bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Serum Facilitates Hepatitis C Virus Infection, and Neutralizing Responses Inversely Correlate with Viral Replication Kinetics at the Acute Phase of Hepatitis C Virus Infection
Authors: Lavillette Dimitri , Morice Yoann , Germanidis Georgios , Donot Peggy , Soulier Alexandre , Pagkalos Emanuil , Sakellariou Georgios , Intrator Liliane , Bartosch Birke , Pawlotsky Jean-Michel , Cosset François-Loïc 
Published: April 2005

ABSTRACT
The factors leading to spontaneous clearance of hepatitis C virus (HCV) or to viral persistence are elusive. Understanding virus-host interactions that enable acute HCV clearance is key to the development of more effective therapeutic and prophylactic strategies. Here, using a sensitive neutralization assay based on infectious HCV pseudoparticles (HCVpp), we have studied the kinetics of humoral responses in a cohort of acute-phase patients infected during a single nosocomial outbreak in a hemodialysis center. The 17 patients were monitored for the spontaneous outcome of HCV infection for 6 months before a treatment decision was made. Blood samples were taken frequently (15 ± 4 per patient). Phylogenetic analysis of the predominant virus(es) revealed infection by only one of two genotype 1b strains. While all patients seroconverted, their sera induced two opposing effects in HCVpp infection assays: inhibition and facilitation. Furthermore, the ability of sera to facilitate or inhibit infection correlated with the presence of either infecting HCV strain and divided the patients into two groups. In group 1, the progressive emergence of a relatively strong neutralizing response correlated with a fluctuating decrease in high initial viremia, leading to control of viral replication. Patients in group 2 failed to reduce viremia within the acute phase, and no neutralizing responses were detected despite seroconversion. Strikingly, sera of group 2, as well as naïve sera, facilitated infection by HCVpp displaying HCV glycoproteins from different genotypes and strains, including those retrieved from patients. These results provide new insights into the mechanisms of viral persistence and immune control of viremia.
The Locus Encompassing the Latency-Associated Transcript of Herpes Simplex Virus Type 1 Interferes with and Delays Interferon Expression in Productively Infected Neuroblastoma Cells and Trigeminal Ganglia of Acutely Infected Mice
Authors: Peng Weiping , Henderson Gail , Inman Melissa , BenMohamed Lbachir , Perng Guey-Chuen , Wechsler Steven L. , Jones Clinton 
Published: April 2005

ABSTRACT
The herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) is the only abundant viral transcript expressed in latently infected neurons. LAT inhibits apoptosis, suggesting that it regulates latency by promoting the survival of infected neurons. The LAT locus also contains a newly described gene (AL), which is antisense to LAT and partially overlaps LAT encoding sequences. When human (SK-N-SH) or mouse (neuro-2A) neuroblastoma cells were infected with a virus that does not express LAT or AL gene products (dLAT2903), beta interferon (IFN-β) and IFN-α RNA expression was detected earlier relative to the same cells infected with HSV-1 strains that express LAT and AL. Infection of neuro-2A cells with dLAT2903 also led to higher levels of IFN-β promoter activity than in cells infected with wild-type (wt) HSV-1. In contrast, IFN RNA expression was the same when human lung fibroblasts were infected with dLAT2903 or wt HSV-1. When BALB/c mice were infected with dLAT2903, IFN-α and IFN-β RNA expression was readily detected in trigeminal ganglia (TG) 4 days after infection. These transcripts were not detected in TG of mice infected with wt HSV-1 or dLAT2903R (marker-rescued dLAT2903) until 6 days postinfection. When TG single-cell suspensions from infected BALB/c mice were prepared and incubated in vitro with wt HSV-1 as a source of antigen, TG cultures prepared from mice infected with dLAT2903 produced and secreted higher levels of IFN protein than wt HSV-1 or dLAT2903R. Collectively, these studies suggest that the LAT locus interferes with and delays IFN expression.
Immunization with the Gene Expressing Woodchuck Hepatitis Virus Nucleocapsid Protein Fused to Cytotoxic-T-Lymphocyte-Associated Antigen 4 Leads to Enhanced Specific Immune Responses in Mice and Woodchucks
Authors: Lu Mengji , Isogawa Masanori , Xu Yang , Hilken Gero 
Published: April 2005

ABSTRACTA number of options are available to modify and improve DNA vaccines. An interesting approach to improve DNA vaccines is to fuse bioactive domains, like cytotoxic-T-lymphocyte-associated protein 4 (CTLA-4), to an antigen. Such fusion antigens are expressed in vivo and directed to immune cells by the specific bioactive domain and therefore possess great potential to induce and modulate antigen-specific immune responses. In the present study, we tested this new approach for immunomodulation against hepadnavirus infection in the woodchuck model. Plasmids expressing the nucleocapsid protein (WHcAg) and e antigen (WHeAg) of woodchuck hepatitis virus (WHV) alone or in fusion to the extracellular domain of woodchuck CTLA-4 and CD28 were constructed. Immunizations of mice with plasmids expressing WHcAg or WHeAg led to a specific immunoglobulin G2a (IgG2a)-dominant antibody response. In contrast, fusions of WHcAg to CTLA-4 and CD28 induced a specific antibody response with comparable levels of IgG1 and IgG2a. Furthermore, the specific IgG1 response to WHcAg/WHeAg developed immediately after a single immunization with the CTLA-4-WHcAg fusion. Woodchucks were immunized with plasmids expressing WHeAg or the CTLA-4-WHcAg fusion and subsequently challenged with WHV. CTLA-4-WHcAg showed an improved efficacy in induction of protective immune responses to WHV. In particular, the anti-WHsAg antibody response developed earlier after challenge in woodchucks that received immunizations with CTLA-4-WHcAg, consistent with the hypothesis that anti-WHs response is dependent on a Th cell response to WHcAg. In conclusion, the use of fusion genes represents a generally applicable strategy to improve DNA vaccination.
Human Immunodeficiency Virus Type 1 Stimulates the Expression and Production of Secretory Leukocyte Protease Inhibitor (SLPI) in Oral Epithelial Cells: a Role for SLPI in Innate Mucosal Immunity
Authors: Jana N. K. , Gray L. R. , Shugars D. C. 
Published: April 2005

ABSTRACT

The innate immune response is a key barrier against pathogenic microorganisms such as human immunodeficiency virus type 1 (HIV-1). Because HIV-1 is rarely transmitted orally, we hypothesized that oral epithelial cells participate in the innate immune defense against this virus. We further hypothesized that secretory leukocyte protease inhibitor (SLPI), a 12-kDa mucosal antiviral protein, is a component of the host immune response to this virus. Here we demonstrated constitutive expression and production of SLPI in immortalized human oral keratinocytes. Brief exposure of cells to HIV-1 BaL and HXB2 significantly increased SLPI mRNA and protein production compared to that in mock-exposed cells (
P
< 0.01), as evaluated by real-time quantitative reverse transcription-PCR and enzyme-linked immunosorbent assay. HIV-1-mediated stimulation of SLPI occurred at the transcriptional level, was dose and time dependent, was elicited by heat-inactivated and infectious viruses, and did not depend on cellular infection. Experiments with purified retroviral proteins showed that the stimulatory effect was induced specifically by external envelope glycoproteins from HIV-1 and simian immunodeficiency virus. SLPI responsiveness to HIV-1 was also observed in an unrelated oral epithelial cell line and in normal (nonimmortalized) human oral epithelial cells isolated from healthy uninfected gingival tissues. In this first report of SLPI regulation by HIV-1, we show that the expression and production of the antimicrobial and anti-inflammatory protein can be stimulated in oral epithelial cells by the virus through interactions with gp120 in the absence of direct infection. These findings indicate that SLPI is a component of the oral mucosal response to HIV-1.
Functional Chimeras of Human Immunodeficiency Virus Type 1 gp120 and Influenza A Virus (H3) Hemagglutinin
Authors: Copeland K. M. , Elliot A. J. , Daniels R. S. 
Published: April 2005

ABSTRACT

In an attempt to produce a protein that will allow determination of the native human immunodeficiency virus type 1 (HIV-1) gp120 (Env) structure in its trimeric state, we fused the globular head of gp120 to the stalk region of influenza virus A (X31) hemagglutinin (HA). The chimeric protein (EnvHA) has been expressed by using a recombinant vaccinia virus system, and its functional characteristics were determined. EnvHA is expressed as a 120- to 150-kDa protein that can oligomerize to form dimers and trimers. It retains the low-pH (5.2 to 5.4) requirement of X31-HA to trigger membrane fusion but, unlike X31-HA, it is not absolutely dependent on exogenously added trypsin for protein processing to release the HA2 fusion peptide. In terms of receptor binding the chimeric protein retains specificity for human CD4 but, in relation to the membrane fusion event, it appears to lose the Env coreceptor specificity of the parental HIV-1 strains: NL43 for CXCR4 and JRFL for CCR5. These properties suggest that stable, functional EnvHAs are being produced and that they may be exploited in terms of structural studies. Further, the potential of introducing the
envHA
genes into influenza viruses, by use of reverse genetics, and their use as a therapeutic vaccine for HIV are discussed.
Accumulation of Amino Acid Substitutions Promotes Irreversible Structural Changes in the Hemagglutinin of Human Influenza AH3 Virus during Evolution
Authors: Nakajima Katsuhisa , Nobusawa Eri , Nagy Alexander , Nakajima Setsuko 
Published: April 2005

ABSTRACT
In order to clarify the effect of an accumulation of amino acid substitutions on the hemadsorption character of the influenza AH3 virus hemagglutinin (HA) protein, we introduced single-point amino acid changes into the HA1 domain of the HA proteins of influenza viruses isolated in 1968 (A/Aichi/2/68) and 1997 (A/Sydney/5/97) by using PCR-based random mutation or site-directed mutagenesis. These substitutions were classified as positive or negative according to their effects on the hemadsorption activity. The rate of positive substitutions was about 50% for both strains. Of 44 amino acid changes that were identical in the two strains with regard to both the substituted amino acids and their positions in the HA1 domain, 22% of the changes that were positive in A/Aichi/2/68 were negative in A/Sydney/5/97 and 27% of the changes that were negative in A/Aichi/2/68 were positive in A/Sydney/5/97. A similar discordance rate was also seen for the antigenic sites. These results suggest that the accumulation of amino acid substitutions in the HA protein during evolution promoted irreversible structural changes and therefore that antigenic changes in the H3HA protein may not be limited.
Functional Characterization of the Genomic Promoter of Borna Disease Virus (BDV): Implications of 3′-Terminal Sequence Heterogeneity for BDV Persistence
Authors: Rosario Debralee , Perez Mar , de la Torre Juan Carlos 
Published: April 2005

ABSTRACTBorna disease virus (BDV) is an enveloped virus with a genome organization characteristic ofMononegavirales. However, based on its unique features, BDV is considered the prototypic member of a new virus family,Bornaviridae, within the orderMononegavirales. We have described the establishment of a reverse genetics system for the rescue of BDV RNA analogues, or minigenomes, that is based on the use of polymerase I/polymerase II. Using this BDV minigenome rescue system, we have examined the functional implications of the reported sequence heterogeneity found at the 5′ and 3′ termini of the BDV genome and also defined the minimal BDV genomic promoter within the 3′-terminal 25 nucleotides. Our results suggest that the accumulation of RNA genome species containing truncations of one to three nucleotides at their 3′ termini may contribute to modulate BDV RNA replication and gene expression during long-term persistence.
Low Levels of Human Immunodeficiency Virus Type 1 DNA in High-Risk Seronegative Men
Authors: Koning Fransje A. , van der Vorst Teun J. K. , Schuitemaker Hanneke 
Published: April 2005

ABSTRACT
We detected human immunodeficiency virus type 1 (HIV-1) DNA at very low levels in sequential peripheral blood mononuclear cell samples of five out of six high-risk, seronegative, homosexual men and five out of five individuals 7.8 to 1.6 years prior to seroconversion. These data indicate a high prevalence of low-level HIV-1 DNA in exposed seronegative individuals.
Residues in the Murine Leukemia Virus Capsid That Differentially Govern Resistance to Mouse
Fv1
and Human
Ref1
Restrictions
Authors: Lassaux Adeline , Sitbon Marc , Battini Jean-Luc 
Published: April 2005

ABSTRACT

We identified new residues within a 101-amino-acid stretch of the murine leukemia virus capsid that differentially modulate resistance and susceptibility to the mouse
Fv1
and human
Ref1
genes. Among these residues, aspartate 92 and histidine 117 are both required for
Fv1

b

resistance, whereas the latter is sufficient to confer
Ref1
resistance.
Failure of the Lamivudine-Resistant rtM204I Hepatitis B Virus Mutants To Efficiently Support Hepatitis Delta Virus Secretion
Authors: Vietheer P. T. K. , Netter H. J. , Sozzi T. , Bartholomeusz A. 
Published: April 2005

ABSTRACTHepatitis delta virus (HDV) is encapsidated by the envelope proteins of hepatitis B virus (HBV). The major HBV lamivudine (LMV)-resistant mutations in the polymerase gene within the reverse transcriptase (rt) region at rtM204V or rtM204I are associated with changes in the overlapping envelope gene products, in particular, the gene encoding small envelope protein (s) at sI195M or sW196L/S/Stop. We have demonstrated that the LMV resistance mutations corresponding to sW196L/S inhibited secretion of HDV particles, while changes corresponding to sI195M did not affect secretion. Differential efficiencies of HBsAg proteins expressed by LMV-resistant HBV to support HDV secretion may have consequences for clinical prognosis as coinfected patients are treated with antiviral agents.
Synthesis, Reactions, Conformation Analysis, and NMR Spectra of 5,10-Epoxy-5ξ,10ξ-estrane-3,17-diones
Authors: Buděšínský Miloš , Fajkoš Jan , Günter Jaroslav , Kasal Alexander 
Published: April 2005

On epoxidation of estr-5(10)-ene-3,17-dione, the 5β,10β-epoxide is the major product. The mixture of epoxides was converted into 5,10β-dihydroxy-5α-estrane-3,17-dione, 10α- and 10β-hydroxyestr-4-ene-3,17-dione, and estrone. Due to the sensitivity of the products, 1H NMR was the best way to monitor the reaction pathway.
The "nations" in the salvific racles of Isaiah
Authors: Croatto Severino J. 
Published: April 2005

AbstractThe purpose of this study is to deconstruct the exegetical tradition that emphasizes the promise of universal salvation for the foreign nations in the book of Isaiah. The real message—scattered all along the book by its final author or Fourth Isaiah—is to affirm the liberation and return of the different Judean diasporas. The nations as such, on the contrary, will receive the negative lot of the reversal of fortunes.
Scoredist: A simple and robust protein sequence distance estimator
Authors: Sonnhammer Erik LL , Hollich Volker 
Published: April 2005

Abstract
Background
Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used.

Results
We propose a correction-based protein sequence estimator called Scoredist. It uses a logarithmic correction of observed divergence based on the alignment score according to the BLOSUM62 score matrix. We evaluated Scoredist and a number of optimal matrix methods using three evolutionary models for both training and testing Dayhoff, Jones-Taylor-Thornton, and Müller-Vingron, as well as Whelan and Goldman solely for testing. Test alignments with known distances between 0.01 and 2 substitutions per position (1–200 PAM) were simulated using ROSE. Scoredist proved as accurate as the optimal matrix methods, yet substantially more robust. When trained on one model but tested on another one, Scoredist was nearly always more accurate. The Jukes-Cantor and Kimura correction methods were also tested, but were substantially less accurate.

Conclusion
The Scoredist distance estimator is fast to implement and run, and combines robustness with accuracy. Scoredist has been incorporated into the Belvu alignment viewer, which is available at ftp://ftp.cgb.ki.se/pub/prog/belvu/.
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR – how well do they correlate?
Authors: Dallas Peter B , Gottardo Nicholas G , Firth Martin J , Beesley Alex H , Hoffmann Katrin , Terry Philippa A , Freitas Joseph R , Boag Joanne M , Cummings Aaron J , Kees Ursula R 
Published: April 2005

Abstract
Background
The use of microarray technology to assess gene expression levels is now widespread in biology. The validation of microarray results using independent mRNA quantitation techniques remains a desirable element of any microarray experiment. To facilitate the comparison of microarray expression data between laboratories it is essential that validation methodologies be critically examined. We have assessed the correlation between expression scores obtained for 48 human genes using oligonucleotide microarrays and the expression levels for the same genes measured by quantitative real-time RT-PCR (qRT-PCR).

Results
Correlations with qRT-PCR data were obtained using microarray data that were processed using robust multi-array analysis (RMA) and the MAS 5.0 algorithm. Our results indicate that when identical transcripts are targeted by the two methods, correlations between qRT-PCR and microarray data are generally strong (r = 0.89). However, we observed poor correlations between qRT-PCR and RMA or MAS 5.0 normalized microarray data for 13% or 16% of genes, respectively.

Conclusion
These results highlight the complementarity of oligonucleotide microarray and qRT-PCR technologies for validation of gene expression measurements, while emphasizing the continuing requirement for caution in interpreting gene expression data.
Structural and Epistemic Parameters in Communities of Practice
Authors: Thompson Mark 
Published: April 2005

If communities of practice (Lave and Wenger 1991) are best understood as fluid social relations, enacted among a self-selected group of participants, then are they best left alone, free from “interference” by organizational managers and policymakers? Or are there ways in which organizations can provide helpful support to such communities, without constraining the delicate dynamic by which they are sustained? This paper supports the latter position, arguing that organizations should sponsor the creation of certain loose organizational structures, around which it is hoped that communities of practice may then interact. However, some recent empirical research is presented suggesting that attempts to control group interaction by introducing too much structure are likely to result in the demise of the community itself. It is therefore proposed that there are lower and upper parameters for structural intervention in communities of practice. It is suggested that such communities also have epistemic parameters, where participants’ willingness to express their ideas as conceptual boundary objects around which others may engage and develop ideas is a minimum requirement, but where too much inward communicative focus is likely to result in gradual loss of meaning, with a negative effect on the community. In developing this position, this paper attempts to deepen our theoretical understanding of the interrelationship between organizational structure and the epistemic activity of members of communities of practice. Several practical implications of these insights are discussed for organizations wishing to cultivate and maintain communities of practice within their own working environments.
Characterization of active oxygen species under oxygen-alkali bleaching conditions
Authors: Yokoyama Tomoya , Matsumoto Yuji , Meshitsuka Gyosuke 
Published: April 2005

Abstract
The reactivities of active oxygen species toward a non-phenolic lignin model compound, 1-(3,4-dimethoxyphenyl)-1,2-ethanediol (veratryl glycol, VG), and a carbo-hydrate model compound, methyl β-D-glucopyranoside (MGP), were examined and compared under practical oxygen bleaching conditions. In this study, active oxygen species were generated in situ by subjecting a phenolic compound, 2,4,6-trimethylphenol, to oxygen oxidation to faithfully simulate practical oxygen bleaching. The results indicated that the time-dependent reaction selectivity of active oxygen species between VG and MGP, k
VG(t)/k
MGP(t), in the early stage of the reaction is 2.1 and 0.3–0.7 at initial pH values of 11.8 and 13.1, respectively. By comparing this value with the of hydroxyl radical obtained by Ek et al. [Holzforschung 43 (1989) 391] we conclude that the active oxygen species in the early stage of the reaction are hydroxyl radicals. The reaction selectivity at higher pH was much lower, which is explained by the fact that an oxyl anion radical, the conjugate base of the hydroxyl radical, predominantly abstracts hydrogen from aliphatic substructures. Chain-type reactions could be mainly responsible for degradation of the model compounds after the middle stage of the reaction. We suggest that the operation of chain-type reactions is not greatly dependent on the pH of the medium, but on the structure of the substrate.
Condensed tannins from steamed Acacia mearnsii bark
Authors: Duan Wengui , Ohara Seiji , Hashida Koh , Makino Rei 
Published: April 2005

Abstract
The optimum steaming conditions for extraction of condensed tannins from Acacia mearnsii bark were explored, after which characterization of proanthocyanidins from bark steamed under optimum conditions was carried out. The optimum conditions were as follows: steaming time, 30 min; steaming temperature, 140°C; and water volume, 75 ml. The total phenolics content obtained under these conditions amounted to 25.31%, which was much higher than the 21.70% obtained by conventional hot water extraction. Six proanthocyanidin dimers were isolated from the steamed bark. Analysis revealed them to be fisetinidol-(4β-8)-catechin, fisetinidol-(4α-8)-catechin, robinetinidol-(4β-8)-catechin, robinetinidol-(4α-8)-catechin, robinetinidol-(4β-8)-gallocatechin, and robinetinidol-(4α-8)-gallocatechin. Proanthocyanidin polymers were found to consist mainly of prorobinetinidin extender units, similar to those obtained from the same bark by conventional extraction with 70% acetone aqueous solution. However, nuclear magnetic resonance and gel permeation chromatography analyses suggested that during steaming the polymers undergo condensation reactions, as well as inversion of the configuration of interflavanoid bonds.