bluuebunny/crossref_metadata_2025 huggingface dataset:
Principles of calibrating the dual-recycled GEO 600
Authors: Hewitson M. , Heinzel G. , Smith J. R. , Strain K. A. , Ward H.
Published: October 2004

GEO 600 is a dual-recycled interferometric gravitational wave detector which uses advanced optical techniques to achieve its design sensitivity. The peak response of GEO is tunable over a range of frequencies within the detection band of the instrument. The accurate calibration of the detector is an essential step in preparing the data for distribution to the various analysis groups in the community as well as allowing for the extraction of science results. Calibrating the dual-recycled interferometer requires the optical response of the instrument to be determined and corrected for on time scales associated with any fluctuations in the response. Due to the optical readout scheme used in GEO 600, any gravitational wave signals seen by the detector are split between two output signals. This means that, in order to recover a calibrated strain signal that has an optimal signal-to-noise ratio, the two outputs need to be combined pre- or postcalibration. This article presents a detailed method for calibrating the dual-recycled GEO configuration. The method builds upon the calibration scheme developed to calibrate the power-recycled GEO configuration. The main focus of this article is on the new aspects of the calibration process: on-line measurement, parameterization, and correction of the optical response of the instrument in an on-line, time-domain calibration pipeline. Some discussion is also given regarding the combination of the two main detector output signals in producing an optimal calibrated strain signal.
Technique to eliminate vibration localization
Authors: Shahruz S. M.
Published: October 2004

In this article, mistuned periodic structures are considered. It is well known that some components of such structures may vibrate with small amplitudes, while some other components may vibrate with significantly large amplitudes. Such a behavior is known as vibration localization and is undesirable. An effective passive technique to eliminate vibration localization is proposed in this article. The elimination is achieved by adding small components between the structure components. It is proved that the added components eliminate vibration localization in mistuned periodic structures. The proof is established by using a dichotomy in the dynamics of the structure to which the small components are added, and by applying the singular perturbation method.
Modulated laser interferometer with picometer resolution for piezoelectric characterization
Authors: Chao Chen , Wang Zhihong , Zhu Weiguang
Published: October 2004

A modified double-beam interferometric measurement system is established and tested for displacement measurement of ferroelectric lead zirconate titanate bulk samples. To overcome the optical path-length drift or laser intensity instability, a modulation technique is introduced, and desired resolution (down to several picometers) and reliability are achieved without the complicated close loop servo system. This modified interferometer provides us a powerful yet easily accessible tool for piezoelectric thin/thick film characterization.
Data coding tools for color-coded vector nanolithography
Authors: Lekki Janusz , Kumar Saveen , Parihar Sunil S. , Grange Sebastien , Baur Charles , Foschia Raphael , Kulik Andrzej
Published: October 2004

We propose and demonstrate the ability and efficiency of using a universal file format for a nanolithography pattern. A problem faced by the physicists working in the field of nanolithography is a lack of a flexible pattern design software (possibly open–source) that could be applied in combination with a broad range of commercial scanning probe microscope (SPM) systems. The current nanolithography software packages are device–specific and not portable. Therefore, it is impossible to make a lithography pattern and share it with fellow physicists working on a networked sub-system. In this paper we describe the software designed to read and interpret a nanolithography pattern stored in a Windows Metafile (WMF) standard graphic format and next to draw it on a substrate using an SPM tip. The nanolithography parameters like height, velocity, feedback force, etc. are coded in the color of the WMF onto the RGB channels of the image establishing a distinct relation between a graphical feature (color) and the used nanolithography scheme (voltage, height, etc.). The concept enables preparation of complex patterns using any standard graphic software and aids an intuitive recognition of the mode and parameters set for a pattern. The advantages of using a WMF over other approaches and the universal scope of the software are discussed.
Frequency-chirped light from an injection-locked diode laser
Authors: Wright M. J. , Gould P. L. , Gensemer S. D.
Published: October 2004

We use current modulation of an external-cavity diode laser in conjunction with optical injection locking of a free-running diode laser to produce a high output power of rapidly frequency-chirped light. Chirp rates exceeding 15 GHz/μs have been demonstrated with this simple system. An important consequence of the injection locking is the significant reduction of amplitude modulation in the output.
Modification of a scanning electron microscope to produce Smith–Purcell radiation
Authors: Kapp Oscar H. , Sun Yin-e , Kim Kwang-Je , Crewe Albert V.
Published: October 2004

We have modified a scanning electron microscope (SEM) in an attempt to produce a miniature free electron laser that can produce radiation in the far infrared region, which is difficult to obtain otherwise. This device is similar to the instrument studied by the Dartmouth group and functions on the basic principles first described by Smith and Purcell. The electron beam of the SEM is passed over a metal grating and should be capable of producing photons either in the spontaneous emission regime or in the superradiance regime if the electron beam is sufficiently bright. The instrument is capable of being continuously tuned by virtue of the period of the metal grating and the choice of accelerating voltage. The emitted Smith–Purcell photons exit the instrument via a polyethylene window and are detected by an infrared bolometer. Although we have obtained power levels exceeding nanowatts in the spontaneous emission regime, we have thus far not been able to detect a clear example of superradiance.
Melt temperature field measurement in single screw extrusion using thermocouple meshes
Authors: Brown E. C. , Kelly A. L. , Coates P. D.
Published: October 2004

The development and validation of a sensor for extrusion melt temperature field measurement is described. A grid of opposing thermocouple wires was constructed and held in position by a supporting frame. Wires were joined together at crossing points to form thermocouple junctions, which were computer monitored. The mesh was used to monitor melt temperature fields during single screw extrusion at the die entrance. Design and construction of the mesh is described in addition to experimental optimization of wire diameter and junction forming. Calibration of the sensor and potential measurement errors including shear heating effects are discussed. Initial results from single screw extrusion are presented for a commercial grade of low density polyethylene using five- and seven-junction thermocouple meshes. The dependence of melt temperature profile on screw speed is illustrated. At low screw speeds melt temperature profiles were flat in shape and higher than set wall temperatures. At higher screw speeds the profiles became more pointed in shape. Use of higher resolution sensors exposed more complex temperature profiles with shoulder regions.
Zeeman effect spectroscopically locked Cs diode laser system for atomic physics
Authors: Overstreet K. R. , Franklin J. , Shaffer J. P.
Published: October 2004

We present a diode laser system for Cs that uses a dichroic atomic vapor laser lock (DAVLL) to obtain stable single frequency operation around 852 nm from a high power quantum well index guided laser diode, >170 mW (JDS Uniphase SDL-5401-G1 and SDL-5421-G1). The laser diode is locked to an external cavity formed by a diffraction grating in the Littrow configuration. Passive stabilization of the laser system resulted in a laser drift of <20 MHz/min over a ∼10 min time scale. Over a 24 h period, the free running laser drift was less than 300 MHz. The diode laser and the external cavity temperature are actively stabilized independently so that temperature may be used to tune the cavity and/or the laser operating wavelength. The DAVLL lock actively stabilizes the external cavity to which the laser is locked by feeding back to piezoelectric transducers upon which the grating is mounted. Rapid fluctuations of the laser system are compensated for by feeding back a high frequency component (>1 kHz) of the error signal generated by the DAVLL signal to the laser current control. The instantaneous linewidth of the system was measured to be 200 kHz. The effective linewidth was 500 kHz root-mean-square while the long term drift was <1.5 MHz/h when the laser system was locked to the DAVLL signal. These results were obtained in a standard laboratory environment without temperature stabilizing the DAVLL spectrometer.
Reactor system for the study of high-temperature short-time sintering of nanoparticles
Authors: Kirchhof Martin J. , Schmid Hans-Joachim , Peukert Wolfgang
Published: October 2004

A high-temperature short residence time flow reactor system has been realized for the investigation of the gas phase sintering kinetics of nanoparticles separated from all other synthesis mechanisms, e.g., chemical reaction, nucleation, coagulation and condensation. Major components are a hot-wall tubular reactor for the production of unsintered aggregates consisting of spherical primary particles in the size range 10–80 nm and a sintering reactor for the investigation of the sintering kinetics at well-defined temperature and residence time history. Therefore, rapid heating and quenching of the particles at the beginning and at the end of the reaction zone, respectively, is maintained. Main parameters in the sintering reactor are: temperatures up to 1873 K and residence times in the range 8–1000 ms. The reactor conditions are characterized by temperature profile measurements with a newly constructed suction thermocouple probe and by computational fluid dynamics simulations of the residence time distributions. Exemplary results of the sintering of silica nanoparticles obtained by transmission electron microscopy analysis are presented.
Environmentally protected hot-stage atomic force microscope for studying thermo-mechanical deformation in microelectronic devices
Authors: Park C. , Shultz T. E. , Dutta I.
Published: October 2004

A commercial atomic force microscope (AFM) was equipped with a hot stage for conducting thermal cycling experiments up to 398 K, as well as a vacuum and purge system to provide a protective environment during heating. Two different hot-stage configurations, one for studying features in the plane of a microelectronic device, and the other for studying features on its cross section, were developed. It is shown that the AFM retains its calibration with no significant introduction of errors at temperatures up to 398 K. Two applications of in situ hot-stage atomic force microscopy, related to microelectronic devices, have been demonstrated. First, the in-plane coefficient of thermal expansion of a low dielectric constant (low-k) thin film dielectric material used in back-end interconnect structures was measured. Second, the equipment was used to conduct in situ studies of deformation of Cu thin film interconnect lines at the back end of silicon chips, under thermo-mechanical loads simulating those imposed on chip-level interconnect structures by a microelectronic package. The design of a bimetallic thermo-mechanical loading stage, which was used for the latter experiments in conjunction with the hot stage, is also discussed.
C
O
2
(λm=10.6 μm) He–Ne (λc=633 nm) two-color laser interferometry for low and medium electron density measurements in the TJ-II Stellarator
Authors: Acedo Pablo , Lamela Horacio , Sánchez Miguel , Estrada Teresa , Sánchez Joaquín
Published: October 2004

In this article we describe the setup, installation, calibration, and operation of the two-color (CO2–HeNe) laser heterodyne interferometer installed in the TJ-II Stellarator. This diagnostic has been routinely working during the last TJ-II experimental campaign (Autumn 2003) in low-density [electron cyclotron resonance (ECRH) heated, ne≅1019 m−3] and medium density [neutral beam injection (NBI) heated, ne≅5×1019 m−3] plasmas with line integral error better than 2×1017 m−2. This work demonstrates the possibility of using low-cost two wavelength laser interferometric diagnostics to measure low and medium-density plasmas instead of the complicated far infrared (FIR) interferometric systems that also suffer from fringe-jumps errors. The issues of low sensitivity to plasma density and mechanical vibration subtraction typical of these laser interferometers are solved through proper calibration of the interferometric system in the machine. First results on NBI heated plasmas measured by the laser interferometric system in the Stellarator TJ-II will be shown.
Study of particle acceleration of Cu plasma
Authors: Belloni F. , Doria D. , Lorusso A. , Nassisi V.
Published: October 2004

The experimental results of particle acceleration by plasma generated using a XeCl laser are described. The laser ion source developed is able to accelerate specific particles and to overcome the plasma effects which occur specially during the application of the accelerating voltage. In order to successfully execute this experiment, plasma expansion was highly necessary before the accelerating voltage application. For this goal an almost hermetic expanding chamber with a hole at its end, used as extraction electrode, was made. In this way arcs were eliminated and specific particles propagate in the drift tube. Time-of-flight and current intensity measurements of the ion beam have been done. The output signal, measured at 147 cm from the target, resulted modulated on ion mass-to-charge ratio and its maximum current was 220 μA at 18 kV accelerating voltage. Under the same accelerating value the bunch charge was estimated to be 4.2 nC.
Large area x-ray and neutron imaging using three-dimensional arrays of microlenses
Authors: Piestrup M. A.
Published: October 2004

Linear arrays of biconcave microlenses have been shown to be capable of imaging small objects using either x rays or neutrons. Because these lenses have small apertures and finite lengths, they are limited in their field of view (FOV). To increase the FOV, we propose that two sets of three-dimensional arrays of these microlenses be used. The spacing of the microlenses is calculated to achieve a complete image with uniform brightness. General design criteria are discussed in situations where either a one-to-one image or a magnified image is required.
Simple, cost effective, in situ sample hot stage for biological atomic force microscopy
Authors: Sattin Bernie D. , Goh M. Cynthia
Published: October 2004

The design and implementation of a hot stage for control of the sample temperature in atomic force microscope (AFM) imaging in fluid is described. This heater design is optimally suited for AFM studies that are biological in nature, where the sample needs to be held near physiological conditions. The ease of assembly, simplicity of design, and low cost makes it suitable for implementation in any laboratory for both research or teaching purposes. The small size and self-contained nature of the device allows it to be incorporated into any AFM system. We demonstrate the ability of the heater to function reliably at elevated temperatures where clear, high resolution images of plasmid DNA under water can be routinely obtained.
W
-band Fabry–Pérot microwave reasonators for optical detected electron paramagnetic resonance and electron nuclear double resonance of paramagnetic defects in solids
Authors: Tkach I. , Rogulis U. , Greulich-Weber S. , Spaeth J.-M.
Published: October 2004

The designs of W-band (∼95 GHz) Fabry–Pérot microwave resonators for optically detected electron paramagnetic resonance (ODEPR) and electron nuclear double resonance (ODENDOR) as well as the ODEPR/ODENDOR spectrometer are described. The Fabry–Pérot resonator was mainly designed for W-band EPR and ENDOR detected via the magnetic circular dichroism of the optical absorption (MCDA), but can also be used with slight modifications for photoluminescence (PL) detection of EPR/ENDOR. The microwave resonators were tested and successfully used for the first high-field MCDA-EPR/ENDOR investigation applied to the investigation of the paramagnetic EL2 defect in semi-insulating GaAs in which higher order effects could be suppressed which prevented the unambiguous analysis of previous K-band experiments. W-band PL-EPR was used to investigate dopants in SiC. The excellent performance of the microwave resonators encourages their use in wider applications of ODEPR and ODENDOR spectroscopy.
On the efficiency of Gore-Tex layer for brain protection from shock wave damage in cranioplasty
Authors: Saito T. , Voinovich P. A. , Nakagawa A. , Hosseini S. H. R. , Takayama K. , Hirano T.
Published: October 2004

The effectiveness of a Gore-Tex layer for protecting soft tissue from damage in shock wave therapy is investigated analytically, numerically and experimentally. Analytical considerations based on the fundamentals of wave dynamics and two-dimensional numerical simulations based on the elastodynamic equations are carried out for underwater shock wave propagation and interaction with Gore-Tex membrane models of different complexity. The results clearly demonstrate that considerable attenuation of shock waves with Gore-Tex is due to the air trapped inside the membrane. The experimental results confirm that a Gore-Tex sheet placed in the liquid reduces the transmitted shock wave peak overpressure significantly, by up to two orders of magnitude. Another experimental series reveals what kind of damage in the rat brain tissue can be caused by shock waves of different intensity.
Development of a system of automatic gap-adjusted electrodes for shock wave generators
Authors: Manousakas Ioannis , Liang Shen-Min , Wan Long-Ray , Wang Chia-Hui
Published: October 2004

In this study, a system of automatic gap-adjusted electrodes is developed for electrohydraulic shock wave generators that can be used both for extracorporeal shock wave lithotripsy (treatment of renal calculi) and for the extracorporeal shock wave therapy for musculo-skeletal disorders. This system is composed of three main components: (1) two electrodes and their bases; (2) servo motors and control software; (3) a high sensitivity CCD camera and image processing program. To verify system performance, in vitro fragmentation tests have been conducted using kidney stone phantoms. Results indicate that the efficiency of stone fragmentation using automatic gap adjustment can be increased up to 55.2%, which is twice more than without automatic gap adjustment (26.7%). This system can be applied to any commercial electrohydraulic extracorporeal shock wave lithotriptor or orthotriptor without difficulty.
Amplification of axially symmetric magnetic field by Bohm particle diffusion
Authors: Lee Tae-Yeon , Ryu Chang-Mo
Published: October 2004

The magnetic induction equation for an axially symmetric magnetic field reveals an interesting feature, when the Bohm plasma diffusion is incorporated. The 1/B dependence of Bohm diffusion allows the induction equation to transform into a simple heat equation which admits an exact solution when the plasma temperature is constant. When the diffusion velocity satisfies a certain condition, the axially symmetric magnetic field can be significantly enhanced.
Stabilizing viscosity contrast effect on miscible displacement in heterogeneous porous media, using lattice Bhatnagar–Gross–Krook simulations
Authors: Talon Laurent , Martin Jérôme , Rakotomalala Nicole , Salin Dominique
Published: October 2004

We analyze the displacement of a viscous fluid by a miscible more viscous one in heterogeneous porous media. We performed lattice Bhatnagar–Gross–Krook simulations, which were previously successfully applied to the study of the dispersion of a passive tracer in a stochastic heterogeneous porous medium. In the present situation, the flow is stable (no viscous fingering) and leads to an overall Gaussian dispersion, the coefficient of which decreases as the viscosity ratio increases. The results are in reasonable agreement with the stochastic approach of Welty and Gelhar.
Two-dimensional fast reconnection in a fluid drift model
Authors: Scott Bruce , Porcelli Franco
Published: October 2004

A simple scenario for two-dimensional reconnection is reexamined in the context of a fluid drift model which treats the pressure and parallel ion velocity independently. The rapid nonlinear establishment of an arbitrarily thin current sheet is unaffected for expected values of the plasma β of a few percent. Eventually the sound wave dynamics should enter to alter the results, but remains insignificant for reasonable β values (gas/magnetic pressure up to 0.1).
Magnetic electron drift waves in electron magnetohydrodynamic plasmas
Authors: Chakrabarti Nikhil , Singh Raghvendra
Published: October 2004

The dynamics of nonuniform, magnetized, cold electron plasma in a stationary charge neutral ion background is considered. In the high frequency limit, electromagnetic modification of electron plasma oscillation is obtained in homogeneous plasma, whereas in inhomogeneous plasma in the low frequency regime a driftlike mode is found. Nonlinear evolution of this mode is derived to describe the two-dimensional (2D) dynamics. The equation has a close resemblance to 2D electrostatic collisionless drift wave equation thereby called as “magnetic electron drift” wave. In addition to the usual small amplitude dispersive modes the stationary state nonlinear vortexlike solutions are also discussed. The magnetic electron drift wave in the electron magnetohydrodynamic regime can find applications in laboratory as well as in space plasmas.
Potential ballistic dispersal of Cytisus scoparius (Fabaceae) seeds
Authors: Malo Juan E.
Published: October 2004

Cytisus scoparius (L.) Link (Fabaceae) has a ballistic type of primary seed-dispersal mechanism in which its legumes dehisce suddenly when they dry. This paper presents an experimental approach to the measurement and modeling of distances reached by seeds under optimum dispersal conditions. Branchlets of the species carrying mature legumes were collected and attached to 1.20-m-high platforms on a flat roof terrace. For 2 weeks, daily measurements were made of distances attained by seeds ejected from legumes in the previous 24 h. Seeds were found at a distance of 2343 ± 113 mm (mean ± s.e., n = 245), with 10.2% of recorded distances greater than 5 m and some about 7 m. The mixture model fitted to the distances traveled by seeds allows the mathematical isolation of two underlying processes, the ballistic projection of seeds by dehiscent legumes (nearly 49% of seeds, reaching 3686 ± 1797 mm) and the barochorous dispersal of the remaining seeds in the platform environs (1254 ± 1254 mm). Modeling shows that seeds dispersed ballistically reach locations at some distance from the shrub crown, with low densities of sibling seeds—a potential advantage for the establishment of new individuals.
Chromosome numbers in Kunzea (Myrtaceae)
Authors: de Lange P. J. , Murray B. G.
Published: October 2004

Documented chromosome counts are reported for the first time for nine Kunzea species and two varieties. Confirmatory counts are provided for K. sinclairii. Counts are also documented for a further nine unnamed variants of the Australasian K. ericoides complex. In addition, counts and chromosome-pairing behaviour are reported for eight putative wild New Zealand Kunzea hybrids, including one example of ×Kunzspermum hirakimata, and artificial hybrids from 21 controlled crosses (18 Kunzea and two controlled Kunzea × Leptospermum). Some chromosomal variation is evident in the New Zealand members of the K. ericoides complex, which helps to support the recognition of additional taxa within this aggregate species.
Mitotic checkpoint function in the formation of gross chromosomal rearrangements in
Saccharomyces cerevisiae
Authors: Myung Kyungjae , Smith Stephanie , Kolodner Richard D.
Published: October 2004

The accumulation of gross chromosomal rearrangements (GCRs) is characteristic of cancer cells. Multiple pathways that prevent GCRs, including S-phase cell cycle checkpoints, homologous recombination, telomere maintenance, suppression of
de novo
telomere addition, chromatin assembly, and mismatch repair, have been identified in
Saccharomyces cerevisiae
. However, pathways that promote the formation of GCRs are not as well understood. Of these, the
de novo
telomere addition pathway and nonhomologous end-joining are the best characterized. Here, we demonstrate that defects in the mitotic checkpoint and the mitotic exit network can suppress GCRs in strains containing defects that increase the GCR rate. These data suggest that functional mitotic checkpoints can play a role in the formation of genome rearrangements.
A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase
Authors: Berkovitch Frederick , Behshad Elham , Tang Kuo-Hsiang , Enns Eva A. , Frey Perry A. , Drennan Catherine L.
Published: October 2004

Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5′-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of
dl
-lysine and of
l
-β-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from
Clostridium sticklandii
. In this structure, a Rossmann domain covalently binds pyridoxal-5′-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, ≈25 Å from the active site. In this mode of pyridoxal-5′-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5′-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.
Loss of Runx3 function in leukocytes is associated with spontaneously developed colitis and gastric mucosal hyperplasia
Authors: Brenner Ori , Levanon Ditsa , Negreanu Varda , Golubkov Olga , Fainaru Ofer , Woolf Eilon , Groner Yoram
Published: October 2004

RUNX transcription factors are key regulators of lineage-specific gene expression and might be involved in autoimmune diseases. Runx3 plays a role during the development of sensory neurons and T cells and regulates transforming growth factor β (TGF-β) signaling in dendritic cells. Here, we report that at 4 weeks of age, Runx3 knockout (KO) mice spontaneously develop inflammatory bowel disease (IBD) characterized by leukocyte infiltration, mucosal hyperplasia, formation of lymphoid clusters, and increased production of IgA. Additionally, at a considerably older age (8 months), the KO mice also develop progressive hyperplasia of the gastric mucosa associated with disturbed epithelial differentiation and cellular hyaline degeneration. Analysis of cytokines in the colonic mucosa of Runx3 KO mice revealed a mixed T helper 1/T helper 2 response. By using immunohistochemistry and RNAin situhybridization, Runx3 expression in the gastrointestinal tract is detected in lymphoid and myeloid populations but not in the epithelium. The data indicate that loss of leukocytic cell-autonomous function of Runx3 results in IBD and gastric lesion in the KO mice. IBD in humans is viewed as a complex genetic disorder. Several susceptibility loci were identified on different human chromosomes including the chromosomal region 1p36 whereRUNX3resides. It is thus tempting to speculate that mutations inRUNX3may constitute an IBD risk factor in humans.
Managerial Perspectives on Government Intervention in Malaysia: Implications for International Business
Authors: Mamman Aminu
Published: October 2004

Globalization has created major opportunities for multinational enterprises (MNEs) – indeed, many observers believe that MNEs are agents of globalization. Undoubtedly their impact will continue to be felt by countries around the globe. However, because their impact and its implications will depend on decisions made by individuals who help shape government policy, it is important to understand the significance of managerial attitudes to government policy. This paper investigates: (a) what managers believe government should or should not do, (b) whether their attitudes depend on their position in the organizational hierarchy; and (c) whether their views are in line with the principles of free market and globalization. The data revealed that the managers are in favour of government intervention in the economy – if it is intended to create a freer operation of the market rather than to restrict it. The implication of the findings for international business, MNEs, and research is discussed.
The Global Export of Risk: Finance and the Film Business
Authors: Phillips Richard
Published: October 2004

This article examines the nature of risk and the limits of risk mitigation in the foreign financing of the US film business. The innovations and motivations through which foreign financial institutions have underwritten the most fundamental risk of the Hollywood model – the high costs of production – are discussed through several cases studies. These meetings of finance and the film business have produced monumental vestiges of corporate bankruptcy, market collapse and the inevitable redistribution of debt. Who paid? The public – and not only by their consumption of US film entertainment and merchandising. Foreign money has supported a portion of the substantial costs of failure created by the big-budget Hollywood production model. This global export of risk has often been placed upon the unknowing tax-payer or insurance-holder following the collapse of different financial institutions. Consequently, the ultimate importance behind the story of finance and the film business lies in its contribution to a broader evaluation about the sources of risk and the limits of risk mitigation in contemporary capitalism.
Upgrading in the Global Clothing Industry: The Transformation of Boyner Holding
Authors: Tokatli Nebahat , Eldener Yonca Boyaci
Published: October 2004

The authors examine the complexity of the structure and corporate practice of Boyner Holding, a Benetton supplier in Turkey as well as a manufacturer and a retailer in its own right. Their analysis has implications concerning the fluid, intricate and dynamic power relationships within the global clothing industry, as well as concerning the availability of upgrading opportunities for corporations in peripheral places such as Turkey. The analysis also points to the current blurring of the traditional distinctions between production-based and distribution-based firms, between full-package manufacturers and original brand name manufacturers and, in fact, between lead firms and their suppliers.
A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
Authors: Ji Yuan , Tsui Kam-Wah , Kim KyungMann
Published: October 2004

Motivation: The classification of samples using gene expression profiles is an important application in areas such as cancer research and environmental health studies. However, the classification is usually based on a small number of samples, and each sample is a long vector of thousands of gene expression levels. An important issue in parametric modeling for so many gene expression levels is the control of the number of nuisance parameters in the model. Large models often lead to intensive or even intractable computation, while small models may be inadequate for complex data.

Methodology: We propose a two-step empirical Bayes classification method as a solution to this issue. At the first step, we use the model-based cluster algorithm with a non-traditional purpose of assigning gene expression levels to form abundance groups. At the second step, by assuming the same variance for all the genes in the same group, we substantially reduce the number of nuisance parameters in our statistical model.

Results: The proposed model is more parsimonious, which leads to efficient computation under an empirical Bayes estimation procedure. We consider two real examples and simulate data using our method. Desired low classification error rates are obtained even when a large number of genes are pre-selected for class prediction.

Availability: Supplemental materials including technical details are available at “http://odin.mdacc.tmc.edu/~yuanj/papers/sup.pdf”. An R program for computation is available upon request by email to Yuan Ji (yuanji@mdanderson.org)

Contact:  yuanji@mdanderson.org
Extracting relations between promoter sequences and their strengths from microarray data
Authors: Kiryu Hisanori , Oshima Taku , Asai Kiyoshi
Published: October 2004

Motivation: The relations between the promoter sequences and their strengths were extensively studied in the 1980s. Although these studies uncovered strong sequence-strength correlations, the cost of their elaborate experimental methods have been too high to be applied to a large number of promoters. On the contrary, a recent increase in the microarray data allows us to compare thousands of gene expressions with their DNA sequences.

Results: We studied the relations between the promoter sequences and their strengths using the Escherichia coli microarray data. We modeled those relations using a simple weight matrix, which was optimized with a novel support vector regression method. It was observed that several non-consensus bases in the ‘−35’ and ‘−10’ regions of promoter sequences act positively on the promoter strength and that certain consensus bases have a minor effect on the strength. We analyzed outliers for which the observed gene expressions deviate from the promoter strength predictions, and identified several genes with enhanced expressions due to multiple promoters and genes under strong regulation by transcription factors. Our method is applicable to other procaryotes for which both the promoter sequences and the microarray data are available.

Contact:  hisano-k@is.aist-nara.ac.jp
Finding regulatory modules through large-scale gene-expression data analysis
Authors: Kloster M. , Tang C. , Wingreen N.S.
Published: October 2004

Motivation: The use of gene microchips has enabled a rapid accumulation of gene-expression data. One of the major challenges of analyzing this data is the diversity, in both size and signal strength, of the various modules in the gene regulatory networks of organisms.

Results: Based on the iterative signature algorithm [Bergmann,S., Ihmels,J. and Barkai,N. (2002) Phys. Rev. E67, 031902], we present an algorithm—the progressive iterative signature algorithm (PISA)—that, by sequentially eliminating modules, allows unsupervised identification of both large and small regulatory modules. We applied PISA to a large set of yeast gene-expression data, and, using the Gene Ontology database as a reference, found that the algorithm is much better able to identify regulatory modules than methods based on high-throughput transcription-factor binding experiments or on comparative genomics.

Contact:  tang@nec-labs.com
Evolutionary optimization with data collocation for reverse engineering of biological networks
Authors: Tsai Kuan-Yao , Wang Feng-Sheng
Published: October 2004

Motivation: Modern experimental biology is moving away from analyses of single elements to whole-organism measurements. Such measured time-course data contain a wealth of information about the structure and dynamic of the pathway or network. The dynamic modeling of the whole systems is formulated as a reverse problem that requires a well-suited mathematical model and a very efficient computational method to identify the model structure and parameters. Numerical integration for differential equations and finding global parameter values are still two major challenges in this field of the parameter estimation of nonlinear dynamic biological systems.

Results: We compare three techniques of parameter estimation for nonlinear dynamic biological systems. In the proposed scheme, the modified collocation method is applied to convert the differential equations to the system of algebraic equations. The observed time-course data are then substituted into the algebraic system equations to decouple system interactions in order to obtain the approximate model profiles. Hybrid differential evolution (HDE) with population size of five is able to find a global solution. The method is not only suited for parameter estimation but also can be applied for structure identification. The solution obtained by HDE is then used as the starting point for a local search method to yield the refined estimates.

Availability: The algorithm, implemented by Compaq Visual Fortran Professional Edition 6.6, and the supplements are available at http://www.che.ccu.edu.tw/~bioproc/index-english.html/. IMSL Math/Library is a commercial library included in Compaq Visual Fortran Professional Edition.

Contact:  chmfsw@ccu.edu.tw
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data
Authors: Jarvis Roger M. , Goodacre Royston
Published: October 2004

Motivation: The major difficulties relating to mathematical modelling of spectroscopic data are inconsistencies in spectral reproducibility and the black box nature of the modelling techniques. For the analysis of biological samples the first problem is due to biological, experimental and machine variability which can lead to sample size differences and unavoidable baseline shifts. Consequently, there is often a requirement for mathematical correction(s) to be made to the raw data if the best possible model is to be formed. The second problem prevents interpretation of the results since the variables that most contribute to the analysis are not easily revealed; as a result, the opportunity to obtain new knowledge from such data is lost.

Methods: We used genetic algorithms (GAs) to select spectral pre-processing steps for Fourier transform infrared (FT-IR) spectroscopic data. We demonstrate a novel approach for the selection of important discriminatory variables by GA from FT-IR spectra for multi-class identification by discriminant function analysis (DFA).

Results: The GA selects sensible pre-processing steps from a total of ∼1010 possible mathematical transformations. Application of these algorithms results in a 16% reduction in the model error when compared against the raw data model. GA-DFA recovers six variables from the full set of 882 spectral variables against which a satisfactory DFA model can be formed; thus inferences can be made as to the biochemical differences that are reflected by these spectral bands.

Availability: Supplementary information, datasets and scripts are available from the corresponding author.

Contact:  roy.goodacre@manchester.ac.uk
Predicting protein localization in budding Yeast
Authors: Chou Kuo-Chen , Cai Yu-Dong
Published: October 2004

Motivation: Most of the existing methods in predicting protein subcellular location were used to deal with the cases limited within the scope from two to five localizations, and only a few of them can be effectively extended to cover the cases of 12–14 localizations. This is because the more the locations involved are, the poorer the success rate would be. Besides, some proteins may occur in several different subcellular locations, i.e. bear the feature of ‘multiplex locations’. So far there is no method that can be used to effectively treat the difficult multiplex location problem. The present study was initiated in an attempt to address (1) how to efficiently identify the localization of a query protein among many possible subcellular locations, and (2) how to deal with the case of multiplex locations.

Results: By hybridizing gene ontology, functional domain and pseudo amino acid composition approaches, a new method has been developed that can be used to predict subcellular localization of proteins with multiplex location feature. A global analysis of the proteins in budding yeast classified into 22 locations was performed by jack-knife cross-validation with the new method. The overall success identification rate thus obtained is 70%. In contrast to this, the corresponding rates obtained by some other existing methods were only 13–14%, indicating that the new method is very powerful and promising. Furthermore, predictions were made for the four proteins whose localizations could not be determined by experiments, as well as for the 236 proteins whose localizations in budding yeast were ambiguous according to experimental observations. However, according to our predicted results, many of these ‘ambiguous proteins’ were found to have the same score and ranking for several different subcellular locations, implying that they may simultaneously exist, or move around, in these locations. This finding is intriguing because it reflects the dynamic feature of these proteins in a cell that may be associated with some special biological functions.

Contact:  kchou@san.rr.com

Supplementary information:  www.pami.sjtu.edu.cn/kcchou
Normalization of two-channel microarray experiments: a semiparametric approach
Authors: Eckel J. E. , Gennings C. , Therneau T. M. , Burgoon L. D. , Boverhof D. R. , Zacharewski T. R.
Published: October 2004

Motivation: An important underlying assumption of any experiment is that the experimental subjects are similar across levels of the treatment variable, so that changes in the response variable can be attributed to exposure to the treatment under study. This assumption is often not valid in the analysis of a microarray experiment due to systematic biases in the measured expression levels related to experimental factors such as spot location (often referred to as a print-tip effect), arrays, dyes, and various interactions of these effects. Thus, normalization is a critical initial step in the analysis of a microarray experiment, where the objective is to balance the individual signal intensity levels across the experimental factors, while maintaining the effect due to the treatment under investigation.

Results: Various normalization strategies have been developed including log-median centering, analysis of variance modeling, and local regression smoothing methods for removing linear and/or intensity-dependent systematic effects in two-channel microarray experiments. We describe a method that incorporates many of these into a single strategy, referred to as two-channel fastlo, and is derived from a normalization procedure that was developed for single-channel arrays. The proposed normalization procedure is applied to a two-channel dose–response experiment.

Availability: The SAS macro for two-channel fastlo is available from the authors upon request and the data used to test the methods is publicly available at http://www.bch.msu.edu/~zacharet/publications/supplementary/ee_dr

Contact:  eckel@mayo.edu
Theoretical and practical advances in genome halving
Authors: Yin Peng , Hartemink Alexander J.
Published: October 2004

Motivation: Duplication of an organism's entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes.

Results: In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.

Availability:  GenomeHalving is available upon email request.

Contact:  py@cs.duke.edu; amink@cs.duke.edu
Identifying differentially expressed genes from microarray experiments via statistic synthesis
Authors: Yang Yee Hwa , Xiao Yuanyuan , Segal Mark R.
Published: October 2004

Motivation: A common objective of microarray experiments is the detection of differential gene expression between samples obtained under different conditions. The task of identifying differentially expressed genes consists of two aspects: ranking and selection. Numerous statistics have been proposed to rank genes in order of evidence for differential expression. However, no one statistic is universally optimal and there is seldom any basis or guidance that can direct toward a particular statistic of choice.

Results: Our new approach, which addresses both ranking and selection of differentially expressed genes, integrates differing statistics via a distance synthesis scheme. Using a set of (Affymetrix) spike-in datasets, in which differentially expressed genes are known, we demonstrate that our method compares favorably with the best individual statistics, while achieving robustness properties lacked by the individual statistics. We further evaluate performance on one other microarray study.

Availability: The approach is implemented in an R package called DEDS, which is available for download from the Bioconductor website (http://www.bioconductor.org/).

Contact:  mark@biostat.ucsf.edu