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Array Data (array + data)

Distribution by Scientific Domains

Medical Sciences	28%
Engineering	21%

Selected Abstracts

Statistical Metrics for Quality Assessment of High-Density Tiling Array Data

BIOMETRICS, Issue 2 2010
Hui Tang
Summary High-density tiling arrays are designed to blanket an entire genomic region of interest using tiled oligonucleotides at very high resolution and are widely used in various biological applications. Experiments are usually conducted in multiple stages, in which unwanted technical variations may be introduced. As tiling arrays become more popular and are adopted by many research labs, it is pressing to develop quality control tools as was done for expression microarrays. We propose a set of statistical quality metrics analogous to those in expression microarrays with application to tiling array data. We also develop a method to estimate the significance level of an observed quality measurement using randomization tests. These methods have been applied to multiple real data sets, including three independent ChIP-chip experiments and one transcriptom mapping study, and they have successfully identified good quality chips as well as outliers in each study. [source]

A transportable mb(Lg) scale for central Europe and implications for low-magnitude Ms,mb discrimination

GEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2005
Howard J. Patton
SUMMARY We have extended the mb(Lg) method of Nuttli using root-mean-square (rms) amplitudes corrected for noise and a ,,1 dependence for geometrical spreading. Lg waves recorded on the German Regional Seismic Network (GRSN) for earthquakes in south-central Europe were used to develop an mb(Lg) formula requiring a new calibration constant Crms to keep rms mb(Lg) on the same baseline as Nuttli's traditional formula based on 3rd-peak amplitudes. GRSN stations had to be calibrated for site terms and for Lg attenuation. Lateral variations in LgQ appear to be significant across the study area, and a regional Q model consisting of constant- Q partitions north, south and in the central Alps was developed using measurements based on interstation and two-event, single-station methods. When plotted against surface wave estimates of Mw, rms mb(Lg) measurements in central Europe are found to be consistent with Mw,mb(Lg) relationships for north America and southern Asia, thus supporting the transportability of our mb(Lg) formula. Frequency,wavenumber processing of Gräfenberg Array data enabled us to extract Rayleigh waves for small events, and regional Ms were measured using the Marshall and Basham formula. Our Ms,mb(Lg) relationship extends to Ms 2.5 and agrees well with observations in other regions including the western United States. The discrimination potential of Ms,mb(Lg) observations was examined under realistic monitoring conditions, where path corrections were inferred from earthquake data and applied uniformly to natural sources and explosions. Under these conditions, mb(Pn, P) are greater than mb(Lg) for large NTS explosions; however, Ms,mb scaling slopes are steeper for P waves than they are for Lg, and Ms,mb observations for NTS explosions converge near mb 4. Thus, allowing for measurement errors and additional uncertainty in mb(Pn) due to regional bias, there is little difference in the discrimination potential for Pn and Lg waves at small magnitudes. As such, a regional Ms,mb discriminant based on Lg might be preferred owing to the better detectability of Lg waves for small earthquakes. These results need to be confirmed for explosions at other test sites. Compared to teleseismic experience, regional Ms,mb observations extend the discrimination capability to lower magnitudes by at least one Ms unit. [source]

HP24 MICRORNA EXPRESSION PROFILES IN BARRETT'S OESOPHAGUS

ANZ JOURNAL OF SURGERY, Issue 2007
D. I. Watson
Purpose The genetic changes that drive the metaplastic change from squamous oesophagus (NO) towards Barrett's oesophagus (BO) and cancer are unclear. microRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression and contribute to cellular differentiation and identity. We sought to determine the role of miRNAs in BO. Methodology Biopsies of NO, BO and cardia were taken from 7 patients and RNA was extracted. miRNA expression profiles of 300 miRNAs were determined by microarray. Guided by the array results, real-time Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) for 8 selected miRNAs enabled their expression to be studied in tissues from another 15 patients. Results Array data revealed that 39 miRNAs were significantly differentially expressed between NO, BO and cardia. A tissue-specific expression profile was confirmed by RT-PCR, with miR-21, 143, 145, 194 and 215 significantly up regulated in BO and cardia (columnar) vs. NO (squamous). A trend towards increased miR-21 expression from NO to BO and adenocarcinoma was observed (p = 0.1). Interestingly, high expression of miR-143, 194 and 215 was seen in BO vs. NO (p < 0.0001), but with subsequent downregulation in cancers (p = 0.1). In contrast, miR-203 and 205 were highly expressed in NO and low in BO and cardia. A database search revealed that these miRNAs potentially target (proto-)oncogenes and tumour suppressor genes. Conclusions Differences in miRNA expression are present between NO, BO, cardia and cancer. Deregulation of certain miRNAs, and their predicted effect on the expression of target genes, might contribute to the metaplastic and neoplastic process in the oesophagus and could serve as novel biomarkers to classify diseased tissues. [source]

Vascular gene expression and phenotypic correlation during differentiation of human embryonic stem cells

DEVELOPMENTAL DYNAMICS, Issue 2 2005
Sharon Gerecht-Nir
Abstract The study of the cascade of events of induction and sequential gene activation that takes place during human embryonic development is hindered by the unavailability of postimplantation embryos at different stages of development. Spontaneous differentiation of human embryonic stem cells (hESCs) can occur by means of the formation of embryoid bodies (EBs), which resemble certain aspects of early embryos to some extent. Embryonic vascular formation, vasculogenesis, is a sequential process that involves complex regulatory cascades. In this study, changes of gene expression along the development of human EBs for 4 weeks were studied by large-scale gene screening. Two main clusters were identified,one of down-regulated genes such as POU5, NANOG, TDGF1/Cripto (TDGF, teratocarcinoma-derived growth factor-1), LIN28, CD24, TERF1 (telomeric repeat binding factor-1), LEFTB (left,right determination, factor B), and a second of up-regulated genes such as TWIST, WNT5A, WT1, AFP, ALB, NCAM1. Focusing on the vascular system development, genes known to be involved in vasculogenesis and angiogenesis were explored. Up-regulated genes include vasculogenic growth factors such as VEGFA, VEGFC, FIGF (VEGFD), ANG1, ANG2, TGF,3, and PDGFB, as well as the related receptors FLT1, FLT4, PDGFRB, TGF,R2, and TGF,R3, other markers such as CD34, VCAM1, PECAM1, VE-CAD, and transcription factors TAL1, GATA2, and GATA3. The reproducibility of the array data was verified independently and illustrated that many genes known to be involved in vascular development are activated during the differentiation of hESCs in culture. Hence, the analysis of the vascular system can be extended to other differentiation pathways, allocating human EBs as an in vitro model to study early human development. Developmental Dynamics 232:487,497, 2005. © 2004 Wiley-Liss, Inc. [source]

Three-dimensional VS profiling using microtremors in Kushiro, Japan

EARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 6 2008
Hiroshi Arai
Abstract A practical method is presented for determining three-dimensional S-wave velocity (VS) profile from microtremor measurements. Frequency,wave number (f,k) spectral analyses of microtremor array records are combined, for this purpose, with microtremor horizontal-to-vertical (H/V) spectral ratio techniques. To demonstrate the effectiveness of the proposed method, microtremor measurements using arrays of sensors were conducted at six sites in the city of Kushiro, Japan. The spectral analyses of the array records yield dispersion characteristics of Rayleigh waves and H/V spectra of surface waves, and joint inversion of these data results in VS profiles down to bedrock at the sites. Conventional microtremor measurements were performed at 230 stations within Kushiro city, resulting in the H/V spectra within the city. Three-dimensional VS structure is then estimated from inversion of the H/V spectra with the VS values determined from the microtremor array data. This reveals three-dimensional VS profile of Kushiro city, together with an unknown hidden valley that crosses the central part of the city. The estimated VS profile is consistent with available velocity logs and results of subsequent borings, indicating the effectiveness of the proposed method. Copyright © 2008 John Wiley & Sons, Ltd. [source]

The effects of torsion and motion coupling in site response estimation

EARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 5 2003
Mohammad R. Ghayamghamian
Abstract Soil amplification characteristics are investigated using data from the Chibaken-Toho-Oki earthquake and its aftershocks recorded at Chiba dense array in Japan. The frequency-dependent amplification function of soil is calculated using uphole-to-downhole spectral ratio analysis, considering the horizontal components of shear wave. The identified spectral ratios consistently demonstrate the splitting of peaks in their resonance frequencies and low amplification values in comparison with a 1D model. The torsional behaviour and horizontal ground motion coupling are clarified as the reasons for these phenomena at the site. To prove the hypothesis, the torsional motion is directly evaluated using the data of the horizontal dense array in different depths at the site. The comparison between Fourier spectra of torsional motion and identified transfer functions reveals the peaks at the same frequencies. The wave equation including torsion and horizontal motion coupling is introduced and solved for the layered media by applying wave propagation theory. Using the developed model, the effects of torsional motion with horizontal motion coupling on soil transfer function are numerically examined. Splitting and low amplification at resonance frequencies are confirmed by the results of numerical analysis. Furthermore, the ground motion in two horizontal directions at the site is simulated using site geotechnical specification and optimizing the model parameters. The simulated and recorded motions demonstrate good agreement that is used to validate the hypothesis. In addition, the spectral density of torsional ground motions are compared with the calculated one and found to be well predicted by the model. Finally, the results are used to explain the overestimation of damping in back-calculation of dynamic soil properties using vertical array data in small strain level. Copyright © 2003 John Wiley & Sons, Ltd. [source]

Genomic and clinical analyses of 2p24 and 12q13-q14 amplification in alveolar rhabdomyosarcoma: A report from the Children's Oncology Group

GENES, CHROMOSOMES AND CANCER, Issue 8 2009
Frederic G. Barr
Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric cancer that is related to the skeletal muscle lineage and characterized by recurrent chromosomal translocations. Within the ARMS category, there is clinical and genetic heterogeneity, consistent with the premise that "primary" genetic events collaborate with "secondary" events to give rise to subsets with varying clinical features. Previous studies demonstrated that genomic amplification occurs frequently in ARMS. In the current study, we used oligonucleotide arrays to localize two common amplicons to the 2p24 and 12q13-q14 chromosomal regions. Based on the copy number array data, we sublocalized the minimum common regions of 2p24 and 12q13-q14 amplification to a 0.83 Mb region containing the DDX1 and MYCN genes, and a 0.55 Mb region containing 27 genes, respectively. Using fluorescent in situ hybridization assays to measure copy number of the 2p24 and 12q13-q14 regions in over 100 cases, we detected these amplicons in 13% and 12% of cases, respectively. Comparison with fusion status revealed that 2p24 amplification occurred preferentially in cases positive for PAX3-FOXO1 or PAX7-FOXO1 while 12q13-q14 amplification occurred preferentially in PAX3-FOXO1 -positive cases. Expression studies demonstrated that MYCN was usually overexpressed in cases with 2p24 amplification while multiple genes were overexpressed in cases with 12q13-q14 amplification. Finally, although 2p24 amplification did not have a significant association with clinical outcome, 12q13-q14 amplification was associated with significantly worse failure-free and overall survival that was independent of gene fusion status. © 2009 Wiley-Liss, Inc. [source]

Array-conditioned deconvolution of multiple-component teleseismic recordings

GEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2010
C.-W. Chen
SUMMARY We investigate the applicability of an array-conditioned deconvolution technique, developed for analysing borehole seismic exploration data, to teleseismic receiver functions and data pre-processing steps for scattered wavefield imaging. This multichannel deconvolution technique constructs an approximate inverse filter to the estimated source signature by solving an overdetermined set of deconvolution equations, using an array of receivers detecting a common source. We find that this technique improves the efficiency and automation of receiver function calculation and data pre-processing workflow. We apply this technique to synthetic experiments and to teleseismic data recorded in a dense array in northern Canada. Our results show that this optimal deconvolution automatically determines and subsequently attenuates the noise from data, enhancing P -to- S converted phases in seismograms with various noise levels. In this context, the array-conditioned deconvolution presents a new, effective and automatic means for processing large amounts of array data, as it does not require any ad-hoc regularization; the regularization is achieved naturally by using the noise present in the array itself. [source]

Upregulation of the tumor suppressor gene menin in hepatocellular carcinomas and its significance in fibrogenesis,

HEPATOLOGY, Issue 5 2006
Pierre J. Zindy
The molecular mechanisms underlying the progression of cirrhosis toward hepatocellular carcinoma were investigated by a combination of DNA microarray analysis and literature data mining. By using a microarray screening of suppression subtractive hybridization cDNA libraries, we first analyzed genes differentially expressed in tumor and nontumor livers with cirrhosis from 15 patients with hepatocellular carcinomas. Seventy-four genes were similarly recovered in tumor (57.8% of differentially expressed genes) and adjacent nontumor tissues (64% of differentially expressed genes) compared with histologically normal livers. Gene ontology analyses revealed that downregulated genes (n = 35) were mostly associated with hepatic functions. Upregulated genes (n = 39) included both known genes associated with extracellular matrix remodeling, cell communication, metabolism, and post-transcriptional regulation gene (e.g., ZFP36L1), as well as the tumor suppressor gene menin (multiple endocrine neoplasia type 1; MEN1). MEN1 was further identified as an important node of a regulatory network graph that integrated array data with array-independent literature mining. Upregulation of MEN1 in tumor was confirmed in an independent set of samples and associated with tumor size (P = .016). In the underlying liver with cirrhosis, increased steady-state MEN1 mRNA levels were correlated with those of collagen ,2(I) mRNA (P < .01). In addition, MEN1 expression was associated with hepatic stellate cell activation during fibrogenesis and involved in transforming growth factor beta (TGF-,),dependent collagen ,2(I) regulation. In conclusion, menin is a key regulator of gene networks that are activated in fibrogenesis associated with hepatocellular carcinoma through the modulation of TGF-, response. (HEPATOLOGY 2006;44:1296,1307.) [source]

Modulation of sulfur mustard induced cell death in human epidermal keratinocytes using IL-10 and TNF-,,,

JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 4 2005
Aziz Qabar
Abstract We compared the effects of overexpressing a tightly regulated anti-inflammatory cytokine, interleukin 10 (IL-10), and the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-,) on sulfur mustard induced cytotoxicity in human epidermal keratinocytes. Both cytokines were overexpressed when compared with the cells transfected with the empty vector as determined by quantitative ELISA. Cells overexpressing interleukin 10 suppressed the pro-inflammatory cytokines interleukin 8 and interleukin 6 following exposure to 50,300 ,M sulfur mustard. These cells exhibited delayed onset of sulfur mustard induced cell death. On the other hand, cells overexpressing tumor necrosis factor alpha induced a sustained elevation in both interleukin 6 and 8 expression following exposure to 50,300 ,M sulfur mustard. These cells were sensitized to the effects of sulfur mustard that resulted in an increased sulfur mustard induced cell death. Normal human epidermal keartinocytes treated with sulfur mustard exhibited elevated levels of tumor necrosis factor alpha expression and increased activity of nuclear factor kappa B. Gene array data indicated that cells overexpressing interleukin 10 induced several genes that are involved in growth promotion and cell-fate determination. We, therefore, identify IL-10 and TNF-, signal transduction pathways and their components as possible candidates for early therapeutic intervention against sulfur mustard induced cell injury. © 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:213,225, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20089 [source]

SAVANT analysis of the microelectronics and photonics testbed solar cell data,

PROGRESS IN PHOTOVOLTAICS: RESEARCH & APPLICATIONS, Issue 2 2005
Robert J. Walters
Abstract An analysis of solar array data from the Microelectronic and Photonic Testbed (MPTB) space experiment is presented. The data are analyzed using the displacement damage dose (Dd) methodology developed by the US Naval Research Laboratory (NRL) as implemented in the Solar Array Verification and Analysis Tool (SAVANT). SAVANT is a WindowsTM -based computer code that predicts the on-orbit performance of a solar cell in a specified Earth orbit. The predicted solar cell performance produced by the SAVANT code are compared with the measured on-orbit data. In addition, the calculated data are compared with onboard dosimeter measurements. The results allow both a validation of the SAVANT code and a comparison of the space environment models with measured on-orbit data. The results show the models to match the measured data within a factor of 2. Published in 2005 by John Wiley & Sons, Ltd. [source]

Simultaneously detection of genomic and expression alterations in prostate cancer using cDNA microarray,

THE PROSTATE, Issue 14 2008
Mei Jiang
Abstract BACKGROUND Prostate cancer is a common disease among men but the knowledge of the prostate carcinogenesis is still limited. METHODS cDNA microarray-based comparative genomic hybridization (CGH) and expression profiling were performed to screen the genomic and the expression changes in prostate cancer respectively. The two data were integrated to study the influence of genomic aberrations on gene expression and seek for the genes with their expression affected by the genomic aberrations. Real-time PCR was performed to evaluate the array data. RESULTS Array-based CGH detected gains at 2q, 3p/q, 5q, 6q, 8q, 9p, 10p/q, 11q, 12p, 14q, and 19p/q and losses at 1p, 2p, 4q, 6p/q, 7p, 11p/q, 12q, 17p/q, 19p/q, and Xp/q in more than 20% prostate tumors and narrowed these aberrations. For example, the gain of 8q was mapped to five minimal regions. Novel aberrations were also identified, such as loss at Xq21.33-q22.2. Expression profiling discovered the significant biological processes involved in the prostate carcinogenesis, such as exogenous antigen presentation via MHC class II and protein ubiquitination. Integration analysis revealed a weak positive correlation between genomic copy number and gene expression level. Fifty-three genes showed their expression directly affected by the genomic aberrations possibly, including more than one member of Ras superfamily and major histocompatibility complex (MHC). These genes are involved in multiple biological processes. CONCLUSIONS Integration of the CGH and expression data provided more information than separate analysis. Although the direct influence of genomic aberrations on gene expression seems weak, the influence can be extended by indirect regulation through a few directly affected genes. Because the influence can be persistent, the genes directly affected by the genomic aberrations may play key roles in the prostate carcinogenesis and are worth further analysis. Prostate 68: 1496,1509, 2008. © 2008 Wiley-Liss, Inc. [source]

THE DISCOVERY OF AN ANGLO-SAXON GRUBENHAUS AT NEW BEWICK, NORTHERN UK USING ELECTRICAL SURVEYING AND PREDICTIVE DECONVOLUTION

ARCHAEOMETRY, Issue 2 2010
P. W. J. GLOVER
Twin-probe and 33-fold multiplexed Wenner electrical resistivity surveys were carried out at New Bewick, northern UK to examine the extent of crop marks and potential Grubenhäuser (sunken-featured buildings, sunken-floored buildings or SFBs). The twin-probe method was faster, but provided data with a lower spatial resolution. However, the Wenner array data was affected by characteristic ,M'- or ,W'-shaped responses over filled excavations such as those expected to represent a Grubenhaus. The raw Wenner array data have been analysed using one-dimensional and two-dimensional predictive deconvolution in order to remove these artefacts. The deconvolution was carried out using an inverse matrix element method. The filtered results indicate the presence of anomalies consistent with the presence of at least six Grubenhäuser and other anomalies concurrent with the linear crop-marks. One particular anomaly measured about 5 m by 4 m and with a pit depth of 0.6 m below 0.3 m of topsoil. This anomaly was subsequently excavated and a Grubenhaus was discovered at the site. The excavated Grubenhaus measured 4.7 m by 3.9 m with a pit depth of 0.5 m below the base of the topsoil, confirming the electrical survey results. [source]