Showing papers by "Yi Chen published in 2000"

Molecular classification of cutaneous malignant melanoma by gene expression profiling

Abstract: The most common human cancers are malignant neoplasms of the skin. Incidence of cutaneous melanoma is rising especially steeply, with minimal progress in non-surgical treatment of advanced disease. Despite significant effort to identify independent predictors of melanoma outcome, no accepted histopathological, molecular or immunohistochemical marker defines subsets of this neoplasm. Accordingly, though melanoma is thought to present with different 'taxonomic' forms, these are considered part of a continuous spectrum rather than discrete entities. Here we report the discovery of a subset of melanomas identified by mathematical analysis of gene expression in a series of samples. Remarkably, many genes underlying the classification of this subset are differentially regulated in invasive melanomas that form primitive tubular networks in vitro, a feature of some highly aggressive metastatic melanomas. Global transcript analysis can identify unrecognized subtypes of cutaneous melanoma and predict experimentally verifiable phenotypic characteristics that may be of importance to disease progression.

Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.

Abstract: Breast cancer cell lines provide a useful starting point for the discovery and functional analysis of genes involved in breast cancer. Here, we studied 38 established breast cancer cell lines by comparative genomic hybridization (CGH) to determine recurrent genetic alterations and the extent to which these cell lines resemble uncultured tumors. The following chromosomal gains were observed: 8q (75%), 1q (61%), 20q (55%), 7p (44%), 3q (39%), 5p (39%), 7q (39%), 17q (33%), 1p (30%), and 20p (30%), and the most common losses were: 8p (58%), 18q (58%), 1p (42%), Xp (42%), Xq (42%), 4p (36%), 11q (36%), 18p (33%), 10q (30%), and 19p (28%). Furthermore, 35 recurrent high-level amplification sites were identified, most often involving 8q23 (37%), 20q13 (29%), 3q25-q26 (24%), 17q22-q23 (16%), 17q23-q24 (16%), 1p13 (11%), 1q32 (11%), 5p13 (11%), 5p14 (11%), 11q13 (11%), 17q12-q21 (11%), and 7q21-q22 (11%). A comparison of DNA copy number changes found in the cell lines with those reported in 17 published studies (698 tumors) of uncultured tumors revealed a substantial degree of overlap. CGH copy number profiles may facilitate identification of important new genes located at the hotspots of such chromosomal alterations. This was illustrated by analyzing expression levels of 1236 genes using cDNA microarrays in four of the cell lines. Several highly overexpressed genes (such as RCH1 at 17q23, TOPO II at 17q21-q22, as well as CAS and MYBL2 at 20q13) were involved in these recurrent DNA amplifications. In conclusion, DNA copy number profiles were generated by CGH for most of the publicly available breast cancer cell lines and were made available on a web site (http://www.nhgri.nih.gov/DIR/CGB/++ +CR2000). This should facilitate the correlative analysis of gene expression and copy number as illustrated here by the finding by cDNA microarrays of several overexpressed genes that were amplified.

Detecting Activation of Ribosomal Protein S6 Kinase by Complementary DNA and Tissue Microarray Analysis

Abstract: Background: Studies by comparative genomic hybridization (CGH) have shown that chromosomal region 17q23 is amplified in up to 20% of primary breast cancers. We used microarray analyses to measure the expression levels of genes in this region and to explore their prognostic importance. Methods: A microarray that contained 4209 complementary DNA (cDNA) clones was used to identify genes that are overexpressed in the MCF-7 breast cancer cell line as compared with normal mammary tissue. Fluorescence in situ hybridization was used to analyze the copy number of one overexpressed gene, ribosomal protein S6 kinase (S6K), and to localize it to the 17q23 region. Northern and western blot analyses were used to measure S6K gene and protein expression, and an enzymatic assay was used to measure S6K activity. Tumor tissue microarray analysis was used to study amplification of S6K and the HER-2 oncogene, another 17q-linked gene, and the relationship between amplification and prognosis was analyzed. The Kaplan-Meier method was used for data analysis, and the log-rank test was used for statistical analysis. All P values are two-sided. Results: S6K was amplified and highly overexpressed in MCF-7 cells relative to normal mammary epithelium, and protein expression and enzyme activity were increased. S6K was amplified in 59 (8.8%) of 668 primary breast tumors, and a statistically significant association between amplification and poor prognosis (P =.0021) was observed. Amplification of both S6K and HER-2 implied particularly poor survival (P =.0001). Conclusions: The combination of CGH information with cDNA and tissue microarray analyses can be used to identify amplified and overexpressed genes and to evaluate the clinical implications of such genes and genomic rearrangements. S6K is likely to be one of the genes at 17q23 that is amplified during oncogenesis and may adversely affect the prognosis of patients with this amplification.

Analysis of DNA fragments by microchip electrophoresis fabricated on poly(methyl methacrylate) substrates using a wire-imprinting method.

Abstract: Microfluidic devices were fabricated on poly(methyl methacrylate) (PMMA) substrate using two small-diameter (79 microm) wires to create a cross impression in plastics softened by low-temperature heating. The resulting channels had a rounded shape and 75 microm in depth. The variability of the channel dimensions was found to be less than 6% from different locations of the same channel and less than 10% between chips. Moreover, the fabricated PMMA chip appeared to sustain an electric field strength up to 300 V/cm without significant Joule heating. The function of resulting devices for electrophoretic injection and separation of a DNA size marker, HaeIII digest of (phiX174, was also characterized. Results indicated that all of the 11 DNA fragments of the size marker could be identified in less than 3 min with relative standard deviations less than 0.4% and 8% for migration time and peak area, respectively. Moreover, with the use of near infrared (IR) dye, fluorescence signals of the higher molecular weight fragments (> 603 bp in length) could be detected at total DNA concentrations as low as 0.1 microg/mL (S/N = 4.2). In conclusion, the performance of wire-imprinted devices on PMMA substrate were comparable to those fabricated by other professional means.

Detection of gene amplification by genomic hybridization to cDNA microarrays.

Abstract: Gene amplification is one of the major mechanisms of oncogene activation in tumorigenesis. To facilitate the identification of genes mapping to amplified regions, we have used a technique based on the hybridization of total genomic DNA to cDNA microarrays. To aid detection of the weak signals generated in this complex hybridization, we have used a tyramide-based technique that allows amplification of a fluorescent signal up to 1000-fold. Dilution experiment suggests that amplifications of 5-fold and higher can be detected by this approach. The technique was validated using cancer cell lines with several known gene amplifications, such as those affecting MYC, MYCN, ERBB2, and CDK4 . In addition to the detection of the known amplifications, we identified a novel amplified gene, ZNF133, in the neuroblastoma cell line NGP. Hybridization of NGP cDNA on an identical array also revealed over expression of ZNF133 . Parallel analysis of genomic DNA for copy number and cDNA for expression now provides rapid approach to the identification of amplified genes and chromosomal regions in tumor cells.

Activities of supported copper oxide catalysts in the NO+CO reaction at low temperatures

Abstract: The activities of copper oxide supported on CeO2, γ-Al2O3 and ceria-modified γ-Al2O3 catalysts for the NO+CO reaction at low temperature (200°C) have been investigated. The results show that the activities of the surface-dispersed copper species are greatly enhanced due to the presence of ceria, whether it was used as a support or as the pre-dispersed species on γ-Al2O3. The activities decrease in the order: CuO/CeO2>CuO/CeO2/γ-Al2O3>CuO/γ-Al2O3. For the CuO/CeO2/γ-Al2O3 catalysts, it is shown that NO conversions are not improved significantly with the increasing of CuO and/or ceria loadings, however, the turn-over number for the catalysts is found to be strongly relative to ceria loadings. By a combination of X-ray diffraction (XRD), electron spin resonance (ESR) and temperature programmed reduction (TPR) results, the states and properties of copper oxide species, as well as the interactions among the surface-dispersed copper oxide species, ceria species and support, are also studied. All the results are tentatively discussed according to the incorporation model proposed previously.

Identification of Tumor‐Suppressor Genes Using Human Melanoma Cell Lines UACC903, UACC903(+6), and SRS3 by Comparison of Expression Profiles

Abstract: The development and progression of cancer are believed to be due to multiple genetic alterations resulting in complex changes in expression of many genes. The parental malignant melanoma cell line UACC903 displays anchorage-independent growth, and the chromosome 6-suppressed subline UACC903(+6) displays anchorage-dependent growth. The anchorage-independent revertant cell line SRS3 derived from UACC903(+6) by retroviral transduction resembles the phenotype of UACC903. In this study, we first compared the expression profiles of 3317 genes between these three cell lines in pairs by cDNA microarrays, resulting in identification of genes with known suppressor activities. We then demonstrated connexin 43 (Cx43)-suppressing anchorage-independent growth of UACC903 on overexpression. Of 3317 genes with informative expression detected by cDNA microarray, 321 (9.68%) showed expression changes between at least one pair of the three cell lines. Notably, 12 genes displayed higher levels of expression in UACC903(+6) than in both UACC903 and SRS3, providing candidates for further identification of melanoma-suppressor genes. Genes encoding Cx43 (suppressor activity), monocyte chemotactic protein 1 (suppressor activity), and cysteine proteinase P32alpha (apoptotic activity) were all upregulated in UACC903(+6), in contrast to both UACC903 and SRS3. Transfection of Cx43, encoded on human chromosome 6q21-q23, a region frequently altered in malignant melanoma, resulted in its overexpression and the suppression of anchorage-independent growth of UACC903. Thus, our result proves the principle that the combination of the ability to alter cellular phenotype by successive genetic alterations and the ability to examine the global expression profiles facilitates the identification of tumor suppressor genes. Mol. Carcinog. 28:119-127, 2000.

A Study on the Surface Properties of Ceria-Supported Tungsten and Copper Oxides

Abstract: Laser Raman spectroscopy (LRS), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), ultraviolet and visible diffuse reflectance spectroscopy (UV-DRS), and temperature-programmed reduction (TPR) are used to characterize a series of WO3/CeO2 samples. The results indicate that the dispersion capacity of tungsten oxide is about 4.8W6+ ions nm-2(CeO2) and the structure of the supported tungsten oxide species is closely related to its loading amount on ceria. For the calcined samples, two distinctly different tungsten species have been identified by various methods. At low WO3 loading, only the highly dispersed tungsten oxide species are found on the surface possibly formed by the incorporation of the dispersed W6+ ions into the surface vacant sites of CeO2. Increasing the loading amount of tungsten oxide to a value above 4.8W6+ ions nm-2(CeO2) leads to the formation of crystalline WO3. LRS and IR results of WO3/CeO2 samples prepared by using differe...

Molecular classification of cutaneous malignant melanoma by gene expression profiling

Abstract: The most common human cancers are malignant neoplasms of the skin. Incidence of cutaneous melanoma is rising especially steeply, with minimal progress in non-surgical treatment of advanced disease. Despite significant effort to identify independent predictors of melanoma outcome, no accepted histopathological, molecular or immunohistochemical marker defines subsets of this neoplasm. Accordingly, though melanoma is thought to present with different 'taxonomic' forms, these are considered part of a continuous spectrum rather than discrete entities. Here we report the discovery of a subset of melanomas identified by mathematical analysis of gene expression in a series of samples. Remarkably, many genes underlying the classification of this subset are differentially regulated in invasive melanomas that form primitive tubular networks in vitro, a feature of some highly aggressive metastatic melanomas. Global transcript analysis can identify unrecognized subtypes of cutaneous melanoma and predict experimentally verifiable phenotypic characteristics that may be of importance to disease progression.

Preparation and characterization of calixarene-coated capillaries for capillary electrophoresis.

Abstract: Preparation and characterization of calixarene-coated capillaries for capillary electrophoresis (CE) were exemplified with p-allylcalix[4]arene (pACX4) which was immobilized to the fused silica surface using gamma-methacryloxypropyl-trimethoxysilane (gamma-MAPS) as linking agent. Successful gamma-ACX4 coating was suggested by the greatly decreased electroosmotic flow (EOF), due to the introduction of phenolic hydroxyl groups on the inner surface of the capillaries. A slight slope of EOF versus pH at pH 6 months at 4

Neural adaptive tracking controller for robot manipulators with unknown dynamics

Abstract: A neural network (NN)-based adaptive control law is proposed for the tracking control of an n-link robot manipulator with unknown dynamic nonlinearities. Basis-function-like networks are employed to approximate the plant nonlinearities, and the bound on the NN reconstruction error is assumed to be unknown. The proposed NN-based adaptive control approach integrates the NN approach and an adaptive implementation of the discrete variable structure control, with a simple estimation mechanism for the upper bound on the NN reconstruction errors and an additional control input as a function of the estimate. Lyapunov stability theory is used to prove the uniform ultimate boundedness of the tracking error, and simulation results demonstrate the applicability of the proposed method to achieve desired performance.

Search for new particles decaying to tt̄ in pp̄ collisions at √s = 1.8 TeV

Abstract: We use 106 pb{sup -1} of data collected with the Collider Detector at Fermilab to search for narrow-width, vector particles decaying to a top and an antitop quark. Model independent upper limits on the cross section for narrow, vector resonances decaying to t{ovr t} are presented. At the 95% confidence level, we exclude the existence of a leptophobic Z' boson in a model of top-color-assisted technicolor with mass M{sub Z'}<480 GeV/c{sup 2} for natural width {Gamma} = 0.012M{sub Z'}, and M{sub Z'}<780 GeV/c{sup 2} for {Gamma} = 0.04M{sub Z'}.

Probing the formation process of aluminium hydroxide nanoparticles prepared by laser ablation with 27Al NMR spectroscopy

Abstract: The 27Al MAS NMR spectra of amorphous alumina exhibit three resonances resulting from aluminium in four-, five-, and six-coordination, whereas samples containing crystalline particles of bayerite, gibbsite, and boehmite show only a single resonance associated with six-coordinate aluminium.

Optical noise correlations and beating the standard quantum limit in advanced gravitational-wave detectors

Abstract: The uncertainty principle, applied naively to the test masses of a laser-interferometer gravitational-wave detector, produces a Standard Quantum Limit (SQL) on the interferometer's sensitivity. It has long been thought that beating this SQL would require a radical redesign of interferometers. However, we show that LIGO-II interferometers, currently planned for 2006, can beat the SQL by as much as a factor two over a bandwidth \Delta f \sim f, if their thermal noise can be pushed low enough. This is due to dynamical correlations between photon shot noise and radiation-pressure noise, produced by the LIGO-II signal-recycling mirror.

Quantifying gene relatedness via nonlinear prediction of gene

Abstract: Relatedness between genes is quantified by constructing nonlinear models predicting gene expression. Effectiveness of the model is evaluated to provide a measurement of the relatedness of genes associated with the model. Various types of models, including full-logic or neural networks can be constructed. A graphical user interface presents results of the analysis to allow evaluation by a user. Each gene's contribution to the measurement of relatedness can be shown on a graph, and graphical representations of models used to predict gene expression can be displayed.

Surface interactions of MoO3/ α-Fe2O3 system

Abstract: α-Fe2O3-supported molybdena catalysts have been prepared by heating a mixture of MoO3 and α-Fe2O3. XRD, XPS, LRS, TG-DTA and Mossbauer spectroscopy were used to characterize the interactions between MoO3 and α-Fe2O3. The dispersion capacity of MoO3 on the surface of α-Fe2O3 determined by XRD and XPS was 0.8 mmol/100m2 α-Fe2O3 in the samples calcined at 420°C. For the sample with low MoO3 loading, LRS and FT-IR results showed that Mo6+ ions were located in the tetrahedral vacant sites on the surface of α-Fe2O3, signed as Mo-I. The amount of Mo-II species, formed by Mo6+ ions incorporated into the octahedral vacant sites, increased with the MoO3 loading. Based on the assumption that the (001) plane of α-Fe2O3 is preferentially exposed, almost all the Mo6+ ions of the dispersed molybdena species existed at the surface octahedral sites for the sample with MoO3 loading close or beyond the dispersion capacity, and formed the Mo-II species. In this case, the capping O2− ions linking with the incorporated Mo6+ ions formed a surface epitaxial structure, which was in good agreement with the results predicted by the incorporation model proposed previously. XRD and Mossbauer spectroscopy of the MoO3 / α-Fe2O3 samples calcined at different temperatures showed that the calcination temperature could strongly influence the interaction extent: (i) at 420°C, MoO3 dispersed on the surface of α-Fe2O3 and formed surface Mo species; (ii) at 500°C, MoO3 reacted with the bulk of α-Fe2O3 and formed Fe2(MoO4)3 compound.

A quality assurance phantom for IMRT dose verification

Abstract: We have investigated a quality assurance (QA) phantom that was specially designed to verify the accuracy of dose distributions calculated by a commercial inverse planning optimization system (CORVUS) and by the Monte Carlo method for intensity-modulated radiotherapy (IMRT). The QA phantom is a PMMA cylinder of 30 cm diameter and 40 cm length with various bone and lung inserts. A procedure was developed to measure the absolute dose at any point inside the QA phantom. Another cylindrical phantom of the same dimensions, but made of water, was used to confirm the results obtained with the PMMA phantom. The PMMA phantom was irradiated by 4, 6 and 15 MV photon beams and the dose was measured using an ionization chamber and compared to the results calculated by CORVUS and by the Monte Carlo method. The results show that the dose distributions calculated by both CORVUS and Monte Carlo agreed well (within 2% of dose maximum) with measured results in the uniform PMMA phantom for both open and intensity-modulated fields. Similar agreement was obtained between Monte Carlo calculation and measured results with the bone and lung heterogeneities inside the PMMA phantom. Following the positive results of this study, our QA phantom has been integrated as a routine QA procedure for patient's IMRT dose verification at Stanford since 1999.

Synthesis, structure, and magnetic properties of Pr 5 Co 19 B 6

Abstract: A compound ${\mathrm{Pr}}_{5}{\mathrm{Co}}_{19}{\mathrm{B}}_{6}$ has been synthesized successfully and its crystal structure has been investigated by x-ray powder diffraction. It belongs to the ${R}_{m+n}{\mathrm{Co}}_{5m+3n}{\mathrm{B}}_{2n}$ $(R=\mathrm{rare}$ earth) family with $m=2$ and $n=3.$ The space group is $P6/mmm.$ The lattice parameters are $a=5.1264(4)\AA{}$ and $c=16.5602(6)\AA{}.$ Each unit cell contains one formula unit of ${\mathrm{Pr}}_{5}{\mathrm{Co}}_{19}{\mathrm{B}}_{6},$ and there are nine kinds of equivalent positions in each unit cell, i.e., $1b,$ $2e(1),$ $2e(2),$ $4h(1),$ $6i(1),$ $6i(2),$ $3f,$ $2d,$ and $4h(2),$ which are occupied by $1{\mathrm{Pr}}^{(1)},$ ${2\mathrm{P}\mathrm{r}}^{(2)},$ ${2\mathrm{P}\mathrm{r}}^{(3)},$ ${4\mathrm{C}\mathrm{o}}^{(1)},$ ${6\mathrm{C}\mathrm{o}}^{(2)},$ ${6\mathrm{C}\mathrm{o}}^{(3)},$ ${3\mathrm{C}\mathrm{o}}^{(4)},$ ${2\mathrm{B}}^{(1)},$ and ${4\mathrm{B}}^{(2)},$ respectively. Magnetic measurements indicate that this compound is ferromagnetic with a Curie temperature of 380 K. Its saturation magnetic moment at 5 K and room temperature are $23.7{\ensuremath{\mu}}_{B}/\mathrm{f}.\mathrm{u}.$ and $11.9{\ensuremath{\mu}}_{B}/\mathrm{f}.\mathrm{u}.,$ respectively. Based on the experimental results of the saturation magnetization, three kinds of Co sites with different magnetic moment are proposed. The ${\mathrm{Pr}}_{5}{\mathrm{Co}}_{19}{\mathrm{B}}_{6}$ compound exhibits huge planar anisotropy with an anisotropy field of 250 kOe at 5 K. No spin reorientation was detected from the temperature dependence of the magnetization and the temperature dependence of the ac susceptibility curves from 5 K to room temperature. The behavior of magnetocrystalline anisotropy is analyzed using the single-ion model.

Syntheses and magnetic properties of Nd/sub 3/Co/sub 13-x/Ni/sub x/B/sub 2/ borides

Abstract: The effect of substitution of Ni for Co in the borides Nd/sub 3/(Co/sub 13-x/Ni/sub x/)B/sub 2/ (x=0, 1, 2, 3, 4, 5) on the crystal structure and magnetic properties has been investigated. The lattice parameter a decreases while c increases with increasing x in the range 0/spl les/x/spl les/5. The Curie temperature and saturation magnetic moment per formula unit in Nd/sub 3/(Co/sub 13-x/Ni/sub x/)B/sub 2/ decrease monotonically as the Ni concentration increases. We have observed spin-reorientation transitions at temperatures that decrease monotonically with increasing Ni concentration. It is noteworthy that the substitution of Ni has a significant effect on the magnetocrystalline anisotropy of the Co sublattice, leading to the change of easy magnetization direction of Nd/sub 3/(Co/sub 13-x/Ni/sub x/)B/sub 2/ compounds from basal plane to the c axis at room temperature when x/spl ges/2. The magnetic phase diagram of the Nd/sub 3/(Co/sub 13-x/Ni/sub x/)B/sub 2/ borides is given, and the behavior of magnetocrystalline anisotropy is analyzed by the single ion model.

Plastic Microchip Electrophoresis for Clinical Applications of DNA Analysis

Abstract: Microfluidic devices were fabricated on poly(methyl methacrylate) (PMMA) substrate using heat embossing method. Results indicated that all of the 11 DNA fragments of the size marker (HaeIII digest of φX174) could be identified in less than 3 minutes with relative standard deviations less than 0.4% and 8% for migration time and peak area, respectively. The characterized microchip was investigated for clinical post-PCR analysis of hepatitis C virus (HCV) using Laser-induced fluorescence. A separation medium composed of 1% HPMC in TBE buffer and 10 µmol/L intercalating dye (TOPRO-3) was demonstrated to resolve the amplicon of HCV with 135 by in length in less than 1.5 minutes with the confidence interval of the migration time less than 1.3%. Analysis of more than 10 patient samples by both the existing method using agarose gel electrophoresis and the current method using microchip electrophoresis showed a 100% correlation. The polymer microchip, with advantages including fast processing time, simple operation, and disposable use, holds great potential for clinical analysis.

Expression ratio statistics and its applications to microarray data analysis

Abstract: Microarray technology makes it possible to monitor expression levels of thousands of genes simultaneously during single or multiple experiments. Routinely, in order to analyze gene expressions level quantitatively, two fluorescent-labeled RNAs are hybridized to an array of cDNA probes on a glass slide. Ratios of gene expression levels arising from two co-hybridized samples are obtained through image segmentation and signal detection methods. During the past three years, we have developed a gene expression analysis system in which ratio statistics have been applied to expression analysis, and a ratio confidence interval has been established to identify ratio outliers. By using local background subtraction and weak target elimination, we have been able to assume that the fluorescent background level does not interfere with ratio measurement; however, experience suggests that ratios derived from either weak targets or in regions of high local background possess greater variation than those from strong targets. This paper proposes a new interaction model between fluorescent background and hybridization signals in which ratio statistics are numerically evaluated and a self-adjusting confidence interval is employed. The self-adjusting confidence interval, which automatically adapts under different signal-to-background ratios, provides a better criterion to further interrogate weak expression levels.