bluuebunny/crossref_metadata_2025 huggingface dataset:
Genotyping of Porcine Endogenous Retroviruses from a Family of Miniature Swine
Authors: Quinn Gary , Wood James , Suling Kristen , Arn Scott , Sachs David H. , Schuurman Henk-Jan , Patience Clive
Published: December 2003

The identification of animals in an inbred miniature swine herd that consistently fail to produce replication- competent humantropic porcine endogenous retrovirus (PERV) has prompted studies on the biology of PERV in transmitter and nontransmitter animals. We analyzed PERV RNA transcript profiles in a family of inbred miniature swine (SLA
d/d
haplotype) in which individual members differed in their capacity to generate humantropic and ecotropic (i.e., pigtropic) virus. We identified unique
Hae
III and
Hpa
II
gag
restriction fragment length polymorphism (RFLP) profiles resulting from single nucleotide polymorphisms in blood cells; these were found only in animals that produced humantropic PERV. These
Hae
III and
Hpa
II
gag
RFLP profiles proved to be components of humantropic PERV as they were transmitted to 293 human target cells in vitro. The humantropic
Hae
III and
Hpa
II
gag
RFLP genotypes in the family of study were not present in other miniature swine in the herd that produced humantropic PERV, indicating that these RFLP profiles relate specifically to this family's lineage.
Cholesterol Removal by Methyl-β-Cyclodextrin Inhibits Poliovirus Entry
Authors: Danthi Pranav , Chow Marie
Published: December 2003

Upon binding to the poliovirus receptor (PVR), the poliovirus 160S particles undergo a conformational transition to generate 135S particles, which are believed to be intermediates in the virus entry process. The 135S particles interact with host cell membranes through exposure of the N termini of VP1 and the myristylated VP4 protein, and successful cytoplasmic delivery of the genomic RNA requires the interaction of these domains with cellular membranes whose identity is unknown. Because detergent-insoluble microdomains (DIMs) in the plasma membrane have been shown to be important in the entry of other picornaviruses, it was of interest to determine if poliovirus similarly required DIMs during virus entry. We show here that methyl-β-cyclodextrin (MβCD), which disrupts DIMs by depleting cells of cholesterol, inhibits virus infection and that this inhibition was partially reversed by partially restoring cholesterol levels in cells, suggesting that MβCD inhibition of virus infection was mediated by removal of cellular cholesterol. However, fractionation of cellular membranes into DIMs and detergent-soluble membrane fractions showed that both PVR and poliovirus capsid proteins localize not to DIMs but to detergent-soluble membrane fractions during entry into the cells, and their localization was unaffected by treatment with MβCD. We further demonstrate that treatment with MβCD inhibits RNA delivery after formation of the 135S particles. These data indicate that the cholesterol status of the cell is important during the process of genome delivery and that these entry pathways are distinct from those requiring DIM integrity.
The Genome of Canarypox Virus
Authors: Tulman E. R. , Afonso C. L. , Lu Z. , Zsak L. , Kutish G. F. , Rock D. L.
Published: December 2003

Here we present the genomic sequence, with analysis, of a canarypox virus (CNPV). The 365-kbp CNPV genome contains 328 potential genes in a central region and in 6.5-kbp inverted terminal repeats. Comparison with the previously characterized fowlpox virus (FWPV) genome revealed avipoxvirus-specific genomic features, including large genomic rearrangements relative to other chordopoxviruses and novel cellular homologues and gene families. CNPV also contains many genomic differences with FWPV, including over 75 kbp of additional sequence, 39 genes lacking FWPV homologues, and an average of 47% amino acid divergence between homologues. Differences occur primarily in terminal and, notably, localized internal genomic regions and suggest significant genomic diversity among avipoxviruses. Divergent regions contain gene families, which overall comprise over 49% of the CNPV genome and include genes encoding 51 proteins containing ankyrin repeats, 26 N1R/p28-like proteins, and potential immunomodulatory proteins, including those similar to transforming growth factor β and β-nerve growth factor. CNPV genes lacking homologues in FWPV encode proteins similar to ubiquitin, interleukin-10-like proteins, tumor necrosis factor receptor, PIR1 RNA phosphatase, thioredoxin binding protein, MyD116 domain proteins, circovirus Rep proteins, and the nucleotide metabolism proteins thymidylate kinase and ribonucleotide reductase small subunit. These data reveal genomic differences likely affecting differences in avipoxvirus virulence and host range, and they will likely be useful for the design of improved vaccine vectors.
EBNA3C Coactivation with EBNA2 Requires a SUMO Homology Domain
Authors: Rosendorff Adam , Illanes Diego , David Gregory , Lin Jeffrey , Kieff Elliott , Johannsen Eric
Published: December 2003

Epstein-Barr virus (EBV) nuclear antigen 3C (EBNA3C) is critical for EBV immortalization of infected B lymphocytes and can coactivate the EBV LMP1 promoter with EBNA2. EBNA3C amino acids 365 to 545 are necessary and sufficient for coactivation and are required for SUMO-1 and SUMO-3 interaction. We found that EBNA3C but not EBNA3CΔ343-545 colocalized with SUMO-1 in nuclear bodies and was modified by SUMO-2, SUMO-3, and SUMO-1. EBNA3C amino acids 545 to 628 and amino acids 30 to 365 were also required for EBNA3C sumolation and nuclear body localization but were dispensable for coactivation, indicating that EBNA3C sumolation is not required for coactivation. Furthermore, EBNA3C amino acids 476 to 992 potently coactivated with EBNA2 but EBNA3C amino acids 516 to 922 lacked activity, indicating that amino acids 476 to 515 are critical for coactivation. EBNA3C amino acids 476 to 515 include DDDVIEV
507-513
, which are similar to SUMO-1 EEDVIEV
84-90
. EBNA3C m1 and m2 point mutations, DDD
507-509
mutated to AAA and DVIEVID
509-513
mutated to AVIAVIA, respectively, diminished SUMO-1 and SUMO-3 interaction in directed yeast two-hybrid and glutathione
S
-transferase pulldown assays. Furthermore, EBNA3C m1 and m2 did not coactivate the LMP1 promoter with EBNA2. Overexpression of wild-type SUMO-1, SUMO-3, and the SUMO-conjugating enzyme UBC9 coactivated the LMP1 promoter with EBNA2. Since EBNA2 activation is dependent on p300/CBP, the possible effect of EBNA3C on p300-mediated transcription was assayed. EBNA3C potentiated transcription of p300 fused to a heterologous DNA binding domain, whereas EBNA3C m1 and m2 did not. All of these data are consistent with a model in which EBNA3C upregulates EBNA2-mediated gene activation by binding to a sumolated repressor and inhibiting repressive effects on p300/CBP and other transcription factor(s) at EBNA2-regulated promoters.
An External Loop Region of Domain III of Dengue Virus Type 2 Envelope Protein Is Involved in Serotype-Specific Binding to Mosquito but Not Mammalian Cells
Authors: Hung Jan-Jong , Hsieh Meng-Ti , Young Ming-Jer , Kao Chuan-Liang , King Chwan-Chuen , Chang Wen
Published: December 2003

Dengue virus (DV) is a flavivirus and infects mammalian cells through mosquito vectors. This study investigates the roles of domain III of DV type 2 envelope protein (EIII) in DV binding to the host cell. Recombinant EIII interferes with DV infection to BHK21 and C6/36 cells by blocking dengue virion adsorption to these cells. Inhibition of EIII on BHK21 cells was broad with no serotype specificity; however, inhibition of EIII on C6/36 cells was relatively serotype specific. Soluble heparin completely blocks binding of EIII to BHK21 cells, suggesting that domain III binds mainly to cell surface heparan sulfates. This suggestion is supported by the observation that EIII binds very weakly to gro2C and sog9 mutant mammalian cell lines that lack heparan sulfate. In contrast, heparin does not block binding of EIII to mosquito cells. Furthermore, a synthetic peptide that includes amino acids (aa) 380 to 389 of EIII, IGVEPGQLKL, inhibits binding of EIII to C6/36 but not BHK21 cells. This peptide corresponds to a lateral loop region on domain III of E protein, indicating a possible role of this loop in binding to mosquito cells. In summary, these results suggest that EIII plays an important role in binding of DV type 2 to host cells. In addition, EIII interacts with heparan sulfates when binding to BHK21 cells, and a loop region containing aa 380 to 389 of EIII may participate in DV type 2 binding to C6/36 cells.
Herpes Simplex Virus Type 1 Primary Envelopment: UL34 Protein Modification and the US3-UL34 Catalytic Relationship
Authors: Ryckman Brent J. , Roller Richard J.
Published: December 2003

The herpes simplex virus type 1 (HSV-1) US3 kinase is likely important for primary envelopment of progeny nucleocapsids since it localizes to the nuclear envelope of infected cells and largely determines the phosphorylation state and localization of the necessary primary envelopment factor, the UL34 protein. In HEp-2 cells, the production of infectious US3 null progeny is delayed and decreased relative to that of the parental strain, HSV-1(F). Furthermore, the US3 kinase affects the morphology of primary envelopment such that in its absence, UL34 protein-containing enveloped virions accumulate within membrane-bound vesicles. These vesicles are most often found along the interior periphery of the nucleus and may be derived from the inner nuclear membrane. Since the US3 and UL34 proteins comprise a kinase-substrate pair, a reasonable hypothesis is that the US3 kinase influences these replication parameters by direct phosphorylation of the UL34 protein. For this report, recombinant viruses were constructed to determine the significance of UL34 protein phosphorylation and US3 catalytic activity on UL34 protein localization, single-step growth, and envelopment morphology in both HEp-2 and Vero cells. The data presented suggest that the significance of UL34 phosphorylation is cell type dependent and that efficient viral morphogenesis requires US3-mediated phosphorylation of an infected cell protein other than UL34.
Structural and Functional Analysis of Human Cytomegalovirus US3 Protein
Authors: Misaghi Shahram , Sun Zhen-Yu J. , Stern Patrick , Gaudet Rachelle , Wagner Gerhard , Ploegh Hidde
Published: December 2003

Human cytomegalovirus (HCMV) unique short region 3 (US3) protein, a type I membrane protein, prevents maturation of class I major histocompatibility complex (MHC) molecules by retaining them in the endoplasmic reticulum (ER) and thus helps inhibit antigen presentation to cytotoxic T cells. US3 molecules bind to class I MHC molecules in a transient fashion but retain them very efficiently in the ER nonetheless. The US3 luminal domain is responsible for ER retention of US3 itself, while both the US3 luminal and transmembrane domains are necessary for retaining class I MHC in the ER. We have expressed the luminal domain of US3 molecule inEscherichia coliand analyzed its secondary structure by using nuclear magnetic resonance. We then predicted the US3 tertiary structure by modeling it based on the US2 structure. Unlike the luminal domain of US2, the US3 luminal domain does not obviously interact with class I MHC molecules. The luminal domain of US3 dynamically oligomerizes in vitro and full-length US3 molecules associate with each other in vivo. We present a model depicting how dynamic oligomerization of US3 may enhance its ability to retain class I molecules within the ER.
Identification and Characterization of Novel, Naturally Processed Measles Virus Class II HLA-DRB1 Peptides
Authors: Ovsyannikova Inna G. , Johnson Kenneth L. , Muddiman David C. , Vierkant Robert A. , Poland Gregory A.
Published: December 2003

Previously, we identified a naturally processed and presented measles virus (MV) 19-amino-acid peptide, ASDVETAEGGEIHELLRLQ (MV-P), derived from the phosphoprotein and eluted from the human leukocyte antigen (HLA) class II molecule by using mass spectrometry. We report here the identification of a 14-amino-acid peptide, SAGKVSSTLASELG, derived from the MV nucleoprotein (MV-N) bound to HLA-DRB1*0301. Peripheral blood mononuclear cells (PBMC) from 281 previously vaccinated measles-mumps-rubella II (MMR-II) subjects (HLA discordant) were studied for peptide recognition by T cells. Significant gamma interferon (IFN-γ) responses to MV-P and MV-N peptides were observed in 55.9 and 15.3% of subjects, respectively. MV-P- and MV-N-specific interleukin-4 (IL-4) responses were detected in 19.2 and 23.1%, respectively, of PBMC samples. Peptide-specific cytokine responses and HLA-DRB1 allele associations revealed that, for the MV-P peptide, the allele with the strongest association with both IFN-γ (P= 0.02) and IL-4 (P= 0.03) secretion was DRB1*0301. For MV-N, the allele with the strongest association with IFN-γ secretion was DRB1*1501 (P= 0.04), and the alleles with the strongest associations with IL-4 secretion were DRB1*1103 and DRB1*1303 (P= 0.01). These results indicate that HLA class II MV proteins can be processed, presented, and identified, and the ability to generate cell-mediated immune responses can be demonstrated. This information is promising for new vaccine design strategies with peptide-based vaccines.
The Rep Protein of Adeno-Associated Virus Type 2 Interacts with Single-Stranded DNA-Binding Proteins That Enhance Viral Replication
Authors: Stracker Travis H. , Cassell Geoffrey D. , Ward Peter , Loo Yueh-Ming , van Breukelen Bas , Carrington-Lawrence Stacy D. , Hamatake Robert K. , van der Vliet Peter C. , Weller Sandra K. , Melendy Thomas , Weitzman Matthew D.
Published: December 2003

Adeno-associated virus (AAV) type 2 is a human parvovirus whose replication is dependent upon cellular proteins as well as functions supplied by helper viruses. The minimal herpes simplex virus type 1 (HSV-1) proteins that support AAV replication in cell culture are the helicase-primase complex of UL5, UL8, and UL52, together with the UL29 gene product ICP8. We show that AAV and HSV-1 replication proteins colocalize at discrete intranuclear sites. Transfections with mutant genes demonstrate that enzymatic functions of the helicase-primase are not essential. The ICP8 protein alone enhances AAV replication in an in vitro assay. We also show localization of the cellular replication protein A (RPA) at AAV centers under a variety of conditions that support replication. In vitro assays demonstrate that the AAV Rep68 and Rep78 proteins interact with the single-stranded DNA-binding proteins (ssDBPs) of Ad (Ad-DBP), HSV-1 (ICP8), and the cell (RPA) and that these proteins enhance binding and nicking of Rep proteins at the origin. These results highlight the importance of intranuclear localization and suggest that Rep interaction with multiple ssDBPs allows AAV to replicate under a diverse set of conditions.
Cultured Peripheral Neuroglial Cells Are Highly Permissive to Sheep Prion Infection
Authors: Archer Fabienne , Bachelin Corinne , Andreoletti Olivier , Besnard Nathalie , Perrot Gregory , Langevin Christelle , Le Dur Annick , Vilette Didier , Baron-Van Evercooren Anne , Vilotte Jean-Luc , Laude Hubert
Published: December 2003

Transmissible spongiform encephalopathies arise as a consequence of infection of the central nervous system (CNS) by prions. Spreading of the infectious agent through the peripheral nervous system (PNS) may represent a crucial step toward CNS neuroinvasion, but the modalities of this process have yet to be clarified. Here we provide further evidence that PNS glial cells are likely targets for infection by prions. Glial cell clones originating from dorsal root ganglia of transgenic mice expressing ovine PrP (tgOv) and simian virus 40 T antigen were found to be readily infectible by sheep scrapie agent. This led us to establish two stable cell lines that exhibited features of Schwann cells. These cells were shown to sustain an efficient and stable replication of sheep prion based on the high level of accumulation of abnormal PrP and infectivity in exposed cultures. We also provide evidence for abnormal PrP deposition in peripheral neuroglial cells from scrapie-infected tgOv mice and sheep. These findings have potential implications in terms of designing new cell systems permissive to prions and of peripheral pathobiology of prion infections.
Chromosome-Protein Interactions in Polyomavirus Virions
Authors: Carbone Mariarosaria , Ascione Giuseppe , Chichiarelli Silvia , Garcia Marie-Isabelle , Eufemi Margherita , Amati Paolo
Published: December 2003

In this work, we sought to determine whether the components of the murine polyomavirus capsid establish specific interactions with the minichromosome encapsidated into the mature viral particles by using the
cis
-diamminedichloroplatinum(II) cross-linking reagent. Our data indicated that VP1, but not minor capsid proteins, interacts with the viral genome in vivo. In addition, semiquantitative PCR assays performed on cross-linked DNA complexes revealed that VP1 binds to all regions of the viral genome but significantly more to the regulatory region. The implications of such an interaction for viral infectivity are discussed.
Failure of Thymidine Kinase-Negative Herpes Simplex Virus To Reactivate from Latency following Efficient Establishment
Authors: Chen Shih-Heng , Pearson Angela , Coen Donald M. , Chen Shun-Hua
Published: December 2003

Thymidine kinase-negative mutants of herpes simplex virus did not reactivate from latency in mouse trigeminal ganglia, even when their latent viral loads were comparable to those that permitted reactivation by wild-type virus. Thus, reduced establishment of latency does not suffice to account for the failure to reactivate.
Tetracycline-Inducible Packaging Cell Line for Production of Flavivirus Replicon Particles
Authors: Harvey Tracey J. , Liu Wen Jun , Wang Xiang Ju , Linedale Richard , Jacobs Michael , Davidson Andrew , Le Thuy T. T. , Anraku Itaru , Suhrbier Andreas , Shi Pei-Yong , Khromykh Alexander A.
Published: December 2003

We have previously developed replicon vectors derived from the Australian flavivirus Kunjin that have a unique noncytopathic nature and have been shown to direct prolonged high-level expression of encoded heterologous genes in vitro and in vivo and to induce strong and long-lasting immune responses to encoded immunogens in mice. To facilitate further applications of these vectors in the form of virus-like particles (VLPs), we have now generated a stable BHK packaging cell line, tetKUNCprME, carrying a Kunjin structural gene cassette under the control of a tetracycline-inducible promoter. Withdrawal of tetracycline from the medium resulted in production of Kunjin structural proteins that were capable of packaging transfected and self-amplified Kunjin replicon RNA into the secreted VLPs at titers of up to 1.6 × 10
9
VLPs per ml. Furthermore, secreted KUN replicon VLPs from tetKUNCprME cells could be harvested continuously for as long as 10 days after RNA transfection, producing a total yield of more than 10
10
VLPs per 10
6
transfected cells. Passaging of VLPs on Vero cells or intracerebral injection into 2- to 4-day-old suckling mice illustrated the complete absence of any infectious Kunjin virus. tetKUNCprME cells were also capable of packaging replicon RNA from closely and distantly related flaviviruses, West Nile virus and dengue virus type 2, respectively. The utility of high-titer KUN replicon VLPs was demonstrated by showing increasing CD8
+
-T-cell responses to encoded foreign protein with increasing doses of KUN VLPs. A single dose of 2.5 × 10
7
VLPs carrying the human respiratory syncytial virus M2 gene induced 1,400 CD8 T cells per 10
6
splenocytes in an ex vivo gamma interferon enzyme-linked immunospot assay. The packaging cell line thus represents a significant advance in the development of the noncytopathic Kunjin virus replicon-based gene expression system and may be widely applicable to the basic studies of flavivirus RNA packaging and virus assembly as well as to the development of gene expression systems based on replicons from different flaviviruses.
Rapid Genetic Engineering of Human Cytomegalovirus by Using a Lambda Phage Linear Recombination System: Demonstration that pp28 (UL99) Is Essential for Production of Infectious Virus
Authors: Britt William J. , Jarvis Michael , Seo Jun-Young , Drummond Derek , Nelson Jay
Published: December 2003

A highly efficient lambda phage recombination system previously utilized for studies of bacterial artificial chromosome (BAC)-maintained mouse chromosomal DNA was adapted for the study of the role of human cytomegalovirus (HCMV)-encoded pp28 (UL99) in virus replication. Incorporating a two-step mutagenesis strategy with blue/white selection in
Escherichia coli
containing a HCMV AD169 BAC, we have shown that we can rapidly introduce point mutations into the HCMV BAC using linear PCR fragments. All manipulations were carried out in bacteria, which greatly accelerated the introduction and analysis of mutations in the viral genome. Our results indicated that HCMV pp28 was essential for the production of infectious virus and that introduction of a single base change that resulted in loss of the myristylation site on pp28 was also associated with the lack of production of infectious virus. Although the block in the viral morphogenesis cannot be determined from these studies, the latter finding suggested that authentic intracellular localization of pp28, not only the expression of the protein, is required for virus assembly.
Epstein-Barr Virus Immediate-Early Protein BZLF1 Inhibits Tumor Necrosis Factor Alpha-Induced Signaling and Apoptosis by Downregulating Tumor Necrosis Factor Receptor 1
Authors: Morrison Thomas E. , Mauser Amy , Klingelhutz Aloysius , Kenney Shannon C.
Published: December 2003

Tumor necrosis factor alpha (TNF-α) is a key mediator of host immune and inflammatory responses and inhibits herpesvirus replication by cytolytic and noncytolytic mechanisms. TNF-α effects are primarily mediated through the major TNF-α receptor, TNF-R1, which is constitutively expressed in most cell types. Here we show that the Epstein-Barr virus (EBV) immediate-early protein BZLF1 prevents TNF-α activation of target genes and TNF-α-induced cell death. These effects are mediated by down-regulation of the promoter forTNF-R1.Additionally, we demonstrate that expression of TNF-R1 is downregulated during the EBV lytic replication cycle. Thus, EBV has developed a novel mechanism for evading TNF-α antiviral effects during lytic reactivation or primary infection.
Selection of Functional 5′
cis
-Acting Elements Promoting Efficient Sindbis Virus Genome Replication
Authors: Gorchakov Rodion , Hardy Richard , Rice Charles M. , Frolov Ilya
Published: December 2003

The 5′ portion of the Sindbis virus (SIN) genome RNA is multifunctional. Besides initiating translation of the nonstructural polyprotein, RNA elements in the 5′ 200 bases of the SIN genome RNA, or its complement at the 3′ end of the negative-strand intermediate, play key roles in the synthesis of both negative- and positive-strand RNAs. We used here a combination of genetic and biochemical approaches to further dissect the functions of this sequence. Replacement of the SIN 5′ end in defective-interfering (DI) and genome RNAs with sequences from a distantly related alphavirus, Semliki Forest virus (SFV), resulted in nonviable chimeras. The addition of five nucleotides from the 5′ terminus of SIN restored negative-strand RNA synthesis in DI genomes but not their replication in vivo. Pseudorevertants of various SFV-SIN chimeras were isolated, and suppressor mutations were mapped to AU-rich sequences added to the 5′ end of the original SFV 5′ sequence or its “deleted” versions. Early pseudorevertants had heterogeneous 5′ termini that were inefficient for replication relative to the parental SIN 5′ sequence. In contrast, passaging of these pseudorevertant viral populations in BHK cells under competitive conditions yielded evolved, more homogeneous 5′-terminal sequences that were highly efficient for negative-strand synthesis and replication. These 5′-terminal sequences always began with 5′-AU, followed by one or more AU repeats or short stretches of oligo(A). Further analysis demonstrated a positive correlation between the number of repeat units and replication efficiency. Interestingly, some 5′ modifications restored high-level viral replication in BHK-21 cells, but these viruses were impaired for replication in the cells of mosquito origin. These studies provide new information on sequence determinants required for SIN RNA replication and suggest new strategies for restricting cell tropism and optimizing the packaging of alphavirus vectors.
Long-Term Transgene Expression in Proliferating Cells Mediated by Episomally Maintained High-Capacity Adenovirus Vectors
Authors: Kreppel Florian , Kochanek Stefan
Published: December 2003

High-capacity “gutless” adenovirus vectors (HC-AdV) mediate long-term transgene expression in resting cells in vitro and in vivo because of low toxicity and immunogenicity. However, in proliferating cells, expression is transient since HC-AdV genomes do not possess elements that allow for replication and segregation of the replicated genomes to daughter cells. We developed a binary HC-AdV system that, under certain conditions, allows for significantly prolonged episomal maintenance of HC-AdV genomes in proliferating tissue culture cells, resulting in sustained transgene expression. After transduction of target cells the linear HC-AdV genomes were circularized by the DNA recombinase FLPe, which was expressed from the second HC-AdV. The
oriP
/EBNA-1 replication system derived from Epstein-Barr virus, as well as the human replication origin from the
lamin B2
locus, were used as
cis
elements to test for replication of the 28-kb circular vector genomes with or without selective pressure. Depending on the system, up to 98% of the circularized genomes were replicated and segregated to daughter cells, as demonstrated by Southern assays and as confirmed by monitoring
EGFP
transgene expression. Surprisingly, in the absence of FLPe recombinase, a small but significant number of HC-AdV genomes spontaneously circularized after transduction of target cells. These circles, found to contain end-to-end joined adenovirus termini, replicated with increased efficiency compared to vectors circularized by FLPe. After further improvements, this HC-AdV system might be suitable for gene therapy applications requiring long-term transgene expression.
Human Immunodeficiency Virus Type 1 Superinfection Was Not Detected following 215 Years of Injection Drug User Exposure
Authors: Tsui Rose , Herring Belinda L. , Barbour Jason D. , Grant Robert M. , Bacchetti Peter , Kral Alex , Edlin Brian R. , Delwart Eric L.
Published: December 2003

Evidence for human immunodeficiency virus type 1 (HIV-1) superinfection was sought among 37 HIV-1-positive street-recruited active injection drug users (IDUs) from the San Francisco Bay area. HIV-1 sequences from pairs of samples collected 1 to 12 years apart, spanning a total of 215 years of exposure, were generated at p17
gag
, the V3-V5 region of
env
, and/or the first exon of
tat
and phylogenetically analyzed. No evidence of HIV-1 superinfection was detected in which a highly divergent HIV-1 variant emerged at a frequency >20% of the serum viral quasispecies. Based on the reported risk behavior of the IDUs and the HIV-1 incidence in uninfected subjects in the same cohort, a total of 3.4 new infections would have been expected if existing infection conferred no protection from superinfection. Adjusted for risk behaviors, the estimated relative risk of superinfection compared with initial infection was therefore 0.0 (95% confidence interval, 0.00, 0.79;
P
= 0.02), indicating that existing infection conferred a statistically significant level of protection against superinfection with an HIV-1 strain of the same subtype, which was between 21 and 100%.
COMBINATION, COOPERATION AND SELECTION OF CLASSIFIERS: A STATE OF THE ART
Authors: GUNES V. , MÉNARD M. , LOONIS P. , PETIT-RENAUD S.
Published: December 2003

When several classifiers are brought to contribute to the same task of recognition, various strategies of decisions, implying these classifiers in different ways, are possible. A first strategy consists in deciding using different opinions: it corresponds to the combination of classifiers. A second strategy consists in using one or more opinions for better guiding other classifiers in their training stages, and/or to improve the decision-making of other classifiers in the classification stage: it corresponds to the cooperation of classifiers. The third and last strategy consists in giving more importance to one or more classifiers according to various criteria or situations: it corresponds to the selection of classifiers. The temporal aspect of Pattern Recognition (PR), i.e. the possible evolution of the classes to be recognized, can be treated by the strategy of selection.
UNCORRELATED PROJECTION DISCRIMINANT ANALYSIS AND ITS APPLICATION TO FACE IMAGE FEATURE EXTRACTION
Authors: YANG JIAN , YANG JING-YU , FRANGI ALEJANDRO F. , ZHANG DAVID
Published: December 2003

In this paper, a novel image projection analysis method (UIPDA) is first developed for image feature extraction. In contrast to Liu's projection discriminant method, UIPDA has the desirable property that the projected feature vectors are mutually uncorrelated. Also, a new LDA technique called EULDA is presented for further feature extraction. The proposed methods are tested on the ORL and the NUST603 face databases. The experimental results demonstrate that: (i) UIPDA is superior to Liu's projection discriminant method and more efficient than Eigenfaces and Fisherfaces; (ii) EULDA outperforms the existing PCA plus LDA strategy; (iii) UIPDA plus EULDA is a very effective two-stage strategy for image feature extraction.
CONNECTIONIST TECHNIQUES FOR THE IDENTIFICATION AND SUPPRESSION OF INTERFERING UNDERLYING FACTORS
Authors: CORCHADO EMILIO , FYFE COLIN
Published: December 2003

We consider the difficult problem of identification of independent causes from a mixture of them when these causes interfere with one another in a particular manner: those considered are visual inputs to a neural network system which are created by independent underlying causes which may occlude each other. The prototypical problem in this area is a mixture of horizontal and vertical bars in which each horizontal bar interferes with the representation of each vertical bar and vice versa. Previous researchers have developed artificial neural networks which can identify the individual causes; we seek to go further in that we create artificial neural networks which identify all the horizontal bars from only such a mixture. This task is a necessary precursor to the development of the concept of "horizontal" or "vertical".
EXTRACTING SALIENT REGIONS AND LEARNING IMPORTANCE SCORES IN REGION-BASED IMAGE RETRIEVAL
Authors: KO BYOUNGCHUL , BYUN HYERAN
Published: December 2003

In this paper, we propose a new method for extracting salient regions and learning their importance scores in region-based image retrieval. In Region-Based Image Retrieval (RBIR), not all the regions are important for retrieving similar images and rather, in retrieval, the user is often interested in performing a query on only one or a few regions rather than the whole image. Therefore, for a successful retrieval system, it is an important issue to specify which regions are important for retrieving an image. To extract salient regions from images automatically, we make three assumptions and determine salient regions with their importance scores. In this paper, we apply the relevance feedback algorithm to the matching process as two different purposes: one is for updating importance scores of salient regions and the other is for updating weights of feature vectors. By using our relevance feedback method, the matching process can improve retrieval performance interactively and allow progressive refinement of query results according to the user's feedback action. Through experiments and comparison with other methods, our proposed method shows good performance as well as easy and semantic interface for region-based image retrieval. The efficacy of our method is validated using a set of 3000 images from Corel-photo CD.
A SIMPLE LOCALLY ADAPTIVE NEAREST NEIGHBOR RULE WITH APPLICATION TO POLLUTION FORECASTING
Authors: NOCK RICHARD , SEBBAN MARC , BERNARD DIDIER
Published: December 2003

In this paper, we propose a thorough investigation of a nearest neighbor rule which we call the "Symmetric Nearest Neighbor (sNN) rule". Basically, it symmetrises the classical nearest neighbor relationship from which are computed the points voting for some instances. Experiments on 29 datasets, most of which are readily available, show that the method significantly outperforms the traditional Nearest Neighbors methods. Experiments on a domain of interest related to tropical pollution normalization also show the greater potential of this method. We finally discuss the reasons for the rule's efficiency, provide methods for speeding-up the classification time, and derive from the sNN rule a reliable and fast algorithm to fix the parameter k in the k-NN rule, a longstanding problem in this field.
GENERAL IMAGE CLASSIFICATION USING ADAPTIVE CELLULAR COLOR DECOMPOSITION
Authors: LO CHIH-HSIEN , CHEN SHU-YUAN
Published: December 2003

In this paper, a coarse-to-fine hierarchical classification method based on the features derived from adaptive cellular color decomposition is proposed. The proposed method is general and can be applied to all kinds of color image databases as long as a sample set of images have been classified. In addition, the number of classes can be as versatile as required. To achieve the goal mentioned above, our method consists of two phases: color quantization and classification. In the color quantization step, cellular decomposition is used to adaptively quantize color images in the HSV color space since H and S components construct a hexagon structure that is same as the cellular pattern. In the classification step, a coarse-to-fine strategy is employed. In the coarse stage, five image-based features extracted directly from the quantization results of the query images are used to prune irrelevant database images. In the fine stage, two cluster-based features are extracted from a small set of candidate images using closest-cluster matching. On the other hand, according to feature evaluation, one image-based and two cluster-based features are selected to derive individual-based similarity measure, which, in turn, is used to measure image-to-image similarity. In addition, class-based similarity measure using class characteristics is proposed to evaluate image-to-class similarity. Candidate images are then sorted according to the similarity measure, which is a combination of individual-based and class-based similarity measures. Finally, k-NN rule is used to assign the query image to a single class according to the sorting results. The effectiveness and practicability of the proposed method have been demonstrated by various experimental results.
AN APPROACH TO NATURAL STROKE EXTRACTION FOR OFF-LINE LOOSELY-CONSTRAINED HANDWRITTEN CHINESE CHARACTERS
Authors: YEUNG DANIEL S. , FONG H. S. , TSANG ERIC C. C. , SHU WENHAO , WANG XIAOLONG
Published: December 2003

This paper proposes a new approach to extracting natural strokes from the skeletons of loosely-constrained, off-line handwritten Chinese characters. It admits the output substrokes from a previously proposed fuzzy substroke extractor as its inputs. By identifying a number of expected ambiguities which include mutual similarities, unstable touches and joint/cross distortions, fuzzy stroke models are constructed and a "hit-all" fuzzy stroke matching strategy is pursued. Fuzzy partitioning technique is used to generate a ranked list of consistent stroke sets from the set of fuzzy strokes being identified. With this approach, a maximum of 20 distinct natural stroke classes can be extracted from each input character, together with an estimate on the actual count of strokes which compose the character. Our system offers a number of performance tuning capabilities such as the computation of the fuzzy scores of each extracted stroke, the adjustment on the fuzzy stroke model parameters, and the potential of incorporating one's personal writing styles into our methodology.
Role of Prostaglandin E Receptor EP
1
Subtype in the Development of Renal Injury in Genetically Hypertensive Rats
Authors: Suganami Takayoshi , Mori Kiyoshi , Tanaka Issei , Mukoyama Masashi , Sugawara Akira , Makino Hisashi , Muro Seiji , Yahata Kensei , Ohuchida Shuichi , Maruyama Takayuki , Narumiya Shuh , Nakao Kazuwa
Published: December 2003

One of the major causes of end-stage renal diseases is hypertensive renal disease, in which enhanced renal prostaglandin (PG) E
2
production has been shown. PGE
2
, a major arachidonic acid metabolite produced in the kidney, acts on 4 receptor subtypes, EP
1
through EP
4
, but the pathophysiological importance of the PGE
2
/EP subtypes in the development of hypertensive renal injury remains to be elucidated. In this study, we investigated whether an orally active EP
1
-selective antagonist (EP
1
A) prevents the progression of renal damage in stroke-prone spontaneously hypertensive rats (SHRSP), a model of human malignant hypertension. Ten-week-old SHRSP, with established hypertension but with minimal renal damage, were given EP
1
A or vehicle for 5 weeks. After the treatment period, vehicle-treated SHRSP showed prominent proliferative lesions in arterioles, characterized by decreased α-smooth muscle actin expression in multilayered vascular smooth muscle cells. Upregulation of transforming growth factor-β expression and tubulointerstitial fibrosis were also observed in vehicle-treated SHRSP. All these changes were dramatically attenuated in EP
1
A-treated SHRSP. Moreover, EP
1
A treatment significantly inhibited both increase in urinary protein excretion and decrease in creatinine clearance but had little effect on systemic blood pressure. These findings indicate that the PGE
2
/EP
1
signaling pathway plays a crucial role in the development of renal injury in SHRSP. This study opens a novel therapeutic potential of selective blockade of EP
1
for the treatment of hypertensive renal disease.
Noninvasive Imaging of Myocardial Viability
Authors: Wu Katherine C. , Lima João A.C.
Published: December 2003

Complete knowledge of myocardial structure, metabolism, and function is crucial to understanding the response of the heart to injury such as ischemia. Increasingly, this type of knowledge is required at multiple levels, from that of the isolated myocyte to the functioning organism, to provide basic scientists and clinical investigators a common framework for translation of findings and information feedback. This article focuses on the utilization of imaging methods to assess myocardial viability in vivo. It discusses the advantages and pitfalls of different imaging techniques, with particular emphasis on available data in humans and large animal models. Because of their novelty and potential for accurate phenotyping of human pathophysiology, magnetic resonance modalities will be highlighted.
Cold cracking studies on low alloy steel weldments: Effect of filler metal composition
Authors: Reddy G. Madhusudhan , Mohandas T. , Sarma D. S.
Published: December 2003

The resistance to hydrogen cracking of Cr - Mo, Ni - Cr - Mo and Si - Mn steels which are employed in armoured vehicle construction was evaluated under implant test conditions. Austenitic stainless steel filler (AWS E312), which is reported to be resistant to hydrogen assisted cracking, was used to study the cracking tendency of all the three steels. Four other fillers, namely a nickel based filler (ENiCrFe-3), a low carbon, low alloy steel, a mild steel (AWS E6013) and a matching filler for Cr - Mo, were employed to evaluate their relative cracking tendency. Cr - Mo and Ni - Cr - Mo steels exhibited high cracking tendency while Si - Mn steel was resistant to cracking with the E312 filler. Cr - Mo steel was resistant to cracking with the nickel based filler, the low carbon, low alloy steel and the matching filler. The observed cracking tendency of the steels is linked to a susceptible interface/fusion boundary microstructure.
Measurement of contact parameters at electrode/sheet interface during resistance spot welding process
Authors: Le Meur G. , Bourouga B. , Dupuy T.
Published: December 2003

The numerical simulation of the resistance spot welding process requires a precise understanding of the thermal conditions at the electrode/sheet interface. This necessitates a knowledge of the thermal contact resistance RTC which prevails at the interface, and the partition coefficient of generated heat flux at the interface α. This coefficient draws its significance from the non-conservative character of the generated heat flux in the disturbed zone of the contact. Consequently, on the macroscopic scale, only a fraction α (α< 1) of the heat flux generated at the interface contributes to the temperature change at the electrode/sheet interface. The present work reports an experimental study relating to the simultaneous estimation of RTC and α at the electrode/sheet interface during the resistance spot welding process. Both parameters, RTC and α, depend on the electrode/sheet interface structure. Consequently, RTC and α are time dependent during the welding process. The results of measurement of temperature as well as the estimations of RTC(t) and α (t) show that the developed experimental methodology is reproducible and reliable. The analysis of the results of the estimations allowed the interpretation of the evolution of RTC and α during the weld cycle as functions of current intensity and electrode force. Although the estimations are based on a one-dimensional heat transfer assumption, the results are in agreement with the physical phenomena that prevail at the electrode/sheet interface.
Analysis of acoustic characteristics for plasma arc cutting
Authors: Xue W. , Kusumoto K. , Nezu K.
Published: December 2003

The sound emitted during plasma arc cutting is closely related to the cutting conditions including cutting speed, arc current, operating gas flowrate, torch standoff height, nozzle shape, etc., and it therefore contains useful information for the evaluation of the plasma arc cutting process. The present work investigates the characteristics of the sound emitted during plasma arc cutting under various cutting conditions, using fast Fourier transformation and probability statistical analyses. An acoustic model of plasma arc cutting, having two jet sound sources, is proposed to interpret this sound. The sensitive frequency band of the cutting sound and the relationship between the cutting sound and the conditions are then revealed. It is shown that the cutting sound is a random signal readily affected by cutting conditions, and its energy is concentrated in the high frequency field and originates mainly from the mixing region of the first sound source and the mixing and transition regions of the second sound source. Experimental results also suggest the possibility of developing an acoustically based monitor system for this plasma arc process, and of reducing the acoustic exposure level, thereby improving working conditions.
Measurement and calculation of arc power and heat transfer efficiency in pulsed gas metal arc welding
Authors: Joseph A. , Harwig D. , Farson D. F. , Richardson R.
Published: December 2003

This study investigates the heat transfer efficiency of the pulsed gas metal arc welding (GMAW-P) process. The arc power and heat input were calculated from arc current and voltage measurements and the heat input was also measured with a liquid nitrogen calorimeter. The measured heat transfer efficiency for GMAW-P varied slightly over a wide range of pulse parameters, with an average value of 70%, a maximum of 72% and a minimum of 68%. Welding heat transfer efficiency based on arc power calculated as the product of average current and voltage was too high (averaging 82%), while that calculated using the product of the root mean square (RMS) of the average current and voltage was too low (averaging 61%). Both also varied significantly with pulsing parameters. Mathematical analysis shows that average instantaneous power values must be used when current and voltage vary significantly with time. The experimental differences between the average instantaneous power and the other calculated values are explained by the relative phases of the pulsed current, voltage and arc resistance waveforms.
Use of thin adherends in adhesively bonded joints under different loading modes
Authors: Kadioglu F. , Es-Souni M.
Published: December 2003

The adhesive bonding technique is especially suited to the joining of thin materials. An adhesive joint consists of a structural adhesive and an adherend. When designing the joint, focusing on the behaviour of the adhesive is important. However, if the material to be joined is thin, then it becomes much more important to concentrate on the material properties. In the present work, two adhesives with different mechanical behaviour and two thin adherend materials, steel and aluminium, were selected for the production of adhesive joints. The single lap joint configuration was subjected to tests under bending load and also under tensile load. The results show that adherend plasticity plays an important part in the joint failure; specimens under bending load experienced high plastic deformation of adherends, depending on the strength of the adherend material. Overlap increase did not seem to affect the joint strength. When the joints were tested under tensile loading, it was observed that the load bearing capacity of adhesives was an important parameter influencing the joint strength, and that an increase in overlap seemed to contribute to the joint performance. In general, the results obtained imply that it is vital that the adherends used remain in their elastic deformation region to obtain a joint strength that reflects the mechanical behaviour of the adhesive used.
Effect of process parameters of micro-plasma arc welding on morphology and quality in stainless steel edge joint welds
Authors: Tseng K. H. , Hsieh S. T. , Tseng C. C.
Published: December 2003

The effects of the process parameters of micro-plasma arc welding (micro-PAW) on the morphology and quality of stainless steel edge joint welds were investigated. Micro-PAW was applied on type 304 stainless steels to produce an edge joint weld. Welding experiments were carried out for various combinations of arc current, welding speed, arc length, shielding gas, and clamp distance, with all other operating conditions held constant. The experimental results indicated that the collimated shape of the low current plasma arc was mainly responsible for the low sensitivity of the weld morphology to variations in the nozzle standoff distances. The arc voltage increased with increasing quantity of added hydrogen in the argon shielding gas. It was also found that satisfactory edge joint welds can be formed using a clamp distance of 0.35 mm, and that the edge joint penetration on a 0.1 mm thickness stainless steel is about 60% of the clamp distance.