bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Conserved RNA Secondary Structures on Hepatitis Delta Virus Genotype I RNA Editing, Replication, and Virus Production
Authors: Jayan Geetha C. , Casey John L.
Published: August 2005

RNA editing of the hepatitis delta virus (HDV) antigenome at the amber/W site by the host RNA adenosine deaminase ADAR1 is a critical step in the HDV replication cycle. Editing is required for production of the viral protein hepatitis delta antigen long form (HDAg-L), which is necessary for viral particle production but can inhibit HDV RNA replication. The RNA secondary structural features in ADAR1 substrates are not completely defined, but base pairing in the 20-nucleotide (nt) region 3′ of editing sites is thought to be important. The 25-nt region 3′ of the HDV amber/W site in HDV genotype I RNA consists of a conserved secondary structure that is mostly base paired but also has asymmetric internal loops and single-base bulges. To understand the effect of this 3′ region on the HDV replication cycle, mutations that either increase or decrease base pairing in this region were created and the effects of these changes on amber/W site editing, RNA replication, and virus production were studied. Increased base pairing, particularly in the region 15 to 25 nt 3′ of the editing site, significantly increased editing; disruption of base pairing in this region had little effect. Increased editing resulted in a dramatic inhibition of HDV RNA synthesis, mostly due to excess HDAg-L production. Although virus production at early times was unaffected by this reduced RNA replication, at later times it was significantly reduced. Therefore, it appears that the conserved RNA secondary structure around the HDV genotype I amber/W site has been selected not for the highest editing efficiency but for optimal viral replication and secretion.
Endothelial Cells Promote Human Immunodeficiency Virus Replication in Nondividing Memory T Cells via Nef-, Vpr-, and T-Cell Receptor-Dependent Activation of NFAT
Authors: Choi Jaehyuk , Walker Jason , Talbert-Slagle Kristina , Wright Paulette , Pober Jordan S. , Alexander Louis
Published: August 2005

Human endothelial cells (ECs) enhance human immunodeficiency virus (HIV) replication within CD4+memory T cells by 50,000-fold in a Nef-dependent manner. Here, we report that EC-mediated HIV type 1 replication is also dependent on an intactvprgene. Moreover, we demonstrate that despite a requirement for engaging major histocompatibility complex (MHC) class II molecules and costimulators, EC-stimulated virus-producing cells (p24highT cells) do not proliferate, nor are they arrested in the cell cycle. Rather, they are minimally activated, sometimes expressing CD69 but not CD25, HLA-DR, VLA-1, or effector cytokines. Blocking antibodies to interleukin 2 (IL-2), IL-6, IL-7, or tumor necrosis factor do not inhibit viral replication. Cyclosporine effectively inhibits viral replication, as does disruption of the NFAT binding site in the viral long terminal repeat. Furthermore, in the presence of ECs, suboptimal T-cell receptor (TCR) stimulation with phytohemagglutinin L supports efficient viral replication, and suboptimal stimulation with toxic shock syndrome toxin 1 leads to viral replication selectively in the TCR-stimulated, Vβ2-expressing T cells. Collectively, these data indicate that ECs provide signals that promote Nef- and Vpr-dependent HIV replication in memory T cells that have been minimally activated through their TCRs. Our studies suggest a mechanism for HIV replication in vivo within the reservoir of circulating memory CD4+T cells that persist despite antiretroviral therapy and further suggest that maintenance of immunological memory by MHC class II-expressing ECs via TCR signaling may contribute to HIV rebound following cessation of antiretroviral therapy.
Role of Plasminogen in Propagation of Scrapie
Authors: Salmona Mario , Capobianco Raffaella , Colombo Laura , De Luigi Ada , Rossi Giacomina , Mangieri Michela , Giaccone Giorgio , Quaglio Elena , Chiesa Roberto , Donati Maria Benedetta , Tagliavini Fabrizio , Forloni Gianluigi
Published: August 2005

To investigate whether plasminogen may feature in scrapie infection, we inoculated plasminogen-deficient (Plg−/−), heterozygous plasminogen-deficient (Plg+/−), and wild-type (Plg+/+) mice by the intracerebral or intraperitoneal (i.p.) route with the RML scrapie strain and monitored the onset of neurological signs of disease, survival time, brain, and accumulation of scrapie disease-associated forms of the prion protein (PrPSc). Only after i.p. inoculation, a slight, although significant, difference in survival (P< 0.05) between Plg−/−and Plg+/+mice was observed. Neuropathological examination and Western blot analysis were carried out when the first signs of disease appeared in Plg+/+animals (175 days after i.p. inoculation) and when mice reached the terminal stage of illness. At the onset of symptoms, PrPScaccumulation was higher in the brain and spleen of Plg+/+and Plg+/−mice than in those of Plg−/−mice, and these differences were paralleled by differences in the severity of spongiform changes and astrogliosis in the cerebral cortex and subcortical gray structures. Immunohistochemical analysis of the spleens before inoculation did not show any impairment of the immune system affecting follicular dendritic or lymphoid cells in Plg−/−mice. Once the disease progressed and mice began to die of infection, differences were no longer apparent in either brains or spleens. In conclusion, our data indicate that plasminogen has no major effect on the survival of scrapie agent-infected mice.
Antigenic Stimulation Specifically Reactivates the Replication of Archived Simian Immunodeficiency Virus Genomes in Chronically Infected Macaques
Authors: Renoux Céline , Wain-Hobson Simon , Hurtrel Bruno , Cheynier Rémi
Published: August 2005

Human immunodeficiency virus/simian immunodeficiency virus (SIV) diversification is a direct consequence of viral replication and occurs principally in secondary lymphoid organs where CD4
+
T cells are activated and proliferate. However, the evolution of viral quasispecies may also be driven by various nonexclusive mechanisms, including adaptation to specific immune responses and modification of viral fitness. Analysis of viral quasispecies in SIV-infected macaques subjected to repeated antigenic stimulations allowed us to demonstrate transient expansions of SIV populations that were highly dependent upon activation of antigen-specific T cells. T-cell clones expanded in response to a particular antigen were infected by a specific viral population and persisted for prolonged periods. Upon a second stimulation by encounter with the same antigen, these specific genomes were at the origin of a new burst of replication, leading to rapid but transient replacement of the viral quasispecies in blood. Finally, longitudinal analysis of SIV sequence variation during and between antigenic stimulations revealed that viral evolution is mostly constrained to periods of strong immunological activity.
Functional Constraints of Influenza A Virus Epitopes Limit Escape from Cytotoxic T Lymphocytes
Authors: Berkhoff E. G. M. , de Wit E. , Geelhoed-Mieras M. M. , Boon A. C. M. , Symons J. , Fouchier R. A. M. , Osterhaus A. D. M. E. , Rimmelzwaan G. F.
Published: August 2005

Viruses can exploit a variety of strategies to evade immune surveillance by cytotoxic T lymphocytes (CTL), including the acquisition of mutations in CTL epitopes. Also for influenza A viruses a number of amino acid substitutions in the nucleoprotein (NP) have been associated with escape from CTL. However, other previously identified influenza A virus CTL epitopes are highly conserved, including the immunodominant HLA-A*0201-restricted epitope from the matrix protein, M158-66. We hypothesized that functional constraints were responsible for the conserved nature of influenza A virus CTL epitopes, limiting escape from CTL. To assess the impact of amino acid substitutions in conserved epitopes on viral fitness and recognition by specific CTL, we performed a mutational analysis of CTL epitopes. Both alanine replacements and more conservative substitutions were introduced at various positions of different influenza A virus CTL epitopes. Alanine replacements for each of the nine amino acids of the M158-66epitope were tolerated to various extents, except for the anchor residue at the second position. Substitution of anchor residues in other influenza A virus CTL epitopes also affected viral fitness. Viable mutant viruses were used in CTL recognition experiments. The results are discussed in the light of the possibility of influenza viruses to escape from specific CTL. It was speculated that functional constraints limit variation in certain epitopes, especially at anchor residues, explaining the conserved nature of these epitopes.
CD46-Utilizing Adenoviruses Inhibit C/EBPβ-Dependent Expression of Proinflammatory Cytokines
Authors: Iacobelli-Martinez Milena , Nepomuceno Ronald R. , Connolly Jodi , Nemerow Glen R.
Published: August 2005

The majority of adenovirus serotypes utilize the coxsackievirus-adenovirus receptor (CAR) for virus-host cell attachment, but subgroup B and subgroup D (adenovirus type 37 [Ad37]) viruses recognize CD46. CD46 is a ubiquitously expressed receptor that serves as a cofactor for the inactivation of the complement components C3b and C4b, and it also serves as a receptor for diverse microbial pathogens. A reported consequence of CD46 engagement is a reduced capability of human immune cells to express interleukin-12 (IL-12), a cytokine involved in both the innate and adaptive immune responses. Studies were thus undertaken to determine whether CD46-utilizing Ads alter the expression of proinflammatory cytokines. Subgroup B (Ad16 and -35) and Ad37, but not Ad2 or -5, significantly reduced IL-12 production by human peripheral blood mononuclear cells stimulated with gamma interferon (IFN-γ) and lipopolysaccharide. IL-12 mRNA (p35 and p40 subunits) levels as well as other cytokine mRNA levels (IL-1α and -β, IL-1Ra, and IL-6) were decreased upon interaction with CD46-utilizing Ads. Analysis of transcription factor activity required for cytokine expression indicated that CD46-utilizing Ads preferentially inhibited IFN-γ-induced C/EBPβ protein expression, consequently reducing its ability to form DNA complexes. Interference with IFN-γ signaling events by CD46-utilizing Ads, but not CAR-utilizing Ads, reveals a potentially critical difference in the host immune response against distinct Ad vectors, a situation that has implications for gene delivery and vaccine development.
Variation in Interferon Sensitivity and Induction among Strains of Eastern Equine Encephalitis Virus
Authors: Aguilar Patricia V. , Paessler Slobodan , Carrara Anne-Sophie , Baron Samuel , Poast Joyce , Wang Eryu , Moncayo Abelardo C. , Anishchenko Michael , Watts Douglas , Tesh Robert B. , Weaver Scott C.
Published: August 2005

Eastern equine encephalitis virus (EEEV) causes human encephalitis in North America (NA), but in South America (SA) it has rarely been associated with human disease, suggesting that SA strains are less virulent. To evaluate the hypothesis that this virulence difference is due to a greater ability of NA strains to evade innate immunity, we compared replication of NA and SA strains in Vero cells pretreated with interferon (IFN). Human IFN-α, -β, and -γ generally exhibited less effect on replication of NA than SA strains, supporting this hypothesis. In the murine model, no consistent difference in IFN induction was observed between NA and SA strains. After infection with most EEEV strains, higher viremia levels and shorter survival times were observed in mice deficient in IFN-α/β receptors than in wild-type mice, suggesting that IFN-α
/
β is important in controlling replication. In contrast, IFN-γ receptor-deficient mice infected with NA and SA strains had similar viremia levels and mortality rates to those of wild-type mice, suggesting that IFN-γ does not play a major role in murine protection. Mice pretreated with poly(I-C), a nonspecific IFN inducer, exhibited dose-dependent protection against fatal eastern equine encephalitis, further evidence that IFN is important in controlling disease. Overall, our in vivo results did not support the hypothesis that NA strains are more virulent in humans due to their greater ability to counteract the IFN response. However, further studies using a better model of human disease are needed to confirm the results of differential human IFN sensitivity obtained in our in vitro experiments.
Evidence that the Respiratory Syncytial Virus Polymerase Is Recruited to Nucleotides 1 to 11 at the 3′ End of the Nucleocapsid and Can Scan To Access Internal Signals
Authors: Cowton Vanessa M. , Fearns Rachel
Published: August 2005

The 3′-terminal end of the respiratory syncytial virus genomic RNA contains a 44-nucleotide leader (Le) region adjoining the gene start signal of the first gene. Previous mapping studies demonstrated that there is a promoter located at the 3′ end of Le, which can signal initiation of antigenome synthesis. The aim of this study was to investigate the role of the 3′ terminus of the RNA template in (i) promoter recognition and (ii) determining the initiation site for antigenome synthesis. A panel of minigenomes containing additional sequence at the 3′ end of the Le were analyzed for their ability to direct antigenome and mRNA synthesis. Minigenomes containing heterologous extensions of 6 nucleotides or more were unable to support efficient RNA synthesis. However, the activity of a minigenome with a 56-nucleotide extension could be restored by insertion of Le nucleotides 1 to 11 or 1 to 13 at the 3′ end, indicating that these nucleotides, in conjunction with the 3′ terminus, are sufficient to recruit polymerase to the template. Northern blot and 5′ rapid amplification of cDNA ends analysis of antigenome RNA indicated that antigenome initiation occurred at the first position of Le, irrespective of the terminal extension. This finding demonstrates that the 3′ terminus of the RNA is not necessary for determining the antigenome initiation site. Data are presented which suggest that following recruitment to a promoter at the 3′ end of Le, the polymerase is able to scan and respond to a promoter signal embedded within the RNA template.
A Severe Acute Respiratory Syndrome-Associated Coronavirus-Specific Protein Enhances Virulence of an Attenuated Murine Coronavirus
Authors: Pewe Lecia , Zhou Haixia , Netland Jason , Tangudu Chandra , Olivares Heidi , Shi Lei , Look Dwight , Gallagher Thomas , Perlman Stanley
Published: August 2005

Most animal species that can be infected with the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) do not reproducibly develop clinical disease, hindering studies of pathogenesis. To develop an alternative system for the study of SARS-CoV, we introduced individual SARS-CoV genes (open reading frames [ORFs]) into the genome of an attenuated murine coronavirus. One protein, the product of SARS-CoV ORF6, converted a sublethal infection to a uniformly lethal encephalitis and enhanced virus growth in tissue culture cells, indicating that SARS-CoV proteins function in the context of a heterologous coronavirus infection. Furthermore, these results suggest that the attenuated murine coronavirus lacks a virulence gene residing in SARS-CoV. Recombinant murine coronaviruses cause a reproducible and well-characterized clinical disease, offer virtually no risk to laboratory personnel, and should be useful for elucidating the role of SARS-CoV nonstructural proteins in viral replication and pathogenesis.
Human Immunodeficiency Virus Type 1 Vpr-Dependent Cell Cycle Arrest through a Mitogen-Activated Protein Kinase Signal Transduction Pathway
Authors: Yoshizuka Naoto , Yoshizuka-Chadani Yuko , Krishnan Vyjayanthi , Zeichner Steven L.
Published: August 2005

The human immunodeficiency virus type 1 (HIV-1) Vpr protein has important functions in advancing HIV pathogenesis via several effects on the host cell. Vpr mediates nuclear import of the preintegration complex, induces host cell apoptosis, and inhibits cell cycle progression at G
2
, which increases HIV gene expression. Some of Vpr's activities have been well described, but some functions, such as cell cycle arrest, are not yet completely characterized, although components of the ATR DNA damage repair pathway and the Cdc25C and Cdc2 cell cycle control mechanisms clearly play important roles. We investigated the mechanisms underlying Vpr-mediated cell cycle arrest by examining global cellular gene expression profiles in cell lines that inducibly express wild-type and mutant Vpr proteins. We found that Vpr expression is associated with the down-regulation of genes in the MEK2-ERK pathway and with decreased phosphorylation of the MEK2 effector protein ERK. Exogenous provision of excess MEK2 reverses the cell cycle arrest associated with Vpr, confirming the involvement of the MEK2-ERK pathway in Vpr-mediated cell cycle arrest. Vpr therefore appears to arrest the cell cycle at G
2
/M through two different mechanisms, the ATR mechanism and a newly described MEK2 mechanism. This redundancy suggests that Vpr-mediated cell cycle arrest is important for HIV replication and pathogenesis. Our findings additionally reinforce the idea that HIV can optimize the host cell environment for viral replication.
Human Cytomegalovirus IE1-72 Activates Ataxia Telangiectasia Mutated Kinase and a p53/p21-Mediated Growth Arrest Response
Authors: Castillo Jonathan P. , Frame Fiona M. , Rogoff Harry A. , Pickering Mary T. , Yurochko Andrew D. , Kowalik Timothy F.
Published: August 2005

Human cytomegalovirus (HCMV) encodes several proteins that can modulate components of the cell cycle machinery. TheUL123gene product, IE1-72, binds the Rb-related, p107 protein and relieves its repression of E2F-responsive promoters; however, it is unable to induce quiescent cells to enter S phase in wild-type (p53+/+) cells. IE1-72 also induces p53 accumulation through an unknown mechanism. We present here evidence suggesting that IE1-72 may activate the p53 pathway by increasing the levels of p19Arfand by inducing the phosphorylation of p53 at Ser15. Phosphorylation of this residue by IE1-72 expression alone or HCMV infection is found to be dependent on the ataxia-telangiectasia mutated kinase. IE2-86 expression leads to p53 phosphorylation and may contribute to this phenotype in HCMV-infected cells. We also found that IE1-72 promotes p53 nuclear accumulation by abrogating p53 nuclear shuttling. These events result in the stimulation of p53 activity, leading to a p53- and p21-dependent inhibition of cell cycle progression from G1to S phase in cells transiently expressing IE1-72. Thus, like many of the small DNA tumor viruses, the first protein expressed upon HCMV infection activates a p53 response by the host cell.
Assembly and Intracellular Localization of the Bluetongue Virus Core Protein VP3
Authors: Kar Alak Kanti , Iwatani Nao , Roy Polly
Published: August 2005

The bluetongue virus (BTV) core protein VP3 plays a crucial role in the virion assembly and replication process. Although the structure of the protein is well characterized, much less is known about the intracellular processing and localization of the protein in the infected host cell. In BTV-infected cells, newly synthesized viral core particles accumulate in specific locations within the host cell in structures known as virus inclusion bodies (VIBs), which are composed predominantly of the nonstructural protein NS2. However, core protein location in the absence of VIBs remains unclear. In this study, we examined VP3 location and degradation both in the absence of any other viral protein and in the presence of NS2 or the VP3 natural associate protein, VP7. To enable real-time tracking and processing of VP3 within the host cell, a fully functional enhanced green fluorescent protein (EGFP)-VP3 chimera was synthesized, and distribution of the fusion protein was monitored in different cell types using specific markers and inhibitors. In the absence of other BTV proteins, EGFP-VP3 exhibited distinct cytoplasmic focus formation. Further evidence suggested that EGFP-VP3 was targeted to the proteasome of the host cells but was dispersed throughout the cytoplasm when MG132, a specific proteasome inhibitor, was added. However, the distribution of the chimeric EGFP-VP3 protein was altered dramatically when the protein was expressed in the presence of the BTV core protein VP7, a normal partner of VP3 during BTV assembly. Interaction of EGFP-VP3 and VP7 and subsequent assembly of core-like particles was further examined by visualizing fluorescent particles and was confirmed by biochemical analysis and by electron microscopy. These data indicated the correct assembly of EGFP-VP3 subcores, suggesting that core formation could be monitored in real time. When EGFP-VP3 was expressed in BTV-infected BSR cells, the protein was not associated with proteasomes but instead was distributed within the BTV inclusion bodies, where it colocalized with NS2. These findings expand our knowledge about VP3 localization and its fate within the host cell and illustrate the assembly capability of a VP3 molecule with a large amino-terminal extension. This also opens up the possibility of application as a delivery system.
Enhancement of Enveloped Virus Entry by Phosphatidylserine
Authors: Coil David A. , Miller A. Dusty
Published: August 2005

Enveloped virus vectors are used in a wide variety of applications. We have discovered that treatment of cultured cells with phosphatidylserine (PS) liposomes can increase virus vector infection by up to 20-fold. This effect does not abrogate virus receptor requirements, is specific to PS compared to other phospholipids, and is limited to enveloped viruses. Furthermore, the enhancement of infection does not occur through increases in virus receptor levels or virus binding, indicating that virus fusion is enhanced. The liposomes are easily generated, store well, and allow enhanced infection with a variety of virus vectors and cell types.
Intracellular Localization of the Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein: Absence of Nucleolar Accumulation during Infection and after Expression as a Recombinant Protein in Vero Cells
Authors: Rowland Raymond R. R. , Chauhan Vinita , Fang Ying , Pekosz Andrew , Kerrigan Maureen , Burton Miriam D.
Published: August 2005

The nucleocapsid (N) protein of several members within the order
Nidovirales
localizes to the nucleolus during infection and after transfection of cells with N genes. However, confocal microscopy of N protein localization in Vero cells infected with the severe acute respiratory syndrome coronavirus (SARS-CoV) or transfected with the SARS-CoV N gene failed to show the presence of N in the nucleoplasm or nucleolus. Amino acids 369 to 389, which contain putative nuclear localization signal (NLS) and nucleolar localization signal motifs, failed to restore nuclear localization to an NLS-minus mutant Rev protein. These data indicate that nuclear localization is not a conserved property among all nidoviruses.
Identification of Quantitative Trait Loci for Susceptibility to Mouse Adenovirus Type 1
Authors: Welton Amanda R. , Chesler Elissa J. , Sturkie Carla , Jackson Anne U. , Hirsch Gwen N. , Spindler Katherine R.
Published: August 2005

Adult SJL/J mice are highly susceptible to mouse adenovirus type 1 (MAV-1) infections, whereas other inbred strains, including BALB/cJ, are resistant (K. R. Spindler, L. Fang, M. L. Moore, C. C. Brown, G. N. Hirsch, and A. K. Kajon, J. Virol.75:12039-12046, 2001). Using congenic mouse strains, we showed that theH-2shaplotype of SJL/J mice is not associated with susceptibility to MAV-1. Susceptibility of MAV-1-infected (BALB/cJ × SJL/J)F1mice was intermediate between that of SJL/J mice and that of BALB/cJ mice, indicating that susceptibility is a genetically controlled quantitative trait. We mapped genetic loci involved in mouse susceptibility to MAV-1 by analysis of 192 backcross progeny in a genome scan with 65 simple sequence length polymorphic markers. A major quantitative trait locus (QTL) was detected on chromosome 15 (Chr 15) with a highly significant logarithm of odds score of 21. The locus on Chr 15 alone accounts for 40% of the total trait variance between susceptible and resistant strains. QTL modeling of the data indicated that there are a number of other QTLs with small effects that together with the major QTL on Chr 15 account for 54% of the trait variance. Identification of the major QTL is the first step in characterizing host genes involved in susceptibility to MAV-1.
A Single Amino Acid Substitution in 1918 Influenza Virus Hemagglutinin Changes Receptor Binding Specificity
Authors: Glaser Laurel , Stevens James , Zamarin Dmitriy , Wilson Ian A. , García-Sastre Adolfo , Tumpey Terrence M. , Basler Christopher F. , Taubenberger Jeffery K. , Palese Peter
Published: August 2005

The receptor binding specificity of influenza viruses may be important for host restriction of human and avian viruses. Here, we show that the hemagglutinin (HA) of the virus that caused the 1918 influenza pandemic has strain-specific differences in its receptor binding specificity. The A/South Carolina/1/18 HA preferentially binds the α2,6 sialic acid (human) cellular receptor, whereas the A/New York/1/18 HA, which differs by only one amino acid, binds both the α2,6 and the α2,3 sialic acid (avian) cellular receptors. Compared to the conserved consensus sequence in the receptor binding site of avian HAs, only a single amino acid at position 190 was changed in the A/New York/1/18 HA. Mutation of this single amino acid back to the avian consensus resulted in a preference for the avian receptor.
Relative Contributions of Measles Virus Hemagglutinin- and Fusion Protein-Specific Serum Antibodies to Virus Neutralization
Authors: de Swart Rik L. , Yüksel Selma , Osterhaus Albert D. M. E.
Published: August 2005

The relative contribution of measles virus hemagglutinin (H)- or fusion protein (F)-specific antibodies to virus neutralization (VN) has not been demonstrated. We have depleted these specific antibodies from sera collected from young adults, who had been vaccinated during childhood, by prolonged incubation with viable transfected human melanoma cells expressing H or F. Simultaneous depletion of antibodies of both specificities completely abrogated VN activity. Depletion of F-specific antibodies only had a minimal effect, whereas removal of H-specific antibodies resulted in almost complete reduction of VN activity. These results demonstrate that measles virus neutralizing antibodies are mainly directed to the H protein.
Genetic diversity among Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars as determined from amplified fragment length polymorphism and simple sequence repeat markers and quantitative agronomic traits
Authors: Iwata Hiroyoshi , Imon Kenta , Tsumura Yoshihiko , Ohsawa Ryo
Published: August 2005

We assessed the genetic diversity in Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers and investigated the relationships between the genetic diversity and agronomic traits. The average expected intracultivar hetero zygosity was 0.303 for AFLP and 0.819 for SSR. The differentiations among agroecotypes, among cultivars within an agroecotype, and among cultivars were small (0.002, 0.024, and 0.026 for SSR and 0.013, 0.013, and 0.026 for AFLP, respectively) but statistically significant from zero except for the SSR differentiation among agroecotypes. In principal coordinates analysis, cultivars within the same agroecotype tended to cluster, indicating that agroecotypes well reflected the genetic relationships among cultivars. In AFLP, the differentiation among the agroecotypes was more distinct than in SSR, and genetic distance showed a moderate correlation with the difference in quantitative traits, indicating that AFLP can resolve the relationships among cultivars with better resolution than SSR. By contrast, SSR may be more sensitive to demographic changes. Four of the five SSR markers showed a significant positive correlation (Kendall's τ = 0.382–0.607) between allelic richness and variation in flowering timing, indicating that cumulative bottleneck events have occurred during the population history, with a decline in the variation of photosensitivity of flowering.Key words: agroecotype, coefficient of gene differentiation, genetic distance, allelic richness, photosensitivity of flowering.
DNA sequence of theEscherichia coliO103 O antigen gene cluster and detection of enterohemorrhagicE. coliO103 by PCR amplification of thewzxandwzygenes
Authors: Fratamico Pina M , DebRoy Chitrita , Strobaugh, Jr. Terence P , Chen Chin-Yi
Published: August 2005

Escherichia coli serogroup O103 has been associated with gastrointestinal illness and hemolytic uremic syndrome. To develop PCR-based methods for detection and identification of this serogroup, the DNA sequence of the 12 033-bp region containing the O antigen gene cluster of Escherichia coli O103 was determined. Of the 12 open reading frames identified, the E. coli O103 wzx (O antigen flippase) and wzy (O antigen polymerase) genes were selected as targets for development of both conventional and real-time PCR assays specific for this serogroup. In addition, a multiplex PCR targeting the Shiga toxin (Stx) 1 (stx1), Shiga toxin 2 (stx2), wzx, and wzy genes was developed to differentiate Stx-producing E. coli O103 from non-toxigenic strains. The PCR assays can be employed to identify E. coli serogroup O103, replacing antigen-based serotyping, and to potentially detect the organism in food, fecal, or environmental samples.Key words: real-time polymerase chain reaction, E. coli typing, E. coli O103, O antigen DNA sequence.
WETTING PHENOMENA AND CONSTANT MEAN CURVATURE SURFACES WITH BOUNDARY
Authors: LÓPEZ RAFAEL
Published: August 2005

In a microscopic scale or microgravity environment, interfaces in wetting phenomena are usually modeled by surfaces with constant mean curvature (CMC surfaces). Usually, the condition regarding the constancy of the contact angle along the line of separation between different phases is assumed. Although the classical capillary boundary condition is the angle made at the contact line, configurations also occur in which a Dirichlet condition is appropriate. In this article, we discuss those with vanishing boundary conditions, such as those that occur on a thin flat portion of a plate of general shape covered with water. In this paper, we review recent works on the existence of CMC surfaces with non-empty boundary, with a special focus on the Dirichlet problem for the constant mean curvature equation.
FREE ENERGY IN THE GENERALIZED SHERRINGTON–KIRKPATRICK MEAN FIELD MODEL
Authors: PANCHENKO DMITRY
Published: August 2005

In [11], Talagrand gave a rigorous proof of the Parisi formula in the classical Sherrington–Kirkpatrick (SK) model. In this paper, we build upon the methodology developed in [11] and extend Talagrand's result to the class of SK type models in which the spins have arbitrary prior distribution on a bounded subset of the real line.
Drell-Yan Production at the Fermilab Tevatron
Authors:   on behalf of CDF and DØ Collaborations., LEE JEDONG
Published: August 2005

Using data from [Formula: see text] collisions at [Formula: see text] collected by the CDF and DØ detectors, we present measurements of the Drell-Yan inclusive differential cross section and forward-backward charge asymmetry as a function of invariant mass. We compare these measurements with Standard Model predictions, and present searches for new physics that could appear as deviations from the Standard Model in the Drell-Yan differential cross section.
ANALYSIS OF DIPHOTON EVENTS AT CDF
Authors:   for the CDF Collaboration., CULBERTSON RAY
Published: August 2005

The Collider Detector at Fermilab Collaboration has analyzed events with two photons in the central detector. The cross section is measured and compared to theoretical models. The diphoton mass spectrum is searched for anomalous narrow peaks and a search for gauge–mediated SUSY is performed with events with two photons and missing Et.
A SEARCH FOR LEPTON FLAVOR VIOLATION IN TAU DECAYS ATBABAR
Authors:   representing the BABAR Collaboration., IGONKINA OLGA
Published: August 2005

We present a recent BABAR search for lepton flavor violation in tau decays. The search for τ → ℓℓℓ(ℓ = e, μ) decays is based on a data sample of 91.6 fb-1. No signal is found in any of six channels and 90% CL upper limits are set in the range of (1 - 3) × 10-7. The search for τ → μγ decay is done with a 63 fb-1data sample. The number of observed events is consistent with expected background level and a preliminary upper limit is set at 2 × 10-6at 90% CL.
B MESON DECAYS TO QUASI-TWO-BODY CHARMLESS FINAL STATES AT BABAR
Authors:   ON BEHALF OF THE BABAR COLLABORATION., LAZZARO ALFIO
Published: August 2005

We present results for measurements of the decays to charmless final states of B0 meson to ηK0, ηω, [Formula: see text] with [Formula: see text], and of B+ to ηρ+, η′π+. Analyses are based on data taken with the BABAR detector at the PEP-II asymmetric e+e- collider at SLAC. We measure the following branching fractions in units of [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]. The charge asymmetries are [Formula: see text] and [Formula: see text]. First error is statistical, the second systematic. All results are preliminary.
A NOVEL CORRELATION FUNCTION FROM DETRENDED FLUCTUATION ANALYSIS
Authors: YANG C. B.
Published: August 2005

A method for investigating the existence of long-range correlations between two sequences is proposed from the detrended fluctuation analysis method. A new correlation function is defined and its behavior is shown for simple examples.
A CLASS OF CLOSED SOLUTIONS FOR THE BOGOLIUBOV EXCITATIONS ON SMOOTH GROUND STATE OF A TRAPPED BOSE–EINSTEIN CONDENSATE
Authors: MA YONG-LI , ZHU HAICHEN
Published: August 2005

Bogoliubov–de Gennes equations (BdGEs) for collective excitations from a trapped Bose–Einstein condensate described by a spatially smooth ground-state wavefunction can be treated analytically. A new class of closed solutions for the BdGEs is obtained for the one-dimensional (1D) and 3D spherically harmonic traps. The solutions of zero-energy mode of the BdGEs are also provided. The eigenfunctions of the excitations consist of zero-energy mode, zero-quantum-number mode and entire excitation modes when the approximate ground state is a background Bose gas sea.
WAVE EQUATION FOR FRACTAL SOLID STRING
Authors: TARASOV VASILY E.
Published: August 2005

We use the fractional integrals to describe fractal solid. We suggest to consider the fractal solid as special (fractional) continuous medium. We replace the fractal solid with fractal mass dimension by some continuous model that is described by fractional integrals. The fractional integrals are considered as approximation of the integrals on fractals. We derive fractional generalization of the action functional and the Euler–Lagrange equation for the fractal solid string. The solution of wave equation for fractal solid string is considered.
SIGNAL DENOISING USING WAVELETS AND BLOCK HIDDEN MARKOV MODEL
Authors: LIAO ZHIWU , TANG Y. Y.
Published: August 2005

This paper presents a new framework for signal denoising based on wavelet-domain hidden Markov models (HMMs). The new framework enables us to concisely model the statistical dependencies and non-Gaussian statistics encountered in real-world signals, and enables us to get a more reliable and local model using blocks. Wavelet-domain HMMs are designed with the intrinsic properties of wavelet transform and provide powerful yet tractable probabilistic signal models. In this paper, we propose a novel wavelet domain HMM using blocks to strike a delicate balance between improving spatial adaptability of contextual HMM (CHMM) and modeling a more reliable HMM. Each wavelet coefficient is modeled as a Gaussian mixture model, and the dependencies among wavelet coefficients in each subband are described by a context structure, then the structure is modified by blocks which are connected areas in a scale conditioned on the same context. Before denoising a signal, efficient Expectation Maximization (EM) algorithms are developed for fitting the HMMs to observational signal data. Parameters of trained HMM are used to modify wavelet coefficients according to the rule of minimizing the mean squared error (MSE) of the signal. Then, reverse wavelet transformation is utilized to modified wavelet coefficients. Finally, experimental results are given. The results show that block hidden Markov model (BHMM) is a powerful yet simple tool in signal denoising.
UNIVERSAL WRITING MODEL FOR RECOVERY OF WRITING SEQUENCE OF STATIC HANDWRITING IMAGES
Authors: LAU KAI KWONG , YUEN PONG CHI , TANG YUAN YAN
Published: August 2005

Online features have been proven to be more robust information for handwriting recognition than an offline static image due to dynamic aspects, such as the writing sequence of strokes. The estimation of temporal information from a static image becomes an important issue. This paper presents a new statistical method to reconstruct the writing order of a handwritten signature from a two-dimensional static image. The reconstruction process consists of two phases, namely the training phase and the testing phase. In the training phase, the writing order with other attributes, such as length and direction, are extracted and analyzed from a set of training online handwritten signatures. A Universal Writing Model (UWM), which consists of a set of distribution functions, is then constructed. In the testing phase, the UWM is applied to reconstruct the writing order of an offline signature. 300 offline signatures with ground truth are used for evaluation. Experimental results show that about one-eighth of the reconstructed writing sequences are the same as the actual writing sequences.
RECTANGULAR MIXED FINITE ELEMENTS FOR ELASTICITY
Authors: ARNOLD DOUGLAS N. , AWANOU GERARD
Published: August 2005

We present a family of stable rectangular mixed finite elements for plane elasticity. Each member of the family consists of a space of piecewise polynomials discretizing the space of symmetric tensor fields in which the stress field is sought, and another to discretize the space of vector fields in which the displacement is sought. These may be viewed as analogues in the case of rectangular meshes of mixed finite elements recently proposed for triangular meshes. As for the triangular case the elements are closely related to a discrete version of the elasticity differential complex.
THE WATER CONVEYANCE PROBLEM: OPTIMAL PURIFICATION OF POLLUTED WATERS
Authors: ALVAREZ-VÁZQUEZ L. J. , MARTÍNEZ A. , MUÑOZ-SOLA R. , RODRÍGUEZ C. , VÁZQUEZ-MÉNDEZ M. E.
Published: August 2005

In this work we deal with the optimal purification of polluted areas of shallow waters by means of the injection of clear water in order to promote seawater exchange. This problem can be formulated as a control constrained optimal control problem where the control is the velocity of the injected water, the state equations are the shallow water equations together with that modelling the contaminant concentration, and the cost function measures the total amount of injected water and the fulfilment of the water quality standards. We analyze the solutions of the optimal control problem and give an optimality condition in order to characterize them. We also discretize the problem by means of a characteristics-mixed finite element method, focusing our attention on both the discrete and the discretized adjoint systems, and propose an algorithm for the numerical resolution of the discrete optimization problem. Finally, we present numerical results for some computational experiments.
STRANGE QUARK MATTER ATTACHED TO THE STRING CLOUD IN THE SPHERICAL SYMMETRIC SPACE–TIME ADMITTING CONFORMAL MOTION
Authors: YAVUZ İLHAMİ , YILMAZ İHSAN , BAYSAL HÜSNÜ
Published: August 2005

In this paper, we have examined charged strange quark matter attached to the string cloud in the spherical symmetric space–time admitting one-parameter group of conformal motions. For this purpose, we have solved Einstein's field equations for spherical symmetric space–time with strange quark matter attached to the string cloud via conformal motions. Also, we have discussed the features of the obtained solutions.
THE PROPERTIES OF AMORPHOUS CARBON NITRIDE THIN FILMS SYNTHESIZED BY PULSED LASER DEPOSITION WITH VARIOUS PREPARATION CONDITIONS
Authors: RUSOP M. , SOGA T. , JIMBO T.
Published: August 2005

Surface morphology, deposition rate, bonding composition, structural, optical and electrical properties of XeCl excimer pulsed laser deposited amorphous carbon nitride ( a-CN x) films using camphoric carbon ( C 10 H 16 O ) target in 0.8 Torr nitrogen ( N ) gas ambient as a function of laser fluences (LF) (from 2.8 to 5.2 J/cm2) with fixed target-to-substrate distances (TSD) at 45 mm and substrate temperatures (ST) at 20°C; TSD (from 25 to 45 mm) with fixed LF at 3.4 J/cm2 and ST at 20°C; and ST (from 20 to 500°C) with fixed LF at 3.4 J/cm2 and TSD at 45 mm are reported. At fixed TSD and ST, the surface roughness, particle density, deposition rate and N content increase, whereas the particle size decreases with higher LF. When the LF and ST are fixed, decreasing TSD results in an increase in the irregular small particle size, particle density, surface roughness, deposition rate, N content. On the other hand, when the LF and TSD are fixed, the surface roughness, particle density and particle size increase, whereas the deposition rate decreases with higher ST. The N content increases with ST up to 400°C and decreases thereafter. We found that the amorphous structure of a-CN x films and the ratio of sp2 trihedral component to sp3 tetrahedral component are strongly dependent on the LF, TSD and ST. The a-CN x films with high N content have relatively high electrical resistivity.
THE STABILITY OF VAPOR CONDENSATION EQUILIBRIUM
Authors: ZHANG SHIMIN
Published: August 2005

The system must get across an energy peak of unstable equilibrium during the condensation of pure vapor; as the supersaturated extent of vapor increases and the temperature decreases, the energy peak shortens and vapor condensation becomes easier. The system must get across an energy peak of unstable equilibrium first, and then get into an energy valley of stable equilibrium during the condensation of impure vapor; as the partial pressure of vapor decreases, the energy peak becomes taller, the energy valley more shallow, vapor condensation becomes more difficult and liquid evaporation becomes easier; when the partial pressure of vapor decreases to a certain extent, the energy peak and the energy valley combine into one, and vapor condensation becomes impossible.
SYNTHESIS AND PROPERTY STUDY OF NANOPARTICLE QUATERNARY SEMICONDUCTOR SiCAlN FILMS WITH CO-SPUTTERING UNDER LOWER TEMPERATURE
Authors: HUANG SHIYONG , XU S. , LONG JIDONG , DAI ZHENHONG , SUN YUANPING
Published: August 2005

Quaternary SiCAlN nanoparticle films were produced by reactive rf magnetron co-sputtering technique with a chemically pure SiC and an Al target under low temperature. The crystalline structure, surface morphology, and element content of the films were studied in terms of sputtering parameters. The element content and chemical states of SiCAlN films were measured by means of energy dispersive X-ray fluorescence (EDX) and X-ray photoelectronic spectroscopy (XPS). Surface morphology of SiCAlN films was investigated by FE-SEM.
THE APPLICATION OF PULSED LASER DEPOSITION IN PRODUCING BIOACTIVE CERAMIC FILMS
Authors: ZHAO YAFAN , CHEN CHUANZHONG , WANG DIANGANG
Published: August 2005

Pulsed laser deposition (PLD) is a relatively new technique for producing thin films. It presents unique advantages for the deposition of bioactive ceramics. The mechanism and characteristics of the technique PLD are introduced. Its applications and current research status in hydroxyapatite and bioglass thin films are reviewed. The effect of processing parameters of PLD, including atmosphere, substrate temperature, laser wavelength and target properties, on the structures and the properties of the hydroxyapatite film, is analyzed in detail. Future application trends are also analyzed.
GIBBS ADSORPTION ISOTHERM FOR CONCENTRATION AS VARIABLE
Authors: ZHANG SHIMIN
Published: August 2005

Gibbs adsorption isotherm of the multicomponent system for concentration instead of chemical potential as independent variables is deduced and explained in a simple way. For the multicomponent system composed of α and β phases with plane interface, if the β phase is a dilute solution, and component k is solvent as well as [Formula: see text], Gibbs adsorption isotherm of component i can be expressed as [Formula: see text] (the dividing surface is placed where the adsorption of component k is zero). The adsorption of some components on the vapor–liquid interface of dilute solution with moderate or low pressure can meet the application condition of this adsorption isotherm. The adsorption of various components on the solid–liquid and liquid–liquid interface of dilute solution can also meet the application condition of this adsorption isotherm if various components of one phase are virtually insoluble in another phase.
PHOTOELECTRICAL PROPERTIES OF p-TYPE AND n-TYPE ELECTRICAL CONDUCTIVITY AMORPHOUS CARBON THIN FILMS FOR APPLICATION IN ECONOMICAL CARBON-BASED SOLAR CELLS
Authors: RUSOP M. , SOGA T. , JIMBO T.
Published: August 2005

The successful deposition of boron ( B )-doped p-type ( p-C:B ) and phosphorous ( P )-doped n-type ( n-C:P ) carbon ( C ) films, and fabrication of p-C:B on silicon ( Si ) substrate ( p-C:B/n-Si ) and n-C:P/p-Si cells by the technique of pulsed laser deposition (PLD) using graphite target is reported. The cells' performances are represented in the dark I–V rectifying curve and I–V working curve under illumination when exposed to AM 1.5 illumination condition (100 mW/cm2, 25°C). The open circuit voltage (V oc ) and short circuit current density (J sc ) for p-C:B/n-Si are observed to vary from 230–250 mV and 1.5–2.2 mA/cm2, respectively, and to vary from 215–265 mV and 7.5–10.5 mA/cm2, respectively, for n-C:P/p-Si cells. The p-C:B/n-Si cell fabricated using the target with the amount of B by 3 Bwt% shows highest energy conversion efficiency, η = 0.20%, and fill factor, FF = 45%, while, the n-C:P/p-Si cell with the amount of P by 7 Pwt% shows highest energy conversion efficiency, η = 1.14%, and fill factor, FF = 41%. The quantum efficiencies (QE) of the p-C:B/n-Si and n-C:P/p-Si cells are observed to improve with Bwt% and Pwt%, respectively. The contributions of QE are suggested to be due to photon absorption by carbon layer in the lower wavelength region (below 750 nm) and Si substrates in the higher wavelength region. The dependence of B and P content on the electrical and optical properties of the deposited films, and the photovoltaic characteristics of the respective p-C:B/n-Si and n-C:P/p-Si heterojunction photovoltaic cells, are discussed.
DISLOCATION GROWTH AND MICROCRYSTAL FORMATION OF MANGANESE MERCURY THIOCYANATE CRYSTALS
Authors: GENG Y. L. , XU D. , WANG X. Q. , YU G. W. , ZHANG G. H.
Published: August 2005

Dislocation growth and microcrystals are investigated on the {110} faces of MMTC crystals grown from aqueous solution. Growth of MMTC crystals occurs in elementary steps (~ 0.81 nm), introduced by both simple and complex dislocation sources. The bright particles with regular sizes and shapes are assumed to be microcrystals transferred from aggregates that deposit on the faces during the crystal growth.