bluuebunny/crossref_metadata_2025_split huggingface dataset:
Murine T Cells Potently Restrict Human Immunodeficiency Virus Infection
Authors: Baumann Jörg G. , Unutmaz Derya , Miller Michael D. , Breun Sabine K. J. , Grill Stacy M. , Mirro Jane , Littman Dan R. , Rein Alan , KewalRamani Vineet N. 
Published: October 2004

ABSTRACTDevelopment of a mouse model for human immunodeficiency virus type 1 (HIV-1) infection has advanced through the progressive identification of host cell factors required for HIV-1 replication. Murine cells lack HIV-1 receptor molecules, do not support efficient viral gene expression, and lack factors necessary for the assembly and release of virions. Many of these blocks have been described using mouse fibroblast cell lines. Here we identify a postentry block to HIV-1 infection in mouse T-cell lines that has not been detected in mouse fibroblasts. While murine fibroblastic lines are comparable to human T-cell lines in permissivity to HIV-1 transduction, infection of murine T cells is 100-fold less efficient. Virus entry occurs efficiently in murine T cells. However, reduced efficiency of the completion of reverse transcription and nuclear transfer of the viral preintegration complex are observed. Although this block has similarities to the restriction of murine retroviruses by Fv1, there is no correlation of HIV-1 susceptibility with cellular Fv1 genotypes. In addition, the block to HIV-1 infection in murine T-cell lines cannot be saturated by a high virus dose. Further studies of this newly identified block may lend insight into the early events of retroviral replication and reveal new targets for antiretroviral interventions.
Coxsackievirus Group B Type 3 Infection Upregulates Expression of Monocyte Chemoattractant Protein 1 in Cardiac Myocytes, Which Leads to Enhanced Migration of Mononuclear Cells in Viral Myocarditis
Authors: Shen Yan , Xu Wei , Chu Yi-Wei , Wang Ying , Liu Quan-Sheng , Xiong Si-Dong 
Published: October 2004

ABSTRACTCoxsackievirus group B type 3 (CVB3) is an important cause of viral myocarditis. The infiltration of mononuclear cells into the myocardial tissue is one of the key events in viral myocarditis. Immediately after CVB3 infects the heart, the expression of chemokine(s) by infected myocardial cells may be the first trigger for inflammatory infiltration and immune response. However, it is unknown whether CVB3 can induce the chemokine expression in cardiac myocytes. Monocyte chemoattractant protein 1 (MCP-1) is a potent chemokine that stimulates the migration of mononuclear cells. The objective of the present study was to investigate the effect of CVB3 infection on MCP-1 expression in murine cardiac myocytes and the role of MCP-1 in migration of mononuclear cells in viral myocarditis. Our results showed that the expression of MCP-1 was significantly increased in cardiac myocytes after wild-type CVB3 infection in a time- and dose-dependent manner, which resulted in enhanced migration of mononuclear cells in mice with viral myocarditis. The migration of mononuclear cells was partially abolished by antibodies specific for MCP-1 in vivo and in vitro. Administration of anti-MCP-1 antibody prevented infiltration of mononuclear cells bearing the MCP-1 receptor CCR2 in mice with viral myocarditis. Infection by UV-irradiated CVB3 induced rapid and transient expression of MCP-1 in cardiac myocytes. In conclusion, our results indicate that CVB3 infection stimulates the expression of MCP-1 in myocardial cells, which subsequently leads to migration of mononuclear cells in viral myocarditis.
Enhanced Cellular Receptor Usage by a Bioselected Variant of Coxsackievirus A21
Authors: Johansson E. Susanne , Xing Li , Cheng R. Holland , Shafren Darren R. 
Published: October 2004

ABSTRACTDecay-accelerating factor (DAF) functions as cell attachment receptor for a wide range of human enteroviruses. The Kuykendall prototype strain of coxsackievirus A21 (CVA21) attaches to DAF but requires interactions with intercellular cell adhesion molecule 1 (ICAM-1) to infect cells. We show here that a bioselected variant of CVA21 (CVA21-DAFv) generated by multiple passages in DAF-expressing, ICAM-1-negative rhabdomyosarcoma (RD) cells acquired the capacity to induce rapid and complete lysis of ICAM-1-deficient cells while retaining the capacity to bind ICAM-1. CVA21-DAFv binding to DAF on RD cells mediated lytic infection and was inhibited by either antibody blockade with a specific anti-DAF SCR1 monoclonal antibody (MAb) or soluble human DAF. Despite being bioselected in RD cells, CVA21-DAFv was able to lytically infect an additional ICAM-1-negative cancer cell line via DAF interactions alone. The finding that radiolabeled CVA21-DAFv virions are less readily eluted from surface-expressed DAF than are parental CVA21 virions during a competitive epitope challenge by an anti-DAF SCR1 MAb suggests that interactions between CVA21-DAFv and DAF are of higher affinity than those of the parental strain. Nucleotide sequence analysis of the capsid-coding region of the CVA21-DAFv revealed the presence of two amino acid substitutions in capsid protein VP3 (R96H and E101A), possibly conferring the enhanced DAF-binding phenotype of CVA21-DAFv. These residues are predicted to be embedded at the interface of VP1, VP2, and VP3 and are postulated to enhance the affinity of DAF interaction occurring outside the capsid canyon. Taken together, the data clearly demonstrate an enhanced DAF-using phenotype and expanded receptor utilization of CVA21-DAFv compared to the parental strain, further highlighting that capsid interactions with DAF alone facilitate rapid multicycle lytic cell infection.
Evolutionary Dynamics of the Glycan Shield of theHuman Immunodeficiency Virus Envelope during Natural Infection andImplications for Exposure of the 2G12Epitope
Authors: Dacheux Laurent , Moreau Alain , Ataman-Önal Yasemin , Biron François , Verrier Bernard , Barin Francis 
Published: October 2004

ABSTRACT
Elucidation
of the kinetics of exposure of neutralizing epitopes on the envelope of
human immunodeficiency virus type 1 (HIV-1) during the course of
infection may provide key information about how HIV escapes the immune
system or why its envelope is such a poor immunogen to induce broadly
efficient neutralizing antibodies. We analyzed the kinetics of exposure
of the epitopes corresponding to the broadly neutralizing human
monoclonal antibodies immunoglobulin G1b12 (IgG1b12), 2G12, and 2F5 at
the quasispecies level during infection. We studied the antigenicity
and sequences of 94 full-length envelope clones present during primary
infection and at least 4 years later in four HIV-1 clade B-infected
patients. No or only minor exposure differences were observed for the
2F5 and IgG1b12 epitopes between the early and late clones. Conversely,
the envelope glycoproteins of the HIV-1 quasispecies present during
primary infection did not expose the 2G12 neutralizing epitope, unlike
those present after several years in three of the four patients.
Sequence analysis revealed major differences at potential N-linked
glycosylation sites between early and late clones, particularly at
positions known to be important for 2G12 binding. Our study, in natural
mutants, confirms that the glycosylation sites N295, N332, and N392 are
essential for 2G12 binding. This study demonstrates the relationship
between the evolving “glycan shield ” of HIV and the
kinetics of exposure of the 2G12 epitope during the course of natural
infection.
Serotype-Specific Entry of Dengue Virus into Liver Cells: Identification of the 37-Kilodalton/67-Kilodalton High-Affinity Laminin Receptor as a Dengue Virus Serotype 1 Receptor
Authors: Thepparit Chutima , Smith Duncan R. 
Published: October 2004

ABSTRACTDengue virus, the causative agent of dengue fever, dengue shock syndrome, and dengue hemorrhagic fever, infects susceptible cells by initially binding to a receptor(s) located on the host cell surface. Evidence to date suggests that receptor usage may be cell and serotype specific, and this study sought to identify dengue virus serotype 1 binding proteins on the surface of liver cells, a known target organ. By using a virus overlay protein binding assay (VOPBA), in both nondenaturing and denaturing gel systems, a putative dengue virus serotype 1 binding protein of approximately 37 kDa expressed on the surface of liver (HepG2) cells was identified. Mass spectrometry analysis identified a candidate protein, the 37/67-kDa high-affinity laminin receptor. Entry of the dengue virus serotype 1 was significantly inhibited in a dose-dependent manner by both antibodies directed against the 37/67-kDa high-affinity laminin receptor and soluble laminin. No inhibition of virus entry was seen with dengue virus serotypes 2, 3, or 4, demonstrating that the 37/67-kDa high-affinity laminin receptor is a serotype-specific receptor for dengue virus entry into liver cells.
Novel Role for Decay-Accelerating Factor in Coxsackievirus A21-Mediated Cell Infectivity
Authors: Newcombe Nicole G. , Beagley Leone G. , Christiansen Dale , Loveland Bruce E. , Johansson E. Susanne , Beagley Ken W. , Barry Richard D. , Shafren Darren R. 
Published: October 2004

ABSTRACTDecay-accelerating factor (DAF) is involved in the cell membrane attachment of many human enteroviruses. Presently, further specific active roles of DAF in mediating productive cell infection and in the pathogenesis of natural enterovirus infection are poorly understood. In an attempt to more fully understand the role of DAF in lytic cell infection we examined the specific interactions of the prototype strain of coxsackievirus A21 (CVA21) with surface-expressed DAF. Investigations into discrete DAF-CVA21 interactions focused on viral binding; viral particle elution with respect to the parameters of time, temperature, and pH; and subsequent cell infection. Radiolabeled-virus binding assays revealed that peak elution of CVA21 from DAF occurred within 15 min of initial attachment and that the DAF-eluted virus increased in a linear fashion with respect to temperature and pH. CVA21 eluted from endogenous surface-expressed DAF was highly infectious, in contrast to CVA21 eluted from intercellular adhesion molecule 1 (ICAM-1), which retained little to no infectivity. Using an adenovirus transduction system, we demonstrate that CVA21 can remain infectious for up to 24 h after DAF binding and is capable of initiating a multicycle lytic infection upon delayed ICAM-1 surface expression. Taken together, the data suggest that a major role of DAF in cell infection by the prototype strain of CVA21 is to provide membrane concentration of infectious virions, effectively increasing viral interactions with endogenous or induced ICAM-1.
The Nucleoprotein Is Required for Efficient Coronavirus Genome Replication
Authors: Almazán Fernando , Galán Carmen , Enjuanes Luis 
Published: October 2004

ABSTRACT

The construction of a set of transmissible gastroenteritis coronavirus (TGEV)-derived replicons as bacterial artificial chromosomes is reported. These replicons were generated by sequential deletion of nonessential genes for virus replication, using a modified TGEV full-length cDNA clone containing unique restriction sites between each pair of consecutive genes. Efficient activity of TGEV replicons was associated with the presence of the nucleoprotein provided either in
cis
or in
trans
. TGEV replicons were functional in several cell lines, including the human cell line 293T, in which no or very low cytopathic effect was observed, and expressed high amounts of heterologous protein.
Characterization of a Novel Close-to-Root Papillomavirus from a Florida Manatee by Using Multiply Primed Rolling-Circle Amplification:
Trichechus manatus latirostris
Papillomavirus Type 1
Authors: Rector Annabel , Bossart Gregory D. , Ghim Shin-Je , Sundberg John P. , Jenson A. Bennett , Van Ranst Marc 
Published: October 2004

ABSTRACT

By using an isothermal multiply primed rolling-circle amplification protocol, the complete genomic DNA of a novel papillomavirus was amplified from a skin lesion biopsy of a Florida manatee (
Trichechus manatus latirostris
), one of the most endangered marine mammals in United States coastal waters. The nucleotide sequence, genome organization, and phylogenetic position of the
Trichechus manatus latirostris
papillomavirus type 1 (TmPV-1) were determined. TmPV-1 is the first virus isolated from the order of
Sirenia
. A phylogenetic analysis shows that TmPV-1 is only distantly related to other papillomavirus sequences, and it appears in our phylogenetic tree as a novel close-to-root papillomavirus genus.
The Phylogeography of Orangutan Foamy Viruses Supports the Theory of Ancient Repopulation of Sumatra
Authors: Verschoor Ernst J. , Langenhuijzen Susan , Bontjer Ilja , Fagrouch Zahra , Niphuis Henk , Warren Kristin S. , Eulenberger K. , Heeney Jonathan L. 
Published: October 2004

ABSTRACT
Phylogenetic analysis of foamy virus sequences obtained from Bornean and Sumatran orangutans showed a distinct clustering pattern. One subcluster was represented by both Bornean and Sumatran orangutan simian foamy viruses (SFV). Combined analysis of host mitochondrial DNA and SFV phylogeny provided evidence for the hypothesis of the repopulation of Sumatra by orangutans from Borneo.
Study of Sequence Variation of Dengue Type 3 Virus in Naturally Infected Mosquitoes and Human Hosts: Implications for Transmission and Evolution
Authors: Lin Su-Ru , Hsieh Szu-Chia , Yueh Yi-Yuan , Lin Ting-Hsiang , Chao Day-Yu , Chen Wei-June , King Chwan-Chuen , Wang Wei-Kung 
Published: October 2004

ABSTRACT

Dengue virus is an arbovirus that replicates alternately in the mosquito vector and human host. We investigated sequences of dengue type 3 virus in naturally infected
Aedes aegypti
mosquitoes and in eight patients from the same outbreak and reported that the extent of sequence variation seen with the mosquitoes was generally lower than that seen with the patients (mean diversity, 0.21 versus 0.38% and 0.09 versus 0.23% for the envelope [E] and capsid [C] genes, respectively). This was further verified with five experimentally infected mosquitoes (mean diversity, 0.09 and 0.10% for the E and C genes, respectively). Examination of the quasispecies structures of the E sequences of the mosquitoes and of the patients revealed that the sequences of the major variants were the same, suggesting that the major variant was transmitted. These findings support our hypothesis that mosquitoes contribute to the evolutionary conservation of dengue virus by maintaining a more homogenous viral population and a dominant variant during transmission.
SECOND ORDER LOGICAL SYSTEM FOR RISK CLASSIFICATION IN A NEWLY DEVELOPED COUNTRY
Authors: WHALEN THOMAS , GIM GWANGYONG 
Published: October 2004

Modern financial institutions require sophisticated risk assessment tools to integrate human expertise and historical data in a market that is changing and broadening qualitatively, quantitatively, and geographically. The need is especially acute in newly developed countries where expertise and data are scarce, and knowledge bases and assumptions imported from the West may be of limited applicability. Second order logical models can be a valuable tool in such situations. They integrate the robustness of neural or statistical modeling of data, the perspicuity of logical rule induction, and the experience and understanding of skilled human experts. The approach is illustrated in the context of risk assessment in the Korean surety insurance industry.
Cognitive Map Formation Through Sequence Encoding by Theta Phase Precession
Authors: Wagatsuma Hiroaki , Yamaguchi Yoko 
Published: October 2004

The rodent hippocampus has been thought to represent the spatial environment as a cognitive map. The associative connections in the hippocampus imply that a neural entity represents the map as a geometrical network of hippocampal cells in terms of a chart. According to recent experimental observations, the cells fire successively relative to the theta oscillation of the local field potential, called theta phase precession, when the animal is running. This observation suggests the learning of temporal sequences with asymmetric connections in the hippocampus, but it also gives rather inconsistent implications on the formation of the chart that should consist of symmetric connections for space coding. In this study, we hypothesize that the chart is generated with theta phase coding through the integration of asymmetric connections. Our computer experiments use a hippocampal network model to demonstrate that a geometrical network is formed through running experiences in a few minutes. Asymmetric connections are found to remain and distribute heterogeneously in the network. The obtained network exhibits the spatial localization of activities at each instance as the chart does and their propagation that represents behavioral motions with multidirectional properties. We conclude that theta phase precession and the Hebbian rule with a time delay can provide the neural principles for learning the cognitive map.
Mean Field and Capacity in Realistic Networks of Spiking Neurons Storing Sparsely Coded Random Memories
Authors: Curti Emanuele , Mongillo Gianluigi , Camera Giancarlo La , Amit Daniel J. 
Published: October 2004

Mean-field (MF) theory is extended to realistic networks of spiking neurons storing in synaptic couplings of randomly chosen stimuli of a given low coding level. The underlying synaptic matrix is the result of a generic, slow, long-term synaptic plasticity of two-state synapses, upon repeated presentation of the fixed set of the stimuli to be stored. The neural populations subtending the MF description are classified by the number of stimuli to which their neurons are responsive (multiplicity). This involves 2p + 1 populations for a network storing p memories. The computational complexity of the MF description is then significantly reduced by observing that at low coding levels (f), only a few populations remain relevant: the population of mean multiplicity –pf and those of multiplicity of order √pf around the mean. The theory is used to produce (predict) bifurcation diagrams (the onset of selective delay activity and the rates in its various stationary states) and to compute the storage capacity of the network (the maximal number of single items used in training for each of which the network can sustain a persistent, selective activity state). This is done in various regions of the space of constitutive parameters for the neurons and for the learning process. The capacity is computed in MF versus potentiation amplitude, ratio of potentiation to depression probability and coding level f. The MF results compare well with recordings of delay activity rate distributions in simulations of the underlying microscopic network of 10,000 neurons.
The Effects of Weld Geometry and Glass-fiber-orientation on the Mechanical Performance of Joints - Part II: Kinetics of Glass-fiber-orientation and Mechanical Performance
Authors: Kagan Val A. , Roth Christopher 
Published: October 2004

The mechanical performance of injection-molded short glass-fiber-reinforced thermoplastic components is anisotropic and is highly dependent on the fiber-orientation and distribution. Similarly, the bulk and short and long-term mechanical performance at the weld is influenced by these fibers and the specific welding technology used as related to melt-pool formation. The purpose of this analysis is to show: 1. the short-fiber-orientation (analytical and simulation data) and distribution at the prewelded bead, ribs, and wall areas; 2. advantages of SigmaSoft injection-molding simulation software, which utilizes full threedimensional fiber representation of any molded part; 3. the mechanical performance of welds with optimized geometry (US Patent 6,447,866). Findings on the mechanical performance of butt-joints with different designs and localized geometry will help designers and technicians with plastic part design optimization. In a previous ANTEC paper (Part I) (Kagan, V.A. and Roth, C. (2002). The Effects of Weld Geometry and Glass-Fiber Orientation on the Mechanical Performance of Joints - Part I: Kinetics of Glass-fiber-orientation and Performance at Bulk and Weld Areas, Design Issues, In: ANTEC Proceedings), we related these findings to the kinetics of welds and part design issues for straight and T-type butt-joints.
Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer
Authors: Nickrent Daniel L , Blarer Albert , Qiu Yin-Long , Vidal-Russell Romina , Anderson Frank E 
Published: October 2004

Abstract
Background
The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.

Results
Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further.

Conclusions
Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.