Update-in-Place Analysis for True Multidimensional Arrays

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Steven M. Fitzgerald

1996-01-01

Full Text Available Applicative languages have been proposed for defining algorithms for parallel architectures because they are implicitly parallel and lack side effects. However, straightforward implementations of applicative-language compilers may induce large amounts of copying to preserve program semantics. The unnecessary copying of data can increase both the execution time and the memory requirements of an application. To eliminate the unnecessary copying of data, the Sisal compiler uses both build-in-place and update-in-place analyses. These optimizations remove unnecessary array copy operations through compile-time analysis. Both build-in-place and update-in-place are based on hierarchical ragged arrays, i.e., the vector-of-vectors array model. Although this array model is convenient for certain applications, many optimizations are precluded, e.g., vectorization. To compensate for this deficiency, new languages, such as Sisal 2.0, have extended array models that allow for both high-level array operations to be performed and efficient implementations to be devised. In this article, we introduce a new method to perform update-in-place analysis that is applicable to arrays stored either in hierarchical or in contiguous storage. Consequently, the array model that is appropriate for an application can be selected without the loss of performance. Moreover, our analysis is more amenable for distributed memory and large software systems.

Hybrid Information Flow Analysis for Programs with Arrays

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Gergö Barany

2016-07-01

Full Text Available Information flow analysis checks whether certain pieces of (confidential data may affect the results of computations in unwanted ways and thus leak information. Dynamic information flow analysis adds instrumentation code to the target software to track flows at run time and raise alarms if a flow policy is violated; hybrid analyses combine this with preliminary static analysis. Using a subset of C as the target language, we extend previous work on hybrid information flow analysis that handled pointers to scalars. Our extended formulation handles arrays, pointers to array elements, and pointer arithmetic. Information flow through arrays of pointers is tracked precisely while arrays of non-pointer types are summarized efficiently. A prototype of our approach is implemented using the Frama-C program analysis and transformation framework. Work on a full machine-checked proof of the correctness of our approach using Isabelle/HOL is well underway; we present the existing parts and sketch the rest of the correctness argument.

Fault Analysis in Solar Photovoltaic Arrays

Science.gov (United States)

Zhao, Ye

Fault analysis in solar photovoltaic (PV) arrays is a fundamental task to increase reliability, efficiency and safety in PV systems. Conventional fault protection methods usually add fuses or circuit breakers in series with PV components. But these protection devices are only able to clear faults and isolate faulty circuits if they carry a large fault current. However, this research shows that faults in PV arrays may not be cleared by fuses under some fault scenarios, due to the current-limiting nature and non-linear output characteristics of PV arrays. First, this thesis introduces new simulation and analytic models that are suitable for fault analysis in PV arrays. Based on the simulation environment, this thesis studies a variety of typical faults in PV arrays, such as ground faults, line-line faults, and mismatch faults. The effect of a maximum power point tracker on fault current is discussed and shown to, at times, prevent the fault current protection devices to trip. A small-scale experimental PV benchmark system has been developed in Northeastern University to further validate the simulation conclusions. Additionally, this thesis examines two types of unique faults found in a PV array that have not been studied in the literature. One is a fault that occurs under low irradiance condition. The other is a fault evolution in a PV array during night-to-day transition. Our simulation and experimental results show that overcurrent protection devices are unable to clear the fault under "low irradiance" and "night-to-day transition". However, the overcurrent protection devices may work properly when the same PV fault occurs in daylight. As a result, a fault under "low irradiance" and "night-to-day transition" might be hidden in the PV array and become a potential hazard for system efficiency and reliability.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

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Moreau Yves

2005-05-01

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

Performance Analysis of Digital loudspeaker Arrays

DEFF Research Database (Denmark)

Pedersen, Bo Rohde; Kontomichos, Fotios; Mourjopoulos, John

2008-01-01

An analysis of digital loudspeaker arrays shows that the ways in which bits are mapped to the drivers influence the quality of the audio result. Specifically, a "bit-summed" rather than the traditional "bit-mapped" strategy greatly reduces the number of times drivers make binary transitions per...... period of the input frequency. Detailed simulations compare the results for a 32-loudspeaker array with a similar configuration with analog excitation of the drivers. Ideally, drivers in digital arrays should be very small and span a small area, but that sets limits on the low-frequency response...

A single lysis solution for the analysis of tissue samples by different proteomic technologies

DEFF Research Database (Denmark)

Gromov, P.; Celis, J.E.; Gromova, I.

2008-01-01

-based proteomics (reverse-phase lysate arrays or direct antibody arrays), allowing the direct comparison of qualitative and quantitative data yielded by these technologies when applied to the same samples. The usefulness of the CLB1 solution for gel-based proteomics was further established by 2D PAGE analysis...... dissease, is driving scientists to increasingly use clinically relevant samples for biomarker and target discovery. Tissues are heterogeneous and as a result optimization of sample preparation is critical for generating accurate, representative, and highly reproducible quantitative data. Although a large...... number of protocols for preparation of tissue lysates has been published, so far no single recipe is able to provide a "one-size fits all" solubilization procedure that can be used to analyse the same lysate using different proteomics technologies. Here we present evidence showing that cell lysis buffer...

Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer.

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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

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC and its application for DNA methylation analysis

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Ottaviani Diego

2008-05-01

Full Text Available Abstract Background The major histocompatibility complex (MHC is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP, methylated DNA immunoprecipitation (MeDIP, array comparative genomic hybridization (aCGH and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs. Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.

The role of acoustic nonlinearity in tissue heating behind a rib cage using a high-intensity focused ultrasound phased array

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Yuldashev, Petr V.; Shmeleva, Svetlana M.; Ilyin, Sergey A.; Sapozhnikov, Oleg A.; Gavrilov, Leonid R.; Khokhlova, Vera A.

2013-04-01

The goal of this study was to investigate theoretically the effects of nonlinear propagation in a high-intensity focused ultrasound (HIFU) field produced by a therapeutic phased array and the resultant heating of tissue behind a rib cage. Three configurations of focusing were simulated: in water, in water with ribs in the beam path and in water with ribs backed by a layer of soft tissue. The Westervelt equation was used to model the nonlinear HIFU field, and a 1 MHz phased array consisting of 254 circular elements was used as a boundary condition to the model. The temperature rise in tissue was modelled using the bioheat equation, and thermally necrosed volumes were calculated using the thermal dose formulation. The shapes of lesions predicted by the modelling were compared with those previously obtained in in vitro experiments at low-power sonications. Intensity levels at the face of the array elements that corresponded to the formation of high-amplitude shock fronts in the focal region were determined as 10 W cm-2 in the free field in water and 40 W cm-2 in the presence of ribs. It was shown that exposures with shocks provided a substantial increase in tissue heating, and its better spatial localization in the main focal region only. The relative effects of overheating ribs and splitting of the focus due to the periodic structure of the ribs were therefore reduced. These results suggest that utilizing nonlinear propagation and shock formation effects can be beneficial for inducing confined HIFU lesions when irradiating through obstructions such as ribs. Design of compact therapeutic arrays to provide maximum power outputs with lower intensity levels at the elements is necessary to achieve shock wave regimes for clinically relevant sonication depths in tissue.

Balanced into array : genome-wide array analysis in 54 patients with an apparently balanced de novo chromosome rearrangement and a meta-analysis

NARCIS (Netherlands)

Feenstra, Ilse; Hanemaaijer, Nicolien; Sikkema-Raddatz, Birgit; Yntema, Helger; Dijkhuizen, Trijnie; Lugtenberg, Dorien; Verheij, Joke; Green, Andrew; Hordijk, Roel; Reardon, William; de Vries, Bert; Brunner, Han; Bongers, Ernie; de Leeuw, Nicole; van Ravenswaaij-Arts, Conny

2011-01-01

High-resolution genome-wide array analysis enables detailed screening for cryptic and submicroscopic imbalances of microscopically balanced de novo rearrangements in patients with developmental delay and/or congenital abnormalities. In this report, we added the results of genome-wide array analysis

Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays

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Heather D. Kissel

2013-01-01

Full Text Available Identifying molecular markers of endometrial hyperplasia (neoplasia progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE hysterectomy specimens (benign indications from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87% FF and 50/51 (98% FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.

Waveguide Phased Array Antenna Analysis and Synthesis

NARCIS (Netherlands)

Visser, H.J.; Keizer, W.P.M.N.

1996-01-01

Results of two software packages for analysis and synthesis of waveguide phased array antennas are shown. The antennas consist of arrays of open-ended waveguides where irises can be placed in the waveguide apertures and multiple dielectric sheets in front of the apertures in order to accomplish a

Determination of catechins and catechin gallates in tissues by liquid chromatography with coulometric array detection and selective solid phase extraction.

Science.gov (United States)

Chu, Kai On; Wang, Chi Chiu; Chu, Ching Yan; Rogers, Michael Scott; Choy, Kwong Wai; Pang, Chi Pui

2004-10-25

Catechins levels in organ tissues, particularly liver, determined by published methods are unexpectedly low, probably due to the release of oxidative enzymes, metal ions and reactive metabolites from tissue cells during homogenization and to the pro-oxidant effects of ascorbic acid during sample processing in the presence of metal ions. We describe a new method for simultaneous analysis of eight catechins in tissue: (+)-catechin (C), (-)-epicatechin (EC), (-)-gallocatechin (GC), (-)-epigallocatechin (EGC), (-)-catechin gallate (CG), (-)-epicatechin gallate (ECG), (-)-gallocatechin gallate (GCG) and (-)-epigallocatechin gallate (EGCG) (Fig. 1). The new extraction procedure utilized a methanol/ethylacetate/dithionite (2:1:3) mixture during homogenization for simultaneous enzyme precipitation and antioxidant protection. Selective solid phase extraction was used to remove most interfering bio-matrices. Reversed phase HPLC with CoulArray detection was used to determine the eight catechins simultaneously within 25 min. Good linearity (>0.9922) was obtained in the range 20-4000 ng/g. The coefficients of variance (CV) were less than 5%. Absolute recovery ranged from 62 to 96%, accuracy 92.5 +/- 4.5 to 104.9 +/- 6%. The detection limit was 5 ng/g. This method is capable for determining catechins in rat tissues of liver, brain, spleen, and kidney. The method is robust, reproducible, with high recovery, and has been validated for both in vitro and in vivo sample analysis.

Application of TMA (Tissue micro-array) in the observation of apoptotic cascade in postradiation damage in avian medicine

International Nuclear Information System (INIS)

Fridman, E.; Skarda, J.; Skardova, I.

2006-01-01

The study of apoptotic cascade by the use of relatively new technique in avian medicine: TMA may help in early detection and prevention of acquired immunodeficiency caused by the influence of a variety of pathogenic and non-pathogenic environmental factors, which may result in severe economical losses in conditions of intensive poultry farming. There has not been any report of applying this method in veterinary medicine. Tissue micro-array (TMA) technology allows rapid visualization of molecular targets in thousands of tissue specimens at a time, either at the DNA, RNA or protein level. The technique facilitates rapid translation of molecular discoveries to clinical applications. This technology has a number of advantages compared with conventional techniques: speed and high throughput, standardization and experimental uniformity, ease of use, all histochemical and molecular detection techniques can be used, decreased assay volume, preservation of original block, and conservation of valuable tissue etc. The aim of the present work were the study of immunosuppression and apoptotic cascade and possibilities of application of tissue micro-array in chicken in experimental condition and diagnostics in avian medicine in general. The selection of samples from avian primary immune organs: thymus and Bursa Fabric was done after gamma irradiation and infectious bursal virus infection (IBDV). (authors)

High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results

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Siggberg Linda

2012-09-01

Full Text Available Abstract Background Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. Methods and Results Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. Conclusions In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

The National NeuroAIDS Tissue Consortium brain gene array: two types of HIV-associated neurocognitive impairment.

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Benjamin B Gelman

Full Text Available The National NeuroAIDS Tissue Consortium (NNTC performed a brain gene expression array to elucidate pathophysiologies of Human Immunodeficiency Virus type 1 (HIV-1-associated neurocognitive disorders.Twenty-four human subjects in four groups were examined A Uninfected controls; B HIV-1 infected subjects with no substantial neurocognitive impairment (NCI; C Infected with substantial NCI without HIV encephalitis (HIVE; D Infected with substantial NCI and HIVE. RNA from neocortex, white matter, and neostriatum was processed with the Affymetrix® array platform.With HIVE the HIV-1 RNA load in brain tissue was three log(10 units higher than other groups and over 1,900 gene probes were regulated. Interferon response genes (IFRGs, antigen presentation, complement components and CD163 antigen were strongly upregulated. In frontal neocortex downregulated neuronal pathways strongly dominated in HIVE, including GABA receptors, glutamate signaling, synaptic potentiation, axon guidance, clathrin-mediated endocytosis and 14-3-3 protein. Expression was completely different in neuropsychologically impaired subjects without HIVE. They had low brain HIV-1 loads, weak brain immune responses, lacked neuronally expressed changes in neocortex and exhibited upregulation of endothelial cell type transcripts. HIV-1-infected subjects with normal neuropsychological test results had upregulation of neuronal transcripts involved in synaptic transmission of neostriatal circuits.Two patterns of brain gene expression suggest that more than one pathophysiological process occurs in HIV-1-associated neurocognitive impairment. Expression in HIVE suggests that lowering brain HIV-1 replication might improve NCI, whereas NCI without HIVE may not respond in kind; array results suggest that modulation of transvascular signaling is a potentially promising approach. Striking brain regional differences highlighted the likely importance of circuit level disturbances in HIV/AIDS. In

HTGR core seismic analysis using an array processor

International Nuclear Information System (INIS)

Shatoff, H.; Charman, C.M.

1983-01-01

A Floating Point Systems array processor performs nonlinear dynamic analysis of the high-temperature gas-cooled reactor (HTGR) core with significant time and cost savings. The graphite HTGR core consists of approximately 8000 blocks of various shapes which are subject to motion and impact during a seismic event. Two-dimensional computer programs (CRUNCH2D, MCOCO) can perform explicit step-by-step dynamic analyses of up to 600 blocks for time-history motions. However, use of two-dimensional codes was limited by the large cost and run times required. Three-dimensional analysis of the entire core, or even a large part of it, had been considered totally impractical. Because of the needs of the HTGR core seismic program, a Floating Point Systems array processor was used to enhance computer performance of the two-dimensional core seismic computer programs, MCOCO and CRUNCH2D. This effort began by converting the computational algorithms used in the codes to a form which takes maximum advantage of the parallel and pipeline processors offered by the architecture of the Floating Point Systems array processor. The subsequent conversion of the vectorized FORTRAN coding to the array processor required a significant programming effort to make the system work on the General Atomic (GA) UNIVAC 1100/82 host. These efforts were quite rewarding, however, since the cost of running the codes has been reduced approximately 50-fold and the time threefold. The core seismic analysis with large two-dimensional models has now become routine and extension to three-dimensional analysis is feasible. These codes simulate the one-fifth-scale full-array HTGR core model. This paper compares the analysis with the test results for sine-sweep motion

Design and Analysis of MEMS Linear Phased Array

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Guoxiang Fan

2016-01-01

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

Analysis of measurements on wind turbine arrays. Vol. 1

International Nuclear Information System (INIS)

Hoeg, E.

1990-12-01

In 1989 a Danish electric power company initiated an analysis of eight wind turbine arrays. Data from this project is presented together with the explained results of the analyses and the output variations for individual arrays and for systems within the arrays. The models for prognosis are compared and evaluated in order to find that which is most effective. (AB)

Glycomic analysis of human respiratory tract tissues and correlation with influenza virus infection.

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Trevenan Walther

2013-03-01

Full Text Available The first step in influenza infection of the human respiratory tract is binding of the virus to sialic (Sia acid terminated receptors. The binding of different strains of virus for the receptor is determined by the α linkage of the sialic acid to galactose and the adjacent glycan structure. In this study the N- and O-glycan composition of the human lung, bronchus and nasopharynx was characterized by mass spectrometry. Analysis showed that there was a wide spectrum of both Sia α2-3 and α2-6 glycans in the lung and bronchus. This glycan structural data was then utilized in combination with binding data from 4 of the published glycan arrays to assess whether these current glycan arrays were able to predict replication of human, avian and swine viruses in human ex vivo respiratory tract tissues. The most comprehensive array from the Consortium for Functional Glycomics contained the greatest diversity of sialylated glycans, but was not predictive of productive replication in the bronchus and lung. Our findings indicate that more comprehensive but focused arrays need to be developed to investigate influenza virus binding in an assessment of newly emerging influenza viruses.

Active Sensor for Microwave Tissue Imaging with Bias-Switched Arrays.

Science.gov (United States)

Foroutan, Farzad; Nikolova, Natalia K

2018-05-06

A prototype of a bias-switched active sensor was developed and measured to establish the achievable dynamic range in a new generation of active arrays for microwave tissue imaging. The sensor integrates a printed slot antenna, a low-noise amplifier (LNA) and an active mixer in a single unit, which is sufficiently small to enable inter-sensor separation distance as small as 12 mm. The sensor’s input covers the bandwidth from 3 GHz to 7.5 GHz. Its output intermediate frequency (IF) is 30 MHz. The sensor is controlled by a simple bias-switching circuit, which switches ON and OFF the bias of the LNA and the mixer simultaneously. It was demonstrated experimentally that the dynamic range of the sensor, as determined by its ON and OFF states, is 109 dB and 118 dB at resolution bandwidths of 1 kHz and 100 Hz, respectively.

Fabrication of plasmonic cavity arrays for SERS analysis

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Li, Ning; Feng, Lei; Teng, Fei; Lu, Nan

2017-05-01

The plasmonic cavity arrays are ideal substrates for surface enhanced Raman scattering analysis because they can provide hot spots with large volume for analyte molecules. The large area increases the probability to make more analyte molecules on hot spots and leads to a high reproducibility. Therefore, to develop a simple method for creating cavity arrays is important. Herein, we demonstrate how to fabricate a V and W shape cavity arrays by a simple method based on self-assembly. Briefly, the V and W shape cavity arrays are respectively fabricated by taking KOH etching on a nanohole and a nanoring array patterned silicon (Si) slides. The nanohole array is generated by taking a reactive ion etching on a Si slide assembled with monolayer of polystyrene (PS) spheres. The nanoring array is generated by taking a reactive ion etching on a Si slide covered with a monolayer of octadecyltrichlorosilane before self-assembling PS spheres. Both plasmonic V and W cavity arrays can provide large hot area, which increases the probability for analyte molecules to deposit on the hot spots. Taking 4-Mercaptopyridine as analyte probe, the enhancement factor can reach 2.99 × 105 and 9.97 × 105 for plasmonic V cavity and W cavity array, respectively. The relative standard deviations of the plasmonic V and W cavity arrays are 6.5% and 10.2% respectively according to the spectra collected on 20 random spots.

Crosstalk analysis of silicon-on-insulator nanowire-arrayed waveguide grating

International Nuclear Information System (INIS)

Li Kai-Li; An Jun-Ming; Zhang Jia-Shun; Wang Yue; Wang Liang-Liang; Li Jian-Guang; Wu Yuan-Da; Yin Xiao-Jie; Hu Xiong-Wei

2016-01-01

The factors influencing the crosstalk of silicon-on-insulator (SOI) nanowire arrayed waveguide grating (AWG) are analyzed using the transfer function method. The analysis shows that wider and thicker arrayed waveguides, outsider fracture of arrayed waveguide, and larger channel space, could mitigate the deterioration of crosstalk. The SOI nanowire AWGs with different arrayed waveguide widths are fabricated by using deep ultraviolet lithography (DUV) and inductively coupled plasma etching (ICP) technology. The measurement results show that the crosstalk performance is improved by about 7 dB through adopting 800 nm arrayed waveguide width. (paper)

Three-dimensional spheroid culture targeting versatile tissue bioassays using a PDMS-based hanging drop array.

Science.gov (United States)

Kuo, Ching-Te; Wang, Jong-Yueh; Lin, Yu-Fen; Wo, Andrew M; Chen, Benjamin P C; Lee, Hsinyu

2017-06-29

Biomaterial-based tissue culture platforms have emerged as useful tools to mimic in vivo physiological microenvironments in experimental cell biology and clinical studies. We describe herein a three-dimensional (3D) tissue culture platform using a polydimethylsiloxane (PDMS)-based hanging drop array (PDMS-HDA) methodology. Multicellular spheroids can be achieved within 24 h and further boosted by incorporating collagen fibrils in PDMS-HDA. In addition, the spheroids generated from different human tumor cells exhibited distinct sensitivities toward drug chemotherapeutic agents and radiation as compared with two-dimensional (2D) cultures that often lack in vivo-like biological insights. We also demonstrated that multicellular spheroids may enable key hallmarks of tissue-based bioassays, including drug screening, tumor dissemination, cell co-culture, and tumor invasion. Taken together, these results offer new opportunities not only to achieve the active control of 3D multicellular spheroids on demand, but also to establish a rapid and cost-effective platform to study anti-cancer therapeutics and tumor microenvironments.

Analysis and synthesis of (SAR) waveguide phased array antennas

Science.gov (United States)

Visser, H. J.

1994-02-01

This report describes work performed due to ESA contract No. 101 34/93/NL/PB. Started is with a literature study on dual polarized waveguide radiators, resulting in the choice for the open ended square waveguide. After a thorough description of the mode matching infinite waveguide array analysis method - including finiteness effects - that forms the basis for all further described analysis and synthesis methods, the accuracy of the analysis software is validated by comparison with measurements on two realized antennas. These antennas have centered irises in the waveguide apertures and a dielectric wide angle impedance matching sheet in front of the antenna. A synthesis method, using simulated annealing and downhill simplex, is described next and different antenna designs, based on the analysis of a single element in an infinite array environment, are presented. Next, designs of subarrays are presented. Shown is the paramount importance of including the array environment in the design of a subarray. A microstrip patch waveguide exciter and subarray feeding network are discussed and the depth of the waveguide radiator is estimated. Chosen is a rectangular grid array with waveguides of 2.5 cm depth without irises and without dielectric sheet, grouped in linear 8 elements subarrays.

An Empirical Study of Precise Interprocedural Array Analysis

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Michael Hind

1994-01-01

Full Text Available In this article we examine the role played by the interprocedural analysis of array accesses in the automatic parallelization of Fortran programs. We use the PTRAN system to provide measurements of several benchmarks to compare different methods of representing interprocedurally accessed arrays. We examine issues concerning the effectiveness of automatic parallelization using these methods and the efficiency of a precise summarization method.

Reliability analysis of the solar array based on Fault Tree Analysis

International Nuclear Information System (INIS)

Wu Jianing; Yan Shaoze

2011-01-01

The solar array is an important device used in the spacecraft, which influences the quality of in-orbit operation of the spacecraft and even the launches. This paper analyzes the reliability of the mechanical system and certifies the most vital subsystem of the solar array. The fault tree analysis (FTA) model is established according to the operating process of the mechanical system based on DFH-3 satellite; the logical expression of the top event is obtained by Boolean algebra and the reliability of the solar array is calculated. The conclusion shows that the hinges are the most vital links between the solar arrays. By analyzing the structure importance(SI) of the hinge's FTA model, some fatal causes, including faults of the seal, insufficient torque of the locking spring, temperature in space, and friction force, can be identified. Damage is the initial stage of the fault, so limiting damage is significant to prevent faults. Furthermore, recommendations for improving reliability associated with damage limitation are discussed, which can be used for the redesigning of the solar array and the reliability growth planning.

Reliability analysis of the solar array based on Fault Tree Analysis

Energy Technology Data Exchange (ETDEWEB)

Wu Jianing; Yan Shaoze, E-mail: yansz@mail.tsinghua.edu.cn [State Key Laboratory of Tribology, Department of Precision Instruments and Mechanology, Tsinghua University,Beijing 100084 (China)

2011-07-19

The solar array is an important device used in the spacecraft, which influences the quality of in-orbit operation of the spacecraft and even the launches. This paper analyzes the reliability of the mechanical system and certifies the most vital subsystem of the solar array. The fault tree analysis (FTA) model is established according to the operating process of the mechanical system based on DFH-3 satellite; the logical expression of the top event is obtained by Boolean algebra and the reliability of the solar array is calculated. The conclusion shows that the hinges are the most vital links between the solar arrays. By analyzing the structure importance(SI) of the hinge's FTA model, some fatal causes, including faults of the seal, insufficient torque of the locking spring, temperature in space, and friction force, can be identified. Damage is the initial stage of the fault, so limiting damage is significant to prevent faults. Furthermore, recommendations for improving reliability associated with damage limitation are discussed, which can be used for the redesigning of the solar array and the reliability growth planning.

Verification of computed tomographic estimates of cochlear implant array position: a micro-CT and histologic analysis.

Science.gov (United States)

Teymouri, Jessica; Hullar, Timothy E; Holden, Timothy A; Chole, Richard A

2011-08-01

To determine the efficacy of clinical computed tomographic (CT) imaging to verify postoperative electrode array placement in cochlear implant (CI) patients. Nine fresh cadaver heads underwent clinical CT scanning, followed by bilateral CI insertion and postoperative clinical CT scanning. Temporal bones were removed, trimmed, and scanned using micro-CT. Specimens were then dehydrated, embedded in either methyl methacrylate or LR White resin, and sectioned with a diamond wafering saw. Histology sections were examined by 3 blinded observers to determine the position of individual electrodes relative to soft tissue structures within the cochlea. Electrodes were judged to be within the scala tympani, scala vestibuli, or in an intermediate position between scalae. The position of the array could be estimated accurately from clinical CT scans in all specimens using micro-CT and histology as a criterion standard. Verification using micro-CT yielded 97% agreement, and histologic analysis revealed 95% agreement with clinical CT results. A composite, 3-dimensional image derived from a patient's preoperative and postoperative CT images using a clinical scanner accurately estimates the position of the electrode array as determined by micro-CT imaging and histologic analyses. Information obtained using the CT method provides valuable insight into numerous variables of interest to patient performance such as surgical technique, array design, and processor programming and troubleshooting.

Analysis of Camera Arrays Applicable to the Internet of Things.

Science.gov (United States)

Yang, Jiachen; Xu, Ru; Lv, Zhihan; Song, Houbing

2016-03-22

The Internet of Things is built based on various sensors and networks. Sensors for stereo capture are essential for acquiring information and have been applied in different fields. In this paper, we focus on the camera modeling and analysis, which is very important for stereo display and helps with viewing. We model two kinds of cameras, a parallel and a converged one, and analyze the difference between them in vertical and horizontal parallax. Even though different kinds of camera arrays are used in various applications and analyzed in the research work, there are few discussions on the comparison of them. Therefore, we make a detailed analysis about their performance over different shooting distances. From our analysis, we find that the threshold of shooting distance for converged cameras is 7 m. In addition, we design a camera array in our work that can be used as a parallel camera array, as well as a converged camera array and take some images and videos with it to identify the threshold.

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

International Nuclear Information System (INIS)

Yang Zhenhua; Liu Quan; Ding Ning; Ning Cheng

2005-01-01

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

Parametric analysis of ATM solar array.

Science.gov (United States)

Singh, B. K.; Adkisson, W. B.

1973-01-01

The paper discusses the methods used for the calculation of ATM solar array performance characteristics and provides the parametric analysis of solar panels used in SKYLAB. To predict the solar array performance under conditions other than test conditions, a mathematical model has been developed. Four computer programs have been used to convert the solar simulator test data to the parametric curves. The first performs module summations, the second determines average solar cell characteristics which will cause a mathematical model to generate a curve matching the test data, the third is a polynomial fit program which determines the polynomial equations for the solar cell characteristics versus temperature, and the fourth program uses the polynomial coefficients generated by the polynomial curve fit program to generate the parametric data.

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

Science.gov (United States)

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

2014-01-01

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

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

Directory of Open Access Journals (Sweden)

Laia Ramos

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

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

Science.gov (United States)

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

2014-01-01

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

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

Science.gov (United States)

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

2010-01-01

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

Sensitivity Analysis of WEC Array Layout Parameters Effect on the Power Performance

DEFF Research Database (Denmark)

Ruiz, Pau Mercadé; Ferri, Francesco; Kofoed, Jens Peter

2015-01-01

This study assesses the effect that the array layout choice has on the power performance. To this end, a sensitivity analysis is carried out with six array layout parameters, as the simulation inputs, the array power performance (q-factor), as the simulation output, and a simulation model special...

ExonMiner: Web service for analysis of GeneChip Exon array data

Directory of Open Access Journals (Sweden)

Imoto Seiya

2008-11-01

Full Text Available Abstract Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1 data normalization, (2 statistical analysis based on two-way ANOVA, (3 finding transcripts with significantly different splice patterns, (4 efficient visualization based on heatmaps and barplots, and (5 meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.

Exome Array Analysis of Nuclear Lens Opacity.

Science.gov (United States)

Loomis, Stephanie J; Klein, Alison P; Lee, Kristine E; Chen, Fei; Bomotti, Samantha; Truitt, Barbara; Iyengar, Sudha K; Klein, Ronald; Klein, Barbara E K; Duggal, Priya

2018-06-01

Nuclear cataract is the most common subtype of age-related cataract, the leading cause of blindness worldwide. It results from advanced nuclear sclerosis, or opacity in the center of the optic lens, and is affected by both genetic and environmental risk factors, including smoking. We sought to understand the genetic factors associated with nuclear sclerosis through interrogation of rare and low frequency coding variants using exome array data. We analyzed Illumina Human Exome Array data for 1,488 participants of European ancestry in the Beaver Dam Eye Study who were without cataract surgery for association with nuclear sclerosis grade, controlling for age and sex. We performed single-variant regression analysis for 32,138 variants with minor allele frequency (MAF) ≥0.003. In addition, gene-based analysis of 11,844 genes containing at least two variants with MAF nuclear sclerosis, the possible association with the RNF149 gene highlights a potential candidate gene for future studies that aim to understand the genetic architecture of nuclear sclerosis.

Improvements in analysis techniques for segmented mirror arrays

Science.gov (United States)

Michels, Gregory J.; Genberg, Victor L.; Bisson, Gary R.

2016-08-01

The employment of actively controlled segmented mirror architectures has become increasingly common in the development of current astronomical telescopes. Optomechanical analysis of such hardware presents unique issues compared to that of monolithic mirror designs. The work presented here is a review of current capabilities and improvements in the methodology of the analysis of mechanically induced surface deformation of such systems. The recent improvements include capability to differentiate surface deformation at the array and segment level. This differentiation allowing surface deformation analysis at each individual segment level offers useful insight into the mechanical behavior of the segments that is unavailable by analysis solely at the parent array level. In addition, capability to characterize the full displacement vector deformation of collections of points allows analysis of mechanical disturbance predictions of assembly interfaces relative to other assembly interfaces. This capability, called racking analysis, allows engineers to develop designs for segment-to-segment phasing performance in assembly integration, 0g release, and thermal stability of operation. The performance predicted by racking has the advantage of being comparable to the measurements used in assembly of hardware. Approaches to all of the above issues are presented and demonstrated by example with SigFit, a commercially available tool integrating mechanical analysis with optical analysis.

Data-flow Analysis of Programs with Associative Arrays

Directory of Open Access Journals (Sweden)

David Hauzar

2014-05-01

Full Text Available Dynamic programming languages, such as PHP, JavaScript, and Python, provide built-in data structures including associative arrays and objects with similar semantics—object properties can be created at run-time and accessed via arbitrary expressions. While a high level of security and safety of applications written in these languages can be of a particular importance (consider a web application storing sensitive data and providing its functionality worldwide, dynamic data structures pose significant challenges for data-flow analysis making traditional static verification methods both unsound and imprecise. In this paper, we propose a sound and precise approach for value and points-to analysis of programs with associative arrays-like data structures, upon which data-flow analyses can be built. We implemented our approach in a web-application domain—in an analyzer of PHP code.

The On-Site Analysis of the Cherenkov Telescope Array

CERN Document Server

Bulgarelli, Andrea; Zoli, Andrea; Aboudan, Alessio; Rodríguez-Vázquez, Juan José; De Cesare, Giovanni; De Rosa, Adriano; Maier, Gernot; Lyard, Etienne; Bastieri, Denis; Lombardi, Saverio; Tosti, Gino; Bergamaschi, Sonia; Beneventano, Domenico; Lamanna, Giovanni; Jacquemier, Jean; Kosack, Karl; Antonelli, Lucio Angelo; Boisson, Catherine; Borkowski, Jerzy; Buson, Sara; Carosi, Alessandro; Conforti, Vito; Colomé, Pep; Reyes, Raquel de los; Dumm, Jon; Evans, Phil; Fortson, Lucy; Fuessling, Matthias; Gotz, Diego; Graciani, Ricardo; Gianotti, Fulvio; Grandi, Paola; Hinton, Jim; Humensky, Brian; Inoue, Susumu; Knödlseder, Jürgen; Flour, Thierry Le; Lindemann, Rico; Malaguti, Giuseppe; Markoff, Sera; Marisaldi, Martino; Neyroud, Nadine; Nicastro, Luciano; Ohm, Stefan; Osborne, Julian; Oya, Igor; Rodriguez, Jerome; Rosen, Simon; Ribo, Marc; Tacchini, Alessandro; Schüssler, Fabian; Stolarczyk, Thierry; Torresi, Eleonora; Testa, Vincenzo; Wegner, Peter

2015-01-01

The Cherenkov Telescope Array (CTA) observatory will be one of the largest ground-based very high-energy gamma-ray observatories. The On-Site Analysis will be the first CTA scientific analysis of data acquired from the array of telescopes, in both northern and southern sites. The On-Site Analysis will have two pipelines: the Level-A pipeline (also known as Real-Time Analysis, RTA) and the level-B one. The RTA performs data quality monitoring and must be able to issue automated alerts on variable and transient astrophysical sources within 30 seconds from the last acquired Cherenkov event that contributes to the alert, with a sensitivity not worse than the one achieved by the final pipeline by more than a factor of 3. The Level-B Analysis has a better sensitivity (not be worse than the final one by a factor of 2) and the results should be available within 10 hours from the acquisition of the data: for this reason this analysis could be performed at the end of an observation or next morning. The latency (in part...

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

Directory of Open Access Journals (Sweden)

Yick Ching Wong

2014-11-01

Full Text Available 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.

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

Science.gov (United States)

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

Automated detection of regions of interest for tissue microarray experiments: an image texture analysis

International Nuclear Information System (INIS)

Karaçali, Bilge; Tözeren, Aydin

2007-01-01

Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. This study presents a high throughput analysis of texture heterogeneity on breast tissue images for the purpose of identifying regions of interest in the tissue for molecular profiling via tissue microarray technology. Image texture of breast histology slides was described in terms of three parameters: the percentage of area occupied in an image block by chromatin (B), percentage occupied by stroma-like regions (P), and a statistical heterogeneity index H commonly used in image analysis. Texture parameters were defined and computed for each of the thousands of image blocks in our dataset using both the gray scale and color segmentation. The image blocks were then classified into three categories using the texture feature parameters in a novel statistical learning algorithm. These categories are as follows: image blocks specific to normal breast tissue, blocks specific to cancerous tissue, and those image blocks that are non-specific to normal and disease states. Gray scale and color segmentation techniques led to identification of same regions in histology slides as cancer-specific. Moreover the image blocks identified as cancer-specific belonged to those cell crowded regions in whole section image slides that were marked by two pathologists as regions of interest for further histological studies. These results indicate the high efficiency of our automated method for identifying pathologic regions of interest on histology slides. Automation of critical region identification will help minimize the inter-rater variability among different raters (pathologists) as hundreds of tumors that are used to develop an array have typically been evaluated (graded) by different pathologists. The region of interest

CGHPRO – A comprehensive data analysis tool for array CGH

Directory of Open Access Journals (Sweden)

Lenzner Steffen

2005-04-01

Full Text Available Abstract Background Array CGH (Comparative Genomic Hybridisation is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios. Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment. Results We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the

Quantitative analysis of transcranial and intraparenchymal light penetration in human cadaver brain tissue.

Science.gov (United States)

Tedford, Clark E; DeLapp, Scott; Jacques, Steven; Anders, Juanita

2015-04-01

Photobiomodulation (PBM) also known as low-level light therapy has been used successfully for the treatment of injury and disease of the nervous system. The use of PBM to treat injury and diseases of the brain requires an in-depth understanding of light propagation through tissues including scalp, skull, meninges, and brain. This study investigated the light penetration gradients in the human cadaver brain using a Transcranial Laser System with a 30 mm diameter beam of 808 nm wavelength light. In addition, the wavelength-dependence of light scatter and absorbance in intraparenchymal brain tissue using 660, 808, and 940 nm wavelengths was investigated. Intact human cadaver heads (n = 8) were obtained for measurement of light propagation through the scalp/skull/meninges and into brain tissue. The cadaver heads were sectioned in either the transverse or mid-sagittal. The sectioned head was mounted into a cranial fixture with an 808 nm wavelength laser system illuminating the head from beneath with either pulsed-wave (PW) or continuous-wave (CW) laser light. A linear array of nine isotropic optical fibers on a 5 mm pitch was inserted into the brain tissue along the optical axis of the beam. Light collected from each fiber was delivered to a multichannel power meter. As the array was lowered into the tissue, the power from each probe was recorded at 5 mm increments until the inner aspect of the dura mater was reached. Intraparenchymal light penetration measurements were made by delivering a series of wavelengths (660, 808, and 940 nm) through a separate optical fiber within the array, which was offset from the array line by 5 mm. Local light penetration was determined and compared across the selected wavelengths. Unfixed cadaver brains provide good anatomical localization and reliable measurements of light scatter and penetration in the CNS tissues. Transcranial application of 808 nm wavelength light penetrated the scalp, skull, meninges, and brain

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

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Astrid Wachter

2015-11-01

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

Analysis and Simulation of Multi-target Echo Signals from a Phased Array Radar

OpenAIRE

Jia Zhen; Zhou Rui

2017-01-01

The construction of digital radar simulation systems has been a research hotspot of the radar field. This paper focuses on theoretical analysis and simulation of multi-target echo signals produced in a phased array radar system, and constructs an array antenna element and a signal generation environment. The antenna element is able to simulate planar arrays and optimizes these arrays by adding window functions. And the signal environment can model and simulate radar transmission signals, rada...

RoboSCell: An automated single cell arraying and analysis instrument

KAUST Repository

Sakaki, Kelly

2009-09-09

Single cell research has the potential to revolutionize experimental methods in biomedical sciences and contribute to clinical practices. Recent studies suggest analysis of single cells reveals novel features of intracellular processes, cell-to-cell interactions and cell structure. The methods of single cell analysis require mechanical resolution and accuracy that is not possible using conventional techniques. Robotic instruments and novel microdevices can achieve higher throughput and repeatability; however, the development of such instrumentation is a formidable task. A void exists in the state-of-the-art for automated analysis of single cells. With the increase in interest in single cell analyses in stem cell and cancer research the ability to facilitate higher throughput and repeatable procedures is necessary. In this paper, a high-throughput, single cell microarray-based robotic instrument, called the RoboSCell, is described. The proposed instrument employs a partially transparent single cell microarray (SCM) integrated with a robotic biomanipulator for in vitro analyses of live single cells trapped at the array sites. Cells, labeled with immunomagnetic particles, are captured at the array sites by channeling magnetic fields through encapsulated permalloy channels in the SCM. The RoboSCell is capable of systematically scanning the captured cells temporarily immobilized at the array sites and using optical methods to repeatedly measure extracellular and intracellular characteristics over time. The instrument\\'s capabilities are demonstrated by arraying human T lymphocytes and measuring the uptake dynamics of calcein acetoxymethylester-all in a fully automated fashion. © 2009 Springer Science+Business Media, LLC.

Analysis of the modal behavior of an antiguide diode laser array with Talbot filter

NARCIS (Netherlands)

van Eijk, P.D.; van Eijk, Pieter D.; Reglat, Muriel; Vassilief, Georges; Krijnen, Gijsbertus J.M.; Driessen, A.; Mouthaan, A.J.

An analysis of the filtering of the array modes in a resonant optical waveguide (ROW) array of antiguides by a diffractive spatial filter (a Talbot filter) is presented. A dispersion relation is derived for the array modes, allowing the calculation of the field distribution. The filtering is

Automated Detection of Connective Tissue by Tissue Counter Analysis and Classification and Regression Trees

Directory of Open Access Journals (Sweden)

Josef Smolle

2001-01-01

Full Text Available Objective: To evaluate the feasibility of the CART (Classification and Regression Tree procedure for the recognition of microscopic structures in tissue counter analysis. Methods: Digital microscopic images of H&E stained slides of normal human skin and of primary malignant melanoma were overlayed with regularly distributed square measuring masks (elements and grey value, texture and colour features within each mask were recorded. In the learning set, elements were interactively labeled as representing either connective tissue of the reticular dermis, other tissue components or background. Subsequently, CART models were based on these data sets. Results: Implementation of the CART classification rules into the image analysis program showed that in an independent test set 94.1% of elements classified as connective tissue of the reticular dermis were correctly labeled. Automated measurements of the total amount of tissue and of the amount of connective tissue within a slide showed high reproducibility (r=0.97 and r=0.94, respectively; p < 0.001. Conclusions: CART procedure in tissue counter analysis yields simple and reproducible classification rules for tissue elements.

Intracavitary ultrasound phased arrays for thermal therapies

Science.gov (United States)

Hutchinson, Erin

Currently, the success of hyperthermia and thermal surgery treatments is limited by the technology used in the design and fabrication of clinical heating devices and the completeness of the thermometry systems used for guidance. For both hyperthermia and thermal surgery, electrically focused ultrasound generated by phased arrays provides a means of controlling localized energy deposition in body tissues. Intracavitary applicators can be used to bring the energy source close to a target volume, such as the prostate, thereby minimizing normal tissue damage. The work performed in this study was aimed at improving noninvasive prostate thermal therapies and utilized three research approaches: (1) Acoustic, thermal and optimization simulations, (2) Design and fabrication of multiple phased arrays, (3) Ex vivo and in vivo experimental testing of the heating capabilities of the phased arrays. As part of this study, a novel aperiodic phased array design was developed which resulted in a 30- 45% reduction in grating lobe levels when compared to conventional phased arrays. Measured acoustic fields generated by the constructed aperiodic arrays agreed closely with the fields predicted by the theoretical simulations and covered anatomically appropriate ranges. The power capabilities of these arrays were demonstrated to be sufficient for the purposes of hyperthermia and thermal surgery. The advantage of using phased arrays in place of fixed focus transducers was shown by demonstrating the ability of electronic scanning to increase the size of the necrosed tissue volume while providing a more uniform thermal dose, which can ultimately reduce patient treatment times. A theoretical study on the feasibility of MRI (magnetic resonance imaging) thermometry for noninvasive temperature feedback control was investigated as a means to improve transient and steady state temperature distributions achieved in hyperthermia treatments. MRI guided ex vivo and in vivo experiments demonstrated

Read margin analysis of crossbar arrays using the cell-variability-aware simulation method

Science.gov (United States)

Sun, Wookyung; Choi, Sujin; Shin, Hyungsoon

2018-02-01

This paper proposes a new concept of read margin analysis of crossbar arrays using cell-variability-aware simulation. The size of the crossbar array should be considered to predict the read margin characteristic of the crossbar array because the read margin depends on the number of word lines and bit lines. However, an excessively high-CPU time is required to simulate large arrays using a commercial circuit simulator. A variability-aware MATLAB simulator that considers independent variability sources is developed to analyze the characteristics of the read margin according to the array size. The developed MATLAB simulator provides an effective method for reducing the simulation time while maintaining the accuracy of the read margin estimation in the crossbar array. The simulation is also highly efficient in analyzing the characteristic of the crossbar memory array considering the statistical variations in the cell characteristics.

Solar array deployment analysis considering path-dependent behavior of a tape spring hinge

Energy Technology Data Exchange (ETDEWEB)

Kim, Kyung Won; Park, Young Jin [KAIST, Daejeon (Korea, Republic of)

2015-05-15

Solar array deployment analysis is conducted considering the path-dependent nonlinear behavior of tape spring hinge. Such hinges offer many advantages over rigid hinges; they are self-deployable, self-locking, lightweight, and simple. However, they show strongly nonlinear behavior with respect to rotation angle, making deployment analysis difficult. To accurately consider the characteristics of tape spring hinges for deployment analysis, a path-dependent path identification (PI) method for tracing the previous path of the moment is introduced. To analyze the deployment motion, the governing equation for solar array deployment is derived within the framework of Kane's dynamic equation for three deployable solar panels. The numerical solution is compared with the Recurdyn's multi-body dynamics analysis solution using experimentally measured moment-rotation profiles. Solar array deployment analysis is conducted by considering and not considering the path-dependent PI method. This simulation example shows that the proposed path-dependent PI method is very effective for accurately predicting the deployment motion.

Comprehensive Survey on Improved Focality and Penetration Depth of Transcranial Magnetic Stimulation Employing Multi-Coil Arrays

Directory of Open Access Journals (Sweden)

Xile Wei

2017-11-01

Full Text Available Multi-coil arrays applied in transcranial magnetic stimulation (TMS are proposed to accurately stimulate brain tissues and modulate neural activities by an induced electric field (EF. Composed of numerous independently driven coils, a multi-coil array has alternative energizing strategies to evoke EFs targeting at different cerebral regions. To improve the locating resolution and the stimulating focality, we need to fully understand the variation properties of induced EFs and the quantitative control method of the spatial arrangement of activating coils, both of which unfortunately are still unclear. In this paper, a comprehensive analysis of EF properties was performed based on multi-coil arrays. Four types of planar multi-coil arrays were used to study the relationship between the spatial distribution of EFs and the structure of stimuli coils. By changing coil-driven strategies in a basic 16-coil array, we find that an EF induced by compactly distributed coils decays faster than that induced by dispersedly distributed coils, but the former has an advantage over the latter in terms of the activated brain volume. Simulation results also indicate that the attenuation rate of an EF induced by the 36-coil dense array is 3 times and 1.5 times greater than those induced by the 9-coil array and the 16-coil array, respectively. The EF evoked by the 36-coil dispense array has the slowest decay rate. This result demonstrates that larger multi-coil arrays, compared to smaller ones, activate deeper brain tissues at the expense of decreased focality. A further study on activating a specific field of a prescribed shape and size was conducted based on EF variation. Accurate target location was achieved with a 64-coil array 18 mm in diameter. A comparison between the figure-8 coil, the planar array, and the cap-formed array was made and demonstrates an improvement of multi-coil configurations in the penetration depth and the focality. These findings suggest

Comprehensive Survey on Improved Focality and Penetration Depth of Transcranial Magnetic Stimulation Employing Multi-Coil Arrays.

Science.gov (United States)

Wei, Xile; Li, Yao; Lu, Meili; Wang, Jiang; Yi, Guosheng

2017-11-14

Multi-coil arrays applied in transcranial magnetic stimulation (TMS) are proposed to accurately stimulate brain tissues and modulate neural activities by an induced electric field (EF). Composed of numerous independently driven coils, a multi-coil array has alternative energizing strategies to evoke EFs targeting at different cerebral regions. To improve the locating resolution and the stimulating focality, we need to fully understand the variation properties of induced EFs and the quantitative control method of the spatial arrangement of activating coils, both of which unfortunately are still unclear. In this paper, a comprehensive analysis of EF properties was performed based on multi-coil arrays. Four types of planar multi-coil arrays were used to study the relationship between the spatial distribution of EFs and the structure of stimuli coils. By changing coil-driven strategies in a basic 16-coil array, we find that an EF induced by compactly distributed coils decays faster than that induced by dispersedly distributed coils, but the former has an advantage over the latter in terms of the activated brain volume. Simulation results also indicate that the attenuation rate of an EF induced by the 36-coil dense array is 3 times and 1.5 times greater than those induced by the 9-coil array and the 16-coil array, respectively. The EF evoked by the 36-coil dispense array has the slowest decay rate. This result demonstrates that larger multi-coil arrays, compared to smaller ones, activate deeper brain tissues at the expense of decreased focality. A further study on activating a specific field of a prescribed shape and size was conducted based on EF variation. Accurate target location was achieved with a 64-coil array 18 mm in diameter. A comparison between the figure-8 coil, the planar array, and the cap-formed array was made and demonstrates an improvement of multi-coil configurations in the penetration depth and the focality. These findings suggest that there is a

SNP Arrays

Directory of Open Access Journals (Sweden)

Jari Louhelainen

2016-10-01

Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

Array analysis of regional Pn and Pg wavefields from the Nevada Test Site

International Nuclear Information System (INIS)

Leonard, M.A.

1991-06-01

Small-aperture high-frequency seismic arrays with dimensions of a few kilometers or less, can improve our ability to seismically monitor compliance with a low-yield Threshold Test Ban Treaty. This work studies the characteristics and effectiveness of array processing of the regional Pn and Pg wavefields generated by underground nuclear explosions at the Nevada Test Site. Waveform data from the explosion HARDIN (m b = 5.5) is recorded at a temporary 12-element, 3-component, 1.5 km-aperture array sited in an area of northern Nevada. The explosions VILLE (m b = 4.4) and SALUT (m b = 5.5) are recorded at two arrays sited in the Mojave desert, one a 96-element vertical-component 7 km-aperture array and the other a 155-element vertical-component 4 km-aperture array. Among the mean spectra for the m b = 5.5 events there are significant differences in low-frequency spectral amplitudes between array sites. The spectra become nearly identical beyond about 6 Hz. Spectral ratios are used to examine seismic source properties and the partitioning of energy between Pn and Pg. Frequency-wavenumber analysis at the 12-element array is used to obtain estimates of signal gain, phase velocity, and source azimuth. This analysis reveals frequency-dependent biases in velocity and azimuth of the coherent Pn and Pg arrivals. Signal correlation, the principal factor governing array performance, is examined in terms of spatial coherence estimates. The coherence is found to vary between the three sites. In all cases the coherence of Pn is greater than that for Pg. 81 refs., 92 figs., 5 tabs

Array analysis of regional Pn and Pg wavefields from the Nevada Test Site

Energy Technology Data Exchange (ETDEWEB)

Leonard, M.A. (California Univ., Berkeley, CA (United States). Dept. of Geology and Geophysics Lawrence Berkeley Lab., CA (United States))

1991-06-01

Small-aperture high-frequency seismic arrays with dimensions of a few kilometers or less, can improve our ability to seismically monitor compliance with a low-yield Threshold Test Ban Treaty. This work studies the characteristics and effectiveness of array processing of the regional Pn and Pg wavefields generated by underground nuclear explosions at the Nevada Test Site. Waveform data from the explosion HARDIN (m{sub b} = 5.5) is recorded at a temporary 12-element, 3-component, 1.5 km-aperture array sited in an area of northern Nevada. The explosions VILLE (m{sub b} = 4.4) and SALUT (m{sub b} = 5.5) are recorded at two arrays sited in the Mojave desert, one a 96-element vertical-component 7 km-aperture array and the other a 155-element vertical-component 4 km-aperture array. Among the mean spectra for the m{sub b} = 5.5 events there are significant differences in low-frequency spectral amplitudes between array sites. The spectra become nearly identical beyond about 6 Hz. Spectral ratios are used to examine seismic source properties and the partitioning of energy between Pn and Pg. Frequency-wavenumber analysis at the 12-element array is used to obtain estimates of signal gain, phase velocity, and source azimuth. This analysis reveals frequency-dependent biases in velocity and azimuth of the coherent Pn and Pg arrivals. Signal correlation, the principal factor governing array performance, is examined in terms of spatial coherence estimates. The coherence is found to vary between the three sites. In all cases the coherence of Pn is greater than that for Pg. 81 refs., 92 figs., 5 tabs.

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

Science.gov (United States)

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

2015-11-01

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

Chronic in vivo stability assessment of carbon fiber microelectrode arrays

Science.gov (United States)

Patel, Paras R.; Zhang, Huanan; Robbins, Matthew T.; Nofar, Justin B.; Marshall, Shaun P.; Kobylarek, Michael J.; Kozai, Takashi D. Y.; Kotov, Nicholas A.; Chestek, Cynthia A.

2016-12-01

Objective. Individual carbon fiber microelectrodes can record unit activity in both acute and semi-chronic (∼1 month) implants. Additionally, new methods have been developed to insert a 16 channel array of carbon fiber microelectrodes. Before assessing the in vivo long-term viability of these arrays, accelerated soak tests were carried out to determine the most stable site coating material. Next, a multi-animal, multi-month, chronic implantation study was carried out with carbon fiber microelectrode arrays and silicon electrodes. Approach. Carbon fibers were first functionalized with one of two different formulations of PEDOT and subjected to accelerated aging in a heated water bath. After determining the best PEDOT formula to use, carbon fiber arrays were chronically implanted in rat motor cortex. Some rodents were also implanted with a single silicon electrode, while others received both. At the end of the study a subset of animals were perfused and the brain tissue sliced. Tissue sections were stained for astrocytes, microglia, and neurons. The local reactive responses were assessed using qualitative and quantitative methods. Main results. Electrophysiology recordings showed the carbon fibers detecting unit activity for at least 3 months with average amplitudes of ∼200 μV. Histology analysis showed the carbon fiber arrays with a minimal to non-existent glial scarring response with no adverse effects on neuronal density. Silicon electrodes showed large glial scarring that impacted neuronal counts. Significance. This study has validated the use of carbon fiber microelectrode arrays as a chronic neural recording technology. These electrodes have demonstrated the ability to detect single units with high amplitude over 3 months, and show the potential to record for even longer periods. In addition, the minimal reactive response should hold stable indefinitely, as any response by the immune system may reach a steady state after 12 weeks.

Clearance Analysis of Node 3 Aft CBM to the Stowed FGB Solar Array

Science.gov (United States)

Liddle, Donn

2014-01-01

In early 2011, the ISS Vehicle Configuration Office began considering the relocation of the Permanent Multipurpose Module (PMM) to the aft facing Common Berthing Mechanism (CBM) on Node 3 to open a berthing location for visiting vehicles on the Node 1 nadir CBM. In this position, computer-aided design (CAD) models indicated that the aft end of the PMM would be only a few inches from the stowed Functional Cargo Block (FGB) port solar array. To validate the CAD model clearance analysis, in the late summer of 2011 the Image Science and Analysis Group (ISAG) was asked to determine the true geometric relationship between the on-orbit aft facing Node 3 CBM and the FGB port solar array. The desired measurements could be computed easily by photogrammetric analysis if current imagery of the ISS hardware were obtained. Beginning in the fall of 2011, ISAG used the Dynamic Onboard Ubiquitous Graphics (DOUG) program to design a way to acquire imagery of the aft face of Node 3, the aft end-cone of Node 1, the port side of pressurized mating adapter 1 (PMA1), and the port side of the FGB out to the tip of the port solar array using cameras on the Space Station Remote Manipulator System (SSRMS). This was complicated by the need to thread the SSRMS under the truss, past Node 3 and the Cupola, and into the space between the aft side of Node 3 and the FGB solar array to acquire more than 100 images from multiple positions. To minimize the number of SSRMS movements, the Special Purpose Dexterous Manipulator (SPDM) would be attached to the SSRMS. This would make it possible to park the SPDM in one position and acquire multiple images by changing the viewing orientation of the SPDM body cameras using the pan/tilt units on which the cameras are mounted. Using this implementation concept, ISAG identified four SSRMS/SPDM positions from which all of the needed imagery could be acquired. Based on a photogrammetric simulation, it was estimated that the location of the FGB solar array could be

Dual-Polarized Planar Phased Array Analysis for Meteorological Applications

Directory of Open Access Journals (Sweden)

Chen Pang

2015-01-01

Full Text Available This paper presents a theoretical analysis for the accuracy requirements of the planar polarimetric phased array radar (PPPAR in meteorological applications. Among many factors that contribute to the polarimetric biases, four factors are considered and analyzed in this study, namely, the polarization distortion due to the intrinsic limitation of a dual-polarized antenna element, the antenna pattern measurement error, the entire array patterns, and the imperfect horizontal and vertical channels. Two operation modes, the alternately transmitting and simultaneously receiving (ATSR mode and the simultaneously transmitting and simultaneously receiving (STSR mode, are discussed. For each mode, the polarimetric biases are formulated. As the STSR mode with orthogonal waveforms is similar to the ATSR mode, the analysis is mainly focused on the ATSR mode and the impacts of the bias sources on the measurement of polarimetric variables are investigated through Monte Carlo simulations. Some insights of the accuracy requirements are obtained and summarized.

Joint Analysis of BICEP2/Keck Array and Planck Data

DEFF Research Database (Denmark)

Ade, P. A. R.; Aghanim, N.; Ahmed, Z.

2015-01-01

We report the results of a joint analysis of data from BICEP2/Keck Array and Planck. BICEP2 and Keck Array have observed the same approximately 400 deg2 patch of sky centered on RA 0 h, Dec. -57.5°. The combined maps reach a depth of 57 nK deg in Stokes Q and U in a band centered at 150 GHz. Planck...... GHz to a lensed-ΛCDM model that includes dust and a possible contribution from inflationary gravitational waves (as parametrized by the tensor-to-scalar ratio r), using a prior on the frequency spectral behavior of polarized dust emission from previous Planck analysis of other regions of the sky. We...... present an alternative analysis which is similar to a map-based cleaning of the dust contribution, and show that this gives similar constraints. The final result is expressed as a likelihood curve for r, and yields an upper limit r 0.05

Blind Time-Frequency Analysis for Source Discrimination in Multisensor Array Processing

National Research Council Canada - National Science Library

Amin, Moeness

1999-01-01

.... We have clearly demonstrated, through analysis and simulations, the offerings of time-frequency distributions in solving key problems in sensor array processing, including direction finding, source...

A novel, flat, electronically-steered phased array transducer for tissue ablation: preliminary results

International Nuclear Information System (INIS)

Ellens, Nicholas P K; Lucht, Benjamin B C; Gunaseelan, Samuel T; Hudson, John M; Hynynen, Kullervo H

2015-01-01

Flat, λ/2-spaced phased arrays for therapeutic ultrasound were examined in silico and in vitro. All arrays were made by combining modules made of 64 square elements with 1.5 mm inter-element spacing along both major axes. The arrays were designed to accommodate integrated, co-aligned diagnostic transducers for targeting and monitoring. Six arrays of 1024 elements (16 modules) and four arrays of 6144 elements (96 modules) were modelled and compared according to metrics such as peak pressure amplitude, focal size, ability to be electronically-steered far off-axis and grating lobe amplitude. Two 1024 element prototypes were built and measured in vitro, producing over 100 W of acoustic power. In both cases, the simulation model of the pressure amplitude field was in good agreement with values measured by hydrophone. Using one of the arrays, it was shown that the peak pressure amplitude dropped by only 24% and 25% of the on-axis peak pressure amplitude when steered to the edge of the array (40 mm) at depths of 30 mm and 50 mm. For the 6144 element arrays studied in in silico only, similarly high steerability was found: even when steered 100 mm off-axis, the pressure amplitude decrease at the focus was less than 20%, while the maximum pressure grating lobe was only 20%. Thermal simulations indicate that the modules produce more than enough acoustic power to perform rapid ablations at physiologically relevant depths and steering angles. Arrays such as proposed and tested in this study have enormous potential: their high electronic steerability suggests that they will be able to perform ablations of large volumes without the need for any mechanical translation. (paper)

Active Micro structured Optical Arrays of Grazing Incidence Reflectors

International Nuclear Information System (INIS)

Willingale, R.; Feldman, Ch.; Michette, A.; Hart, D.; McFaul, Ch; Morrison, G.R.; Pfauntsch, S.; Powell, A.K.; Sahraei, Sh.; Shand, M.T.; Button, T.; Rodriguez-Sanmartin, D.; Zhang, D.; Dunare, C.; Parkes, W.; Stevenson, T.; Folkard, M.; Vojnovic, B.; Vojnovic, B.

2011-01-01

The UK Smart X-Ray Optics (SXO) programme is developing active/adaptive optics for terrestrial applications. One of the technologies proposed is micro structured optical arrays (MOAs), which focus X-rays using grazing incidence reflection through consecutive aligned arrays of microscopic channels. Although such arrays are similar in concept to poly capillary and microchannel plate optics, they can be bent and adjusted using piezoelectric actuators providing control over the focusing and inherent aberrations. Custom configurations can be designed, using ray tracing and finite element analysis, for applications from sub-keV to several-keV X-rays, and the channels of appropriate aspect ratios can be made using deep silicon etching. An exemplar application will be in the micro probing of biological cells and tissue samples using Ti Ka radiation (4.5?keV) in studies related to radiation-induced cancers. This paper discusses the optical design, modelling, and manufacture of such optics

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

Directory of Open Access Journals (Sweden)

Sri Jaya LAKSHMI

2015-05-01

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

Combined Bisulfite Restriction Analysis for brain tissue identification.

Science.gov (United States)

Samsuwan, Jarunya; Muangsub, Tachapol; Yanatatsaneejit, Pattamawadee; Mutirangura, Apiwat; Kitkumthorn, Nakarin

2018-05-01

According to the tissue-specific methylation database (doi: 10.1016/j.gene.2014.09.060), methylation at CpG locus cg03096975 in EML2 has been preliminarily proven to be specific to brain tissue. In this study, we enlarged sample size and developed a technique for identifying brain tissue in aged samples. Combined Bisulfite Restriction Analysis-for EML2 (COBRA-EML2) technique was established and validated in various organ samples obtained from 108 autopsies. In addition, this technique was also tested for its reliability, minimal DNA concentration detected, and use in aged samples and in samples obtained from specific brain compartments and spinal cord. COBRA-EML2 displayed 100% sensitivity and specificity for distinguishing brain tissue from other tissues, showed high reliability, was capable of detecting minimal DNA concentration (0.015ng/μl), could be used for identifying brain tissue in aged samples. In summary, COBRA-EML2 is a technique to identify brain tissue. This analysis is useful in criminal cases since it can identify the vital organ tissues from small samples acquired from criminal scenes. The results from this analysis can be counted as a medical and forensic marker supporting criminal investigations, and as one of the evidences in court rulings. Copyright © 2018 Elsevier B.V. All rights reserved.

Cluster Computing For Real Time Seismic Array Analysis.

Science.gov (United States)

Martini, M.; Giudicepietro, F.

A seismic array is an instrument composed by a dense distribution of seismic sen- sors that allow to measure the directional properties of the wavefield (slowness or wavenumber vector) radiated by a seismic source. Over the last years arrays have been widely used in different fields of seismological researches. In particular they are applied in the investigation of seismic sources on volcanoes where they can be suc- cessfully used for studying the volcanic microtremor and long period events which are critical for getting information on the volcanic systems evolution. For this reason arrays could be usefully employed for the volcanoes monitoring, however the huge amount of data produced by this type of instruments and the processing techniques which are quite time consuming limited their potentiality for this application. In order to favor a direct application of arrays techniques to continuous volcano monitoring we designed and built a small PC cluster able to near real time computing the kinematics properties of the wavefield (slowness or wavenumber vector) produced by local seis- mic source. The cluster is composed of 8 Intel Pentium-III bi-processors PC working at 550 MHz, and has 4 Gigabytes of RAM memory. It runs under Linux operating system. The developed analysis software package is based on the Multiple SIgnal Classification (MUSIC) algorithm and is written in Fortran. The message-passing part is based upon the LAM programming environment package, an open-source imple- mentation of the Message Passing Interface (MPI). The developed software system includes modules devote to receiving date by internet and graphical applications for the continuous displaying of the processing results. The system has been tested with a data set collected during a seismic experiment conducted on Etna in 1999 when two dense seismic arrays have been deployed on the northeast and the southeast flanks of this volcano. A real time continuous acquisition system has been simulated by

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

Data.gov (United States)

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

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

Data.gov (United States)

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

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

Science.gov (United States)

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.

Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization.

Science.gov (United States)

Liao, Can; Fu, Fang; Yang, Xin; Sun, Yi-Min; Li, Dong-Zhi

2011-06-01

Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis. Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction. All the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene. The results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

Mass accretion and nested array dynamics from Ni-Clad Ti-Al wire array Z pinches

International Nuclear Information System (INIS)

Jones, Brent Manley; Jennings, Christopher A.; Coverdale, Christine Anne; Cuneo, Michael Edward; Maron, Yitzhak; LePell, Paul David; Deeney, Christopher

2010-01-01

Analysis of 50 mm diameter wire arrays at the Z Accelerator has shown experimentally the accretion of mass in a stagnating z pinch and provided insight into details of the radiating plasma species and plasma conditions. This analysis focused on nested wire arrays with a 2:1 (outeninner) mass, radius, and wire number ratio where Al wires were fielded on the outer array and Ni-clad Ti wires were fielded on the inner array.In this presentation, we will present analysis of data from other mixed Al/Ni-clad Ti configurations to further evaluate nested wire array dynamics and mass accretion. These additional configurations include the opposite configuration to that described above (Ni-clad Ti wires on the outer array, with Al wires on the inner array) as well as higher wire number Al configurations fielded to vary the interaction of the two arrays. These same variations were also assessed for a smaller diameter nested array configuration (40 mm). Variations in the emitted radiation and plasma conditions will be presented, along with a discussion of what the results indicate about the nested array dynamics. Additional evidence for mass accretion will also be presented.

Gravitational wave detection and data analysis for pulsar timing arrays

NARCIS (Netherlands)

Haasteren, Rutger van

2011-01-01

Long-term precise timing of Galactic millisecond pulsars holds great promise for measuring long-period (months-to-years) astrophysical gravitational waves. In this work we develop a Bayesian data analysis method for projects called pulsar timing arrays; projects aimed to detect these gravitational

Combined spectroscopic imaging and chemometric approach for automatically partitioning tissue types in human prostate tissue biopsies

Science.gov (United States)

Haka, Abigail S.; Kidder, Linda H.; Lewis, E. Neil

2001-07-01

We have applied Fourier transform infrared (FTIR) spectroscopic imaging, coupling a mercury cadmium telluride (MCT) focal plane array detector (FPA) and a Michelson step scan interferometer, to the investigation of various states of malignant human prostate tissue. The MCT FPA used consists of 64x64 pixels, each 61 micrometers 2, and has a spectral range of 2-10.5 microns. Each imaging data set was collected at 16-1 resolution, resulting in 512 image planes and a total of 4096 interferograms. In this article we describe a method for separating different tissue types contained within FTIR spectroscopic imaging data sets of human prostate tissue biopsies. We present images, generated by the Fuzzy C-Means clustering algorithm, which demonstrate the successful partitioning of distinct tissue type domains. Additionally, analysis of differences in the centroid spectra corresponding to different tissue types provides an insight into their biochemical composition. Lastly, we demonstrate the ability to partition tissue type regions in a different data set using centroid spectra calculated from the original data set. This has implications for the use of the Fuzzy C-Means algorithm as an automated technique for the separation and examination of tissue domains in biopsy samples.

Analysis of radiation damage in on-orbit solar array of Venus explorer Akatsuki

International Nuclear Information System (INIS)

Toyota, Hiroyuki; Shimada, Takanobu; Takahashi, You; Imamura, Takeshi; Hada, Yuko; Ishii, Takako T.; Isobe, Hiroaki; Asai, Ayumi; Shiota, Daikou

2013-01-01

This paper describes an analysis of radiation damage in solar array of Venus explorer Akatsuki observed on orbit. The output voltage of the solar array have shown sudden drops, which are most reasonably associated with radiation damage, three times since its launch. The analysis of these radiation damages is difficult, because no direct observation data of the spectra and the amount of the high-energy particles is available. We calculated the radiation damage using the relative damage coefficient (RDC) method assuming a typical spectral shape of protons. (author)

Numeric-modeling sensitivity analysis of the performance of wind turbine arrays

Energy Technology Data Exchange (ETDEWEB)

Lissaman, P.B.S.; Gyatt, G.W.; Zalay, A.D.

1982-06-01

An evaluation of the numerical model created by Lissaman for predicting the performance of wind turbine arrays has been made. Model predictions of the wake parameters have been compared with both full-scale and wind tunnel measurements. Only limited, full-scale data were available, while wind tunnel studies showed difficulties in representing real meteorological conditions. Nevertheless, several modifications and additions have been made to the model using both theoretical and empirical techniques and the new model shows good correlation with experiment. The larger wake growth rate and shorter near wake length predicted by the new model lead to reduced interference effects on downstream turbines and hence greater array efficiencies. The array model has also been re-examined and now incorporates the ability to show the effects of real meteorological conditions such as variations in wind speed and unsteady winds. The resulting computer code has been run to show the sensitivity of array performance to meteorological, machine, and array parameters. Ambient turbulence and windwise spacing are shown to dominate, while hub height ratio is seen to be relatively unimportant. Finally, a detailed analysis of the Goodnoe Hills wind farm in Washington has been made to show how power output can be expected to vary with ambient turbulence, wind speed, and wind direction.

Rapid prenatal diagnosis of cytogenetic abnormalities by array CGH analysis

Science.gov (United States)

Array CGH analysis has been shown to be highly accurate for rapid detection of chromosomal aneuploidies and submicroscopic deletions or duplications on fetal DNA samples in a clinical prenatal diagnostic setting. The objective of this study is to present our "post-validation phase" experience with ...

Segmentation and Quantitative Analysis of Epithelial Tissues.

Science.gov (United States)

Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

2016-01-01

Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

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

Science.gov (United States)

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.

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

Directory of Open Access Journals (Sweden)

Settles Matthew L

2009-05-01

Full Text Available Abstract Background Natural antisense transcripts (NATs are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded or a different locus (trans-encoded. They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept. Results By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense

Fast photoacoustic imaging system based on 320-element linear transducer array

International Nuclear Information System (INIS)

Yin Bangzheng; Xing Da; Wang Yi; Zeng Yaguang; Tan Yi; Chen Qun

2004-01-01

A fast photoacoustic (PA) imaging system, based on a 320-transducer linear array, was developed and tested on a tissue phantom. To reconstruct a test tomographic image, 64 time-domain PA signals were acquired from a tissue phantom with embedded light-absorption targets. A signal acquisition was accomplished by utilizing 11 phase-controlled sub-arrays, each consisting of four transducers. The results show that the system can rapidly map the optical absorption of a tissue phantom and effectively detect the embedded light-absorbing target. By utilizing the multi-element linear transducer array and phase-controlled imaging algorithm, we thus can acquire PA tomography more efficiently, compared to other existing technology and algorithms. The methodology and equipment thus provide a rapid and reliable approach to PA imaging that may have potential applications in noninvasive imaging and clinic diagnosis

Re-Punching Tissue Microarrays Is Possible: Why Can This Be Useful and How to Do It

Directory of Open Access Journals (Sweden)

Aurélien Lacombe

2015-05-01

Full Text Available Tissue microarray (TMA methodology allows the concomitant analysis of hundreds of tissue specimens arrayed in the same manner on a recipient block. Subsequently, all samples can be processed under identical conditions, such as antigen retrieval procedure, reagent concentrations, incubation times with antibodies/probes, and escaping the inter-assays variability. Therefore, the use of TMA has revolutionized histopathology translational research projects and has become a tool very often used for putative biomarker investigations. TMAs are particularly relevant for large scale analysis of a defined disease entity. In the course of these exploratory studies, rare subpopulations can be discovered or identified. This can refer to subsets of patients with more particular phenotypic or genotypic disease with low incidence or to patients receiving a particular treatment. Such rare cohorts should be collected for more specific investigations at a later time, when, possibly, more samples of a rare identity will be available as well as more knowledge derived from concomitant, e.g., genetic, investigations will have been acquired. In this article we analyze for the first time the limits and opportunities to construct new TMA blocks using tissues from older available arrays and supplementary donor blocks. In summary, we describe the reasons and technical details for the construction of rare disease entities arrays.

OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging

DEFF Research Database (Denmark)

de Raad, Markus; de Rond, Tristan; Rübel, Oliver

2017-01-01

://openmsinersc.gov), a platform for storing, sharing, and analyzing MSI data. By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone without programming experience yet allows experienced users to leverage all features. OMAAT was :evaluated by analyzing an MSI data set of a high-throughput glycoside...... processing tools for the analysis of large arrayed MSI sample sets. The OpenMSI Arrayed Analysis Toolkit (OMAAT) is a software package that addresses the challenges of analyzing spatially defined samples in MSI data sets. OMAAT is written in Python and is integrated with OpenMSI (http...

The tissue micro-array data exchange specification: a web based experience browsing imported data

Science.gov (United States)

Nohle, David G; Hackman, Barbara A; Ayers, Leona W

2005-01-01

Background The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11

MTF measurement and analysis of linear array HgCdTe infrared detectors

Science.gov (United States)

Zhang, Tong; Lin, Chun; Chen, Honglei; Sun, Changhong; Lin, Jiamu; Wang, Xi

2018-01-01

The slanted-edge technique is the main method for measurement detectors MTF, however this method is commonly used on planar array detectors. In this paper the authors present a modified slanted-edge method to measure the MTF of linear array HgCdTe detectors. Crosstalk is one of the major factors that degrade the MTF value of such an infrared detector. This paper presents an ion implantation guard-ring structure which was designed to effectively absorb photo-carriers that may laterally defuse between adjacent pixels thereby suppressing crosstalk. Measurement and analysis of the MTF of the linear array detectors with and without a guard-ring were carried out. The experimental results indicated that the ion implantation guard-ring structure effectively suppresses crosstalk and increases MTF value.

ArrayExpress update--trends in database growth and links to data analysis tools.

Science.gov (United States)

Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Ison, Jon; Keays, Maria; Kurbatova, Natalja; Malone, James; Mani, Roby; Mupo, Annalisa; Pedro Pereira, Rui; Pilicheva, Ekaterina; Rung, Johan; Sharma, Anjan; Tang, Y Amy; Ternent, Tobias; Tikhonov, Andrew; Welter, Danielle; Williams, Eleanor; Brazma, Alvis; Parkinson, Helen; Sarkans, Ugis

2013-01-01

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue.

Science.gov (United States)

Kjeldsen, Henrik D; Kaiser, Marcus; Whittington, Miles A

2015-09-30

Brain function is dependent upon the concerted, dynamical interactions between a great many neurons distributed over many cortical subregions. Current methods of quantifying such interactions are limited by consideration only of single direct or indirect measures of a subsample of all neuronal population activity. Here we present a new derivation of the electromagnetic analogy to near-field acoustic holography allowing high-resolution, vectored estimates of interactions between sources of electromagnetic activity that significantly improves this situation. In vitro voltage potential recordings were used to estimate pseudo-electromagnetic energy flow vector fields, current and energy source densities and energy dissipation in reconstruction planes at depth into the neural tissue parallel to the recording plane of the microelectrode array. The properties of the reconstructed near-field estimate allowed both the utilization of super-resolution techniques to increase the imaging resolution beyond that of the microelectrode array, and facilitated a novel approach to estimating causal relationships between activity in neocortical subregions. The holographic nature of the reconstruction method allowed significantly better estimation of the fine spatiotemporal detail of neuronal population activity, compared with interpolation alone, beyond the spatial resolution of the electrode arrays used. Pseudo-energy flow vector mapping was possible with high temporal precision, allowing a near-realtime estimate of causal interaction dynamics. Basic near-field electromagnetic holography provides a powerful means to increase spatial resolution from electrode array data with careful choice of spatial filters and distance to reconstruction plane. More detailed approaches may provide the ability to volumetrically reconstruct activity patterns on neuronal tissue, but the ability to extract vectored data with the method presented already permits the study of dynamic causal interactions

PATMA: parser of archival tissue microarray

Directory of Open Access Journals (Sweden)

Lukasz Roszkowiak

2016-12-01

Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

Progress on conformal microwave array applicators for heating chestwall disease

Science.gov (United States)

Stauffer, P. R.; Maccarini, P. F.; Juang, T.; Jacobsen, S. K.; Gaeta, C. J.; Schlorff, J. L.; Milligan, A. J.

2007-02-01

Previous studies have reported the computer modeling, CAD design, and theoretical performance of single and multiple antenna arrays of Dual Concentric Conductor (DCC) square slot radiators driven at 915 and 433 MHz. Subsequently, practical CAD designs of microstrip antenna arrays constructed on thin and flexible printed circuit board (PCB) material were reported which evolved into large Conformal Microwave Array (CMA) sheets that could wrap around the surface of the human torso for delivering microwave energy to large areas of superficial tissue. Although uniform and adjustable radiation patterns have been demonstrated from multiple element applicators radiating into simple homogeneous phantom loads, the contoured and heterogeneous tissue loads typical of chestwall recurrent breast cancer have required additional design efforts to achieve good coupling and efficient heating from the increasingly larger conformal array applicators used to treat large area contoured patient anatomy. Thus recent work has extended the theoretical optimization of DCC antennas to improve radiation efficiency of each individual aperture and reduce mismatch reflections, radiation losses, noise, and cross coupling of the feedline distribution network of large array configurations. Design improvements have also been incorporated into the supporting bolus structure to maintain effective coupling of DCC antennas into contoured anatomy and to monitor and control surface temperatures under the entire array. New approaches for non-invasive monitoring of surface and sub-surface tissue temperatures under each independent heat source are described that make use of microwave radiometry and flexible sheet grid arrays of thermal sensors. Efforts to optimize the clinical patient interface and move from planar rectangular shapes to contoured vest applicators that accommodate entire disease in a larger number of patients are summarized. By applying heat more uniformly to large areas of contoured anatomy

A Flexible Nested Sodium and Proton Coil Array with Wideband Matching for Knee Cartilage MRI at 3 Tesla

Science.gov (United States)

Brown, Ryan; Lakshmanan, Karthik; Madelin, Guillaume; Alon, Leeor; Chang, Gregory; Sodickson, Daniel K.; Regatte, Ravinder R.; Wiggins, Graham C.

2015-01-01

Purpose We describe a 6×2 channel sodium/proton array for knee MRI at 3 Tesla. Multi-element coil arrays are desirable because of well-known signal-to-noise ratio advantages over volume and single-element coils. However, low coil-tissue coupling that is characteristic of coils operating at low frequency can make the potential gains from a phased array difficult to realize. Methods The issue of low coil-tissue coupling in the developed six channel sodium receive array was addressed by implementing 1) a mechanically flexible former to minimize coil-to-tissue distance and reduce the overall diameter of the array and 2) a wideband matching scheme that counteracts preamplifier noise degradation caused by coil coupling and a high quality factor. The sodium array was complemented with a nested proton array to enable standard MRI. Results The wideband matching scheme and tight-fitting mechanical design contributed to greater than 30% central SNR gain on the sodium module over a mono-nuclear sodium birdcage coil, while the performance of the proton module was sufficient for clinical imaging. Conclusion We expect the strategies presented in this work to be generally relevant in high density receive arrays, particularly in x-nuclei or small animal applications, or in those where the array is distant from the targeted tissue. PMID:26502310

Spacecraft Multiple Array Communication System Performance Analysis

Science.gov (United States)

Hwu, Shian U.; Desilva, Kanishka; Sham, Catherine C.

2010-01-01

The Communication Systems Simulation Laboratory (CSSL) at the NASA Johnson Space Center is tasked to perform spacecraft and ground network communication system simulations, design validation, and performance verification. The CSSL has developed simulation tools that model spacecraft communication systems and the space and ground environment in which the tools operate. In this paper, a spacecraft communication system with multiple arrays is simulated. Multiple array combined technique is used to increase the radio frequency coverage and data rate performance. The technique is to achieve phase coherence among the phased arrays to combine the signals at the targeting receiver constructively. There are many technical challenges in spacecraft integration with a high transmit power communication system. The array combining technique can improve the communication system data rate and coverage performances without increasing the system transmit power requirements. Example simulation results indicate significant performance improvement can be achieved with phase coherence implementation.

Seismic Background Noise Analysis of BRTR (PS-43) Array

Science.gov (United States)

Ezgi Bakir, Mahmure; Meral Ozel, Nurcan; Umut Semin, Korhan

2015-04-01

The seismic background noise variation of BRTR array, composed of two sub arrays located in Ankara and in Ankara-Keskin, has been investigated by calculating Power Spectral Density and Probability Density Functions for seasonal and diurnal noise variations between 2005 and 2011. PSDs were computed within the frequency range of 100 s - 10 Hz. The results show us a little change in noise conditions in terms of time and location. Especially, noise level changes were observed at 3-5 Hz in diurnal variations at Keskin array and there is a 5-7 dB difference in day and night time in cultural noise band (1-10 Hz). On the other hand, noise levels of medium period array is high in 1-2 Hz frequency rather than short period array. High noise levels were observed in daily working times when we compare it to night-time in cultural noise band. The seasonal background noise variation at both sites also shows very similar properties to each other. Since these stations are borehole instruments and away from the coasts, we saw a small change in noise levels caused by microseism. Comparison between Keskin short period array and Ankara medium period array show us Keskin array is quiter than Ankara array.

In-air micro-pixe analysis of tissue samples

International Nuclear Information System (INIS)

Tanaka, A.; Ishii, K.; Komori, Y.

2002-01-01

Micro-PIXE is capable of providing spatial distributions of elements in the micro-meter scale and its application to biology is useful to elucidate the cellular metabolism. Since, in this method, a sample target is usually irradiated with proton or α-particle beams in vacuum, beam heating results in evaporation of volatile elements an shrinking of the sample. In order to avoid these side effects, we previously developed a technique of in-air micro-PIXE analysis for samples of cultured cells. In addition to these, analysis of exposed tissue samples from living subjects is highly desirable in biological and medical research. Here, we describe a technique of in-air micro-PIXE analysis of such tissue samples. The target samples of exposed tissue slices from a Donryu rat, in which a tumor had been transplanted, were analyzed with proton micro-beams of 2.6 MeV. We report that the shape of cells and the distribution of volatile elements in the tissue sample remain uncharged when using a target preparation based on a freeze-drying method. (author)

Discrimination of honeys using colorimetric sensor arrays, sensory analysis and gas chromatography techniques.

Science.gov (United States)

Tahir, Haroon Elrasheid; Xiaobo, Zou; Xiaowei, Huang; Jiyong, Shi; Mariod, Abdalbasit Adam

2016-09-01

Aroma profiles of six honey varieties of different botanical origins were investigated using colorimetric sensor array, gas chromatography-mass spectrometry (GC-MS) and descriptive sensory analysis. Fifty-eight aroma compounds were identified, including 2 norisoprenoids, 5 hydrocarbons, 4 terpenes, 6 phenols, 7 ketones, 9 acids, 12 aldehydes and 13 alcohols. Twenty abundant or active compounds were chosen as key compounds to characterize honey aroma. Discrimination of the honeys was subsequently implemented using multivariate analysis, including hierarchical clustering analysis (HCA) and principal component analysis (PCA). Honeys of the same botanical origin were grouped together in the PCA score plot and HCA dendrogram. SPME-GC/MS and colorimetric sensor array were able to discriminate the honeys effectively with the advantages of being rapid, simple and low-cost. Moreover, partial least squares regression (PLSR) was applied to indicate the relationship between sensory descriptors and aroma compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar.

Science.gov (United States)

Ko, Jae-Heung; Kim, Hyun-Tae; Hwang, Ildoo; Han, Kyung-Hwan

2012-06-01

Plant biotechnology offers a means to create novel phenotypes. However, commercial application of biotechnology in crop improvement programmes is severely hindered by the lack of utility promoters (or freedom to operate the existing ones) that can drive gene expression in a tissue-specific or temporally controlled manner. Woody biomass is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, developing xylem (DX)-specific modification of the feedstock is highly desirable. To develop utility promoters that can drive transgene expression in a DX-specific manner, we used the Affymetrix Poplar Genome Arrays to obtain tissue-type-specific transcriptomes from poplar stems. Subsequent bioinformatics analysis identified 37 transcripts that are specifically or strongly expressed in DX cells of poplar. After further confirmation of their DX-specific expression using semi-quantitative PCR, we selected four genes (DX5, DX8, DX11 and DX15) for in vivo confirmation of their tissue-specific expression in transgenic poplars. The promoter regions of the selected DX genes were isolated and fused to a β-glucuronidase (GUS)-reported gene in a binary vector. This construct was used to produce transgenic poplars via Agrobacterium-mediated transformation. The GUS expression patterns of the resulting transgenic plants showed that these promoters were active in the xylem cells at early seedling growth and had strongest expression in the developing xylem cells at later growth stages of poplar. We conclude that these DX promoters can be used as a utility promoter for DX-specific biomass engineering. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

Near Infrared Spectroscopy Systems for Tissue Oximetry

DEFF Research Database (Denmark)

Petersen, Søren Dahl

for other medical applications. The tissue oximeters are realised by incorporation of pn-diodes into the silicon in order to form arrays of infrared detectors. These arrays can then be used for spatially resolved spectroscopy measurements, with the targeted end user being prematurely born infant children...

Growth versus metabolic tissue replacement in mouse tissues determined by stable carbon and nitrogen isotope analysis

Science.gov (United States)

Macavoy, S. E.; Jamil, T.; Macko, S. A.; Arneson, L. S.

2003-12-01

Stable isotope analysis is becoming an extensively used tool in animal ecology. The isotopes most commonly used for analysis in terrestrial systems are those of carbon and nitrogen, due to differential carbon fractionation in C3 and C4 plants, and the approximately 3‰ enrichment in 15N per trophic level. Although isotope signatures in animal tissues presumably reflect the local food web, analysis is often complicated by differential nutrient routing and fractionation by tissues, and by the possibility that large organisms are not in isotopic equilibrium with the foods available in their immediate environment. Additionally, the rate at which organisms incorporate the isotope signature of a food through both growth and metabolic tissue replacement is largely unknown. In this study we have assessed the rate of carbon and nitrogen isotopic turnover in liver, muscle and blood in mice following a diet change. By determining growth rates, we were able to determine the proportion of tissue turnover caused by growth versus that caused by metabolic tissue replacement. Growth was found to account for approximately 10% of observed tissue turnover in sexually mature mice (Mus musculus). Blood carbon was found to have the shortest half-life (16.9 days), followed by muscle (24.7 days). Liver carbon turnover was not as well described by the exponential decay equations as other tissues. However, substantial liver carbon turnover was observed by the 28th day after diet switch. Surprisingly, these tissues primarily reflect the carbon signature of the protein, rather than carbohydrate, source in their diet. The nitrogen signature in all tissues was enriched by 3 - 5‰ over their dietary protein source, depending on tissue type, and the isotopic turnover rates were comparable to those observed in carbon.

Transient three-dimensional thermal-hydraulic analysis of nuclear reactor fuel rod arrays: general equations and numerical scheme

International Nuclear Information System (INIS)

Wnek, W.J.; Ramshaw, J.D.; Trapp, J.A.; Hughes, E.D.; Solbrig, C.W.

1975-11-01

A mathematical model and a numerical solution scheme for thermal-hydraulic analysis of fuel rod arrays are given. The model alleviates the two major deficiencies associated with existing rod array analysis models, that of a correct transverse momentum equation and the capability of handling reversing and circulatory flows. Possible applications of the model include steady state and transient subchannel calculations as well as analysis of flows in heat exchangers, other engineering equipment, and porous media

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

Science.gov (United States)

Watanabe, Leandro; Myers, Chris J

2016-08-19

The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime.

Noise analysis and performance of a selfscanned linear InSb detector array

International Nuclear Information System (INIS)

Finger, G.; Meyer, M.; Moorwood, A.F.M.

1987-01-01

A noise model for detectors operated in the capacitive discharge mode is presented. It is used to analyze the noise performance of the ESO nested timing readout technique applied to a linear 32-element InSb array which is multiplexed by a silicon switched-FET shift register. Analysis shows that KTC noise of the videoline is the major noise contribution; it can be eliminated by weighted double-correlated sampling. Best noise performance of this array is achieved at the smallest possible reverse bias voltage (not more than 20 mV) whereas excess noise is observed at higher reverse bias voltages. 5 references

Long-lived tissue resident HIV-1 specific memory CD8+ T cells are generated by skin immunization with live virus vectored microneedle arrays

OpenAIRE

Zaric, Marija; Becker, Pablo Daniel; Hervouet, Catherine; Kalcheva, Petya; Ibarzo Yus, Barbara; Cocita, Clement; O'Neill, Lauren Alexandra; Kwon, Sung-Yun; Klavinskis, Linda Sylvia

2017-01-01

The generation of tissue resident memory (TRM) cells at the body surfaces to provide a front line defence against invading pathogens represents an important goal in vaccine development for a wide variety of pathogens. It has been widely assumed that local vaccine delivery to the mucosae is necessary to achieve that aim. Here we characterise a novel micro-needle array (MA) delivery system fabricated to deliver a live recombinant human adenovirus type 5 vaccine vector (AdHu5) encoding HIV-1 gag...

Numerical analysis of natural convection and radiation heat transfer from various shaped thin fin-arrays placed on a horizontal plate-a conjugate analysis

International Nuclear Information System (INIS)

Dogan, M.; Sivrioglu, Mecit; Yılmaz, Onder

2014-01-01

Highlights: • Optimum fin shape is determined for natural convection and radiation heat transfer. • Fin array with the optimum shape has a much greater average heat transfer coefficient. • The most important factors affecting the heat transfer coefficient are determined. - Abstract: Steady state natural convection and radiation heat transfer from various shaped thin fin-arrays on a horizontal base plate has been numerically investigated. A conjugate analysis has been carried out in which the conservation equations of mass, momentum and energy for the fluid in the two fin enclosure are solved together with the heat conduction equation in the fin and the base plate. Heat transfer by radiation is also considered in analysis. The heat transfer coefficient has been determined for each of the fin array considered in the present study at the same base and the same total area. The results of the analysis show that there are some important geometrical factors affecting the design of fin arrays. Taking into consideration these factors, an optimum fin shape that yields the highest average heat transfer coefficient has been determined

Fiber-optic microsphere-based antibody array for the analysis of inflammatory cytokines in saliva.

Science.gov (United States)

Blicharz, Timothy M; Siqueira, Walter L; Helmerhorst, Eva J; Oppenheim, Frank G; Wexler, Philip J; Little, Frédéric F; Walt, David R

2009-03-15

Antibody microarrays have emerged as useful tools for high-throughput protein analysis and candidate biomarker screening. We describe here the development of a multiplexed microsphere-based antibody array capable of simultaneously measuring 10 inflammatory protein mediators. Cytokine-capture microspheres were fabricated by covalently coupling monoclonal antibodies specific for cytokines of interest to fluorescently encoded 3.1 microm polymer microspheres. An optical fiber bundle containing approximately 50,000 individual 3.1 microm diameter fibers was chemically etched to create microwells in which cytokine-capture microspheres could be deposited. Microspheres were randomly distributed in the wells to produce an antibody array for performing a multiplexed sandwich immunoassay. The array responded specifically to recombinant cytokine solutions in a concentration-dependent fashion. The array was also used to examine endogenous mediator patterns in saliva supernatants from patients with pulmonary inflammatory diseases such as asthma and chronic obstructive pulmonary disease (COPD). This array technology may prove useful as a laboratory-based platform for inflammatory disease research and diagnostics, and its small footprint could also enable integration into a microfluidic cassette for use in point-of-care testing.

Array-CGH Analysis in a Cohort of Phenotypically Well-Characterized Individuals with "Essential" Autism Spectrum Disorders

Science.gov (United States)

Napoli, Eleonora; Russo, Serena; Casula, Laura; Alesi, Viola; Amendola, Filomena Alessandra; Angioni, Adriano; Novelli, Antonio; Valeri, Giovanni; Menghini, Deny; Vicari, Stefano

2018-01-01

Copy-number variants (CNVs) are associated with susceptibility to autism spectrum disorder (ASD). To detect the presence of CNVs, we conducted an array-comparative genomic hybridization (array-CGH) analysis in 133 children with "essential" ASD phenotype. Genetic analyses documented that 12 children had causative CNVs (C-CNVs), 29…

Vibrational Micro-Spectroscopy of Human Tissues Analysis: Review.

Science.gov (United States)

Bunaciu, Andrei A; Hoang, Vu Dang; Aboul-Enein, Hassan Y

2017-05-04

Vibrational spectroscopy (Infrared (IR) and Raman) and, in particular, micro-spectroscopy and micro-spectroscopic imaging have been used to characterize developmental changes in tissues, to monitor these changes in cell cultures and to detect disease and drug-induced modifications. The conventional methods for biochemical and histophatological tissue characterization necessitate complex and "time-consuming" sample manipulations and the results are rarely quantifiable. The spectroscopy of molecular vibrations using mid-IR or Raman techniques has been applied to samples of human tissue. This article reviews the application of these vibrational spectroscopic techniques for analysis of biological tissue published between 2005 and 2015.

Evaluation of Influenza-Specific Humoral Response by Microbead Array Analysis

Directory of Open Access Journals (Sweden)

Yoav Keynan

2011-01-01

Full Text Available RATIONALE: Quantitation and determination of antigen specificity of systemic and mucosal immune responses to influenza vaccination is beneficial for future vaccine development. Previous methods to acquire this information were costly, time consuming and sample exhaustive. The benefits of suspension microbead array (MBA analysis are numerous. The multiplex capabilities of the system conserve time, money and sample, while generating statistically powerful data.

Cyclotron-Resonance-Maser Arrays

International Nuclear Information System (INIS)

Kesar, A.; Lei, L.; Dikhtyar, V.; Korol, M.; Jerby, E.

1999-01-01

The cyclotron-resonance-maser (CRM) array [1] is a radiation source which consists of CRM elements coupled together under a common magnetic field. Each CRM-element employs a low-energy electron-beam which performs a cyclotron interaction with the local electromagnetic wave. These waves can be coupled together among the CRM elements, hence the interaction is coherently synchronized in the entire array. The implementation of the CRM-array approach may alleviate several technological difficulties which impede the development of single-beam gyro-devices. Furthermore, it proposes new features, such as the phased-array antenna incorporated in the CRM-array itself. The CRM-array studies may lead to the development of compact, high-power radiation sources operating at low-voltages. This paper introduces new conceptual schemes of CRM-arrays, and presents the progress in related theoretical and experimental studies in our laboratory. These include a multi-mode analysis of a CRM-array, and a first operation of this device with five carbon-fiber cathodes

Cochlear pathology following reimplantation of a multichannel scala tympani electrode array in the macaque.

Science.gov (United States)

Shepherd, R K; Clark, G M; Xu, S A; Pyman, B C

1995-03-01

The histopathologic consequence of removing and reimplanting intracochlear electrode arrays on residual auditory nerve fibers is an important issue when evaluating the safety of cochlear prostheses. The authors have examined this issue by implanting multichannel intracochlear electrodes in macaque monkeys. Macaques were selected because of the similarity of the surgical technique used to insert electrodes into the cochlea compared to that in humans, in particular the ability to insert the arrays into the upper basal turn. Five macaques were bilaterally implanted with the Melbourne/Cochlear banded electrode array. Following a minimum implant period of 5 months, the electrode array on one side of each animal was removed and another immediately implanted. The animals were sacrificed a minimum of 5 months following the reinsertion procedure, and the cochleas prepared for histopathologic analysis. Long-term implantation of the electrode resulted in a relatively mild tissue response within the cochlea. Results also showed that inner and outer hair cell survival, although significantly reduced adjacent to the array, was normal in 8 of the 10 cochleas apicalward. Moreover, the electrode reinsertion procedure did not appear to adversely affect this apical hair cell population. Significant new bone formation was frequently observed in both control and reimplanted cochleas close to the electrode fenestration site and was associated with trauma to the endosteum and/or the introduction of bone chips into the cochlea at the time of surgery. Electrode insertion trauma, involving the osseous spiral lamina or basilar membrane, was more commonly observed in reimplanted cochleas. This damage was usually restricted to the lower basal turn and resulted in a more extensive ganglion cell loss. Finally, in a number of cochleas part of the electrode array was located within the scala media or scala vestibuli. These electrodes did not appear to evoke a more extensive tissue response or

Degree-of-Freedom Strengthened Cascade Array for DOD-DOA Estimation in MIMO Array Systems.

Science.gov (United States)

Yao, Bobin; Dong, Zhi; Zhang, Weile; Wang, Wei; Wu, Qisheng

2018-05-14

In spatial spectrum estimation, difference co-array can provide extra degrees-of-freedom (DOFs) for promoting parameter identifiability and parameter estimation accuracy. For the sake of acquiring as more DOFs as possible with a given number of physical sensors, we herein design a novel sensor array geometry named cascade array. This structure is generated by systematically connecting a uniform linear array (ULA) and a non-uniform linear array, and can provide more DOFs than some exist array structures but less than the upper-bound indicated by minimum redundant array (MRA). We further apply this cascade array into multiple input multiple output (MIMO) array systems, and propose a novel joint direction of departure (DOD) and direction of arrival (DOA) estimation algorithm, which is based on a reduced-dimensional weighted subspace fitting technique. The algorithm is angle auto-paired and computationally efficient. Theoretical analysis and numerical simulations prove the advantages and effectiveness of the proposed array structure and the related algorithm.

Stochastic resolution analysis of co-prime arrays in radar

NARCIS (Netherlands)

Pribic, R; Coutiño Minguez, M.A.; Leus, G.J.T.

2016-01-01

Resolution from co-prime arrays and from a full ULA of the size equal to the virtual size of co-prime arrays is investigated. We take into account not only the resulting beam width but also the fact that fewer measurements are acquired by co-prime arrays. This fact is relevant in compressive

Analysis of oligonucleotide array experiments with repeated measures using mixed models

Directory of Open Access Journals (Sweden)

Getchell Thomas V

2004-12-01

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

Romanian earthquakes analysis using BURAR seismic array

International Nuclear Information System (INIS)

Borleanu, Felix; Rogozea, Maria; Nica, Daniela; Popescu, Emilia; Popa, Mihaela; Radulian, Mircea

2008-01-01

Bucovina seismic array (BURAR) is a medium-aperture array, installed in 2002 in the northern part of Romania (47.61480 N latitude, 25.21680 E longitude, 1150 m altitude), as a result of the cooperation between Air Force Technical Applications Center, USA and National Institute for Earth Physics, Romania. The array consists of ten elements, located in boreholes and distributed over a 5 x 5 km 2 area; nine with short-period vertical sensors and one with a broadband three-component sensor. Since the new station has been operating the earthquake survey of Romania's territory has been significantly improved. Data recorded by BURAR during 01.01.2005 - 12.31.2005 time interval are first processed and analyzed, in order to establish the array detection capability of the local earthquakes, occurred in different Romanian seismic zones. Subsequently a spectral ratios technique was applied in order to determine the calibration relationships for magnitude, using only the information gathered by BURAR station. The spectral ratios are computed relatively to a reference event, considered as representative for each seismic zone. This method has the advantage to eliminate the path effects. The new calibration procedure is tested for the case of Vrancea intermediate-depth earthquakes and proved to be very efficient in constraining the size of these earthquakes. (authors)

Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

Directory of Open Access Journals (Sweden)

Gillings Michael R

2006-01-01

Full Text Available Abstract Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be. Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. Results The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes. It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene

TH-CD-206-01: Expectation-Maximization Algorithm-Based Tissue Mixture Quantification for Perfusion MRI

International Nuclear Information System (INIS)

Han, H; Xing, L; Liang, Z; Li, L

2016-01-01

Purpose: To investigate the feasibility of estimating the tissue mixture perfusions and quantifying cerebral blood flow change in arterial spin labeled (ASL) perfusion MR images. Methods: The proposed perfusion MR image analysis framework consists of 5 steps: (1) Inhomogeneity correction was performed on the T1- and T2-weighted images, which are available for each studied perfusion MR dataset. (2) We used the publicly available FSL toolbox to strip off the non-brain structures from the T1- and T2-weighted MR images. (3) We applied a multi-spectral tissue-mixture segmentation algorithm on both T1- and T2-structural MR images to roughly estimate the fraction of each tissue type - white matter, grey matter and cerebral spinal fluid inside each image voxel. (4) The distributions of the three tissue types or tissue mixture across the structural image array are down-sampled and mapped onto the ASL voxel array via a co-registration operation. (5) The presented 4-dimensional expectation-maximization (4D-EM) algorithm takes the down-sampled three tissue type distributions on perfusion image data to generate the perfusion mean, variance and percentage images for each tissue type of interest. Results: Experimental results on three volunteer datasets demonstrated that the multi-spectral tissue-mixture segmentation algorithm was effective to initialize tissue mixtures from T1- and T2-weighted MR images. Compared with the conventional ASL image processing toolbox, the proposed 4D-EM algorithm not only generated comparable perfusion mean images, but also produced perfusion variance and percentage images, which the ASL toolbox cannot obtain. It is observed that the perfusion contribution percentages may not be the same as the corresponding tissue mixture volume fractions estimated in the structural images. Conclusion: A specific application to brain ASL images showed that the presented perfusion image analysis method is promising for detecting subtle changes in tissue perfusions

TH-CD-206-01: Expectation-Maximization Algorithm-Based Tissue Mixture Quantification for Perfusion MRI

Energy Technology Data Exchange (ETDEWEB)

Han, H; Xing, L [Stanford University, Palo Alto, CA (United States); Liang, Z [Stony Brook University, Stony Brook, NY (United States); Li, L [City University of New York College of Staten Island, Staten Island, NY (United States)

2016-06-15

Purpose: To investigate the feasibility of estimating the tissue mixture perfusions and quantifying cerebral blood flow change in arterial spin labeled (ASL) perfusion MR images. Methods: The proposed perfusion MR image analysis framework consists of 5 steps: (1) Inhomogeneity correction was performed on the T1- and T2-weighted images, which are available for each studied perfusion MR dataset. (2) We used the publicly available FSL toolbox to strip off the non-brain structures from the T1- and T2-weighted MR images. (3) We applied a multi-spectral tissue-mixture segmentation algorithm on both T1- and T2-structural MR images to roughly estimate the fraction of each tissue type - white matter, grey matter and cerebral spinal fluid inside each image voxel. (4) The distributions of the three tissue types or tissue mixture across the structural image array are down-sampled and mapped onto the ASL voxel array via a co-registration operation. (5) The presented 4-dimensional expectation-maximization (4D-EM) algorithm takes the down-sampled three tissue type distributions on perfusion image data to generate the perfusion mean, variance and percentage images for each tissue type of interest. Results: Experimental results on three volunteer datasets demonstrated that the multi-spectral tissue-mixture segmentation algorithm was effective to initialize tissue mixtures from T1- and T2-weighted MR images. Compared with the conventional ASL image processing toolbox, the proposed 4D-EM algorithm not only generated comparable perfusion mean images, but also produced perfusion variance and percentage images, which the ASL toolbox cannot obtain. It is observed that the perfusion contribution percentages may not be the same as the corresponding tissue mixture volume fractions estimated in the structural images. Conclusion: A specific application to brain ASL images showed that the presented perfusion image analysis method is promising for detecting subtle changes in tissue perfusions

Vertical nanowire arrays as a versatile platform for protein detection and analysis

DEFF Research Database (Denmark)

Rostgaard, Katrine R.; Frederiksen, Rune S.; Liu, Yi-Chi

2013-01-01

solutions. Here we show that vertical arrays of nanowires (NWs) can overcome several bottlenecks of using nanoarrays for extraction and analysis of proteins. The high aspect ratio of the NWs results in a large surface area available for protein immobilization and renders passivation of the surface between...

TLD array for precise dose measurements in stereotactic radiation techniques

International Nuclear Information System (INIS)

Ertl, A.; Kitz, K.; Griffitt, W.; Hartl, R.F.E.; Zehetmayer, M.

1996-01-01

We developed a new TLD array for precise dose measurement and verification of the spatial dose distribution in small radiation targets. It consists of a hemicylindrical, tissue-equivalent rod made of polystyrene with 17 parallel moulds for an exact positioning of each TLD. The spatial resolution of the TLD array was evaluated using the Leskell spherical phantom. Dose planning was performed with KULA 4.4 under stereotactic conditions on axial CT images. In the Leksell gamma unit the TLD array was irradiated with a maximal dose of 10 Gy with an unplugged 14 mm collimator. The doses delivered to the TLDs were rechecked by diode detector and film dosimetry and compared to the computer-generated dose profile. We found excellent agreement of our measured values, even at the critical penumbra decline. For the 14 mm and 18 mm collimator and for the 11 mm collimator combination we compared the measured and calculated data at full width at half maximum. This TLD array may be useful for phantom or tissue model studies on the spatial dose distribution in confined radiation targets as used in stereotactic radiotherapy. (author)

OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging

Energy Technology Data Exchange (ETDEWEB)

de Raad, Markus [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); de Rond, Tristan [Univ. of California, Berkeley, CA (United States); Rübel, Oliver [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Keasling, Jay D. [Univ. of California, Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Technical Univ. of Denmark, Lyngby (Denmark); Northen, Trent R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Bowen, Benjamin P. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2017-05-03

Mass spectrometry imaging (MSI) has primarily been applied in localizing biomolecules within biological matrices. Although well-suited, the application of MSI for comparing thousands of spatially defined spotted samples has been limited. One reason for this is a lack of suitable and accessible data processing tools for the analysis of large arrayed MSI sample sets. In this paper, the OpenMSI Arrayed Analysis Toolkit (OMAAT) is a software package that addresses the challenges of analyzing spatially defined samples in MSI data sets. OMAAT is written in Python and is integrated with OpenMSI (http://openmsi.nersc.gov), a platform for storing, sharing, and analyzing MSI data. By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone without programming experience yet allows experienced users to leverage all features. OMAAT was evaluated by analyzing an MSI data set of a high-throughput glycoside hydrolase activity screen comprising 384 samples arrayed onto a NIMS surface at a 450 μm spacing, decreasing analysis time >100-fold while maintaining robust spot-finding. The utility of OMAAT was demonstrated for screening metabolic activities of different sized soil particles, including hydrolysis of sugars, revealing a pattern of size dependent activities. Finally, these results introduce OMAAT as an effective toolkit for analyzing spatially defined samples in MSI. OMAAT runs on all major operating systems, and the source code can be obtained from the following GitHub repository: https://github.com/biorack/omaat.

Electron probe microanalysis for clinical investigations: Microdrop and soft tissue analysis

International Nuclear Information System (INIS)

Ingram, M.J.; Ingram, F.D.

1984-01-01

The most important advantage offered by electron probe microanalysis (EPA) for clinical investigations is the ability to analyze smaller volumes of tissue than is possible with conventional techniques. The sample can be a biological soft tissue specimen, which involves subcellular localization, or a picoliter fluid droplet. In either case, the analysis can be nondestructive and permit multiple analyses for a number of elements in a given sample. The most highly developed electron microprobe analytical technique is fluid drop analysis, popularly referred to as microdrop analysis. This method provides the investigator with an analytic capability that has an accuracy of measurement often 1% or better on 20 to 30 picoliter fluid droplets. Electron microprobe techniques have been used for studies of animal hard tissue and for studies that involve insoluble inclusions. However, the development of techniques for studies of labile constituents in animal soft tissue has been much slower. It has been necessary not only to develop appropriate methods of tissue preparation, but also to establish sound techniques for tissue collection. Although there are adequate methods for collection of most types of tissue from laboratory animals, many of these methods are not suitable for human subjects. In order to provide the reader with a better understanding of the capabilities and potential for the application of electron microprobe methodology to problems in clinical medicine, the authors discuss some of their experiences with liquid droplet analysis and quantitative electrolyte distribution measurements in animal soft tissue

Knowledge Enrichment Analysis for Human Tissue- Specific Genes Uncover New Biological Insights

Directory of Open Access Journals (Sweden)

Gong Xiu-Jun

2012-06-01

Full Text Available The expression and regulation of genes in different tissues are fundamental questions to be answered in biology. Knowledge enrichment analysis for tissue specific (TS and housekeeping (HK genes may help identify their roles in biological process or diseases and gain new biological insights.In this paper, we performed the knowledge enrichment analysis for 17,343 genes in 84 human tissues using Gene Set Enrichment Analysis (GSEA and Hypergeometric Analysis (HA against three biological ontologies: Gene Ontology (GO, KEGG pathways and Disease Ontology (DO respectively.The analyses results demonstrated that the functions of most gene groups are consistent with their tissue origins. Meanwhile three interesting new associations for HK genes and the skeletal muscle tissuegenes are found. Firstly, Hypergeometric analysis against KEGG database for HK genes disclosed that three disease terms (Parkinson’s disease, Huntington’s disease, Alzheimer’s disease are intensively enriched.Secondly, Hypergeometric analysis against the KEGG database for Skeletal Muscle tissue genes shows that two cardiac diseases of “Hypertrophic cardiomyopathy (HCM” and “Arrhythmogenic right ventricular cardiomyopathy (ARVC” are heavily enriched, which are also considered as no relationship with skeletal functions.Thirdly, “Prostate cancer” is intensively enriched in Hypergeometric analysis against the disease ontology (DO for the Skeletal Muscle tissue genes, which is a much unexpected phenomenon.

A microfluidic chip with a U-shaped microstructure array for multicellular spheroid formation, culturing and analysis

International Nuclear Information System (INIS)

Fu, Chien-Yu; Chang, Hwan-You; Tseng, Sheng-Yang; Yang, Shih-Mo; Hsu, Long; Liu, Cheng-Hsien

2014-01-01

Multicellular spheroids (MCS), formed by self-assembly of single cells, are commonly used as a three-dimensional cell culture model to bridge the gap between in vitro monolayer culture and in vivo tissues. However, current methods for MCS generation and analysis still suffer drawbacks such as being labor-intensive and of poor controllability, and are not suitable for high-throughput applications. This study demonstrates a novel microfluidic chip to facilitate MCS formation, culturing and analysis. The chip contains an array of U-shaped microstructures fabricated by photopolymerizing the poly(ethylene glycol) diacrylate hydrogel through defining the ultraviolet light exposure pattern with a photomask. The geometry of the U-shaped microstructures allowed trapping cells into the pocket through the actions of fluid flow and the force of gravity. The hydrogel is non-adherent for cells, promoting the formation of MCS. Its permselective property also facilitates exchange of nutrients and waste for MCS, while providing protection of MCS from shearing stress during the medium perfusion. Heterotypic MCS can be formed easily by manipulating the cell trapping steps. Subsequent drug susceptibility analysis and long-term culture could also be achieved within the same chip. This MCS formation and culture platform can be used as a micro-scale bioreactor and applied in many cell biology and drug testing studies. (paper)

TiArA: a virtual appliance for the analysis of Tiling Array data.

Directory of Open Access Journals (Sweden)

Jason A Greenbaum

2010-04-01

Full Text Available Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Tiling Array Analyzer (TiArA is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara.

Single-electron tunnel junction array

International Nuclear Information System (INIS)

Likharev, K.K.; Bakhvalov, N.S.; Kazacha, G.S.; Serdyukova, S.I.

1989-01-01

The authors have carried out an analysis of statics and dynamics of uniform one-dimensional arrays of ultrasmall tunnel junctions. The correlated single-electron tunneling in the junctions of the array results in its behavior qualitatively similar to that of the Josephson transmission line. In particular, external electric fields applied to the array edges can inject single-electron-charged solitons into the array interior. Shape of such soliton and character of its interactions with other solitons and the array edges are very similar to those of the Josephson vortices (sine-Gordon solitons) in the Josephson transmission line. Under certain conditions, a coherent motion of the soliton train along the array is possible, resulting in generation of narrowband SET oscillations with frequency f/sub s/ = /e where is the dc current flowing along the array

Fiber-array based optogenetic prosthetic system for stimulation therapy

Science.gov (United States)

Gu, Ling; Cote, Chris; Tejeda, Hector; Mohanty, Samarendra

2012-02-01

Recent advent of optogenetics has enabled activation of genetically-targeted neuronal cells using low intensity blue light with high temporal precision. Since blue light is attenuated rapidly due to scattering and absorption in neural tissue, optogenetic treatment of neurological disorders may require stimulation of specific cell types in multiple regions of the brain. Further, restoration of certain neural functions (vision, and auditory etc) requires accurate spatio-temporal stimulation patterns rather than just precise temporal stimulation. In order to activate multiple regions of the central nervous system in 3D, here, we report development of an optogenetic prosthetic comprising of array of fibers coupled to independently-controllable LEDs. This design avoids direct contact of LEDs with the brain tissue and thus does not require electrical and heat isolation, which can non-specifically stimulate and damage the local brain regions. The intensity, frequency, and duty cycle of light pulses from each fiber in the array was controlled independently using an inhouse developed LabView based program interfaced with a microcontroller driving the individual LEDs. While the temporal profile of the light pulses was controlled by varying the current driving the LED, the beam profile emanating from each fiber tip could be sculpted by microfabrication of the fiber tip. The fiber array was used to stimulate neurons, expressing channelrhodopsin-2, in different locations within the brain or retina. Control of neural activity in the mice cortex, using the fiber-array based prosthetic, is evaluated from recordings made with multi-electrode array (MEA). We also report construction of a μLED array based prosthetic for spatio-temporal stimulation of cortex.

Transcriptomic Analysis of Intestinal Tissues from Two 90-Day Feeding Studies in Rats Using Genetically Modified MON810 Maize Varieties.

Science.gov (United States)

Sharbati, Jutta; Bohmer, Marc; Bohmer, Nils; Keller, Andreas; Backes, Christina; Franke, Andre; Steinberg, Pablo; Zeljenková, Dagmar; Einspanier, Ralf

2017-01-01

Background: Global as well as specific expression profiles of selected rat tissues were characterized to assess the safety of genetically modified (GM) maize MON810 containing the insecticidal protein Cry1Ab. Gene expression was evaluated by use of Next Generation Sequencing (NGS) as well as RT-qPCR within rat intestinal tissues based on mandatory 90-day rodent feeding studies. In parallel to two 90-day feeding studies, the transcriptional response of rat tissues was assessed as another endpoint to enhance the mechanistic interpretation of GM feeding studies and/or to facilitate the generation of a targeted hypothesis. Rats received diets containing 33% GM maize (MON810) or near-isogenic control maize. As a site of massive exposure to ingested feed the transcriptomic response of ileal and colonic tissue was profiled via RT-qPCR arrays targeting apoptosis, DNA-damage/repair, unfolded protein response (UPR). For global RNA profiling of rat ileal tissue, we applied NGS. Results: No biological response to the GM-diet was observed in male and in female rat tissues. Transcriptome wide analysis of gene expression by RNA-seq confirmed these findings. Nevertheless, gene ontology (GO) analysis clearly associated a set of distinctly regulated transcripts with circadian rhythms. We confirmed differential expression of circadian clock genes using RT-qPCR and immunoassays for selected factors, thereby indicating physiological effects caused by the time point of sampling. Conclusion: Prediction of potential unintended effects of GM-food/feed by transcriptome based profiling of intestinal tissue presents a novel approach to complement classical toxicological testing procedures. Including the detection of alterations in signaling pathways in toxicity testing procedures may enhance the confidence in outcomes of toxicological trials. In this study, no significant GM-related changes in intestinal expression profiles were found in rats fed GM-maize MON810. Relevant alterations of

Flat-plate photovoltaic array design optimization

Science.gov (United States)

Ross, R. G., Jr.

1980-01-01

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

An Introduction to MAMA (Meta-Analysis of MicroArray data) System.

Science.gov (United States)

Zhang, Zhe; Fenstermacher, David

2005-01-01

Analyzing microarray data across multiple experiments has been proven advantageous. To support this kind of analysis, we are developing a software system called MAMA (Meta-Analysis of MicroArray data). MAMA utilizes a client-server architecture with a relational database on the server-side for the storage of microarray datasets collected from various resources. The client-side is an application running on the end user's computer that allows the user to manipulate microarray data and analytical results locally. MAMA implementation will integrate several analytical methods, including meta-analysis within an open-source framework offering other developers the flexibility to plug in additional statistical algorithms.

Performance analysis of solar cell arrays in concentrating light intensity

International Nuclear Information System (INIS)

Xu Yongfeng; Li Ming; Lin Wenxian; Wang Liuling; Xiang Ming; Zhang Xinghua; Wang Yunfeng; Wei Shengxian

2009-01-01

Performance of concentrating photovoltaic/thermal system is researched by experiment and simulation calculation. The results show that the I-V curve of the GaAs cell array is better than that of crystal silicon solar cell arrays and the exergy produced by 9.51% electrical efficiency of the GaAs solar cell array can reach 68.93% of the photovoltaic/thermal system. So improving the efficiency of solar cell arrays can introduce more exergy and the system value can be upgraded. At the same time, affecting factors of solar cell arrays such as series resistance, temperature and solar irradiance also have been analyzed. The output performance of a solar cell array with lower series resistance is better and the working temperature has a negative impact on the voltage in concentrating light intensity. The output power has a -20 W/V coefficient and so cooling fluid must be used. Both heat energy and electrical power are then obtained with a solar trough concentrating photovoltaic/thermal system. (semiconductor devices)

Ex Vivo Model of Human Penile Transplantation and Rejection: Implications for Erectile Tissue Physiology.

Science.gov (United States)

Sopko, Nikolai A; Matsui, Hotaka; Lough, Denver M; Miller, Devin; Harris, Kelly; Kates, Max; Liu, Xiaopu; Billups, Kevin; Redett, Richard; Burnett, Arthur L; Brandacher, Gerald; Bivalacqua, Trinity J

2017-04-01

Penile transplantation is a potential treatment option for severe penile tissue loss. Models of human penile rejection are lacking. Evaluate effects of rejection and immunosuppression on cavernous tissue using a novel ex vivo mixed lymphocyte reaction (MLR) model. Cavernous tissue and peripheral blood mononuclear cells (PBMCs) from 10 patients undergoing penile prosthesis operations and PBMCs from a healthy volunteer were obtained. Ex vivo MLRs were prepared by culturing cavernous tissue for 48h in media alone, in media with autologous PBMCs, or in media with allogenic PBMCs to simulate control, autotransplant, and allogenic transplant conditions with or without 1μM cyclosporine A (CsA) or 20nM tacrolimus (FK506) treatment. Rejection was characterized by PBMC flow cytometry and gene expression transplant array. Cavernous tissues were evaluated by histomorphology and myography to assess contraction and relaxation. Data were analyzed using two-way analysis of variance and unpaired Student t test. Flow cytometry and tissue array demonstrated allogenic PBMC activation consistent with rejection. Rejection impaired cavernous tissue physiology and was associated with cellular infiltration and apoptosis. CsA prevented rejection but did not improve tissue relaxation. CsA treatment impaired relaxation in tissues cultured without PBMCs compared with media and FK506. Study limitations included the use of penile tissue with erectile dysfunction and lack of cross-matching data. This model could be used to investigate the effects of penile rejection and immunosuppression. Additional studies are needed to optimize immunosuppression to prevent rejection and maximize corporal tissue physiology. This report describes a novel ex vivo model of human penile transplantation rejection. Tissue rejection impaired erectile tissue physiology. This report suggests that cyclosporin A might hinder corporal physiology and that other immunosuppressant agents, such as FK506, might be better suited

A prototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics.

Science.gov (United States)

Chen, Wenjin; Reiss, Michael; Foran, David J

2004-06-01

The tissue microarray (TMA) technique enables researchers to extract small cylinders of tissue from histological sections and arrange them in a matrix configuration on a recipient paraffin block such that hundreds can be analyzed simultaneously. TMA offers several advantages over traditional specimen preparation by maximizing limited tissue resources and providing a highly efficient means for visualizing molecular targets. By enabling researchers to reliably determine the protein expression profile for specific types of cancer, it may be possible to elucidate the mechanism by which healthy tissues are transformed into malignancies. Currently, the primary methods used to evaluate arrays involve the interactive review of TMA samples while they are viewed under a microscope, subjectively evaluated, and scored by a technician. This process is extremely slow, tedious, and prone to error. In order to facilitate large-scale, multi-institutional studies, a more automated and reliable means for analyzing TMAs is needed. We report here a web-based prototype which features automated imaging, registration, and distributed archiving of TMAs in multiuser network environments. The system utilizes a principal color decomposition approach to identify and characterize the predominant staining signatures of specimens in color space. This strategy was shown to be reliable for detecting and quantifying the immunohistochemical expression levels for TMAs.

Tissue chemical analysis with muonic X-rays

International Nuclear Information System (INIS)

Hutson, R.L.; Reidy, J.J.; Springer, K.; Daniel, H.; Knowles, H.B.

1976-01-01

The stopped muon channel at the Clinton P. Anderson Meson Physics Facility (LAMPF) was used as a source of muons for studying the elemental composition of tissue with muonic X rays. The X ray spectra from several types of tissue were used to determine the amounts of carbon, nitrogen, and oxygen present. These determinations agree with the results of more conventional chemical analysis. The results show that muonic X rays offer a non-invasive technique for determining the amounts of the more abundant elements present in selected regions of the body. (orig.) [de

Projection neuron circuits resolved using correlative array tomography

Directory of Open Access Journals (Sweden)

Daniele eOberti

2011-04-01

Full Text Available Assessment of three-dimensional morphological structure and synaptic connectivity is essential for a comprehensive understanding of neural processes controlling behavior. Different microscopy approaches have been proposed based on light microcopy (LM, electron microscopy (EM, or a combination of both. Correlative array tomography (CAT is a technique in which arrays of ultrathin serial sections are repeatedly stained with fluorescent antibodies against synaptic molecules and neurotransmitters and imaged with LM and EM (Micheva and Smith, 2007. The utility of this correlative approach is limited by the ability to preserve fluorescence and antigenicity on the one hand, and EM tissue ultrastructure on the other. We demonstrate tissue staining and fixation protocols and a workflow that yield an excellent compromise between these multimodal imaging constraints. We adapt CAT for the study of projection neurons between different vocal brain regions in the songbird. We inject fluorescent tracers of different colors into afferent and efferent areas of HVC in zebra finches. Fluorescence of some tracers is lost during tissue preparation but recovered using anti-dye antibodies. Synapses are identified in EM imagery based on their morphology and ultrastructure and classified into projection neuron type based on fluorescence signal. Our adaptation of array tomography, involving the use of fluorescent tracers and heavy-metal rich staining and embedding protocols for high membrane contrast in EM will be useful for research aimed at statistically describing connectivity between different projection neuron types and for elucidating how sensory signals are routed in the brain and transformed into a meaningful motor output.

Vrancea seismic source analysis using a small-aperture array

International Nuclear Information System (INIS)

Popescu, E.; Popa, M.; Radulian, M.; Placinta, A.O.

2005-01-01

A small-aperture seismic array (BURAR) was installed in 1999 in the northern part of the Romanian territory (Bucovina area). Since then, the array has been in operation under a joint cooperation programme between Romania and USA. The array consists of 10 stations installed in boreholes (nine short period instruments and one broadband instrument) with enough high sensitivity to properly detect earthquakes generated in Vrancea subcrustal domain (at about 250 km epicentral distance) with magnitude M w below 3. Our main purpose is to investigate and calibrate the source parameters of the Vrancea intermediate-depth earthquakes using specific techniques provided by the BURAR array data. Forty earthquakes with magnitudes between 2.9 and 6.0 were selected, including the recent events of September 27, 2004 (45.70 angle N, 26.45 angle E, h = 166 km, M w = 4.7), October 27, 2004 (45.84 angle N, 26.63 angle E, h = 105 km, M w = 6.0) and May 14, 2005 (45.66 angle N, 26.52 angle E, h = 146 km, M w = 5.1), which are the best ever recorded earthquakes on the Romanian territory: Empirical Green's function deconvolution and spectral ratio methods are applied for pairs of collocated events with similar focal mechanism. Stability tests are performed for the retrieved source time function using the array elements. Empirical scaling and calibration relationships are also determined. Our study shows the capability of the BURAR array to determine the source parameters of the Vrancea intermediate-depth earthquakes as a stand alone station and proves that the recordings of this array alone provides reliable and useful tools to efficiently constrain the source parameters and consequently source scaling properties. (authors)

Intracellular Protein Delivery and Gene Transfection by Electroporation Using a Microneedle Electrode Array

Science.gov (United States)

Choi, Seong-O; Kim, Yeu-Chun; Lee, Jeong Woo; Park, Jung-Hwan

2012-01-01

The impact of many biopharmaceuticals, including protein- and gene-based therapies, has been limited by the need for better methods of delivery into cells within tissues. Here, we present intracellular delivery of molecules and transfection with plasmid DNA by electroporation using a novel microneedle electrode array designed for targeted treatment of skin and other tissue surfaces. The microneedle array is molded out of polylactic acid. Electrodes and circuitry required for electroporation are applied to the microneedle array surface by a new metal-transfer micromolding method. The microneedle array maintains mechanical integrity after insertion into pig cadaver skin and is able to electroporate human prostate cancer cells in vitro. Quantitative measurements show that increasing electroporation pulse voltage increases uptake efficiency of calcein and bovine serum albumin, whereas increasing pulse length has lesser effects over the range studied. Uptake of molecules by up to 50 % of cells and transfection of 12 % of cells with a gene for green fluorescent protein is demonstrated at high cell viability. We conclude that the microneedle electrode array is able to electroporate cells, resulting in intracellular uptake of molecules, and has potential applications to improve intracellular delivery of proteins, DNA and other biopharmaceuticals. PMID:22328093

Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

Directory of Open Access Journals (Sweden)

Thomas Jensen

2016-01-01

Full Text Available Background: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. Methods: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. Results: It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. Conclusion: The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework.

Indoor air quality inspection and analysis system based on gas sensor array

Science.gov (United States)

Gao, Xiang; Wang, Mingjiang; Fan, Binwen

2017-08-01

A detection and analysis system capable of measuring the concentration of four major gases in indoor air is designed. It uses four gas sensors constitute a gas sensor array, to achieve four indoor gas concentration detection, while the detection of data for further processing to reduce the cross-sensitivity between the gas sensor to improve the accuracy of detection.

Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

Directory of Open Access Journals (Sweden)

Alicia Lundby

2012-08-01

Full Text Available Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.

The OncoArray Consortium

DEFF Research Database (Denmark)

Amos, Christopher I; Dennis, Joe; Wang, Zhaoming

2017-01-01

by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy...... among centers and by ethnic background. RESULTS: The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring...

Analyzing Array Manipulating Programs by Program Transformation

Science.gov (United States)

Cornish, J. Robert M.; Gange, Graeme; Navas, Jorge A.; Schachte, Peter; Sondergaard, Harald; Stuckey, Peter J.

2014-01-01

We explore a transformational approach to the problem of verifying simple array-manipulating programs. Traditionally, verification of such programs requires intricate analysis machinery to reason with universally quantified statements about symbolic array segments, such as "every data item stored in the segment A[i] to A[j] is equal to the corresponding item stored in the segment B[i] to B[j]." We define a simple abstract machine which allows for set-valued variables and we show how to translate programs with array operations to array-free code for this machine. For the purpose of program analysis, the translated program remains faithful to the semantics of array manipulation. Based on our implementation in LLVM, we evaluate the approach with respect to its ability to extract useful invariants and the cost in terms of code size.

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

International Nuclear Information System (INIS)

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

2009-01-01

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

Assessment of tissue viability by polarization spectroscopy

Science.gov (United States)

Nilsson, G.; Anderson, C.; Henricson, J.; Leahy, M.; O'Doherty, J.; Sjöberg, F.

2008-09-01

A new and versatile method for tissue viability imaging based on polarization spectroscopy of blood in superficial tissue structures such as the skin is presented in this paper. Linearly polarized light in the visible wavelength region is partly reflected directly by the skin surface and partly diffusely backscattered from the dermal tissue matrix. Most of the directly reflected light preserves its polarization state while the light returning from the deeper tissue layers is depolarized. By the use of a polarization filter positioned in front of a sensitive CCD-array, the light directly reflected from the tissue surface is blocked, while the depolarized light returning from the deeper tissue layers reaches the detector array. By separating the colour planes of the detected image, spectroscopic information about the amount of red blood cells (RBCs) in the microvascular network of the tissue under investigation can be derived. A theory that utilizes the differences in light absorption of RBCs and bloodless tissue in the red and green wavelength region forms the basis of an algorithm for displaying a colour coded map of the RBC distribution in a tissue. Using a fluid model, a linear relationship (cc. = 0.99) between RBC concentration and the output signal was demonstrated within the physiological range 0-4%. In-vivo evaluation using transepidermal application of acetylcholine by the way of iontophoresis displayed the heterogeneity pattern of the vasodilatation produced by the vasoactive agent. Applications of this novel technology are likely to be found in drug and skin care product development as well as in the assessment of skin irritation and tissue repair processes and even ultimately in a clinic case situation.

Increased expression of resistin in ectopic endometrial tissue of women with endometriosis.

Science.gov (United States)

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.

Array capabilities and future arrays

International Nuclear Information System (INIS)

Radford, D.

1993-01-01

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

Tissue Microarray Analysis Applied to Bone Diagenesis

OpenAIRE

Barrios Mello, Rafael; Regis Silva, Maria Regina; Seixas Alves, Maria Teresa; Evison, Martin; Guimarães, Marco Aurélio; Francisco, Rafaella Arrabaça; Dias Astolphi, Rafael; Miazato Iwamura, Edna Sadayo

2017-01-01

Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens....

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis.

Science.gov (United States)

Peeters, M; Huang, C L; Vonk, L A; Lu, Z F; Bank, R A; Helder, M N; Doulabi, B Zandieh

2016-11-01

Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised.Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016

Clinical utility of an array comparative genomic hybridization analysis for Williams syndrome.

Science.gov (United States)

Yagihashi, Tatsuhiko; Torii, Chiharu; Takahashi, Reiko; Omori, Mikimasa; Kosaki, Rika; Yoshihashi, Hiroshi; Ihara, Masahiro; Minagawa-Kawai, Yasuyo; Yamamoto, Junichi; Takahashi, Takao; Kosaki, Kenjiro

2014-11-01

To reveal the relation between intellectual disability and the deleted intervals in Williams syndrome, we performed an array comparative genomic hybridization analysis and standardized developmental testing for 11 patients diagnosed as having Williams syndrome based on fluorescent in situ hybridization testing. One patient had a large 4.2-Mb deletion spanning distally beyond the common 1.5-Mb intervals observed in 10/11 patients. We formulated a linear equation describing the developmental age of the 10 patients with the common deletion; the developmental age of the patient with the 4.2-Mb deletion was significantly below the expectation (developmental age = 0.51 × chronological age). The large deletion may account for the severe intellectual disability; therefore, the use of array comparative genomic hybridization may provide practical information regarding individuals with Williams syndrome. © 2014 Japanese Teratology Society.

An analysis of seismic background noise variation and evaluation of detection capability of Keskin Array (BRTR PS-43) in Turkey

Science.gov (United States)

Bakir, M. E.; Ozel, N. M.; Semin, K. U.

2011-12-01

Bogazici University, Kandilli Observatory and Earthquake Research Institute (KOERI) is currently operating the Keskin seismic array (BRTR-PS 43) located in town Keskin, providing real-time data to IDC. The instrumentaion of seismic array includes six short period borehole seismometers and one broadband borehole seismometer. The seismic background noise variation of Keskin array are studied in order to estimate the local and regional event detection capability in the frequency range from 1 Hz to 10 Hz. The Power density spectrum and also probability density function of Keskin array data were computed for seasonal and diurnal noise variations between 2008 and 2010. The computation will be extended to cover the period between 2005 and 2008. We attempt to determine the precise frequency characteristics of the background noise, which will help us to assess the station sensitivity. Minimum detectable magnitude versus distance for Keskin seismic array will be analyzed based on the seismic noise analysis. Detailed analysis results of seismic background noise and detection capability will be presented by this research.

Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice.

Science.gov (United States)

Chopra, Pankaj; Papale, Ligia A; White, Andrew T J; Hatch, Andrea; Brown, Ryan M; Garthwaite, Mark A; Roseboom, Patrick H; Golos, Thaddeus G; Warren, Stephen T; Alisch, Reid S

2014-02-13

Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymethylcytosine (5-hmC), in both stem cells and post-mitotic neurons, raises new questions as to the role of this base in mediating epigenetic effects. Genomic studies of these marks using model systems are limited, particularly with array-based tools, because the standard method of detecting DNA methylation cannot distinguish between 5-mC and 5-hmC and most methods have been developed to only survey the human genome. We show that non-human data generated using the optimization of a widely used human DNA methylation array, designed only to detect 5-mC, reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R(2) > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressor genes finds 76 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Similarly, adapting the assay to detect 5-hmC finds highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus > mouse). Annotation of 5-hmC with respect to gene structure reveals a significant prevalence in the 3'UTR and an association with chromatin-related ontological terms, suggesting an epigenetic feedback loop mechanism for 5-hmC. Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems

Second-order Data by Flow Injection Analysis with Spectrophotometric Diode-array Detection and Incorporated Gel-filtration Chromatographic Column

DEFF Research Database (Denmark)

Bechmann, Iben Ellegaard

1997-01-01

A flow injection analysis (FIA) system furnished with a gel-filtration chromatographic column and with photodiode-array detection was used for the generation of second-order data. The system presented is a model system in which the analytes are blue dextran, potassium hexacyanoferrate(III) and he......A flow injection analysis (FIA) system furnished with a gel-filtration chromatographic column and with photodiode-array detection was used for the generation of second-order data. The system presented is a model system in which the analytes are blue dextran, potassium hexacyanoferrate...

Transcriptomic Analysis of Intestinal Tissues from Two 90-Day Feeding Studies in Rats Using Genetically Modified MON810 Maize Varieties

Directory of Open Access Journals (Sweden)

Jutta Sharbati

2017-12-01

Full Text Available Background: Global as well as specific expression profiles of selected rat tissues were characterized to assess the safety of genetically modified (GM maize MON810 containing the insecticidal protein Cry1Ab. Gene expression was evaluated by use of Next Generation Sequencing (NGS as well as RT-qPCR within rat intestinal tissues based on mandatory 90-day rodent feeding studies. In parallel to two 90-day feeding studies, the transcriptional response of rat tissues was assessed as another endpoint to enhance the mechanistic interpretation of GM feeding studies and/or to facilitate the generation of a targeted hypothesis. Rats received diets containing 33% GM maize (MON810 or near-isogenic control maize. As a site of massive exposure to ingested feed the transcriptomic response of ileal and colonic tissue was profiled via RT-qPCR arrays targeting apoptosis, DNA-damage/repair, unfolded protein response (UPR. For global RNA profiling of rat ileal tissue, we applied NGS.Results: No biological response to the GM-diet was observed in male and in female rat tissues. Transcriptome wide analysis of gene expression by RNA-seq confirmed these findings. Nevertheless, gene ontology (GO analysis clearly associated a set of distinctly regulated transcripts with circadian rhythms. We confirmed differential expression of circadian clock genes using RT-qPCR and immunoassays for selected factors, thereby indicating physiological effects caused by the time point of sampling.Conclusion: Prediction of potential unintended effects of GM-food/feed by transcriptome based profiling of intestinal tissue presents a novel approach to complement classical toxicological testing procedures. Including the detection of alterations in signaling pathways in toxicity testing procedures may enhance the confidence in outcomes of toxicological trials. In this study, no significant GM-related changes in intestinal expression profiles were found in rats fed GM-maize MON810. Relevant

A Raman spectroscopy bio-sensor for tissue discrimination in surgical robotics.

Science.gov (United States)

Ashok, Praveen C; Giardini, Mario E; Dholakia, Kishan; Sibbett, Wilson

2014-01-01

We report the development of a fiber-based Raman sensor to be used in tumour margin identification during endoluminal robotic surgery. Although this is a generic platform, the sensor we describe was adapted for the ARAKNES (Array of Robots Augmenting the KiNematics of Endoluminal Surgery) robotic platform. On such a platform, the Raman sensor is intended to identify ambiguous tissue margins during robot-assisted surgeries. To maintain sterility of the probe during surgical intervention, a disposable sleeve was specially designed. A straightforward user-compatible interface was implemented where a supervised multivariate classification algorithm was used to classify different tissue types based on specific Raman fingerprints so that it could be used without prior knowledge of spectroscopic data analysis. The protocol avoids inter-patient variability in data and the sensor system is not restricted for use in the classification of a particular tissue type. Representative tissue classification assessments were performed using this system on excised tissue. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fabrication and biological evaluation of uniform extracellular matrix coatings on discontinuous photolithography generated micropallet arrays.

Science.gov (United States)

Gunn, Nicholas M; Bachman, Mark; Li, Guann-Pyng; Nelson, Edward L

2010-11-01

The recent identification of rare cell populations within tissues that are associated with specific biological behaviors, for example, progenitor cells, has illuminated a limitation of current technologies to study such adherent cells directly from primary tissues. The micropallet array is a recently developed technology designed to address this limitation by virtue of its capacity to isolate and recover single adherent cells on individual micropallets. The capacity to apply this technology to primary tissues and cells with restricted growth characteristics, particularly adhesion requirements, is critically dependent on the capacity to generate functional extracellular matrix (ECM) coatings. The discontinuous nature of the micropallet array surface provides specific constraints on the processes for generating the desired ECM coatings that are necessary to achieve the full functional capacity of the micropallet array. We have developed strategies, reported herein, to generate functional coatings with various ECM protein components: fibronectin, EHS tumor basement membrane extract, collagen, and laminin-5; confirmed by evaluation for rapid cellular adherence of four dissimilar cell types: fibroblast, breast epithelial, pancreatic epithelial, and myeloma. These findings are important for the dissemination and expanded use of micropallet arrays and similar microtechnologies requiring the integrated use of ECM protein coatings to promote cellular adherence.

Adaptive Injection-locking Oscillator Array for RF Spectrum Analysis

International Nuclear Information System (INIS)

Leung, Daniel

2011-01-01

A highly parallel radio frequency receiver using an array of injection-locking oscillators for on-chip, rapid estimation of signal amplitudes and frequencies is considered. The oscillators are tuned to different natural frequencies, and variable gain amplifiers are used to provide negative feedback to adapt the locking band-width with the input signal to yield a combined measure of input signal amplitude and frequency detuning. To further this effort, an array of 16 two-stage differential ring oscillators and 16 Gilbert-cell mixers is designed for 40-400 MHz operation. The injection-locking oscillator array is assembled on a custom printed-circuit board. Control and calibration is achieved by on-board microcontroller.

GeLC-MS: A Sample Preparation Method for Proteomics Analysis of Minimal Amount of Tissue.

Science.gov (United States)

Makridakis, Manousos; Vlahou, Antonia

2017-10-10

Application of various proteomics methodologies have been implemented for the global and targeted proteome analysis of many different types of biological samples such as tissue, urine, plasma, serum, blood, and cell lines. Among the aforementioned biological samples, tissue has an exceptional role into clinical research and practice. Disease initiation and progression is usually located at the tissue level of different organs, making the analysis of this material very important for the understanding of the disease pathophysiology. Despite the significant advances in the mass spectrometry instrumentation, tissue proteomics still faces several challenges mainly due to increased sample complexity and heterogeneity. However, the most prominent challenge is attributed to the invasive procedure of tissue sampling which restricts the availability of fresh frozen tissue to minimal amounts and limited number of samples. Application of GeLC-MS sample preparation protocol for tissue proteomics analysis can greatly facilitate making up for these difficulties. In this chapter, a step by step guide for the proteomics analysis of minute amounts of tissue samples using the GeLC-MS sample preparation protocol, as applied by our group in the analysis of multiple different types of tissues (vessels, kidney, bladder, prostate, heart) is provided.

Tetranectin positive expression in tumour tissue leads to longer survival in Danish women with ovarian cancer. Results from the 'Malova' ovarian cancer study

DEFF Research Database (Denmark)

Heeran, Mel C; Rask, Lene; Høgdall, Claus K

2015-01-01

of the disease. Using tissue arrays we analysed the expression levels in tissues from 166 women with borderline ovarian tumours (BOTs) and 592 women with ovarian cancer (OC). A panel of three antibodies was used for immunohistochemistry: a polyclonal and two monoclonal antibodies. Serum TN was measured using...... found to imply longer OS (p Kaplan-Meier survival analysis performed on all OC cases showed a significantly longer OS (p = 0...

Array coding for large data memories

Science.gov (United States)

Tranter, W. H.

1982-01-01

It is pointed out that an array code is a convenient method for storing large quantities of data. In a typical application, the array consists of N data words having M symbols in each word. The probability of undetected error is considered, taking into account three symbol error probabilities which are of interest, and a formula for determining the probability of undetected error. Attention is given to the possibility of reading data into the array using a digital communication system with symbol error probability p. Two different schemes are found to be of interest. The conducted analysis of array coding shows that the probability of undetected error is very small even for relatively large arrays.

The effect of micro-ECoG substrate footprint on the meningeal tissue response

Science.gov (United States)

Schendel, Amelia A.; Nonte, Michael W.; Vokoun, Corinne; Richner, Thomas J.; Brodnick, Sarah K.; Atry, Farid; Frye, Seth; Bostrom, Paige; Pashaie, Ramin; Thongpang, Sanitta; Eliceiri, Kevin W.; Williams, Justin C.

2014-08-01

Objective. There is great interest in designing implantable neural electrode arrays that maximize function while minimizing tissue effects and damage. Although it has been shown that substrate geometry plays a key role in the tissue response to intracortically implanted, penetrating neural interfaces, there has been minimal investigation into the effect of substrate footprint on the tissue response to surface electrode arrays. This study investigates the effect of micro-electrocorticography (micro-ECoG) device geometry on the longitudinal tissue response. Approach. The meningeal tissue response to two micro-ECoG devices with differing geometries was evaluated. The first device had each electrode site and trace individually insulated, with open regions in between, while the second device had a solid substrate, in which all 16 electrode sites were embedded in a continuous insulating sheet. These devices were implanted bilaterally in rats, beneath cranial windows, through which the meningeal tissue response was monitored for one month after implantation. Electrode site impedance spectra were also monitored during the implantation period. Main results. It was observed that collagenous scar tissue formed around both types of devices. However, the distribution of the tissue growth was different between the two array designs. The mesh devices experienced thick tissue growth between the device and the cranial window, and minimal tissue growth between the device and the brain, while the solid device showed the opposite effect, with thick tissue forming between the brain and the electrode sites. Significance. These data suggest that an open architecture device would be more ideal for neural recording applications, in which a low impedance path from the brain to the electrode sites is critical for maximum recording quality.

Probe suppression in conformal phased array

CERN Document Server

Singh, Hema; Neethu, P S

2017-01-01

This book considers a cylindrical phased array with microstrip patch antenna elements and half-wavelength dipole antenna elements. The effect of platform and mutual coupling effect is included in the analysis. The non-planar geometry is tackled by using Euler's transformation towards the calculation of array manifold. Results are presented for both conducting and dielectric cylinder. The optimal weights obtained are used to generate adapted pattern according to a given signal scenario. It is shown that array along with adaptive algorithm is able to cater to an arbitrary signal environment even when the platform effect and mutual coupling is taken into account. This book provides a step-by-step approach for analyzing the probe suppression in non-planar geometry. Its detailed illustrations and analysis will be a useful text for graduate and research students, scientists and engineers working in the area of phased arrays, low-observables and stealth technology.

Scattering Analysis of a Compact Dipole Array with Series and Parallel Feed Network including Mutual Coupling Effect

Directory of Open Access Journals (Sweden)

H. L. Sneha

2013-01-01

Full Text Available The current focus in defense arena is towards the stealth technology with an emphasis to control the radar cross-section (RCS. The scattering from the antennas mounted over the platform is of prime importance especially for a low-observable aerospace vehicle. This paper presents the analysis of the scattering cross section of a uniformly spaced linear dipole array. Two types of feed networks, that is, series and parallel feed networks, are considered. The total RCS of phased array with either kind of feed network is obtained by following the signal as it enters through the aperture and travels through the feed network. The RCS estimation of array is done including the mutual coupling effect between the dipole elements in three configurations, that is, side-by-side, collinear, and parallel-in-echelon. The results presented can be useful while designing a phased array with optimum performance towards low observability.

Microelectrode array-induced neuronal alignment directs neurite outgrowth: analysis using a fast Fourier transform (FFT).

Science.gov (United States)

Radotić, Viktorija; Braeken, Dries; Kovačić, Damir

2017-12-01

Many studies have shown that the topography of the substrate on which neurons are cultured can promote neuronal adhesion and guide neurite outgrowth in the same direction as the underlying topography. To investigate this effect, isotropic substrate-complementary metal-oxide-semiconductor (CMOS) chips were used as one example of microelectrode arrays (MEAs) for directing neurite growth of spiral ganglion neurons. Neurons were isolated from 5 to 7-day-old rat pups, cultured 1 day in vitro (DIV) and 4 DIV, and then fixed with 4% paraformaldehyde. For analysis of neurite alignment and orientation, fast Fourier transformation (FFT) was used. Results revealed that on the micro-patterned surface of a CMOS chip, neurons orient their neurites along three directional axes at 30, 90, and 150° and that neurites aligned in straight lines between adjacent pillars and mostly followed a single direction while occasionally branching perpendicularly. We conclude that the CMOS substrate guides neurites towards electrodes by means of their structured pillar organization and can produce electrical stimulation of aligned neurons as well as monitoring their neural activities once neurites are in the vicinity of electrodes. These findings are of particular interest for neural tissue engineering with the ultimate goal of developing a new generation of MEA essential for improved electrical stimulation of auditory neurons.

Dynamical analysis of surface-insulated planar wire array Z-pinches

Science.gov (United States)

Li, Yang; Sheng, Liang; Hei, Dongwei; Li, Xingwen; Zhang, Jinhai; Li, Mo; Qiu, Aici

2018-05-01

The ablation and implosion dynamics of planar wire array Z-pinches with and without surface insulation are compared and discussed in this paper. This paper first presents a phenomenological model named the ablation and cascade snowplow implosion (ACSI) model, which accounts for the ablation and implosion phases of a planar wire array Z-pinch in a single simulation. The comparison between experimental data and simulation results shows that the ACSI model could give a fairly good description about the dynamical characteristics of planar wire array Z-pinches. Surface insulation introduces notable differences in the ablation phase of planar wire array Z-pinches. The ablation phase is divided into two stages: insulation layer ablation and tungsten wire ablation. The two-stage ablation process of insulated wires is simulated in the ACSI model by updating the formulas describing the ablation process.

AnovArray: a set of SAS macros for the analysis of variance of gene expression data

Directory of Open Access Journals (Sweden)

Renard Jean-Paul

2005-06-01

Full Text Available Abstract Background Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility to evaluate multiple sources of variation in an experiment. Results AnovArray is a package implementing ANOVA for gene expression data using SAS® statistical software. The originality of the package is 1 to quantify the different sources of variation on all genes together, 2 to provide a quality control of the model, 3 to propose two models for a gene's variance estimation and to perform a correction for multiple comparisons. Conclusion AnovArray is freely available at http://www-mig.jouy.inra.fr/stat/AnovArray and requires only SAS® statistical software.

Backscattering analysis of high frequency ultrasonic imaging for ultrasound-guided breast biopsy

Science.gov (United States)

Cummins, Thomas; Akiyama, Takahiro; Lee, Changyang; Martin, Sue E.; Shung, K. Kirk

2017-03-01

A new ultrasound-guided breast biopsy technique is proposed. The technique utilizes conventional ultrasound guidance coupled with a high frequency embedded ultrasound array located within the biopsy needle to improve the accuracy in breast cancer diagnosis.1 The array within the needle is intended to be used to detect micro- calcifications indicative of early breast cancers such as ductal carcinoma in situ (DCIS). Backscattering analysis has the potential to characterize tissues to improve localization of lesions. This paper describes initial results of the application of backscattering analysis of breast biopsy tissue specimens and shows the usefulness of high frequency ultrasound for the new biopsy related technique. Ultrasound echoes of ex-vivo breast biopsy tissue specimens were acquired by using a single-element transducer with a bandwidth from 41 MHz to 88 MHz utilizing a UBM methodology, and the backscattering coefficients were calculated. These values as well as B-mode image data were mapped in 2D and matched with each pathology image for the identification of tissue type for the comparison to the pathology images corresponding to each plane. Microcalcifications were significantly distinguished from normal tissue. Adenocarcinoma was also successfully differentiated from adipose tissue. These results indicate that backscattering analysis is able to quantitatively distinguish tissues into normal and abnormal, which should help radiologists locate abnormal areas during the proposed ultrasound-guided breast biopsy with high frequency ultrasound.

Terabyte IDE RAID-5 Disk Arrays

Energy Technology Data Exchange (ETDEWEB)

David A. Sanders et al.

2003-09-30

High energy physics experiments are currently recording large amounts of data and in a few years will be recording prodigious quantities of data. New methods must be developed to handle this data and make analysis at universities possible. We examine some techniques that exploit recent developments in commodity hardware. We report on tests of redundant arrays of integrated drive electronics (IDE) disk drives for use in offline high energy physics data analysis. IDE redundant array of inexpensive disks (RAID) prices now are less than the cost per terabyte of million-dollar tape robots! The arrays can be scaled to sizes affordable to institutions without robots and used when fast random access at low cost is important.

Efficient Full-Wave Analysis of Waveguide Arrays on Cylindrical Surfaces.

NARCIS (Netherlands)

Gerini, G.; Guglielmi, M.; Rozzi, T.; Zappelli, L.

1999-01-01

Conformal open-ended waveguide arrays received great attention in the early seventies. Recently, dielectric loaded waveguide radiators have been again proposed to achieve high dety microwave packaging [1], [2]. The efficient design of highly integrated array solutions, however, require fast and

Hybrid Arrays for Chemical Sensing

Science.gov (United States)

Kramer, Kirsten E.; Rose-Pehrsson, Susan L.; Johnson, Kevin J.; Minor, Christian P.

In recent years, multisensory approaches to environment monitoring for chemical detection as well as other forms of situational awareness have become increasingly popular. A hybrid sensor is a multimodal system that incorporates several sensing elements and thus produces data that are multivariate in nature and may be significantly increased in complexity compared to data provided by single-sensor systems. Though a hybrid sensor is itself an array, hybrid sensors are often organized into more complex sensing systems through an assortment of network topologies. Part of the reason for the shift to hybrid sensors is due to advancements in sensor technology and computational power available for processing larger amounts of data. There is also ample evidence to support the claim that a multivariate analytical approach is generally superior to univariate measurements because it provides additional redundant and complementary information (Hall, D. L.; Linas, J., Eds., Handbook of Multisensor Data Fusion, CRC, Boca Raton, FL, 2001). However, the benefits of a multisensory approach are not automatically achieved. Interpretation of data from hybrid arrays of sensors requires the analyst to develop an application-specific methodology to optimally fuse the disparate sources of data generated by the hybrid array into useful information characterizing the sample or environment being observed. Consequently, multivariate data analysis techniques such as those employed in the field of chemometrics have become more important in analyzing sensor array data. Depending on the nature of the acquired data, a number of chemometric algorithms may prove useful in the analysis and interpretation of data from hybrid sensor arrays. It is important to note, however, that the challenges posed by the analysis of hybrid sensor array data are not unique to the field of chemical sensing. Applications in electrical and process engineering, remote sensing, medicine, and of course, artificial

Neutron activation analysis of medullar and cortical bone tissues from animals

International Nuclear Information System (INIS)

Takata, Marcelo Kazuo; Saiki, Mitiko

2000-01-01

In this work, neutron activation analysis was applied in the determination of the elements Ba, Br, Ca, Cl, Cr, Fe, K, Mg, Mn, Na, P, Rb, Sb, Sc, Sr and Zn present in animal bone tissues. The obtained results indicated a significant difference between the elemental concentrations present in medullar and cortical tissues. The results obtained for bone tissues from distinct animal species were also different. (author)

Thermal analysis for folded solar array of spacecraft in orbit

International Nuclear Information System (INIS)

Yang, W.H.; Cheng, H.E.; Cai, A.

2004-01-01

The combined radiation-conduction heat transfer in folded solar array was considered as a three-dimensional anisotropic conduction without inner heat source. The three-dimensional equivalent conductivity in cell plate were obtained. The especially discrete equation coefficients of the nodes on the surfaces of adjacent cell plates were deduced by utilizing the simplified radiation network among the two adjacent cell plate surfaces and the deep cold space. All the thermal influence factors on the temperature response of the folded solar array were considered carefully. SIP method was used to solve the discrete equation. By comparing the calculation results under three cases, the temperature response and the maximum average difference of the folded solar array was obtained during the period of throw-radome of the launch vehicle and spread of the folded solar array. The obtained result is a valuable reference for the selection of the launch time of the spacecraft

Preconcentration of plutonium and americium using the Actinide-CUTM Resin for human tissue analysis

International Nuclear Information System (INIS)

Qu, H.; Stuit, D.; Glover, S.E.; Love, S.F.; Filby, R.H.; Washington State Univ., Pullman, WA

1998-01-01

A method for the preconcentration of Am and Pu from human tissue solutions (liver, lung, bone etc) using the Actinide-CU Resin (EIChroM Industries) has been developed for their alpha-spectrometric determination. With near 100% recoveries were obtained by preconcentration, subsequent decomposition methods for eluent were developed. Good agreement for Pu and Am determination with the USTUR anion-exchange/solvent extraction method was demonstrated using previously analyzed human tissue solutions and NIST SRMs. The advantages of the preconcentration method applied to human tissue analysis are simplicity of operation, shorter analysis time compared to anion exchange/solvent extraction methods, and capacity to analyze large tissue samples (up to 15 g bone ash per analysis and 500 g soft tissue). (author)

Long-term stability of intracortical recordings using perforated and arrayed Parylene sheath electrodes

Science.gov (United States)

Hara, Seth A.; Kim, Brian J.; Kuo, Jonathan T. W.; Lee, Curtis D.; Meng, Ellis; Pikov, Victor

2016-12-01

Objective. Acquisition of reliable and robust neural recordings with intracortical neural probes is a persistent challenge in the field of neuroprosthetics. We developed a multielectrode array technology to address chronic intracortical recording reliability and present in vivo recording results. Approach. The 2 × 2 Parylene sheath electrode array (PSEA) was microfabricated and constructed from only Parylene C and platinum. The probe includes a novel three-dimensional sheath structure, perforations, and bioactive coatings that improve tissue integration and manage immune response. Coatings were applied using a sequential dip-coating method that provided coverage over the entire probe surface and interior of the sheath structure. A sharp probe tip taper facilitated insertion with minimal trauma. Fabricated probes were subject to examination by optical and electron microscopy and electrochemical testing prior to implantation. Main results. 1 × 2 arrays were successfully fabricated on wafer and then packaged together to produce 2 × 2 arrays. Then, probes having electrode sites with adequate electrochemical properties were selected. A subset of arrays was treated with bioactive coatings to encourage neuronal growth and suppress inflammation and another subset of arrays was implanted in conjunction with a virally mediated expression of Caveolin-1. Arrays were attached to a custom-made insertion shuttle to facilitate precise insertion into the rat motor cortex. Stable electrophysiological recordings were obtained during the period of implantation up to 12 months. Immunohistochemical evaluation of cortical tissue around individual probes indicated a strong correlation between the electrophysiological performance of the probes and histologically observable proximity of neurons and dendritic sprouting. Significance. The PSEA demonstrates the scalability of sheath electrode technology and provides higher electrode count and density to access a greater volume for recording

Analysis of O-glycans as 9-fluorenylmethyl derivatives and its application to the studies on glycan array.

Science.gov (United States)

Yamada, Keita; Hirabayashi, Jun; Kakehi, Kazuaki

2013-03-19

A method is proposed for the analysis of O-glycans as 9-fluorenylmethyl (Fmoc) derivatives. After releasing the O-glycans from the protein backbone in the presence of ammonia-based media, the glycosylamines thus formed are conveniently labeled with Fmoc-Cl and analyzed by HPLC and MALDI-TOF MS after easy purification. Fmoc labeled O-glycans showed 3.5 times higher sensitivities than those labeled with 2-aminobenzoic acid in fluorescent detection. Various types of O-glycans having sialic acids, fucose, and/or sulfate residues were successfully labeled with Fmoc and analyzed by HPLC and MALDI-TOF MS. The method was applied to the comprehensive analysis of O-glycans expressed on MKN45 cells (human gastric adenocarcinoma). In addition, Fmoc-derivatized O-glycans were easily converted to free hemiacetal or glycosylamine-form glycans that are available for fabrication of glycan array and neoglycoproteins. To demonstrate the availability of our methods, we fabricate the glycan array with Fmoc labeled glycans derived from mucin samples and cancer cells. The model studies using the glycan array showed clear interactions between immobilized glycans and some lectins.

Analysis of mean time to data loss of fault-tolerant disk arrays RAID-6 based on specialized Markov chain

Science.gov (United States)

Rahman, P. A.; D'K Novikova Freyre Shavier, G.

2018-03-01

This scientific paper is devoted to the analysis of the mean time to data loss of redundant disk arrays RAID-6 with alternation of data considering different failure rates of disks both in normal state of the disk array and in degraded and rebuild states, and also nonzero time of the disk replacement. The reliability model developed by the authors on the basis of the Markov chain and obtained calculation formula for estimation of the mean time to data loss (MTTDL) of the RAID-6 disk arrays are also presented. At last, the technique of estimation of the initial reliability parameters and examples of calculation of the MTTDL of the RAID-6 disk arrays for the different numbers of disks are also given.

Calculation of microplanar beam dose profiles in a tissue/lung/tissue phantom

International Nuclear Information System (INIS)

Company, F.Z.; Allen, B.J.

1998-01-01

Recent advances in synchrotron generated x-ray beams with a high fluence rate permit investigation of the application of an array of closely spaced, parallel or converging microplanar beams in radiotherapy. The proposed technique takes advantage of the hypothesized repair mechanism of capillary cells between alternate microbeam zones, which regenerates the lethally irradiated endothelial cells. The lateral and depth doses of 100 keV microplanar beams are investigated for different beam dimensions and spacings in a tissue, lung and tissue/lung/tissue phantom. The EGS4 Monte Carlo code is used to calculate dose profiles at different depths and bundles of beams (up to 20x20cm square cross section). The maximum dose on the beam axis (peak) and the minimum interbeam dose (valley) are compared at different depths, bundles, heights, widths and beam spacings. (author)

Ceramic ball grid array package stress analysis

Science.gov (United States)

Badri, S. H. B. S.; Aziz, M. H. A.; Ong, N. R.; Sauli, Z.; Alcain, J. B.; Retnasamy, V.

2017-09-01

The ball grid array (BGA), a form of chip scale package (CSP), was developed as one of the most advanced surface mount devices, which may be assembled by an ordinary surface ball bumps are used instead of plated nickel and gold (Ni/Au) bumps. Assembly and reliability of the BGA's printed circuit board (PCB), which is soldered by conventional surface mount technology is considered in this study. The Ceramic Ball Grid Array (CBGA) is a rectangular ceramic package or square-shaped that will use the solder ball for external electrical connections instead of leads or wire for connections. The solder balls will be arranged in an array or grid at the bottom of the ceramic package body. In this study, ANSYS software is used to investigate the stress on the package for 2 balls and 4 balls of the CBGA package with the various force range of 1-3 Newton applied to the top of the die, top of the substrate and side of the substrate. The highest maximum stress was analyzed and the maximum equivalent stress was observed on the solder ball and the die. From the simulation result, the CBGA package with less solder balls experience higher stress compared to the package with many solder balls. Therefore, less number of solder ball on the CBGA package results higher stress and critically affect the reliability of the solder balls itself, substrate and die which can lead to the solder crack and also die crack.

Neutron activation analysis of trace elements in biological tissue

Energy Technology Data Exchange (ETDEWEB)

Velandia, J A; Perkons, A K

1974-01-01

Thermal Neutron Activation Analysis with Instrumental Ge(Li) Gamma Spectrometry was used to determine the amounts of more than 30 trace constituents in heart tissue of rats and kidney tissue of rabbits. The results were confirmed by a rapid ion-exchange group separation method in the initial stages of the experiments. The samples were exposed to thermal neutrons for periods between 3 minutes and 14 hours. Significant differences in the amounts and types of trace elements in the two different tissue types are apparent, however, are probably due to specific diets. Tables of relevant nuclear data, standard concentrations, radiochemical separation recoveries, and quantitative analytical results are presented. The ion-exchange group separation scheme and typical examples of the instrumental gamma ray spectra are shown. The techniques developed in this study are being used for a large scale constituent survey of various diseased and healthy human tissues.

Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

DEFF Research Database (Denmark)

Jensen, Thomas; Holten-Rossing, Henrik; Svendsen, Ida M H

2016-01-01

to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including...... staining may benefit. METHODS: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm......BACKGROUND: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar...

Proteomic Analysis of Human Tendon and Ligament: Solubilization and Analysis of Insoluble Extracellular Matrix in Connective Tissues.

Science.gov (United States)

Sato, Nori; Taniguchi, Takako; Goda, Yuichiro; Kosaka, Hirofumi; Higashino, Kosaku; Sakai, Toshinori; Katoh, Shinsuke; Yasui, Natsuo; Sairyo, Koichi; Taniguchi, Hisaaki

2016-12-02

Connective tissues such as tendon, ligament and cartilage are mostly composed of extracellular matrix (ECM). These tissues are insoluble, mainly due to the highly cross-linked ECM proteins such as collagens. Difficulties obtaining suitable samples for mass spectrometric analysis render the application of modern proteomic technologies difficult. Complete solubilization of them would not only elucidate protein composition of normal tissues but also reveal pathophysiology of pathological tissues. Here we report complete solubilization of human Achilles tendon and yellow ligament, which is achieved by chemical digestion combined with successive protease treatment including elastase. The digestion mixture was subjected to liquid chromatography-mass spectrometry. The low specificity of elastase was overcome by accurate mass analysis achieved using FT-ICR-MS. In addition to the detailed proteome of both tissues, we also quantitatively determine the major protein composition of samples, by measuring peak area of some characteristic peptides detected in tissue samples and in purified proteins. As a result, differences between human Achilles tendon and yellow ligament were elucidated at molecular level.

GENE ARRAY ANALYSIS OF THE VENTRAL PROSTATE IN RATS EXPOSED TO EITHER VINCLOZOLIN OR PROCYMIDONE

Science.gov (United States)

GENE ARRAY ANALYSIS OF THE VENTRAL PROSTATE IN RATS EXPOSED TO EITHER VINCLOZOLIN OR PROCYMIDONE. MB Rosen, VS Wilson, JE Schmid, and LE Gray Jr. US EPA, ORD, NHEERL, RTP, NC.Vinclozolin (Vi) and procymidone (Pr) are antiandrogenic fungicides. While changes in gene expr...

Microscopic histological characteristics of soft tissue sarcomas: analysis of tissue features and electrical resistance.

Science.gov (United States)

Tosi, A L; Campana, L G; Dughiero, F; Forzan, M; Rastrelli, M; Sieni, E; Rossi, C R

2017-07-01

Tissue electrical conductivity is correlated with tissue characteristics. In this work, some soft tissue sarcomas (STS) excised from patients have been evaluated in terms of histological characteristics (cell size and density) and electrical resistance. The electrical resistance has been measured using the ex vivo study on soft tissue tumors electrical characteristics (ESTTE) protocol proposed by the authors in order to study electrical resistance of surgical samples excised by patients in a fixed measurement setup. The measurement setup includes a voltage pulse generator (700 V, 100 µs long at 5 kHz, period 200 µs) and an electrode with 7 needles, 20 mm-long, with the same distance arranged in a fixed hexagonal geometry. In the ESTTE protocol, the same voltage pulse sequence is applied to each different tumor mass and the corresponding resistance has been evaluated from voltage and current recorded by the equipment. For each tumor mass, a histological sample of the volume treated by means of voltage pulses has been taken for histological analysis. Each mass has been studied in order to identify the sarcoma type. For each histological sample, an image at 20× or 40× of magnification was acquired. In this work, the electrical resistance measured for each tumor has been correlated with tissue characteristics like the type, size and density of cells. This work presents a preliminary study to explore possible correlations between tissue characteristics and electrical resistance of STS. These results can be helpful to adjust the pulse voltage intensity in order to improve the electrochemotherapy efficacy on some histotype of STS.

Genetic evidence reveals improvement opportunities for tissue preparation in forensic analysis

OpenAIRE

Romero, Rosa Elena; Sandoval, Alejandro; Arango, Juliana; Camargo, Martha Lucia

2016-01-01

Introduction: Paraffin embedded tissues are an excellent alternative to obtain dna, especially when it is not possible to have fresh samples or when the tissue storage and preservation is not feasible; therefore, this sample is the only item available for matching purposes. The success in any genetic analysis implies having adequate tissue fixation and suitable dna extraction methods that allow to obtain good quality and quantity molecules, free of biological, chemical and microbiological con...

Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study

Directory of Open Access Journals (Sweden)

Beltrame Francesco

2010-11-01

Full Text Available Abstract Background Tissue MicroArray technology aims to perform immunohistochemical staining on hundreds of different tissue samples simultaneously. It allows faster analysis, considerably reducing costs incurred in staining. A time consuming phase of the methodology is the selection of tissue areas within paraffin blocks: no utilities have been developed for the identification of areas to be punched from the donor block and assembled in the recipient block. Results The presented work supports, in the specific case of a primary subtype of breast cancer (tubular breast cancer, the semi-automatic discrimination and localization between normal and pathological regions within the tissues. The diagnosis is performed by analysing specific morphological features of the sample such as the absence of a double layer of cells around the lumen and the decay of a regular glands-and-lobules structure. These features are analysed using an algorithm which performs the extraction of morphological parameters from images and compares them to experimentally validated threshold values. Results are satisfactory since in most of the cases the automatic diagnosis matches the response of the pathologists. In particular, on a total of 1296 sub-images showing normal and pathological areas of breast specimens, algorithm accuracy, sensitivity and specificity are respectively 89%, 84% and 94%. Conclusions The proposed work is a first attempt to demonstrate that automation in the Tissue MicroArray field is feasible and it can represent an important tool for scientists to cope with this high-throughput technique.

Lectin-Array Blotting.

Science.gov (United States)

Pazos, Raquel; Echevarria, Juan; Hernandez, Alvaro; Reichardt, Niels-Christian

2017-09-01

Aberrant protein glycosylation is a hallmark of cancer, infectious diseases, and autoimmune or neurodegenerative disorders. Unlocking the potential of glycans as disease markers will require rapid and unbiased glycoproteomics methods for glycan biomarker discovery. The present method is a facile and rapid protocol for qualitative analysis of protein glycosylation in complex biological mixtures. While traditional lectin arrays only provide an average signal for the glycans in the mixture, which is usually dominated by the most abundant proteins, our method provides individual lectin binding profiles for all proteins separated in the gel electrophoresis step. Proteins do not have to be excised from the gel for subsequent analysis via the lectin array but are transferred by contact diffusion from the gel to a glass slide presenting multiple copies of printed lectin arrays. Fluorescently marked glycoproteins are trapped by the printed lectins via specific carbohydrate-lectin interactions and after a washing step their binding profile with up to 20 lectin probes is analyzed with a fluorescent scanner. The method produces the equivalent of 20 lectin blots in a single experiment, giving detailed insight into the binding epitopes present in the fractionated proteins. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Tissue microarrays and their use for preparation of reference slides ...

African Journals Online (AJOL)

Use of Tissue array was first applied in 1998, and has received a significant amount of attention from the research community ever since. In this technique, a large number (up to 1000) of cylindrical tissue core extracted from \\"donor\\" paraffin block are deposited into \\"recipient\\" block. The aim was modification of the ...

Phased-array design for MST and ST radars

Science.gov (United States)

Ecklund, W. L.

1986-01-01

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

Intraneural stimulation using wire-microelectrode arrays: analysis of force steps in recruitment curves

NARCIS (Netherlands)

Smit, J.P.A.; Rutten, Wim; Boom, H.B.K.

1996-01-01

In acute experiments on six Wistar rats, a wire-microelectrode array was inserted into the common peroneal nerve. A 5-channel array and a 24-channel array were available. Each electrode in the array was used to generate a twitch contraction force recruitment curve for the extensor digitorum longus

Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs.

Directory of Open Access Journals (Sweden)

Maarten Sonnaert

Full Text Available To progress the fields of tissue engineering (TE and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial 'design of experiments' approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology.

Tissue preservation with mass spectroscopic analysis: Implications for cancer diagnostics.

Science.gov (United States)

Hall, O Morgan; Peer, Cody J; Figg, William D

2018-05-17

Surgical intervention is a common treatment modality for localized cancer. Post-operative analysis involves evaluation of surgical margins to assess whether all malignant tissue has been resected because positive surgical margins lead to a greater likelihood of recurrence. Secondary treatments are utilized to minimize the negative effects of positive surgical margins. Recently, in Science Translational Medicine, Zhang et al describe a new mass spectroscopic technique that could potentially decrease the likelihood of positive surgical margins. Their nondestructive in vivo tissue sampling leads to a highly accurate and rapid cancer diagnosis with great precision between healthy and malignant tissue. This new tool has the potential to improve surgical margins and accelerate cancer diagnostics by analyzing biomolecular signatures of various tissues and diseases.

Long-lived tissue resident HIV-1 specific memory CD8+ T cells are generated by skin immunization with live virus vectored microneedle arrays.

Science.gov (United States)

Zaric, Marija; Becker, Pablo Daniel; Hervouet, Catherine; Kalcheva, Petya; Ibarzo Yus, Barbara; Cocita, Clement; O'Neill, Lauren Alexandra; Kwon, Sung-Yun; Klavinskis, Linda Sylvia

2017-12-28

The generation of tissue resident memory (T RM ) cells at the body surfaces to provide a front line defence against invading pathogens represents an important goal in vaccine development for a wide variety of pathogens. It has been widely assumed that local vaccine delivery to the mucosae is necessary to achieve that aim. Here we characterise a novel micro-needle array (MA) delivery system fabricated to deliver a live recombinant human adenovirus type 5 vaccine vector (AdHu5) encoding HIV-1 gag. We demonstrate rapid dissolution kinetics of the microneedles in skin. Moreover, a consequence of MA vaccine cargo release was the generation of long-lived antigen-specific CD8 + T cells that accumulate in mucosal tissues, including the female genital and respiratory tract. The memory CD8 + T cell population maintained in the peripheral mucosal tissues was attributable to a MA delivered AdHu5 vaccine instructing CD8 + T cell expression of CXCR3 + , CD103 +, CD49a + , CD69 + , CD127 + homing, retention and survival markers. Furthermore, memory CD8 + T cells generated by MA immunization significantly expanded upon locally administered antigenic challenge and showed a predominant poly-functional profile producing high levels of IFNγ and Granzyme B. These data demonstrate that skin vaccine delivery using microneedle technology induces mobilization of long lived, poly-functional CD8 + T cells to peripheral tissues, phenotypically displaying hallmarks of residency and yields new insights into how to design and deliver effective vaccine candidates with properties to exert local immunosurveillance at the mucosal surfaces. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Wind loads on flat plate photovoltaic array fields

Science.gov (United States)

Miller, R. D.; Zimmerman, D. K.

1981-01-01

The results of an experimental analysis (boundary layer wind tunnel test) of the aerodynamic forces resulting from winds acting on flat plate photovoltaic arrays are presented. Local pressure coefficient distributions and normal force coefficients on the arrays are shown and compared to theoretical results. Parameters that were varied when determining the aerodynamic forces included tilt angle, array separation, ground clearance, protective wind barriers, and the effect of the wind velocity profile. Recommended design wind forces and pressures are presented, which envelop the test results for winds perpendicular to the array's longitudinal axis. This wind direction produces the maximum wind loads on the arrays except at the array edge where oblique winds produce larger edge pressure loads. The arrays located at the outer boundary of an array field have a protective influence on the interior arrays of the field. A significant decrease of the array wind loads were recorded in the wind tunnel test on array panels located behind a fence and/or interior to the array field compared to the arrays on the boundary and unprotected from the wind. The magnitude of this decrease was the same whether caused by a fence or upwind arrays.

Data in support of proteomic analysis of pneumococcal pediatric clinical isolates to construct a protein array

Directory of Open Access Journals (Sweden)

Alfonso Olaya-Abril

2016-03-01

Full Text Available Surface proteins play key roles in the interaction between cells and their environment, and in pathogenic microorganisms they are the best targets for drug or vaccine discovery and/or development. In addition, surface proteins can be the basis for serodiagnostic tools aiming at developing more affordable techniques for early diagnosis of infection in patients. We carried out a proteomic analysis of a collection of pediatric clinical isolates of Streptococcus pneumoniae, an important human pathogen responsible for more than 1.5 million child deaths worldwide. For that, cultured live bacterial cells were “shaved” with trypsin, and the recovered peptides were analyzed by LC/MS/MS. We selected 95 proteins to be produced as recombinant polypeptides, and printed them on an array. We probed the protein array with a collection of patient sera to define serodiagnostic antigens. The mass spectrometry proteomics data correspond to those published in [1] and have been deposited to the ProteomeXchange Consortium [2] via the PRIDE partner repository [3] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD001740. The protein array raw data are provided as supplemental material in this article. Keywords: Pneumococcus, Protein arrays, Proteomics, Diagnostics

ESPRIT And Uniform Linear Arrays

Science.gov (United States)

Roy, R. H.; Goldburg, M.; Ottersten, B. E.; Swindlehurst, A. L.; Viberg, M.; Kailath, T.

1989-11-01

Abstract ¬â€?ESPRIT is a recently developed and patented technique for high-resolution estimation of signal parameters. It exploits an invariance structure designed into the sensor array to achieve a reduction in computational requirements of many orders of magnitude over previous techniques such as MUSIC, Burg's MEM, and Capon's ML, and in addition achieves performance improvement as measured by parameter estimate error variance. It is also manifestly more robust with respect to sensor errors (e.g. gain, phase, and location errors) than other methods as well. Whereas ESPRIT only requires that the sensor array possess a single invariance best visualized by considering two identical but other-wise arbitrary arrays of sensors displaced (but not rotated) with respect to each other, many arrays currently in use in various applications are uniform linear arrays of identical sensor elements. Phased array radars are commonplace in high-resolution direction finding systems, and uniform tapped delay lines (i.e., constant rate A/D converters) are the rule rather than the exception in digital signal processing systems. Such arrays possess many invariances, and are amenable to other types of analysis, which is one of the main reasons such structures are so prevalent. Recent developments in high-resolution algorithms of the signal/noise subspace genre including total least squares (TLS) ESPRIT applied to uniform linear arrays are summarized. ESPRIT is also shown to be a generalization of the root-MUSIC algorithm (applicable only to the case of uniform linear arrays of omni-directional sensors and unimodular cisoids). Comparisons with various estimator bounds, including CramerRao bounds, are presented.

Challenging aspects of contemporary cochlear implant electrode array design.

Science.gov (United States)

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

2017-12-01

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

Automated flow quantification in valvular heart disease based on backscattered Doppler power analysis: implementation on matrix-array ultrasound imaging systems.

Science.gov (United States)

Buck, Thomas; Hwang, Shawn M; Plicht, Björn; Mucci, Ronald A; Hunold, Peter; Erbel, Raimund; Levine, Robert A

2008-06-01

Cardiac ultrasound imaging systems are limited in the noninvasive quantification of valvular regurgitation due to indirect measurements and inaccurate hemodynamic assumptions. We recently demonstrated that the principle of integration of backscattered acoustic Doppler power times velocity can be used for flow quantification in valvular regurgitation directly at the vena contracta of a regurgitant flow jet. We now aimed to accomplish implementation of automated Doppler power flow analysis software on a standard cardiac ultrasound system utilizing novel matrix-array transducer technology with detailed description of system requirements, components and software contributing to the system. This system based on a 3.5 MHz, matrix-array cardiac ultrasound scanner (Sonos 5500, Philips Medical Systems) was validated by means of comprehensive experimental signal generator trials, in vitro flow phantom trials and in vivo testing in 48 patients with mitral regurgitation of different severity and etiology using magnetic resonance imaging (MRI) for reference. All measurements displayed good correlation to the reference values, indicating successful implementation of automated Doppler power flow analysis on a matrix-array ultrasound imaging system. Systematic underestimation of effective regurgitant orifice areas >0.65 cm(2) and volumes >40 ml was found due to currently limited Doppler beam width that could be readily overcome by the use of new generation 2D matrix-array technology. Automated flow quantification in valvular heart disease based on backscattered Doppler power can be fully implemented on board a routinely used matrix-array ultrasound imaging systems. Such automated Doppler power flow analysis of valvular regurgitant flow directly, noninvasively, and user independent overcomes the practical limitations of current techniques.

Trend Analysis of Organ and Tissue Donation for Transplantation.

Science.gov (United States)

Dos Santos, M J; Leal de Moraes, E; Santini Martins, M; Carlos de Almeida, E; Borges de Barros E Silva, L; Urias, V; Silvano Corrêa Pacheco Furtado, M C; Brito Nunes, Á; El Hage, S

2018-03-01

The goal of this study was to identify the tendency toward donations of tissue and organs from donors with brain death between 2001 and 2016 as registered by an organ procurement organization in São Paulo City. This quantitative, retrospective, exploratory study encompassed all Tissue and Organ Donation Terms signed between 2001 and 2016. A logistic regression model was applied to verify whether there was an upward or downward trend in donation. After statistical analysis, a significant change trend was identified in skin, bones, valve, vessel, heart, lung, and pancreas donations, indicating an increase in the donation rate through the years. The donation rate did not show changes over the years for donations of liver, kidneys, and corneas. The decision-making process regarding organ and tissue donation is restricted not only to the dilemma of whether to donate but another question then arises as well: which organs and tissues are to be donated? The discrepancy between the authorization for organ donation and the authorization for tissue donation, as well as the option for one or another organ and/or tissue, must be thoroughly examined because these factors directly affect the number of transplants and acquirements effectively accomplished. These factors may be related to explaining to one's relatives aspects of the surgery, body reassembling, and usage of such organs and/or tissues. They may also be related to the lack of knowledge concerning organ donation and the symbolism represented by the organ and/or tissue, among other factors. Copyright © 2018 Elsevier Inc. All rights reserved.

Modeling of transdermal drug delivery with a microneedle array

Science.gov (United States)

Lv, Y.-G.; Liu, J.; Gao, Y.-H.; Xu, B.

2006-11-01

Transdermal drug delivery is generally limited by the extraordinary barrier properties of the stratum corneum, the outer 10-15 µm layer of skin. A conventional needle inserted across this barrier and into deeper tissues could effectively deliver drugs. However, it would lead to infection and cause pain, thereby reducing patient compliance. In order to administer a frequent injection of insulin and other therapeutic agents more efficiently, integrated arrays with very short microneedles were recently proposed as very good candidates for painless injection or extraction. A variety of microneedle designs have thus been made available by employing the fabrication tools of the microelectronics industry and using materials such as silicon, metals, polymers and glass with feature sizes ranging from sub-micron to nanometers. At the same time, experiments were also made to test the capability of the microneedles to inject drugs into tissues. However, due to the difficulty encountered in measurement, a detailed understanding of the spatial and transient drug delivery process still remains unclear up to now. To better grasp the mechanisms involved, quantitative theoretical models were developed in this paper to simultaneously characterize the flow and drug transport, and numerical solutions were performed to predict the kinetics of dispersed drugs injected into the skin from a microneedle array. Calculations indicated that increasing the initial injection velocity and accelerating the blood circulation in skin tissue with high porosity are helpful to enhance the transdermal drug delivery. This study provides the first quantitative simulation of fluid injection through a microneedle array and drug species transport inside the skin. The modeling strategy can also possibly be extended to deal with a wider range of clinical issues such as targeted nanoparticle delivery for therapeutics or molecular imaging.

Effect of wire shape on wire array discharge

International Nuclear Information System (INIS)

Shimomura, N.; Tanaka, Y.; Yushita, Y.; Nagata, M.; Teramoto, Y.; Katsuki, S.; Akiyama, H.

2001-01-01

Although considerable investigations have been reported on z-pinches to achieve nuclear fusion, little attention has been given from the point of view of how a wire array consisting of many parallel wires explodes. Instability existing in the wire array discharge has been shown. In this paper, the effect of wire shape in the wire array on unstable behavior of the wire array discharge is represented by numerical analysis. The claws on the wire formed in installation of wire may cause uniform current distribution on wire array. The effect of error of wire diameter in production is computed by Monte Carlo Method. (author)

Effect of wire shape on wire array discharge

Energy Technology Data Exchange (ETDEWEB)

Shimomura, N.; Tanaka, Y.; Yushita, Y.; Nagata, M. [University of Tokushima, Department of Electrical and Electronic Engineering, Tokushima (Japan); Teramoto, Y.; Katsuki, S.; Akiyama, H. [Kumamoto University, Department of Electrical and Computer Engineering, Kumamoto (Japan)

2001-09-01

Although considerable investigations have been reported on z-pinches to achieve nuclear fusion, little attention has been given from the point of view of how a wire array consisting of many parallel wires explodes. Instability existing in the wire array discharge has been shown. In this paper, the effect of wire shape in the wire array on unstable behavior of the wire array discharge is represented by numerical analysis. The claws on the wire formed in installation of wire may cause uniform current distribution on wire array. The effect of error of wire diameter in production is computed by Monte Carlo Method. (author)

RAPID PROCESSING OF ARCHIVAL TISSUE SAMPLES FOR PROTEOMIC ANALYSIS USING PRESSURE-CYCLING TECHNOLOGY

Directory of Open Access Journals (Sweden)

Vinuth N. Puttamallesh1,2

2017-06-01

Full Text Available Advent of mass spectrometry based proteomics has revolutionized our ability to study proteins from biological specimen in a high-throughput manner. Unlike cell line based studies, biomedical research involving tissue specimen is often challenging due to limited sample availability. In addition, investigation of clinically relevant research questions often requires enormous amount of time for sample collection prospectively. Formalin fixed paraffin embedded (FFPE archived tissue samples are a rich source of tissue specimen for biomedical research. However, there are several challenges associated with analysing FFPE samples. Protein cross-linking and degradation of proteins particularly affects proteomic analysis. We demonstrate that barocycler that uses pressure-cycling technology enables efficient protein extraction and processing of small amounts of FFPE tissue samples for proteomic analysis. We identified 3,525 proteins from six 10µm esophageal squamous cell carcinoma (ESCC tissue sections. Barocycler allows efficient protein extraction and proteolytic digestion of proteins from FFPE tissue sections at par with conventional methods.

Criticality safety of low-density storage arrays

International Nuclear Information System (INIS)

Bauer, T. H.; Nuclear Engineering Division

2005-01-01

This paper proposes a straightforward bounding method for the criticality safety analysis of fissionable materials configured into large arrays of standard containers. While criticality-safe storage limits have been well established for single containers, even under flooded conditions, it is also necessary to rule out any potential for criticality arising from neutronic interactions among multiple containers that might build up over long distances in a large array. Traditionally, the array problem has been approached by individual Monte Carlo analyses of explicit arrangements of single units and their surroundings. Deemphasizing specific configurations, the present technique takes advantage of low average density of fissionable material in typical storage arrays to separate neutron interactions that take place in the neutron's 'birth unit' from subsequent interactions in a dilute array. Numerous explicit Monte Carlo analyses show that array effects may be conservatively calculated by analyses that homogenize fissionable contents and depend only on the overall array shape, size, and reflective boundary

Criticality safety of low-density storage arrays

International Nuclear Information System (INIS)

Bauer, T.H.

1996-01-01

This paper proposes a straightforward bounding method for the criticality safety analysis of fissionable materials configured into large arrays of standard containers. While criticality-safe storage limits have been well established for single containers, even under flooded conditions, it is also necessary to rule out any potential for criticality arising from neutronic interactions among multiple containers that might build up over long distances in a large array. Traditionally, the array problem has been approached by individual Monte Carlo analyses of explicit arrangements of single units and their surroundings. Deemphasizing specific configurations, the present technique takes advantage of low average density of fissionable material in typical storage arrays to separate neutron interactions that take place in the neutron's open-quotes birth unitclose quotes from subsequent interactions in a dilute array. Numerous explicit Monte Carlo analyses show that array effects may be conservatively calculated by analyses that homogenize fissionable contents and depend only on the overall array shape, size, and reflective boundary

Adapting Controlled-source Coherence Analysis to Dense Array Data in Earthquake Seismology

Science.gov (United States)

Schwarz, B.; Sigloch, K.; Nissen-Meyer, T.

2017-12-01

Exploration seismology deals with highly coherent wave fields generated by repeatable controlled sources and recorded by dense receiver arrays, whose geometry is tailored to back-scattered energy normally neglected in earthquake seismology. Owing to these favorable conditions, stacking and coherence analysis are routinely employed to suppress incoherent noise and regularize the data, thereby strongly contributing to the success of subsequent processing steps, including migration for the imaging of back-scattering interfaces or waveform tomography for the inversion of velocity structure. Attempts have been made to utilize wave field coherence on the length scales of passive-source seismology, e.g. for the imaging of transition-zone discontinuities or the core-mantle-boundary using reflected precursors. Results are however often deteriorated due to the sparse station coverage and interference of faint back-scattered with transmitted phases. USArray sampled wave fields generated by earthquake sources at an unprecedented density and similar array deployments are ongoing or planned in Alaska, the Alps and Canada. This makes the local coherence of earthquake data an increasingly valuable resource to exploit.Building on the experience in controlled-source surveys, we aim to extend the well-established concept of beam-forming to the richer toolbox that is nowadays used in seismic exploration. We suggest adapted strategies for local data coherence analysis, where summation is performed with operators that extract the local slope and curvature of wave fronts emerging at the receiver array. Besides estimating wave front properties, we demonstrate that the inherent data summation can also be used to generate virtual station responses at intermediate locations where no actual deployment was performed. Owing to the fact that stacking acts as a directional filter, interfering coherent wave fields can be efficiently separated from each other by means of coherent subtraction. We

A 63 element 1.75 dimensional ultrasound phased array for the treatment of benign prostatic hyperplasia

Directory of Open Access Journals (Sweden)

Smith Nadine

2005-06-01

Full Text Available Abstract Background Prostate cancer and benign prostatic hyperplasia are very common diseases in older American men, thus having a reliable treatment modality for both diseases is of great importance. The currently used treating options, mainly surgical ones, have numerous complications, which include the many side effects that accompany such procedures, besides the invasive nature of such techniques. Focused ultrasound is a relatively new treating modality that is showing promising results in treating prostate cancer and benign prostatic hyperplasia. Thus this technique is gaining more attention in the past decade as a non-invasive method to treat both diseases. Methods In this paper, the design, construction and evaluation of a 1.75 dimensional ultrasound phased array to be used for treating prostate cancer and benign prostatic hyperplasia is presented. With this array, the position of the focus can be controlled by changing the electrical power and phase to the individual elements for electronically focusing and steering in a three dimensional volume. The array was designed with a maximum steering angle of ± 13.5° in the transverse direction and a maximum depth of penetration of 11 cm, which allows the treatment of large prostates. The transducer piezoelectric ceramic, matching layers and cable impedance have been designed for maximum power transfer to tissue. Results To verify the capability of the transducer for focusing and steering, exposimetry was performed and the results correlated well with the calculated field. Ex vivo experiments using bovine tissue were performed with various lesion sizes and indicated the capability of the transducer to ablate tissue using short sonications. Conclusion A 1.75 dimensional array, that overcame the drawbacks associated with one-dimensional arrays, has been designed, built and successfully tested. Design issues, such as cable and ceramic capacitances, were taken into account when designing this

Measuring levels of biogenic amines and their metabolites in rat brain tissue using high-performance liquid chromatography with photodiode array detection.

Science.gov (United States)

Gu, Min-Jung; Jeon, Ji-Hyun; Oh, Myung Sook; Hong, Seon-Pyo

2016-01-01

We developed a method to detect biogenic amines and their metabolites in rat brain tissue using simultaneous high-performance liquid chromatography and a photodiode array detection. Measurements were made using a Hypersil Gold C-18 column (250 × 2.1 mm, 5 µm). The mobile phase was 5 mM perchloric acid containing 5 % acetonitrile. The correlation coefficient was 0.9995-0.9999. LODs (S/N = 3) and LOQs (S/N = 10) were as follows: dopamine 0.4 and 1.3 pg, 3, 4-dihydroxyphenylacetic acid 8.4 and 28.0 pg, serotonin 0.4 and 1.3 pg, 5-hydroxyindolacetic acid 3.4 and 11.3 pg, and homovanillic acid 8.4 and 28.0 pg. This method does not require derivatization steps, and is more sensitive than the widely used HPLC-UV method.

Two-Stage MAS Technique for Analysis of DRA Elements and Arrays on Finite Ground Planes

DEFF Research Database (Denmark)

Larsen, Niels Vesterdal; Breinbjerg, Olav

2007-01-01

A two-stage Method of Auxiliary Sources (MAS) technique is proposed for analysis of dielectric resonator antenna (DRA) elements and arrays on finite ground planes (FGPs). The problem is solved by first analysing the DRA on an infinite ground plane (IGP) and then using this solution to model the FGP...

Criticality safety of low-density storage arrays

International Nuclear Information System (INIS)

Bauer, T.H.

1996-01-01

This note proposes a straightforward and simple method for the criticality safety analysis of fissionable materials configured into large arrays of standard containers. While criticality-safe storage limits have been well-established for standard containers--even under flooded conditions, it is also necessary to rule out the potential for criticality arising from neutronic interactions among multiple containers that might build up over long distances in a large array. Traditionally, the array problem has been approached by individual Monte Carlo analyses of explicit arrangements of single units and their surroundings. Here, the authors show how multiple Monte Carlo analyses can be usefully combined for wide-ranging general application. The technique takes advantage of low average density of fissionable material in typical storage arrays to separate neutron interactions that take place in the neutron's ''birth unit'' from subsequent interactions in a highly dilute array. Effects of array size, in particular, are conservatively calculated by straightforward analyses which simply smear array contents uniformly across the extent of the array. For given unit loadings in standard containers, practical expressions for neutron multiplication depend only on overall array shape, size and reflective boundary

Capillary electrophoresis - Mass spectrometry metabolomics analysis revealed enrichment of hypotaurine in rat glioma tissues.

Science.gov (United States)

Gao, Peng; Ji, Min; Fang, Xueyan; Liu, Yingyang; Yu, Zhigang; Cao, Yunfeng; Sun, Aijun; Zhao, Liang; Zhang, Yong

2017-11-15

Glioma is one of the most lethal brain malignancies with unknown etiologies. Many metabolomics analysis aiming at diverse kinds of samples had been performed. Due to the varied adopted analytical platforms, the reported disease-related metabolites were not consistent across different studies. Comparable metabolomics results are more likely to be acquired by analyzing the same sample types with identical analytical platform. For tumor researches, tissue samples metabolomics analysis own the unique advantage that it can gain more direct insight into disease-specific pathological molecules. In this light, a previous reported capillary electrophoresis - mass spectrometry human tissues metabolomics analysis method was employed to profile the metabolome of rat C6 cell implantation gliomas and the corresponding precancerous tissues. It was found that 9 metabolites increased in the glioma tissues. Of them, hypotaurine was the only metabolite that enriched in the malignant tissues as what had been reported in the relevant human tissues metabolomics analysis. Furthermore, hypotaurine was also proved to inhibit α-ketoglutarate-dependent dioxygenases (2-KDDs) through immunocytochemistry staining and in vitro enzymatic activity assays by using C6 cell cultures. This study reinforced the previous conclusion that hypotaurine acted as a competitive inhibitor of 2-KDDs and proved the value of metabolomics in oncology studies. Copyright © 2017. Published by Elsevier Inc.

Diagnostics of the BIOMASS feed array prototype

DEFF Research Database (Denmark)

Cappellin, Cecilia; Pivnenko, Sergey; Pontoppidan, Kennie Nybo

2013-01-01

The 3D reconstruction algorithm is applied to the prototype feed array of the BIOMASS synthetic aperture radar, recently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility in Denmark. Careful analysis of the measured feed array data has shown that the test support structure...

Induction and Analysis of Bronchus-Associated Lymphoid Tissue.

Science.gov (United States)

Fleige, Henrike; Förster, Reinhold

2017-01-01

Bronchus-associated lymphoid tissue (BALT) forms spontaneously in the lung after pulmonary infection and has been identified as a highly organized lymphoid structure supporting the efficient priming of T cells in the lung. To explore the mechanisms and instructive signals controlling BALT neogenesis we used both, a single dose of vaccinia virus MVA and repeated inhalations of heat-inactivated Pseudomonas aeruginosa (P. aeruginosa). Intranasal administration of both pathogens induces highly organized BALT but distinct pathways and molecules are used to promote the development of BALT. Here, we describe the induction and phenotype of the distinct types of BALT as well as the immunofluorescence microscopy-based analysis of the induced lymphoid tissue in the lung.

Soft tissue artifact in canine kinematic gait analysis

NARCIS (Netherlands)

Schwencke, M.; Smolders, L.A.; Bergknut, N.; Gustas, P.; Meij, B.P.; Hazewinkel, H.A.W.

2012-01-01

Vet Surg. 2012 Oct;41(7):829-37. doi: 10.1111/j.1532-950X.2012.01021.x. Soft tissue artifact in canine kinematic gait analysis. Schwencke M, Smolders LA, Bergknut N, Gustås P, Meij BP, Hazewinkel HA. Source Department of Clinical Sciences of Companion Animals,, Faculty of Veterinary Medicine,

Raman spectroscopic analysis of human skin tissue sections ex-vivo: evaluation of the effects of tissue processing and dewaxing

Science.gov (United States)

Ali, Syed M.; Bonnier, Franck; Tfayli, Ali; Lambkin, Helen; Flynn, Kathleen; McDonagh, Vincent; Healy, Claragh; Clive Lee, T.; Lyng, Fiona M.; Byrne, Hugh J.

2013-06-01

Raman spectroscopy coupled with K-means clustering analysis (KMCA) is employed to elucidate the biochemical structure of human skin tissue sections and the effects of tissue processing. Both hand and thigh sections of human cadavers were analyzed in their unprocessed and formalin-fixed, paraffin-processed (FFPP), and subsequently dewaxed forms. In unprocessed sections, KMCA reveals clear differentiation of the stratum corneum (SC), intermediate underlying epithelium, and dermal layers for sections from both anatomical sites. The SC is seen to be relatively rich in lipidic content; the spectrum of the subjacent layers is strongly influenced by the presence of melanin, while that of the dermis is dominated by the characteristics of collagen. For a given anatomical site, little difference in layer structure and biochemistry is observed between samples from different cadavers. However, the hand and thigh sections are consistently differentiated for all cadavers, largely based on lipidic profiles. In dewaxed FFPP samples, while the SC, intermediate, and dermal layers are clearly differentiated by KMCA of Raman maps of tissue sections, the lipidic contributions to the spectra are significantly reduced, with the result that respective skin layers from different anatomical sites become indistinguishable. While efficient at removing the fixing wax, the tissue processing also efficiently removes the structurally similar lipidic components of the skin layers. In studies of dermatological processes in which lipids play an important role, such as wound healing, dewaxed samples are therefore not appropriate. Removal of the lipids does however accentuate the spectral features of the cellular and protein components, which may be more appropriate for retrospective analysis of disease progression and biochemical analysis using tissue banks.

Ultrasound beam characteristics of a symmetric nodal origami based array

Science.gov (United States)

Bilgunde, Prathamesh N.; Bond, Leonard J.

2018-04-01

Origami-the ancient art of paper folding-is being explored in acoustics for effective focusing of sound. In this short communication, we present a numerical investigation of beam characteristics for an origami based ultrasound array. A spatial re-configuration of array elements is performed based upon the symmetric nodal origami. The effect of fold angle on the ultrasound beam is evaluated using frequency domain and transient finite element analysis. It was found that increase in the fold angle reduces near field length by 58% and also doubles the beam intensity as compared to the linear array. Transient analysis also indicated 80% reduction in the -6dB beam width, which can improve the lateral resolution of phased array. Such a spatially re-configurable array could potentially be used in the future to reduce the cost of electronics in the phased array instrumentation.

A Fusion Approach to Feature Extraction by Wavelet Decomposition and Principal Component Analysis in Transient Signal Processing of SAW Odor Sensor Array

Directory of Open Access Journals (Sweden)

Prashant SINGH

2011-03-01

Full Text Available This paper presents theoretical analysis of a new approach for development of surface acoustic wave (SAW sensor array based odor recognition system. The construction of sensor array employs a single polymer interface for selective sorption of odorant chemicals in vapor phase. The individual sensors are however coated with different thicknesses. The idea of sensor coating thickness variation is for terminating solvation and diffusion kinetics of vapors into polymer up to different stages of equilibration on different sensors. This is expected to generate diversity in information content of the sensors transient. The analysis is based on wavelet decomposition of transient signals. The single sensor transients have been used earlier for generating odor identity signatures based on wavelet approximation coefficients. In the present work, however, we exploit variability in diffusion kinetics due to polymer thicknesses for making odor signatures. This is done by fusion of the wavelet coefficients from different sensors in the array, and then applying the principal component analysis. We find that the present approach substantially enhances the vapor class separability in feature space. The validation is done by generating synthetic sensor array data based on well-established SAW sensor theory.

SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

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Davies Jonathan J

2006-12-01

Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Spatial cluster analysis of nanoscopically mapped serotonin receptors for classification of fixed brain tissue

Science.gov (United States)

Sams, Michael; Silye, Rene; Göhring, Janett; Muresan, Leila; Schilcher, Kurt; Jacak, Jaroslaw

2014-01-01

We present a cluster spatial analysis method using nanoscopic dSTORM images to determine changes in protein cluster distributions within brain tissue. Such methods are suitable to investigate human brain tissue and will help to achieve a deeper understanding of brain disease along with aiding drug development. Human brain tissue samples are usually treated postmortem via standard fixation protocols, which are established in clinical laboratories. Therefore, our localization microscopy-based method was adapted to characterize protein density and protein cluster localization in samples fixed using different protocols followed by common fluorescent immunohistochemistry techniques. The localization microscopy allows nanoscopic mapping of serotonin 5-HT1A receptor groups within a two-dimensional image of a brain tissue slice. These nanoscopically mapped proteins can be confined to clusters by applying the proposed statistical spatial analysis. Selected features of such clusters were subsequently used to characterize and classify the tissue. Samples were obtained from different types of patients, fixed with different preparation methods, and finally stored in a human tissue bank. To verify the proposed method, samples of a cryopreserved healthy brain have been compared with epitope-retrieved and paraffin-fixed tissues. Furthermore, samples of healthy brain tissues were compared with data obtained from patients suffering from mental illnesses (e.g., major depressive disorder). Our work demonstrates the applicability of localization microscopy and image analysis methods for comparison and classification of human brain tissues at a nanoscopic level. Furthermore, the presented workflow marks a unique technological advance in the characterization of protein distributions in brain tissue sections.

Robust immunohistochemical staining of several classes of proteins in tissues subjected to autolysis.

Science.gov (United States)

Maleszewski, Joseph; Lu, Jie; Fox-Talbot, Karen; Halushka, Marc K

2007-06-01

Despite the common use of immunohistochemistry in autopsy tissues, the stability of most proteins over extended time periods is unknown. The robustness of signal for 16 proteins (MMP1, MMP2, MMP3, MMP9, TIMP1, TIMP2, TIMP3, AGER, MSR, SCARB1, OLR1, CD36, LTF, LGALS3, LYZ, and DDOST) and two measures of advanced glycation end products (AGE, CML) was evaluated. Two formalin-fixed, paraffin-embedded human tissue arrays containing 16 tissues each were created to evaluate 48 hr of autolysis in a warm or cold environment. For these classes of proteins, matrix metalloproteinases and their inhibitors, scavenger receptors, and advanced glycation end product receptors, we saw no systematic diminution of signal intensity during a period of 24 hr. Analysis was performed by two independent observers and confirmed for a subset of proteins by digital analysis and Western blotting. We conclude that these classes of proteins degrade slowly and faithfully maintain their immunohistochemistry characteristics over at least a 24-hr time interval in devitalized tissues. This study supports the use of autopsy tissues with short postmortem intervals for immunohistochemical studies for diseases such as diabetic vascular disease, cancer, Alzheimer's disease, atherosclerosis, and other pathological states. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

Can intrinsic human tissue radiosensitivity be correlated with late responding gene RNA expression in white blood cells using a 96 gene micro-array?

International Nuclear Information System (INIS)

Schmidt, D.; Streeter, O.; Dagliyan, G.; Hill, C.K.; Williams-Hill, D.M.

2003-01-01

Radiation is widely used in the treatment of cancers. It is generally believed there is a sigmoid relationship between radiation dose and probability of cure. There is also a sigmoid relationship between radiation dose and normal tissue response. Generally total radiation dose to a tumor is limited by normal tissue tolerance. It has been postulated that up to 70% of inter-individual differences in radiosensitivity may be due to genetic predisposition (Tureson I. Et al, IJROBP, 1996;36:1065). However, to date, clinicians have no way of estimating or predicting an individual's normal tissue response to radiation exposure. Thus the prescribed dose cannot be tailored to an individuals actual expected response but is an empirically derived compromise based on experience. Although a number of studies using cellular techniques have shown that human cell radiosensitivity can be measured, none of these can be performed quick enough to be used in the clinic. In this study we are looking at gene expression that occurs some 24 hours after an exposure compared to expression before any exposure in peripheral white blood cells from patients undergoing radiotherapy for various tumors. The patients will be followed for overt radiation sensitivity by standard criteria by clinicians in the Department. The main aims are: does RNA expression level in a 96 gene micro-array vary before and after radiation and do these changes in RNA expression correlate with the objective measurements of acute radiation response observed by the clinicians in the patients. The USC IRB recently approved the protocol and human consent for this study to enter 50 patients in the next 12 months using mostly head and neck and endometrial cancer patients where we can get a normal tissue sample to examine as well as the blood sample. We will present the rationale, protocol, methods and early results in detail

Genetic analysis of presbycusis by arrayed primer extension.

Science.gov (United States)

Rodriguez-Paris, Juan; Ballay, Charles; Inserra, Michelle; Stidham, Katrina; Colen, Tahl; Roberson, Joseph; Gardner, Phyllis; Schrijver, Iris

2008-01-01

Using the Hereditary Hearing Loss arrayed primer extension (APEX) array, which contains 198 mutations across 8 hearing loss-associated genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5, 12S-rRNA, and tRNA Ser), we compared the frequency of sequence variants in 94 individuals with early presbycusis to 50 unaffected controls and aimed to identify possible genetic contributors. This cross-sectional study was performed at Stanford University with presbycusis samples from the California Ear Institute. The patients were between ages 20 and 65 yr, with adult-onset sensorineural hearing loss of unknown etiology, and carried a clinical diagnosis of early presbycusis. Exclusion criteria comprised known causes of hearing loss such as significant noise exposure, trauma, ototoxic medication, neoplasm, and congenital infection or syndrome, as well as congenital or pediatric onset. Sequence changes were identified in 11.7% and 10% of presbycusis and control alleles, respectively. Among the presbycusis group, these solely occurred within the GJB2 and SLC26A4 genes. Homozygous and compound heterozygous pathogenic mutations were exclusively seen in affected individuals. We were unable to detect a statistically significant difference between our control and affected populations regarding the frequency of sequence variants detected with the APEX array. Individuals who carry two mild mutations in the GJB2 gene possibly have an increased risk of developing early presbycusis.

Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues

International Nuclear Information System (INIS)

Cifola, Ingrid; Magni, Fulvio; Signorini, Stefano; Battaglia, Cristina; Perego, Roberto A; Bianchi, Cristina; Mangano, Eleonora; Bombelli, Silvia; Frascati, Fabio; Fasoli, Ester; Ferrero, Stefano; Di Stefano, Vitalba; Zipeto, Maria A

2011-01-01

Clear cell renal cell carcinoma (ccRCC) is characterized by recurrent copy number alterations (CNAs) and loss of heterozygosity (LOH), which may have potential diagnostic and prognostic applications. Here, we explored whether ccRCC primary cultures, established from surgical tumor specimens, maintain the DNA profile of parental tumor tissues allowing a more confident CNAs and LOH discrimination with respect to the original tissues. We established a collection of 9 phenotypically well-characterized ccRCC primary cell cultures. Using the Affymetrix SNP array technology, we performed the genome-wide copy number (CN) profiling of both cultures and corresponding tumor tissues. Global concordance for each culture/tissue pair was assayed evaluating the correlations between whole-genome CN profiles and SNP allelic calls. CN analysis was performed using the two CNAG v3.0 and Partek software, and comparing results returned by two different algorithms (Hidden Markov Model and Genomic Segmentation). A very good overlap between the CNAs of each culture and corresponding tissue was observed. The finding, reinforced by high whole-genome CN correlations and SNP call concordances, provided evidence that each culture was derived from its corresponding tissue and maintained the genomic alterations of parental tumor. In addition, primary culture DNA profile remained stable for at least 3 weeks, till to third passage. These cultures showed a greater cell homogeneity and enrichment in tumor component than original tissues, thus enabling a better discrimination of CNAs and LOH. Especially for hemizygous deletions, primary cultures presented more evident CN losses, typically accompanied by LOH; differently, in original tissues the intensity of these deletions was weaken by normal cell contamination and LOH calls were missed. ccRCC primary cultures are a reliable in vitro model, well-reproducing original tumor genetics and phenotype, potentially useful for future functional approaches

Focal plane array with modular pixel array components for scalability

Science.gov (United States)

Kay, Randolph R; Campbell, David V; Shinde, Subhash L; Rienstra, Jeffrey L; Serkland, Darwin K; Holmes, Michael L

2014-12-09

A modular, scalable focal plane array is provided as an array of integrated circuit dice, wherein each die includes a given amount of modular pixel array circuitry. The array of dice effectively multiplies the amount of modular pixel array circuitry to produce a larger pixel array without increasing die size. Desired pixel pitch across the enlarged pixel array is preserved by forming die stacks with each pixel array circuitry die stacked on a separate die that contains the corresponding signal processing circuitry. Techniques for die stack interconnections and die stack placement are implemented to ensure that the desired pixel pitch is preserved across the enlarged pixel array.

Analysis of seismic waves crossing the Santa Clara Valley using the three-component MUSIQUE array algorithm

Science.gov (United States)

Hobiger, Manuel; Cornou, Cécile; Bard, Pierre-Yves; Le Bihan, Nicolas; Imperatori, Walter

2016-10-01

We introduce the MUSIQUE algorithm and apply it to seismic wavefield recordings in California. The algorithm is designed to analyse seismic signals recorded by arrays of three-component seismic sensors. It is based on the MUSIC and the quaternion-MUSIC algorithms. In a first step, the MUSIC algorithm is applied in order to estimate the backazimuth and velocity of incident seismic waves and to discriminate between Love and possible Rayleigh waves. In a second step, the polarization parameters of possible Rayleigh waves are analysed using quaternion-MUSIC, distinguishing retrograde and prograde Rayleigh waves and determining their ellipticity. In this study, we apply the MUSIQUE algorithm to seismic wavefield recordings of the San Jose Dense Seismic Array. This array has been installed in 1999 in the Evergreen Basin, a sedimentary basin in the Eastern Santa Clara Valley. The analysis includes 22 regional earthquakes with epicentres between 40 and 600 km distant from the array and covering different backazimuths with respect to the array. The azimuthal distribution and the energy partition of the different surface wave types are analysed. Love waves dominate the wavefield for the vast majority of the events. For close events in the north, the wavefield is dominated by the first harmonic mode of Love waves, for farther events, the fundamental mode dominates. The energy distribution is different for earthquakes occurring northwest and southeast of the array. In both cases, the waves crossing the array are mostly arriving from the respective hemicycle. However, scattered Love waves arriving from the south can be seen for all earthquakes. Combining the information of all events, it is possible to retrieve the Love wave dispersion curves of the fundamental and the first harmonic mode. The particle motion of the fundamental mode of Rayleigh waves is retrograde and for the first harmonic mode, it is prograde. For both modes, we can also retrieve dispersion and ellipticity

Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae.

Science.gov (United States)

Göttert, Hendrikje; Mattiazzi Usaj, Mojca; Rosebrock, Adam P; Andrews, Brenda J

2018-01-01

Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains. We also present an alternative pipeline for the analysis of R-SGA output strains using flow cytometry of cells in liquid culture. Data normalization for both pipelines is discussed.

Timed arrays wideband and time varying antenna arrays

CERN Document Server

Haupt, Randy L

2015-01-01

Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

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

Directory of Open Access Journals (Sweden)

Xu Li

2016-09-01

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

Analysis of DNA methylation in various swine tissues.

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Chun Yang

Full Text Available DNA methylation is known to play an important role in regulating gene expression during biological development and tissue differentiation in eukaryotes. In this study, we used the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP method to assess the extent and pattern of cytosine methylation in muscle, heart, liver, spleen, lung, kidney and stomach from the swine strain Laiwu, and we also examined specific methylation patterns in the seven tissues. In total, 96,371 fragments, each representing a recognition site cleaved by either or both EcoRI + HpaII and EcoRI + MspI, the HpaII and MspI are isoschizomeric enzymes, were amplified using 16 pairs of selective primers. A total of 50,094 sites were found to be methylated at cytosines in seven tissues. The incidence of DNA methylation was approximately 53.99% in muscle, 51.24% in the heart, 50.18% in the liver, 53.31% in the spleen, 51.97% in the lung, 51.15% in the kidney and 53.39% in the stomach, as revealed by the incidence of differential digestion. Additionally, differences in DNA methylation levels imply that such variations may be related to specific gene expression during tissue differentiation, growth and development. Three types of bands were generated in the F-MSAP profile, the total numbers of these three types of bands in the seven tissues were 46,277, 24,801 and 25,293, respectively.In addition, different methylation patterns were observed in seven tissues from pig, and almost all of the methylation patterns detected by F-MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrated that the F-MSAP technique can be adapted for use in large-scale DNA methylation detection in the pig genome.

Breast tissue classification using x-ray scattering measurements and multivariate data analysis

Science.gov (United States)

Ryan, Elaine A.; Farquharson, Michael J.

2007-11-01

This study utilized two radiation scatter interactions in order to differentiate malignant from non-malignant breast tissue. These two interactions were Compton scatter, used to measure the electron density of the tissues, and coherent scatter to obtain a measure of structure. Measurements of these parameters were made using a laboratory experimental set-up comprising an x-ray tube and HPGe detector. The breast tissue samples investigated comprise five different tissue classifications: adipose, malignancy, fibroadenoma, normal fibrous tissue and tissue that had undergone fibrocystic change. The coherent scatter spectra were analysed using a peak fitting routine, and a technique involving multivariate analysis was used to combine the peak fitted scatter profile spectra and the electron density values into a tissue classification model. The number of variables used in the model was refined by finding the sensitivity and specificity of each model and concentrating on differentiating between two tissues at a time. The best model that was formulated had a sensitivity of 54% and a specificity of 100%.

Breast tissue classification using x-ray scattering measurements and multivariate data analysis

Energy Technology Data Exchange (ETDEWEB)

Ryan, Elaine A; Farquharson, Michael J [School of Allied Health Sciences, City University, Charterhouse Square, London EC1M 6PA (United Kingdom)

2007-11-21

This study utilized two radiation scatter interactions in order to differentiate malignant from non-malignant breast tissue. These two interactions were Compton scatter, used to measure the electron density of the tissues, and coherent scatter to obtain a measure of structure. Measurements of these parameters were made using a laboratory experimental set-up comprising an x-ray tube and HPGe detector. The breast tissue samples investigated comprise five different tissue classifications: adipose, malignancy, fibroadenoma, normal fibrous tissue and tissue that had undergone fibrocystic change. The coherent scatter spectra were analysed using a peak fitting routine, and a technique involving multivariate analysis was used to combine the peak fitted scatter profile spectra and the electron density values into a tissue classification model. The number of variables used in the model was refined by finding the sensitivity and specificity of each model and concentrating on differentiating between two tissues at a time. The best model that was formulated had a sensitivity of 54% and a specificity of 100%.

Analysis of growth and tissue replacement rates by stable sulfur isotope turnover.

Science.gov (United States)

Arneson, L. S.; Macko, S. A.; Macavoy, S. E.

2003-12-01

Stable isotope analysis has become a powerful tool to study animal ecology. Analysis of stable isotope ratios of elements such as carbon, nitrogen, sulfur, hydrogen, oxygen and others have been used to trace migratory routes, reconstruct dietary sources and determine the physiological condition of individual animals. The isotopes most commonly used are carbon, due to differential carbon fractionation in C3 and C4 plants, and nitrogen, due to the approximately 3% enrichment in 15N per trophic level. Although all cells express sulfur-containing compounds, such as cysteine, methionine, and coenzyme A, the turnover rate of sulfur in tissues has not been examined in most studies, owing to the difficulty in determining the δ 34S signature. In this study, we have assessed the rate of sulfur isotopic turnover in mouse tissues following a diet change from terrestrial (7%) to marine (19%) source. Turnover models reflecting both growth rate and metabolic tissue replacement will be developed for blood, liver, fat and muscle tissues.

Definition of pertinent parameters for the evaluation of articular cartilage repair tissue with high-resolution magnetic resonance imaging

International Nuclear Information System (INIS)

Marlovits, Stefan; Striessnig, Gabriele; Resinger, Christoph T.; Aldrian, Silke M.; Vecsei, Vilmos; Imhof, Herwig; Trattnig, Siegfried

2004-01-01

To evaluate articular cartilage repair tissue after biological cartilage repair, we propose a new technique of non-invasive, high-resolution magnetic resonance imaging (MRI) and define a new classification system. For the definition of pertinent variables the repair tissue of 45 patients treated with three different techniques for cartilage repair (microfracture, autologous osteochondral transplantation, and autologous chondrocyte transplantation) was analyzed 6 and 12 months after the procedure. High-resolution imaging was obtained with a surface phased array coil placed over the knee compartment of interest and adapted sequences were used on a 1 T MRI scanner. The analysis of the repair tissue included the definition and rating of nine pertinent variables: the degree of filling of the defect, the integration to the border zone, the description of the surface and structure, the signal intensity, the status of the subchondral lamina and subchondral bone, the appearance of adhesions and the presence of synovitis. High-resolution MRI, using a surface phased array coil and specific sequences, can be used on every standard 1 or 1.5 T MRI scanner according to the in-house standard protocols for knee imaging in patients who have had cartilage repair procedures without substantially prolonging the total imaging time. The new classification and grading system allows a subtle description and suitable assessment of the articular cartilage repair tissue

ArrayBridge: Interweaving declarative array processing with high-performance computing

Energy Technology Data Exchange (ETDEWEB)

Xing, Haoyuan [The Ohio State Univ., Columbus, OH (United States); Floratos, Sofoklis [The Ohio State Univ., Columbus, OH (United States); Blanas, Spyros [The Ohio State Univ., Columbus, OH (United States); Byna, Suren [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prabhat, Prabhat [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wu, Kesheng [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brown, Paul [Paradigm4, Inc., Waltham, MA (United States)

2017-05-04

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.

Angular photogrammetric analysis of the soft-tissue facial profile of Indian adults

Directory of Open Access Journals (Sweden)

K Saravana Pandian

2018-01-01

Full Text Available Introduction: Soft-tissue analysis has become an important component of orthodontic diagnosis and treatment planning. Photographic evaluation of an orthodontic patient is a very close representation of the appearance of the person. The previously established norms for soft-tissue analysis will vary for different ethnic groups. Thus, there is a need to develop soft-tissue facial profile norms pertaining to Indian ethnic groups. Aim and Objectives: The aim of this study is to establish the angular photogrammetric standards of soft-tissue facial profile for Indian males and females and also to compare sexual dimorphism present between them. Materials and Methods: The lateral profile photographs of 300 random participants (150 males and 150 females between ages 18 and 25 years were taken and analyzed using FACAD tracing software. Inclusion criteria were angles Class I molar occlusion with acceptable crowding and proclination, normal growth and development with well-aligned dental arches, and full complements of permanent teeth irrespective of third molar status. This study was conducted in Indian population, and samples were taken from various cities across India. Descriptive statistical analysis was carried out, and sexual dimorphism was evaluated by Student's t-test between males and females. Results: The results of the present study showed statistically significant (P < 0.05 gender difference in 5 parameters out of 12 parameters in Indian population. Conclusion: In the present study, soft-tissue facial measurements were established by means of photogrammetric analysis to facilitate orthodontists to carry out more quantitative evaluation and make disciplined decisions. The mean values obtained can be used for comparison with records of participants with the same characteristics by following this photogrammetric technique.

Tests of operating conditions for metrological application of HTS Josephson arrays

International Nuclear Information System (INIS)

Sosso, A; Lacquaniti, V; Andreone, D; Cerri, R; Klushin, A M

2006-01-01

We report on an experimental study of metrological properties of High Temperature Superconductor arrays, made of shunted bicrystal YBCO Josephson junctions, to assess their accuracy. A detailed analysis of measurement errors is presented, mainly based on a direct comparison of an HTS array against a low temperature array. Owing to the high sensitivity of the comparison, we were able to measure the changes in the HTS array voltage on a step at nanovolt level. A precise estimate of the dependence of the HTS array step width on operating conditions was obtained. Differences were observed with respect to the results provided by the usual, low sensitivity, techniques, confirming that the method we adopted is necessary in the study of HTS arrays for metrology. The high sensitivity analysis was applied in the derivation of the temperature dependence of the critical current as well, providing some insights on the behaviour of the HTS array

Analysis of feature stability for laser-based determination of tissue thickness

Science.gov (United States)

Ernst, Floris; Schweikard, Achim; Stüber, Patrick; Bruder, Ralf; Wagner, Benjamin; Wissel, Tobias

2015-03-01

Localisation of the cranium is necessary for accurate stereotactic radiotherapy of malign lesions in the brain. This is achieved by immobilizing the patient's head (typically by using thermoplastic masks, bite blocks or combinations thereof) and x-ray imaging to determine the actual position of the patient with respect to the treatment device. In previous work we have developed a novel method for marker-less and non-invasive tracking of the skull using a combination of laser-based surface triangulation and the analysis of backscattered feature patterns of a tightly collimated NIR laser beam scanned over the patient's forehead. An HDR camera is coupled into the beam path of the laser scanning system to acquire one image per projected laser point. We have demonstrated that this setup is capable of accurately determining the tissue thickness for each triangulation point and consequently allows detecting the surface of the cranial bone with sub-millimetre accuracy. Typical clinical settings (treatment times of 15-90 min) require feature stability over time, since the determination of tissue thickness is achieved by machine learning methods trained on initial feature scans. We have collected initial scans of the forehead as well as long-term backscatter data (20 images per seconds over 30 min) from five subjects and extracted the relevant tissue features from the image streams. Based on the knowledge of the relationship between the tissue feature values and the tissue thickness, the analysis of the long-term data showed that the noise level is low enough to allow robust discrimination of tissue thicknesses of 0.5 mm.

Developing 3D microstructures for tissue engineering

DEFF Research Database (Denmark)

Mohanty, Soumyaranjan

casting process to generate various large scale tissue engineering constructs with single pore geometry with the desired mechanical stiffness and porosity. In addition, a new technique was developed to fa bricate dual-pore scaffolds for various tissue-engineering applications where 3D printing...... materials have been developed and tested for enhancing the differentiation of hiPSC-derived hepatocytes and fabricating biodegradable scaffolds for in-vivo tissue engineering applications. Along with various scaffolds fabrication methods we finally presented an optimized study of hepatic differentiation...... of hiPSC-derived DE cells cultured for 25 days in a 3D perfusion bioreactor system with an array of 16 small-scale tissue-bioreactors with integrated dual-pore pore scaffolds and flow rates. Hepatic differentiation and functionality of hiPSC-derived hepatocytes were successfully assessed and compared...

Evaluation of phased array UT conditions using ultrasonic visualization technique

International Nuclear Information System (INIS)

Furukawa, Takashi; Komura, Ichirou

2008-01-01

Phased array provides many advantages over conventional ultrasonic testing method, but phased array has also limitations. This paper describes typical results of the experimental sound field analysis generated from the array probe. A photo-elastic ultrasonic visualization technique was applied in this study. The sound fields of shear wave generated from the array probe was equivalent to that from the fixed angle probe. (author)

Infrared spectroscopy with multivariate analysis to interrogate endometrial tissue: a novel and objective diagnostic approach.

Science.gov (United States)

Taylor, S E; Cheung, K T; Patel, I I; Trevisan, J; Stringfellow, H F; Ashton, K M; Wood, N J; Keating, P J; Martin-Hirsch, P L; Martin, F L

2011-03-01

Endometrial cancer is the most common gynaecological malignancy in the United Kingdom. Diagnosis currently involves subjective expert interpretation of highly processed tissue, primarily using microscopy. Previous work has shown that infrared (IR) spectroscopy can be used to distinguish between benign and malignant cells in a variety of tissue types. Tissue was obtained from 76 patients undergoing hysterectomy, 36 had endometrial cancer. Slivers of endometrial tissue (tumour and tumour-adjacent tissue if present) were dissected and placed in fixative solution. Before analysis, tissues were thinly sliced, washed, mounted on low-E slides and desiccated; 10 IR spectra were obtained per slice by attenuated total reflection Fourier-transform IR (ATR-FTIR) spectroscopy. Derived data was subjected to principal component analysis followed by linear discriminant analysis. Post-spectroscopy analyses, tissue sections were haematoxylin and eosin-stained to provide histological verification. Using this approach, it is possible to distinguish benign from malignant endometrial tissue, and various subtypes of both. Cluster vector plots of benign (verified post-spectroscopy to be free of identifiable pathology) vs malignant tissue indicate the importance of the lipid and secondary protein structure (Amide I and Amide II) regions of the spectrum. These findings point towards the possibility of a simple objective test for endometrial cancer using ATR-FTIR spectroscopy. This would facilitate earlier diagnosis and so reduce the morbidity and mortality associated with this disease.

MFDFA and Lacunarity Analysis of Synthetic Multifractals and Pre-Cancerous Tissues

Science.gov (United States)

Roy, A.; Das, N.; Ghosh, N.

2017-12-01

Multifractal Detrended Fluctuation Analysis (MFDFA) has been employed for evaluating complex variations in the refractive index (RI) of human pre-cancerous tissues. While this was primarily aimed towards the early diagnosis of cancer in the human cervix, question remains whether multifractal analysis alone can be conclusively used for distinguishing between various grades of pre-cancerous tissues. Lacunarity is a parameter that was developed for multiscale analysis of data and has been shown to be theoretically related to the correlation dimension, D2, by dlog(L)/dlog(x) = D2 - 2. Further, research has proven that not only can Lacunarity be used as a preliminary indicator of multifractal behavior but it also distinguishes between images with similar correlation dimension values. In order to compare the efficacy of the two approaches namely, MFDFA and Lacunarity, in distinguishing between pre-cancerous tissues of various grades, we test these techniques on a set of 2-dimensional theoretical random multifractal fields. MFDFA is employed for computing the width of the singularity spectrum f(α), which is a measure of multifractal behavior. A weighted mean of the log-transformed lacunarity values at different scales is employed for differentiating between patterns with the same correlation dimension but differences in texture. The two different techniques are then applied to images containing RI values of biopsy samples from human cervical tissues that were histo-pathologically characterized as grade-I and grade-II pre-cancerous cells. The results show that the two approaches are complementary to one another when it comes to multi-scale analysis of complex natural patterns manifested in the images of such pre-cancerous cells.

X ray photoelectron spectroscopy (XPS) analysis of Photosensitive ZrO2 array

Science.gov (United States)

Li, Y.; Zhao, G.; Zhu, R.; Kou, Z.

2018-03-01

Based on organic zirconium source as the starting material, by adding chemical modifiers which are made up with photosensitive ZrO2 sol. A uniformed ZrO2 array dot was fabricated with a mean diameter of around 800 nm. By using UV-vis spectra and X-ray photoelectron spectroscopy analysis method, studies the photosensitive ZrO2 gel film of photochemical reaction process and the photosensitive mechanism, to determine the zirconium atom centered chelate structure, reaction formed by metal chelate Zr atom for the center, and to establish the molecular model of the chelate. And studied the ultraviolet light in the process of the variation of the XPS spectra, Zr3d5/2 to 184.9 eV corresponding to the binding energy of the as the combination of state peak gradually reduce; By combining with the status of Zr-O peak gradually increase; The strength of the peak is gradually decline. This suggests that in the process of ultraviolet light photo chemical reaction happened. This study is of great significance to the micro fabrication of ZrO2 array not only to the memory devices but also to the optical devices.

Analysis of Correlation in MEMS Gyroscope Array and its Influence on Accuracy Improvement for the Combined Angular Rate Signal

Directory of Open Access Journals (Sweden)

Liang Xue

2018-01-01

Full Text Available Obtaining a correlation factor is a prerequisite for fusing multiple outputs of a mircoelectromechanical system (MEMS gyroscope array and evaluating accuracy improvement. In this paper, a mathematical statistics method is established to analyze and obtain the practical correlation factor of a MEMS gyroscope array, which solves the problem of determining the Kalman filter (KF covariance matrix Q and fusing the multiple gyroscope signals. The working principle and mathematical model of the sensor array fusion is briefly described, and then an optimal estimate of input rate signal is achieved by using of a steady-state KF gain in an off-line estimation approach. Both theoretical analysis and simulation show that the negative correlation factor has a favorable influence on accuracy improvement. Additionally, a four-gyro array system composed of four discrete individual gyroscopes was developed to test the correlation factor and its influence on KF accuracy improvement. The result showed that correlation factors have both positive and negative values; in particular, there exist differences for correlation factor between the different units in the array. The test results also indicated that the Angular Random Walk (ARW of 1.57°/h0.5 and bias drift of 224.2°/h for a single gyroscope were reduced to 0.33°/h0.5 and 47.8°/h with some negative correlation factors existing in the gyroscope array, making a noise reduction factor of about 4.7, which is higher than that of a uncorrelated four-gyro array. The overall accuracy of the combined angular rate signal can be further improved if the negative correlation factors in the gyroscope array become larger.

Value of amniocentesis versus fetal tissue for cytogenetic analysis in cases of fetal demise.

Science.gov (United States)

Bryant Borders, Ann E; Greenberg, Jessica; Plaga, Stacey; Shepard-Hinton, Megan; Yates, Carin; Elias, Sherman; Shulman, Lee P

2009-01-01

Use of fetal tissue for cytogenetic analysis in cases of second- and third-trimester fetal demise frequently results in unacceptably high failure rates. We reviewed our ongoing use of amniocentesis prior to uterine evacuation to determine if this provided a better source of cells for cytogenetic analysis. We compared cytogenetic results using fetal tissues obtained following uterine evacuation to our ongoing use of amniotic fluid cell obtained by transabdominal amniocentesis prior to uterine evacuation from 2003 to 2008. In 49 of the 63 cases evaluated by fetal tissue biopsies performed after uterine evacuation, a karyotypic analysis was obtained (77.8%). Among the 38 cases evaluated by amniocentesis, an amniotic fluid sample and fetal cytogenetic results were obtained in all 38 (100%) cases. Our findings indicate that amniocentesis is a more reliable source of cytogenetic information than fetal tissue in cases of second- and third-trimester fetal demise.

Soft tissue cephalometric analysis applied to Himachali ethnic population

Directory of Open Access Journals (Sweden)

Isha Aggarwal

2016-01-01

Full Text Available Introduction: The modern society considers facial attractiveness as an important physical attribute. The great variance in soft tissue drape of the human face complicates accurate assessment of the soft tissue profile, and it is a known fact that facial features of different ethnic groups differ significantly. This study was undertaken to establish norms for Himachali ethnic population. Materials and Methods: The sample comprised lateral cephalograms taken in natural head position of 100 normal individuals (50 males, 50 females. The cephalograms were analyzed by Arnett soft tissue cephalometric analysis for orthodontic diagnosis and treatment planning. Student's t-test was used to compare the means of the two groups. Results: Statistically significant differences were found between Himachali males and females in certain key parameters. Males have thicker soft tissue structures and a more acute nasolabial angle than females. Males have longer faces and females have greater interlabial gap and maxillary incisor exposure. Males have more deep-set facial structures than females. Conclusions: Statistically significant differences were found between Himachali males and females in certain key parameters. Differences were also noted between other ethnic groups and Himachali faces.

Thermal crosstalk in heated microcantilever arrays

International Nuclear Information System (INIS)

Kim, Hoe Joon; Dai, Zhenting; King, William P

2013-01-01

We report on a detailed characterization and analysis of thermal crosstalk in a heated microcantilever array. The fabricated heated cantilever array consists of five identical independently controlled heated cantilevers. The temperature of each cantilever can be controlled over a large temperature range, up to 900 °C, by means of an integrated solid-state resistive heater. We analyze thermal crosstalk in steady and transient operating conditions when the heated cantilever array is either in contact with a substrate or freely suspended in air. The thermal conductance between neighboring cantilevers is as high as 0.61 µW °C −1 , resulting in non-negligible temperature increases in neighboring cantilevers, depending upon the operating conditions. By understanding and accounting for thermal crosstalk, it is possible to improve temperature control and temperature measurements with heated microcantilever arrays. (paper)

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

Science.gov (United States)

1983-01-01

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

Improved Protein Arrays for Quantitative Systems Analysis of the Dynamics of Signaling Pathway Interactions

Energy Technology Data Exchange (ETDEWEB)

Yang, Chin-Rang [National Inst. of Health (NIH), Bethesda, MD (United States). National Heart, Lung and Blood Inst.

2013-12-11

Astronauts and workers in nuclear plants who repeatedly exposed to low doses of ionizing radiation (IR, <10 cGy) are likely to incur specific changes in signal transduction and gene expression in various tissues of their body. Remarkable advances in high throughput genomics and proteomics technologies enable researchers to broaden their focus from examining single gene/protein kinetics to better understanding global gene/protein expression profiling and biological pathway analyses, namely Systems Biology. An ultimate goal of systems biology is to develop dynamic mathematical models of interacting biological systems capable of simulating living systems in a computer. This Glue Grant is to complement Dr. Boothman’s existing DOE grant (No. DE-FG02-06ER64186) entitled “The IGF1/IGF-1R-MAPK-Secretory Clusterin (sCLU) Pathway: Mediator of a Low Dose IR-Inducible Bystander Effect” to develop sensitive and quantitative proteomic technology that suitable for low dose radiobiology researches. An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states for systems biology modeling is presented. The signals are amplified by a confocal laser Quantum dot scanner resulting in ~1000-fold more sensitivity than traditional Western blots and show the good linearity that is impossible for the signals of HRP-amplification. Therefore this improved protein array technology is suitable to detect weak responses of low dose radiation. Software is developed to facilitate the quantitative readout of signaling network activities. Kinetics of EGFRvIII mutant signaling was analyzed to quantify cross-talks between EGFR and other signaling pathways.

Proteomic analysis of tissue samples in translational breast cancer research

DEFF Research Database (Denmark)

Gromov, Pavel; Moreira, José; Gromova, Irina

2014-01-01

In the last decade, many proteomic technologies have been applied, with varying success, to the study of tissue samples of breast carcinoma for protein expression profiling in order to discover protein biomarkers/signatures suitable for: characterization and subtyping of tumors; early diagnosis...... the translation of basic discoveries into the daily breast cancer clinical practice. In particular, we address major issues in experimental design by reviewing the strengths and weaknesses of current proteomic strategies in the context of the analysis of human breast tissue specimens....

Circular Array of Magnetic Sensors for Current Measurement: Analysis for Error Caused by Position of Conductor.

Science.gov (United States)

Yu, Hao; Qian, Zheng; Liu, Huayi; Qu, Jiaqi

2018-02-14

This paper analyzes the measurement error, caused by the position of the current-carrying conductor, of a circular array of magnetic sensors for current measurement. The circular array of magnetic sensors is an effective approach for AC or DC non-contact measurement, as it is low-cost, light-weight, has a large linear range, wide bandwidth, and low noise. Especially, it has been claimed that such structure has excellent reduction ability for errors caused by the position of the current-carrying conductor, crosstalk current interference, shape of the conduction cross-section, and the Earth's magnetic field. However, the positions of the current-carrying conductor-including un-centeredness and un-perpendicularity-have not been analyzed in detail until now. In this paper, for the purpose of having minimum measurement error, a theoretical analysis has been proposed based on vector inner and exterior product. In the presented mathematical model of relative error, the un-center offset distance, the un-perpendicular angle, the radius of the circle, and the number of magnetic sensors are expressed in one equation. The comparison of the relative error caused by the position of the current-carrying conductor between four and eight sensors is conducted. Tunnel magnetoresistance (TMR) sensors are used in the experimental prototype to verify the mathematical model. The analysis results can be the reference to design the details of the circular array of magnetic sensors for current measurement in practical situations.

Tissue strands as "bioink" for scale-up organ printing.

Science.gov (United States)

Yu, Yin; Ozbolat, Ibrahim T

2014-01-01

Organ printing, takes tissue spheroids as building blocks together with additive manufacturing technique to engineer tissue or organ replacement parts. Although a wide array of cell aggregation techniques has been investigated, and gained noticeable success, the application of tissue spheroids for scale-up tissue fabrication is still worth investigation. In this paper, we introduce a new micro-fabrication technique to create tissue strands at the scale of 500-700μm as a "bioink" for future robotic tissue printing. Printable alginate micro-conduits are used as semi-permeable capsules for tissue strand fabrication. Mouse insulinoma beta TC3 cell tissue strands were formed upon 4 days post fabrication with reasonable mechanical strength, high cell viability close to 90%, and tissue specific markers expression. Fusion was readily observed between strands when placing them together as early as 24h. Also, tissue strands were deposited with human umbilical vein smooth muscle cells (HUVSMCs) vascular conduits together to fabricated miniature pancreatic tissue analog. Our study provided a novel technique using tissue strands as "bioink" for scale-up bioprinting of tissues or organs.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

Science.gov (United States)

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples.

Science.gov (United States)

Donczo, Boglarka; Szarka, Mate; Tovari, Jozsef; Ostoros, Gyorgyi; Csanky, Eszter; Guttman, Andras

2017-06-01

Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ctrl+Shift+Enter mastering Excel array formulas a book about building efficient formulas, advanced formulas, and array formulas for data analysis

CERN Document Server

Girvin, Mike

2013-01-01

Designed with Excel gurus in mind, this handbook outlines how to create formulas that can be used to solve everyday problems with a series of data values that standard Excel formulas cannot or would be too arduous to attempt. Beginning with an introduction to array formulas, this manual examines topics such as how they differ from ordinary formulas, the benefits and drawbacks of their use, functions that can and cannot handle array calculations, and array constants and functions. Among the practical applications surveyed include how to extract data from tables and unique lists, how to get resu

MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

Science.gov (United States)

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

2012-03-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.

Biophotofuel cell anode containing self-organized titanium dioxide nanotube array

Energy Technology Data Exchange (ETDEWEB)

Gan, Yong X., E-mail: yong.gan@utoledo.edu [Mechanical, Industrial and Manufacturing Engineering, College of Engineering, University of Toledo, 2801 W Bancroft Street, Toledo, OH 43606 (United States); Gan, Bo J. [Ottawa Hills High School, 2532 Evergreen Road, Toledo, OH 43606 (United States); Su Lusheng [Mechanical, Industrial and Manufacturing Engineering, College of Engineering, University of Toledo, 2801 W Bancroft Street, Toledo, OH 43606 (United States)

2011-09-15

Graphical abstract: Highlights: {center_dot} A photoactive anode containing highly ordered TiO{sub 2} nanotube array was made and the formation mechanism of self-organized TiO{sub 2} nanotube array on Ti was revealed. {center_dot} Effect of electrolyte concentration and voltage on the size distribution of the nanotubes was investigated. {center_dot} Self-organized TiO{sub 2} nanotube array anode possesses good photo-catalytic behavior of biomass decomposition under ultraviolet (UV) radiation. {center_dot} The fuel cell generates electricity and hydrogen via photoelectrochemical decomposition of ethanol, apple vinegar, sugar and tissue paper. - Abstract: We made a biophotofuel cell consisting of a titanium dioxide nanotube array photosensitive anode for biomass decomposition, and a low-hydrogen overpotential metal, Pt, as the cathode for hydrogen production. The titanium dioxide nanotubes (TiO{sub 2} NTs) were prepared via electrochemical oxidation of pure Ti in NaF solutions. Scanning electron microscopy was used to analyze the morphology of the nanotubes. The average diameter, wall thickness and length of the as-prepared TiO{sub 2} NTs were 88 {+-} 16 nm, 10 {+-} 2 nm and 491 {+-} 56 nm, respectively. Such dimensions are affected by the NaF concentration and the applied voltage during processing. Higher NaF concentrations result in the formation of longer and thicker nanotubes. The higher the voltage is, the thicker the nanotubes. The photosensitive anode made from the highly ordered TiO{sub 2} NTs has good photo-catalytic property, as can be seen from the test results of ethanol, apple vinegar, sugar and tissue paper decomposition under ultraviolet (UV) radiation. It is concluded that the biophotofuel cell with the TiO{sub 2} nanotube photoanode and a Pt cathode can generate electricity, hydrogen and clean water depending on the pH value and the oxygen presence in the solutions.

Performances of the UNDERground SEISmic array for the analysis of seismicity in Central Italy

Directory of Open Access Journals (Sweden)

R. Scarpa

2006-06-01

Full Text Available This paper presents the first results from the operation of a dense seismic array deployed in the underground Physics Laboratories at Gran Sasso (Central Italy. The array consists of 13 short-period, three-component seismometers with an aperture of about 550 m and average sensor spacing of 90 m. The reduced sensor spacing, joined to the spatially-white character of the background noise allows for quick and reliable detection of coherent wavefront arrivals even under very poor SNR conditions. We apply high-resolution frequency-slowness and polarization analyses to a set of 27 earthquakes recorded between November, 2002, and September, 2003, at epicentral distances spanning the 20-140 km interval. We locate these events using inversion of P- and S-wave backazimuths and S-P delay times, and compare the results with data from the Centralized National Seismic Network catalog. For the case of S-wave, the discrepancies among the two set of locations never exceed 10 km; the largest errors are instead observed for the case of P-waves. This observation may be due to the fact that the small array aperture does not allow for robust assessment of waves propagating at high apparent velocities. This information is discussed with special reference to the directions of future studies aimed at elucidating the location of seismogenetic structures in Central Italy from extended analysis of the micro-seismicity.

A Multimode Equivalent Network Approach for the Analysis of a 'Realistic' Finite Array of Open Ended Waveguides

NARCIS (Netherlands)

Neto, A.; Bolt, R.; Gerini, G.; Schmitt, D.

2003-01-01

In this contribution we present a theoretical model for the analysis of finite arrays of open-ended waveguides mounted on finite mounting platforms or having radome coverages. This model is based on a Multimode Equivalent Network (MEN) [1] representation of the radiating waveguides complete with

Suppression of 3D coherent noise by areal geophone array; Menteki jushinki array ni yoru sanjigen coherent noise no yokusei

Energy Technology Data Exchange (ETDEWEB)

Murayama, R; Nakagami, K; Tanaka, H [Japan National Oil Corp., Tokyo (Japan). Technology Research Center

1996-05-01

For improving the quality of data collected by reflection seismic exploration, a lattice was deployed at one point of a traverse line, and the data therefrom were used to study the 3D coherent noise suppression effect of the areal array. The test was conducted at a Japan National Oil Corporation test field in Kashiwazaki City, Niigata Prefecture. The deployed lattice had 144 vibration receiving points arrayed at intervals of 8m composing an areal array, and 187 vibration generating points arrayed at intervals of 20m extending over 6.5km. Data was collected at the vibration receiving points in the lattice, each point acting independently from the others, and processed for the composition of a large areal array, with the said data from plural vibration receiving points added up therein. As the result of analysis of the records covering the data collected at the receiving points in the lattice, it is noted that an enlarged areal array leads to a higher S/N ratio and that different reflection waves are emphasized when the array direction is changed. 1 ref., 6 figs.

Development and field practical performance of smart array probe

International Nuclear Information System (INIS)

Maeda, Kotaro; Shimone, Junri; Akagawa, Junichi; Nagata, Yasuyuki; Harada, Yutaka; Sera, Takehiko; Hirano, Shinro

2011-01-01

In 1999, NEL developed the transmit-receive type ECT array probe for steam generator (SG) tubing, called 'X-probe', in cooperation with foreign firms. Recently NEL has developed the advanced ECT array probe, 'Smart Array Probe', characterized with a significantly improved resolution for circumferential cracks. The doubled channels in the circumferential mode have greatly improved the circumferential resolution of Smart Array Probe. With all the circumferential mode channels on the same circle, there is no need for axial position correction of inspection data. This report describes both the field practical performance and the compliance assessment to a Japanese SG-ECT guideline 'JEAG4208' of Smart Array ECT System, composed of Smart Array Probe, pusher-in-tester 'OMNI-200', and NEL's ECT Analysis System. (author)

Application of cluster analysis and unsupervised learning to multivariate tissue characterization

International Nuclear Information System (INIS)

Momenan, R.; Insana, M.F.; Wagner, R.F.; Garra, B.S.; Loew, M.H.

1987-01-01

This paper describes a procedure for classifying tissue types from unlabeled acoustic measurements (data type unknown) using unsupervised cluster analysis. These techniques are being applied to unsupervised ultrasonic image segmentation and tissue characterization. The performance of a new clustering technique is measured and compared with supervised methods, such as a linear Bayes classifier. In these comparisons two objectives are sought: a) How well does the clustering method group the data?; b) Do the clusters correspond to known tissue classes? The first question is investigated by a measure of cluster similarity and dispersion. The second question involves a comparison with a supervised technique using labeled data

Physics of tissue harmonic imaging by ultrasound

Science.gov (United States)

Jing, Yuan

Tissue Harmonic Imaging (THI) is an imaging modality that is currently deployed on diagnostic ultrasound scanners. In THI the amplitude of the ultrasonic pulse that is used to probe the tissue is large enough that the pulse undergoes nonlinear distortion as it propagates into the tissue. One result of the distortion is that as the pulse propagates energy is shifted from the fundamental frequency of the source pulse into its higher harmonics. These harmonics will scatter off objects in the tissue and images formed from the scattered higher harmonics are considered to have superior quality to the images formed from the fundamental frequency. Processes that have been suggested as possibly responsible for the improved imaging in THI include: (1) reduced sensitivity to reverberation, (2) reduced sensitivity to aberration, and (3) reduction in side lobes. By using a combination of controlled experiments and numerical simulations, these three reasons have been investigated. A single element transducer and a clinical ultrasound scanner with a phased array transducer were used to image a commercial tissue-mimicking phantom with calibrated targets. The higher image quality achieved with THI was quantified in terms of spatial resolution and "clutter" signals. A three-dimensional model of the forward propagation of nonlinear sound beams in media with arbitrary spatial properties (a generalized KZK equation) was developed. A time-domain code for solving the KZK equation was validated with measurements of the acoustic field generated by the single element transducer and the phased array transducer. The code was used to investigate the impact of aberration using tissue-like media with three-dimensional variations in all acoustic properties. The three-dimensional maps of tissue properties were derived from the datasets available through the Visible Female project. The experiments and simulations demonstrated that second harmonic imaging (1) suffers less clutter associated with

Simulating the Sky as Seen by the Square Kilometer Array using the MIT Array Performance Simulator (MAPS)

Science.gov (United States)

Matthews, Lynn D.; Cappallo, R. J.; Doeleman, S. S.; Fish, V. L.; Lonsdale, C. J.; Oberoi, D.; Wayth, R. B.

2009-05-01

The Square Kilometer Array (SKA) is a proposed next-generation radio telescope that will operate at frequencies of 0.1-30 GHz and be 50-100 times more sensitive than existing radio arrays. Meeting the performance goals of this instrument will require innovative new hardware and software developments, a variety of which are now under consideration. Key to evaluating the performance characteristics of proposed SKA designs and testing the feasibility of new data calibration and processing algorithms is the ability to carry out realistic simulations of radio wavelength arrays under a variety of observing conditions. The MIT Array Performance Simulator (MAPS) (http://www.haystack.mit.edu/ast/arrays/maps/index.html) is an observations simulation package designed to achieve this goal. MAPS accepts an input source list or sky model and generates a model visibility set for a user-defined "virtual observatory'', incorporating such factors as array geometry, primary beam shape, field-of-view, and time and frequency resolution. Optionally, effects such as thermal noise, out-of-beam sources, variable station beams, and time/location-dependent ionospheric effects can be included. We will showcase current capabilities of MAPS for SKA applications by presenting results from an analysis of the effects of realistic sky backgrounds on the achievable image fidelity and dynamic range of SKA-like arrays comprising large numbers of small-diameter antennas.

Excitation-scanning hyperspectral imaging as a means to discriminate various tissues types

Science.gov (United States)

Deal, Joshua; Favreau, Peter F.; Lopez, Carmen; Lall, Malvika; Weber, David S.; Rich, Thomas C.; Leavesley, Silas J.

2017-02-01

Little is currently known about the fluorescence excitation spectra of disparate tissues and how these spectra change with pathological state. Current imaging diagnostic techniques have limited capacity to investigate fluorescence excitation spectral characteristics. This study utilized excitation-scanning hyperspectral imaging to perform a comprehensive assessment of fluorescence spectral signatures of various tissues. Immediately following tissue harvest, a custom inverted microscope (TE-2000, Nikon Instruments) with Xe arc lamp and thin film tunable filter array (VersaChrome, Semrock, Inc.) were used to acquire hyperspectral image data from each sample. Scans utilized excitation wavelengths from 340 nm to 550 nm in 5 nm increments. Hyperspectral images were analyzed with custom Matlab scripts including linear spectral unmixing (LSU), principal component analysis (PCA), and Gaussian mixture modeling (GMM). Spectra were examined for potential characteristic features such as consistent intensity peaks at specific wavelengths or intensity ratios among significant wavelengths. The resultant spectral features were conserved among tissues of similar molecular composition. Additionally, excitation spectra appear to be a mixture of pure endmembers with commonalities across tissues of varied molecular composition, potentially identifiable through GMM. These results suggest the presence of common autofluorescent molecules in most tissues and that excitationscanning hyperspectral imaging may serve as an approach for characterizing tissue composition as well as pathologic state. Future work will test the feasibility of excitation-scanning hyperspectral imaging as a contrast mode for discriminating normal and pathological tissues.

Null stream analysis of Pulsar Timing Array data: localisation of resolvable gravitational wave sources

Science.gov (United States)

Goldstein, Janna; Veitch, John; Sesana, Alberto; Vecchio, Alberto

2018-04-01

Super-massive black hole binaries are expected to produce a gravitational wave (GW) signal in the nano-Hertz frequency band which may be detected by pulsar timing arrays (PTAs) in the coming years. The signal is composed of both stochastic and individually resolvable components. Here we develop a generic Bayesian method for the analysis of resolvable sources based on the construction of `null-streams' which cancel the part of the signal held in common for each pulsar (the Earth-term). For an array of N pulsars there are N - 2 independent null-streams that cancel the GW signal from a particular sky location. This method is applied to the localisation of quasi-circular binaries undergoing adiabatic inspiral. We carry out a systematic investigation of the scaling of the localisation accuracy with signal strength and number of pulsars in the PTA. Additionally, we find that source sky localisation with the International PTA data release one is vastly superior than what is achieved by its constituent regional PTAs.

Fabrication of cell container arrays with overlaid surface topographies.

Science.gov (United States)

Truckenmüller, Roman; Giselbrecht, Stefan; Escalante-Marun, Maryana; Groenendijk, Max; Papenburg, Bernke; Rivron, Nicolas; Unadkat, Hemant; Saile, Volker; Subramaniam, Vinod; van den Berg, Albert; van Blitterswijk, Clemens; Wessling, Matthias; de Boer, Jan; Stamatialis, Dimitrios

2012-02-01

This paper presents cell culture substrates in the form of microcontainer arrays with overlaid surface topographies, and a technology for their fabrication. The new fabrication technology is based on microscale thermoforming of thin polymer films whose surfaces are topographically prepatterned on a micro- or nanoscale. For microthermoforming, we apply a new process on the basis of temporary back moulding of polymer films and use the novel concept of a perforated-sheet-like mould. Thermal micro- or nanoimprinting is applied for prepatterning. The novel cell container arrays are fabricated from polylactic acid (PLA) films. The thin-walled microcontainer structures have the shape of a spherical calotte merging into a hexagonal shape at their upper circumferential edges. In the arrays, the cell containers are arranged densely packed in honeycomb fashion. The inner surfaces of the highly curved container walls are provided with various topographical micro- and nanopatterns. For a first validation of the microcontainer arrays as in vitro cell culture substrates, C2C12 mouse premyoblasts are cultured in containers with microgrooved surfaces and shown to align along the grooves in the three-dimensional film substrates. In future stem-cell-biological and tissue engineering applications, microcontainers fabricated using the proposed technology may act as geometrically defined artificial microenvironments or niches.

Prevention of hyperglycemia in Zucker diabetic fatty rats by exercise training: effects on gene expression in insulin-sensitive tissues determined by high-density oligonucleotide microarray analysis

DEFF Research Database (Denmark)

Colombo, Michele; Gregersen, Soeren; Kruhoeffer, Mogens

2005-01-01

, blood samples, soleus muscle, liver, visceral fat (epididymal fat pads), and islet tissue were collected. Gene expression was quantified with Affymetrix RG-U34A array (16 chips). Exercise training ameliorates the development of hyperglycemia and reduces plasma free fatty acid and the level of glucagon...

Spatiotemporal norepinephrine mapping using a high-density CMOS microelectrode array.

Science.gov (United States)

Wydallis, John B; Feeny, Rachel M; Wilson, William; Kern, Tucker; Chen, Tom; Tobet, Stuart; Reynolds, Melissa M; Henry, Charles S

2015-10-21

A high-density amperometric electrode array containing 8192 individually addressable platinum working electrodes with an integrated potentiostat fabricated using Complementary Metal Oxide Semiconductor (CMOS) processes is reported. The array was designed to enable electrochemical imaging of chemical gradients with high spatiotemporal resolution. Electrodes are arranged over a 2 mm × 2 mm surface area into 64 subarrays consisting of 128 individual Pt working electrodes as well as Pt pseudo-reference and auxiliary electrodes. Amperometric measurements of norepinephrine in tissue culture media were used to demonstrate the ability of the array to measure concentration gradients in complex media. Poly(dimethylsiloxane) microfluidics were incorporated to control the chemical concentrations in time and space, and the electrochemical response at each electrode was monitored to generate electrochemical heat maps, demonstrating the array's imaging capabilities. A temporal resolution of 10 ms can be achieved by simultaneously monitoring a single subarray of 128 electrodes. The entire 2 mm × 2 mm area can be electrochemically imaged in 64 seconds by cycling through all subarrays at a rate of 1 Hz per subarray. Monitoring diffusional transport of norepinephrine is used to demonstrate the spatiotemporal resolution capabilities of the system.

Analytical Kinematics and Coupled Vibrations Analysis of Mechanical System Operated by Solar Array Drive Assembly

Science.gov (United States)

Sattar, M.; Wei, C.; Jalali, A.; Sattar, R.

2017-07-01

To address the impact of solar array (SA) anomalies and vibrations on performance of precision space-based operations, it is important to complete its accurate jitter analysis. This work provides mathematical modelling scheme to approximate kinematics and coupled micro disturbance dynamics of rigid load supported and operated by solar array drive assembly (SADA). SADA employed in analysis provides a step wave excitation torque to activate the system. Analytical investigations into kinematics is accomplished by using generalized linear and Euler angle coordinates, applying multi-body dynamics concepts and transformations principles. Theoretical model is extended, to develop equations of motion (EoM), through energy method (Lagrange equation). The main emphasis is to research coupled frequency response by determining energies dissipated and observing dynamic behaviour of internal vibratory systems of SADA. The disturbance model captures discrete active harmonics of SADA, natural modes and vibration amplifications caused by interactions between active harmonics and structural modes of mechanical assembly. The proposed methodology can help to predict true micro disturbance nature of SADA operating rigid load. Moreover, performance outputs may be compared against actual mission requirements to assess precise spacecraft controller design to meet next space generation stringent accuracy goals.

Improved SNR of phased-array PERES coils via simulation study

International Nuclear Information System (INIS)

RodrIguez, Alfredo O; Medina, LucIa

2005-01-01

A computational comparison of signal-to-noise ratio (SNR) was performed between a conventional phased array of two circular-shaped coils and a petal resonator surface array. The quasi-static model and phased-array optimum SNR were combined to derive an SNR formula for each array. Analysis of mutual inductance between coil petals was carried out to compute the optimal coil separation and optimum number of petal coils. Mutual interaction between coil arrays was not included in the model because this does not drastically affect coil performance. Phased arrays of PERES coils show a 114% improvement in SNR over that of the simplest circular configuration. (note)

Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

Directory of Open Access Journals (Sweden)

Daniel P Riordan

Full Text Available Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the

Array processing for seismic surface waves

Energy Technology Data Exchange (ETDEWEB)

Marano, S.

2013-07-01

This dissertation submitted to the Swiss Federal Institute of Technology ETH in Zurich takes a look at the analysis of surface wave properties which allows geophysicists to gain insight into the structure of the subsoil, thus avoiding more expensive invasive techniques such as borehole drilling. This thesis aims at improving signal processing techniques for the analysis of surface waves in various directions. One main contribution of this work is the development of a method for the analysis of seismic surface waves. The method also deals with the simultaneous presence of multiple waves. Several computational approaches to minimize costs are presented and compared. Finally, numerical experiments that verify the effectiveness of the proposed cost function and resulting array geometry designs are presented. These lead to greatly improved estimation performance in comparison to arbitrary array geometries.

Array processing for seismic surface waves

International Nuclear Information System (INIS)

Marano, S.

2013-01-01

This dissertation submitted to the Swiss Federal Institute of Technology ETH in Zurich takes a look at the analysis of surface wave properties which allows geophysicists to gain insight into the structure of the subsoil, thus avoiding more expensive invasive techniques such as borehole drilling. This thesis aims at improving signal processing techniques for the analysis of surface waves in various directions. One main contribution of this work is the development of a method for the analysis of seismic surface waves. The method also deals with the simultaneous presence of multiple waves. Several computational approaches to minimize costs are presented and compared. Finally, numerical experiments that verify the effectiveness of the proposed cost function and resulting array geometry designs are presented. These lead to greatly improved estimation performance in comparison to arbitrary array geometries

Determination of trace elements in human brain tissues using neutron activation analysis

International Nuclear Information System (INIS)

Leite, R.E.P.; Jacob-Filho, W.; Grinberg, L.T.; Ferretti, R.E.L.

2008-01-01

Neutron activation analysis was applied to assess trace element concentrations in brain tissues from normal (n = 21) and demented individuals (n = 21) of both genders aged more than 50 years. Concentrations of the elements Br, Fe, K, Na, Rb, Se and Zn were determined. Comparisons were made between the results obtained for the hippocampus and frontal cortex tissues, as well as, those obtained in brains of normal and demented individuals. Certified reference materials, NIST 1566b Oyster Tissue and NIST 1577b Bovine Liver were analyzed for quality of the analytical results. (author)

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Directory of Open Access Journals (Sweden)

Krasnogor Natalio

2009-10-01

Full Text Available Abstract Background Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

Batch fabrication of disposable screen printed SERS arrays.

Science.gov (United States)

Qu, Lu-Lu; Li, Da-Wei; Xue, Jin-Qun; Zhai, Wen-Lei; Fossey, John S; Long, Yi-Tao

2012-03-07

A novel facile method of fabricating disposable and highly reproducible surface-enhanced Raman spectroscopy (SERS) arrays using screen printing was explored. The screen printing ink containing silver nanoparticles was prepared and printed on supporting materials by a screen printing process to fabricate SERS arrays (6 × 10 printed spots) in large batches. The fabrication conditions, SERS performance and application of these arrays were systematically investigated, and a detection limit of 1.6 × 10(-13) M for rhodamine 6G could be achieved. Moreover, the screen printed SERS arrays exhibited high reproducibility and stability, the spot-to-spot SERS signals showed that the intensity variation was less than 10% and SERS performance could be maintained over 12 weeks. Portable high-throughput analysis of biological samples was accomplished using these disposable screen printed SERS arrays.

Heat-rejection design for large concentrating solar arrays

Science.gov (United States)

French, E. P.

1980-01-01

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

Array Detector Modules for Spent Fuel Verification

Energy Technology Data Exchange (ETDEWEB)

Bolotnikov, Aleksey

2018-05-07

Brookhaven National Laboratory (BNL) proposes to evaluate the arrays of position-sensitive virtual Frisch-grid (VFG) detectors for passive gamma-ray emission tomography (ET) to verify the spent fuel in storage casks before storing them in geo-repositories. Our primary objective is to conduct a preliminary analysis of the arrays capabilities and to perform field measurements to validate the effectiveness of the proposed array modules. The outcome of this proposal will consist of baseline designs for the future ET system which can ultimately be used together with neutrons detectors. This will demonstrate the usage of this technology in spent fuel storage casks.

Development and Evaluation of Micro-Electrocorticography Arrays for Neural Interfacing Applications

Science.gov (United States)

Schendel, Amelia Ann

Neural interfaces have great promise for both electrophysiological research and therapeutic applications. Whether for the study of neural circuitry or for neural prosthetic or other therapeutic applications, micro-electrocorticography (micro-ECoG) arrays have proven extremely useful as neural interfacing devices. These devices strike a balance between invasiveness and signal resolution, an important step towards eventual human application. The objective of this research was to make design improvements to micro-ECoG devices to enhance both biocompatibility and device functionality. To best evaluate the effectiveness of these improvements, a cranial window imaging method for in vivo monitoring of the longitudinal tissue response post device implant was developed. Employment of this method provided valuable insight into the way tissue grows around micro-ECoG arrays after epidural implantation, spurring a study of the effects of substrate geometry on the meningeal tissue response. The results of the substrate footprint comparison suggest that a more open substrate geometry provides an easy path for the tissue to grow around to the top side of the device, whereas a solid device substrate encourages the tissue to thicken beneath the device, between the electrode sites and the brain. The formation of thick scar tissue between the recording electrode sites and the neural tissue is disadvantageous for long-term recorded signal quality, and thus future micro-ECoG device designs should incorporate open-architecture substrates for enhanced longitudinal in vivo function. In addition to investigating improvements for long-term device reliability, it was also desired to enhance the functionality of micro-ECoG devices for neural electrophysiology research applications. To achieve this goal, a completely transparent graphene-based device was fabricated for use with the cranial window imaging method and optogenetic techniques. The use of graphene as the conductive material provided

Comparison of diagnostic efficacy between CLE, tissue sampling, and CLE combined with tissue sampling for undetermined pancreaticobiliary strictures: a meta-analysis.

Science.gov (United States)

Gao, Ya-Dong; Qu, Ya-Wei; Liu, Hai-Feng

2018-04-01

The accurate diagnosis of undetermined pancreaticobiliary strictures remains challenging. Current ERCP-guided tissue sampling methods are of low sensitivity. Confocal laser endomicroscopy (CLE) is a new procedure and allows real optical biopsies that may improve the diagnosis of undetermined pancreaticobiliary strictures. The aim of this meta-analysis was to determine the diagnostic yield of CLE, tissue sampling, and CLE combined with tissue sampling for undetermined pancreaticobiliary strictures. Pubmed, Embase, and the Cochrane Library database were reviewed for relevant studies. Pooled estimates of sensitivity and specificity with 95% confidence intervals (CIs) were calculated using the random-effects meta-analysis model. The summary receiver-operating characteristic (SROC) curve was constructed, and the area under the receiver operating characteristic curve (AUC) was calculated. Twelve studies involving 591 patients were enrolled in our analysis. The overall sensitivity and the specificity estimate of CLE for discriminating benign and malignant pancreaticobiliary strictures were 87% (95%CI, 83-91%) and 76% (95%CI, 70-81%), respectively. The AUC to assess the diagnostic efficacy was 0.8705. For tissue sampling, the overall sensitivity and the specificity estimate were 64% (95%CI, 57-70%) and 94% (95%CI, 90-97%), respectively. The AUC to assess the diagnostic efficacy was 0.8040. A combination of both methods increased the sensitivity (93%; 95%CI, 88-96%) with a specificity of 82% (95%CI, 74-89%). The AUC to assess the diagnostic efficacy was 0.9377. There was no publication bias by Deeks' Funnel Plot with p = .936. Compared with tissue sampling, CLE may increase the sensitivity for the diagnosis of malignant pancreaticobiliary strictures. A combination of both can effectively diagnose malignant pancreaticobiliary strictures.

Hyperspectral Imaging and SPA-LDA Quantitative Analysis for Detection of Colon Cancer Tissue

Science.gov (United States)

Yuan, X.; Zhang, D.; Wang, Ch.; Dai, B.; Zhao, M.; Li, B.

2018-05-01

Hyperspectral imaging (HSI) has been demonstrated to provide a rapid, precise, and noninvasive method for cancer detection. However, because HSI contains many data, quantitative analysis is often necessary to distill information useful for distinguishing cancerous from normal tissue. To demonstrate that HSI with our proposed algorithm can make this distinction, we built a Vis-NIR HSI setup and made many spectral images of colon tissues, and then used a successive projection algorithm (SPA) to analyze the hyperspectral image data of the tissues. This was used to build an identification model based on linear discrimination analysis (LDA) using the relative reflectance values of the effective wavelengths. Other tissues were used as a prediction set to verify the reliability of the identification model. The results suggest that Vis-NIR hyperspectral images, together with the spectroscopic classification method, provide a new approach for reliable and safe diagnosis of colon cancer and could lead to advances in cancer diagnosis generally.

High throughput assessment of cells and tissues: Bayesian classification of spectral metrics from infrared vibrational spectroscopic imaging data.

Science.gov (United States)

Bhargava, Rohit; Fernandez, Daniel C; Hewitt, Stephen M; Levin, Ira W

2006-07-01

Vibrational spectroscopy allows a visualization of tissue constituents based on intrinsic chemical composition and provides a potential route to obtaining diagnostic markers of diseases. Characterizations utilizing infrared vibrational spectroscopy, in particular, are conventionally low throughput in data acquisition, generally lacking in spatial resolution with the resulting data requiring intensive numerical computations to extract information. These factors impair the ability of infrared spectroscopic measurements to represent accurately the spatial heterogeneity in tissue, to incorporate robustly the diversity introduced by patient cohorts or preparative artifacts and to validate developed protocols in large population studies. In this manuscript, we demonstrate a combination of Fourier transform infrared (FTIR) spectroscopic imaging, tissue microarrays (TMAs) and fast numerical analysis as a paradigm for the rapid analysis, development and validation of high throughput spectroscopic characterization protocols. We provide an extended description of the data treatment algorithm and a discussion of various factors that may influence decision-making using this approach. Finally, a number of prostate tissue biopsies, arranged in an array modality, are employed to examine the efficacy of this approach in histologic recognition of epithelial cell polarization in patients displaying a variety of normal, malignant and hyperplastic conditions. An index of epithelial cell polarization, derived from a combined spectral and morphological analysis, is determined to be a potentially useful diagnostic marker.

Analysis and Optimization of a Novel 2-D Magnet Array with Gaps and Staggers for a Moving-Magnet Planar Motor

Science.gov (United States)

Chen, Xuedong; Zeng, Lizhan

2018-01-01

This paper presents a novel 2-D magnet array with gaps and staggers, which is especially suitable for magnetically levitated planar motor with moving magnets. The magnetic flux density distribution is derived by Fourier analysis and superposition. The influences of gaps and staggers on high-order harmonics and flux density were analyzed, and the optimized design is presented. Compared with the other improved structures based on traditional Halbach magnet arrays, the proposed design has the lowest high-order harmonics percentage, and the characteristics of flux density meet the demand of high acceleration in horizontal directions. It is also lightweight and easy to manufacture. The proposed magnet array was built, and the calculation results have been verified with experiment. PMID:29300323

An Error Analysis of Structured Light Scanning of Biological Tissue

DEFF Research Database (Denmark)

Jensen, Sebastian Hoppe Nesgaard; Wilm, Jakob; Aanæs, Henrik

2017-01-01

This paper presents an error analysis and correction model for four structured light methods applied to three common types of biological tissue; skin, fat and muscle. Despite its many advantages, structured light is based on the assumption of direct reflection at the object surface only......, statistical linear model based on the scan geometry. As such, scans can be corrected without introducing any specially designed pattern strategy or hardware. We can effectively reduce the error in a structured light scanner applied to biological tissue by as much as factor of two or three........ This assumption is violated by most biological material e.g. human skin, which exhibits subsurface scattering. In this study, we find that in general, structured light scans of biological tissue deviate significantly from the ground truth. We show that a large portion of this error can be predicted with a simple...

Analysis of 3-D effects in segmented cylindrical quasi-Halbach magnet arrays

NARCIS (Netherlands)

Meessen, K.J.; Paulides, J.J.H.; Lomonova, E.

2011-01-01

To improve the performance of permanent magnet (PM) machines, quasi-Halbach PM arrays are used to increase the magnetic loading in these machines. In tubular PM actuators, these arrays are often approximated using segmented magnets resulting in a 3-D magnetic field effect. This paper describes the

Intracavitary ultrasound phased arrays for prostate thermal therapies: MRI compatibility and in vivo testing.

Science.gov (United States)

Hutchinson, E B; Hynynen, K

1998-12-01

A 62 element MRI-compatible linear phased array was designed and constructed to investigate the feasibility of using transrectal ultrasound for the thermal therapeutic treatment of prostate cancer and benign prostatic hyperplasia. An aperiodic design technique developed in a previous study was used in the design of this array, which resulted in reduced grating lobe levels by using an optimized random distribution of unequally sized elements. The element sizes used in this array were selected to be favorable for both grating lobe levels as determined by array aperiodicity and array efficiency as determined by width to thickness ratios. The heating capabilities and MRI compatibility of the array were tested with in vivo rabbit thigh muscle heating experiments using MRI temperature monitoring. The array produced therapeutic temperature elevations in vivo at depths of 3-6 cm and axial locations up to 3 cm off the central axis and increased the size of the heated volume with electronic scanning of a single focus. The ability of this array to be used for ultrasound surgery was demonstrated by creating necrosed tissue lesions in vivo using short high-power sonications. The ability of the array to be used for hyperthermia was demonstrated by inducing therapeutic temperature elevations for longer exposures. Based on the acoustic and heating performance of this array, it has the potential to be clinically useful for delivering thermal therapies to the prostate and other target volumes close to body cavities.

Micro-hole array fluorescent sensor based on AC-Dielectrophoresis (DEP) for simultaneous analysis of nano-molecules

Science.gov (United States)

Kim, Hye Jin; Kang, Dong-Hoon; Lee, Eunji; Hwang, Kyo Seon; Shin, Hyun-Joon; Kim, Jinsik

2018-02-01

We propose a simple fluorescent bio-chip based on two types of alternative current-dielectrophoretic (AC-DEP) force, attractive (positive DEP) and repulsive (negative DEP) force, for simultaneous nano-molecules analysis. Various radius of micro-holes on the bio-chip are designed to apply the different AC-DEP forces, and the nano-molecules are concentrated inside the micro-hole arrays according to the intensity of the DEP force. The bio-chip was fabricated by Micro Electro Mechanical system (MEMS) technique, and was composed of two layers; a SiO2 layer and Ta/Pt layer were accomplished for an insulation layer and a top electrode with micro-hole arrays to apply electric fields for DEP force, respectively. Each SiO2 and Ta/Pt layers were deposited by thermal oxidation and sputtering, and micro-hole arrays were fabricated with Inductively Coupled Plasma (ICP) etching process. For generation of each positive and negative DEP at micro-holes, we applied two types of sine-wave AC voltage with different frequency range alternately. The intensity of the DEP force was controlled by the radius of the micro-hole and size of nano-molecule, and calculated with COMSOL multi-physics. Three types of nano-molecules labelled with different fluorescent dye were used and the intensity of nano-molecules was examined by the fluorescent optical analysis after applying the DEP force. By analyzing the fluorescent intensities of the nano-molecules, we verify the various nano-molecules in analyte are located successfully inside corresponding micro-holes with different radius according to their size.

Micro-arrayed human embryonic stem cells-derived cardiomyocytes for in vitro functional assay.

Directory of Open Access Journals (Sweden)

Elena Serena

Full Text Available INTRODUCTION: The heart is one of the least regenerative organs in the body and any major insult can result in a significant loss of heart cells. The development of an in vitro-based cardiac tissue could be of paramount importance for many aspects of the cardiology research. In this context, we developed an in vitro assay based on human cardiomyocytes (hCMs and ad hoc micro-technologies, suitable for several applications: from pharmacological analysis to physio-phatological studies on transplantable hCMs. We focused on the development of an assay able to analyze not only hCMs viability, but also their functionality. METHODS: hCMs were cultured onto a poly-acrylamide hydrogel with tunable tissue-like mechanical properties and organized through micropatterning in a 20×20 array. Arrayed hCMs were characterized by immunofluorescence, GAP-FRAP analyses and live and dead assay. Their functionality was evaluated monitoring the excitation-contraction coupling. RESULTS: Micropatterned hCMs maintained the expression of the major cardiac markers (cTnT, cTnI, Cx43, Nkx2.5, α-actinin and functional properties. The spontaneous contraction frequency was (0.83±0.2 Hz, while exogenous electrical stimulation lead to an increase up to 2 Hz. As proof of concept that our device can be used for screening the effects of pathological conditions, hCMs were exposed to increasing levels of H(2O(2. Remarkably, hCMs viability was not compromised with exposure to 0.1 mM H(2O(2, but hCMs contractility was dramatically suppressed. As proof of concept, we also developed a microfluidic platform to selectively treat areas of the cell array, in the perspective of performing multi-parametric assay. CONCLUSIONS: Such system could be a useful tool for testing the effects of multiple conditions on an in vitro cell model representative of human heart physiology, thus potentially helping the processes of therapy and drug development.

Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues.

Science.gov (United States)

Cifola, Ingrid; Bianchi, Cristina; Mangano, Eleonora; Bombelli, Silvia; Frascati, Fabio; Fasoli, Ester; Ferrero, Stefano; Di Stefano, Vitalba; Zipeto, Maria A; Magni, Fulvio; Signorini, Stefano; Battaglia, Cristina; Perego, Roberto A

2011-06-13

Clear cell renal cell carcinoma (ccRCC) is characterized by recurrent copy number alterations (CNAs) and loss of heterozygosity (LOH), which may have potential diagnostic and prognostic applications. Here, we explored whether ccRCC primary cultures, established from surgical tumor specimens, maintain the DNA profile of parental tumor tissues allowing a more confident CNAs and LOH discrimination with respect to the original tissues. We established a collection of 9 phenotypically well-characterized ccRCC primary cell cultures. Using the Affymetrix SNP array technology, we performed the genome-wide copy number (CN) profiling of both cultures and corresponding tumor tissues. Global concordance for each culture/tissue pair was assayed evaluating the correlations between whole-genome CN profiles and SNP allelic calls. CN analysis was performed using the two CNAG v3.0 and Partek software, and comparing results returned by two different algorithms (Hidden Markov Model and Genomic Segmentation). A very good overlap between the CNAs of each culture and corresponding tissue was observed. The finding, reinforced by high whole-genome CN correlations and SNP call concordances, provided evidence that each culture was derived from its corresponding tissue and maintained the genomic alterations of parental tumor. In addition, primary culture DNA profile remained stable for at least 3 weeks, till to third passage. These cultures showed a greater cell homogeneity and enrichment in tumor component than original tissues, thus enabling a better discrimination of CNAs and LOH. Especially for hemizygous deletions, primary cultures presented more evident CN losses, typically accompanied by LOH; differently, in original tissues the intensity of these deletions was weaken by normal cell contamination and LOH calls were missed. ccRCC primary cultures are a reliable in vitro model, well-reproducing original tumor genetics and phenotype, potentially useful for future functional approaches

Application of neural networks to digital pulse shape analysis for an array of silicon strip detectors

Energy Technology Data Exchange (ETDEWEB)

Flores, J.L. [Dpto de Ingeniería Eléctrica y Térmica, Universidad de Huelva (Spain); Martel, I. [Dpto de Física Aplicada, Universidad de Huelva (Spain); CERN, ISOLDE, CH 1211 Geneva, 23 (Switzerland); Jiménez, R. [Dpto de Ingeniería Electrónica, Sist. Informáticos y Automática, Universidad de Huelva (Spain); Galán, J., E-mail: jgalan@diesia.uhu.es [Dpto de Ingeniería Electrónica, Sist. Informáticos y Automática, Universidad de Huelva (Spain); Salmerón, P. [Dpto de Ingeniería Eléctrica y Térmica, Universidad de Huelva (Spain)

2016-09-11

The new generation of nuclear physics detectors that used to study nuclear reactions is considering the use of digital pulse shape analysis techniques (DPSA) to obtain the (A,Z) values of the reaction products impinging in solid state detectors. This technique can be an important tool for selecting the relevant reaction channels at the HYDE (HYbrid DEtector ball array) silicon array foreseen for the Low Energy Branch of the FAIR facility (Darmstadt, Germany). In this work we study the feasibility of using artificial neural networks (ANNs) for particle identification with silicon detectors. Multilayer Perceptron networks were trained and tested with recent experimental data, showing excellent identification capabilities with signals of several isotopes ranging from {sup 12}C up to {sup 84}Kr, yielding higher discrimination rates than any other previously reported.

Tissue Harmonic Synthetic Aperture Ultrasound Imaging

DEFF Research Database (Denmark)

Hemmsen, Martin Christian; Rasmussen, Joachim; Jensen, Jørgen Arendt

2014-01-01

Synthetic aperture sequential beamforming (SASB) and tissue har- monic imaging (THI) are combined to improve the image quality of medical ultrasound imaging. The technique is evaluated in a compar- ative study against dynamic receive focusing (DRF). The objective is to investigate if SASB combined...... with THI improves the image qual- ity compared to DRF-THI. The major benet of SASB is a reduced bandwidth between the probe and processing unit. A BK Medical 2202 Ultraview ultrasound scanner was used to acquire beamformed RF data for oine evaluation. The acquisition was made interleaved between methods......, and data were recorded with and without pulse inversion for tissue harmonic imaging. Data were acquired using a Sound Technol- ogy 192 element convex array transducer from both a wire phantom and a tissue mimicking phantom to investigate spatial resolution and pen- etration. In-vivo scans were also...

Power balance and loss mechanism analysis in RF transmit coil arrays.

Science.gov (United States)

Kuehne, Andre; Goluch, Sigrun; Waxmann, Patrick; Seifert, Frank; Ittermann, Bernd; Moser, Ewald; Laistler, Elmar

2015-10-01

To establish a framework for transmit array power balance calculations based on power correlation matrices to accurately quantify the loss contributions from different mechanisms such as coupling, lumped components, and radiation. Starting from Poynting's theorem, power correlation matrices are derived for all terms in the power balance, which is formulated as a matrix equation. Finite-difference time-domain simulations of two 7 T eight-channel head array coils at 297.2 MHz are used to verify the theoretical considerations and demonstrate their application. Care is taken to accurately incorporate all loss mechanisms. The power balance for static B1 phase shims as well as two-dimensional spatially selective transmit SENSE pulses is shown. The simulated power balance shows an excellent agreement with theory, with a maximum power imbalance of less than 0.11%. Power loss contributions from the different loss mechanisms vary significantly between the investigated setups, and depending on the excitation mode imposed on the coil. The presented approach enables a straightforward loss evaluation for an arbitrary excitation of transmit coil arrays. Worst-case power imbalance and losses are calculated in a straightforward manner. This allows for deeper insight into transmit array loss mechanisms, incorporation of radiated power components in specific absorption rate calculations and verification of electromagnetic simulations. © 2014 Wiley Periodicals, Inc.

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

Science.gov (United States)

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

2006-12-22

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

Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

Science.gov (United States)

Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2013-12-03

We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

Directory of Open Access Journals (Sweden)

Zhang Wei

2009-09-01

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

Meshless methods in biomechanics bone tissue remodelling analysis

CERN Document Server

Belinha, Jorge

2014-01-01

This book presents the complete formulation of a new advanced discretization meshless technique: the Natural Neighbour Radial Point Interpolation Method (NNRPIM). In addition, two of the most popular meshless methods, the EFGM and the RPIM, are fully presented. Being a truly meshless method, the major advantages of the NNRPIM over the FEM, and other meshless methods, are the remeshing flexibility and the higher accuracy of the obtained variable field. Using the natural neighbour concept, the NNRPIM permits to determine organically the influence-domain, resembling the cellulae natural behaviour. This innovation permits the analysis of convex boundaries and extremely irregular meshes, which is an advantage in the biomechanical analysis, with no extra computational effort associated.   This volume shows how to extend the NNRPIM to the bone tissue remodelling analysis, expecting to contribute with new numerical tools and strategies in order to permit a more efficient numerical biomechanical analysis.

Lung counting: Comparison of a four detector array that has either metal or carbon fiber end caps, and the effect on array performance characteristics

International Nuclear Information System (INIS)

Sabbir Ahmed, Asm; Kramer, Gary H.

2011-01-01

This study described the performance of an array of HPGe detectors, made by ORTEC. In the existing system, a metal end cap was used in the detector construction. In general, the natural metal contains some radioactive materials, create high background noises and signals during in vivo counting. ORTEC proposed a novel carbon fiber to be used in end cap, without any radio active content. This paper described the methodology of developing a model of the given HPGe array-detectors, comparing the detection efficiency and cross talk among the detectors using two end cap materials: either metal or carbon fiber and to provide a recommendation about the end cap material. The detector's counting efficiency were studied using point and plane sources. The cross talk among the array detectors were studied using a homogeneous attenuating medium made of tissue equivalent material. The cross talk was significant when single or multiple point sources (simulated to heterogeneous hot spots) were embedded inside the attenuating medium. With carbon fiber, the cross talk increased about 100% for photon energy at about 100 keV. For a uniform distribution of radioactive material, the cross talk increased about 5-10% when the end cap was made of carbon instead of steel. Metal end cap was recommended for the array of HPGe detectors.

Cyclic Loading of Growing Tissue in a Bioreactor: Mathematical Model and Asymptotic Analysis

KAUST Repository

Pohlmeyer, J. V.

2013-10-24

A simplified 2D mathematical model for tissue growth within a cyclically-loaded tissue engineering scaffold is presented and analyzed. Such cyclic loading has the potential to improve yield and functionality of tissue such as bone and cartilage when grown on a scaffold within a perfusion bioreactor. The cyclic compression affects the flow of the perfused nutrient, leading to flow properties that are inherently unsteady, though periodic, on a timescale short compared with that of tissue proliferation. A two-timescale analysis based on these well-separated timescales is exploited to derive a closed model for the tissue growth on the long timescale of proliferation. Some sample numerical results are given for the final model, and discussed. © 2013 Society for Mathematical Biology.

Fluorescence suppression using wavelength modulated Raman spectroscopy in fiber-probe-based tissue analysis.

Science.gov (United States)

Praveen, Bavishna B; Ashok, Praveen C; Mazilu, Michael; Riches, Andrew; Herrington, Simon; Dholakia, Kishan

2012-07-01

In the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30  s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species.

Protein Profiling of Preeclampsia Placental Tissues

OpenAIRE

Shu, Chang; Liu, Zitao; Cui, Lifeng; Wei, Chengguo; Wang, Shuwen; Tang, Jian Jenny; Cui, Miao; Lian, Guodong; Li, Wei; Liu, Xiufen; Xu, Hongmei; Jiang, Jing; Lee, Peng; Zhang, David Y.; He, Jin

2014-01-01

Preeclampsia is a multi-system disorder involved in pregnancy without an effective treatment except delivery. The precise pathogenesis of this complicated disorder is still not completely understood. The objective of this study is to evaluate the alterations of protein expression and phosphorylations that are important in regulating placental cell function in preterm and term preeclampsia. Using the Protein Pathway Array, 38 proteins in placental tissues were found to be differentially expres...

Pathology interface for the molecular analysis of tissue by mass spectrometry

Directory of Open Access Journals (Sweden)

Jeremy L Norris

2016-01-01

Full Text Available Background: Imaging mass spectrometry (IMS generates molecular images directly from tissue sections to provide better diagnostic insights and expand the capabilities of clinical anatomic pathology. Although IMS technology has matured over recent years, the link between microscopy imaging currently used by pathologists and MS-based molecular imaging has not been established. Methods: We adapted the Vanderbilt University Tissue Core workflow for IMS into a web-based system that facilitates remote collaboration. The platform was designed to perform within acceptable web response times for viewing, annotating, and processing high resolution microscopy images. Results: We describe a microscopy-driven approach to tissue analysis by IMS. Conclusion: The Pathology Interface for Mass Spectrometry is designed to provide clinical access to IMS technology and deliver enhanced diagnostic value.

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-10-15

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

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

Directory of Open Access Journals (Sweden)

Lo Fang-Yi

2012-06-01

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

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

International Nuclear Information System (INIS)

Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

2012-01-01

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

Space solar array reliability: A study and recommendations

Science.gov (United States)

Brandhorst, Henry W., Jr.; Rodiek, Julie A.

2008-12-01

Providing reliable power over the anticipated mission life is critical to all satellites; therefore solar arrays are one of the most vital links to satellite mission success. Furthermore, solar arrays are exposed to the harshest environment of virtually any satellite component. In the past 10 years 117 satellite solar array anomalies have been recorded with 12 resulting in total satellite failure. Through an in-depth analysis of satellite anomalies listed in the Airclaim's Ascend SpaceTrak database, it is clear that solar array reliability is a serious, industry-wide issue. Solar array reliability directly affects the cost of future satellites through increased insurance premiums and a lack of confidence by investors. Recommendations for improving reliability through careful ground testing, standardization of testing procedures such as the emerging AIAA standards, and data sharing across the industry will be discussed. The benefits of creating a certified module and array testing facility that would certify in-space reliability will also be briefly examined. Solar array reliability is an issue that must be addressed to both reduce costs and ensure continued viability of the commercial and government assets on orbit.

CFD Analysis of a Finite Linear Array of Savonius Wind Turbines

Science.gov (United States)

Belkacem, Belabes; Paraschivoiu, Marius

2016-09-01

Vertical axis wind turbines such as Savonius rotors have been shown to be suitable for low wind speeds normally associated with wind resources in all corners of the world. However, the efficiency of the rotor is low. This paper presents results of Computational Fluid Dynamics (CFD) simulations for an array of Savonius rotors that show a significant increase in efficiency. It looks at identifying the effect on the energy yield of a number of turbines placed in a linear array. Results from this investigation suggest that an increase in the energy yield could be achieved which can reach almost two times than the conventional Savonius wind turbine in the case of an array of 11turbines with a distance of 1.4R in between them. The effect of different TSR values and different wind inlet speeds on the farm has been studied for both a synchronous and asynchronous wind farm.

Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array--comparative genomic hybridization

DEFF Research Database (Denmark)

Isinger-Ekstrand, Anna; Johansson, Jan; Ohlsson, Mattias

2010-01-01

15, 13q34, and 12q13, whereas different profiles with gains at 5p15, 7p22, 2q35, and 13q34 characterized gastric cancers. CDK6 and EGFR were identified as putative target genes in cancers of the esophagus and the gastroesophageal junction, with upregulation in one quarter of the tumors. Gains......We aimed to characterize the genomic profiles of adenocarcinomas in the gastroesophageal junction in relation to cancers in the esophagus and the stomach. Profiles of gains/losses as well as gene expression profiles were obtained from 27 gastroesophageal adenocarcinomas by means of 32k high......-resolution array-based comparative genomic hybridization and 27k oligo gene expression arrays, and putative target genes were validated in an extended series. Adenocarcinomas in the distal esophagus and the gastroesophageal junction showed strong similarities with the most common gains at 20q13, 8q24, 1q21-23, 5p...

Thermal analysis of laser interstitial thermotherapy in ex vivo fibro-fatty tissue using exponential functions

Energy Technology Data Exchange (ETDEWEB)

Salas, Nelson Jr. [Biomedical Optics and Laser Laboratory, Department of Biomedical Engineering, University of Miami College of Engineering, PO Box 248294, Coral Gables, FL 33124 (United States); Manns, Fabrice [Biomedical Optics and Laser Laboratory, Department of Biomedical Engineering, University of Miami College of Engineering, PO Box 248294, Coral Gables, FL 33124 (United States); Milne, Peter J [Ophthalmic Biophysics Center, Bascom Palmer Eye Institute, University of Miami School of Medicine, 1638 NW 10th Ave, McKnight Bldg, Miami, FL 33136 (United States); Denham, David B [Ophthalmic Biophysics Center, Bascom Palmer Eye Institute, University of Miami School of Medicine, 1638 NW 10th Ave, McKnight Bldg, Miami, FL 33136 (United States); Minhaj, Ahmed M [Biomedical Optics and Laser Laboratory, Department of Biomedical Engineering, University of Miami College of Engineering, PO Box 248294, Coral Gables, FL 33124 (United States); Parel, Jean-Marie [Biomedical Optics and Laser Laboratory, Department of Biomedical Engineering, University of Miami College of Engineering, PO Box 248294, Coral Gables, FL 33124 (United States); Robinson, David S [Center for Breast Care, St Luke' s Hospital of Kansas City, 4400 Broadway, Suite 509, Kansas City, MO 64111 (United States)

2004-05-07

A therapeutic procedure to treat small, surface breast tumours up to 10 mm in radius plus a 5 mm margin of healthy, surrounding tissue using laser interstitial thermotherapy (LITT) is currently being investigated. The purpose of this study is to analyse and model the thermal and coagulative response of ex vivo fibro-fatty tissue, a model for breast tissue, during experimental laser interstitial thermotherapy at 980 nm. Laser radiation at 980 nm was delivered interstitially through a diffusing tip optical fibre inserted into a fibro-fatty tissue model to produce controlled heating at powers ranging from 3.2 to 8.0 W. Tissue temperature was measured with thermocouples placed at 15 positions around the fibre. The induced coagulation zone was measured on gross anatomical sections. Thermal analysis indicates that a finite sum of exponential functions is an approximate solution to the heat conduction equation that more accurately predicts the time-temperature dependence in tissue prior to carbonization (T < 100 deg. C) during LITT than the traditional model using a single exponential function. Analysis of the ellipsoid coagulation volume induced in tissue indicates that the 980 nm wavelength does not penetrate deep enough in fibro-fatty tissue to produce a desired 30 mm diameter (14.1 x 10{sup 3} mm{sup 3}) coagulation volume without unwanted tissue liquefaction and carbonization.

DNA-barcode directed capture and electrochemical metabolic analysis of single mammalian cells on a microelectrode array.

Science.gov (United States)

Douglas, Erik S; Hsiao, Sonny C; Onoe, Hiroaki; Bertozzi, Carolyn R; Francis, Matthew B; Mathies, Richard A

2009-07-21

A microdevice is developed for DNA-barcode directed capture of single cells on an array of pH-sensitive microelectrodes for metabolic analysis. Cells are modified with membrane-bound single-stranded DNA, and specific single-cell capture is directed by the complementary strand bound in the sensor area of the iridium oxide pH microelectrodes within a microfluidic channel. This bifunctional microelectrode array is demonstrated for the pH monitoring and differentiation of primary T cells and Jurkat T lymphoma cells. Single Jurkat cells exhibited an extracellular acidification rate of 11 milli-pH min(-1), while primary T cells exhibited only 2 milli-pH min(-1). This system can be used to capture non-adherent cells specifically and to discriminate between visually similar healthy and cancerous cells in a heterogeneous ensemble based on their altered metabolic properties.

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

International Nuclear Information System (INIS)

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

1987-09-01

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

Impedance Changes and Fibrous Tissue Growth after Cochlear Implantation Are Correlated and Can Be Reduced Using a Dexamethasone Eluting Electrode.

Directory of Open Access Journals (Sweden)

Maciej Wilk

Full Text Available The efficiency of cochlear implants (CIs is affected by postoperative connective tissue growth around the electrode array. This tissue formation is thought to be the cause behind post-operative increases in impedance. Dexamethasone (DEX eluting CIs may reduce fibrous tissue growth around the electrode array subsequently moderating elevations in impedance of the electrode contacts.For this study, DEX was incorporated into the silicone of the CI electrode arrays at 1% and 10% (w/w concentration. Electrodes prepared by the same process but without dexamethasone served as controls. All electrodes were implanted into guinea pig cochleae though the round window membrane approach. Potential additive or synergistic effects of electrical stimulation (60 minutes were investigated by measuring impedances before and after stimulation (days 0, 7, 28, 56 and 91. Acoustically evoked auditory brainstem responses were recorded before and after CI insertion as well as on experimental days 7, 28, 56, and 91. Additionally, histology performed on epoxy embedded samples enabled measurement of the area of scala tympani occupied with fibrous tissue.In all experimental groups, the highest levels of fibrous tissue were detected in the basal region of the cochlea in vicinity to the round window niche. Both DEX concentrations, 10% and 1% (w/w, significantly reduced fibrosis around the electrode array of the CI. Following 3 months of implantation impedance levels in both DEX-eluting groups were significantly lower compared to the control group, the 10% group producing a greater effect. The same effects were observed before and after electrical stimulation.To our knowledge, this is the first study to demonstrate a correlation between the extent of new tissue growth around the electrode and impedance changes after cochlear implantation. We conclude that DEX-eluting CIs are a means to reduce this tissue reaction and improve the functional benefits of the implant by attenuating

Metabolomics reveals the heterogeneous secretome of two entomopathogenic fungi to ex vivo cultured insect tissues.

Directory of Open Access Journals (Sweden)

Charissa de Bekker

Full Text Available Fungal entomopathogens rely on cellular heterogeneity during the different stages of insect host infection. Their pathogenicity is exhibited through the secretion of secondary metabolites, which implies that the infection life history of this group of environmentally important fungi can be revealed using metabolomics. Here metabolomic analysis in combination with ex vivo insect tissue culturing shows that two generalist isolates of the genus Metarhizium and Beauveria, commonly used as biological pesticides, employ significantly different arrays of secondary metabolites during infectious and saprophytic growth. It also reveals that both fungi exhibit tissue specific strategies by a distinguishable metabolite secretion on the insect tissues tested in this study. In addition to showing the important heterogeneous nature of these two entomopathogens, this study also resulted in the discovery of several novel destruxins and beauverolides that have not been described before, most likely because previous surveys did not use insect tissues as a culturing system. While Beauveria secreted these cyclic depsipeptides when encountering live insect tissues, Metarhizium employed them primarily on dead tissue. This implies that, while these fungi employ comparable strategies when it comes to entomopathogenesis, there are most certainly significant differences at the molecular level that deserve to be studied.

Fabrication and characterization of CaP-coated nanotube arrays

International Nuclear Information System (INIS)

Kung, Kuan-Chen; Chen, Jia-Ling; Liu, Yen-Ting; Lee, Tzer-Min

2015-01-01

Modified anodization techniques have been shown to improve the biocompatibility of titanium. This study demonstrated the anodic formation of self-organized nanotube arrays on titanium from an electrolyte solution containing 1 M H 3 PO 4 and 1 wt% hydrofluoric acid (HF). Our aim was to investigate the effects of sputter-deposited CaP on nanotube arrays. SEM images revealed a surface with uniform morphology and an average pore diameter of 29 nm. XRD results indicated that the phase of the nanotube arrays was amorphous. Electron spectroscopy for chemical analysis (ESCA) confirmed that the nanotube arrays were coated with calcium and phosphorus. Cell culture experiments using human osteosarcoma (HOS) cells demonstrated that the CaP/nanotube arrays had a pronounced effect on initial cell attachment as well as on the number of cells at 1, 7, and 14 days. Compared to as-polished titanium, the CaP/nanotube arrays accelerated cell proliferation, attachment, and spreading. Our results demonstrate the pronounced effects of CaP/nanotube arrays on the biological responses of HOS cells. - Highlights: • Self-organized nanotube arrays were anodically formed on titanium. • Surfaces of nanotube arrays exhibited uniform morphology and pore size. • According to ESCA results, Ca and P were successfully coated on nanotube arrays. • CaP/nanotube arrays accelerated the attachment and spreading of cells. • CaP/nanotube arrays were shown to affect biological responses of cells

Fabrication and characterization of CaP-coated nanotube arrays

Energy Technology Data Exchange (ETDEWEB)

Kung, Kuan-Chen; Chen, Jia-Ling [Institute of Oral Medicine, National Cheng Kung University, Tainan 701, Taiwan (China); Liu, Yen-Ting [Department of Materials Science and Engineering, National Cheng Kung University, Tainan 701, Taiwan (China); Lee, Tzer-Min, E-mail: tmlee@mail.ncku.edu.tw [Institute of Oral Medicine, National Cheng Kung University, Tainan 701, Taiwan (China); Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan (China); School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan (China)

2015-03-01

Modified anodization techniques have been shown to improve the biocompatibility of titanium. This study demonstrated the anodic formation of self-organized nanotube arrays on titanium from an electrolyte solution containing 1 M H{sub 3}PO{sub 4} and 1 wt% hydrofluoric acid (HF). Our aim was to investigate the effects of sputter-deposited CaP on nanotube arrays. SEM images revealed a surface with uniform morphology and an average pore diameter of 29 nm. XRD results indicated that the phase of the nanotube arrays was amorphous. Electron spectroscopy for chemical analysis (ESCA) confirmed that the nanotube arrays were coated with calcium and phosphorus. Cell culture experiments using human osteosarcoma (HOS) cells demonstrated that the CaP/nanotube arrays had a pronounced effect on initial cell attachment as well as on the number of cells at 1, 7, and 14 days. Compared to as-polished titanium, the CaP/nanotube arrays accelerated cell proliferation, attachment, and spreading. Our results demonstrate the pronounced effects of CaP/nanotube arrays on the biological responses of HOS cells. - Highlights: • Self-organized nanotube arrays were anodically formed on titanium. • Surfaces of nanotube arrays exhibited uniform morphology and pore size. • According to ESCA results, Ca and P were successfully coated on nanotube arrays. • CaP/nanotube arrays accelerated the attachment and spreading of cells. • CaP/nanotube arrays were shown to affect biological responses of cells.

THE MURCHISON WIDEFIELD ARRAY 21 cm POWER SPECTRUM ANALYSIS METHODOLOGY

Energy Technology Data Exchange (ETDEWEB)

Jacobs, Daniel C.; Beardsley, A. P.; Bowman, Judd D. [Arizona State University, School of Earth and Space Exploration, Tempe, AZ 85287 (United States); Hazelton, B. J.; Sullivan, I. S.; Barry, N.; Carroll, P. [University of Washington, Department of Physics, Seattle, WA 98195 (United States); Trott, C. M.; Pindor, B.; Briggs, F.; Gaensler, B. M. [ARC Centre of Excellence for All-sky Astrophysics (CAASTRO) (Australia); Dillon, Joshua S.; Oliveira-Costa, A. de; Ewall-Wice, A.; Feng, L. [MIT Kavli Institute for Astrophysics and Space Research, Cambridge, MA 02139 (United States); Pober, J. C. [Brown University, Department of Physics, Providence, RI 02912 (United States); Bernardi, G. [Department of Physics and Electronics, Rhodes University, Grahamstown 6140 (South Africa); Cappallo, R. J.; Corey, B. E. [MIT Haystack Observatory, Westford, MA 01886 (United States); Emrich, D., E-mail: daniel.c.jacobs@asu.edu [International Centre for Radio Astronomy Research, Curtin University, Perth, WA 6845 (Australia); and others

2016-07-10

We present the 21 cm power spectrum analysis approach of the Murchison Widefield Array Epoch of Reionization project. In this paper, we compare the outputs of multiple pipelines for the purpose of validating statistical limits cosmological hydrogen at redshifts between 6 and 12. Multiple independent data calibration and reduction pipelines are used to make power spectrum limits on a fiducial night of data. Comparing the outputs of imaging and power spectrum stages highlights differences in calibration, foreground subtraction, and power spectrum calculation. The power spectra found using these different methods span a space defined by the various tradeoffs between speed, accuracy, and systematic control. Lessons learned from comparing the pipelines range from the algorithmic to the prosaically mundane; all demonstrate the many pitfalls of neglecting reproducibility. We briefly discuss the way these different methods attempt to handle the question of evaluating a significant detection in the presence of foregrounds.

Texture analysis of speckle in optical coherence tomography images of tissue phantoms

International Nuclear Information System (INIS)

Gossage, Kirk W; Smith, Cynthia M; Kanter, Elizabeth M; Hariri, Lida P; Stone, Alice L; Rodriguez, Jeffrey J; Williams, Stuart K; Barton, Jennifer K

2006-01-01

Optical coherence tomography (OCT) is an imaging modality capable of acquiring cross-sectional images of tissue using back-reflected light. Conventional OCT images have a resolution of 10-15 μm, and are thus best suited for visualizing tissue layers and structures. OCT images of collagen (with and without endothelial cells) have no resolvable features and may appear to simply show an exponential decrease in intensity with depth. However, examination of these images reveals that they display a characteristic repetitive structure due to speckle.The purpose of this study is to evaluate the application of statistical and spectral texture analysis techniques for differentiating living and non-living tissue phantoms containing various sizes and distributions of scatterers based on speckle content in OCT images. Statistically significant differences between texture parameters and excellent classification rates were obtained when comparing various endothelial cell concentrations ranging from 0 cells/ml to 25 million cells/ml. Statistically significant results and excellent classification rates were also obtained using various sizes of microspheres with concentrations ranging from 0 microspheres/ml to 500 million microspheres/ml. This study has shown that texture analysis of OCT images may be capable of differentiating tissue phantoms containing various sizes and distributions of scatterers

Analysis of X-ray iron and nickel radiation and jets from planar wire arrays and X-pinches

International Nuclear Information System (INIS)

Safronova, A S; Kantsyrev, V L; Esaulov, A A; Ouart, N D; Shlyaptseva, V; Williamson, K M; Shrestha, I; Osborne, G C; Weller, M E

2010-01-01

University-scale Z-pinch devices are able to produce plasmas with a broad range of sizes, temperatures, densities, their gradients, and opacity properties. Radiative properties of such plasmas depend on material, mass, and configuration of the wire array loads. Experiments with two different types of loads, double planar wire arrays (DPWA) and X-pinches, performed on the 1 MA Zebra generator at UNR are analyzed. X-pinches are made from Stainless Steel (69% Fe, 20% Cr, and 9% Ni) wires. Combined DPWAs consist of one plane from SS wires and another plane from Alumel (95% Ni, 2% Al, 2% Si) wires. The main focus of this work is on the analysis of plasma jets at the early phase of plasma formation and the K-and L-shell radiation generation at the implosion and stagnation phases in experiments with the two aforementioned wire loads. The relevant theoretical tools that guide the data analysis include non-LTE collisional-radiative and wire ablation dynamics models. The astrophysical relevance of the plasma jets as well as of spectroscopic and imaging studies are demonstrated.

Benchmark Evaluation of Plutonium Nitrate Solution Arrays

International Nuclear Information System (INIS)

Marshall, M.A.; Bess, J.D.

2011-01-01

In October and November of 1981 thirteen approach-to-critical experiments 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(reg s ign) 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 of 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 performed to fill a gap in experimental data regarding criticality limits for storing and handling arrays of Pu solution in reprocessing facilities. Of the thirteen approach-to-critical experiments eleven resulted in extrapolations to critical configurations. Four of the approaches were extrapolated to the critical number of bottles; these were not evaluated further due to the large uncertainty associated with the modeling of a fraction of a bottle. The remaining seven approaches were extrapolated to critical array spacing of 3-4 and 4-4 arrays; these seven critical configurations were evaluation for inclusion as acceptable benchmark experiments in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. Detailed and simple models of these configurations were created and the associated bias of these simplifications was determined to range from 0.00116 and 0.00162 ± 0.00006 ?keff. Monte Carlo analysis of all models was completed using MCNP5 with ENDF/BVII.0 neutron cross section libraries. A thorough uncertainty analysis of all critical, geometric, and material parameters was performed using parameter

Flat-plate solar array project. Volume 8: Project analysis and integration

Science.gov (United States)

Mcguire, P.; Henry, P.

1986-01-01

Project Analysis and Integration (PA&I) performed planning and integration activities to support management of the various Flat-Plate Solar Array (FSA) Project R&D activities. Technical and economic goals were established by PA&I for each R&D task within the project to coordinate the thrust toward the National Photovoltaic Program goals. A sophisticated computer modeling capability was developed to assess technical progress toward meeting the economic goals. These models included a manufacturing facility simulation, a photovoltaic power station simulation and a decision aid model incorporating uncertainty. This family of analysis tools was used to track the progress of the technology and to explore the effects of alternative technical paths. Numerous studies conducted by PA&I signaled the achievement of milestones or were the foundation of major FSA project and national program decisions. The most important PA&I activities during the project history are summarized. The PA&I planning function is discussed and how it relates to project direction and important analytical models developed by PA&I for its analytical and assessment activities are reviewed.

Diagnosis of breast cancer by tissue analysis

Institute of Scientific and Technical Information of China (English)

Debnath Bhattacharyya; Samir Kumar Bandyopadhyay; Tai-hoon Kim

2013-01-01

In this paper,we propose a technique to locate abnormal growth of cells in breast tissue and suggest further pathological test,when require.We compare normal breast tissue with malignant invasive breast tissue by a series of image processing steps.Normal ductal epithelial cells and ductal/lobular invasive carcinogenic cells also consider for comparison here in this paper.In fact,features of cancerous breast tissue (invasive) are extracted and analyses with normal breast tissue.We also suggest the breast cancer recognition technique through image processing and prevention by controlling p53 gene mutation to some extent.

SU-F-T-458: Tracking Trends of TG-142 Parameters Via Analysis of Data Recorded by 2D Chamber Array

Energy Technology Data Exchange (ETDEWEB)

Alexandrian, A; Kabat, C; Defoor, D; Saenz, D; Rasmussen, K; Kirby, N; Gutierrez, A; Papanikolaou, N; Stathakis, S [University of Texas HSC SA, San Antonio, TX (United States)

2016-06-15

Purpose: With increasing QA demands of medical physicists in clinical radiation oncology, the need for an effective method of tracking clinical data has become paramount. A tool was produced which scans through data automatically recorded by a 2D chamber array and extracts relevant information recommended by TG-142. Using this extracted information a timely and comprehensive analysis of QA parameters can be easily performed enabling efficient monthly checks on multiple linear accelerators simultaneously. Methods: A PTW STARCHECK chamber array was used to record several months of beam outputs from two Varian 2100 series linear accelerators and a Varian NovalisTx−. In conjunction with the chamber array, a beam quality phantom was used to simultaneously to determine beam quality. A minimalist GUI was created in MatLab that allows a user to set the file path of the data for each modality to be analyzed. These file paths are recorded to a MatLab structure and then subsequently accessed by a script written in Python (version 3.5.1) which then extracts values required to perform monthly checks as outlined by recommendations from TG-142. The script incorporates calculations to determine if the values recorded by the chamber array fall within an acceptable threshold. Results: Values obtained by the script are written to a spreadsheet where results can be easily viewed and annotated with a “pass” or “fail” and saved for further analysis. In addition to creating a new scheme for reviewing monthly checks, this application allows for able to succinctly store data for follow up analysis. Conclusion: By utilizing this tool, parameters recommended by TG-142 for multiple linear accelerators can be rapidly obtained and analyzed which can be used for evaluation of monthly checks.

Angular photogrammetric soft tissue facial profile analysis of Bangladeshi young adults

Directory of Open Access Journals (Sweden)

Lubna Akter

2017-01-01

Full Text Available Introduction: Angular photogrammetric soft tissue facial profile analysis provides a permanent record for the actual appearance of a person, which would also serve to establish an ideal esthetic treatment goal. The aim of the present study was to evaluate the average angular variables that define the soft tissue facial profile of a Bangladeshi sample. Materials and Methods: This cross-sectional study was carried out at Department of Orthodontics and Dentofacial Orthopedics of Dhaka Dental College and Hospital, Bangladesh, from July to December 2015. Soft tissue facial profiles of 200 participants (100 males and 100 females between 18 and 25 years of age, with a dental Class I occlusal relationship and harmonious soft tissue profile, were selected by convenience sampling among students, doctors, and patients of Dhaka Dental College. Standardized photographs of 200 samples were taken in the natural head position. The photographic records were analyzed with the software for Windows, Microsoft Visio 2007, Standard Edition. All data were analyzed through standard methods using Statistical Package for the Statistical Package for Social Science Software (SPSS Version-20, IBM Corp, USA. Results: The average angular measurements for nasofrontal, total facial angle, facial angle, upper lip angle, projection of lower lip to chin, and mentolabial angle were wider in females. The mean value for nose tip angle, nasolabial angle, nasomental angle, and projection of upper lip to chin angle was higher in males compared to females. Nasofrontal angle (G-N-Nd (P = 0.000 and mentolabial angle (Li-Sm-Pg (P = 0.001 showed statistically significant differences. The greatest variability was found for mentolabial angle. Conclusion: The study of angular photogrammetric soft tissue facial profile analysis of Bangladeshi young adults contributes to the establishment of standardized normal values for the population. This study provides data which can be used in treatment

Life on magnets: stem cell networking on micro-magnet arrays.

Science.gov (United States)

Zablotskii, Vitalii; Dejneka, Alexandr; Kubinová, Šárka; Le-Roy, Damien; Dumas-Bouchiat, Frédéric; Givord, Dominique; Dempsey, Nora M; Syková, Eva

2013-01-01

Interactions between a micro-magnet array and living cells may guide the establishment of cell networks due to the cellular response to a magnetic field. To manipulate mesenchymal stem cells free of magnetic nanoparticles by a high magnetic field gradient, we used high quality micro-patterned NdFeB films around which the stray field's value and direction drastically change across the cell body. Such micro-magnet arrays coated with parylene produce high magnetic field gradients that affect the cells in two main ways: i) causing cell migration and adherence to a covered magnetic surface and ii) elongating the cells in the directions parallel to the edges of the micro-magnet. To explain these effects, three putative mechanisms that incorporate both physical and biological factors influencing the cells are suggested. It is shown that the static high magnetic field gradient generated by the micro-magnet arrays are capable of assisting cell migration to those areas with the strongest magnetic field gradient, thereby allowing the build up of tunable interconnected stem cell networks, which is an elegant route for tissue engineering and regenerative medicine.

Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

International Nuclear Information System (INIS)

Gunn, Shelly; Gorre, Mercedes; Mohammed, Mansoor; Yeh, I-Tien; Lytvak, Irina; Tirtorahardjo, Budi; Dzidic, Natasha; Zadeh, Soheila; Kim, Jaeweon; McCaskill, Chris; Lim, Lony

2010-01-01

HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin), remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods. In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE) tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms. Array-based comparative genomic hybridization (array CGH) analysis of chromosome 17 resolved HER2 gene status in [20/20] (100%) of cases and revealed additional chromosome 17 copy number changes in [18/20] (90%) of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to 'ratio skewing' caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability. These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17 abnormalities in these cases suggests that the two

Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration

Directory of Open Access Journals (Sweden)

Kelemen Arpad

2008-08-01

Full Text Available Abstract Background This paper addresses key biological problems and statistical issues in the analysis of large gene expression data sets that describe systemic temporal response cascades to therapeutic doses in multiple tissues such as liver, skeletal muscle, and kidney from the same animals. Affymetrix time course gene expression data U34A are obtained from three different tissues including kidney, liver and muscle. Our goal is not only to find the concordance of gene in different tissues, identify the common differentially expressed genes over time and also examine the reproducibility of the findings by integrating the results through meta analysis from multiple tissues in order to gain a significant increase in the power of detecting differentially expressed genes over time and to find the differential differences of three tissues responding to the drug. Results and conclusion Bayesian categorical model for estimating the proportion of the 'call' are used for pre-screening genes. Hierarchical Bayesian Mixture Model is further developed for the identifications of differentially expressed genes across time and dynamic clusters. Deviance information criterion is applied to determine the number of components for model comparisons and selections. Bayesian mixture model produces the gene-specific posterior probability of differential/non-differential expression and the 95% credible interval, which is the basis for our further Bayesian meta-inference. Meta-analysis is performed in order to identify commonly expressed genes from multiple tissues that may serve as ideal targets for novel treatment strategies and to integrate the results across separate studies. We have found the common expressed genes in the three tissues. However, the up/down/no regulations of these common genes are different at different time points. Moreover, the most differentially expressed genes were found in the liver, then in kidney, and then in muscle.

Analysis of lung tissue particles among silicosis cases

Directory of Open Access Journals (Sweden)

B Case

2005-10-01

Full Text Available Background and Aims:Lung tissue samples of several miners, millers, sandblaster, welders andconstruction workers with historical exposure to mineral particles were analyzed. These subjectshad significant respiratory exposure to silica particles and demanded compensation foroccupational lung diseases.Method: Lung tissue samples were observed under an Electron microscope with 10000Xmagnification. Mineral particles were sized and analyzed by EDS detector based on X-rayspectrophotometry.Results: The results have indicated that the lung particle burden of the subjects was closelyrelated to their occupational history. The highest level of mineral silica particles were found in thelungs of miners and sandblasters. The highest concentration of metallic particles was found in thelungs of welders and miners in ferric mining industry. Severity of lung fibrosis was directlyrelated to the lung free silica concentration. However, no association was found between particlediameter and severity of fibrosis. In addition, lung particle burden of silicotic cases with lungcancer contained a much higher concentration of metallic particles and asbestos fibres that thelung of those subject with silicosis only.Conclusion: Although workers in mining and construction may be predominantly exposed tosilica particles including quartz, the role of other mineral particles including asbestos fibres,metallic fibres and other minerals should be taken into account in the genesis of occupational lungdisease in particular lung cancer. Lung tissue sample analysis can provide valuable informationto assess the legal and compensation cases.

CFD Analysis of a Finite Linear Array of Savonius Wind Turbines

International Nuclear Information System (INIS)

Belkacem, Belabes; Paraschivoiu, Marius

2016-01-01

Vertical axis wind turbines such as Savonius rotors have been shown to be suitable for low wind speeds normally associated with wind resources in all corners of the world. However, the efficiency of the rotor is low. This paper presents results of Computational Fluid Dynamics (CFD) simulations for an array of Savonius rotors that show a significant increase in efficiency. It looks at identifying the effect on the energy yield of a number of turbines placed in a linear array. Results from this investigation suggest that an increase in the energy yield could be achieved which can reach almost two times than the conventional Savonius wind turbine in the case of an array of 11turbines with a distance of 1.4R in between them. The effect of different TSR values and different wind inlet speeds on the farm has been studied for both a synchronous and asynchronous wind farm. (paper)

TLR9 expression in glioma tissues correlated to glioma progression and the prognosis of GBM patients

International Nuclear Information System (INIS)

Wang, Chao; Cao, Shouqiang; Yan, Ying; Ying, Qiao; Jiang, Tao; Xu, Ke; Wu, Anhua

2010-01-01

Our study aims to evaluate the expression of TLR9 in glioma tissues, examine the association between TLR9 expression, clinicopathological variables, and glioma patient outcome, we further characterized the direct effects of TLR9 agonist CpG ODN upon the proliferation and invasion of glioma cells in vitro. RT-PCR and immunofluorescence were used to determine the expression of TLR9 in glioma cell lines and clinical glioma samples. Tissue microarry and immunohistochemistry were applied to evaluated TLR9 expression in 292 newly diagnosed glioma and 13 non-neoplastic brain tissues. We further investigated the effect of CpG ODN on the proliferation and invasion of glioma cells in vitro with MTT assays and matrigel transwell assay respectively. RT-PCR showed that TLR9 expressed in all the glioma samples and glioma cell lines we examined. The tissue array analysis indicated that TLR9 expression is correlated with malignancy of glioma (p < 0.01). Multivariate Cox regression analysis revealed that TLR9 expression is an independent prognostic factor for PFS of GBM patients(P = 0.026). TLR9 agonist CpG ODN has no significant effect on glioma proliferation, but matrigel transwell analysis showed that TLR9 agonist CpG ODN can significantly enhance glioma invasion in vitro. Our data indicated that TLR9 expression increases according to the histopathological grade of glioma, and the TLR9 expression level is related to the PFS of GBM patients. In addition, our findings warrant caution in the directly injection of TLR9 agonist CpG ODN into glioma tissues for the glioma immunotherapy

Analysis of Chloroquine and Metabolites Directly from Whole-body Animal Tissue Sections by Liquid Extraction Surface Analysis (LESA) and Tandem Mass Spectrometry

Energy Technology Data Exchange (ETDEWEB)

Parson, Whitney B [ORNL; Koeniger, Stormy L [Abbott Laboratories; Johnson, Robert W [Abbott Laboratories; Erickson, Jamie [Abbott Laboratories; Tian, Yu [Abbott Laboratories; Stedman, Christopher A. [Abbott Laboratories; Schwartz, Annette [Abbott Laboratories; Tarcsa, Edit [Abbott Laboratories; Cole, Roderic [ORNL; Van Berkel, Gary J [ORNL

2012-01-01

The rapid and direct analysis of the amount and spatial distribution of exogenous chloroquine and chloroquine metabolites from tissue sections by liquid extraction surface sampling analysis coupled with tandem mass spectrometry (LESA-MS) was demonstrated. LESA-MS results compared well with previously published chloroquine quantification data collected by organ excision, extraction and fluorescent detection. The ability to directly sample and analyze spatially-resolved exogenous molecules from tissue sections with minimal sample preparation and analytical method development has the potential to facilitate the assessment of target tissue penetration of pharmaceutical compounds, to establish pharmacokinetic/pharmacodynamic (PK/PD) relationships, and to complement established pharmacokinetic methods used in the drug discovery process during tissue distribution assessment.

Synthesis and characterization of Mn-doped ZnO column arrays

International Nuclear Information System (INIS)

Yang Mei; Guo Zhixing; Qiu Kehui; Long Jianping; Yin Guangfu; Guan Denggao; Liu Sutian; Zhou Shijie

2010-01-01

Mn-doped ZnO column arrays were successfully synthesized by conventional sol-gel process. Effect of Mn/Zn atomic ratio and reaction time were investigated, and the morphology, tropism and optical properties of Mn-doped ZnO column arrays were characterized by SEM, XRD and photoluminescence (PL) spectroscopy. The result shows that a Mn/Zn atomic ratio of 0.1 and growth time of 12 h are the optimal condition for the preparation of densely distributed ZnO column arrays. XRD analysis shows that Mn-doped ZnO column arrays are highly c-axis oriented. As for Mn-doped ZnO column arrays, obvious increase of photoluminescence intensity is observed at the wavelength of ∼395 nm and ∼413 nm, compared to pure ZnO column arrays.

Coupling in reflector arrays

DEFF Research Database (Denmark)

Appel-Hansen, Jørgen

1968-01-01

In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present communic......In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present...

Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media.

Science.gov (United States)

Chen, Zhen; Dorfman, Kevin D

2014-02-01

Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such "tilted" post arrays is superior to the standard "un-tilted" approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low-electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the "free path," i.e. the average distance of ballistic trajectories of point-sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomics analysis of apoptosis-regulating proteins in tissues with different radiosensitivity

International Nuclear Information System (INIS)

An, Jeung-Hee; Seong, Jin-Sil

2006-01-01

The aim of this study was to identify of radiosusceptibility proteins in tissues with different radiosensitivity. C3H/HeJ mice were exposed to 10 Gy. The tissues were processed for proteins extraction and were analyzed by 2-dimensional electrophoresis. The proteins were identified by matrix-assisted laser desorption ionizing time-of-flight mass spectrometry and validated by immunohistochemical staining and Western blotting. The peaks of apoptosis levels were 35.3±1.7% and 0.6±0.2% in the spleen and the liver, respectively, after ionizing radiation. Analysis of liver tissue showed that the expression level of reactive oxygen species (ROS) related proteins such as cytochrome c, glutathione S transferase, NADH dehydrogenase and peroxiredoxin VI increased after radiation. The expression level of cytochrome c increased to 3-fold after ionizing radiation in both tissues. However in spleen tissue, the expression level of various kinds of apoptosis regulating proteins increased after radiation. These involved iodothyronine, CD 59A glycoprotein precursor, fas antigen and tumor necrosis factor -inducible protein TSG-6nprecursor after radiation. The difference in the apoptosis index between the liver and spleen tissues is closely associated with the expression of various kinds of apoptosis-related proteins. The result suggests that the expression of apoptosis-related protein and redox proteins play important roles in this radiosusceptibility. (author)

Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

Energy Technology Data Exchange (ETDEWEB)

Brückner, Michael [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Becker, Katja [Justus Liebig University Giessen, Biochemistry and Molecular Biology, 35392 Giessen (Germany); Popp, Jürgen [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany); Frosch, Torsten, E-mail: torsten.frosch@uni-jena.de [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany)

2015-09-24

A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

International Nuclear Information System (INIS)

Brückner, Michael; Becker, Katja; Popp, Jürgen; Frosch, Torsten

2015-01-01

A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

Report for Development of a Census Array and Evaluation of the Array to Detect Biothreat Agents and Environmental Samples for DHS

Energy Technology Data Exchange (ETDEWEB)

Jaing, C; Jackson, P

2011-04-14

The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Census Array. We designed a Census/Detection Array to detect all sequenced viruses (including phage), bacteria (eubacteria), and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to be unique relative to the human genome. A combination of 'detection' probes with high levels of conservation within a family plus 'census' probes targeting strain/isolate specific regions enabled detection and taxonomic classification from the level of family down to the strain. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. We tested the array with purified bacterial and viral DNA/RNA samples, artificial mixes of known bacterial/viral samples, spiked DNA against complex background including BW aerosol samples and soil samples, and environmental samples to evaluate the array's sensitivity and forensic capability. The data were analyzed using our novel maximum likelihood software. For most of the organisms tested, we have achieved at least species level discrimination.

Bioanalytical and chemical sensors using living taste, olfactory, and neural cells and tissues: a short review.

Science.gov (United States)

Wu, Chunsheng; Lillehoj, Peter B; Wang, Ping

2015-11-07

Biosensors utilizing living tissues and cells have recently gained significant attention as functional devices for chemical sensing and biochemical analysis. These devices integrate biological components (i.e. single cells, cell networks, tissues) with micro-electro-mechanical systems (MEMS)-based sensors and transducers. Various types of cells and tissues derived from natural and bioengineered sources have been used as recognition and sensing elements, which are generally characterized by high sensitivity and specificity. This review summarizes the state of the art in tissue- and cell-based biosensing platforms with an emphasis on those using taste, olfactory, and neural cells and tissues. Many of these devices employ unique integration strategies and sensing schemes based on sensitive transducers including microelectrode arrays (MEAs), field effect transistors (FETs), and light-addressable potentiometric sensors (LAPSs). Several groups have coupled these hybrid biosensors with microfluidics which offers added benefits of small sample volumes and enhanced automation. While this technology is currently limited to lab settings due to the limited stability of living biological components, further research to enhance their robustness will enable these devices to be employed in field and clinical settings.

Photon activation analysis of soft tissues of marine invertebrates

International Nuclear Information System (INIS)

Fukushima, M.; Tamate, H.

2001-01-01

We have determined levels of elements in soft tissues of 23 species of marine invertebrates by photon activation analysis and atomic absorption spectrometry. Concentration levels of Mg and Rb were almost same for all samples determined. On the contrary, relatively high concentration of elements were observed for Ni in mid-gut gonads of ear shells, As in gills, hepatopancreas, and muscles of several species of Crustaceans. (author)

Celebrating 10 Years of Delivering EarthScope USArray Transportable Array Data from the Array Network Facility (ANF)

Science.gov (United States)

Eakins, J. A.; Vernon, F.; Astiz, L.; Davis, G. A.; Reyes, J. C.; Martynov, V. G.; Tytell, J.; Cox, T. A.; Meyer, J.

2013-12-01

Since 2004, the Array Network Facility (ANF) has been responsible for generation and delivery of the metadata as well as collection and initial quality control and the transmission of the seismic, and more recently infrasound and meteorological data, for the Earthscope USArray Transportable Array. As of August 2013, we have managed data from over 1600 stations. Personnel at the ANF provide immediate eyes on the data to improve quality control as well as interact with the individual stations via calibrations, mass recentering, baler data retrieval and event analysis. Web-based tools have been developed, and rewritten over the years, to serve the needs of both station engineers and the public. Many lessons on the needs for scalability have been learned. Analysts continue to review all seismic events recorded on 7 or more TA stations making associations against externally available bulletins and/or generating ANF authored locations which are available at both the ANF and IRIS-DMC. The US Array pressure data have several unique characteristics that are allowing us to conduct a rigorous analysis of the spatio-temporal variations in the pressure field on time scales of less than an hour across the eastern United States. With the installation of the infrasound and atmospheric pressure sensors, starting in 2010, observations of gust fronts, near misses of tornados at individual stations, and of the mesoscale gravity waves showing the value and utility of the US Array pressure data will be presented.

Trace element analysis of wild rodent tissues using the PIXE method

International Nuclear Information System (INIS)

Hill, M.W.; Mangelson, N.F.; Ryder, J.F.; Atwood, N.D.; Wood, B.W.

1980-01-01

Five species of rodents have been collected in an area near Lake Powell Utah. Common names of the five species are: Long-tailed Mouse, Small Pocket Mouse, Deer Mouse, Antelope Ground Squirrel and Kangaroo Rat. Liver, lung, kidney and hair tissues from each animal were analyzed for trace element content by proton particle-induced x-ray emission (proton PIXE) analysis. Mean concentrations for the following elements were established for the tissues of each animal type: K, Ca, Ti, Mn, Fe, Ni, Cu, Zn, Se, Br, Rb and Pb. Analyses of variance were performed on the set of elements common to all tissues. Some significant differences in element concentrations were found between animal species and between tissue types. These differences lead to the following orders based on element concentration: Long-tailed Mouse greater than or equal to Antelope Ground Squirrel greater than or equal to Kangaroo Rat greater than or equal to Small Pocket Mouse and liver greater than or equal to kidney greater than or equal to lung greater than or equal to hair. Linear regression analyses were also performed on mean elemental concentrations in tissues. These analyses lead to several conclusions. First, the pattern of trace element concentrations in each of the four tissues is the same in all five species. Second, the pattern of trace element concentrations is the same in all four tissues of one species with the exception of Ti and Fe in hair. Third, the variation of an element in the hair cannot predict the variation of that same element in the other three tissues. Only K, Ca, Ti, Mn, Fe, Cu, and Zn were included in the third study

Tectonic Tremor analysis with the Taiwan Chelungpu-Fault Drilling Program (TCDP) downhole seismometer array

Science.gov (United States)

Lin, Y.; Hillers, G.; Ma, K.; Campillo, M.

2011-12-01

We study tectonic tremor activity in the Taichung area, Taiwan, analyzing continuous seismic records from 6 short-period sensors of the TCDP borehole array situated around 1 km depth. The low background noise level facilitates the detection of low-amplitude tectonic tremor and low-frequency earthquake (LFE) waveforms. We apply a hierarchical analysis to first detect transient amplitude increases, and to subsequently verify its tectonic origin, i.e. to associate it with tremor signals. The frequency content of tremor usually exceeds the background noise around 2-8 Hz; hence, in the first step, we use BHS1, BHS4 and BHS7 (top, center, bottom sensor) records to detect amplitude anomalies in this frequency range. We calculate the smoothed spectra of 30 second non-overlapping windows taken daily from 5 night time hours to avoid increased day time amplitudes associated with cultural activities. Amplitude detection is then performed on frequency dependent median values of 5 minute advancing, 10 minute long time windows, yielding a series of threshold dependent increased-energy spectra-envelopes, indicating teleseismic waveforms, potential tremor records, or other transients related to anthropogenic or natural sources. To verify the transients' tectonic origin, potential tremor waveforms detected by the amplitude method are manually picked in the time domain. We apply the Brown et al. (2008) LFE matched filter technique to three-component data from the 6 available sensors. Initial few-second templates are taken from the analyst-picked, minute-long segments, and correlated component-wise with 24-h data. Significantly increased similarity between templates and matched waveform segments is detected using the array-average 7-fold MAD measure. Harvested waveforms associated with this initial `weak' detection are stacked, and the thus created master templates are used in an iterative correlation procedure to arrive at robust LFE detections. The increased similarity of waveforms

CRISPRDetect: A flexible algorithm to define CRISPR arrays.

Science.gov (United States)

Biswas, Ambarish; Staals, Raymond H J; Morales, Sergio E; Fineran, Peter C; Brown, Chris M

2016-05-17

CRISPR (clustered regularly interspaced short palindromic repeats) RNAs provide the specificity for noncoding RNA-guided adaptive immune defence systems in prokaryotes. CRISPR arrays consist of repeat sequences separated by specific spacer sequences. CRISPR arrays have previously been identified in a large proportion of prokaryotic genomes. However, currently available detection algorithms do not utilise recently discovered features regarding CRISPR loci. We have developed a new approach to automatically detect, predict and interactively refine CRISPR arrays. It is available as a web program and command line from bioanalysis.otago.ac.nz/CRISPRDetect. CRISPRDetect discovers putative arrays, extends the array by detecting additional variant repeats, corrects the direction of arrays, refines the repeat/spacer boundaries, and annotates different types of sequence variations (e.g. insertion/deletion) in near identical repeats. Due to these features, CRISPRDetect has significant advantages when compared to existing identification tools. As well as further support for small medium and large repeats, CRISPRDetect identified a class of arrays with 'extra-large' repeats in bacteria (repeats 44-50 nt). The CRISPRDetect output is integrated with other analysis tools. Notably, the predicted spacers can be directly utilised by CRISPRTarget to predict targets. CRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.

Identification of catecholamine neurotransmitters using fluorescence sensor array

Energy Technology Data Exchange (ETDEWEB)

Ghasemi, Forough [Department of Chemistry, Sharif University of Technology, Tehran 11155-9516 (Iran, Islamic Republic of); Hormozi-Nezhad, M. Reza, E-mail: hormozi@sharif.edu [Department of Chemistry, Sharif University of Technology, Tehran 11155-9516 (Iran, Islamic Republic of); Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Mahmoudi, Morteza, E-mail: mahmoudi@stanford.edu [Department of Nanotechnology and Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551 (Iran, Islamic Republic of); Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305-5101 (United States)

2016-04-21

A nano-based sensor array has been developed for identification and discrimination of catecholamine neurotransmitters based on optical properties of their oxidation products under alkaline conditions. To produce distinct fluorescence response patterns for individual catecholamine, quenching of thioglycolic acid functionalized cadmium telluride (CdTe) quantum dots, by oxidation products, were employed along with the variation of fluorescence spectra of oxidation products. The spectral changes were analyzed with hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify catecholamine patterns. The proposed sensor could efficiently discriminate the individual catecholamine (i.e., dopamine, norepinephrine, and L-DOPA) and their mixtures in the concentration range of 0.25–30 μmol L{sup −1}. Finally, we found that the sensor had capability to identify the various catecholamines in urine sample. - Highlights: • We have proposed a fluorescence sensor array to detect catecholamine neurotransmitters. • Visual differentiation of catecholamines is provided by fluorescence array fingerprints. • Discrimination of catecholamines from each other, and from their mixture is obtained on a PCA plot. • Proposed sensor array can be used for detection of catecholamines in urine samples.

The Cherenkov Telescope Array production system for Monte Carlo simulations and analysis

Science.gov (United States)

Arrabito, L.; Bernloehr, K.; Bregeon, J.; Cumani, P.; Hassan, T.; Haupt, A.; Maier, G.; Moralejo, A.; Neyroud, N.; pre="for the"> CTA Consortium, DIRAC Consortium,

2017-10-01

The Cherenkov Telescope Array (CTA), an array of many tens of Imaging Atmospheric Cherenkov Telescopes deployed on an unprecedented scale, is the next-generation instrument in the field of very high energy gamma-ray astronomy. An average data stream of about 0.9 GB/s for about 1300 hours of observation per year is expected, therefore resulting in 4 PB of raw data per year and a total of 27 PB/year, including archive and data processing. The start of CTA operation is foreseen in 2018 and it will last about 30 years. The installation of the first telescopes in the two selected locations (Paranal, Chile and La Palma, Spain) will start in 2017. In order to select the best site candidate to host CTA telescopes (in the Northern and in the Southern hemispheres), massive Monte Carlo simulations have been performed since 2012. Once the two sites have been selected, we have started new Monte Carlo simulations to determine the optimal array layout with respect to the obtained sensitivity. Taking into account that CTA may be finally composed of 7 different telescope types coming in 3 different sizes, many different combinations of telescope position and multiplicity as a function of the telescope type have been proposed. This last Monte Carlo campaign represented a huge computational effort, since several hundreds of telescope positions have been simulated, while for future instrument response function simulations, only the operating telescopes will be considered. In particular, during the last 18 months, about 2 PB of Monte Carlo data have been produced and processed with different analysis chains, with a corresponding overall CPU consumption of about 125 M HS06 hours. In these proceedings, we describe the employed computing model, based on the use of grid resources, as well as the production system setup, which relies on the DIRAC interware. Finally, we present the envisaged evolutions of the CTA production system for the off-line data processing during CTA operations and

Numerical study of read scheme in one-selector one-resistor crossbar array

Science.gov (United States)

Kim, Sungho; Kim, Hee-Dong; Choi, Sung-Jin

2015-12-01

A comprehensive numerical circuit analysis of read schemes of a one selector-one resistance change memory (1S1R) crossbar array is carried out. Three schemes-the ground, V/2, and V/3 schemes-are compared with each other in terms of sensing margin and power consumption. Without the aid of a complex analytical approach or SPICE-based simulation, a simple numerical iteration method is developed to simulate entire current flows and node voltages within a crossbar array. Understanding such phenomena is essential in successfully evaluating the electrical specifications of selectors for suppressing intrinsic drawbacks of crossbar arrays, such as sneaky current paths and series line resistance problems. This method provides a quantitative tool for the accurate analysis of crossbar arrays and provides guidelines for developing an optimal read scheme, array configuration, and selector device specifications.

Multiple Seismic Array Observations for Tracing Deep Tremor Activity in Western Shikoku, Japan

Science.gov (United States)

Takeda, T.; Matsuzawa, T.; Shiomi, K.; Obara, K.

2011-12-01

Deep non-volcanic tremors become very active during episodic slow-slip events in western Japan and Cascadia. The episodic tremor and slow-slip events in western Shikoku, Japan, occur at a typical interval of 6 months. Recently, it has been reported that tremor migration activity is complex and shows different migrating directions depending on time scales (Ghosh et al., 2010). Such characteristics of tremor are important to understand the mechanism of tremor and the relationship between tremor and SSEs. However it is difficult to determine the location of tremors with high accuracy because tremors show faint signals and make the identification of P/S-wave arrivals difficult. Seismic array analysis is useful to evaluate tremor activity, especially to estimate the arrival direction of seismic energy (e.g. Ueno et al., 2010, Ghosh et al., 2010), as it can distinguish multiple tremor sources occurring simultaneously. Here, we have conducted seismic array observation and analyzed seismic data during tremor activity by applying the MUSIC method to trace tremor location and its migration in western Shikoku. We have installed five seismic arrays in western Shikoku since January 2011. One of the arrays contains 30 stations with 3-component seismometers with a natural frequency of 2 Hz (Type-L array). The array aperture size is 2 km and the mean interval between stations is approximately 200 m. Each of the other arrays (Type-S array) contains 9 seismic stations with the same type of seismometers of the Type-L array, and is deployed surrounding the Type-L array. The small array aperture size is 800 m and its mean station interval is approximately 150 m. All array stations have recorded continuous waveform data at a sampling of 200Hz. In May 2011, an episodic tremor and a short-term slip event occurred for the first time during the observation period. We could retrieve the array seismic data during the whole tremor episode. The analysis of data from the type-L array confirms

Detecting Outlier Microarray Arrays by Correlation and Percentage of Outliers Spots

Directory of Open Access Journals (Sweden)

Song Yang

2006-01-01

Full Text Available We developed a quality assurance (QA tool, namely microarray outlier filter (MOF, and have applied it to our microarray datasets for the identification of problematic arrays. Our approach is based on the comparison of the arrays using the correlation coefficient and the number of outlier spots generated on each array to reveal outlier arrays. For a human universal reference (HUR dataset, which is used as a technical control in our standard hybridization procedure, 3 outlier arrays were identified out of 35 experiments. For a human blood dataset, 12 outlier arrays were identified from 185 experiments. In general, arrays from human blood samples displayed greater variation in their gene expression profiles than arrays from HUR samples. As a result, MOF identified two distinct patterns in the occurrence of outlier arrays. These results demonstrate that this methodology is a valuable QA practice to identify questionable microarray data prior to downstream analysis.

Post-Irradiation Examination of Array Targets - Part I

Energy Technology Data Exchange (ETDEWEB)

Icenhour, A.S.

2004-01-23

During FY 2001, two arrays, each containing seven neptunium-loaded targets, were irradiated at the Advanced Test Reactor in Idaho to examine the influence of multi-target self-shielding on {sup 236}Pu content and to evaluate fission product release data. One array consisted of seven targets that contained 10 vol% NpO{sub 2} pellets, while the other array consisted of seven targets that contained 20 vol % NpO{sub 2} pellets. The arrays were located in the same irradiation facility but were axially separated to minimize the influence of one array on the other. Each target also contained a dosimeter package, which consisted of a small NpO{sub 2} wire that was inside a vanadium container. After completion of irradiation and shipment back to the Oak Ridge National Laboratory, nine of the targets (four from the 10 vol% array and five from the 20 vol% array) were punctured for pressure measurement and measurement of {sup 85}Kr. These nine targets and the associated dosimeters were then chemically processed to measure the residual neptunium, total plutonium production, {sup 238}Pu production, and {sup 236}Pu concentration at discharge. The amount and isotopic composition of fission products were also measured. This report provides the results of the processing and analysis of the nine targets.

Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue.

Science.gov (United States)

Thompson, Seonaid M; Craven, Rachel A; Nirmalan, Niroshini J; Harnden, Patricia; Selby, Peter J; Banks, Rosamonde E

2013-04-01

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ordered arrays of polymeric nanopores by using inverse nanostructured PTFE surfaces

International Nuclear Information System (INIS)

Martín, Jaime; Martín-González, Marisol; Del Campo, Adolfo; Reinosa, Julián J; Fernández, José Francisco

2012-01-01

We present a simple, efficient, and high-throughput methodology for the fabrication of ordered nanoporous polymeric surfaces with areas in the range of cm 2 . The procedure is based on a two-stage replication of a master nanostructured pattern. The process starts with the preparation of an ordered array of poly(tetrafluoroethylene) (PTFE) free-standing nanopillars by wetting self-ordered porous anodic aluminum oxide templates with molten PTFE. The nanopillars are 120 nm in diameter and approximately 350 nm long, while the array extends over cm 2 . The PTFE nanostructuring process induces surface hydrocarbonation of the nanopillars, as revealed by confocal Raman microscopy/spectroscopy, which enhances the wettability of the originally hydrophobic material and facilitates its subsequent use as an inverse pattern. Thus, the PTFE nanostructure is then used as a negative master for the fabrication of macroscopic hexagonal arrays of nanopores composed of biocompatible poly(vinylalcohol). In this particular case, the nanopores are 130–140 nm in diameter and the interpore distance is around 430 nm. Features of such characteristic dimensions are known to be easily recognized by living cells. Moreover, the inverse mold is not destroyed in the pore array demolding process and can be reused for further pore array fabrication. Therefore, the developed method allows the high-throughput production of cm 2 -scale biocompatible nanoporous surfaces that could be interesting as two-dimensional scaffolds for tissue repair or wound healing. Moreover, our approach can be extrapolated to the fabrication of almost any polymer and biopolymer ordered pore array. (paper)

3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

Science.gov (United States)

Cho, Nam-Hoon; Choi, Heung-Kook

2014-01-01

One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system. PMID:25371701

3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

Directory of Open Access Journals (Sweden)

Tae-Yun Kim

2014-01-01

Full Text Available One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system.

Quantization of liver tissue in dual kVp computed tomography using linear discriminant analysis

Science.gov (United States)

Tkaczyk, J. Eric; Langan, David; Wu, Xiaoye; Xu, Daniel; Benson, Thomas; Pack, Jed D.; Schmitz, Andrea; Hara, Amy; Palicek, William; Licato, Paul; Leverentz, Jaynne

2009-02-01

Linear discriminate analysis (LDA) is applied to dual kVp CT and used for tissue characterization. The potential to quantitatively model both malignant and benign, hypo-intense liver lesions is evaluated by analysis of portal-phase, intravenous CT scan data obtained on human patients. Masses with an a priori classification are mapped to a distribution of points in basis material space. The degree of localization of tissue types in the material basis space is related to both quantum noise and real compositional differences. The density maps are analyzed with LDA and studied with system simulations to differentiate these factors. The discriminant analysis is formulated so as to incorporate the known statistical properties of the data. Effective kVp separation and mAs relates to precision of tissue localization. Bias in the material position is related to the degree of X-ray scatter and partial-volume effect. Experimental data and simulations demonstrate that for single energy (HU) imaging or image-based decomposition pixel values of water-like tissues depend on proximity to other iodine-filled bodies. Beam-hardening errors cause a shift in image value on the scale of that difference sought between in cancerous and cystic lessons. In contrast, projection-based decomposition or its equivalent when implemented on a carefully calibrated system can provide accurate data. On such a system, LDA may provide novel quantitative capabilities for tissue characterization in dual energy CT.

An efficient method for evaluating RRAM crossbar array performance

Science.gov (United States)

Song, Lin; Zhang, Jinyu; Chen, An; Wu, Huaqiang; Qian, He; Yu, Zhiping

2016-06-01

An efficient method is proposed in this paper to mitigate computational burden in resistive random access memory (RRAM) array simulation. In the worst case scenario, a 4 Mb RRAM array with line resistance is greatly reduced using this method. For 1S1R-RRAM array structures, static and statistical parameters in both reading and writing processes are simulated. Error analysis is performed to prove the reliability of the algorithm when line resistance is extremely small compared with the junction resistance. Results show that high precision is maintained even if the size of RRAM array is reduced by one thousand times, which indicates significant improvements in both computational efficiency and memory requirements.

Spectroscopic analysis of bladder cancer tissues using Fourier transform infrared spectroscopy

Science.gov (United States)

Al-Muslet, Nafie A.; Ali, Essam E.

2012-03-01

Bladder cancer is one of the most common cancers in Africa. It takes several days to reach a diagnosis using histological examinations of specimens obtained by endoscope, which increases the medical expense. Recently, spectroscopic analysis of bladder cancer tissues has received considerable attention as a diagnosis technique due to its sensitivity to biochemical variations in the samples. This study investigated the use of Fourier transform infrared (FTIR) spectroscopy to analyze a number of bladder cancer tissues. Twenty-two samples were collected from 11 patients diagnosed with bladder cancer from different hospitals without any pretreatment. From each patient two samples were collected, one normal and another cancerous. FTIR spectrometer was used to differentiate between normal and cancerous bladder tissues via changes in spectra of these samples. The investigations detected obvious changes in the bands of proteins (1650, 1550 cm-1), lipids (2925, 2850 cm-1), and nucleic acid (1080, 1236 cm-1). The results show that FTIR spectroscopy is promising as a rapid, accurate, nondestructive, and easy to use alternative method for identification and diagnosis of bladder cancer tissues.

Read/write schemes analysis for novel complementary resistive switches in passive crossbar memory arrays

International Nuclear Information System (INIS)

Yu Shimeng; Liang Jiale; Wu Yi; Wong, H-S Philip

2010-01-01

Recently a prototype of complementary resistive switches has been proposed to solve the sneak-path problem in passive crossbar memory arrays. To further evaluate the potential of this novel cell structure for practical applications, we present a modeling analysis to capture its switching dynamics and analyze its unique read/write schemes. The model is corroborated by experimental data. We found a trade-off between the read voltage window and write voltage window. The constraint from avoiding disturbance on unselected cells is critical for proper functionality, which in turn limits the writing speed.

A pattern recognition approach to transistor array parameter variance

Science.gov (United States)

da F. Costa, Luciano; Silva, Filipi N.; Comin, Cesar H.

2018-06-01

The properties of semiconductor devices, including bipolar junction transistors (BJTs), are known to vary substantially in terms of their parameters. In this work, an experimental approach, including pattern recognition concepts and methods such as principal component analysis (PCA) and linear discriminant analysis (LDA), was used to experimentally investigate the variation among BJTs belonging to integrated circuits known as transistor arrays. It was shown that a good deal of the devices variance can be captured using only two PCA axes. It was also verified that, though substantially small variation of parameters is observed for BJT from the same array, larger variation arises between BJTs from distinct arrays, suggesting the consideration of device characteristics in more critical analog designs. As a consequence of its supervised nature, LDA was able to provide a substantial separation of the BJT into clusters, corresponding to each transistor array. In addition, the LDA mapping into two dimensions revealed a clear relationship between the considered measurements. Interestingly, a specific mapping suggested by the PCA, involving the total harmonic distortion variation expressed in terms of the average voltage gain, yielded an even better separation between the transistor array clusters. All in all, this work yielded interesting results from both semiconductor engineering and pattern recognition perspectives.

Phased laser diode array permits selective excitation of ultrasonic guided waves in coated bone-mimicking tubes

Science.gov (United States)

Moilanen, Petro; Salmi, Ari; Kilappa, Vantte; Zhao, Zuomin; Timonen, Jussi; Hæggström, Edward

2017-10-01

This paper validates simulation predictions, which state that specific modes could be enhanced in quantitative ultrasonic bone testing. Tunable selection of ultrasonic guided wave excitation is useful in non-destructive testing since it permits the mediation of energy into diagnostically useful modes while reducing the energy mediated into disturbing contributions. For instance, it is often challenging to distinguish and extract the useful modes from ultrasound signals measured in bone covered by a soft tissue. We show that a laser diode array can selectively excite ultrasound in bone mimicking phantoms. A fiber-coupled diode array (4 elements) illuminated two solid tubes (2-3 mm wall thickness) embraced by an opaque soft-tissue mimicking elastomer coating (5 mm thick). A predetermined time delay matching the selected mode and frequency was employed between the outputs of the elements. The generated ultrasound was detected by a 215 kHz piezo receiver. Our results suggest that this array reduces the disturbances caused by the elastomer cover and so pave way to permit non-contacting in vivo guided wave ultrasound assessment of human bones. The implementation is small, inexpensive, and robust in comparison with the conventional pulsed lasers.

Concurrent array-based queue

Science.gov (United States)

Heidelberger, Philip; Steinmacher-Burow, Burkhard

2015-01-06

According to one embodiment, a method for implementing an array-based queue in memory of a memory system that includes a controller includes configuring, in the memory, metadata of the array-based queue. The configuring comprises defining, in metadata, an array start location in the memory for the array-based queue, defining, in the metadata, an array size for the array-based queue, defining, in the metadata, a queue top for the array-based queue and defining, in the metadata, a queue bottom for the array-based queue. The method also includes the controller serving a request for an operation on the queue, the request providing the location in the memory of the metadata of the queue.

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

Science.gov (United States)

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

2014-02-15

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

Multi-terabyte EIDE disk arrays running Linux RAID5

International Nuclear Information System (INIS)

Sanders, D.A.; Cremaldi, L.M.; Eschenburg, V.; Godang, R.; Joy, M.D.; Summers, D.J.; Petravick, D.L.

2004-01-01

High-energy physics experiments are currently recording large amounts of data and in a few years will be recording prodigious quantities of data. New methods must be developed to handle this data and make analysis at universities possible. Grid Computing is one method; however, the data must be cached at the various Grid nodes. We examine some storage techniques that exploit recent developments in commodity hardware. Disk arrays using RAID level 5 (RAID-5) include both parity and striping. The striping improves access speed. The parity protects data in the event of a single disk failure, but not in the case of multiple disk failures. We report on tests of dual-processor Linux Software RAID-5 arrays and Hardware RAID-5 arrays using a 12-disk 3ware controller, in conjunction with 250 and 300 GB disks, for use in offline high-energy physics data analysis. The price of IDE disks is now less than $1/GB. These RAID-5 disk arrays can be scaled to sizes affordable to small institutions and used when fast random access at low cost is important

Multi-terabyte EIDE disk arrays running Linux RAID5

Energy Technology Data Exchange (ETDEWEB)

Sanders, D.A.; Cremaldi, L.M.; Eschenburg, V.; Godang, R.; Joy, M.D.; Summers, D.J.; /Mississippi U.; Petravick, D.L.; /Fermilab

2004-11-01

High-energy physics experiments are currently recording large amounts of data and in a few years will be recording prodigious quantities of data. New methods must be developed to handle this data and make analysis at universities possible. Grid Computing is one method; however, the data must be cached at the various Grid nodes. We examine some storage techniques that exploit recent developments in commodity hardware. Disk arrays using RAID level 5 (RAID-5) include both parity and striping. The striping improves access speed. The parity protects data in the event of a single disk failure, but not in the case of multiple disk failures. We report on tests of dual-processor Linux Software RAID-5 arrays and Hardware RAID-5 arrays using a 12-disk 3ware controller, in conjunction with 250 and 300 GB disks, for use in offline high-energy physics data analysis. The price of IDE disks is now less than $1/GB. These RAID-5 disk arrays can be scaled to sizes affordable to small institutions and used when fast random access at low cost is important.

Human soft tissue analysis using x-ray or gamma-ray techniques

International Nuclear Information System (INIS)

Theodorakou, C; Farquharson, M J

2008-01-01

This topical review is intended to describe the x-ray techniques used for human soft tissue analysis. X-ray techniques have been applied to human soft tissue characterization and interesting results have been presented over the last few decades. The motivation behind such studies is to provide improved patient outcome by using the data obtained to better understand a disease process and improve diagnosis. An overview of theoretical background as well as a complete set of references is presented. For each study, a brief summary of the methodology and results is given. The x-ray techniques include x-ray diffraction, x-ray fluorescence, Compton scattering, Compton to coherent scattering ratio and attenuation measurements. The soft tissues that have been classified using x-rays or gamma rays include brain, breast, colon, fat, kidney, liver, lung, muscle, prostate, skin, thyroid and uterus. (topical review)

Measurement of cytokine and adhesion molecule expression in synovial tissue by digital image analysis

NARCIS (Netherlands)

Kraan, M. C.; Smith, M. D.; Weedon, H.; Ahern, M. J.; Breedveld, F. C.; Tak, P. P.

2001-01-01

Digital image analysis (DIA) offers the opportunity to quantify the stained area and staining intensity when synovial tissue (ST) is investigated by immunohistochemical analysis. This study aimed at determining the sensitivity of DIA compared with semiquantitative analysis (SQA). Paired ST samples

Phased Array Ultrasonic Evaluation of Space Shuttle Main Engine (SSME) Nozzle Weld

Science.gov (United States)

James, Steve; Engel, J.; Kimbrough, D.; Suits, M.; Hopson, George (Technical Monitor)

2001-01-01

This viewgraph presentation gives an overview of the phased array ultrasonic evaluation of the Space Shuttle Main Engine (SSME) nozzle weld. Details are given on the nondestructive testing evaluation approach, conventional shear wave and phased array techniques, and an x-ray versus phased array risk analysis. The field set-up was duplicated to the greatest extent possible in the laboratory and the phased array ultrasonic technique was developed and validated prior to weld evaluation. Results are shown for the phased array ultrasonic evaluation and conventional ultrasonic evaluation results.

Study and operating conditions of HTS Josephson arrays for metrological application

International Nuclear Information System (INIS)

Sosso, A.; Lacquaniti, V.; Andreone, D.; Cerri, R.; Klushin, A.M.

2006-01-01

We report an experimental study of metrological properties of high-temperature superconductor arrays, made of shunted bicrystal YBCO Josephson junctions. The work is mainly based on a direct comparison against a low temperature array. Owing to the high sensitivity of the measurements, we observed at nanovolt level the changes in the HTS array voltage on a step. A precise estimate of the dependence of the HTS array step width on operating conditions was obtained. Differences were observed with respect to the results of low sensitivity techniques, confirming that our method is necessary in the study of HTS arrays for metrology. The high sensitivity analysis was also applied in the derivation of the temperature dependence of the critical current, providing insights on the behavior of the HTS array

ZnO nanorod arrays grown under different pressures and their photoluminescence properties

Energy Technology Data Exchange (ETDEWEB)

Meng Xiuqing [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic ZoneChangchun 130033 (China); Graduate School of the Chinese Academy of Sciences (China); Zhao Dongxu [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic ZoneChangchun 130033 (China)]. E-mail: dxzhao2000@yahoo.com.cn; Shen Dezhen [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic ZoneChangchun 130033 (China); Zhang Jiying [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic ZoneChangchun 130033 (China); Li Binghui [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic ZoneChangchun 130033 (China); Wang Xiaohua [National Key Laboratory of High Power Semiconductor Laser, Changchun University of Science and technology, 7089 Weixing Road Changchun (China); Fan Xiwu [Key Laboratory of Excited State Processes, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 16 East Nan-Hu Road, Open Economic ZoneChangchun 130033 (China)

2007-01-15

The ZnO nanorod arrays were synthesized via a simple vapor deposition method on Si (1 1 1) substrates at a low growth temperature of 520 deg. C. By selecting different source materials under different growth pressures, well-aligned hexagonal-shaped ZnO nanorod arrays were obtained under both conditions. X-ray diffraction (XRD) analysis confirmed the nanorods are c-axis orientated. Selected area electron diffraction (SAED) and transmission electron microscopy (TEM) analysis demonstrated the individual nanorod is single crystal. Photoluminescence (PL) analyses show the superior optical properties of the nanorod arrays.

ZnO nanorod arrays grown under different pressures and their photoluminescence properties

International Nuclear Information System (INIS)

Meng Xiuqing; Zhao Dongxu; Shen Dezhen; Zhang Jiying; Li Binghui; Wang Xiaohua; Fan Xiwu

2007-01-01

The ZnO nanorod arrays were synthesized via a simple vapor deposition method on Si (1 1 1) substrates at a low growth temperature of 520 deg. C. By selecting different source materials under different growth pressures, well-aligned hexagonal-shaped ZnO nanorod arrays were obtained under both conditions. X-ray diffraction (XRD) analysis confirmed the nanorods are c-axis orientated. Selected area electron diffraction (SAED) and transmission electron microscopy (TEM) analysis demonstrated the individual nanorod is single crystal. Photoluminescence (PL) analyses show the superior optical properties of the nanorod arrays

Numerical Signal Analysis of Thermo-Cyclically Operated MOG Gas Sensor Arrays for Early Identification of Emissions from Overloaded Electric Cables

Directory of Open Access Journals (Sweden)

Rolf Seifert

2015-10-01

Full Text Available A thermo-cyclically operated multi metal oxide gas sensor (MOG array is introduced together with a novel signal analysis approach (SimSens for identifying the emissions from overheated isolation cable materials thereby detecting the fires originated in electrical cabinets at early stages. The MOG array can yield specific conductance signatures appropriate to specifically identify gases. The obtained results bear good capability for detection and identification of pyrolysis gas emissions at relatively low sample heating temperatures even before a visible color-change of the polyvinyl chloride (PVC-isolation material. The dynamic conductance signals were evaluated using SimSens, a numerical analysis tool designed for simultaneous evaluation of conductance profiles. The results show promising pyrolysis gas identification and concentration determination capabilities in relation to the conductance profile shapes of model gases like carbon monoxide (CO and propene.

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

Science.gov (United States)

Rauschenbach, H. S.

1980-01-01

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

Development of stereotactically guided laser interstitial thermotherapy of breast cancer: in situ measurement and analysis of the temperature field in ex vivo and in vivo adipose tissue.

Science.gov (United States)

Milne, P J; Parel, J M; Manns, F; Denham, D B; Gonzalez-Cirre, X; Robinson, D S

2000-01-01

The size (0.5-1.0 cm) of early nonpalpable breast tumors currently detected by mammography and confirmed by stereotactic core biopsy is of the order of the penetration depth of near infrared photons in breast tissue. In principle, stereotactically biopsied tumors, therefore, could be safely and efficiently treated with laser thermotherapy. The aim of the current study is to confirm the controlled heating produced by clinically relevant power levels delivered with an interstitial laser fiber optic probe adapted for use with stereotactic mammography and biopsy procedures. Temperature increases and the resultant thermal field produced by the irradiation of ex vivo (porcine and human) and in vivo (porcine) tissue models appropriate to the treatment of human breast tissue by using cw Nd:YAG laser radiation delivered with a interstitial fiber optic probe with a quartz diffusing tip, were recorded with an array of fifteen 23-gauge needle thermocouple probes connected to a laboratory computer-based data acquisition system. By using a stepwise decreasing power cycle to avoid tissue charring, acceptably symmetric thermal fields of repeatable volumetric dimensions were obtained. Reproducible thermal gradients and predictable tissue necrosis without carbonization could be induced in a 3-cm-diameter region around the fiber probe during a single treatment lasting only 3 minutes. The time-dependences of the temperature rise of the thermocouples surrounding the LITT probe were quantitatively modeled with simple linear functions during the applied laser heating cycles. Analysis of our experimental results show that reproducible, symmetric and predictable volumetric temperature increases in time can be reliably produced by interstitial laser thermotherapy. Copyright 2000 Wiley-Liss, Inc.

Analysis of tooth tissues using Raman spectroscopy

International Nuclear Information System (INIS)

Timchenko, E.V.; Timchenko, P.E.; Kulabukhova, A.Yu.; Volova, L.T.; Rosenbaum, A.Yu.

2016-01-01

The results of experimental studies of healthy tooth tissue and tooth tissues during caries disease are presented. Features of Raman spectrum of tooth tissues during caries disease are obtained: the main changes are detected at wavenumbers 956 cm -1 .1069 cm -1 . corresponding to phosphates. and 1241 cm -1 . 1660 cm -1 . corresponding to collagen III and collagen I. respectively. Were introduced criteria allowing to detect caries and to identify weakening of tooth tissues. preceding the caries. The reliability of research results is confirmed by scanning electron microscopy. (paper)

Creation of Cardiac Tissue Exhibiting Mechanical Integration of Spheroids Using 3D Bioprinting.

Science.gov (United States)

Ong, Chin Siang; Fukunishi, Takuma; Nashed, Andrew; Blazeski, Adriana; Zhang, Huaitao; Hardy, Samantha; DiSilvestre, Deborah; Vricella, Luca; Conte, John; Tung, Leslie; Tomaselli, Gordon; Hibino, Narutoshi

2017-07-02

This protocol describes 3D bioprinting of cardiac tissue without the use of biomaterials, using only cells. Cardiomyocytes, endothelial cells and fibroblasts are first isolated, counted and mixed at desired cell ratios. They are co-cultured in individual wells in ultra-low attachment 96-well plates. Within 3 days, beating spheroids form. These spheroids are then picked up by a nozzle using vacuum suction and assembled on a needle array using a 3D bioprinter. The spheroids are then allowed to fuse on the needle array. Three days after 3D bioprinting, the spheroids are removed as an intact patch, which is already spontaneously beating. 3D bioprinted cardiac patches exhibit mechanical integration of component spheroids and are highly promising in cardiac tissue regeneration and as 3D models of heart disease.

Topology optimization of Halbach magnet arrays using isoparametric projection

International Nuclear Information System (INIS)

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

2017-01-01

Highlights: • Design method of Halbach magnet array is proposed using topology optimization. • Magnet strength and direction are simultaneously optimized by isoparametric projection. • For manufacturing feasibility of magnet, penalization and extrusion schemes are proposed. • Design results of circular shaped Halbach arrays are provided. • Halbach arrays in linear actuator are optimized to maximize magnetic force. - Abstract: Topology optimization using isoparametric projection for the design of permanent magnet patterns in Halbach arrays is proposed. Based on isoparametric shape functions used in the finite element analysis, the permanent magnet strength and magnetization directions in a Halbach array are simultaneously optimized for a given design goal. To achieve fabrication feasibility of a designed Halbach magnet array, two design schemes are combined with the isoparametric projection method. First, a penalization scheme is proposed for designing the permanent magnets to have discrete magnetization direction angles. Second, an extrusion scheme is proposed for the shape regularization of the permanent magnet segments. As a result, the method systematically finds the optimal permanent magnet patterns of a Halbach array considering manufacturing feasibility. In two numerical examples, a circular shaped permanent magnet Halbach array is designed to minimize the magnitude of the magnetic flux density and to maximize the upward direction magnetic flux density inside the magnet array. Logical extension of the method to the design of permanent magnet arrays in linear actuators is provided, where the design goal is to maximize the actuator magnetic force.

Topology optimization of Halbach magnet arrays using isoparametric projection

Energy Technology Data Exchange (ETDEWEB)

Lee, Jaewook, E-mail: jaewooklee@gist.ac.kr [School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005 (Korea, Republic of); Nomura, Tsuyoshi [Toyota Central R& D Labs., Inc., 41-1 Yokomichi, Aichi 480-1192 (Japan); Toyota Research Institute of North America, 1555 Woodridge Avenue, Ann Arbor, MI 48105 (United States); Dede, Ercan M. [Toyota Research Institute of North America, 1555 Woodridge Avenue, Ann Arbor, MI 48105 (United States)

2017-06-15

Highlights: • Design method of Halbach magnet array is proposed using topology optimization. • Magnet strength and direction are simultaneously optimized by isoparametric projection. • For manufacturing feasibility of magnet, penalization and extrusion schemes are proposed. • Design results of circular shaped Halbach arrays are provided. • Halbach arrays in linear actuator are optimized to maximize magnetic force. - Abstract: Topology optimization using isoparametric projection for the design of permanent magnet patterns in Halbach arrays is proposed. Based on isoparametric shape functions used in the finite element analysis, the permanent magnet strength and magnetization directions in a Halbach array are simultaneously optimized for a given design goal. To achieve fabrication feasibility of a designed Halbach magnet array, two design schemes are combined with the isoparametric projection method. First, a penalization scheme is proposed for designing the permanent magnets to have discrete magnetization direction angles. Second, an extrusion scheme is proposed for the shape regularization of the permanent magnet segments. As a result, the method systematically finds the optimal permanent magnet patterns of a Halbach array considering manufacturing feasibility. In two numerical examples, a circular shaped permanent magnet Halbach array is designed to minimize the magnitude of the magnetic flux density and to maximize the upward direction magnetic flux density inside the magnet array. Logical extension of the method to the design of permanent magnet arrays in linear actuators is provided, where the design goal is to maximize the actuator magnetic force.

LIBS analysis of artificial calcified tissues matrices.

Science.gov (United States)

Kasem, M A; Gonzalez, J J; Russo, R E; Harith, M A

2013-04-15

In most laser-based analytical methods, the reproducibility of quantitative measurements strongly depends on maintaining uniform and stable experimental conditions. For LIBS analysis this means that for accurate estimation of elemental concentration, using the calibration curves obtained from reference samples, the plasma parameters have to be kept as constant as possible. In addition, calcified tissues such as bone are normally less "tough" in their texture than many samples, especially metals. Thus, the ablation process could change the sample morphological features rapidly, and result in poor reproducibility statistics. In the present work, three artificial reference sample sets have been fabricated. These samples represent three different calcium based matrices, CaCO3 matrix, bone ash matrix and Ca hydroxyapatite matrix. A comparative study of UV (266 nm) and IR (1064 nm) LIBS for these three sets of samples has been performed under similar experimental conditions for the two systems (laser energy, spot size, repetition rate, irradiance, etc.) to examine the wavelength effect. The analytical results demonstrated that UV-LIBS has improved reproducibility, precision, stable plasma conditions, better linear fitting, and the reduction of matrix effects. Bone ash could be used as a suitable standard reference material for calcified tissue calibration using LIBS with a 266 nm excitation wavelength. Copyright © 2013 Elsevier B.V. All rights reserved.

Discriminant analysis of normal and malignant breast tissue based upon INAA investigation of elemental concentration

International Nuclear Information System (INIS)

Kwanhoong Ng; Senghuat Ong; Bradley, D.A.; Laimeng Looi

1997-01-01

Discriminant analysis of six trace element concentrations measured by instrumental neutron activation analysis (INAA) in 26 paired-samples of malignant and histologically normal human breast tissues shows the technique to be a potentially valuable clinical tool for making malignant-normal classification. Nonparametric discriminant analysis is performed for the data obtained. Linear and quadratic discriminant analyses are also carried out for comparison. For this data set a formal analysis shows that the elements which may be useful in distinguishing between malignant and normal tissues are Ca, Rb and Br, providing correct classification for 24 out of 26 normal samples and 22 out of 26 malignant samples. (Author)

Programmable cellular arrays. Faults testing and correcting in cellular arrays

International Nuclear Information System (INIS)

Cercel, L.

1978-03-01

A review of some recent researches about programmable cellular arrays in computing and digital processing of information systems is presented, and includes both combinational and sequential arrays, with full arbitrary behaviour, or which can realize better implementations of specialized blocks as: arithmetic units, counters, comparators, control systems, memory blocks, etc. Also, the paper presents applications of cellular arrays in microprogramming, in implementing of a specialized computer for matrix operations, in modeling of universal computing systems. The last section deals with problems of fault testing and correcting in cellular arrays. (author)

Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays

Directory of Open Access Journals (Sweden)

Nixon Tamara J

2008-05-01

Full Text Available Abstract Background Tumor-predominant splice isoforms were identified during comparative in silico sequence analysis of EST clones, suggesting that global aberrant alternative pre-mRNA splicing may be an epigenetic phenomenon in cancer. We used an exon expression array to perform an objective, genome-wide survey of glioma-specific splicing in 24 GBM and 12 nontumor brain samples. Validation studies were performed using RT-PCR on glioma cell lines, patient tumor and nontumor brain samples. Results In total, we confirmed 14 genes with glioma-specific splicing; seven were novel events identified by the exon expression array (A2BP1, BCAS1, CACNA1G, CLTA, KCNC2, SNCB, and TPD52L2. Our data indicate that large changes (> 5-fold in alternative splicing are infrequent in gliomagenesis ( Conclusion While we observed some tumor-specific alternative splicing, the number of genes showing exclusive tumor-specific isoforms was on the order of tens, rather than the hundreds suggested previously by in silico mining. Given the important role of alternative splicing in neural differentiation, there may be selective pressure to maintain a majority of splicing events in order to retain glial-like characteristics of the tumor cells.

Electronic tongue - an array of non-specific chemical sensors - for analysis of radioactive solutions

International Nuclear Information System (INIS)

Legin, A.; Rudnitskaya, A.; Babain, V.

2006-01-01

Multisensor systems, combining chemical sensor arrays with multivariate data processing engines (electronic tongue) rapidly and successfully developing in the last years are capable of simultaneous quantitative analysis of several species, e.g. metals, in complex real solutions. The expansion of the metals (metal ions) and species to be detected in radioactive waste requires permanent enhancement of sensing materials and sensors, with seriously different properties from those known earlier. A prospective direction of R and D of novel sensing materials is exploitation of radiochemical extraction systems and application of extraction substances as active components of new sensors. The sensors based on bidentate phosphorous organic compounds and their combinations with chlorinated cobalt dicarbollide displayed high sensitivity and selectivity to rare-earth metal ions La 3+ , Pr 3+ , Nd 3+ , Eu 3+ . The results indicated good promise for the development of novel analytical tools for detection of multivalent metal cations in different media, particularly in corrosive solutions such as radioactive wastes and solutions derived from spent nuclear fuel. The sensors and sensor arrays made on their basis can play an important role in the development of 'electronic tongue' systems for rapid analytical determinations of different components in complex radioactive solutions

Aligned Carbon Nanotube Arrays Bonded to Solid Graphite Substrates: Thermal Analysis for Future Device Cooling Applications

Directory of Open Access Journals (Sweden)

Betty T. Quinton

2018-05-01

Full Text Available Carbon nanotubes (CNTs are known for high thermal conductivity and have potential use as nano-radiators or heat exchangers. This paper focuses on the thermal performance of carpet-like arrays of vertically aligned CNTs on solid graphite substrates with the idea of investigating their behavior as a function of carpet dimensions and predicting their performance as thermal interface material (TIM for electronic device cooling. Vertically aligned CNTs were grown on highly oriented pyrolytic graphite (HOPG substrate, which creates a robust and durable all-carbon hierarchical structure. The multi-layer thermal analysis approach using Netzsch laser flash analysis system was used to evaluate their performance as a function of carpet height, from which their thermal properties can be determined. It was seen that the thermal resistance of the CNT array varies linearly with CNT carpet height, providing a unique way of decoupling the properties of the CNT carpet from its interface. This data was used to estimate the thermal conductivity of individual multi-walled nanotube strands in this carpet, which was about 35 W/m-K. The influence of CNT carpet parameters (aerial density, diameter, and length on thermal resistance of the CNT carpet and its potential advantages and limitations as an integrated TIM are discussed.

Telescoping Solar Array Concept for Achieving High Packaging Efficiency

Science.gov (United States)

Mikulas, Martin; Pappa, Richard; Warren, Jay; Rose, Geoff

2015-01-01

Lightweight, high-efficiency solar arrays are required for future deep space missions using high-power Solar Electric Propulsion (SEP). Structural performance metrics for state-of-the art 30-50 kW flexible blanket arrays recently demonstrated in ground tests are approximately 40 kW/cu m packaging efficiency, 150 W/kg specific power, 0.1 Hz deployed stiffness, and 0.2 g deployed strength. Much larger arrays with up to a megawatt or more of power and improved packaging and specific power are of interest to mission planners for minimizing launch and life cycle costs of Mars exploration. A new concept referred to as the Compact Telescoping Array (CTA) with 60 kW/cu m packaging efficiency at 1 MW of power is described herein. Performance metrics as a function of array size and corresponding power level are derived analytically and validated by finite element analysis. Feasible CTA packaging and deployment approaches are also described. The CTA was developed, in part, to serve as a NASA reference solar array concept against which other proposed designs of 50-1000 kW arrays for future high-power SEP missions could be compared.

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Directory of Open Access Journals (Sweden)

Rasley Amy

2006-06-01

Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

Implantable liquid metal-based flexible neural microelectrode array and its application in recovering animal locomotion functions

Science.gov (United States)

Guo, Rui; Liu, Jing

2017-10-01

With significant advantages in rapidly restoring the nerve function, electrical stimulation of nervous tissue is a crucial treatment of peripheral nerve injuries leading to common movement disorder. However, the currently available stimulating electrodes generally based on rigid conductive materials would cause a potential mechanical mismatch with soft neural tissues which thus reduces long-term effects of electrical stimulation. Here, we proposed and fabricated a flexible neural microelectrode array system based on the liquid metal GaIn alloy (75.5% Ga and 24.5% In by weight) and via printing approach. Such an alloy with a unique low melting point (10.35 °C) owns excellent electrical conductivity and high compliance, which are beneficial to serve as implantable flexible neural electrodes. The flexible neural microelectrode array embeds four liquid metal electrodes and stretchable interconnects in a PDMS membrane (500 µm in thickness) that possess a lower elastic modulus (1.055 MPa), which is similar to neural tissues with elastic moduli in the 0.1-1.5 MPa range. The electrical experiments indicate that the liquid metal interconnects could sustain over 7000 mechanical stretch cycles with resistance approximately staying at 4 Ω. Over the conceptual experiments on animal sciatic nerve electrical stimulation, the dead bullfrog implanted with flexible neural microelectrode array could even rhythmically contract and move its lower limbs under the electrical stimulations from the implant. This demonstrates a highly efficient way for quickly recovering biological nerve functions. Further, the good biocompatibility of the liquid metal material was justified via a series of biological experiments. This liquid metal modality for neural stimulation is expected to play important roles as biologic electrodes to overcome the fundamental mismatch in mechanics between biological tissues and electronic devices in the coming time.

Implantable liquid metal-based flexible neural microelectrode array and its application in recovering animal locomotion functions

International Nuclear Information System (INIS)

Guo, Rui; Liu, Jing

2017-01-01

With significant advantages in rapidly restoring the nerve function, electrical stimulation of nervous tissue is a crucial treatment of peripheral nerve injuries leading to common movement disorder. However, the currently available stimulating electrodes generally based on rigid conductive materials would cause a potential mechanical mismatch with soft neural tissues which thus reduces long-term effects of electrical stimulation. Here, we proposed and fabricated a flexible neural microelectrode array system based on the liquid metal GaIn alloy (75.5% Ga and 24.5% In by weight) and via printing approach. Such an alloy with a unique low melting point (10.35 °C) owns excellent electrical conductivity and high compliance, which are beneficial to serve as implantable flexible neural electrodes. The flexible neural microelectrode array embeds four liquid metal electrodes and stretchable interconnects in a PDMS membrane (500 µ m in thickness) that possess a lower elastic modulus (1.055 MPa), which is similar to neural tissues with elastic moduli in the 0.1–1.5 MPa range. The electrical experiments indicate that the liquid metal interconnects could sustain over 7000 mechanical stretch cycles with resistance approximately staying at 4 Ω. Over the conceptual experiments on animal sciatic nerve electrical stimulation, the dead bullfrog implanted with flexible neural microelectrode array could even rhythmically contract and move its lower limbs under the electrical stimulations from the implant. This demonstrates a highly efficient way for quickly recovering biological nerve functions. Further, the good biocompatibility of the liquid metal material was justified via a series of biological experiments. This liquid metal modality for neural stimulation is expected to play important roles as biologic electrodes to overcome the fundamental mismatch in mechanics between biological tissues and electronic devices in the coming time. (paper)

Wound healing with nonthermal microplasma jets generated in arrays of hourglass microcavity devices

Science.gov (United States)

Hum Park, Chan; Lee, Joong Seob; Heui Kim, Ji; Kim, Dong-Kyu; Lee, Ok Joo; Ju, Hyung Woo; Moon, Bo Mi; Cho, Jin Hoon; Kim, Min Hwan; Sun, Peter Peng; Park, Sung-Jin; Eden, J. Gary

2014-10-01

Clinical studies are reported in which artificial wounds in rat epidermal and dermal tissue have been treated by arrays of sub-500 µm diameter, low temperature plasma microjets. Fabricated in Al/nanoporous alumina (Al2O3) by wet chemical and microablation processes, each plasma jet device has a double parabolic (hourglass) structure, and arrays as large as 6  ×  6 devices with 500 µm diameter apertures have been tested to date. Treatment of 1 cm2 acute epidermal wounds for 20-40 s daily with an array of microplasma jets generated in He feedstock gas promoted wound recovery significantly, as evidenced by tissue histology and measured wound area. Seven days after wound formation, the wound area of the untreated control was 40  ±  2% of its initial value, whereas that for an identical wound treated twice daily for 20 s was 9  ±  2% of its original surface area. No histological distinctions were observed between wounds treated twice each day for 10 or 20 s - only the full recovery time differed. Spectra produced in the visible and ultraviolet by He jets in room air are dominated by atomic oxygen (3p 5P → 3s 5S) at 777 nm and violet fluorescence (391.4 nm) from N2+, a species produced when the He (2s 3S1) metastable is deactivated by Penning ionization of N2. Although the combined cross-sectional area of the jets in the array is only 7% of the wound area, the microplasma treatment results in spatially uniform, and accelerated, wound healing. Both effects are attributed to the increased surface area of the jet array (relative to a single jet having an equivalent diameter) and the concomitant enhancement in the generation of molecular radicals, and metastable atoms and molecules (such as {{\\text{N}}2}≤ft(A{}{}3 Σ \\text{u}+\\right) ).

Wound healing with nonthermal microplasma jets generated in arrays of hourglass microcavity devices

International Nuclear Information System (INIS)

Park, Chan Hum; Lee, Joong Seob; Kim, Ji Heui; Kim, Dong-Kyu; Lee, Ok Joo; Ju, Hyung Woo; Moon, Bo Mi; Cho, Jin Hoon; Kim, Min Hwan; Sun, Peter Peng; Park, Sung-Jin; Eden, J Gary

2014-01-01

Clinical studies are reported in which artificial wounds in rat epidermal and dermal tissue have been treated by arrays of sub-500 µm diameter, low temperature plasma microjets. Fabricated in Al/nanoporous alumina (Al 2 O 3 ) by wet chemical and microablation processes, each plasma jet device has a double parabolic (hourglass) structure, and arrays as large as 6  ×  6 devices with 500 µm diameter apertures have been tested to date. Treatment of 1 cm 2 acute epidermal wounds for 20–40 s daily with an array of microplasma jets generated in He feedstock gas promoted wound recovery significantly, as evidenced by tissue histology and measured wound area. Seven days after wound formation, the wound area of the untreated control was 40  ±  2% of its initial value, whereas that for an identical wound treated twice daily for 20 s was 9  ±  2% of its original surface area. No histological distinctions were observed between wounds treated twice each day for 10 or 20 s – only the full recovery time differed. Spectra produced in the visible and ultraviolet by He jets in room air are dominated by atomic oxygen (3p 5 P → 3s 5 S) at 777 nm and violet fluorescence (391.4 nm) from N 2 + , a species produced when the He (2s 3 S 1 ) metastable is deactivated by Penning ionization of N 2 . Although the combined cross-sectional area of the jets in the array is only 7% of the wound area, the microplasma treatment results in spatially uniform, and accelerated, wound healing. Both effects are attributed to the increased surface area of the jet array (relative to a single jet having an equivalent diameter) and the concomitant enhancement in the generation of molecular radicals, and metastable atoms and molecules (such as N 2 (A 3 Σ u + )). (paper)

SEP solar array Shuttle flight experiment

Science.gov (United States)

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.

Multielement analysis by neutron activation of tissues from swine administered copper supplemented diets

International Nuclear Information System (INIS)

Stroube, W.B. Jr.; Cunningham, W.C.; Tanner, J.T.; Bradley, B.D.; Graber, G.

1982-01-01

Instrumental neutron activation analysis was used to determine Co, Cu, Fe, Mg, Mn, Se and Zn in tissues from swine fed copper supplemented diets. Elemental abundances of the seven elements in the kidney tissues are all within normal ranges. No trends are observed between the groups of animals which received different levels of dietary copper. Dietary copper values of 70 to 90 ppm increase liver copper abundance for certain animals. (author)

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

Science.gov (United States)

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

2012-03-01

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

On the interference rejection capabilities of triangular antenna array for cellular base stations

KAUST Repository

Atat, Rachad; Shakir, Muhammad; Alouini, Mohamed-Slim

2012-01-01

In this paper, we present the performance analysis of the triangular antenna arrays in terms of the interference rejection capability. In this context, we derive an expression to calculate the spatial interference suppression coefficient for the triangular antenna array with variable number of antenna elements. The performance of the triangular antenna array has been compared with the circular antenna array with respect to interference suppression performance, steering beam pattern, beamwidth and directivity. Simulation results show that the triangular array with large number of elements produces a sharper beamwidth and better interference suppression performance than the circular antenna array. © 2012 IEEE.