors is located at the Lujan Center at the Los Alamos Neutron Science Center (LANSCE). Accurate measurements of neutron capture data are important for many current applications as well as for basic understanding of neutron capture. The gamma rays following neutron capture reactions have been studied by the time-of-flight technique using the DANCE array. The high granularity of the array allows measurements of the gamma-ray multiplicity. The gamma-ray multiplicities and energy spectramore » for different multiplicities can be measured and analyzed for spin and parity determination of the resolved resonances.« less

Ultrasonic brain therapy: First trans-skull in vivo experiments on sheep using adaptive focusing

NASA Astrophysics Data System (ADS)

Pernot, Mathieu; Aubry, Jean-Francois; Tanter, Michael; Fink, Mathias; Boch, Anne-Laure; Kujas, Michèle

2004-05-01

A high-power prototype dedicated to trans-skull therapy has been tested in vivo on 20 sheep. The array is made of 200 high-power transducers working at 1-MHz central and is able to reach 260 bars at focus in water. An echographic array connected to a Philips HDI 1000 system has been inserted in the therapeutic array in order to perform real-time monitoring of the treatment. A complete craniotomy has been performed on half of the treated animal models in order to get a reference model. On the other animals, a minimally invasive surgery has been performed thanks to a time-reversal experiment: a hydrophone was inserted at the target inside the brain thanks to a 1-mm2 craniotomy. A time-reversal experiment was then conducted through the skull bone with the therapeutic array to treat the targeted point. For all the animals a specified region around the target was treated thanks to electronic beam steering. Animals were finally divided into three groups and sacrificed, respectively, 0, 1, and 2 weeks after treatment. Finally, histological examination confirmed tissue damage. These in vivo experiments highlight the strong potential of high-power time-reversal technology.

MARE-l in Milan: Status and Perspectives

NASA Technical Reports Server (NTRS)

Ferri, E.; Arnaboldi, C.; Ceruti, G.; Faverzani, M.; Gatti, C.; Giachero, A.; Gotti, C.; Kilbourne, C.; Kraft-Bermuth, S.; Nucciotti, A.;

Design and Characterization of Dual-Curvature 1.5-Dimensional High-Intensity Focused Ultrasound Phased-Array Transducer

PubMed Central

Chen, Gin-Shin; Lin, Che-Yu; Jeong, Jong Seob; Cannata, Jonathan M.; Lin, Win-Li; Chang, Hsu; Shung, K. Kirk

2013-01-01

A dual-curvature focused ultrasound phased-array transducer with a symmetric control has been developed for noninvasive ablative treatment of tumors. The 1.5-D array was constructed in-house and the electro-acoustic conversion efficiency was measured to be approximately 65%. In vitro experiments demonstrated that the array uses 256 independent elements to achieve 2-D wide-range high-intensity electronic focusing. PMID:22293745

Telescope Array Results on UHE Cosmic Rays and the Plan

NASA Astrophysics Data System (ADS)

Sagawa, Hiroyuki

The Telescope Array (TA) is the largest experiment in the Northern Hemisphere studying the origin and nature of ultra-high-energy cosmic rays. The TA detector consists of a surface array of 507 scintillation counters covering approximately 700 km2, and 38 fluorescence telescopes located at three sites looking over the surface array. Here, recent TA results using the first five years of data and our ongoing and near-future plans are presented.

Functional convergence of Akt protein with VEGFR-1 in human endothelial progenitor cells exposed to sera from patient with type 2 diabetes mellitus.

PubMed

Hassanpour, Mehdi; Rezabakhsh, Aysa; Rahbarghazi, Reza; Nourazarian, Alireza; Nouri, Mohammad; Avci, Çığır Biray; Ghaderi, Shahrooz; Alidadyani, Neda; Bagca, Bakiye Goker; Bagheri, Hesam Saghaei

2017-11-01

Diabetes mellitus type 2 predisposes patients to various microvascular complications. In the current experiment, the potent role of diabetes mellitus was investigated on the content of VEGFR-1, -2, Tie-1 and -2, and Akt in human endothelial progenitor cells. The gene expression profile of mTOR and Hedgehog signaling pathways were measured by PCR array. The possible crosstalk between RTKs, mTOR and Hedgehog signaling was also studied by bioinformatic analysis. Endothelial progenitor cells were incubated with serum from normal and diabetic for 7days. Compared to non-treated cells, diabetic serum-induced cell apoptosis (~2-fold) and prohibited cell migration toward bFGF (p<0.001). ELISA analysis showed that diabetes exposed cells had increased abundance of Tie-1, -2 and VEGFR-2 and reduced amount of VEGFR-1 (p<0.0001) in diabetic cells. Western blotting showed a marked reduction in the protein level of Akt after cells exposure to serum from diabetic subjects (p<0.0001). PCR array revealed a significant stimulation of both mTOR and Hedgehog signaling pathways in diabetic cells (p<0.05). According to data from bioinformatic datasets, we showed VEGFR-1, -2 and Tie-2, but not Tie-1, are master regulators of angiogenesis. There is a crosstalk between RTKs and mTOR signaling by involving P62, GABARAPL1, and HTT genes. It seems that physical interaction and co-expression of Akt decreased the level of VEGFR-1 in diabetic cells. Regarding data from the present experiment, diabetic serum contributed to uncontrolled induction of both mTOR and Hedgehog signaling in endothelial progenitor cells. Diabetes mellitus induces mTOR pathway by involving receptor tyrosine kinases while Hedgehog stimulation is independent of these receptors. Copyright © 2017 Elsevier Inc. All rights reserved.

The interactions of solar arrays with electric thrusters

NASA Technical Reports Server (NTRS)

Kaufman, H. R.; Isaacson, G. C.; Domitz, S.

1976-01-01

The generation of a charge-exchange plasma by a thruster, the transport of this plasma to the solar array, and the interaction of the solar array with the plasma after it arrives are all described. The generation of this plasma can be described accurately from thruster geometry and operating conditions. The transport of the charge-exchange plasma was studied experimentally with a 15 cm thruster. A model was developed for simple thruster-array configurations. A variety of experiments were surveyed for the interaction of the plasma at the solar array.

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

PubMed Central

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

2014-01-01

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

Stress alters the expression of cancer-related genes in the prostate.

PubMed

Flores, Ivan E; Sierra-Fonseca, Jorge A; Davalos, Olinamyr; Saenz, Luis A; Castellanos, Maria M; Zavala, Jaidee K; Gosselink, Kristin L

2017-09-05

Prostate cancer is a major contributor to mortality worldwide, and significant efforts are being undertaken to decipher specific cellular and molecular pathways underlying the disease. Chronic stress is known to suppress reproductive function and promote tumor progression in several cancer models, but our understanding of the mechanisms through which stress contributes to cancer development and progression is incomplete. We therefore examined the relationship between stress, modulation of the gonadotropin-releasing hormone (GnRH) system, and changes in the expression of cancer-related genes in the rat prostate. Adult male rats were acutely or repeatedly exposed to restraint stress, and compared to unstressed controls and groups that were allowed 14 days of recovery from the stress. Prostate tissue was collected and frozen for gene expression analyses by PCR array before the rats were transcardially perfused; and brain tissues harvested and immunohistochemically stained for Fos to determine neuronal activation. Acute stress elevated Fos expression in the paraventricular nucleus of the hypothalamus (PVH), an effect that habituated with repeated stress exposure. Data from the PCR arrays showed that repeated stress significantly increases the transcript levels of several genes associated with cellular proliferation, including proto-oncogenes. Data from another array platform showed that both acute and repeated stress can induce significant changes in metastatic gene expression. The functional diversity of genes with altered expression, which includes transcription factors, growth factor receptors, apoptotic genes, and extracellular matrix components, suggests that stress is able to induce aberrant changes in pathways that are deregulated in prostate cancer. Our findings further support the notion that stress can affect cancer outcomes, perhaps by interfering with neuroendocrine mechanisms involved in the control of reproduction.

Effects of simulated microgravity on gene expression and biological phenotypes of a single generation Caenorhabditis elegans cultured on 2 different media

NASA Astrophysics Data System (ADS)

Tee, Ling Fei; Neoh, Hui-min; Then, Sue Mian; Murad, Nor Azian; Asillam, Mohd Fairos; Hashim, Mohd Helmy; Nathan, Sheila; Jamal, Rahman

2017-11-01

Studies of multigenerational Caenorhabditis elegans exposed to long-term spaceflight have revealed expression changes of genes involved in longevity, DNA repair, and locomotion. However, results from spaceflight experiments are difficult to reproduce as space missions are costly and opportunities are rather limited for researchers. In addition, multigenerational cultures of C. elegans used in previous studies contribute to mixture of gene expression profiles from both larvae and adult worms, which were recently reported to be different. Usage of different culture media during microgravity simulation experiments might also give rise to differences in the gene expression and biological phenotypes of the worms. In this study, we investigated the effects of simulated microgravity on the gene expression and biological phenotype profiles of a single generation of C. elegans worms cultured on 2 different culture media. A desktop Random Positioning Machine (RPM) was used to simulate microgravity on the worms for approximately 52 to 54 h. Gene expression profile was analysed using the Affymetrix GeneChip® C. elegans 1.0 ST Array. Only one gene (R01H2.2) was found to be downregulated in nematode growth medium (NGM)-cultured worms exposed to simulated microgravity. On the other hand, eight genes were differentially expressed for C. elegans Maintenance Medium (CeMM)-cultured worms in microgravity; six were upregulated, while two were downregulated. Five of the upregulated genes (C07E3.15, C34H3.21, C32D5.16, F35H8.9 and C34F11.17) encode non-coding RNAs. In terms of biological phenotype, we observed that microgravity-simulated worms experienced minimal changes in terms of lifespan, locomotion and reproductive capabilities in comparison with the ground controls. Taking it all together, simulated microgravity on a single generation of C. elegans did not confer major changes to their gene expression and biological phenotype. Nevertheless, exposure of the worms to microgravity lead to higher expression of non-coding RNA genes, which may play an epigenetic role in the worms during longer terms of microgravity exposure.

The Air-Shower Experiment KASCADE-Grande

NASA Astrophysics Data System (ADS)

Haungs, A.; Apel, W. D.; Arteaga, J. C.; Badea, F.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Brüggemann, M.; Buchholz, P.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuhrmann, D.; Ghia, P. L.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Heck, D.; Hörandel, J. R.; Huege, T.; Isar, P. G.; Kampert, K.-H.; Kang, D.; Kickelbick, D.; Klages, H. O.; Kolotaev, Y.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Navarra, G.; Nehls, S.; Oehlschläger, J.; Ostapchenko, S.; Over, S.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schröder, F.; Sima, O.; Stümpert, M.; Toma, G.; Trinchero, G.; Ulrich, H.; Walkowiak, W.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.; KASCADE-Grande Collaboration

2009-12-01

KASCADE-Grande is an extensive air shower experiment at the Forschungszentrum Karlsruhe, Germany. Main parts of the experiment are the Grande array spread over an area of 700×700 m, the original KASCADE array covering 200×200 m with unshielded and shielded detectors, and additional muon tracking devices. This multi-detector system allows to investigate the energy spectrum, composition, and anisotropies of cosmic rays in the energy range up to 1 EeV. An overview on the performance of the apparatus and first results will be given.

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

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean. To evaluate the utility...

Expression and Production of SH2 Domain Proteins.

PubMed

Liu, Bernard A; Ogiue-Ikeda, Mari; Machida, Kazuya

2017-01-01

The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP). We describe stepwise protocols for expression and purification of SH2 domains using GST or poly His-tags, two widely adopted affinity tags. In addition, we address alternative approaches, challenges, and validation studies for assessing protein quality and provide general characteristics of purified human SH2 domains.

DESCANT - The DEuterated SCintillator Array for Neutron Tagging

NASA Astrophysics Data System (ADS)

Bildstein, Vinzenz; Garrett, P. E.; Bandyopadhay, D.; Bangay, J.; Bianco, L.; Demand, G.; Hadinia, B.; Leach, K. G.; Sumithrarachchi, C.; Turko, J.; Wong, J.; Ashley, S. F.; Crider, B. P.; McEllistrem, M. T.; Peters, E. E.; Prados-Estévez, F. M.; Yates, S. W.; Vanhoy, J. R.; Ball, G. C.; Bishop, D. P.; Garnsworthy, A. B.; Hackman, G.; Pearson, C. J.; Shaw, B.; Saran, F.

2016-09-01

The DESCANT array at TRIUMF is designed to detect neutrons from RIB experiments. DESCANT is composed of 70 close-packed deuterated organic liquid scintillators coupled to digital fast read-out ADC modules. This configuration will permit online pulse-shape discrimination between neutron and γ-ray events. A prototype detector has been tested with monoenergetic neutrons at the accelerator laboratory of the University of Kentucky. A first commissioning experiment of the full array, using the decay of 145-146Cs, will be performed in August 2016. The results of the tests and a preliminary analysis of the commissioning experiment will be presented. Work supported by the Canada Foundation for Innovation, the Natural Sciences and Engineering Research Council of Canada, the National Research Council of Canada and the Canadian Research Chairs program.

Analysis of modified SMI method for adaptive array weight control

NASA Technical Reports Server (NTRS)

Dilsavor, R. L.; Moses, R. L.

1989-01-01

An adaptive array is applied to the problem of receiving a desired signal in the presence of weak interference signals which need to be suppressed. A modification, suggested by Gupta, of the sample matrix inversion (SMI) algorithm controls the array weights. In the modified SMI algorithm, interference suppression is increased by subtracting a fraction F of the noise power from the diagonal elements of the estimated covariance matrix. Given the true covariance matrix and the desired signal direction, the modified algorithm is shown to maximize a well-defined, intuitive output power ratio criterion. Expressions are derived for the expected value and variance of the array weights and output powers as a function of the fraction F and the number of snapshots used in the covariance matrix estimate. These expressions are compared with computer simulation and good agreement is found. A trade-off is found to exist between the desired level of interference suppression and the number of snapshots required in order to achieve that level with some certainty. The removal of noise eigenvectors from the covariance matrix inverse is also discussed with respect to this application. Finally, the type and severity of errors which occur in the covariance matrix estimate are characterized through simulation.

Continuous-Time Random Walk Models of DNA Electrophoresis in a Post Array: II. Mobility and Sources of Band Broadening

PubMed Central

Olson, Daniel W.; Dutta, Sarit; Laachi, Nabil; Tian, Mingwei; Dorfman, Kevin D.

2011-01-01

Using the two-state, continuous-time random walk model, we develop expressions for the mobility and the plate height during DNA electrophoresis in an ordered post array that delineate the contributions due to (i) the random distance between collisions and (ii) the random duration of a collision. These contributions are expressed in terms of the means and variances of the underlying stochastic processes, which we evaluate from a large ensemble of Brownian dynamics simulations performed using different electric fields and molecular weights in a hexagonal array of 1 μm posts with a 3 μm center-to-center distance. If we fix the molecular weight, we find that the collision frequency governs the mobility. In contrast, the average collision duration is the most important factor for predicting the mobility as a function of DNA size at constant Péclet number. The plate height is reasonably well-described by a single post rope-over-pulley model, provided that the extension of the molecule is small. Our results only account for dispersion inside the post array and thus represent a theoretical lower bound on the plate height in an actual device. PMID:21290387

Low dark current InGaAs detector arrays for night vision and astronomy

NASA Astrophysics Data System (ADS)

MacDougal, Michael; Geske, Jon; Wang, Chad; Liao, Shirong; Getty, Jonathan; Holmes, Alan

2009-05-01

Aerius Photonics has developed large InGaAs arrays (1K x 1K and greater) with low dark currents for use in night vision applications in the SWIR regime. Aerius will present results of experiments to reduce the dark current density of their InGaAs detector arrays. By varying device designs and passivations, Aerius has achieved a dark current density below 1.0 nA/cm2 at 280K on small-pixel, detector arrays. Data is shown for both test structures and focal plane arrays. In addition, data from cryogenically cooled InGaAs arrays will be shown for astronomy applications.

ASSESSMENT OF DIFFERENTIAL GENE EXPRESSION IN SHEEPSHEAD MINNOWS EXPOSED TO ENVIRONMENTAL ESTROGENS

EPA Science Inventory

Gene arrays and quantitative real-time PCR (Q-PRC) are sensitive methods for assessing exposure of fish and other wildlife to environmental contaminants by measuring changes in gene expression. Several genes normally induced by estradiol in female fish, those for vitellogenins (...

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

PubMed Central

2012-01-01

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings. PMID:16964229

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.

PubMed

Lepre, Jorge; Rice, J Jeremy; Tu, Yuhai; Stolovitzky, Gustavo

2004-05-01

Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).

Tumour necrosis factor α (TNF)–TNF receptor 1-inducible cytoprotective proteins in the mouse liver: relevance of suppressors of cytokine signalling

PubMed Central

Sass, Gabriele; Shembade, Noula D.; Tiegs, Gisa

2004-01-01

TNF (tumour necrosis factor α) induces tolerance towards itself in experimental liver injury. Tolerance induction has been shown to be dependent on TNFR1 (TNF receptor 1) signalling, but mechanisms and mediators of TNF-induced hepatic tolerance are unknown. We investigated the TNF-inducible gene-expression profile in livers of TNFR2−/− mice, using cDNA array technology. We found that, out of 793 investigated genes involved in inflammation, cell cycle and signal transduction, 282 were expressed in the mouse liver in response to TNF via TNFR1. Among those, expression of 78 genes was induced, while expression of 60 genes was reduced. We investigated further the cellular expression of the 27 most prominently induced genes, and found that 20 of these genes were up-regulated directly in parenchymal liver cells, representing potentially protective proteins and possible mediators of TNF tolerance. In vitro experiments revealed that overexpression of SOCS1 (silencer of cytokine signalling 1), a member of the SOCS family of proteins, as well as of HO-1 (haem oxygenase-1), but not of SOCS2 or SOCS3, protected isolated primary mouse hepatocytes from TNF-induced apoptosis. The identification of protective genes in hepatocytes is the prerequisite for future development of gene therapies for immune-mediated liver diseases. PMID:15554901

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

PubMed Central

2012-01-01

Background Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. Results Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development. Conclusion The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process. PMID:23256600

A Fourier Method for Sidelobe Reduction in Equally Spaced Linear Arrays

NASA Astrophysics Data System (ADS)

Safaai-Jazi, Ahmad; Stutzman, Warren L.

2018-04-01

Uniformly excited, equally spaced linear arrays have a sidelobe level larger than -13.3 dB, which is too high for many applications. This limitation can be remedied by nonuniform excitation of array elements. We present an efficient method for sidelobe reduction in equally spaced linear arrays with low penalty on the directivity. The method involves the following steps: construction of a periodic function containing only the sidelobes of the uniformly excited array, calculation of the Fourier series of this periodic function, subtracting the series from the array factor of the original uniformly excited array after it is truncated, and finally mitigating the truncation effects which yields significant increase in sidelobe level reduction. A sidelobe reduction factor is incorporated into element currents that makes much larger sidelobe reductions possible and also allows varying the sidelobe level incrementally. It is shown that such newly formed arrays can provide sidelobe levels that are at least 22.7 dB below those of the uniformly excited arrays with the same size and number of elements. Analytical expressions for element currents are presented. Radiation characteristics of the sidelobe-reduced arrays introduced here are examined, and numerical results for directivity, sidelobe level, and half-power beam width are presented for example cases. Performance improvements over popular conventional array synthesis methods, such as Chebyshev and linear current tapered arrays, are obtained with the new method.

Weight Vector Fluctuations in Adaptive Antenna Arrays Tuned Using the Least-Mean-Square Error Algorithm with Quadratic Constraint

NASA Astrophysics Data System (ADS)

Zimina, S. V.

2015-06-01

We present the results of statistical analysis of an adaptive antenna array tuned using the least-mean-square error algorithm with quadratic constraint on the useful-signal amplification with allowance for the weight-coefficient fluctuations. Using the perturbation theory, the expressions for the correlation function and power of the output signal of the adaptive antenna array, as well as the formula for the weight-vector covariance matrix are obtained in the first approximation. The fluctuations are shown to lead to the signal distortions at the antenna-array output. The weight-coefficient fluctuations result in the appearance of additional terms in the statistical characteristics of the antenna array. It is also shown that the weight-vector fluctuations are isotropic, i.e., identical in all directions of the weight-coefficient space.

In-phased second harmonic wave array generation with intra-Talbot-cavity frequency-doubling.

PubMed

Hirosawa, Kenichi; Shohda, Fumio; Yanagisawa, Takayuki; Kannari, Fumihiko

2015-03-23

The Talbot cavity is one promising method to synchronize the phase of a laser array. However, it does not achieve the lowest array mode with the same phase but the highest array mode with the anti-phase between every two adjacent lasers, which is called out-phase locking. Consequently, their far-field images exhibit 2-peak profiles. We propose intra-Talbot-cavity frequency-doubling. By placing a nonlinear crystal in a Talbot cavity, the Talbot cavity generates an out-phased fundamental wave array, which is converted into an in-phase-locked second harmonic wave array at the nonlinear crystal. We demonstrate numerical calculations and experiments on intra-Talbot-cavity frequency-doubling and obtain an in-phase-locked second harmonic wave array for a Nd:YVO₄ array laser.

Ebola virus infection induces irregular dendritic cell gene expression.

PubMed

Melanson, Vanessa R; Kalina, Warren V; Williams, Priscilla

2015-02-01

Filoviruses subvert the human immune system in part by infecting and replicating in dendritic cells (DCs). Using gene arrays, a phenotypic profile of filovirus infection in human monocyte-derived DCs was assessed. Monocytes from human donors were cultured in GM-CSF and IL-4 and were infected with Ebola virus Kikwit variant for up to 48 h. Extracted DC RNA was analyzed on SuperArray's Dendritic and Antigen Presenting Cell Oligo GEArray and compared to uninfected controls. Infected DCs exhibited increased expression of cytokine, chemokine, antiviral, and anti-apoptotic genes not seen in uninfected controls. Significant increases of intracellular antiviral and MHC I and II genes were also noted in EBOV-infected DCs. However, infected DCs failed to show any significant difference in co-stimulatory T-cell gene expression from uninfected DCs. Moreover, several chemokine genes were activated, but there was sparse expression of chemokine receptors that enabled activated DCs to home to lymph nodes. Overall, statistically significant expression of several intracellular antiviral genes was noted, which may limit viral load but fails to stop replication. EBOV gene expression profiling is of vital importance in understanding pathogenesis and devising novel therapeutic treatments such as small-molecule inhibitors.

CEBS object model for systems biology data, SysBio-OM.

PubMed

Xirasagar, Sandhya; Gustafson, Scott; Merrick, B Alex; Tomer, Kenneth B; Stasiewicz, Stanley; Chan, Denny D; Yost, Kenneth J; Yates, John R; Sumner, Susan; Xiao, Nianqing; Waters, Michael D

2004-09-01

To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Array servo scanning micro EDM of 3D micro cavities

NASA Astrophysics Data System (ADS)

Tong, Hao; Li, Yong; Yi, Futing

2011-05-01

Micro electro discharge machining (Micro EDM) is a non-traditional processing technology with the special advantages of low set-up cost and few cutting force in machining any conductive materials regardless of their hardness. As well known, die-sinking EDM is unsuitable for machining the complex 3D micro cavity less than 1mm due to the high-priced fabrication of 3D microelectrode itself and its serous wear during EDM process. In our former study, a servo scanning 3D micro-EDM (3D SSMEDM) method was put forward, and our experiments showed it was available to fabricate complex 3D micro-cavities. In this study, in order to improve machining efficiency and consistency accuracy for array 3D micro-cavities, an array-servo-scanning 3D micro EDM (3D ASSMEDM) method is presented considering the complementary advantages of the 3D SSMEDM and the array micro electrodes with simple cross-section. During 3D ASSMEDM process, the array cavities designed by CAD / CAM system can be batch-manufactured by servo scanning layer by layer using array-rod-like micro tool electrodes, and the axial wear of the array electrodes is compensated in real time by keeping discharge gap. To verify the effectiveness of the 3D ASSMEDM, the array-triangle-micro cavities (side length 630 μm) are batch-manufactured on P-doped silicon by applying the array-micro-electrodes with square-cross-section fabricated by LIGA process. Our exploratory experiment shows that the 3D ASSMEDM provides a feasible approach for the batch-manufacture of 3D array-micro-cavities of conductive materials.

Strategies in Landmark Use by Children, Adults, and Marmoset Monkeys

ERIC Educational Resources Information Center

MacDonald, Suzanne E.; Spetch, Marcia L.; Kelly, Debbie M.; Cheng, Ken

2004-01-01

Common marmosets ("Callithrix jacchus jacchus"), human children, and human adults learned to find a goal that was located in the center of a square array of four identical landmarks. The location of the landmark array and corresponding goal varied across trials, so the task could not be solved without using the landmark array. In Experiment 1, a…

Response effects in the perception of conjunctions of colour and form.

PubMed

Chmiel, N

1989-01-01

Two experiments addressed the question whether visual search for a target defined by a conjunction of colour and form requires a central, serial, attentional process, but detection of a single feature, such as colour, is preattentive, as proposed by the feature-integration theory of attention. Experiment 1 investigated conjunction and feature search using small array sizes of up to five elements, under conditions which precluded eye-movements, in contrast to previous studies. The results were consistent with the theory. Conjunction search showed the effect of adding distractors to the display, the slopes of the curves relating RT to array size were in the approximate ratio of 2:1, consistent with a central, serial search process, exhaustive for absence responses and self-terminating for presence responses. Feature search showed no significant effect of distractors for presence responses. Experiment 2 manipulated the response requirements in conjunction search, using vocal response in a GO-NO GO procedure, in contrast to Experiment 1, which used key-press responses in a YES-NO procedure. Strikingly, presence-response RT was not affected significantly by the number of distractors in the array. The slope relating RT to array size was 3.92. The absence RT slope was 30.56, producing a slope ratio of approximately 8:1. There was no interaction of errors with array size and the presence and absence conditions, implying that RT-error trade-offs did not produce this slope ratio. This result suggests that feature-integration theory is at least incomplete.

Move to learn: Integrating spatial information from multiple viewpoints.

PubMed

Holmes, Corinne A; Newcombe, Nora S; Shipley, Thomas F

2018-05-11

Recalling a spatial layout from multiple orientations - spatial flexibility - is challenging, even when the global configuration can be viewed from a single vantage point, but more so when it must be viewed piecemeal. In the current study, we examined whether experiencing the transition between multiple viewpoints enhances spatial memory and flexible recall for a spatial configuration viewed simultaneously (Exp. 1) and sequentially (Exp. 2), whether the type of transition matters, and whether action provides an additional advantage over passive experience. In Experiment 1, participants viewed an array of dollhouse furniture from four viewpoints, but with all furniture simultaneously visible. In Experiment 2, participants viewed the same array piecemeal, from four partitioned viewpoints that allowed for viewing only a segment at a time. The transition between viewpoints involved rotation of the array or participant movement around it. Rotation and participant movement were passively experienced or actively generated. The control condition presented the dollhouse as a series of static views. Across both experiments, participant movement significantly enhanced spatial memory relative to array rotation or static views. However, in Exp. 2, there was a further advantage for actively walking around the array compared to being passively pushed. These findings suggest that movement around a stable environment is key to spatial memory and flexible recall, with action providing an additional boost to the integration of temporally segmented spatial events. Thus, spatial memory may be more flexible than prior data indicate, when studied under more natural acquisition conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

microRNA-342, microRNA-191 and microRNA-510 are differentially expressed in T regulatory cells of type 1 diabetic patients.

PubMed

Hezova, Renata; Slaby, Ondrej; Faltejskova, Petra; Mikulkova, Zuzana; Buresova, Ivana; Raja, K R Muthu; Hodek, Jan; Ovesna, Jaroslava; Michalek, Jaroslav

2010-01-01

Regulatory T cells (Tregs) are critical regulators of autoimmune diseases, including type 1 diabetes mellitus. It is hypothesised that Tregs' function can be influenced by changes in the expression of specific microRNAs (miRNAs). Thus, we performed miRNAs profiling in a population of Tregs separated from peripheral blood of five type 1 diabetic patients and six healthy donors. For more detailed molecular characterisation of Tregs, we additionally compared miRNAs expression profiles of Tregs and conventional T cells. Tregs were isolated according to CD3+, CD4+, CD25(hi)+ and CD127- by flow cytometry, and miRNA expression profiling was performed using TaqMan Array Human MicroRNA Panel-1 (384-well low density array). In Tregs of diabetic patients we found significantly increased expression of miRNA-510 (p=0.05) and decreased expression of both miRNA-342 (p<0.0001) and miRNA-191 (p=0.0079). When comparing Tregs and T cells, we revealed that Tregs had significant higher expression of miRNA-146a and lower expression of eight specific miRNAs (20b, 31, 99a, 100, 125b, 151, 335, and 365). To our knowledge, this is the first study demonstrating changes in miRNA expression profiles occurring in Tregs of T1D patients and a miRNAs signature of adult Tregs.

Ka-band MMIC array system for ACTS aeronautical terminal experiment (Aero-X)

NASA Technical Reports Server (NTRS)

Raquet, Charles A.; Zakrajsek, Robert J.; Lee, Richard Q.; Andro, Monty; Turtle, John P.

1995-01-01

During the summer of 1994, the Advanced Communication Technology Satellite (ACTS) Aeronautical Terminal Experiment (Aero-X) was successfully completed by the NASA Lewis Research Center (LeRC) and the Jet Propulsion Laboratory (JPL). 4.8 and 9.6 Kbps duplex voice links were established between the LeRC Learjet and the ACTS Link Evaluation Terminal (LET) in Cleveland, Ohio, via the ACTS. The antenna system used in this demonstration was developed by LeRC and featured LeRC and US Air Force experimental arrays using GaAs MMIC devices at each radiating element for electronic beam steering and distributed power amplification. The antenna system consisted of three arrays mounted inside the LeRC Learjet, pointing out through the windows. An open loop tracking controller developed by LeRC used information from the aircraft position and attitude sensors to automatically steer the arrays toward ACTS during flight JPL ACTS Mobile Terminal (AMT) system hardware was used as transceivers both on the aircraft and at the LET. The single 32 element MMIC transmit array developed by NASA/LeRC and Texas Instruments has an EIRP of 23.4 dBW at boresight. The two 20 GHz MMIC receive arrays were developed in a cooperative effort with the USAF Rome Laboratory/Electronic System Center, taking advantage of existing USAF array development contracts with Boeing and Martin Marietta. The Boeing array has 23 elements and a G/T of 16/6 db/degK at boresight. The Martin Marietta array has 16 elements and a G/T of 16.1 db/degK at boresight. The three proof-of-concept arrays, the array control system and their integration and operation in the Learjet for Aero-X are described.

Methods for monitoring multiple gene expression

DOEpatents

Berka, Randy; Bachkirova, Elena; Rey, Michael

2013-10-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Methods for monitoring multiple gene expression

DOEpatents

Berka, Randy [Davis, CA; Bachkirova, Elena [Davis, CA; Rey, Michael [Davis, CA

2012-05-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Methods for monitoring multiple gene expression

DOEpatents

Berka, Randy [Davis, CA; Bachkirova, Elena [Davis, CA; Rey, Michael [Davis, CA

2008-06-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

The Upper Atmosphere Research Satellite In-Flight Dynamics

NASA Technical Reports Server (NTRS)

Woodard, Stanley E.

1997-01-01

Upper Atmosphere Research Satellite flight data from the first 737 days after launch (September 1991) was used to investigate spacecraft disturbances and responses. The investigation included two in-flight dynamics experiments (approximately three orbits each). Orbital and configuration influences on spacecraft dynamic response were also examined. Orbital influences were due to temperature variation from crossing the Earth's terminator and variation of the solar incident energy as the orbit precessed. During the terminator crossing, the rapid ambient temperature change caused the spacecraft's two flexible appendages to experience thermal elastic bending (thermal snap). The resulting response was dependent upon the orientation of the solar array and the solar incident energy. Orbital influences were also caused by on-board and environmental disturbances and spacecraft configuration changes resulting in dynamic responses which were repeated each orbit. Configuration influences were due to solar array rotation changing spacecraft modal properties. The investigation quantified the spacecraft dynamic response produced by the solar array and high gain antenna harmonic drive disturbances. The solar array's harmonic drive output resonated two solar array modes. Friction in the solar array gear drive provided sufficient energy dissipation which prevented the solar panels from resonating catastrophically; however, the solar array vibration amplitude was excessively large. The resulting vibration had a latitude-specific pattern.

Color waveguide transparent screen using lens array holographic optical element

NASA Astrophysics Data System (ADS)

Liu, Siqi; Sun, Peng; Wang, Chang; Zheng, Zhenrong

2017-11-01

A color transparent screen was designed in this paper, a planar glass was used as a waveguide structure and the lens array holographic optical element (HOE) was used as a display unit. The lens array HOE was exposed by two coherent beams. One was the reference wave which directly illuminated on the holographic material and the other was modulated by the micro lens array. The lens array HOE can display the images with see-through abilities. Unlike the conventional lens array HOE, a planar glass was adopted as the waveguide in the experiment. The projecting light was totally internal-reflected in the planar glass to eliminate the undesired zero-order diffracted light. By using waveguide, it also brings advantage of compact structure. Colorful display can be realized in our system as the holographic materials were capable for multi-wavelength display. In this paper, a color transparent screen utilizing the lens array HOE and waveguide were designed. Experiment results showed a circular display area on the transparent screen. The diameter of the area is 20 mm and it achieved the pixel resolution of 100 μm. This simple and effective method could be an alternative in the augment reality (AR) applications, such as transparent phone and television.

Latent Herpes Simplex Virus Infection of Sensory Neurons Alters Neuronal Gene Expression

PubMed Central

Kramer, Martha F.; Cook, W. James; Roth, Frederick P.; Zhu, Jia; Holman, Holly; Knipe, David M.; Coen, Donald M.

2003-01-01

The persistence of herpes simplex virus (HSV) and the diseases that it causes in the human population can be attributed to the maintenance of a latent infection within neurons in sensory ganglia. Little is known about the effects of latent infection on the host neuron. We have addressed the question of whether latent HSV infection affects neuronal gene expression by using microarray transcript profiling of host gene expression in ganglia from latently infected versus mock-infected mouse trigeminal ganglia. 33P-labeled cDNA probes from pooled ganglia harvested at 30 days postinfection or post-mock infection were hybridized to nylon arrays printed with 2,556 mouse genes. Signal intensities were acquired by phosphorimager. Mean intensities (n = 4 replicates in each of three independent experiments) of signals from mock-infected versus latently infected ganglia were compared by using a variant of Student's t test. We identified significant changes in the expression of mouse neuronal genes, including several with roles in gene expression, such as the Clk2 gene, and neurotransmission, such as genes encoding potassium voltage-gated channels and a muscarinic acetylcholine receptor. We confirmed the neuronal localization of some of these transcripts by using in situ hybridization. To validate the microarray results, we performed real-time reverse transcriptase PCR analyses for a selection of the genes. These studies demonstrate that latent HSV infection can alter neuronal gene expression and might provide a new mechanism for how persistent viral infection can cause chronic disease. PMID:12915567

Ultrasonic Phased Array Inspection Experiments and Simulations for AN Isogrid Structural Element with Cracks

NASA Astrophysics Data System (ADS)

Roth, D. J.; Tokars, R. P.; Martin, R. E.; Rauser, R. W.; Aldrin, J. C.; Schumacher, E. J.

2010-02-01

In this investigation, a T-shaped aluminum alloy isogrid stiffener element used in aerospace applications was inspected with ultrasonic phased array methods. The isogrid stiffener element had various crack configurations emanating from bolt holes. Computational simulation methods were used to mimic the experiments in order to help understand experimental results. The results of this study indicate that it is at least partly feasible to interrogate this type of geometry with the given flaw configurations using phased array ultrasonics. The simulation methods were critical in helping explain the experimental results and, with some limitation, can be used to predict inspection results.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, ...

A liquid crystal microlens array with aluminum and graphene electrodes for plenoptic imaging

NASA Astrophysics Data System (ADS)

Lei, Yu; Tong, Qing; Luo, Jun; Zhang, Xinyu; Sang, Hongshi; Xie, Changsheng

2015-12-01

Currently, several semiconducting oxide materials such as typical indium tin oxide are widely used as the transparent conducting electrodes (TCEs) in liquid crystal microlens arrays. In this paper, we fabricate a liquid crystal microlens array using graphene rather than semiconducting oxides as the TCE. Common optical experiments are carried out to acquire the focusing features of the graphene-based liquid crystal microlens array (GLCMLA) driven electrically. The acquired optical fields show that the GLCMLA can converge incident collimating lights efficiently. The relationship between the focal length and the applied voltage signal is presented. Then the GLCMLA is deployed in a plenoptic camera prototype and the raw images are acquired so as to verify their imaging capability. Our experiments demonstrate that graphene has already presented a broad application prospect in the area of adaptive optics.

An OSSE Study for Deep Argo Array using the GFDL Ensemble Coupled Data Assimilation System

NASA Astrophysics Data System (ADS)

Chang, You-Soon; Zhang, Shaoqing; Rosati, Anthony; Vecchi, Gabriel A.; Yang, Xiaosong

2018-03-01

An observing system simulation experiment (OSSE) using an ensemble coupled data assimilation system was designed to investigate the impact of deep ocean Argo profile assimilation in a biased numerical climate system. Based on the modern Argo observational array and an artificial extension to full depth, "observations" drawn from one coupled general circulation model (CM2.0) were assimilated into another model (CM2.1). Our results showed that coupled data assimilation with simultaneous atmospheric and oceanic constraints plays a significant role in preventing deep ocean drift. However, the extension of the Argo array to full depth did not significantly improve the quality of the oceanic climate estimation within the bias magnitude in the twin experiment. Even in the "identical" twin experiment for the deep Argo array from the same model (CM2.1) with the assimilation model, no significant changes were shown in the deep ocean, such as in the Atlantic meridional overturning circulation and the Antarctic bottom water cell. The small ensemble spread and corresponding weak constraints by the deep Argo profiles with medium spatial and temporal resolution may explain why the deep Argo profiles did not improve the deep ocean features in the assimilation system. Additional studies using different assimilation methods with improved spatial and temporal resolution of the deep Argo array are necessary in order to more thoroughly understand the impact of the deep Argo array on the assimilation system.

Receptor Activator of Nuclear Factor Kappa B (RANK) and Clinicopathological Variables in Endometrial Cancer: A Study at Protein and Gene Level.

PubMed

Gómez, Raúl; Castro, Ana; Martínez, Jessica; Rodríguez-García, Víctor; Burgués, Octavio; Tarín, Juan J; Cano, Antonio

2018-06-22

The system integrated by the receptor activator of nuclear factor kappa B (RANK) and its ligand, RANKL, modulates the role of hormones in the genesis and progression of breast tumors. We investigated whether the expression of RANK was related with clinicopathological features of primary endometrial tumors. Immunohistochemistry was used in an endometrial cancer tissue array containing samples from 36 tumors. The amount of RANK mRNA was examined in a tissue scan cDNA array containing cDNA from 40 tumors. Normal endometrium was examined for comparison. Immunohistochemical analyses showed that RANK expression was higher in malignant than in normal endometrium ( p < 0.05). RANK expression was related to histological grade (Pearson correlation index = 0.484, p < 0.001), but not to tumor stage or to age of the women. The gene expression was similar in malignant and normal endometrium. The study of RANK isoforms confirmed that the overall relative abundance of the three clearly identified transcripts was similar in normal and pathological endometrium. RANK protein expression increased from normal to malignant endometrium, and the expression level was related with tumor grade but not with stage or the age of subjects in endometrial cancer. In contrast, similar comparisons showed no change in RANK gene expression.

Optimum sensor placement for microphone arrays

NASA Astrophysics Data System (ADS)

Rabinkin, Daniel V.

Microphone arrays can be used for high-quality sound pickup in reverberant and noisy environments. Sound capture using conventional single microphone methods suffers severe degradation under these conditions. The beamforming capabilities of microphone array systems allow highly directional sound capture, providing enhanced signal-to-noise ratio (SNR) when compared to single microphone performance. The overall performance of an array system is governed by its ability to locate and track sound sources and its ability to capture sound from desired spatial volumes. These abilities are strongly affected by the spatial placement of microphone sensors. A method is needed to optimize placement for a specified number of sensors in a given acoustical environment. The objective of the optimization is to obtain the greatest average system SNR for sound capture in the region of interest. A two-step sound source location method is presented. In the first step, time delay of arrival (TDOA) estimates for select microphone pairs are determined using a modified version of the Omologo-Svaizer cross-power spectrum phase expression. In the second step, the TDOA estimates are used in a least-mean-squares gradient descent search algorithm to obtain a location estimate. Statistics for TDOA estimate error as a function of microphone pair/sound source geometry and acoustic environment are gathered from a set of experiments. These statistics are used to model position estimation accuracy for a given array geometry. The effectiveness of sound source capture is also dependent on array geometry and the acoustical environment. Simple beamforming and time delay compensation (TDC) methods provide spatial selectivity but suffer performance degradation in reverberant environments. Matched filter array (MFA) processing can mitigate the effects of reverberation. The shape and gain advantage of the capture region for these techniques is described and shown to be highly influenced by the placement of array sensors. A procedure is developed to evaluate a given array configuration based on the above-mentioned metrics. Constrained placement optimizations are performed that maximize SNR for both TDC and MFA capture methods. Results are compared for various acoustic environments and various enclosure sizes. General guidelines are presented for placement strategy and bandwidth dependence, as they relate to reverberation levels, ambient noise, and enclosure geometry. An overall performance function is described based on these metrics. Performance of the microphone array system is also constrained by the design limitations of the supporting hardware. Two newly developed hardware architectures are presented that support the described algorithms. A low- cost 8-channel system with off-the-shelf componentry was designed and its performance evaluated. A massively parallel 512-channel custom-built system is in development-its capabilities and the rationale for its design are described.

NUP98-PHF23 is a chromatin modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD domain histone reader function

PubMed Central

Gough, Sheryl M; Lee, Fan; Yang, Fan; Walker, Robert L; Zhu, Yeulin J; Pineda, Marbin; Onozawa, Masahiro; Chung, Yang Jo; Bilke, Sven; Wagner, Elise K; Denu, John M; Ning, Yi; Xu, Bowen; Wang, Gang Greg; Meltzer, Paul S; Aplan, Peter D

2014-01-01

In this report, we show that expression of a NUP98-PHF23 (NP23) fusion, associated with acute myeloid leukemia (AML) in humans, leads to myeloid, erythroid, T-cell, and B-cell leukemia in mice. The leukemic and pre-leukemic tissues display a stem cell-like expression signature including Hoxa, Hoxb, and Meis1 genes. The PHF23 PHD domain is known to bind H3K4me3 residues, and chromatin immunoprecipitation experiments demonstrated that the NP23 protein bound chromatin at a specific subset of H3K4me3 sites, including Hoxa, Hoxb, and Meis1. Treatment of NP23 cells with disulfiram, which inhibits the binding of PHD domains to H3K4me3 residues, rapidly and selectively killed NP23 myeloblasts; cell death was preceded by decreased expression of Hoxa, Hoxb, and Meis1. Furthermore, AML driven by a related fusion gene, NUP98-JARID1A (NJL), was also sensitive to disulfiram. Thus, the NP23 mouse provides a platform to evaluate compounds that disrupt binding of oncogenic PHD proteins to H3K4me3. PMID:24535671

Research integrity: the experience of a doubting Thomas.

PubMed

Hettinger, Thomas P

2014-04-01

The sensational "reactome array" paper published in Science in 2009 was investigated in Spain by the Ethics Committee of Consejo Superior de Investigaciones Cientificas (CSIC) after Science issued an editorial expression of concern. The paper was retracted in 2010 because of "skepticism" due to "errors" in chemistry. The "errors" were so profound that many readers expressed doubt that they were really errors, but part of an elaborate hoax. I conducted a forensic analysis of mass spectrometry data in the paper's Supporting Online Material (SOM) and was able to prove that thousands of data values were in fact fabricated. The SOM contains signatures of improper extensive spreadsheet manipulations of incorrect atomic and molecular mass values as well as impossibly repetitive deviations of found molecular mass values from their expected values. No evidence of real mass spectrometry data was detected. Both CSIC and Science have been content to retract the paper without acknowledging the fabrications or assigning responsibility for them. Neither CSIC nor Science has expressed interest in having an independent investigation determining how the paper came to be written, reviewed and published. Their weak response to this episode is a daunting signal that there is an impending crisis in research integrity and science journalism.

Identification of copy number variation-driven genes for liver cancer via bioinformatics analysis.

PubMed

Lu, Xiaojie; Ye, Kun; Zou, Kailin; Chen, Jinlian

2014-11-01

To screen out copy number variation (CNV)-driven differentially expressed genes (DEGs) in liver cancer and advance our understanding of the pathogenesis, an integrated analysis of liver cancer-related CNV data from The Cancer Genome Atlas (TCGA) and gene expression data from EBI Array Express database were performed. The DEGs were identified by package limma based on the cut-off of |log2 (fold-change)|>0.585 and adjusted p-value<0.05. Using hg19 annotation information provided by UCSC, liver cancer-related CNVs were then screened out. TF-target gene interactions were also predicted with information from UCSC using DAVID online tools. As a result, 25 CNV-driven genes were obtained, including tripartite motif containing 28 (TRIM28) and RanBP-type and C3HC4-type zinc finger containing 1 (RBCK1). In the transcriptional regulatory network, 8 known cancer-related transcription factors (TFs) interacted with 21 CNV-driven genes, suggesting that the other 8 TFs may be involved in liver cancer. These genes may be potential biomarkers for early detection and prevention of liver cancer. These findings may improve our knowledge of the pathogenesis of liver cancer. Nevertheless, further experiments are still needed to confirm our findings.

Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting.

PubMed

Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying

2015-06-01

In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. Copyright © 2015 Elsevier Inc. All rights reserved.

Sound-field reproduction systems using fixed-directivity loudspeakers.

PubMed

Poletti, M; Fazi, F M; Nelson, P A

2010-06-01

Sound reproduction systems using open arrays of loudspeakers in rooms suffer from degradations due to room reflections. These reflections can be reduced using pre-compensation of the loudspeaker signals, but this requires calibration of the array in the room, and is processor-intensive. This paper examines 3D sound reproduction systems using spherical arrays of fixed-directivity loudspeakers which reduce the sound field radiated outside the array. A generalized form of the simple source formulation and a mode-matching solution are derived for the required loudspeaker weights. The exterior field is derived and expressions for the exterior power and direct to reverberant ratio are derived. The theoretical results and simulations confirm that minimum interference occurs for loudspeakers which have hyper-cardioid polar responses.

Gene chips and arrays revealed: a primer on their power and their uses.

PubMed

Watson, S J; Akil, H

1999-03-01

This article provides an overview and general explanation of the rapidly developing area of gene chips and expression array technology. These are methods targeted at allowing the simultaneous study of thousands of genes or messenger RNAs under various physiological and pathological states. Their technical basis grows from the Human Genome Project. Both methods place DNA strands on glass computer chips (or microscope slides). Expression arrays start with complementary DNA (cDNA) clones derived from the EST data base, whereas Gene Chips synthesize oligonucleotides directly on the chip itself. Both are analyzed using image analysis systems, are capable of reading values from two different individuals at any one site, and can yield quantitative data for thousands of genes or mRNAs per slide. These methods promise to revolutionize molecular biology, cell biology, neuroscience and psychiatry. It is likely that this technology will radically open up our ability to study the actions and structure of the multiple genes involved in the complex genetics of brain disorders.

Cost competitiveness of a solar cell array power source for ATS-6 educational TV terminal

NASA Technical Reports Server (NTRS)

Masters, R. M.

1975-01-01

A cost comparison is made between a terrestrial solar cell array power system and a variety of other power sources for the ATS-6 Satellite Instructional Television Experiment (SITE) TV terminals in India. The solar array system was sized for a typical Indian location, Lahore. Based on present capital and fuel costs, the solar cell array power system is a close competitor to the least expensive alternate power system. A feasibility demonstration of a terrestrial solar cell array system powering an ATS-6 receiver terminal at Cleveland, Ohio is described.

Interaction of a solar array with an ion thruster due to the charge-exchange plasma

NASA Technical Reports Server (NTRS)

Kaufman, H. R.

1976-01-01

The generation of a charge exchange plasma by a thruster, the transport of this plasma to the solar array, and the interaction of the solar array with the plasma after it arrives are all described. The generation of this plasma is described accurately from thruster geometry and operating conditions. The transport of the charge exchange plasma was studied experimentally with a 15 cm thruster. A model was developed for simple thruster array configurations. A variety of experiments were surveyed for the interaction of the plasma at the solar array.

Voluntary eyeblinks disrupt iconic memory.

PubMed

Thomas, Laura E; Irwin, David E

2006-04-01

In the present research, we investigated whether eyeblinks interfere with cognitive processing. In Experiment 1, the participants performed a partial-report iconic memory task in which a letter array was presented for 106 msec, followed 50, 150, or 750 msec later by a tone that cued recall of onerow of the array. At a cue delay of 50 msec between array offset and cue onset, letter report accuracy was lower when the participants blinked following array presentation than under no-blink conditions; the participants made more mislocation errors under blink conditions. This result suggests that blinking interferes with the binding of object identity and object position in iconic memory. Experiment 2 demonstrated that interference due to blinks was not due merely to changes in light intensity. Experiments 3 and 4 demonstrated that other motor responses did not interfere with iconic memory. We propose a new phenomenon, cognitive blink suppression, in which blinking inhibits cognitive processing. This phenomenon may be due to neural interference. Blinks reduce activation in area V1, which may interfere with the representation of information in iconic memory.

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.

PubMed

Sanges, Remo; Cordero, Francesca; Calogero, Raffaele A

2007-12-15

OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. Affymetrix 3' expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines. http://www.bioconductor.org/packages/2.0/bioc/html/oneChannelGUI.html

Phased Array Radar Network Experiment for Severe Weather

NASA Astrophysics Data System (ADS)

Ushio, T.; Kikuchi, H.; Mega, T.; Yoshikawa, E.; Mizutani, F.; Takahashi, N.

2017-12-01

Phased Array Weather Radar (PAWR) was firstly developed in 2012 by Osaka University and Toshiba under a grant of NICT using the Digital Beamforming Technique, and showed a impressive thunderstorm behavior with 30 second resolution. After that development, second PAWR was installed in Kobe city about 60 km away from the first PAWR site, and Tokyo Metropolitan University, Osaka Univeristy, Toshiba and the Osaka Local Government started a new project to develop the Osaka Urban Demonstration Network. The main sensor of the Osaka Network is a 2-node Phased Array Radar Network and lightning location system. Data products that are created both in local high performance computer and Toshiba Computer Cloud, include single and multi-radar data, vector wind, quantitative precipitation estimation, VIL, nowcasting, lightning location and analysis. Each radar node is calibarated by the baloon measurement and through the comparison with the GPM (Global Precipitation Measurement)/ DPR (Dual Frequency Space borne Radar) within 1 dB. The attenuated radar reflectivities obtained by the Phased Array Radar Network at X band are corrected based on the bayesian scheme proposed in Shimamura et al. [2016]. The obtained high resolution (every 30 seconds/ 100 elevation angles) 3D reflectivity and rain rate fields are used to nowcast the surface rain rate up to 30 minutes ahead. These new products are transferred to Osaka Local Government in operational mode and evaluated by several section in Osaka Prefecture. Furthermore, a new Phased Array Radar with polarimetric function has been developed in 2017, and will be operated in the fiscal year of 2017. In this presentation, Phased Array Radar, network architecuture, processing algorithm, evalution of the social experiment and first Multi-Prameter Phased Array Radar experiment are presented.

Streamwise Evolution of Statistical Events in a Model Wind-Turbine Array

NASA Astrophysics Data System (ADS)

Viestenz, Kyle; Cal, Raúl Bayoán

2016-02-01

Hot-wire anemometry data, obtained from a wind-tunnel experiment containing a 3 × 3 model wind-turbine array, are used to conditionally average the Reynolds stresses. Nine profiles at the centreline behind the array are analyzed to characterize the turbulent velocity statistics of the wake flow. Quadrant analysis yields statistical events occurring in the wake of the wind farm where quadrants 2 and 4 produce ejections and sweeps, respectively. The scaled difference between these two events is expressed via the Δ R0 parameter and is based on the Δ S0 quantity as introduced by M. R. Raupach (J Fluid Mech 108:363-382, 1981). Δ R0 attains a maximum value at hub height and changes sign near the top of the rotor. The ratio of quadrant events of upward momentum flux to those of the downward flux, known as the exuberance, is examined and reveals the effect of root vortices persisting to eight rotor diameters downstream. These events are then associated with the triple correlation term present in the turbulent kinetic energy equation of the fluctuations where it is found that ejections play the dual role of entraining mean kinetic energy while convecting turbulent kinetic energy out of the turbine canopy. The development of these various quantities possesses significance in closure models, and is assessed in light of wake remediation, energy transport and power fluctuations, where it is found that the maximum fluctuation is about 30% of the mean power produced.

Two CMOS gate arrays for the EPACT experiment

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

Winkert, G.

1992-08-01

Two semicustom CMOS digital gate arrays are described in this paper which have been developed for the Energetic Particles: Acceleration, Composition, and Transport (EPACT) experiment. The first device, the 'Event Counters: 16 by 24-bit' (EC1624), implements sixteen 24-bit ripple counters and has flexible counting and readout options. The second device, the 'Serial Transmitter/Receiver' (SXR), is a multi-personality chip that can be used at either end of a serial, synchronous communications data link. It can be configured as a master in a central control unit, or as one of many slaves within remote assemblies. Together a network of SXRs allows formore » commanding and verification of distributed control signals. Both gate arrays are radiation hardened and qualified for space flight use. The architecture of each chip is presented and the benefits to the experiment summarized.« less

Flight Experience from Space Photovoltaic Concentrator Arrays and its Implication on Terrestrial Concentrator Systems

NASA Technical Reports Server (NTRS)

Piszczor, Michael F., Jr.

2003-01-01

Nearly all photovoltaic solar arrays flown in space have used a planar (non- concentrating) design. However, there have been a few notable exceptions where photovoltaic concentrators have been tested and used as the mission s primary power source. Among these are the success experienced by the SCARLET (Solar Concentrator Array with Refractive Linear Element Technology) concept used to power NASA's Deep Space 1 mission and the problems encountered by the original Boeing 702 reflective trough concentrator design. This presentation will give a brief overview of past photovoltaic concentrator systems that have flown in space, specifically addressing the valuable lessons learned from flight experience, and other viable concentrator concepts that are being proposed for the future. The general trends of this flight experience will be noted and discussed with regard to its implications on terrestrial photovoltaic concentrator designs.

A New Individually Addressable Micro-LED Array for Photogenetic Neural Stimulation.

PubMed

McGovern, B; Berlinguer Palmini, R; Grossman, N; Drakakis, E; Poher, V; Neil, M A A; Degenaar, P

2010-12-01

Here, we demonstrate the use of a micro light emitting diode (LED) array as a powerful tool for complex spatiotemporal control of photosensitized neurons. The array can generate arbitrary, 2-D, excitation patterns with millisecond and micrometer resolution. In particular, we describe an active matrix control address system to allow simultaneous control of 256 individual micro LEDs. We present the system optically integrated into a microscope environment and patch clamp electrophysiology. The results show that the emitters have sufficient radiance at the required wavelength to stimulate neurons expressing channelrhodopsin-2 (ChR2).

On the current drive capability of low dimensional semiconductors: 1D versus 2D

DOE PAGES

Zhu, Y.; Appenzeller, J.

2015-10-29

Low-dimensional electronic systems are at the heart of many scaling approaches currently pursuit for electronic applications. Here, we present a comparative study between an array of one-dimensional (1D) channels and its two-dimensional (2D) counterpart in terms of current drive capability. Lastly, our findings from analytical expressions derived in this article reveal that under certain conditions an array of 1D channels can outperform a 2D field-effect transistor because of the added degree of freedom to adjust the threshold voltage in an array of 1D devices.

Landsat 7 Solar Array Testing Experiences

NASA Technical Reports Server (NTRS)

Helfrich, Daniel

2000-01-01

This paper covers the extensive Landsat 7 solar array flight qualification testing effort. Details of the mechanical design of the solar array and its retention/release system are presented. A testing chronology is provided beginning with the onset of problems encountered at the subsystem level and carrying through the third and final powered-spacecraft ground deployment test. Design fixes and other changes are explained in the same order as they became necessary to flight-qualify the array. Some interesting lessons learned are included along with key references.

Fluorescence-based bioassays for the detection and evaluation of food materials.

PubMed

Nishi, Kentaro; Isobe, Shin-Ichiro; Zhu, Yun; Kiyama, Ryoiti

2015-10-13

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

Fluorescence-Based Bioassays for the Detection and Evaluation of Food Materials

PubMed Central

Nishi, Kentaro; Isobe, Shin-Ichiro; Zhu, Yun; Kiyama, Ryoiti

2015-01-01

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials. PMID:26473869

Topographical cone photopigment gene expression in deutan-type red-green color vision defects.

PubMed

Bollinger, Kathryn; Sjoberg, Stacy A; Neitz, Maureen; Neitz, Jay

2004-01-01

Eye donors were identified who had X-chromosome photopigment gene arrays like those of living deuteranomalous men; the arrays contained two genes encoding long-wavelength sensitive (L) pigments as well as genes to encode middle-wavelength sensitive (M) photopigment. Ultrasensitive methods failed to detect the presence of M photopigment mRNA in the retinas of these deutan donors. This provides direct evidence that deuteranomaly is caused by the complete absence of M pigment mRNA. Additionally, for those eyes with mRNA corresponding to two different L-type photopigments, the ratio of mRNA from the first vs. downstream L genes was analyzed across the retinal topography. Results show that the pattern of first relative to downstream L gene expression in the deuteranomalous retina is similar to the pattern of L vs. M gene expression found in normal retinas.

Increased expression of resistin in ectopic endometrial tissue of women with endometriosis.

PubMed

Oh, Yoon Kyung; Ha, Young Ran; Yi, Kyong Wook; Park, Hyun Tae; Shin, Jung-Ho; Kim, Tak; Hur, Jun-Young

2017-11-01

Inflammation is a key process in the establishment and progression of endometriosis. Resistin, an adipocytokine, has biological properties linked to immunologic functions, but its role in endometriosis is unclear. Resistin gene expression was examined in eutopic and ectopic endometrial tissues from women with (n=25) or without (n=25) endometriosis. Resistin mRNA and protein levels were determined in endometrial tissue using quantitative real-time reverse transcription PCR and Western blotting, following adipokine profiling arrays. Resistin protein was detected in human endometrial tissues using an adipokine array test. Resistin mRNA and protein levels were significantly higher in ectopic endometrial tissue of patients with endometriosis than in normal eutopic endometrial tissue. Our results indicate that resistin is differentially expressed in endometrial tissues from women with endometriosis and imply a role for resistin in endometriosis-associated pelvic inflammation. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Organization of Synthetic Alphoid DNA Array in Human Artificial Chromosome (HAC) with a Conditional Centromere

PubMed Central

Kouprina, Natalay; Samoshkin, Alexander; Erliandri, Indri; Nakano, Megumi; Lee, Hee-Sheung; Fu, Haiging; Iida, Yuichi; Aladjem, Mirit; Oshimura, Mitsuo; Masumoto, Hiroshi; Earnshaw, William C.; Larionov, Vladimir

2012-01-01

Human artificial chromosomes (HACs) represent a novel promising episomal system for functional genomics, gene therapy and synthetic biology. HACs are engineered from natural and synthetic alphoid DNA arrays upon transfection into human cells. The use of HACs for gene expression studies requires the knowledge of their structural organization. However, none of de novo HACs constructed so far has been physically mapped in detail. Recently we constructed a synthetic alphoidtetO-HAC that was successfully used for expression of full-length genes to correct genetic deficiencies in human cells. The HAC can be easily eliminated from cell populations by inactivation of its conditional kinetochore. This unique feature provides a control for phenotypic changes attributed to expression of HAC-encoded genes. This work describes organization of a megabase-size synthetic alphoid DNA array in the alphoidtetO-HAC that has been formed from a ~50 kb synthetic alphoidtetO-construct. Our analysis showed that this array represents a 1.1 Mb continuous sequence assembled from multiple copies of input DNA, a significant part of which was rearranged before assembling. The tandem and inverted alphoid DNA repeats in the HAC range in size from 25 to 150 kb. In addition, we demonstrated that the structure and functional domains of the HAC remains unchanged after several rounds of its transfer into different host cells. The knowledge of the alphoidtetO-HAC structure provides a tool to control HAC integrity during different manipulations. Our results also shed light on a mechanism for de novo HAC formation in human cells. PMID:23411994

Use of Geometric Properties of Landmark Arrays for Reorientation Relative to Remote Cities and Local Objects

ERIC Educational Resources Information Center

Mou, Weimin; Nankoo, Jean-François; Zhou, Ruojing; Spetch, Marcia L.

2014-01-01

Five experiments investigated how human adults use landmark arrays in the immediate environment to reorient relative to the local environment and relative to remote cities. Participants learned targets' directions with the presence of a proximal 4 poles forming a rectangular shape and an array of more distal poles forming a rectangular shape. Then…

Status and Integrated Focal Plane Characterization of Simons Array - Cosmic Microwave Background Polarimetry Experiment

NASA Astrophysics Data System (ADS)

Roberts, Hayley; POLARBEAR

2018-06-01

Simons Array is a cosmic microwave background (CMB) polarization experiment located at 5,200 meter altitude site in the Atacama desert in Chile. The science goals of the Simons Array are to characterize the CMB B-mode signal from gravitational lensing, and search for B-mode polarization generated from inflationary gravitational waves.In 2012, POLARBEAR-1 (PB-1) began observations and the POLARBEAR team has published the first measurements of non-zero polarization B-mode polarization angular power spectrum where gravitational lensing of CMB is the dominant signal.POLARBEAR-2A (PB-2A), the first of three receivers of Simons Array, will have 7,588 polarization sensitive Transition Edge Sensor (TES) bolometers with frequencies 90 GHz and 150 GHz. This represents a factor of 6 increase in detector count compared to PB-1. Once Simons Array is fully deployed, the focal plane array will consist 22,764 TES bolometers across 90 GHz, 150 GHz, 220 GHz, and 270 GHz with a projected instantaneous sensitivity of 2.5 µK√s. Here we present the status of PB-2A and characterization of the integrated focal plane to be deployed summer of 2018.

Solar array flight experiment

NASA Technical Reports Server (NTRS)

1986-01-01

Emerging satellite designs require increasing amounts of electrical power to operate spacecraft instruments and to provide environments suitable for human habitation. In the past, electrical power was generated by covering rigid honeycomb panels with solar cells. This technology results in unacceptable weight and volume penalties when large amounts of power are required. To fill the need for large-area, lightweight solar arrays, a fabrication technique in which solar cells are attached to a copper printed circuit laminated to a plastic sheet was developed. The result is a flexible solar array with one-tenth the stowed volume and one-third the weight of comparably sized rigid arrays. An automated welding process developed to attack the cells to the printed circuit guarantees repeatable welds that are more tolerant of severe environments than conventional soldered connections. To demonstrate the flight readiness of this technology, the Solar Array Flight Experiment (SAFE) was developed and flown on the space shuttle Discovery in September 1984. The tests showed the modes and frequencies of the array to be very close to preflight predictions. Structural damping, however, was higher than anticipated. Electrical performance of the active solar panel was also tested. The flight performance and postflight data evaluation are described.

Synthetic aperture ultrasound imaging with a ring transducer array: preliminary ex vivo results.

PubMed

Qu, Xiaolei; Azuma, Takashi; Yogi, Takeshi; Azuma, Shiho; Takeuchi, Hideki; Tamano, Satoshi; Takagi, Shu

2016-10-01

The conventional medical ultrasound imaging has a low lateral spatial resolution, and the image quality depends on the depth of the imaging location. To overcome these problems, this study presents a synthetic aperture (SA) ultrasound imaging method using a ring transducer array. An experimental ring transducer array imaging system was constructed. The array was composed of 2048 transducer elements, and had a diameter of 200 mm and an inter-element pitch of 0.325 mm. The imaging object was placed in the center of the ring transducer array, which was immersed in water. SA ultrasound imaging was then employed to scan the object and reconstruct the reflection image. Both wire phantom and ex vivo experiments were conducted. The proposed method was found to be capable of producing isotropic high-resolution images of the wire phantom. In addition, preliminary ex vivo experiments using porcine organs demonstrated the ability of the method to reconstruct high-quality images without any depth dependence. The proposed ring transducer array and SA ultrasound imaging method were shown to be capable of producing isotropic high-resolution images whose quality was independent of depth.

Gene expression profiling defined pathways correlated with fibroblast cell proliferation induced by Opisthorchis viverrini excretory/secretory product.

PubMed

Thuwajit, Chanitra; Thuwajit, Peti; Uchida, Kazuhiko; Daorueang, Daoyot; Kaewkes, Sasithorn; Wongkham, Sopit; Miwa, Masanao

2006-06-14

To investigate the mechanism of fibroblast cell proliferation stimulated by the Opisthorchis viverrini excretory/secretory (ES) product. NIH-3T3, mouse fibroblast cells were treated with O. viverrini ES product by non-contact co-cultured with the adult parasites. Total RNA from NIH-3T3 treated and untreated with O. viverrini was extracted, reverse transcribed and hybridized with the mouse 15K complementary DNA (cDNA) array. The result was analyzed by ArrayVision version 5 and GeneSpring version 5 softwares. After normalization, the ratios of gene expression of parasite treated to untreated NIH-3T3 cells of 2-and more-fold upregulated was defined as the differentially expressed genes. The expression levels of the signal transduction genes were validated by semi-quantitative SYBR-based real-time RT-PCR. Among a total of 15,000 genes/ESTs, 239 genes with established cell proliferation-related function were 2 fold-and more-up-regulated by O. viverrini ES product compared to those in cells without exposure to the parasitic product. These genes were classified into groups including energy and metabolism, signal transduction, protein synthesis and translation, matrix and structural protein, transcription control, cell cycle and DNA replication. Moreover, the expressions of serine-threonine kinase receptor, receptor tyrosine kinase and collagen production-related genes were up-regulated by O. viverrini ES product. The expression level of signal transduction genes; pkC, pdgfr alpha, jak 1, eps 8, tgf beta 1i4, strap and h ras measured by real-time RT-PCR confirmed their expression levels to those obtained from cDNA array. However, only the up-regulated expression of pkC, eps 8 and tgfbeta 1i4 which are the downstream signaling molecules of either epidermal growth factor (EGF) or transforming growth factor-beta (TGF-beta) showed statistical significance (P < 0.05). O. viverrini ES product stimulates the significant changes of gene expression in several functional categories and these mainly include transcripts related to cell proliferation. The TGF-beta and EGF signal transduction pathways are indicated as the possible pathways of O. viverrini-driven cell proliferation.

Differential gene expression in anterior pituitary glands from anestrous and cycling postpartum beef cows

USDA-ARS?s Scientific Manuscript database

Oligionucleotide microarrays (GeneChip Bovine Genome Arrays, Affymetrix Inc., Santa Clara, CA) were used to evaluate gene expression profiles in anterior pituitary glands collected from 4 anestrous and 4 cycling postpartum primiparous beef cows to provide insight into genes associated with transitio...

APPLICATION OF DNA MICROARRAYS TO REPRODUCTIVE TOXICOLOGY AND THE DEVELOPMENT OF A TESTIS ARRAY

EPA Science Inventory

With the advent of sequence information for entire mammalian genomes, it is now possible to analyze gene expression and gene polymorphisms on a genomic scale. The primary tool for analysis of gene expression is the DNA microarray. We have used commercially available cDNA micro...

High-voltage space-plasma interactions measured on the PASP Plus test arrays

NASA Astrophysics Data System (ADS)

Guidice, Donald A.

1995-10-01

The Photovoltaic Array Space Power Plus Diagnostics (PASP Plus) experiment was developed by the Air Force's Phillips Laboratory with support from NASA's Lewis Research Center. It was launched on the Advanced Photovoltaic and Electronics EXperiments (APEX) satellite on August 3, 1994 into a 70 degree inclination, 363 km by 2550 km elliptical orbit. This orbit allows the investigation of space plasma effects on high-voltage operation (leakage current at positive voltages and arcing at negative voltages) in the perigee region. PASP Plus is testing twelve solar arrays. There are four planar Si arrays: an old standard type (used as a reference), the large-cell Space Station Freedom (SSF) array, a thin 'APSA' array, and an amorphous Si array. Next are three GaAs on Ge planar arrays and three new material planar arrays, including InP and two multijunction types. Finally, there are two concentrator arrays: a reflective-focusing Mini-Cassegrainian and a Fresnel-lens focusing Mini-Dome. PASP Plus's diagnostic sensors include: Langmuir probe to measure plasma density, an electrostatic analyzer (ESA) to measure the 30 eV to 30 KeV electron/ion spectra and determine vehicle negative potential during positive biasing, and a transient pulse monitor (TPM) to characterize the arcs that occur during the negative biasing. Through positive biasing of its test arrays, PASP Plus investigated the snapover phenomenon, which took place over the range of +100 to +300 V. It was found that array configurations where the interconnects are shielded from the space plasma (i.e., the concentrators or arrays with 'wrap-through' connectors) have lower leakage current. The concentrators exhibited negligible leakage current over the whole range up to +500 V. In the case of two similar GaAs on Ge arrays, the one with 'wrap-through' connectors had lower leakage current than the one with conventional interconnects. Through negative biasing, PASP Plus investigated the arcing rates of its test arrays. The standard Si array, with its old construction (exposed rough-surface interconnects), arced significantly over a wide voltage and plasma-density range. The other arrays arced at very low rates, mostly at voltages greater than -350 V and plasma densities near or greater than 10(exp 5)/cm(exp -3). AS expected according to theory, arcing was more prevalent when array temperatures were cold (based on biasing in eclipse).

High-voltage space-plasma interactions measured on the PASP Plus test arrays

NASA Technical Reports Server (NTRS)

Guidice, Donald A.

1995-01-01

The Photovoltaic Array Space Power Plus Diagnostics (PASP Plus) experiment was developed by the Air Force's Phillips Laboratory with support from NASA's Lewis Research Center. It was launched on the Advanced Photovoltaic and Electronics EXperiments (APEX) satellite on August 3, 1994 into a 70 degree inclination, 363 km by 2550 km elliptical orbit. This orbit allows the investigation of space plasma effects on high-voltage operation (leakage current at positive voltages and arcing at negative voltages) in the perigee region. PASP Plus is testing twelve solar arrays. There are four planar Si arrays: an old standard type (used as a reference), the large-cell Space Station Freedom (SSF) array, a thin 'APSA' array, and an amorphous Si array. Next are three GaAs on Ge planar arrays and three new material planar arrays, including InP and two multijunction types. Finally, there are two concentrator arrays: a reflective-focusing Mini-Cassegrainian and a Fresnel-lens focusing Mini-Dome. PASP Plus's diagnostic sensors include: Langmuir probe to measure plasma density, an electrostatic analyzer (ESA) to measure the 30 eV to 30 KeV electron/ion spectra and determine vehicle negative potential during positive biasing, and a transient pulse monitor (TPM) to characterize the arcs that occur during the negative biasing. Through positive biasing of its test arrays, PASP Plus investigated the snapover phenomenon, which took place over the range of +100 to +300 V. It was found that array configurations where the interconnects are shielded from the space plasma (i.e., the concentrators or arrays with 'wrap-through' connectors) have lower leakage current. The concentrators exhibited negligible leakage current over the whole range up to +500 V. In the case of two similar GaAs on Ge arrays, the one with 'wrap-through' connectors had lower leakage current than the one with conventional interconnects. Through negative biasing, PASP Plus investigated the arcing rates of its test arrays. The standard Si array, with its old construction (exposed rough-surface interconnects), arced significantly over a wide voltage and plasma-density range. The other arrays arced at very low rates, mostly at voltages greater than -350 V and plasma densities near or greater than 10(exp 5)/cm(exp -3). AS expected according to theory, arcing was more prevalent when array temperatures were cold (based on biasing in eclipse).

PV modules for ground testing

NASA Technical Reports Server (NTRS)

1986-01-01

The main objective was to design and build a minimum of three photovoltaic test panels for plasma interaction experiments. These experiments are intended to provide data on the interactions between high-voltage solar arrays and the space plasma environment. Data gathered will significantly contribute to the development of design criteria for the space station solar arrays. Electrical isolation between the solar cell strings and the module mounting plate is required for high-voltage bias.

New Planar Wire Array Experiments on the LTD Generator at U Michigan

NASA Astrophysics Data System (ADS)

Weller, M. E.; Safronova, A. S.; Kantsyrev, V. L.; Shrestha, I.; Shlyaptseva, V. V.; Cooper, M. C.; Lorance, M. Y.; Stafford, A.; Petkov, E. E.; Jordan, N. M.; Patel, S. G.; Steiner, A. M.; Yager-Elorriaga, D. A.; Gilgenbach, R. M.

2014-10-01

Experiments on planar wire array z-pinches have been carried out on the MAIZE Linear Transformer Driver (LTD) generator at the University of Michigan (UM) for the first time. Specifically, Al (Al 5056, 95% Al, 5% Mg) double planar wire arrays (DPWAs) comprising six wires in each plane with interplanar gaps of 3.0 mm and 6.0 mm and interwire gaps of 0.7 mm and 1.0 mm were imploded with x-ray time-integrated spectra indicating electron temperatures of over 450 eV for K-shell Al and Mg, while producing mostly optically thin lines. In addition to x-ray time-integrated spectra, the diagnostics included x-ray time-integrated pinhole cameras, two silicon diodes, and shadowgraphy, which are analyzed and compared. The MAIZE LTD is capable of supplying up 1.0 MA, 100 kV pulses with 100 ns rise time into a matched load. However, for these experiments the LTD was charged to +-70 kV resulting in up to 0.5 MA with a current rise time of approximately 150 ns. Future experiments and the importance of studying planar wire arrays on LTD devices are discussed. This work supported by NNSA under DOE Cooperative Agreement DE-NA0001984. S. Patel & A. Steiner supported by Sandia. D. Yager-Elorriaga supported by NSF GF.

Arrays of microscopic organic LEDs for high-resolution optogenetics

PubMed Central

Steude, Anja; Witts, Emily C.; Miles, Gareth B.; Gather, Malte C.

2016-01-01

Optogenetics is a paradigm-changing new method to study and manipulate the behavior of cells with light. Following major advances of the used genetic constructs over the last decade, the light sources required for optogenetic control are now receiving increased attention. We report a novel optogenetic illumination platform based on high-density arrays of microscopic organic light-emitting diodes (OLEDs). Because of the small dimensions of each array element (6 × 9 μm2) and the use of ultrathin device encapsulation, these arrays enable illumination of cells with unprecedented spatiotemporal resolution. We show that adherent eukaryotic cells readily proliferate on these arrays, and we demonstrate specific light-induced control of the ionic current across the membrane of individual live cells expressing different optogenetic constructs. Our work paves the way for the use of OLEDs for cell-specific optogenetic control in cultured neuronal networks and for acute brain slices, or as implants in vivo. PMID:27386540

Proof of Concept Study to Assess Fetal Gene Expression in Amniotic Fluid by NanoArray PCR

PubMed Central

Massingham, Lauren J.; Johnson, Kirby L.; Bianchi, Diana W.; Pei, Shermin; Peter, Inga; Cowan, Janet M.; Tantravahi, Umadevi; Morrison, Tom B.

2011-01-01

Microarray analysis of cell-free RNA in amniotic fluid (AF) supernatant has revealed differential fetal gene expression as a function of gestational age and karyotype. Once informative genes are identified, research moves to a more focused platform such as quantitative reverse transcriptase-PCR. Standardized NanoArray PCR (SNAP) is a recently developed gene profiling technology that enables the measurement of transcripts from samples containing reduced quantities or degraded nucleic acids. We used a previously developed SNAP gene panel as proof of concept to determine whether fetal functional gene expression could be ascertained from AF supernatant. RNA was extracted and converted to cDNA from 19 AF supernatant samples of euploid fetuses between 15 to 20 weeks of gestation, and transcript abundance of 21 genes was measured. Statistically significant differences in expression, as a function of advancing gestational age, were observed for 5 of 21 genes. ANXA5, GUSB, and PPIA showed decreasing gene expression over time, whereas CASC3 and ZNF264 showed increasing gene expression over time. Statistically significantly increased expression of MTOR and STAT2 was seen in female compared with male fetuses. This study demonstrates the feasibility of focused fetal gene expression analysis using SNAP technology. In the future, this technique could be optimized to examine specific genes instrumental in fetal organ system function, which could be a useful addition to prenatal care. PMID:21827969

Weighted analysis of paired microarray experiments.

PubMed

Kristiansson, Erik; Sjögren, Anders; Rudemo, Mats; Nerman, Olle

2005-01-01

In microarray experiments quality often varies, for example between samples and between arrays. The need for quality control is therefore strong. A statistical model and a corresponding analysis method is suggested for experiments with pairing, including designs with individuals observed before and after treatment and many experiments with two-colour spotted arrays. The model is of mixed type with some parameters estimated by an empirical Bayes method. Differences in quality are modelled by individual variances and correlations between repetitions. The method is applied to three real and several simulated datasets. Two of the real datasets are of Affymetrix type with patients profiled before and after treatment, and the third dataset is of two-colour spotted cDNA type. In all cases, the patients or arrays had different estimated variances, leading to distinctly unequal weights in the analysis. We suggest also plots which illustrate the variances and correlations that affect the weights computed by our analysis method. For simulated data the improvement relative to previously published methods without weighting is shown to be substantial.

A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data.

PubMed

Bikel, Shirley; Jacobo-Albavera, Leonor; Sánchez-Muñoz, Fausto; Cornejo-Granados, Fernanda; Canizales-Quinteros, Samuel; Soberón, Xavier; Sotelo-Mundo, Rogerio R; Del Río-Navarro, Blanca E; Mendoza-Vargas, Alfredo; Sánchez, Filiberto; Ochoa-Leyva, Adrian

2017-01-01

In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays. We extracted the RNA from 16 children leukocyte samples (nine males and seven females, ages 6-10 years). An Affymetrix Gene Chip Human Gene 1.0 ST Array was carried out for each sample and the fluorescence of 124 genes of the Y chromosome was used to calculate the absolute gene expression threshold. After that, several expressed and non-expressed genes according to our absolute gene expression threshold were compared against the expression obtained using real-time quantitative polymerase chain reaction (RT-qPCR). From the 124 genes of the Y chromosome, three genes (DDX3Y, TXLNG2P and EIF1AY) that displayed significant differences between sexes were used to calculate the absolute gene expression threshold. Using this threshold, we selected 13 expressed and non-expressed genes and confirmed their expression level by RT-qPCR. Then, we selected the top 5% most expressed genes and found that several KEGG pathways were significantly enriched. Interestingly, these pathways were related to the typical functions of leukocytes cells, such as antigen processing and presentation and natural killer cell mediated cytotoxicity. We also applied this method to obtain the absolute gene expression threshold in already published microarray data of liver cells, where the top 5% expressed genes showed an enrichment of typical KEGG pathways for liver cells. Our results suggest that the three selected genes of the Y chromosome can be used to calculate an absolute gene expression threshold, allowing a transcriptome profiling of microarray data without the need of an additional reference experiment. Our approach based on the establishment of a threshold for absolute gene expression analysis will allow a new way to analyze thousands of microarrays from public databases. This allows the study of different human diseases without the need of having additional samples for relative expression experiments.

How to reduce the effect of framing on messages about health.

PubMed

Garcia-Retamero, Rocio; Galesic, Mirta

2010-12-01

Patients must be informed about risks before any treatment can be implemented. Yet serious problems in communicating these risks occur because of framing effects. To investigate the effects of different information frames when communicating health risks to people with high and low numeracy and determine whether these effects can be countered or eliminated by using different types of visual displays (i.e., icon arrays, horizontal bars, vertical bars, or pies). Experiment on probabilistic, nationally representative US (n = 492) and German (n = 495) samples, conducted in summer 2008. Participants' risk perceptions of the medical risk expressed in positive (i.e., chances of surviving after surgery) and negative (i.e., chances of dying after surgery) terms. Although low-numeracy people are more susceptible to framing than those with high numeracy, use of visual aids is an effective method to eliminate its effects. However, not all visual aids were equally effective: pie charts and vertical and horizontal bars almost completely removed the effect of framing. Icon arrays, however, led to a smaller decrease in the framing effect. Difficulties with understanding numerical information often do not reside in the mind, but in the representation of the problem.

Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti.

PubMed

Adelman, Zach N; Jasinskiene, Nijole; Vally, K J M; Peek, Corrie; Travanty, Emily A; Olson, Ken E; Brown, Susan E; Stephens, Janice L; Knudson, Dennis L; Coates, Craig J; James, Anthony A

2004-10-01

The Class II transposable element, piggyBac, was used to transform the yellow fever mosquito, Aedes aegypti. In two transformed lines only 15-30% of progeny inherited the transgene, with these individuals displaying mosaic expression of the EGFP marker gene. Southern analyses, gene amplification of genomic DNA, and plasmid rescue experiments provided evidence that these lines contained a high copy number of piggyBac transformation constructs and that much of this DNA consisted of both donor and helper plasmids. A detailed analysis of one line showed that the majority of piggyBac sequences were unit-length donor or helper plasmids arranged in a large tandem array that could be lost en masse in a single generation. Despite the presence of a transposase source and many intact donor elements, no conservative (cut and paste) transposition of piggyBac was observed in these lines. These results reveal one possible outcome of uncontrolled and/or unexpected recombination in this mosquito, and support the conclusion that further investigation is necessary before transposable elements such as piggyBac can be used as genetic drive mechanisms to move pathogen-resistance genes into mosquito populations.

Identification of Differentially Expressed Thyroid Hormone Responsive Genes from the Brain of the Mexican Axolotl (Ambystoma mexicanum) ✧

PubMed Central

Huggins, P; Johnson, CK; Schoergendorfer, A; Putta, S; Bathke, AC; Stromberg, AJ; Voss, SR

2011-01-01

The Mexican axolotl (Ambystoma mexicanum) presents an excellent model to investigate mechanisms of brain development that are conserved among vertebrates. In particular, metamorphic changes of the brain can be induced in free-living aquatic juveniles and adults by simply adding thyroid hormone (T4) to rearing water. Whole brains were sampled from juvenile A. mexicanum that were exposed to 0, 8, and 18 days of 50 nM T4, and these were used to isolate RNA and make normalized cDNA libraries for 454 DNA sequencing. A total of 1,875,732 high quality cDNA reads were assembled with existing ESTs to obtain 5,884 new contigs for human RefSeq protein models, and to develop a custom Affymetrix gene expression array (Amby_002) with approximately 20,000 probe sets. The Amby_002 array was used to identify 303 transcripts that differed statistically (p < 0.05, fold change > 1.5) as a function of days of T4 treatment. Further statistical analyses showed that Amby_002 performed concordantly in comparison to an existing, small format expression array. This study introduces a new A. mexicanum microarray resource for the community and the first lists of T4-responsive genes from the brain of a salamander amphibian. PMID:21457787

Identification of differentially expressed thyroid hormone responsive genes from the brain of the Mexican Axolotl (Ambystoma mexicanum).

PubMed

Huggins, P; Johnson, C K; Schoergendorfer, A; Putta, S; Bathke, A C; Stromberg, A J; Voss, S R

2012-01-01

The Mexican axolotl (Ambystoma mexicanum) presents an excellent model to investigate mechanisms of brain development that are conserved among vertebrates. In particular, metamorphic changes of the brain can be induced in free-living aquatic juveniles and adults by simply adding thyroid hormone (T4) to rearing water. Whole brains were sampled from juvenile A. mexicanum that were exposed to 0, 8, and 18 days of 50 nM T4, and these were used to isolate RNA and make normalized cDNA libraries for 454 DNA sequencing. A total of 1,875,732 high quality cDNA reads were assembled with existing ESTs to obtain 5884 new contigs for human RefSeq protein models, and to develop a custom Affymetrix gene expression array (Amby_002) with approximately 20,000 probe sets. The Amby_002 array was used to identify 303 transcripts that differed statistically (p<0.05, fold change >1.5) as a function of days of T4 treatment. Further statistical analyses showed that Amby_002 performed concordantly in comparison to an existing, small format expression array. This study introduces a new A. mexicanum microarray resource for the community and the first lists of T4-responsive genes from the brain of a salamander amphibian. Copyright © 2011 Elsevier Inc. All rights reserved.

Study of array plasma antenna parameters

NASA Astrophysics Data System (ADS)

Kumar, Rajneesh; Kumar, Prince

2018-04-01

This paper is aimed to investigate the array plasma antenna parameters to help the optimization of an array plasma antenna. Single plasma antenna is transformed into array plasma antenna by changing the operating parameters. The re-configurability arises in the form of striations, due to transverse bifurcation of plasma column by changing the operating parameters. Each striation can be treated as an antenna element and system performs like an array plasma antenna. In order to achieve the goal of this paper, three different configurations of array plasma antenna (namely Array 1, Array 2 and Array 3) are simulated. The observations are made on variation in antenna parameters like resonance frequency, radiation pattern, directivity and gain with variation in length and number of antenna elements for each array plasma antenna. Moreover experiments are also performed and results are compared with simulation. Further array plasma antenna parameters are also compared with monopole plasma antenna parameters. The study of present paper invoke the array plasma antenna can be applied for steering and controlling the strength of Wi-Fi signals as per requirement.

Analysis of cellular response by exposure to acute or chronic radiation in human lymphoblastoid TK-6 cells

NASA Astrophysics Data System (ADS)

Ohnishi, T.; Yasumoto, J.; Takahashi, A.; Ohnishi, K.

To clarify the biological effects of low-dose rate radiation on human health for long-term stay in space, we analyzed the induction of apoptosis and apoptosis-related gene expression after irradiation with different dose-rate in human lymphoblastoid TK-6 cells harboring wild-type p53 gene. We irradiated TK-6 cells by X-ray at 1.5 Gy (1 Gy/min) and then sampled at 25 hr after culturing. We also irradiated by gamma-ray at 1.5 Gy (1 mGy/min) and then sampled immediately or 25 hr after irradiation. For DNA ladder analysis, we extracted DNA from these samples and electrophoresed with 2% agarose gel. In addition, we extracted mRNA from these samples for DNA-array analysis. mRNA from non-irradiated cells was used as a control. After labeling the cDNA against mRNA with [α -33P]-dCTP and hybridizing onto DNA array (Human Apoptosis Expression Array, R&D Systems), we scanned the profiles of the spots by a phosphorimager (BAS5000, FUJI FILM) and calculated using a NIH Image program. The data of each DNA-array were normalized with eight kinds of house keeping genes. We analyzed the expression level of apoptosis-related genes such as p53-related, Bcl-2 family, Caspase family and Fas-related genes. DNA ladders were obviously detected in the cells exposed to a high dose-rate radiation. We detected the induction of the gene expression of apoptosis-promotive genes. In contrast, almost no apoptosis was observed in the cells exposed to the chronic radiation at a low dose-rate. In addition, we detected the induction of the gene expression of apoptosis-suppressive genes as compared with apoptosis promotive-genes immediately after chronic irradiation. These results lead the importance of biological meaning of exposure to radiation at low dose-rate from an aspect of carcinogenesis. Finally, the effects of chronic irradiation become a highly important issue in space radiation biology for human health.

An All Silicon Feedhorn-Coupled Focal Plane for Cosmic Microwave Background Polarimetry

NASA Technical Reports Server (NTRS)

Hubmayr, J.; Appel, J. W.; Austermann, J. E.; Beall, J. A.; Becker, D.; Benson, B. A.; Bleem, L. E.; Carlstrom, J. E.; Chang, C. L.; Cho, H. M.;

Small Arrays for Seismic Intruder Detections: A Simulation Based Experiment

NASA Astrophysics Data System (ADS)

Pitarka, A.

2014-12-01

Seismic sensors such as geophones and fiber optic have been increasingly recognized as promising technologies for intelligence surveillance, including intruder detection and perimeter defense systems. Geophone arrays have the capability to provide cost effective intruder detection in protecting assets with large perimeters. A seismic intruder detection system uses one or multiple arrays of geophones design to record seismic signals from footsteps and ground vehicles. Using a series of real-time signal processing algorithms the system detects, classify and monitors the intruder's movement. We have carried out numerical experiments to demonstrate the capability of a seismic array to detect moving targets that generate seismic signals. The seismic source is modeled as a vertical force acting on the ground that generates continuous impulsive seismic signals with different predominant frequencies. Frequency-wave number analysis of the synthetic array data was used to demonstrate the array's capability at accurately determining intruder's movement direction. The performance of the array was also analyzed in detecting two or more objects moving at the same time. One of the drawbacks of using a single array system is its inefficiency at detecting seismic signals deflected by large underground objects. We will show simulation results of the effect of an underground concrete block at shielding the seismic signal coming from an intruder. Based on simulations we found that multiple small arrays can greatly improve the system's detection capability in the presence of underground structures. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344

Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology.

PubMed

Malenke, J R; Milash, B; Miller, A W; Dearing, M D

2013-07-01

Massively parallel sequencing has enabled the creation of novel, in-depth genetic tools for nonmodel, ecologically important organisms. We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) using the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). We tested the microarray with three experiments: one across species with similar habitat (thus, dietary) niches, one across species with different habitat niches and one across populations within a species. The resulting one-colour arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). There were a multitude of expression differences across the woodrat treatments, many of which related to biotransformation processes and activities. The pattern and function of the differences indicate shared ecological pressures, and not merely phylogenetic distance, play an important role in shaping gene expression profiles of woodrat species and populations. The quality and functionality of the woodrat transcriptome and custom microarray suggest these tools will be valuable for expanding the scope of herbivore biology, as well as the exploration of conceptual topics in ecology. © 2013 John Wiley & Sons Ltd.

Numerical study of the properties of optical vortex array laser tweezers.

PubMed

Kuo, Chun-Fu; Chu, Shu-Chun

2013-11-04

Chu et al. constructed a kind of Ince-Gaussian modes (IGM)-based vortex array laser beams consisting of p x p embedded optical vortexes from Ince-Gaussian modes, IG(e)(p,p) modes [Opt. Express 16, 19934 (2008)]. Such an IGM-based vortex array laser beams maintains its vortex array profile during both propagation and focusing, and is applicable to optical tweezers. This study uses the discrete dipole approximation (DDA) method to study the properties of the IGM-based vortex array laser tweezers while it traps dielectric particles. This study calculates the resultant force exerted on the spherical dielectric particles of different sizes situated at the IGM-based vortex array laser beam waist. Numerical results show that the number of trapping spots of a structure light (i.e. IGM-based vortex laser beam), is depended on the relation between the trapped particle size and the structure light beam size. While the trapped particle is small comparing to the beam size of the IGM-based vortex array laser beams, the IGM-based vortex array laser beams tweezers are suitable for multiple traps. Conversely, the tweezers is suitable for single traps. The results of this study is useful to the future development of the vortex array laser tweezers applications.

Mechanical Designs and Developement of Advanced ACT: A Transfomative Upgrade to the ACTPol Receiver on the Atacama Cosmology Telescope.

NASA Astrophysics Data System (ADS)

Ward, Jonathan; Advanced ACT Collaboration, NASA Space Technology Research Fellowship

2017-06-01

The Atacama Cosmology Telescope is a six-meter diameter telescope located at 17,000 feet (5,200 meters) on Cerro Toco in the Andes Mountains of northern Chile. The next generation Advanced ACT (AdvACT) experiment is currently underway and will consist of three multichroic TES bolometer arrays operating together, totaling 5800 detectors on the sky. Each array will be sensitive to two frequency bands: a high frequency (HF) array at 150 and 230 GHz, two middle frequency (MF) arrays at 90 and 150 GHz, and a low frequency (LF) array at 28 and 41 GHz. The AdACT detector arrays will feature a revamped design when compared to ACTPol, including a transition to 150mm wafers equipped with multichroic pixels, allowing for a more densely packed focal plane. Each set of detectors consists of a feedhorn array of stacked silicon wafers which form a corrugated profile leading to each pixel. This is then followed by a four-piece detector stack assembly of silicon wafers which includes a waveguide interface plate, detector wafer, backshort cavity plate, and backshort cap. Each array is housed in a custom designed structure manufactured out of gold-plated, high purity copper. In addition to the detector array assembly, the array package also encloses the majority of our readout electronics. We present the full mechanical design of the AdvACT HF and MF detector array packages along with a detailed look at the detector array assemblies. We also highlight the use of continuously rotating warm half-wave plates (HWPs) at the front of the AdvACT receiver. We review the design of the rotation system and also early pipeline data analysis results. This experiment will also make use of extensive hardware and software previously developed for ACT, which will be modified to incorporate the new AdvACT instruments. Therefore, we discuss the integration of all AdvACT instruments with pre-existing ACTPol infrastructure.

Acoustic imaging of aircraft wake vortex dynamics

DOT National Transportation Integrated Search

2005-06-01

The experience in utilizing a phased microphone array to passively image aircraft wake : vortices is highlighted. It is demonstrated that the array can provide visualization of wake : dynamics similar to smoke release or natural condensation of vorti...

EAS thermal neutron detection with the PRISMA-LHAASO-16 experiment

NASA Astrophysics Data System (ADS)

Li, B.-B.; Alekseenko, V. V.; Cui, S.-w.; Chen, T.-L.; Dangzengluobu; Feng, S.-H.; Gao, Q.; Liu, Y.; Huang, Q.-C.; He, Y.-Y.; Liu, M.-Y.; Ma, X.-H.; Pozdnyakov, E. I.; Shchegolev, O. B.; Shen, F.-Z.; Stenkin, Yu. V.; Stepanov, V. I.; Yanin, Ya. V.; Yao, J.-D.; Zhou, R.

2017-12-01

EAS (extensive air shower) thermal neutron measurement gives advantages to study energy and mass composition of primary cosmic rays especially in the knee region. After the success of the PRISMA-YBJ experiment, we build a new EAS thermal neutron detection array at Tibet University, Lhasa, China (3700 m a.s.l.) in March, 2017. This prototype array so called "PRISMA-LHAASO-16" consists of 16 EAS EN-detectors ("EN" is abbreviation for electron and neutron) measuring two main EAS components: hadronic and electromagnetic ones. Different from PRISMA-YBJ, these detectors use a thin layer of a novel type of ZnS(Ag) scintillator alloyed with natural boron compound for thermal neutron capture. PRISMA-LHAASO-16 will be moved to the LHAASO site in the near future. In this paper, we introduce principle of the detection technique, deployment of the array, and the test results of the array.

Discharge transient coupling in large space power systems

NASA Technical Reports Server (NTRS)

Stevens, N. John; Stillwell, R. P.

1990-01-01

Experiments have shown that plasma environments can induce discharges in solar arrays. These plasmas simulate the environments found in low earth orbits where current plans call for operation of very large power systems. The discharges could be large enough to couple into the power system and possibly disrupt operations. Here, the general concepts of the discharge mechanism and the techniques of coupling are discussed. Data from both ground and flight experiments are reviewed to obtain an expected basis for the interactions. These concepts were applied to the Space Station solar array and distribution system as an example of the large space power system. The effect of discharges was found to be a function of the discharge site. For most sites in the array discharges would not seriously impact performance. One location at the negative end of the array was identified as a position where discharges could couple to charge stored in system capacitors. This latter case could impact performance.

Experimental test of liquid droplet radiator performance

NASA Astrophysics Data System (ADS)

Mattick, A. T.; Simon, M. A.

The liquid droplet radiator (LDR) is a heat rejection system for space power systems wherein an array of heated liquid droplets radiates energy directly to space. The use of submillimeter droplets provides large radiating area-to-mass ratio, resulting in radiator systems which are several times lighter than conventional solid surface radiators. An experiment is described in which the power radiated by an array of 2300 streams of silicone oil droplets is measured to test a previously developed theory of the LDR radiation process. This system would be capable of rejecting several kW of heat in space. Furthermore, it would be suitable as a modular unit of an LDR designed for 100-kW power levels. The experiment provided confirmation of the theoretical dependence of droplet array emissivity on optical depth. It also demonstrated the ability to create an array of more than 1000 droplet streams having a divergence less than 1 degree.

Experimental test of liquid droplet radiator performance

NASA Technical Reports Server (NTRS)

Mattick, A. T.; Simon, M. A.

1987-01-01

The liquid droplet radiator (LDR) is a heat rejection system for space power systems wherein an array of heated liquid droplets radiates energy directly to space. The use of submillimeter droplets provides large radiating area-to-mass ratio, resulting in radiator systems which are several times lighter than conventional solid surface radiators. An experiment is described in which the power radiated by an array of 2300 streams of silicone oil droplets is measured to test a previously developed theory of the LDR radiation process. This system would be capable of rejecting several kW of heat in space. Furthermore, it would be suitable as a modular unit of an LDR designed for 100-kW power levels. The experiment provided confirmation of the theoretical dependence of droplet array emissivity on optical depth. It also demonstrated the ability to create an array of more than 1000 droplet streams having a divergence less than 1 degree.

Study of soft X-ray emission during wire array implosion under plasma focus conditions at the PF-3 facility

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

Dan’ko, S. A.; Mitrofanov, K. N., E-mail: mitrofan@triniti.ru; Krauz, V. I.

2015-11-15

Results of measurements of soft X-ray emission with photon energies of <1 keV under conditions of a plasma focus (PF) experiment are presented. The experiments were carried out at the world’s largest PF device—the PF-3 Filippov-type facility (I ⩽ 3 MA, T/4 ≈ 15–20 µs, W{sub 0} ⩽ 3 MJ). X-ray emission from both a discharge in pure neon and with a tungsten wire array placed on the axis of the discharge chamber was detected. The wire array imploded under the action of the electric current intercepted from the plasma current sheath of the PF discharge in neon. The measuredmore » soft X-ray powers from a conventional PF discharge in gas and a PF discharge in the presence of a wire array were compared for the first time.« less

A novel serrated columnar phased array ultrasonic transducer

NASA Astrophysics Data System (ADS)

Zou, Cheng; Sun, Zhenguo; Cai, Dong; Song, Hongwei; Chen, Qiang

2016-02-01

Traditionally, wedges are required to generate transverse waves in a solid specimen and mechanical rotation device is needed for interrogation of a specimen with a hollow bore, such as high speed railway locomotive axles, turbine rotors, etc. In order to eliminate the mechanical rotation process, a novel array pattern of phased array ultrasonic transducers named as serrated columnar phased array ultrasonic transducer (SCPAUT) is designed. The elementary transducers are planar rectangular, located on the outside surface of a cylinder. This layout is aimed to generate electrically rotating transverse waveforms so as to inspect the longitudinal cracks on the outside surface of a specimen which has a hollow bore at the center, such as the high speed railway locomotive axles. The general geometry of the SCPAUT and the inspection system are illustrated. A FEM model and mockup experiment has been carried out. The experiment results are in good agreement with the FEM simulation results.

Experimental implementation of array-compressed parallel transmission at 7 tesla.

PubMed

Yan, Xinqiang; Cao, Zhipeng; Grissom, William A

2016-06-01

To implement and validate a hardware-based array-compressed parallel transmission (acpTx) system. In array-compressed parallel transmission, a small number of transmit channels drive a larger number of transmit coils, which are connected via an array compression network that implements optimized coil-to-channel combinations. A two channel-to-eight coil array compression network was developed using power splitters, attenuators and phase shifters, and a simulation was performed to investigate the effects of coil coupling on power dissipation in a simplified network. An eight coil transmit array was constructed using induced current elimination decoupling, and the coil and network were validated in benchtop measurements, B1+ mapping scans, and an accelerated spiral excitation experiment. The developed attenuators came within 0.08 dB of the desired attenuations, and reflection coefficients were -22 dB or better. The simulation demonstrated that up to 3× more power was dissipated in the network when coils were poorly isolated (-9.6 dB), versus well-isolated (-31 dB). Compared to split circularly-polarized coil combinations, the additional degrees of freedom provided by the array compression network led to 54% lower squared excitation error in the spiral experiment. Array-compressed parallel transmission was successfully implemented in a hardware system. Further work is needed to develop remote network tuning and to minimize network power dissipation. Magn Reson Med 75:2545-2552, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Large membrane “Furoshiki Satellite” applied to phased array antenna and its sounding rocket experiment

NASA Astrophysics Data System (ADS)

Nakasuka, Shinichi; Funase, Ryu; Nakada, Kenji; Kaya, Nobuyuki; Mankins, John C.

2006-04-01

University of Tokyo and Kobe University are planning a sounding rocket experiment of large membrane "Furoshiki Satellite" extension and large phased array RF transmission. The paper will describe the concept of "Furoshiki Satellite," its application to phased array antenna, and the scenario of micro gravity experiment using a small sounding rocket. University of Tokyo has been proposing the idea of "Furoshiki Satellite," a large membrane or a net structure, say 1km×1km in size, extended by satellites which hold its corners. The attitude and the shape of the membrane or net structure is controlled by these corner satellites. As one application of Furoshiki Satellite, a large phased array antenna can be configured by several RF transmitters placed on several parts of the large net structure. It is difficult to control the position and attitude of the RF transmitters precisely, but using the "retro-directive" method, the tolerance of such position and attitude disturbance will be relaxed by large. This is one of promising systems' concept of the future large solar power satellite or large antenna, because quite a large area can be obtained without any hard structure, and the weight will not depend very much on the size [S. Motohashi, T. Nagamura, Large scaled membrane structure Furoshiki Satellite—its concept and orbital/attitude dynamics, in: Proceedings of 20th International Symposium on Space Technology and Science (ISTS), 1996, p. 96-n-14]. To demonstrate the feasibility of the extension of large net structure and phased array performance, micro-gravity experiment is planned using a sounding rocket of ISAS/JAXA, Japan.

Transcriptional profiling reveals regulated genes in the hippocampus during memory formation

NASA Technical Reports Server (NTRS)

Donahue, Christine P.; Jensen, Roderick V.; Ochiishi, Tomoyo; Eisenstein, Ingrid; Zhao, Mingrui; Shors, Tracey; Kosik, Kenneth S.

2002-01-01

Transcriptional profiling (TP) offers a powerful approach to identify genes activated during memory formation and, by inference, the molecular pathways involved. Trace eyeblink conditioning is well suited for the study of regional gene expression because it requires the hippocampus, whereas the highly parallel task, delay conditioning, does not. First, we determined when gene expression was most regulated during trace conditioning. Rats were exposed to 200 trials per day of paired and unpaired stimuli each day for 4 days. Changes in gene expression were most apparent 24 h after exposure to 200 trials. Therefore, we profiled gene expression in the hippocampus 24 h after 200 trials of trace eyeblink conditioning, on multiple arrays using additional animals. Of 1,186 genes on the filter array, seven genes met the statistical criteria and were also validated by real-time polymerase chain reaction. These genes were growth hormone (GH), c-kit receptor tyrosine kinase (c-kit), glutamate receptor, metabotropic 5 (mGluR5), nerve growth factor-beta (NGF-beta), Jun oncogene (c-Jun), transmembrane receptor Unc5H1 (UNC5H1), and transmembrane receptor Unc5H2 (UNC5H2). All these genes, except for GH, were downregulated in response to trace conditioning. GH was upregulated; therefore, we also validated the downregulation of the GH inhibitor, somatostatin (SST), even though it just failed to meet criteria on the arrays. By during situ hybridization, GH was expressed throughout the cell layers of the hippocampus in response to trace conditioning. None of the genes regulated in trace eyeblink conditioning were similarly affected by delay conditioning, a task that does not require the hippocampus. These findings demonstrate that transcriptional profiling can exhibit a repertoire of genes sensitive to the formation of hippocampal-dependent associative memories.