bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunological and genetic characterization of Borrelia burgdorferi BapA and EppA proteins
Authors: Miller Jennifer C. , Stevenson Brian
Published: May 2003

A large majority of examined Lyme disease spirochaete isolates were demonstrated to contain one or both of the paralogous genesbapAandeppA. Immunological analyses of serum samples collected from infected patients coupled with comparative sequence analyses indicated thatbapAgene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but vary widely in sequence between different bacteria. Considerable evidence of insertion, deletion and other mutations withineppAgenes was observed. A number of significant recombination events were also found to have occurred in regions flankingbapAgenes, while the genes themselves rarely exhibited evidence of mutation, suggesting strong selective pressure to maintain BapA sequences within narrow limits. Data from these and other studies suggest important roles for BapA and EppA during theBorrelia burgdorferiinfectious cycle.
Fur is not the global regulator of iron uptake genes in Rhizobium leguminosarum
Authors: Wexler M. , Todd J. D. , Kolade O. , Bellini D. , Hemmings A. M. , Sawers G. , Johnston A. W. B.
Published: May 2003

Rhizobium leguminosarum fur mutants were unaffected in Fe-dependent regulation of several operons that specify different Fe uptake systems, yet cloned R. leguminosarum fur partially corrected an Escherichia coli fur mutant and R. leguminosarum Fur protein bound to canonical fur boxes. The lack of a phenotype in fur mutants is not due to functional redundancy with Irr, another member of the Fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in Fe-responsive regulation of several operons involved in Fe uptake. Neither Irr nor Fur is needed for symbiotic N2 fixation on peas. As in Bradyrhizobium japonicum, irr mutants accumulated protoporphyrin IX. R. leguminosarum irr is not regulated by Fur and its Irr protein lacks the motif needed for haem-dependent post-translational modification that occurs in B. japonicum Irr. The similarities and differences in the Fur superfamily in the rhizobia and other Gram-negative bacteria are discussed.
Heterologous expression of laccase cDNA from Ceriporiopsis subvermispora yields copper-activated apoprotein and complex isoform patterns
Authors: Larrondo Luis F. , Avila Marcela , Salas Loreto , Cullen Dan , Vicuña Rafael
Published: May 2003

Analysis of genomic clones encoding a putative laccase in homokaryon strains ofCeriporiopsis subvermisporaled to the identification of an allelic variant of the previously describedlcs-1gene. A cDNA clone corresponding to this gene was expressed inAspergillus nidulansand inAspergillus niger. Enzyme assays and Western blots showed that both hosts secreted active laccase. Relative to the isozymic forms of the nativeC. subvermisporaenzyme, theA. niger-produced laccase had a higher molecular mass and gave a single band on IEF gels. In contrast,A. nidulanstransformants secreted several isoforms remarkably similar to those of the native system. Considered together with previously reported Southern blots and protein sequencing, expression inA. nidulanssupports the view thatC. subvermisporahas a single laccase gene and that multiple isoforms result from post-translational processes. In addition, several lines of evidence strongly suggest that under copper limitation,A. nidulanssecretes apoprotein which can be reconstituted by a short incubation with Cu(I) and to a lesser extent with Cu(II).
Diurnal expression of hetR and diazocyte development in the filamentous non-heterocystous cyanobacterium Trichodesmium erythraeum
Authors: El-Shehawy R. , Lugomela C. , Ernst A. , Bergman B.
Published: May 2003

The marine non-heterocystous cyanobacteriumTrichodesmiumfixes atmospheric N2aerobically in light.In situimmunolocalization/light microscopy of NifH revealed that lighter, non-granulated cell regions observed correspond to the nitrogenase-containing diazocyte clusters inTrichodesmiumIMS101. The number of diazocyte clusters per trichome varied from 0 to 4 depending on trichome length. The constant percentage of diazocytes (approx. 15 %) in cultured strains and five natural populations suggests a developmentally regulated differentiation process. Real-time RT-PCR showed thatntcA, encoding the global nitrogen regulator in cyanobacteria, andhetR, the key regulatory gene in heterocyst differentiation, are both constitutively expressed during a 12 h/12 h light/dark cycle.hetRin addition showed a distinct peak in the dark (close to midnight) whilenifHexpression commenced 6–8 h later. The expression of all three genes was negatively affected by addition of ammonia. Some early heterocyst differentiation genes were also identified in the genome ofTrichodesmium. The data suggest thathetRandntcAmay be required for development and function of diazocytes inTrichodesmium.
Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes
Authors: Subramanian Sankar , Kumar Sudhir
Published: May 2003

Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%–60% higher mutation rate in exons than in noncoding DNA. We propose a differential CpG content hypothesis to explain this fundamental, and seemingly unintuitive, pattern. We find that the increased exonic rate is the result of the relative overabundance of synonymous sites involved in CpG dinucleotides, as the evolutionary divergence in non-CpG sites is similar in noncoding DNA and synonymous sites of exons. Expectations and predictions of our hypothesis are confirmed in comparisons involving more distantly related species, including human–orangutan, human–baboon, and human–macaque. Our results suggest an underlying mechanism for higher mutation rate in GC-rich genomic regions, predict nonlinear accumulation of mutations in pseudogenes over time, and provide a possible explanation for the observed higher diversity of single nucleotide polymorphisms (SNPs) in the synonymous sites of exons compared to the noncoding regions.
Haplotype Structure, LD Blocks, and Uneven Recombination Within the LRP5 Gene
Authors: Twells Rebecca C.J. , Mein Charles A. , Phillips Michael S. , Hess J. Fred , Veijola Riitta , Gilbey Matthew , Bright Matthew , Metzker Michael , Lie Benedicte A. , Kingsnorth Amanda , Gregory Edward , Nakagawa Yusuke , Snook Hywel , Wang William Y.S. , Masters Jennifer , Johnson Gillian , Eaves Iain , Howson Joanna M.M. , Clayton David , Cordell Heather J. , Nutland Sarah , Rance Helen , Carr Philippa , Todd John A.
Published: May 2003

Patterns of linkage disequilibrium (LD) in the human genome are beginning to be characterized, with a paucity of haplotype diversity in “LD blocks,” interspersed by apparent “hot spots” of recombination. Previously, we cloned and physically characterized thelow-density lipoprotein-receptor-related protein 5(LRP5) gene. Here, we have extensively analysed bothLRP5 and its flanking three genes, spanning 269 kb, for single nucleotide polymorphisms (SNPs), and we present a comprehensive SNP map comprising 95 polymorphisms. Analysis revealed high levels of recombination across LRP5, including a hot-spot region from intron 1 to intron 7 of LRP5, where there are 109 recombinants/Mb (4882 meioses), in contrast to flanking regions of 14.6 recombinants/Mb. This region of high recombination could be delineated into three to four hot spots, one within a 601-bp interval. ForLRP5, three haplotype blocks were identified, flanked by the hot spots. Each LD block comprised over 80% common haplotypes, concurring with a previous study of 14 genes that showed that common haplotypes account for at least 80% of all haplotypes. The identification of hot spots in between these LD blocks provides additional evidence that LD blocks are separated by areas of higher recombination.

[Supplementary material: primers are available from our Web site:http://www-gene.cimr.cam.ac.uk/todd/human_data.shtml.]
Parallel Evolution by Gene Duplication in the Genomes of Two Unicellular Fungi
Authors: Hughes Austin L. , Friedman Robert
Published: May 2003

Phylogenetic analysis of conserved gene families in fission yeastSchizosaccharomyces pombeand brewer's yeastSaccharomyces cerevisiaeshowed that gene duplications have occurred independently in the same families in each of these two lineages to a far greater extent than expected by chance. These species represent distinct lineages of the phylum Ascomycota that independently evolved a “yeast” life cycle with a unicellular thallus that reproduces by budding, and many of the genes that have duplicated independently in the two lineages are known to be involved in crucial aspects of this life cycle. Parallel gene duplication thus appears to have played a role in the independent origin of similar adaptations in the two species. The results indicate that using phylogenetic analysis to test for parallel gene duplication in different species may help in identifying genes responsible for similar but independently evolved adaptations.
Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature
Authors: Pozzoli Uberto , Elgar Greg , Cagliani Rachele , Riva Laura , Comi Giacomo P. , Bresolin Nereo , Bardoni Alessandra , Sironi Manuela
Published: May 2003

The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes(pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

[Supplemental material is available online at www.genome.org.]
LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics
Authors: Hampson Steve , McLysaght Aoife , Gaut Brandon , Baldi Pierre
Published: May 2003

The identification of homologous regions between chromosomes forms the basis for studies of genome organization, comparative genomics, and evolutionary genomics. Identification of these regions can be based on either synteny or colinearity, but there are few methods to test statistically for significant evidence of homology. In the present study, we improve a preexisting method that used colinearity as the basis for statistical tests. Improvements include computational efficiency and a relaxation of the colinearity assumption. Two algorithms perform the method: FullPermutation, which searches exhaustively for runs of markers, and FastRuns, which trades faster run times for exhaustive searches. The algorithms described here are available in the LineUp package (http://www.igb.uci.edu/∼baldig/lineup). We explore the performance of both algorithms on simulated data and also on genetic map data from maize (Zea mays ssp. mays). The method has reasonable power to detect a homologous region; for example, in >90% of simulations, both algorithms detect a homologous region of 10 markers buried in a random background, even when the homologous regions have diverged by numerous inversion events. The methods were applied to four maize molecular maps. All maps indicate that the maize genome contains extensive regions of genomic duplication and multiplication. Nonetheless, maps differ substantially in the location of homologous regions, probably reflecting the incomplete nature of genetic map data. The variation among maps has important implications for evolutionary inference from genetic map data.
Tn7-Based Genome-Wide Random Insertional Mutagenesis of Candida glabrata
Authors: Castaño Irene , Kaur Rupinder , Pan Shihjung , Cregg Robert , Peñas Alejandro De Las , Guo Nini , Biery Matthew C. , Craig Nancy L. , Cormack Brendan P.
Published: May 2003

We describe and characterize a method for insertional mutagenesis of the yeast pathogen Candida glabrata using the bacterial transposon Tn7. Tn7 was used to mutagenize a C. glabrata genomic fosmid library. Pools of random Tn7insertions in individual fosmids were recovered by transformation intoEscherichia coli. Subsequently, these were introduced by recombination into the C. glabrata genome. We found thatC. glabrata genomic fragments carrying a Tn7insertion could integrate into the genome by nonhomologous recombination, by single crossover (generating a duplication of the insertionally mutagenized locus), and by double crossover, yielding an allele replacement. We were able to generate a highly representative set of ∼104 allele replacements in C. glabrata, and an initial characterization of these shows that a wide diversity of genes were targeted in the mutagenesis. Because the identity of disrupted genes for any mutant of interest can be rapidly identified, this method should be of general utility in functional genomic characterization of this important yeast pathogen. In addition, the method might be broadly applicable to mutational analysis of other organisms.
Discovering Novel cis-Regulatory Motifs Using Functional Networks
Authors: Ettwiller Laurence M. , Rung Johan , Birney Ewan
Published: May 2003

We combined functional information such as protein–protein interactions or metabolic networks with genome information inSaccaromyces cerevisiae to predict cis-regulatory motifs in the upstream region of genes. We developed a new scoring metric combining these two information sources and used this metric in motif discovery. To estimate the statistical significance of this metric, we used brute-force randomization, which shows a consistent well-behaved trend. In contrast, real data showed complex nonrandom behavior. With conservative parameters we were able to find 42 degenerate motifs (that touch 40% of yeast genes) based on 647 original patterns, five of which are well known. Some of these motifs also show limited spatial position in the promoter, indicative of a true motif. We also tested the metric on other known motifs and show that this metric is a good discriminator of real motifs. As well as a pragmatic motif discovery method, with many applications beyond this work, these results also show that interacting proteins are often coordinated at the level of transcription, even in the absence of obvious coregulation in gene expression data sets.

[Supplemental material is available online athttp://www.ebi.ac.uk/∼ettwille/genome_research_paper_2003/result_overlap.html. Program available upon request.]
Retroposed Copies of the HMG Genes: A Window to Genome Dynamics
Authors: Strichman-Almashanu Liora Z. , Bustin Michael , Landsman David
Published: May 2003

Retroposed copies (RPCs) of genes are functional (intronless paralogs) or nonfunctional (processed pseudogenes) copies derived from mRNA through a process of retrotransposition. Previous studies found that gene families involved in mRNA translation or nuclear function were more likely to have large numbers of RPCs. Here we characterize RPCs of the few families coding for the abundant high-mobility-group (HMG) proteins in humans. Using an algorithm we developed, we identified and studied 219 HMG RPCs. For slightly more than 10% of these RPCs, we found evidence indicating expression. Furthermore, eight of these are potentially new members of the HMG families of proteins. For three RPCs, the evidence indicated expression as part of other transcripts; in all of these, we found the presence of alternative splicing or multiple polyadenylation signals. RPC distribution among the HMGs was not even, with 33–65 each for HMGB1, HMGB3, HMGN1, and HMGN2, and 0–6 each for HMGA1, HMGA2, HMGB2, and HMGN3. Analysis of the sequences flanking the RPCs revealed that the junction between the target site duplications and the 5′-flanking sequences exhibited the same TT/AAAA consensus found for the L1 endonuclease, supporting an L1-mediated retrotransposition mechanism. Finally, because our algorithm included aligning RPC flanking sequences with the corresponding HMG genomic sequence, we were able to identify transcribed regions of HMG genes that were not part of the published mRNA sequences.
Exo-Proofreading, A Versatile SNP Scoring Technology
Authors: Cahill Patrick , Bakis Michele , Hurley James , Kamath Veena , Nielsen William , Weymouth Dina , Dupuis Josée , Doucette-Stamm Lynn , Smith Douglas R.
Published: May 2003

We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3′-to-5′ exonuclease proofreading activity of many DNA polymerases. The assay uses one or more primers labeled on the 3′ nucleotide base, and can be implemented in a variety of formats including a one-step PCR reaction that allows SNP typing directly from genomic DNA samples. The detection of genotypes can be accomplished by means of fluorescence detection on assays that have been purified to remove excess primer, or by means of fluorescence polarization without any additional cleanup. We also demonstrate that the Exo-Proofreading SNP assay can be used on pooled samples to obtain allele frequency data.
Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA
Authors: Hellmann Ines , Zöllner Sebastian , Enard Wolfgang , Ebersberger Ingo , Nickel Birgit , Pääbo Svante
Published: May 2003

To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with intergenic chimpanzee DNA sequences and data on human single-nucleotide polymorphisms in the genes studied, this allows us to gauge the extent to which selection affects human genes at a genome-wide scale. The comparison to intergenic DNA sequences indicates that about 39% of silent sites in protein-coding regions are deleterious and subject to negative selection. Further, when the divergence between human and chimpanzee is compared with the extent of nucleotide polymorphisms among humans in the same sequences, there is significantly higher divergence in the 5′ untranslated regions (UTRs) but not in other parts of the transcript. This indicates that positive selection may have had a considerable influence on 5′UTRs. The dinucleotide CG (CpG) also exhibits a different substitution pattern within 5′UTRs as compared with other parts of the genome.
Vortex shedding over a rectangular cylinder with ground effect: flow and heat transfer characteristics
Authors: Shuja S.Z. , Yilbas B.S. , Budair M.O.
Published: May 2003

The vortex shedding from a rectangular cylinder improves the heat transfer rates. Introducing a ground effect in such a flow system alters the shedding frequency, which in turn enables to vary the cooling rates of the cylinder. In the present study a laminar flow passing over a rectangular cylinder with a ground effect is considered. The flow and energy equations are solved numerically using a control volume approach. Strouhal and Stanton number variations due to gap height are computed and the influence of Strouhal number on Stanton number variation behind the cylinder is examined. The study is extended to include the predictions of entropy generation in the solution domain. It is found that shedding frequency increases as gap height reduces and further reduction in gap height results in diminishing of vortex shedding, in which case confined flow is developed in the gap. Heat transfer rates improve when Strouhal number is maximum. In the case of confined flow situation, heat transfer rates enhance substantially in the region close to the top corner of the cylinder, in which case, non‐uniform cooling of the surface is resulted.
Comparison of linear and quadratic shape functions for a hybrid control‐volume finite element method
Authors: Stry Y. , Hainke M. , Jung Th.
Published: May 2003

A control‐volume based method for the numerical calculation of axisymmetric incompressible fluid flow and heat transfer is presented. The proposed method extends the staggered grid approach to unstructured triangular meshes. The velocities are stored at the vertices and the edges of a triangle, pressure and temperature are stored at the vertices. Accordingly, velocities are interpolated in a quadratic way, pressure and temperature linearly. The accuracy of the proposed method is examined for a number of different testproblems. Compared to a linear interpolation scheme implemented in the same code, more accurate solutions and smaller computation times are obtained for the proposed quadratic scheme. The method was designed for and is about to be applied to the numerical simulation of crystal growth.
Inverse estimation of steady‐state surface temperature on a three‐dimensional body
Authors: Kyoung Kim Sun , Il Lee Woo
Published: May 2003

This work aims to estimate the unknown surface temperature distribution on the boundary of a heat conducting solid body from temperature measurements taken from another boundary where convective boundary condition is also known. A steady inverse heat conduction problem is described for an arbitrary three‐dimensional body. A gradient‐based inverse method combined with B‐spline function specification is employed to solve the inverse problem. The validity of the proposed method is verified with computational results.
Effect of Subgrid Modeling on the In-Cylinder Unsteady Mixing Process in a Direct Injection Engine
Authors: Sone K. , Menon S.
Published: May 2003

Fuel-air mixing in a direct injection spark ignition (DISI) engine occurs in a highly unsteady, turbulent and three-dimensional flow. As a result, any cycle-to-cycle unsteady variation in the mixing process can directly impact the performance of the DISI engine. To study the unsteady process in these engines, we have developed and implemented a large-eddy simulation (LES) approach with an innovative subgrid scalar mixing model based on the linear-eddy mixing (LEM) model into a commercial IC engine code (KIVA-3V). Time-averaged results of the simulations using the new LES version (KIVALES) are compared to the steady-state predictions of the original KIVA-3V. Significantly different in-cylinder turbulent fuel-air mixing is predicted by these two methods. Analysis shows that KIVALES resolves spatial features larger than the grid and that the subgrid kinetic energy adjusts to the LES resolution. As a result, KIVALES captures a highly unsteady, anisotropic fuel-air mixing process whereas a more diffused mixed field is predicted by the original KIVA-3V. This ability of KIVALES is attributed to the subgrid closure which scales the subgrid dissipation with the local grid size and thus, decreases the overall dissipation in the flow.
Manifold Gas Dynamics Modeling and Its Coupling With Single-Cylinder Engine Models Using Simulink
Authors: Zhang G. Q. , Assanis D. N.
Published: May 2003

A flexible model for computing one-dimensional, unsteady manifold gas dynamics in single-cylinder spark-ignition and diesel engines has been developed. The numerical method applies an explicit, finite volume formulation and a shock-capturing total variation diminishing scheme. The numerical model has been validated against the method of characteristics for valve flows without combustion prior to coupling with combustion engine simulations. The coupling of the gas-dynamics model with single-cylinder, spark-ignition and diesel engine modules is accomplished using the graphical MATLAB-SIMULINK environment. Comparisons between predictions of the coupled model and measurements shows good agreement for both spark ignition and diesel engines. Parametric studies demonstrating the effect of varying the intake runner length on the volumetric efficiency of a diesel engine illustrate the model use.
The Formation of a Combustible Mixture During the First Cycle of Cranking and Startup in a Port-Fuel-Injected Spark-Ignition Engine
Authors: Cowart J. S.
Published: May 2003

As automotive engine emission standards continue to become more stringent, excellent cranking, and startup fuel control will become imperative in order to achieve minimum engine-out emissions. Optimized engine starting requires the generation of a strong first firing cycle. Fortunately, an engine’s first cycle event is physically less complex than future engine cycles, providing the opportunity for accurate modeling. A physically based crank mixture preparation model coupled with a multicomponent fuel model was developed to provide insights into the fuel vapor generation process during the first cycle of engine starting. Excellent agreement with experimental data is obtained over a range of operating conditions. Model results show that for increased engine temperatures, fuel distillation becomes of comparable importance to the convective mass transfer fuel vapor formation mechanism. Additionally, the modeling work suggests that fuel pooling near the intake valve is occurring at rich fueling levels. The important effect of engine speed during intake is correctly predicted by the model.
Improvement of the Dynamic Characteristic of an Automotive Engine by a Turbocharger Assisted by an Electric Motor
Authors: Katrasˇnik T. , Rodman S. , Trenc F. , Hribernik A. , Medica V.
Published: May 2003

Turbocharging and subsequent charge cooling of the working medium usually causes increase of the mean effective pressure in an automotive diesel engine. Poor performance during the engine load increase is attributed to the nature of energy exchange between the engine and the turbocharger. Filling of the intake and exhaust manifolds, as well as consequent increase of the pressure and acceleration of the rotating components of the turbocharger require a certain period of time. Dynamic performance of the turbocharger can be substantially improved by means of an electric motor attached directly to the turbo shaft. A new concept of asynchronous electric motor with a very thin rotor was applied to support the turbocharger during the transient operation of the engine. The experimental work of matching an electrically assisted turbocharger to an engine is rather expensive; it was therefore decided to determine general characteristic of the electric motor separately through experiments, whereas transient response of the turbocharged and intercooled diesel engine was simulated by a zero-dimensional filling and emptying computer simulation method. A lot of experimentally obtained data and empirical formulae for the compressor, gas turbine, flow coefficients of the engine valves, intercooler, high-pressure fuel pump with the pneumatic control device (LDA), combustion parameters, etc., were applied to overcome deficiency introduced by the zero-dimensional simulation model. As the result a reliable and accurate program compatible with the experimental results in steady and transient engine operation was developed and is presented in the work. Faster transient response, i.e., better load acceptance of the engine was obtained by applying an adequate electric motor to assist the turbocharger; three versions of electric motors with different torque to mass moment of inertia ratios and different operating regimes were introduced in the simulation program to investigate their influence on the transient behavior of the engine.
Dynamic Response of Automotive Catalytic Converters to Variations in Air-Fuel Ratio
Authors: Shamim T. , Medisetty V. C.
Published: May 2003

The automotive catalytic converters, which are employed to reduce engine exhaust emissions, operate in transient conditions under all modes of operation. The fluctuation in air-fuel ratio is a major contributor to these transients. The consideration of these transients is essential in accurate modeling of catalyst operation during actual driving conditions. In this work, a numerical investigation is carried out to comprehend the dynamic response of three-way catalytic converters subjected to changes in air-fuel ratio. The mathematical model considers the coupling effect of heat and mass transfer with the catalyst reactions as exhaust gases flow through the catalyst. The converter dynamic response is studied by considering a converter operating under steady conditions, which is suddenly subjected to air-fuel ratio variations. Two types of imposed fluctuations (sinusoidal and step changes) are considered. The catalyst response is predicted by using a detailed chemical mechanism. The paper elucidates the effect of air-fuel modulations on the catalyst HC, CO, and NO conversion efficiencies.
Fast x-ray spectroscopy study of ethene on clean and SO4 precovered Pt{111}
Authors: Lee Adam F. , Wilson Karen
Published: May 2003

The adsorption and decomposition of ethylene over a Pt{111} single crystal surface has been investigated by fast x-ray spectroscopy. At 100 K ethene displays precursor-mediated adsorption kinetics, adopting a single environment with a saturation C2H4 coverage of 0.25 ML and binding energy of 283.2 eV. Thermal decomposition proceeds above 240 K via dehydrogenation to ethylidyne with an activation barrier of 57±3 kJ mol−1 and preexponential factor ν=1×1010±0.5 s−1. Site-blocking by preadsorbed SO4 reduces the saturation ethene coverage but induces a new, less reactive π-bonded ethene species centered around 283.9 eV, which in turn decomposes to ethylidyne at 350 K.
Effect of thermal annealing on the electronic properties of nitrogen doped amorphous carbon/p-type crystalline silicon heterojunction diodes
Authors: Valentini L. , Lozzi L. , Salerni V. , Armentano I. , Kenny J. M. , Santucci S.
Published: May 2003

Heterojunction diodes with hydrogenated amorphous carbon (a-C:H) and nitrogen doped amorphous carbon (a-C:H:N) films on p-type silicon were prepared by means of plasma enhanced chemical vapor deposition. The electronic and structural properties of the films are analyzed as a function of nitrogen doping as well as thermal treatment after deposition. X-ray photoelectron spectroscopy valence band spectra reveal that the electronic structure of the prepared a-C:H:N films depends on thermal annealing. The nature of the heterojunction is confirmed by the rectifying current–voltage characteristic of the carbonaceous deposit/p-Si junction with a heterojunction structure showing a behavior dependent on the amount of both nitrogen concentration and thermal annealing. In particular, the photovoltaic effect is observed only from annealed a-C:H:N heterojunction structures. Raman spectroscopy performed on heterojunction diodes after thermal treatment indicates that this behavior is most likely due to an extended graphitization.
Metal deposition with femtosecond light pulses at atmospheric pressure
Authors: Haight R. , Longo P. , Wagner A.
Published: May 2003

Femtosecond pulses of 400 nm light have been used to deposit Cr from adsorbed layers of Cr(CO)6 on both transparent and absorbing substrates, in air. Highly reflective Cr metal lines were deposited on fused silica substrates with linewidths as small as 200 nm and smaller still for Cr deposition on Au substrates. Metal deposition results from a multiphoton dissociation process which decomposes the metal hexacarbonyl in the adsorbed layer. Deposition of subsequent Cr layers reveals a change in the dissociation mechanism.
Deposition of plasma polymerized perfluoromethylene-dominated films showing oil-repellency
Authors: Chase J. E. , Boerio F. J.
Published: May 2003

Plasma polymerized fluorocarbon films were deposited onto polyethylene (PE) substrates to increase oil-repellency of PE. Depositions were performed using the monomer, 1H,1H,2H-perfluoro-1-dodecene in a parallel-plate, radio frequency (rf) reactor, with variable continuous-wave power ranging from 2 to 160 W. The film deposition rate and morphology were strongly dependent on the applied rf power. Most importantly, the chemical structure of the deposited films was also altered, resulting in changes in contact angles of various liquids and the surface energy. Films deposited at low power were composed mainly of perfluoromethylene (CF2) species (up to 67.2%), as shown by x-ray photoelectron spectroscopy (XPS). With an increase in rf power, CF2 content in the film decreased as further fragmentation of the monomer occurred. For each deposition at varying rf powers, even at powers as low as 2 W, the C=C and C–H bonds in the monomer were dissociated by the plasma and not incorporated into the films, as shown by Fourier transform infrared spectroscopy. Oil-repellency, as shown by increased contact angles of hydrocarbon liquids, was found to increase as the amount of CF2 species increased in the film structure. A low critical surface energy (2.7 mJ/m2) was calculated for the film deposited with only 2 W of rf power. Adhesion of the plasma-polymerized films to the PE was also evaluated and found to be poor for films with a high concentration of CF2 species, where cohesive failure within the film occurred. However, adhesion increased as a function of rf power, where the film structure showed more cross-linking. There was a compromise between producing a film with high oleophobicity (oil-repellency) while maintaining adhesion of the film to PE, as some disruption of the CF2 chains in the films was necessary for cohesion through cross-linking.
Structural and electrical characteristics of W–N thin films prepared by reactive rf sputtering
Authors: Jiang Pei-Chuen , Chen J. S. , Lin Y. K.
Published: May 2003

The crystal structure, chemical bonding state, composition, and electrical resistivity of W–N films deposited by reactive rf sputtering are investigated by x-ray diffraction, x-ray photoelectron spectroscopy, Auger electron spectroscopy, Rutherford backscattering spectrometry, and four-point probe. Using 150 W of sputtering power and 25% of N2 partial flow rate, the deposition rate and resistivity of W–N films decrease with increasing negative substrate bias. When the substrate bias is set at −100 V, resistivity of W–N films increases while the deposition rate decreases with increasing N2 partial flow rate. W+W2N mix phase, W2N phase, and W2N+WN mix phase are obtained at 10%, 15%–25%, and 40% of N2 partial flow rate, respectively. When the N2 partial flow rate is greater than 40%, the films become amorphous like. Nitrogen concentration in the W–N films increases continuously with increasing N2 partial flow rate, and the W 4f core-level electrons change gradually from metallic W bondings to WN bondings. By reducing the sputtering power to 50 W, we have found that film resistivity also rises with increasing N2 partial flow rate but crystalline W2N phase can be obtained with 10%–50% of N2 partial flow rate. The connection between the process conditions, structural change and electrical resistivity of the sputtered W–N thin films is discussed.
Reaction sequence of Co/Ni/Si(001) system
Authors: Guo S. S. , Tsai C. J.
Published: May 2003

The influence of a Ni interlayer on the formation of cobalt silicides is investigated. By substrate curvature measurements, x-ray diffraction, and Auger electron spectroscopy, a detailed reaction sequence for the Co(90 nm)/Ni(9 nm)/Si(001) system annealed at a ramp rate of 5 °C/min is revealed. For the relatively thick Ni interlayer, the reaction sequence began with the formation of Ni2Si and was followed by the formation of Co2Si on top of the Ni2Si. As the temperature rose, the layer of Ni2Si transformed into NiSi and the formation of CoSi occurred quickly. After, the occurrence of the (NixCo1−x)Si2 phase began at the interface of NiSi/CoSi. The initial phase formation of cobalt silicides occurred via the diffusion of Si through the layer of nickel silicides. It is only when the (NixCo1−x)Si2 phase formed that both Co and Si became mobile in the layer and a CoSi2–(NixCo1−x)Si2–CoSi2 structure developed. The structure exhibits a preferred (400) orientation for the bottom CoSi2 layer.
Degradation of CrN films at high temperature under controlled atmosphere
Authors: Lu Fu-Hsing , Chen Hong-Ying , Hung Chih-Hung
Published: May 2003

The degradation of CrN films was investigated over temperatures of 400–1200 °C in air, nitrogen, and forming gas (N2/H2=9) by analyzing changes in color and appearance, as well as microstructures. The degradation mainly included color changes and cracks occurring on the film surface. The color change resulting from low-temperature/short-time annealing was due to the formation of an additional Cr2N phase, as well as a thin oxide overlayer. The color change appearing at higher temperatures/longer times stemmed from the formation of a thicker Cr2O3 layer, whose content depended on the pN2/pO2 ratio in the atmosphere. The driving force of the oxidation was the Gibbs free-energy change for CrN and Cr2O3. Cracks that showed up at relatively high temperatures were attributed to the large thermal mismatch between the CrN film and Cr2O3 overlayer. The thermal stresses were calculated and discussed. The degradation diagrams were generated based on the above analyzed results.
Experimental study of outgassing from textile materials
Authors: Barni R. , Riccardi C. , Fontanesi M.
Published: May 2003

We have performed a careful analysis of the pumpdown curves measured in our vacuum reactors for radio frequency plasma treatment of materials at low pressure. The characterization of the device pumping behavior both in the viscous and in the molecular regimes makes it possible to study the outgassing flow rates of several textile materials. Estimates of the relevant flow rates in different pressure ranges and measurements of the flow composition have been obtained. Such data can be interpreted in the framework of simplified desorption models and could be used in order to design the pumping system needed for vacuum treatment of such materials, both in batch and in continuously fed-in processes. In particular direct application of existing cold plasma treatments, such as chemical vapor deposition, plasma etching, activation, and grafting, at an industrial scale can be foreseen in view of our data, which can be straightforwardly used to estimate the costs of the required vacuum technology.
Surface and bulk chemistry of calcined UO2 powders
Authors: Nelson A. J. , Meier T. C. , Saw C. K. , Griffith L. V.
Published: May 2003

High-resolution x-ray photoemission spectroscopy (XPS) was used to examine the surface composition and chemical bonding of calcined UO2 powders as a function of process parameters. It is believed that the surface composition of the powder grains ultimately affects packing density. XPS quantitative analysis revealed O/U ratios indicative of mixed uranium valences. In addition, high-resolution U 4f7/2,5/2 core-level spectra revealed reoxidation of U4+ to U6+ for the lower temperatures, and a reduction of U6+ to U4+ for the higher temperatures using 4% H2/Ar. Reoxidation can also be affected by the presence of water or OH, and the powder samples calcined at the lower temperatures have the highest OH−/O2− peak area ratio. The valence-band electronic structure for the higher-temperature calcinations clearly shows a stronger 5f emission peak near the Fermi edge, a feature that is indicative of a highly localized state. Bulk structural analysis using x-ray diffraction also indicates a number of uranium oxide phases produced by calcination. However, at 600 °C the UO2 cubic phase resulted.
Evolution of chemical bonding configuration in ultrathin SiOxNy layers grown by low-temperature plasma nitridation
Authors: Lai Yi-Sheng , Chen J. S.
Published: May 2003

Ultrathin silicon oxynitride (SiOxNy) less than 25 Å has been grown by low-temperature (at 450 °C) N2O and NH3 plasma immersion on a Si surface. The bonding structures and their distribution in depth, as well as the quantity of nitrogen in SiOxNy layers are studied by x-ray photoelectron spectroscopy. A good coincidence is established in SiOxNy thickness extracted from the attenuated Si 2p3/2 photoelectron signal and high-resolution transmission electron micrograph. The increase of SiOxNy thickness is fast at the initial growth and slows down as the oxynitride thickens. It is found that nitrogen atoms are concentrated at the SiOxNy/Si interface. The binding energy (BE) of N 1s core levels shows that N atoms are mostly bonded to three Si atoms (the N–Si3 state). Long-time growth of oxynitride will shift N and O 1s core levels to a higher BE due to increments of oxygen in the SiOxNy layer. Exploration of (N2O+NH3) plasma nitridation suggests that the nitrogen content increases with increasing NH3/N2O ratio, whereas the deposition rate of oxynitride decreases. With the understanding of plasma nitridation basics, control of chemical binding structure, nitrogen content, as well as thickness of the SiOxNy layer, is therefore realized.
Molecular desorption of a nonevaporable getter St 707 irradiated at room temperature with synchrotron radiation of 194 eV critical photon energy
Authors: Le Pimpec F. , Gröbner O. , Laurent J. M.
Published: May 2003

Photon stimulated molecular desorption from a nonevaporable getter (NEG) St 707® (SAES Getters™) surface after conditioning and after saturation with isotopic carbon monoxide [cf. nomenclature in Handbook of Chemistry and Physics, 74th edition, edited by D. R. Lide (CRC Press, Boca Raton, 1994)] C13O18, has been studied on a dedicated beamline at the EPA ring at CERN. The synchrotron radiation of 194 eV critical energy and with an average photon intensity of ∼1×1017 photons s−1 was impinging on the sample at perpendicular incidence. It is found that the desorption yields η (molecules/photon) of the characteristic gases in an UHV system (hydrogen, methane, carbon monoxide, and carbon dioxide) for a freshly activated NEG and for a NEG fully saturated with C13O18 are lower than that of 300 °C baked stainless steel.
Effects of W doping and annealing parameters on the ferroelectricity and fatigue properties of sputtered Bi3.25La0.75Ti3O12 films
Authors: Lin Wen-Tai , Chiu Ta-Wei , Yu Hsiao-Hsuan , Lin Jian-Long , Lin Meng-Shian
Published: May 2003

The ferroelectricity and fatigue properties of Bi3.25La0.75Ti3O12 (BLT) and W-doped BLT (BLTWx) films, x=0.01, 0.03, 0.05, and 0.1, annealed in air as a function of annealing temperature and time were studied. Most of the polarization–electric-field (P–E) loops of BLT and BLTWx films measured immediately after annealing showed leaky behavior. Upon aging at room temperature for 1–4 h, the P–E loops became saturated. The excess oxygen vacancies remained in the films after annealing and subsequent quenching may be responsible for the leaky behavior. Annealing in O2 at 700 °C and below enhanced the formation of pyrochlore Bi2Ti2O7 and thus degraded the ferroelectricity of the films. The remnant polarization (2Pr) of the samples annealed at a temperature of 675–700 °C for 10–60 min increased with the annealing time, while that of the samples annealed at 750 °C were reduced due to the loss of Bi. The 2Pr of BLTWx films increased with the W concentration up to x=0.03 and then decreased, revealing that W doping induces two contrary effects on Pr, i.e., reducing the amount of oxygen vacancies and causing less structure distortion. In addition, W doping significantly improved the fatigue properties of BLTWx films. The leakage current of BLTWx films was in the order of 10−7 A/cm2 at the field of 200 kV/cm, being at least an order of magnitude lower than that of BLT films.
Hydrogen contamination in Ge-doped SiO2 thin films prepared by helicon activated reactive evaporation
Authors: Li W. T. , Bulla D. A. P. , Love J. , Luther-Davies B. , Charles C. , Boswell R.
Published: May 2003

Germanium-doped silicon oxide thin films were deposited at low temperature by using an improved helicon plasma assisted reactive evaporation technique. The origins of hydrogen contamination in the film were investigated, and were found to be H incorporation during deposition and postdeposition water absorption. The H incorporation during deposition was avoided by using an effective method to eliminate the residual hydrogen present in the deposition system. The microstructure, chemical bonds, chemical etch rate, and optical index of the films were studied as a function of the deposition conditions. Granular microstructures were observed in low-density films, and were found to be the cause of postdeposition water absorption. The granular microstructure was eliminated and the film was densified by increasing the helicon plasma power and substrate bias during deposition. A high-density film was shown to have no postdeposition water absorption and no OH detected by using a Fourier-transform infrared spectrometer.
Closing of the Nucleotide Pocket of Kinesin-Family Motors upon Binding to Microtubules
Authors: Naber Nariman , Minehardt Todd J. , Rice Sarah , Chen Xiaoru , Grammer Jean , Matuska Marija , Vale Ronald D. , Kollman Peter A. , Car Roberto , Yount Ralph G. , Cooke Roger , Pate Edward
Published: May 2003

We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor·diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide–binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy–yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.
A Molecular Einstein Ring: Imaging a Starburst Disk Surrounding a Quasi-Stellar Object
Authors: Carilli C. L. , Lewis G. F. , Djorgovski S. G. , Mahabal A. , Cox P. , Bertoldi F. , Omont A.
Published: May 2003

Images of the molecular CO 2-1 line emission and the radio continuum emission from the redshift 4.12 gravitationally lensed quasi-stellar object (QSO) PSS J2322+1944 reveal an Einstein ring with a diameter of 1.5″. These observations are modeled as a star-forming disk surrounding the QSO nucleus with a radius of 2 kiloparsecs. The implied massive star formation rate is 900 solar masses per year. At this rate, a substantial fraction of the stars in a large elliptical galaxy could form on a dynamical time scale of 10
8
years. The observation of active star formation in the host galaxy of a high-redshift QSO supports the hypothesis of coeval formation of supermassive black holes and stars in spheroidal galaxies.
Cooperation Between RNA Polymerase Molecules in Transcription Elongation
Authors: Epshtein Vitaly , Nudler Evgeny
Published: May 2003

Transcription elongation is responsible for rapid synthesis of RNA chains of thousands of nucleotides in vivo. In contrast, a single round of transcription performed in vitro is frequently interrupted by pauses and arrests that drastically reduce the elongation rate and the yield of the full-length transcript. Here we demonstrate that most transcriptional delays disappear if more than one RNA polymerase (RNAP) molecule initiates from the same promoter. Anti-arrest and anti-pause effects of trailing RNAP are due to forward translocation of leading (backtracked) complexes. Such cooperation between RNAP molecules links the rate of elongation to the rate of initiation and explains why elongation is still fast and processive in vivo even without anti-arrest factors.