bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantized writing processes in quantum magnetic disks (abstract)
Authors: Suriono Usman , Chou Stephen Y. 
Published: July 2002

It has been suggested that the writing process in quantum magnetic disks (QMDs) is quantized: a write head either writes perfectly the entire bit which is a discrete single-domain element isolated from other bits with nonmagnetic materials, or it does not write the bit at all. This article presents the micromagnetics demonstration of this quantized writing process. In the simulation, each QMD bit is assumed to be a polycrystalline cobalt bar of 700 nm long, 50 nm wide, and 30 nm thick, and to be oriented parallel to the disk surface. To obtain the dynamic motion of the magnetization structure of the bit, iterative energy minimization algorithm and the Landau–Lifshitz–Gilbert equation were used. The write head field is assumed to be parallel to the long axis of the bar and uniform with a strength of 2.5 times the bar coercivity. The write field has a width the same as that of the bar but a length that is only three-quarters of the cobalt bar length. It was found that even though the writing field size was smaller than the size of the bar, the magnetic moment of the entire single-domain bar can be switched from one direction to another, giving a perfect writing. The switching process occurred roughly in two stages. First, the magnetic moments got reversed in the region where the write field was applied. Second, driven by exchange force and shape anisotropy, the reversal propagated out of the write field region and reached the entire bit.
It was also found that if the overlap of the writing field with the bar was less than one-quarter of the bar length in the bar long axis or four-fifths of the bar width in the bar short axis, the writing field would only temporarily perturbs the magnetic moment distribution of the bar. When the write field was removed from the bar, the magnetic moment of the bar would return to its original state. The quantized writing process in the QMD will allow the use of a smaller and therefore faster write head, can avoid the errors due to misplacement and fringing field, hence is suitable for ultrahigh-density storage.
Spin-resolved electron spectroscopies of epitaxial magnetite (001) (abstract)
Authors: Shaw Kimberly A. , Lochner Eric , Lind David M. , DiBari Rebecca C. , Stoyanov Plamen , Singer Brian 
Published: July 2002

We will present the first spin-resolving electron spectroscopic studies of a magnetite (Fe3O4)(001) surface. Magnetite is a semimetal with a high density of states in the minority band, but a large band gap in the majority states at the Fermi energy. The polarization of the secondary emission cascade is measured using spin-resolved secondary electron emission spectroscopy (SRSEES), and reflects the semimetallic spin structure of Fe3O4. The polarization plateau of spin-resolved secondary emission (29.8%) matches the average 3D band polarization of stoichiometric Fe3O4 as determined from spin-resolved band structure calculations (34.2%). An enhancement of the polarization of the secondary electrons at lowest energies will also be discussed. Spin-resolved Auger emission spectroscopy (SRAES) of the Fe3O4 films have been measured and show correlation effects in the valence-valence Auger transitions. Suppressed intensity and polarization of M23M45M45 Auger emission relative to M1M45M45 Auger emission is observed, as well as strong resonant emission with shake-up. Conversely, no spin polarization is detected in the spin-resolved oxygen LMM Auger features, although oxygen Auger emission (in which we can distinguish between adsorbed and bonded oxygen) is used to verify surface cleanliness of the samples.
The synthesis of Fe3O4 films grown on magnesium oxide (001) substrates using oxygen plasma-assisted molecular beam epitaxy will be discussed, as will thin-film characterization using SQUID magnetometry and x-ray and electron diffraction. A unique angle-, energy-, and spin-resolved electron spectrometer has been designed and built for the study of magnetic surfaces, and these studies represent its’ first use. That spectrometer is based on a tandem configuration of an energy-dispersive energy analyzer and Mott spin polarimeter.
Magnetic properties of fcc-Fe multilayer (invited) (abstract)
Authors: Matsui M. , Doi M. , Kida A. , Yamada Y. 
Published: July 2002

Recently, magnetic properties of fcc-Fe ultrathin films have been extensively investigated. The results, however, are complicated and inconsistent with one another. These are antiferromagnetism, ferromagnetism, different Fe magnetic moment for different atomic sites in film or a rearrangement of surface Fe atoms etc. In this article the recent results for fcc-Fe multilayers will be reported and discussed to obtain a unified picture for magnetism of fcc-Fe ultrathin films. Epitaxially grown multilayers of fcc-Fe with Cu or Cu-M (M=Au,Ni) spacer on Cu(001) and Cu(111) substrates were prepared by molecular beam epitaxy method. The Cu-M spacer was adopted to change the mean interatomic distance between Fe atoms at interfaces by changing the composition of M (=Au,Ni), where Au was used to increase the distance and Ni to decrease it. Fe layers on a pure Cu spacer were fcc and the magnetic moment was at most 2.0μB. Fe layers on a Cu-Au spacer, however, were fct with c/a&lt;1 and those on Cu-Ni with c/a≳1, where a is the in-plane lattice constant and c is the out of plane one. Then a mean magnetic moment of Fe atoms (μ) as a function of Fe atomic volume (V) was obtained. The moment μ continuously increases with increasing V by the so-called magnetovolume effect. The maximum μ value is 2.7μB for about ΔV=4% (ΔV is a change of V from pure Cu volume). And μ=0 for ΔV=−2%. The Mössbauer effect and EXAFS were also measured.
The measurements revealed that the samples for the ΔV≤0 region contain two kinds of Fe (mixture state), high spin state with 2.0μB and nonmagnetic low spin state. Thus it is concluded that the high to low spin state transition is the first kind as theoretically suggested by Moruzzi et al. We also performed band calculations for fcc-Fe/Cu multilayers changing V. Next, the reason for the mixture state is discussed. It is found that a well defined smooth Cu substrate surface promotes a rearrangment of surface Fe atoms due to the surface diffusion, preferring the low spin state and the rough surface obstructs the rearrangement and provides the fcc circumstance by surrounding Cu atoms, which results in the high spin state. Recent inconsistent results for fcc-Fe ultra thin films could be explained by the two spin state model, the surface Fe atomic rearrangement, and the magnetovolume effect.
Twin screw extrusion of a metal particle dispersion
Authors: Göktürk H. , Maki K. 
Published: July 2002

Twin screw extruder is employed as a mechanical dispersion tool in the processing of particulate media incorporating high specific surface area (SSA) pigments. In this study, the effectiveness of a typical screw configuration used in the processing of formulations containing acicular iron particles of SSA=50 m2/g was experimentally investigated. During a steady state mixing operation, the extruder was brought to a dead stop, the screws were pulled out and material samples were collected from nine different screw sections. These samples were analyzed to determine the progress of the mixing process as the dispersion flows from section to section. Using SEM micrographs of the material samples, magnetic particle distributions corresponding to different screw sections were identified. The microstructure was observed to change from a granular appearance of aggregates and voids to a coagulated but relatively more uniform distribution of magnetic particles. The state of the dispersion was also magnetically evaluated by probing the magnetostatic interaction in the dispersion samples. Both hysteresis curves and remanence curves of the samples were utilized for this purpose. Interaction parameters associated with the hysteresis curves, such as coercivity, did not exhibit clear trends from section to section. The remanence curves were found to be more appropriate to analyze the state of the dispersion.
Peak ΔM values calculated from the remanence curves followed the changes that were observed in the microstructure. It was concluded from the overall results that the extrusion process could be further improved by changes in the screw configuration.
Oxidant–antioxidant profiles of platelet rich plasma in smokers
Authors: Gökkusu C. , Ademoglu E. , Tamer S. , Alkan G. 
Published: July 2002

AbstractCigarette smoke is a major risk factor for both coronary heart disease and peripheral vascular disease and has been reported to contain many oxidizing agents that lead to generation of free radicals. In this study, we investigated the levels of lipid peroxides (LPO) and antioxidant vitamins (C and E), total thiol content (t‐SH), the activities of superoxide dismutase (SOD), glutathione S‐transferase (GST) and glutathione peroxidase (GPx) in the platelet‐rich plasma (PRP) and plasma of 50 smokers and 30 non‐smokers. Total cholesterol (TC), low density‐cholesterol (LDL‐C), triglyceride (TG) and phospholipid (PL) levels of the plasma were significantly higher (p < 0.001) and high density‐cholesterol (HDL‐C) levels were significantly lower in smokers (p < 0.001) when compared with non‐smokers. In plasma and PRP, LPO levels, GST and SOD activities were found to be increased (p < 0.001) in smokers, whereas GPx activity, vitamin C levels and t‐SH content were found to be decreased. On the other hand, the levels of vitamin E was unchanged in plasma and PRP. The relationships between plasma levels of lipids, LPO and antioxidant systems were also investigated in both groups. A strong positive correlation was found between TC and Vit E (r = 0.5575; p < 0.001), LPO and PL (r = 0.4270; p < 0.01), LPO and GST (r = 0.3770; p < 0.01) and t‐SH and GPx (r = 0.3781; p < 0.01) in smokers. These findings reveal a disturbance of oxidant‐antioxidant balance by free radicals present in cigarette smoke, which may cause reduction in platelet hyperreactivity and endothelial dysfunction in smokers.
Phorbol Esters and SDF-1 Induce Rapid Endocytosis and Down Modulation of the Chemokine Receptor CXCR4
Authors: Signoret Natalie , Oldridge Joanne , Pelchen-Matthews Annegret , Klasse Per J. , Tran Thanh , Brass Lawrence F. , Rosenkilde Mette M. , Schwartz Thue W. , Holmes William , Dallas Walt , Luther Michael A. , Wells Timothy N.C. , Hoxie James A. , Marsh Mark 
Published: July 2002

The chemokine receptor CXCR4 is required, together with CD4, for entry by some isolates of HIV-1, particularly those that emerge late in infection. The use of CXCR4 by these viruses likely has profound effects on viral host range and correlates with the evolution of immunodeficiency. Stromal cell-derived factor-1 (SDF-1), the ligand for CXCR4, can inhibit infection by CXCR4-dependent viruses. To understand the mechanism of this inhibition, we used a monoclonal antibody that is specific for CXCR4 to analyze the effects of phorbol esters and SDF-1 on surface expression of CXCR4. On human T cell lines SupT1 and BC7, CXCR4 undergoes slow constitutive internalization (1.0% of the cell surface pool/min). Addition of phorbol esters increased this endocytosis rate &gt;6-fold and reduced cell surface CXCR4 expression by 60 to 90% over 120 min. CXCR4 was internalized through coated pits and coated vesicles and subsequently localized in endosomal compartments from where it could recycle to the cell surface after removal of the phorbol ester. SDF-1 also induced the rapid down modulation (half time ∼5 min) of CXCR4. Using mink lung epithelial cells expressing CXCR4 and a COOH-terminal deletion mutant of CXCR4, we found that an intact cytoplasmic COOH-terminal domain was required for both PMA and ligand-induced CXCR4 endocytosis. However, experiments using inhibitors of protein kinase C indicated that SDF-1 and phorbol esters trigger down modulation through different cellular mechanisms.
SDF-1 inhibited HIV-1 infection of mink cells expressing CD4 and CXCR4. The inhibition of infection was less efficient for CXCR4 lacking the COOH-terminal domain, suggesting at least in part that SDF-1 inhibition of virus infection was mediated through ligand-induced internalization of CXCR4. Significantly, ligand induced internalization of CXCR4 but not CD4, suggesting that CXCR4 and CD4 do not normally physically interact on the cell surface. Together these studies indicate that endocytosis can regulate the cell-surface expression of CXCR4 and that SDF-1–mediated down regulation of cell-surface coreceptor expression contributes to chemokine-mediated inhibition of HIV infection.
Atrophin-1, the Dentato-Rubral and Pallido-Luysian Atrophy Gene Product, Interacts with Eto/Mtg8 in the Nuclear Matrix and Represses Transcription
Authors: Wood Jonathan D. , Nucifora Frederick C. , Duan Kui , Zhang Chuanyi , Wang Jianxiang , Kim Yujin , Schilling Gabriele , Sacchi Nicoletta , Liu Johnson M. , Ross Christopher A. 
Published: July 2002

Dentato-rubral and pallido-luysian atrophy (DRPLA) is one of the family of neurodegenerative diseases caused by expansion of a polyglutamine tract. The drpla gene product, atrophin-1, is widely expressed, has no known function or activity, and is found in both the nuclear and cytoplasmic compartments of neurons. Truncated fragments of atrophin-1 accumulate in neuronal nuclei in a transgenic mouse model of DRPLA, and may underlie the disease phenotype.
Using the yeast two-hybrid system, we identified ETO/MTG8, a component of nuclear receptor corepressor complexes, as an atrophin-1–interacting protein. When cotransfected into Neuro-2a cells, atrophin-1 and ETO/MTG8 colocalize in discrete nuclear structures that contain endogenous mSin3A and histone deacetylases. These structures are sodium dodecyl sulfate–soluble and associated with the nuclear matrix. Cotransfection of ETO/MTG8 with atrophin-1 recruits atrophin-1 to the nuclear matrix, while atrophin-1 and ETO/MTG8 cofractionate in nuclear matrix preparations from brains of DRPLA transgenic mice. Furthermore, in a cell transfection–based assay, atrophin-1 represses transcription. Together, these results suggest that atrophin-1 associates with nuclear receptor corepressor complexes and is involved in transcriptional regulation.
Emerging links between disease-associated polyglutamine proteins, nuclear receptors, translocation-leukemia proteins, and the nuclear matrix may have important repercussions for the pathobiology of this family of neurodegenerative disorders.
The Persuasion Knowledge Model: How People Cope with Persuasion Attempts
Authors: Friestad Marian , Wright Peter 
Published: July 2002

Abstract
In theories and studies of persuasion, people's personal knowledge about persuasion agents' goals and tactics, and about how to skillfully cope with these, has been ignored. We present a model of how people develop and use persuasion knowledge to cope with persuasion attempts. We discuss what the model implies about how consumers use marketers' advertising and selling attempts to refine their product attitudes and attitudes toward the marketers themselves. We also explain how this model relates to prior research on consumer behavior and persuasion and what it suggests about the future conduct of consumer research.
Stem Trace: an interactive visual tool for comparative RNA structure analysis.
Authors: Kasprzak W , Shapiro B 
Published: July 2002

Abstract
MOTIVATION: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. RESULTS: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stem Trace elucidates preservation of structures in this region across the various strains of HIV. AVAILABILITY: The program can be made available upon request. It runs on SUN, SGI and DEC (Compaq) Unix workstations.
E-CELL: software environment for whole-cell simulation.
Authors: Tomita M , Hashimoto K , Takahashi K , Shimizu T S , Matsuzaki Y , Miyoshi F , Saito K , Tanida S , Yugi K , Venter J C , Hutchison C A 
Published: July 2002

Abstract
MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.
MaskerAid : a performance enhancement to RepeatMasker
Authors: Bedell Joseph A. , Korf Ian , Gish Warren 
Published: July 2002

Abstract
Summary: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid , a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting.
Availability: On request from the authors (see http://sapiens.wustl.edu/MaskerAid).
Contact: maskeraid@watson.wustl.edu
These authors contributed equally to this work.
* To whom correspondence should be addressed.
** Current address: Incyte Genomics, 4633 World Parkway Cir., St. Louis, MO 63134 USA, jbedell@incyte.com
RDP: detection of recombination amongst aligned sequences
Authors: Martin Darren , Rybicki Ed 
Published: July 2002

Abstract
Summary: Recombination Detection Program (RDP) is a program that applies a pairwise scanning approach to the detection of recombination amongst a group of aligned DNA sequences. The software runs under Windows95 and combines highly automated screening of large numbers of sequences with a highly interactive interface for examining the results of the analyses.
Availability: For academic purposes RDP is available free of charge from: http://www.uct.ac.za/depts/microbiology/microdescription.htm
Contact: darren@molbiol.uct.ac.za
The massively parallel genetic algorithm for RNA folding: MIMD

implementation and population variation
Authors: Shapiro Bruce A. , Wu Jin Chu , Bengali David , Potts Mark J. 
Published: July 2002

Abstract
A massively parallel Genetic Algorithm (GA) has been applied to RNA sequence folding on three different computer architectures. The GA, an evolution-like algorithm that is applied to a large population of RNA structures based on a pool of helical stems derived from an RNA sequence, evolves this population in parallel. The algorithm was originally designed and developed for a 16384 processor SIMD (Single Instruction Multiple Data) MasPar MP-2. More recently it has been adapted to a 64 processor MIMD (Multiple Instruction Multiple Data) SGI ORIGIN 2000, and a 512 processor MIMD CRAY T3E. The MIMD version of the algorithm raises issues concerning RNA structure data-layout and processor communication. In addition, the effects of population variation on the predicted results are discussed. Also presented are the scaling properties of the algorithm from the perspective of the number of physical processors utilized and the number of virtual processors (RNA structures) operated upon.
Contact: bshapiro@ncifcrf.gov; jcwu@ncifcrf.gov; bengalid@ncifcrf.gov; mark.potts@ieee.org
* To whom correspondence should be addressed.
4 Current address: HPC Applications Inc., 10080 Old Frederick Road, Ellicott City, MD 21042, USA.
Cell cycle‐dependent expression of cyclooxygenase‐2 in human fibroblasts
Authors: Gilroy Derek W. , Saunders Michael A. , Sansores‐Garcia Leticia , Matijevic‐Aleksic Nena , Wu Kenneth K. 
Published: July 2002

ABSTRACTThe purpose of this investigation is to determine whether the levels of cyclooxygenase‐2 (COX‐2) expression are cell cycle dependent. We used a serum‐starved human foreskin fibroblast model to determine changes in COX‐2 mRNA, protein, and promoter activity in response to stimulation with interleukin‐1β (IL‐1β) and phorbol 12‐myristate 13‐acetate (PMA) at G0, G1, S and G2/M phases of the cell cycle. IL‐1β (1 ng/ml) and PMA (100 nM) induced robust COX‐2 expression in the G0 cells, and the level of COX‐2 expression declined progressively after the cells had entered the cell cycle. The COX‐2 mRNA level at G1, S and G2/M phases of the cell cycle was 76%, 46%, and 30% of that at G0, respectively. A 5’‐flanking promoter fragment of COX‐2 constructed into a luciferase expression vector was transfected into cells. The promoter activity in response to PMA stimulation was significantly higher in G0 than in S phase cells. These results imply that G0 cells are the key players in inflammation and other COX‐2‐dependent pathophysiological processes. When the cells are in the proliferative phase, COX‐2 inducibility becomes restrained probably by an endogenous control mechanism to avoid COX‐2 mediated oxidative DNA damage.