bluuebunny/crossref_metadata_2025 huggingface dataset:
The nature of citizenship education provision: an initial study
Authors: Leighton Ralph
Published: August 2004

While compulsory citizenship education has apparently been accepted and, in some quarters, regarded as overdue, in schools there has been little opportunity to discuss the meaning of ‘citizenship’. This article reports an initial study of four schools, with a focus on one of them. From this study it was evident that teachers and students have different views about what they are offering and being offered. Some implications of the spaces between these differences are aired in the conclusion of the article.
A Swedish cost-effectiveness analysis of community-based Chlamydia trachomatis PCR testing of postal urine specimens obtained at home
Authors: Novak Daniel P. , Lindholm Lars , Jonsson Monica , Karlsson Roger B.
Published: August 2004

Aims: A study was undertaken to assess the cost-effectiveness of identifying and treating asymptomatic carriers of Chlamydia trachomatis when using community-based testing of urine specimens obtained at home and mailed to a central laboratory. Methods: A total of 100 males and 100 females aged 20 - 24 living in Umeå were randomly sampled from the population registry. A societal cost-effective analysis was carried out, based on screening and medical care costs in Sweden. Results: With a participation rate of 55% (45% males and 65% females), the female screening became cost-saving as the C. trachomatis prevalence exceeded 5.1%, and the male screening became cost-saving with over 12.3% prevalence. Conclusion: Postal screening for C. trachomatis in an asymptomatic young population can be cost-effective only at prevalences higher than at present.
Humour seen from a public health perspective
Authors: Cernerud Lars , Olsson Henny
Published: August 2004

Humour is to be regarded as a salutogenic factor. As with other such factors there are reasons to believe that humour is a part of the individual's personality with the possibility of being strengthened by influences from the family, school, and workplace. The use of humour in population-based health promotive intervention strategies is a field lacking evidence-based knowledge.
Activities of daily living decrease similarly in hospital-treated patients with a hip fracture or a vertebral fracture: a one-year prospective study in 151 patients
Authors: Theander Eva , Jarnlo Gun-Britt , Ornstein Ewald , Karlsson Magnus K.
Published: August 2004

Aims: A hip fracture is commonly regarded as the most devastating fragility fracture, as regards both morbidity and mortality, while a vertebral fracture is usually regarded as having lower general morbidity. The purpose of this study was to investigate whether hospitalized patients with a hip or a vertebral fracture experience similar functional deterioration following the fracture as regards activity of daily living (ADL) and experienced quality of life (QOL). Methods: Eighty-seven women and 22 men, mean age 81 (range 66 - 96), with a hip fracture and 34 women and 8 men, mean age 81 (range 68 - 92), with a vertebral fracture were followed up for 12 months. ADL before fracture and at 4 and 12 months after the fracture were evaluated as well as QOL at 4 and 12 months after the fracture, by questionnaires. Results: A hip and a vertebral fracture in community dwellers within the same age range confers a similar decrease in ADL during the four months following the fracture. No restoration was seen in ADL or total QOL during the year following the fracture. Patients with a vertebral fracture had a lower QOL than patients with a hip fracture 4 and 12 months after the fracture. Conclusion: The need for external community assistance for patients with a vertebral fracture that forces them to have hospital treatment may be similar to the need following a hip fracture.
Case-mix adjustment and efficiency measurement
Authors: Björkgren Magnus A. , Fries Brant E. , Häkkinen Unto , Brommels Mats
Published: August 2004

Aims: The importance of using valid case-mix systems in long-term care is addressed by comparing the predictive power of different case-mix models, and by applying them in the calculation of technical efficiency scores of care units. Methods: To construct different case-mix models a statistical clustering technique (Automatic Interaction Detection) was used. Technical efficiency score were calculated using data envelopment analysis (DEA). Results: The Resource Utilization Groups (RUG-III/22) classification explained 39% of resident specific cost, compared with 16% for a functional dependency scale in the Finnish patient information system HILMO. Conclusion: When assessing the economic performance of long-term care units it is important to pay attention to the predictive validity of the case-mix measure to be used. The choice of case-mix measure significantly affected how units were rated in efficiency.
Social determinants for infant mortality in the Nordic countries, 1980 - 2001
Authors: Arntzen Annett , Andersen Anne Marie Nybo
Published: August 2004

Aim: Social equity in health is an important goal of public health policies in the Nordic countries. Infant mortality is often used as an indicator of the health of societies, and has decreased substantially in the Nordic welfare states over the past 20 years. To identify social patterns in infant mortality in this context the authors set out to review the existing epidemiological literature on associations between social indicators and infant mortality in Denmark, Finland, Norway, and Sweden during the period 1980 - 2000. Methods: Nordic epidemiological studies in the databases ISI Web of Science, PubMed, and OVID, published between 1980 and 2000 focusing on social indicators of infant, neonatal, and postneonatal mortality, were identified. The selected keywords on social indicators were: education, income, occupation, social factors, socioeconomic status, social position, and social class. Results: Social inequality in infant mortality was reported from Denmark, Finland, Norway, and Sweden, and it was found that these increased during the study period. Post-neonatal mortality showed a stronger association with social indicators than neonatal mortality. Some studies showed that neonatal mortality was associated with social indicators in a non-linear fashion, with high rates of mortality in both the lowest and highest social strata. The pattern differed, however, between countries with Finland and Sweden showing consistently less social inequalities than Denmark and Norway. While the increased inequality shown in most studies was an increase in relative risk, a single study from Denmark demonstrated an absolute increase in infant mortality among children born to less educated women. Conclusions: Social inequalities in infant mortality are observed in all four countries, irrespective of social indicators used in the studies. It is, however, difficult to draw inferences from the comparisons between countries, since different measures of social position and different inclusion criteria are used in the studies. Nordic collaborative analyses of social gradients in infant death are needed, taking advantage of the population-covering registers in longitudinal designs, to explore the mechanisms behind the social patterns in infant mortality.
Suicide trends in South Africa, 1968 - 90
Authors: Flisher Alan J. , Liang Holan , Laubscher Ria , Lombard Carl F.
Published: August 2004

Aims: A study was undertaken to investigate suicide rates and proportional mortality trends in South Africa from 1968 to 1990. Methods: Suicide rates per 100,000 population per year and suicide proportional mortality rates per year were calculated. The analyses were stratified by race, sex, and age group. Trends were interpreted using graphs depicting smoothed sex/race-specific suicide rates and proportional mortality rates over time. Regression models for suicide rates were fitted within specific age groups to test the effects of race, sex, and time. Further analysis was done within the specific age and race groups, if any interaction was found with time. Results: There were increases in suicide rate in the young (particularly for white males) and for whites aged 65 years and above (particularly for males). Conclusions: The finding that suicide among the young and elderly in South Africa is increasing suggests that preventive efforts are indicated, especially for white males. Trends for young South Africans mirror those in Europe and the USA, and attention to trends in these countries may predict future trends in youth suicide in South Africa.
Increase in Methicillin-Resistant Staphylococcus aureus Acquisition Rate and Change in Pathogen Pattern Associated with an Outbreak of Severe Acute Respiratory Syndrome
Authors: Yap Florence H. Y. , Gomersall Charles D. , Fung Kitty S. C. , Ho Pak-Leung , Ho Oi-Man , Lam Phillip K. N. , Lam Doris T. C. , Lyon Donald J. , Joynt Gavin M.
Published: August 2004

Background. An outbreak of severe acute respiratory syndrome (SARS) occurred in our 22-bed intensive care unit (ICU; Prince of Wales Hospital, Hong Kong, HKSAR, China) from 12 March to 31 May 2003, when only patients with SARS were admitted. This period was characterized by the upgrading of infection control precautions, which included the wearing of gloves and gowns all the time, an extensive use of steroids, and a change in antibiotic prescribing practices. The pattern of endemic pathogenic organisms, the rates of acquisition of methicillin-resistant Staphylococcus aureus (MRSA), and the rates of ventilator-associated pneumonia (VAP) were compared with those of the pre-SARS and post-SARS periods.

Methods. Data on pathogenic isolates were obtained from the microbiology department (Prince of Wales Hospital). Data on MRSA acquisition and VAP rates were collected prospectively. MRSA screening was performed for all ICU patients. A case of MRSA carriage was defined as an instance in which MRSA was recovered from any site in a patient, and cases were classified as imported or ICU-acquired if the first MRSA isolate was recovered within 72 h of ICU admission or after 72 h in the ICU, respectively.

Results. During the SARS period in the ICU, there was an increase in the rate of isolation of MRSA and Stenotrophomonas and Candida species but a disappearance of Pseudomonas and Klebsiella species. The MRSA acquisition rate was also increased: it was 3.53% (3.53 cases per 100 admissions) during the pre-SARS period, 25.30% during the SARS period, and 2.21% during the post-SARS period (P < .001). The VAP rate was high, at 36.5 episodes per 1000 ventilator-days, and 47% of episodes were caused by MRSA.

Conclusions. A SARS outbreak in the ICU led to changes in the pathogen pattern and the MRSA acquisition rate. The data suggest that MRSA cross-transmission may be increased if gloves and gowns are worn all the time.
Comparative analysis of methods for representing and searching for transcription factor binding sites
Authors: Osada Robert , Zaslavsky Elena , Singh Mona
Published: August 2004

Motivation: An important step in unravelling the transcriptional regulatory network of an organism is to identify, for each transcription factor, all of its DNA binding sites. Several approaches are commonly used in searching for a transcription factor's binding sites, including consensus sequences and position-specific scoring matrices. In addition, methods that compute the average number of nucleotide matches between a putative site and all known sites can be employed. Such basic approaches can all be naturally extended by incorporating pairwise nucleotide dependencies and per-position information content. In this paper, we evaluate the effectiveness of these basic approaches and their extensions in finding binding sites for a transcription factor of interest without erroneously identifying other genomic sequences.

Results: In cross-validation testing on a dataset of Escherichia coli transcription factors and their binding sites, we show that there are statistically significant differences in how well various methods identify transcription factor binding sites. The use of per-position information content improves the performance of all basic approaches. Furthermore, including local pairwise nucleotide dependencies within binding site models results in statistically significant performance improvements for approaches based on nucleotide matches. Based on our analysis, the best results when searching for DNA binding sites of a particular transcription factor are obtained by methods that incorporate both information content and local pairwise correlations.

Availability: The software is available at http://compbio.cs.princeton.edu/bindsites
limmaGUI: A graphical user interface for linear modeling of microarray data
Authors: Wettenhall James M. , Smyth Gordon K.
Published: August 2004

Summary:  limmaGUI is a graphical user interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of differential expression in complex experiments. limmaGUI provides an interface to the statistical methods of the limma package for R, and is itself implemented as an R package. The software provides point and click access to a range of methods for background correction, graphical display, normalization, and analysis of microarray data. Arbitrarily complex microarray experiments involving multiple RNA sources can be accomodated using linear models and contrasts. Empirical Bayes shrinkage of the gene-wise residual variances is provided to ensure stable results even when the number of arrays is small. Integrated support is provided for quantitative spot quality weights, control spots, within-array replicate spots and multiple testing. limmaGUI is available for most platforms on the which R runs including Windows, Mac and most flavors of Unix.

Availability:  http://bioinf.wehi.edu.au/limmaGUI
Highly specific prediction of phosphorylation sites in proteins
Authors: Koenig Matthias , Grabe Niels
Published: August 2004

Summary: The prediction of significant short functional protein sequences has inherent problems. In predicting phosphorylation sites, problems came from the shortness of phosphorylation sites, the difficulties in maintaining many different predefined models of binding sites, and the difficulties of obtaining highly sensitive predictions and of obtaining predictions with a constant sensitivity and specificity. The algorithm presented in this paper overcomes these problems.

The proposed algorithm PHOSITE is based on the case-based sequence analysis. This enables the prediction of phosphorylation sites with constant specificity and sensitivity. Furthermore, this method leads not only to the prediction of phosphorylation sites in general but also predicts the most probable type of kinase involved.

Availability: The tool PHOSITE implementing the presented method can be evaluated under the website http://www.phosite.com
GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
Authors: Boyle Elizabeth I. , Weng Shuai , Gollub Jeremy , Jin Heng , Botstein David , Cherry J. Michael , Sherlock Gavin
Published: August 2004

Summary: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script.

Availability: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/
Haploview: analysis and visualization of LD and haplotype maps
Authors: Barrett J. C. , Fry B. , Maller J. , Daly M. J.
Published: August 2004

Summary: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.

Availability:  http://www.broad.mit.edu/mpg/haploview/

Contact:  jcbarret@broad.mit.edu
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Authors: Samuelsson Jim , Dalevi Daniel , Levander Fredrik , Rögnvaldsson Thorsteinn
Published: August 2004

Summary: A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified.

Motivation: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public.

Results: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools.

Availability: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/

Supplementary information: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/staff/bioinf/
How many samples are needed to build a classifier: a general sequential approach
Authors: Fu Wenjiang J. , Dougherty Edward R. , Mallick Bani , Carroll Raymond J.
Published: August 2004

Motivation: The standard paradigm for a classifier design is to obtain a sample of feature-label pairs and then to apply a classification rule to derive a classifier from the sample data. Typically in laboratory situations the sample size is limited by cost, time or availability of sample material. Thus, an investigator may wish to consider a sequential approach in which there is a sufficient number of patients to train a classifier in order to make a sound decision for diagnosis while at the same time keeping the number of patients as small as possible to make the studies affordable.

Results: A sequential classification procedure is studied via the martingale central limit theorem. It updates the classification rule at each step and provides stopping criteria to ensure with a certain confidence that at stopping a future subject will have misclassification probability smaller than a predetermined threshold. Simulation studies and applications to microarray data analysis are provided. The procedure possesses several attractive properties: (1) it updates the classification rule sequentially and thus does not rely on distributions of primary measurements from other studies; (2) it assesses the stopping criteria at each sequential step and thus can substantially reduce cost via early stopping; and (3) it is not restricted to any particular classification rule and therefore applies to any parametric or non-parametric method, including feature selection or extraction.

Availability: R-code for the sequential stopping rule is available at http://stat.tamu.edu/~wfu/microarray/sequential/R-code.html

Contact:  wfu@stat.tamu.edu
University decentralization as regional policy: the Swedish
experiment
Authors: Andersson Roland , Quigley John M. , Wilhelmson Mats
Published: August 2004

During the past 15 years, Swedish higher education policy has emphasized the spatial decentralization of post-secondary education. We investigate the economic effects of this decentralization policy on productivity and output per worker. We rely upon a 14-year panel of output and employment for Sweden's 285 municipalities, together with data on the location of university-based researchers and students, to estimate the effects of exogenous changes in educational policy upon regional development. We find important and significant effects of this policy upon the average productivity of workers, suggesting that the economic effects of the decentralization on regional development are economically important. We also find evidence of highly significant, but extremely localized, externalities in productivity. This is consistent with recent findings (e.g., Rosenthal and Strange, 2003) on agglomeration in ‘knowledge industries.’
Mosaic hepatitis B virus core particles presenting the complete preS sequence of the viral envelope on their surface
Authors: Kazaks Andris , Borisova Galina , Cvetkova Svetlana , Kovalevska Larisa , Ose Velta , Sominskaya Irina , Pumpens Paul , Skrastina Dace , Dislers Andris
Published: August 2004

The sequence of the preS domain of the hepatitis B virus (HBV, genotype D) envelope was inserted into the major immunodominant region (MIR) of the C-terminally truncated HBV core (HBc) protein. In Escherichia coli, the HBc–preS fusion protein was partially soluble and did not produce particles. Co-expression of the wild-type HBc as a helper protein along with the fusion protein led to the formation of mosaic HBc particles that exhibited HBc, preS1 and preS2 antigenicity. Two alternative combinations of medium- and high-copy plasmids were used for co-expression of fusion and helper proteins, in an attempt to improve mosaic particle production. However, the preS fusion content of the particles remained the same in both expression combinations. In a third co-expression in which the modified HBc helper lacked aa 76–85 in the MIR, the incorporation level of HBc–preS fusion into the particles was noticeably lower. Purified chimeric particles were immunogenic in mice.
Risk of scrapie in British sheep of different prion protein genotype
Authors: Baylis M. , Chihota C. , Stevenson E. , Goldmann W. , Smith A. , Sivam K. , Tongue S. , Gravenor M. B.
Published: August 2004

There is a well-established association between sheep prion protein (PrP) genotype and the risk of death from scrapie. Certain genotypes are clearly associated with susceptibility to the disease and others to resistance. However, there have been no attempts to quantify the disease risk for all 15 PrP genotypes. Here, datasets of the PrP genotypes of nearly 14 000 British sheep and of more than 1500 confirmed scrapie cases were combined to yield an estimate of scrapie risk (reported cases per annum per million sheep of the genotype, or RCAM) for British sheep. The greatest scrapie risk by far, ranging from 225 to 545 RCAM, was for the VRQ-encoding genotypes ARQ/VRQ, ARH/VRQ and VRQ/VRQ. The next greatest risk (37 RCAM) was for the ARQ/ARQ genotype. The ARR/ARR genotype was the only numerically significant genotype for which no scrapie cases have been reported. The AHQ allele conferred resistance and the risk of scrapie in AHQ/VRQ sheep was very low (0·7 RCAM), although there was a higher and moderate risk for the AHQ homozygote (5 RCAM). The ARH allele appeared to confer susceptibility when encoded with VRQ, but possible resistance when encoded with other alleles. Scrapie risk varied with age: for VRQ/VRQ and ARH/VRQ the risk peaked at 2 years of age; that for ARQ/VRQ peaked at 3 years. There was some evidence that, following the lower risk at 4 and 5 years, a second rise occurred from about 6 years. Comparison with other published data indicated that the scrapie risk of certain PrP genotypes may differ between Great Britain and other countries.
Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity
Authors: Chen Yiping , Sharp Paul M. , Fowkes Mary , Kocher Olivier , Joseph Jeffrey T. , Koralnik Igor J.
Published: August 2004

To determine the variability of BK virus (BKV)in vivo, the sequences of nine full-length molecular clones from the striated muscle and heart DNA of a patient with BKV-associated capillary leak syndrome (BKVCAP), as well as three clones each from the urine of one human immunodeficiency virus type 2-positive (BKVHI) and one healthy control subject (BKVHC), were analysed. The regulatory region of all clones corresponded to the archetypal regulatory region usually found in urine isolates. Analysis of the predicted conformation of BKVCAPproteins did not suggest any structural differences on the surface of the viral particles compared with BKVHIand BKVHCclones. No amino acid changes common to most BKVCAPclones could be identified that have not already been reported in non-vasculotropic strains. However, the coding region of each clone had unique nucleotide substitutions, and intra-host variability was greater among BKVCAPclones, with a mean difference of 0·29 % per site compared with 0·16 % for BKVHIand 0·14 % for BKVHC. The clones from each strain formed monophyletic clades, suggesting a single source of infection for each subject. The most divergent BKVCAPclones differed at 0·55 % of sites, implying a rate of nucleotide substitution of approximately 5×10−5substitutions per site per year, which is two orders of magnitude faster than estimated for the other human polyomavirus, JC virus.
Enterovirus 68 is associated with respiratory illness and shares biological features with both the enteroviruses and the rhinoviruses
Authors: Oberste M. Steven , Maher Kaija , Schnurr David , Flemister Mary R. , Lovchik Judith C. , Peters Heather , Sessions Wendy , Kirk Carol , Chatterjee Nando , Fuller Susan , Hanauer J. Michael , Pallansch Mark A.
Published: August 2004

Enterovirus (EV) 68 was originally isolated in California in 1962 from four children with respiratory illness. Since that time, reports of EV68 isolation have been very uncommon. Between 1989 and 2003, 12 additional EV68 clinical isolates were identified and characterized, all of which were obtained from respiratory specimens of patients with respiratory tract illnesses. No EV68 isolates from enteric specimens have been identified from these same laboratories. These recent isolates, as well as the original California strains and human rhinovirus (HRV) 87 (recently shown to be an isolate of EV68 and distinct from the other human rhinoviruses), were compared by partial nucleotide sequencing in three genomic regions (partial sequencing of the 5′-non-translated region and 3D polymerase gene, and complete sequencing of the VP1 capsid gene). The EV68 isolates, including HRV87, were monophyletic in all three regions of the genome. EV68 isolates and HRV87 grew poorly at 37 °C relative to growth at 33 °C and their titres were reduced by incubation at pH 3·0, whereas the control enterovirus, echovirus 11, grew equally well at 33 and 37 °C and its titre was not affected by treatment at pH 3·0. Acid lability and a lower optimum growth temperature are characteristic features of the human rhinoviruses. It is concluded that EV68 is primarily an agent of respiratory disease and that it shares important biological and molecular properties with both the enteroviruses and the rhinoviruses.
Quantitative analysis of foot-and-mouth disease virus RNA loads in bovine tissues: implications for the site of viral persistence
Authors: Zhang Zhidong , Alexandersen Soren
Published: August 2004

To understand better the pathogenesis of foot-and-mouth disease (FMD), the levels of viral RNA in various bovine tissues during the acute and persistent stages of FMD virus (FMDV) infection were investigated by using quantitative RT-PCR. The viral RNA levels in the tissues examined had peaked by day 1 post-infection (p.i.) and were markedly different among the tissues examined. The epithelium collected from sites of lesion development, i.e. the interdigital area and coronary band on the feet, and the tongue, contained the highest level of viral RNA, indicating the predominant tissue sites of viral infection and amplification during the acute stage of infection. Clearance of viral RNA from most of the tissues occurred relatively rapidly and the rate of clearance was largely independent of the level of viral RNA. The viral RNA load in most of the tissues declined slower than in serum, in which viral clearance is rapid. Beyond 28 days p.i., a proportion of pharyngeal region tissues (soft palate, pharynx, tonsil and mandibular lymph node) from infected animals still contained a detectable level of viral RNA, while viral RNA in non-pharyngeal region tissues was generally only detectable for variable periods ranging from 4 to 14 days p.i. The presence of viral RNA in dorsal soft palate tissue had a good correlation with the presence of infectious virus in oesophageal-pharyngeal fluid (OP-fluid) samples, a finding indicative of the specific tissue sites of FMDV persistence.
GB virus B infection of the common marmoset (Callithrix jacchus) and associated liver pathology
Authors: Jacob James R. , Lin Kuei-Chin , Tennant Bud C. , Mansfield Keith G.
Published: August 2004

GB virus B (GBV-B) is a flavivirus that is related closely to hepatitis C virus (HCV) and induces an acute hepatitis when inoculated into several species of New World primates. Common marmosets (Callithrix jacchus) are a widely available, non-endangered primate species that is susceptible to GBV-B infection and develops a characteristic acute hepatitis. Here, animals were found to be susceptible to serially passaged serum and GBV-B transcripts. Hepatic pathology and peripheral viraemia could be quantified biochemically, immunophenotypically and morphologically, and persisted for periods of up to 6 months in some animals. Hepatitis was characterized by a marked influx of CD3+ CD8+ T lymphocytes and CD20+ B cells within the first 2 months of primary infection. The results of this study document the marmoset as another small, non-human primate species in which the pathogenesis of GBV-B can be studied and used as a surrogate model of HCV infection for investigation of pathogenesis and antiviral drug development.
Inhibition of human immunodeficiency virus type 1 replication by Z-100, an immunomodulator extracted from human-type tubercle bacilli, in macrophages
Authors: Emori Yutaka , Ikeda Tamako , Ohashi Takashi , Masuda Takao , Kurimoto Tadashi , Takei Mineo , Kannagi Mari
Published: August 2004

Z-100 is an arabinomannan extracted fromMycobacterium tuberculosisthat has various immunomodulatory activities, such as the induction of interleukin 12, interferon gamma (IFN-γ) andβ-chemokines. The effects of Z-100 on human immunodeficiency virus type 1 (HIV-1) replication in human monocyte-derived macrophages (MDMs) are investigated in this paper. In MDMs, Z-100 markedly suppressed the replication of not only macrophage-tropic (M-tropic) HIV-1 strain (HIV-1JR-CSF), but also HIV-1 pseudotypes that possessed amphotropic Moloney murine leukemia virus or vesicular stomatitis virus G envelopes. Z-100 was found to inhibit HIV-1 expression, even when added 24 h after infection. In addition, it substantially inhibited the expression of the pNL43lucΔenv vector (in which theenvgene is defective and thenefgene is replaced with the firefly luciferase gene) when this vector was transfected directly into MDMs. These findings suggest that Z-100 inhibits virus replication, mainly at HIV-1 transcription. However, Z-100 also downregulated expression of the cell surface receptors CD4 and CCR5 in MDMs, suggesting some inhibitory effect on HIV-1 entry. Further experiments revealed that Z-100 induced IFN-βproduction in these cells, resulting in induction of the 16-kDa CCAAT/enhancer binding protein (C/EBP)βtranscription factor that represses HIV-1 long terminal repeat transcription. These effects were alleviated by SB 203580, a specific inhibitor of p38 mitogen-activated protein kinases (MAPK), indicating that the p38 MAPK signalling pathway was involved in Z-100-induced repression of HIV-1 replication in MDMs. These findings suggest that Z-100 might be a useful immunomodulator for control of HIV-1 infection.
Macaques infected long-term with attenuated simian immunodeficiency virus (SIVmac) remain resistant to wild-type challenge, despite declining cytotoxic T lymphocyte responses to an immunodominant epitope
Authors: Sharpe Sally A. , Cope Alethea , Dowall Stuart , Berry Neil , Ham Claire , Heeney Jonathan L. , Hopkins Donna , Easterbrook Linda , Dennis Mike , Almond Neil , Cranage Martin
Published: August 2004

To further investigate mechanisms of protective immunity that are induced by live, attenuated simian immunodeficiency virus (SIV), three macaques were infected with SIVmacGX2, anef-disrupted molecular clone. In two of these animals, which expressed the MamuA*01 major histocompatibility complex class I allele, loss of functional activity against an SIV-Gag-encoded immunodominant cytotoxic T lymphocyte (CTL) epitope was observed following prolonged infection. Nonetheless, all three animals were resistant to challenge with an uncloned pool of wild-type SIVmac, whereas four naïve controls became infected. Tetramer staining revealed the rapid generation of CD8+T-cell responses againstgag- andtat-encoded immunodominant epitopes in MamuA*01+challenge controls. The dynamics of these T-cell responses to the wild-type virus were similar to those observed following primary infection of the vaccine group with attenuated virus. In contrast, neither tetramer staining nor gamma interferon ELISpot assay revealed an immediate, systemic, anamnestic response in the wild-type-challenged, attenuated SIV-infected animals. Functional CTL capacity had not been lost in this group, as lytic activity was still evident 17 weeks after challenge. Both attenuated and wild-type viruses induced a disseminated CD8+T-cell response, which was of a higher magnitude in lymphoid tissues than in the periphery. These results suggest that, at least as measured in the periphery, protection against wild-type infection that is induced by live, attenuated SIV is not dependent on a rechallenge-driven expansion of immunodominant epitope-specific CD8+T cells and, therefore, pre-existing activity may be sufficient to prevent superinfection.
Expression of hepatitis C virus proteins in epithelial intestinal cells in vivo
Authors: Deforges Séverine , Evlashev Alexey , Perret Magali , Sodoyer Mireille , Pouzol Stéphane , Scoazec Jean-Yves , Bonnaud Bertrand , Diaz Olivier , Paranhos-Baccalà Glaucia , Lotteau Vincent , André Patrice
Published: August 2004

Previous work on hepatitis C virus (HCV) led to the discovery of a new form of virus particle associating virus and lipoprotein elements. These hybrid particles (LVP for lipo-viro-particles) are enriched in triglycerides and contain at least apolipoprotein B (apoB), HCV RNA and core protein. These findings suggest that LVP synthesis could occur in liver and intestine, the two main organs specialized in the production of apoB-containing lipoprotein. To identify the site of LVP production, the genetic diversity and phylogenetic relationship of HCV quasispecies from purified LVP, whole serum and liver biopsies from chronically infected patients were studied. HCV quasispecies from LVP and liver differed significantly, suggesting that LVP were not predominantly synthesized in the liver but might also originate in the intestine. The authors therefore searched for the presence of HCV in the small intestine. Paraffin-embedded intestinal biopsies from 10 chronically HCV-infected patients and from 12 HCV RNA-negative controls (10 anti-HCV antibody-negative and two anti-HCV antibody-positive patients) were tested for HCV protein expression. HCV NS3 and NS5A proteins were stained in small intestine epithelial cells in four of the 10 chronically infected patients, and not in controls. Cells expressing HCV proteins were apoB-producing enterocytes but not mucus-secreting cells. These data indicate that the small intestine can be infected by HCV, and identify this organ as a potential reservoir and replication site. This further emphasizes the interaction between lipoprotein metabolism and HCV, and offers new insights into hepatitis C infection and pathophysiology.
Detection of antibodies against a human papillomavirus (HPV) type 16 peptide that differentiate high-risk from low-risk HPV-associated low-grade squamous intraepithelial lesions
Authors: Rocha-Zavaleta Leticia , Ambrosio Juana P. , Mora-Garcia Maria de Lourdes , Cruz-Talonia Fernando , Hernandez-Montes Jorge , Weiss-Steider Benny , Ortiz-Navarrete Vianney , Monroy-Garcia Alberto
Published: August 2004

A nonapeptide (16L1) was derived from the human papillomavirus type 16 (HPV-16) major capsid protein and tested for detection of potential cross-reactive serum IgG and cervical IgA antibodies in low- and high-risk HPV-associated low-grade squamous intraepithelial lesions (LSIL) and cervical cancer patients by ELISA. The IgG response was similar in women with low-risk HPV-associated LSIL and controls (P=0·1). In contrast, more than 90 % of patients with high-risk HPV-associated LSIL were seropositive. Although tumours from cancer patients were all positive for the presence of high-risk HPV DNA, the level of seropositivity decreased significantly in this group (P<0·0001). Cervical IgA antibodies were also detected in a significantly high proportion of women with high-risk HPV-associated LSIL compared with controls. However, the proportion of IgA-positive patients was lower than the proportion of IgG seropositives. In conclusion, the 16L1 peptide appears to be a high-risk type-common epitope that induces cross-reactive antibodies in high-risk, but not low-risk, HPV-associated LSIL patients, allowing differentiation of high- and low-risk infected women at this stage of infection.
Efficient internalization into low-passage glioma cell lines using adenoviruses other than type 5: an approach for improvement of gene delivery to brain tumours
Authors: Skog Johan , Edlund Karin , Widegren Bengt , Salford Leif G. , Wadell Göran , Mei Ya-Fang
Published: August 2004

There is a need for improvement of the commonly used adenovirus vectors based on serotype 5. This study was performed on three adenovirus serotypes with a CAR-binding motif (Ad4p, Ad5p and Ad17p) and three non-CAR-binding serotypes (Ad11p, Ad16p and Ad21p). The capacity of these alternative adenovirus vector candidates to deliver DNA into low-passage glioma cell lines from seven different donors was evaluated. The non-CAR-binding serotype Ad16p was the most efficient serotype with regard to import of its DNA, as well as initiation of hexon protein expression. Ad16p established hexon expression in 60–80 % of the cell population in gliomas from all donors tested. The other non-CAR-binding serotypes, Ad11p and Ad21p, showed hexon expression in 25–60 and 40–80 % of cells, respectively. The corresponding figure for the best CAR-binding serotype, Ad5p, was only 25–65 %, indicating greater variability between cells from different donors than serotype Ad16p had. The other CAR-binding serotypes, Ad4p and Ad17p, were refractory to some of the gliomas, giving a maximum of only 45 and 40 % hexon expression, respectively, in the most permissive cells. Interestingly, the transduction capacity of the CAR-binding serotypes was not correlated to the level of CAR expression on the cells.
Transcriptional downregulation of DC-SIGN in human herpesvirus 6-infected dendritic cells
Authors: Niiya Hironari , Azuma Taichi , Jin Lei , Uchida Naoyuki , Inoue Atsushi , Hasegawa Hitoshi , Fujita Shigeru , Tohyama Mikiko , Hashimoto Koji , Yasukawa Masaki
Published: August 2004

DC-SIGN expressed on dendritic cells (DCs) efficiently binds and transmits various pathogens, including human immunodeficiency virus, to lymphoid tissues and permissive cells. Consequently, alteration of DC-SIGN expression may affect susceptibility and resistance to pathogens. The present study shows that infection with human herpesvirus 6 (HHV-6) induces downregulation of DC-SIGN expression on immature DCs. Expression levels of DC-SIGN mRNA and intracellular protein appeared to decrease following infection with HHV-6, indicating that downregulation of surface DC-SIGN occurs at the transcriptional level. Downregulation of DC-SIGN was not induced by inoculation of UV-inactivated HHV-6 or culture supernatant of HHV-6-infected DCs, indicating that replication of HHV-6 in DCs is required for downregulation of DC-SIGN. The present study demonstrates for the first time that expression of DC-SIGN is altered at the transcriptional level by virus infection.
Downmodulation of CD3ε expression in CD8α + β − T cells of feline immunodeficiency virus-infected cats
Authors: Nishimura Yorihiro , Shimojima Masayuki , Sato Eiji , Izumiya Yoshihiro , Tohya Yukinobu , Mikami Takeshi , Miyazawa Takayuki
Published: August 2004

Feline immunodeficiency virus (FIV) infection in cats is associated with an increase of feline CD (fCD)8α+β−and fCD8α+βlowcells in peripheral blood. To investigate these cells in more detail, an anti-fCD3εmAb, termed NZM1, was generated, which recognizes the extracellular epitope of the fCD3εmolecule. The anti-fCD3εmAb proved to be more suitable for identifying feline T cells than the anti-fCD5 one, which has been used as a pan-T-cell reagent in cats, because of the presence of fCD5+fCD3ε−cells among lymphocytes. Although the fCD8α+β−and fCD8α+βlowcells in the FIV-infected cats expressed fCD3ε, a subset of fCD8α+β−cells expressed fCD3εantigen at a lower level than the T cells whose phenotype was fCD4+, or fCD8α+βlow. The lower expression of fCD3εmay be associated with the immune status of fCD8α+β−T cells.
Sequence and secondary structure requirements in a highly conserved element for foot-and-mouth disease virus internal ribosome entry site activity and eIF4G binding
Authors: Bassili Gergis , Tzima Eleni , Song Yutong , Saleh Lanja , Ochs Kerstin , Niepmann Michael
Published: August 2004

Foot-and-mouth disease virus (FMDV) and other picornaviruses initiate translation of their positive-strand RNA genomes at the highly structured internal ribosome entry site (IRES), which mediates ribosome recruitment to an internal site of the virus RNA. This process is facilitated by eukaryotic translation initiation factors (eIFs), such as eIF4G and eIF4B. In the eIF4G-binding site, a characteristic, discontinuous sequence element is highly conserved within the cardio- and aphthovirus subgroup (including FMDV) of the picornaviruses. This conserved element was mutated in order to investigate its primary sequence and secondary structure requirements for IRES function. Both binding of eIF4G to the IRES and IRES-directed translation are seriously impaired by mutations in two unpaired dinucleotide stretches that are exposed from the double-stranded (ds)RNA. In the base-paired regions of the conserved element, maintenance of the double-stranded secondary structure is essential, whilst in some cases, the primary sequence within the dsRNA regions is also important for IRES function. Extra eIF4F added to the translation reaction does not restore full IRES activity or eIF4G binding, indicating that disturbances in the structure of this conserved element cannot be overcome by increased initiation factor concentrations.
Fusion PCR generated Japanese encephalitis virus/dengue 4 virus chimera exhibits lack of neuroinvasiveness, attenuated neurovirulence, and a dual-flavi immune response in mice
Authors: Mathenge Edward Gitau Matumbi , Parquet Maria del Carmen , Funakoshi Yasutomo , Houhara Seiji , Wong Pooi Fong , Ichinose Akitoyo , Hasebe Futoshi , Inoue Shingo , Morita Kouichi
Published: August 2004

The first flavivirus chimera encoding dengue 4 virus (D4) PrM and E structural proteins in a Japanese encephalitis virus (JEV) backbone was successfully generated using the long-PCR based cDNA-fragment stitching (LPCRcFS) technique, demonstrating the technique's applicability for rapid preparation of flavivirus chimeras. The JEV/D4 chimera multiplied at levels equal to JEV and D4 in the mosquito cell line C6/36, while in a mouse neuronal cell line (N2a) JEV replicated efficiently, but JEV/D4 and D4 did not. In mouse challenge experiments, JEV/D4 showed a lack of neuroinvasiveness similar to D4 when inoculated intraperitoneally, but demonstrated attenuated neurovirulence (LD50=3·17×104 f.f.u.) when inoculated intracranially. It was also noted that mice receiving intraperitoneal challenge with JEV/D4 possessed D4-specific neutralization antibody and in addition clearly showed resistance to JEV intraperitoneal challenge (at 100×LD50). This suggests that immunity to anti-JEV non-structural protein(s) offers protection against JEV infectionin vivo. Dengue secondary infection was also simulated by challenging mice pre-immunized with dengue 2 virus, with D4 or JEV/D4. Mice showed higher secondary antibody response to challenge with JEV/D4 than to D4, at 210 000 and 37 000 averaged ELISA units, respectively. Taken together, aside from demonstrating the LPCRcFS technique, it could be concluded that the PrM and E proteins are the major determinant of neuroinvasiveness for JEV. It is also expected that the JEV/D4 chimera with its pathogenicity in mice and atypical immune profile, could have applications in dengue prophylactic research,in vivoefficacy assessment of dengue vaccines and development of animal research on models of dengue secondary infection.
Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus
Authors: Tan Zhongyang , Wada Yasuhiko , Chen Jishuang , Ohshima Kazusato
Published: August 2004

A recombination map of the genome ofTurnip mosaic virus(TuMV) was assembled using data from 19 complete genomic sequences, previously reported, and a composite sample of three regions of the genome, one-third in total, of a representative Asia-wide collection of 70 isolates. Thus, a total of 89 isolates of worldwide origin was analysed for recombinants. Eighteen recombination sites were found spaced throughout the 5′ two-thirds of the genome, but there were only two in the 3′ one-third; thus, 24 and 35 % of the P1 and NIa-VPg gene sequences examined were recombinants, whereas only 1 % of the corresponding NIa-Pro and CP gene sequences were recombinants. Recombinants with parents from the same or from different lineages were found, and some recombination sites characterized particular lineages. Most of the strain BR recombinants belonged to the Asian-BR group, as defined previously, and it was concluded that this lineage resulted from a recent migration, whereas many of the strain B recombinants from Asia fell into the world-B group. Again, a large proportion of isolates in this group were recombinants. Some recombination sites were found only in particular lineages, and hence seemed more likely to be the surviving progeny from single recombinational events, rather than the progeny of multiple events occurring at recombination hotspots. It seems that the presence of recombination sites, as well as sequence similarities, may be used to trace the migration and evolution of TuMV.