Showing papers by "Yi Chen published in 1998"

Gene Expression Profiling of Alveolar Rhabdomyosarcoma with cDNA Microarrays

Abstract: Several forms of human sarcoma, lymphoma, and leukemia are characterized by somatically acquired chromosome translocations that result in fusion genes that encode chimeric transcription factors with oncogenic properties. We have used cDNA microarrays containing 1238 cDNAs to investigate the gene expression profile of a group of seven alveolar rhabdomyosarcoma (ARMS) cell lines characterized by the presence of the PAX3-FKHR fusion gene. Using the method of multidimensional scaling to represent the relationships among the cell lines in two-dimensional Euclidean space, we determined that ARMS cells show a consistent pattern of gene expression, which allows the cells to be clustered together. By searching across the seven ARMS cell lines, we found that 37 of 1238 genes were most consistently expressed in ARMS relative to a reference cell line. Only three of these genes have been previously reported to be expressed in ARMS. Among these 37 were genes related to both primary (PAX3-FKHR) and secondary (CDK4) genetic alterations in ARMS. These results in ARMS demonstrate the potential of cDNA microarray technology to elucidate tumor-specific gene expression profiles in human cancers.

Data management and analysis for gene expression arrays

Abstract: Microarray technology makes it possible to simultaneously study the expression of thousands of genes during a single experiment. We have developed an information system, ArrayDB, to manage and analyse large-scale expression data. The underlying relational database was designed to allow flexibility in the nature and structure of data input and also in the generation of standard or customized reports through a web-browser interface. ArrayDB provides varied options for data retrieval and analysis tools that should facilitate the interpretation of complex hybridization results. A sampling of ArrayDB storage, retrieval and analysis capabilities is available ( http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/ ), along with information on a set of approximately 15,000 genes used to fabricate several widely used microarrays. Information stored in ArrayDB is used to provide integrated gene expression reports by linking array target sequences with NCBI's Entrez retrieval system, UniGene and KEGG pathway views. The integration of external information resources is essential in interpreting intrinsic patterns and relationships in large-scale gene expression data.

Termination of Ca2+ release by a local inactivation of ryanodine receptors in cardiac myocytes

Abstract: In heart, a robust regulatory mechanism is required to counteract the regenerative Ca2+-induced Ca2+ release from the sarcoplasmic reticulum. Several mechanisms, including inactivation, adaptation, and stochastic closing of ryanodine receptors (RyRs) have been proposed, but no conclusive evidence has yet been provided. We probed the termination process of Ca2+ release by using a technique of imaging local Ca2+ release, or “Ca2+ spikes”, at subcellular sites; and we tracked the kinetics of Ca2+ release triggered by L-type Ca2+ channels. At 0 mV, Ca2+ release occurred and terminated within 40 ms after the onset of clamp pulses (0 mV). Increasing the open-duration and promoting the reopenings of Ca2+ channels with the Ca2+ channel agonist, FPL64176, did not prolong or trigger secondary Ca2+ spikes, even though two-thirds of the sarcoplasmic reticulum Ca2+ remained available for release. Latency of Ca2+ spikes coincided with the first openings but not with the reopenings of L-type Ca2+ channels. After an initial maximal release, even a multi-fold increase in unitary Ca2+ current induced by a hyperpolarization to −120 mV failed to trigger additional release, indicating absolute refractoriness of RyRs. When the release was submaximal (e.g., at +30 mV), tail currents did activate additional Ca2+ spikes; confocal images revealed that they originated from RyRs unfired during depolarization. These results indicate that Ca2+ release is terminated primarily by a highly localized, use-dependent inactivation of RyRs but not by the stochastic closing or adaptation of RyRs in intact ventricular myocytes.

Measurement of the W Boson Mass with the Collider Detector at Fermilab

Abstract: We present a measurement of the W boson mass using data collected with the CDF detector during the 1994-1995 collider run at the Fermilab Tevatron. A fit to the transverse mass spectrum of a sample of 30115 W --> ev events recorded in an integrated luminosity of 84 pb(-1) gives a mass M-W=80.473 +/-0.065(stat) +/-0.092(syst) GeV/c(2). A fit to the transverse mass spectrum of a sample of 14740 W --> muv events from 80 pb(-1) gives a mass M-W=80,465 +/-0.100(stat)+/-0.103(syst) Ge V/c(2) The dominant contributions to the systematic uncertainties are the uncertainties in the electron energy scale and the muon momentum scale, 0.075 GeV/c(2) and 0.085 GeV/c(2), respectively. The combined value for the electron and muon channel is M-W=80.470 +/-0.089-GeV/c(2). When combined with previously published CDF measurements, we obtain M-W=80.433 +/-0.079 GeV/c(2).

Calibration of BC501A liquid scintillator cells with monochromatic neutron beams

Abstract: The recoil proton energy response has been measured by exposing cylindrical cells, filled with BC501A BICRON liquid scintillator, to mono-energetic neutron reference fields. We determine the required calibration parameters and report the detailed procedures for the experimental data handling. A dedicated Monte Carlo simulation of the detector response and efficiency has been performed. It showed good agreement with the measured quantities. The results from this calibration are necessary for a detailed study of the neutron spectrum at the underground Gran Sasso Laboratory, with a neutron detector made of 32 liquid scintillator cells, like those used during the calibration.

The structure and surface acidity of zirconia-supported tungsten oxides

Abstract: The structure and surface acidity of zirconia-supported tungsten oxide are studied by using BET, XRD, FT Raman, Tian–Calvet microcalorimetry as well as XPS Three different crystal forms of ZrO2 and their hydroxide precursors were prepared in a controllable way It was found that the starting material and preparing conditions used have a significant effect on the structure of ZrO2 obtained The tungstate species on zirconium hydroxide generally promote the transformation of the hydroxide precursor into tetragonal ZrO2, while the same species on the pre-calcined ZrO2 has less effect during calcination A bulk-phase WO3 existed in the samples prepared by initially impregnating the monoclinic, tetragonal and cubic ZrO2 or the hydroxide precursors of m- and t-ZrO2, while no crystalline WO3 was present in the samples prepared by initially impregnating the hydroxide precursor of c-ZrO2 Raman results revealed that the surface tungstate(s) on three different zirconium hydroxides or their respective zirconia have similar structural features before calcination The surface tungsten oxides and some WO3 bulk phase are the detectable tungsten species in the final samples, the ratio of each component is strongly dependent on the preparation history and the nature of the support Creation of very strong acidic sites on the zirconia-supported tungsten oxide is related to the crystal form of zirconia itself, the type of tungsten oxide species, and the cooperation between the surface tungsten oxide overlayer and zirconia The strong acidic sites can be completely poisoned by the remaining sodium ion impurities, but have not been appreciably influenced by added yttrium component The crystalline WO3 seems of little importance in building up the strong surface acidity

Catalytic properties of ultrafine molybdenum-cerium oxide particles prepared by the sol-gel method

Abstract: The structure and catalytic properties of ultrafine Mo-Ce oxide particles prepared by the sol-gel method have been studied by using X-ray diffraction, transmission electron microscopy, temperature-programmed reduction, laser Raman spectroscopy and microreactor tests. It has been shown that for selective oxidation of toluene to benzaldehyde the ultrafine Mo-Ce oxide particles exhibit higher catalytic activity than the larger oxide particles prepared by a conventional coprecipitation method. The unique catalytic properties of ultrafine Mo-Ce oxide particles may be correlated not only to the interaction between molybdenum oxide and cerium oxide, but also to the higher reactivity of lattice oxygen species in the ultrafine oxide matrix.

Monte Carlo simulation of ion implantation into topographically complex structures

Abstract: A new physically based Monte Carlo ion implantation simulator has been developed and implemented in UT-MARLOWE The new simulator is capable of simulating 2-D and 3-D implants into arbitrary topography with multiple layers, both crystalline and amorphous Emphasis has been placed on computational efficiency, and improvements over previous simulators ranging from 1-3 orders of magnitude in CPU time have been observed The accuracy of the simulation is observed not to be compromised by the algorithms for improved computational efficiency

Ultrafine La–Mo and Ce–Mo complex oxide particle catalysts for selective oxidation of toluene

Abstract: It has been found that by decreasing the particle size of La–Mo and Ce–Mo complex oxides to nanoscale, the reactivity of lattice oxygen ions and thus the selectivity for oxidation of toluene to benzaldehyde can be remarkably improved.

Performance evaluation of a hit finding algorithm for the ICARUS detector

Abstract: A procedure to filter the ICARUS digitized data is presented. The final multi-kiloton detector will provide raw data at a rate of the order of 100 Gbytes/s and therefore a crucial element of the acquisition chain will be the on-line data reduction system. A filter has been developed to process the signals and to tag the meaningful data. The hit detection efficiency has been evaluated on a sample of signals obtained from cosmic rays events in the 3 t ICARUS prototype. Its robustness has been tested also on simulated events with different signal to noise ratio. The hit finder hardware implementation is also presented.

Formation of Surface Basicity through the Decomposition of Alkali Metal Nitrates on γ-Al2O3

Abstract: The γ-Al2O3-supported alkali metal nitrate samples with various loadings were prepared by the incipient wetness impregnation method. Differential thermal analysis (DTA), X-ray diffraction (XRD), and magic-angle-spinning (MAS) 23Na and 27Al NMR were conducted regarding the decomposition of supported nitrates and the chemical states of alkali metals on γ-Al2O3. The surface basicity and acidity of these samples evacuated at different temperatures were determined by microcalorimetric adsorption of CO2 and NH3, which were correlated to the states of alkali metals, as revealed by the various physical characterizations.

Logical structural filters

Abstract: Binary granulometric filters are formed from unions of parameterized openings, a point passing the filter if and only if a translate of at least one structuring element fits in the image and contains the point. A granulometry induces a reconstructive granulometry by passing any image component not eliminated by the granulometry. As historically studied in the context of Matheron's granulometric theory, reconstructive granulometries appear as unions of reconstructive parameterized openings. The theory is extended to a much wider class of filters: a logical structural filter (LSF) is formed as a union of intersections of both reconstructive and complementary reconstructive openings. A reconstructive opening passes a component if and only if at least one translate of the structuring element fits inside; a complementary reconstructive opening passes a component if and only if no translate of the structuring element fits inside. The original reconstructive granulometries form the special class of disjunctive LSFs. Complement-free LSFsform granulometries in a slightly more general sense; LSFs containing complements are not increasing and therefore not openings. Along with the relevant algebraic representations for LSFs, the theories of optimal and adaptive granulometric filters are extended to LSFs, a systematic formulation of adaptive transitions is given, transition probabilities for adaptation are found, and two applications to biological imaging are presented.

New analytic models and efficient parameter extraction for computationally efficient 1-D and 2-D ion implantation modeling

Abstract: The rapid progress of CMOS process technology has led to increased process complexity and fabrication cost and has created a strong need for accurate and computationally efficient ion implantation models. In this paper, we propose new and improved analytic models for as-implanted impurity and damage profiles in one and two dimensions. The development of models for the as-implanted damage profile is becoming increasingly important, since it is well known that the implant-induced damage has a significant impact on the diffusion of impurities during subsequent thermal treatment, especially under minimal thermal budget conditions. A new approach to 2-D analytic ion implant simulation that takes into account implant-induced damage, and generates 2-D interstitial/vacancy profiles in addition to impurity profiles, is also described. Finally, a methodology is discussed for automating the extraction of model parameters for generating lookup tables.

Studies of the roles of Sn or Fe on γ-Al 2 O 3 -supported Pt catalysts by CO adsorption microcalorimetry and dehydrogenation reaction of C 4 alkanes

Abstract: CO adsorption microcalorimetry was employed in the study of γ-Al2O3-supported Pt, Pt-Sn and Pt-Fe catalysts. The results indicated that the initial differential heat of CO adsorption of the Pt/γ-Al2O3 catalyst was 125 kJ/mol. As CO coverage increased, the differential heat of adsorption decreased. At higher coverages, the differential heat of adsorption decreased significantly. 60% of the differential heat of CO adsorption on the Pt/γ-N2O3 catalyst was higher than 100 kJ/mol. No significant effect on the initial differential heat was found after adding Sn and Fe to the Pt/γ-Al2O3 catalyst. The amount of strong CO adsorption sites decreased, while the portion of CO adsorption sites with differential heat of 60–110 kJ/mol increased after increasing the Sn or Fe content. This indicates that the surface adsorption energy was changed by adding Sn or Fe to Pt/γ-N2O3. The distribution of differential heat of CO adsorption on the Pt-Sn(C)/γ-Al2O3 catalyst was broad and homogeneous. Comparison of the dehydrogenation performance of C4 alkanes with the number of CO adsorption sites with differential heat of 60–110 kJ/mol showed a good correlation. These results indicate that the surface Pt centers with differential heats of 60–110 kJ/mol for CO adsorption possess superior activity for the dehydrogenation of alkanes.

Electrophoretic Separation of Antisense DNA using Polymer-Solution Filled Capillary by Cross-Injection

Abstract: Different lengths of antisense DNA are normally separated by Polyacrylamide gelfilled column using capillary electrophoresis. The rigid gel bed, however, has a limited lifetime due to the forming of air bubbles and clogging particularly when a real sample with complex matrix is analyzed. An alternative is to replace the gel with a replenishable polymer solution. In this work, a capillary electrophoresis system using a microcross (10 nL ) connected with four 75 μm i.d. fused-silica capillaries and operated under high-voltage shunting is described to implement the PEG sieving medium for the separation of antisense DNAs. Both the separation and injection capillaries were filled with polyethylene glycol (PEG) in tris-borate buffer and the separation was performed with pinched-mode. The PEG medium was found to resolve the 15–20mers of antisense DNA under a conventional linear configuration. Substantial band broadening, however, was observed when using the cross configuration under the same separation conditions. A better control of the injection time as well as the applied voltage is required to minimize the sample diffusion.

The Role of Terminal MoO Bonds in Selective Oxidation of Toluene over a Complex Ce–Mo Oxide in the Absence of Molecular Oxygen

Abstract: The role of terminal MoO bonds in selective oxidation of toluene over a complex Ce–Mo oxide is studied by using a pulse microreactor in the absence of molecular oxygen together with in situ Raman spectroscopy, and it is found that the terminal MoO bonds are mainly responsible for the formation of benzaldehyde.

Theoretical simulation and experimental research on optical coherence tomography (OCT)

Abstract: Utilizing the ultra-fast laser or superluminescence diode (SLD) as the light source, optical coherence tomography (OCT) is a new tomographic imaging technique. It has great applying foreground in many fields such as medicine, biology, material and so on. We founded an OCT system and applied it in biological imaging successfully. Furthermore, we found a potential great application for this technique in measuring the inner structure of bedded samples such as paint films. The experiment in OCT has made prompt development, while only a little work has been done on the theoretical analysis. Some experimental results, thus, can't be explained clearly. In this paper, we use the Monte-Carlo simulation method to analyze OCT image. The differences between single scattered (or least scattered) light and multiply scattered light and its influence to the quality of OCT image are discussed in detail. To show an example, our simulating calculation object is a conduit immersing in a high scattering medium that can be regarded as the approximation of blood vessel. After programming and calculating we get the theoretical result as the form of pseudo color image. The images of conduit immersing in the high scattering medium are clearly seen. Comparing with the experimental imaging of vein they are accordant basically. All above prove the Monte-Carlo simulation method correct and effective in theoretical research of OCT. Many significant results, which are very helpful for experimental research, are draw through this method.

Selective Oxidation of Toluene Catalysed by Ultrafine Fe–Mo Oxide Particles

Abstract: It has been found that by decreasing the size of both Fe2O3 and Fe2(MoO4)3 particles in complex Fe–Mo oxide to nanometric order, the catalytic activity of the mixed oxide in toluene oxidation is remarkably improved.

Adaptive design of logical structure filters

Abstract: A binary granulometry is formed as a union of parameterized openings. It induces a reconstructive granulometry by passing image components it does not fully eliminate. Reconstructive granulometries have historically been formed as unions of reconstructive parameterized openings. The theory has been extended to the new class of logical structure filters (LSF). These are unions of intersections of both reconstructive and complementary reconstructive openings. Reconstructive granulometries form the special class of disjunctive LSFs. This paper covers adaptive methods to design parameterized LSFs. A systematic formulation of adaptive transitions is given and applications are provided.© (1998) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Use of cDNA Microarrays to Assess DNA Gene Expression Patterns in Cancer

Abstract: It is no longer controversial to state that genomic alterations are of fundamental importance in carcinogenesis. However, it remains difficult to determine the spectrum of genomic changes in any given tumor and even more difficult to determine the impact of these changes on gene expression. As a result of progress in the Human Genome Project, significant advances have been made which offer the potential to solve this problem. These techniques utilize human genome maps, cloned resources, and sequence data in conjunction with fluorescence based technologies to enable the genome wide analysis of tumor cells. One such technique, cDNA microarray hybridization1,2, has the potential to provide large scale analysis of gene expression. This novel system for massively parallel cDNA hybridization is based upon robotic printing of DNAs on glass slides and simultaneous two-color fluorescence hybridization. For studies of gene expression, it is possible to utilize the vast resource of arrayed cDNA clones which have been developed as part of the Expressed Sequence Tag (EST) project to produce microarrays containing tens of thousands of genes3–6. When fluorescent probes generated by reverse transcription of tumor cell mRNA are hybridized to the array, the level of expression of every array element is simultaneously determined with respect to a reference probe labeled in a second color. Although the processing of such large quantities of data is challenging in itself, microarray technology will provide a far more detailed picture of gene expression than has previously been possible. The availability of this information has ramifications which will affect virtually all areas of cancer biology. This chapter will provide an overview of the current status of cDNA microarray technology and discuss its potential applications to problems in cancer biology.

Queueing interpretation of adaptive reconstructive multiparameter τ-opening filters

Abstract: A multiparameter binary (tau) -opening is a union of parameterized openings in which parameters for each opening are individually defined and a structuring element can be parameterized relative to both size and shape. The reconstructive filter corresponding to an opening is defined by fully passing any grain not eliminated by the opening and deleting all other grains. Adaptive design results from treating the parameter vector of a reconstructive multiparameter (tau) -opening as the state space of a Markov chain. The present paper considers the relationship between Markovian queueing networks and adaptive multiparameter (tau) - openings for the signal-union-noise model.

Selective Oxidation of Toluene over Complex Fe—Mo Oxides in the Absence of Molecular Oxygen.

Abstract: Fe–Mo catalysts prepared by a sol–gel method for selective oxidation of toluene are studied in the absence of molecular oxygen; a high benzaldehyde yield and high specific activity are achieved at an atomic ratio (Mo∶Fe) of about 1.0.

Experimental verification of a new physically based low energy (<5 keV) ion implant model

Abstract: Accurate modeling of ultra-low energy ion implantation is becoming increasingly more important as MOS devices shrink to deep submicron dimensions, and the required junction depths become shallower than 50 nm. To this end, an efficient Monte Carlo ion implantation model based on a substantially modified Binary Collision Approximation (BCA) has been developed and implemented in UT-MARLOWE. The model removes several of the limitations of the BCA at low energies, such as the asymptotic path approximation and the decoupling of nuclear and electronic stopping usually employed in BCA models. Additionally, multi-body interactions are important at very low energies, and are modeled explicitly for the 3-body case. The modified BCA gives very good agreement with experimental data and is a significant improvement over the classical BCA, particularly for heavy species and well-channeled implants. In this paper, we report on the experimental verification of the model, as well as refinements and corrections subsequently introduced. Surface effects are also discussed, and their impact on the dose-dependence of the profiles is examined. The model has been verified for arsenic and boron, for energies down to 2 keV and 1 keV, respectively. This new model is found to he in very good agreement with the experimental data.