bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Liquid-Pool Simulation of Droplet Combustion in a Swirl
Flow
Authors: Hou S.-S. , Lin T.-H. 
Published: April 2008

Abstract
The influence of flow rotation on droplet combustion and evaporation are experimentally studied by using a burning liquid-pool system, and numerically investigated by considering a nonreactive, rotating, stagnation-point flow, respectively. The experiment involves measurements of flame temperature, flame position and evaporation rate of the liquid pool, observations of the recirculation zone and the soot layer, and identification of flame extinction. A finite-volume method is employed to numerically solve the corresponding transport equations. Calculated results show that in the vicinity of the liquid surface, both convection and diffusion transports are weakened by the flow rotation, resulting in the suppression of the evaporation strength of liquid; the recirculation zone can be identified and compared with experimental observation. For the steady burning of an ethanol pool in a swirling air jet, it is found that as the angular velocity increases, the diffusion flame shifts closer to the upper burner, has a larger flame thickness, experiences a smaller flame stretch, but suffers from the reduction of mass diffusion of ethanol vapor to the flame. However, the evaporation rate of ethanol is usually decreased with increasing angular velocity. In the flame extinction experiment, the critical volumetric oxygen concentration at extinction first decreases to a minimum value and then increases with angular velocity. It is generally concluded that flow rotation reduces the rates of both droplet combustion and evaporation.
Helical Buckling of Pipes in Extended Reach and Horizontal Wells—Part
1: Preventing Helical Buckling
Authors: Wu J. , Juvkam-Wold H. C. , Lu R. 
Published: April 2008

Abstract
This paper studies the helical buckling of pipes (drillstring and tubing) in extended reach and horizontal wells, theoretically and experimentally, resulting in new equations to correctly predict and effectively prevent the helical buckling of pipes in such wells. The theoretical study shows that the so-called helical buckling load that appears in the current literature is only the average axial load in the helical buckling development process. The laboratory experiments confirm the theoretical analysis. The new helical buckling load equations are formulated by combining the theoretical analysis and the experimental results, thereby resolving the existing assumption-and result inconsistency in the current literature. The new equation predicts the true helical buckling load to be about 1.3 times the so-called helical buckling load in the current literature, and about 1.8 times the critical buckling load that predicts the onset of sinusoidal buckling. Consequently, larger bit weights or packer setting loads can be applied to increase the drilling rate or to ensure a proper seal, before the helical buckling of the pipes can occur.
Helical Buckling of Pipes in Extended Reach and Horizontal Wells—Part
2: Frictional Drag Analysis
Authors: Wu J. , Juvkam-Wold H. C. 
Published: April 2008

Abstract
This paper studies the frictional drag of helically buckled pipes (drillstring and tubing) in extended reach and horizontal wells to correctly predict the actual bit weight or packer load, in cases where helical buckling of pipes may have occurred. Helical buckling of pipes in such wells may occur, since large axial loads are often required. The differential equation of axial force balance with consideration of the axial friction for helically buckled pipes is resolved, and the solution shows that when the pipes are helically buckled, the frictional drag will become very large. The actual bit weight for drilling or packer load for well completion may therefore become much smaller than estimated under the unbuckled pipe conditions. The analytical solution is also shown to agree with the results from laboratory experiments, which simulate the real wellbore-pipe conditions. An example is provided to show the calculation procedure and the importance of the results.
Interlaboratory Comparison of Results of an Anthrax Lethal Toxin Neutralization Assay for Assessment of Functional Antibodies in Multiple Species
Authors: Omland Kristian S. , Brys April , Lansky David , Clement Kristin , Lynn Freyja 
Published: April 2008

ABSTRACT

The anthrax lethal toxin neutralization assay (TNA) will likely be used to correlate the protection offered by new anthrax vaccines in animal models to the immunogenicity that will be provided in humans. TNA data are being generated in several different laboratories to measure the immune responses in rabbits, nonhuman primates, and humans. In order to compare data among species and laboratories, a collaborative study was conducted in which 108 samples from the three species were analyzed in seven independent laboratories. Six of the seven laboratories had participated in an interlaboratory technology transfer of the TNA. Analysis of the titration curves generated by samples from each species indicated that the behaviors of the samples from all species were similar; the upper and lower asymptotes and the slopes of the curves were less than 30% divergent from those for human reference material. Dilutional linearity was consistent among samples from each species, with spike to effective dilution at 50% inhibition (ED
50
) slopes of less than 1.2 for all species. Agreement among the laboratories with consensus values was within 10% of the ED
50
s for all samples and within 7.5% of the quotients of the test sample ED
50
and the reference standard ED
50
(NF
50
s) for all samples. The relative standard deviations obtained when data from all laboratories and for all species were combined were 45% for the ED
50
s and 35% for the NF
50
s. These precision data suggest that the NF
50
readout may normalize the values generated by different laboratories. This study demonstrates that the TNA is a panspecies assay that can be performed in several different laboratories with a high degree of quantitative agreement and precision.
Characterization of In Vitro-Generated and Clinical Optochin-Resistant Strains of
Streptococcus pneumoniae
Isolated from Argentina
Authors: Cortes Paulo R. , Orio Andrea G. Albarracín , Regueira Mabel , Piñas Germán E. , Echenique José 
Published: April 2008

ABSTRACT

Optochin susceptibility is a key test used for pneumococcal diagnosis, but optochin-resistant (Opt
r
) pneumococci have been reported in the last 2 decades. In this work, we characterized eight Opt
r
clinical strains which presented a new mutation, G47V, a predominant A49S mutation (recently reported in Brazil) and A49T. These mutations were found in the
c
subunit of the F
0
F
1
ATPase encoded by the
atpC
gene, and W206C was found in the
a
subunit encoded by the
atpA
gene. The Opt
r
clinical isolates were analyzed by BOX PCR, multilocus sequence typing, and serotype and antimicrobial resistance profiles, and they showed no epidemiological relationship. To characterize the Opt
r
mutations that could emerge among clinical strains, we studied a pool of spontaneous Opt
r
colonies obtained in vitro from the virulent D39 strain. We compared the
atpAC
mutations of these Opt
r
pneumococci (with or without passage through C57BL/6 mice) with those described in the clinical isolates. This analysis revealed three new mutations, G47V and L26M in the
c
subunit and L184S in the
a
subunit. Most of the mutations identified in the laboratory-generated Opt
r
strains were also found in clinical strains, with the exception of the L26M and L184S mutations, and we suppose that both mutations could emerge among invasive strains in the future. Considering that
atpAC
are essential genes, we propose that all spontaneous mutations that confer in vitro optochin resistance would not present severe physiological alterations in
S. pneumoniae
and may be carried by circulating pneumococcal strains.
Coronavirus Nonstructural Protein 16 Is a Cap-0 Binding Enzyme Possessing (Nucleoside-2′
O
)-Methyltransferase Activity
Authors: Decroly Etienne , Imbert Isabelle , Coutard Bruno , Bouvet Mickaël , Selisko Barbara , Alvarez Karine , Gorbalenya Alexander E. , Snijder Eric J. , Canard Bruno 
Published: April 2008

ABSTRACT

The coronavirus family of positive-strand RNA viruses includes important pathogens of livestock, companion animals, and humans, including the severe acute respiratory syndrome coronavirus that was responsible for a worldwide outbreak in 2003. The unusually complex coronavirus replicase/transcriptase is comprised of 15 or 16 virus-specific subunits that are autoproteolytically derived from two large polyproteins. In line with bioinformatics predictions, we now show that feline coronavirus (FCoV) nonstructural protein 16 (nsp16) possesses an
S
-adenosyl-
l
-methionine (AdoMet)-dependent RNA (nucleoside-2′
O
)-methyltransferase (2′
O
-MTase) activity that is capable of cap-1 formation. Purified recombinant FCoV nsp16 selectively binds to short capped RNAs. Remarkably, an N7-methyl guanosine cap (
7Me
GpppAC
3-6
) is a prerequisite for binding. High-performance liquid chromatography analysis demonstrated that nsp16 mediates methyl transfer from AdoMet to the 2′
O
position of the first transcribed nucleotide, thus converting
7Me
GpppAC
3-6
into
7Me
GpppA
2′

O

Me
C
3-6
. The characterization of 11 nsp16 mutants supported the previous identification of residues K45, D129, K169, and E202 as the putative K-D-K-E catalytic tetrad of the enzyme. Furthermore, residues Y29 and F173 of FCoV nsp16, which may be the functional counterparts of aromatic residues involved in substrate recognition by the vaccinia virus MTase VP39, were found to be essential for both substrate binding and 2′
O
-MTase activity. Finally, the weak inhibition profile of different AdoMet analogues indicates that nsp16 has evolved an atypical AdoMet binding site. Our results suggest that coronavirus mRNA carries a cap-1, onto which 2′
O
methylation follows an order of events in which 2′
O
-methyl transfer must be preceded by guanine N7 methylation, with the latter step being performed by a yet-unknown N7-specific MTase.
A Conserved Sequence within the H2 Subunit of the Vaccinia Virus Entry/Fusion Complex Is Important for Interaction with the A28 Subunit and Infectivity
Authors: Nelson Gretchen E. , Wagenaar Timothy R. , Moss Bernard 
Published: April 2008

ABSTRACT
The recently described vaccinia virus entry/fusion complex (EFC) comprises at least eight polypeptides that are conserved in all poxviruses. Neither the structure of the complex nor the roles of individual subunits are known. Here we provide evidence for an interaction between the H2 and A28 subunits in the context of a virus infection as well as in uninfected cells transfected with plasmids expressing the corresponding genes. We focused on a highly conserved 21-amino acid-segment in H2 that is flanked by cysteine residues. The effect of amino acid substitutions within the 21-amino-acid segment was determined by an infectivity complementation assay using a conditional H2-null mutant of vaccinia virus. Mutations that had no, moderate, or large negative effects on complementation were found. The latter group included glutamic acid substitutions of leucine and individual glycines and alanine substitution of both glycines within a LGYSG sequence. Mutations with the most pronounced effect on infectivity disrupted the interaction of H2 with A28 to the greatest extent in both infected and uninfected cells. These data indicate that the LGYSG sequence is important for the interaction of H2 with A28 and suggest that this sequence is buried within the EFC complex.
Bovine Papillomavirus Type 1: from Clathrin to Caveolin
Authors: Laniosz Valerie , Holthusen Kirsten A. , Meneses Patricio I. 
Published: April 2008

ABSTRACT
Viruses may infect cells through clathrin-dependent, caveolin-dependent, or clathrin- and caveolin-independent endocytosis. Bovine papillomavirus type 1 (BPV1) entry into cells has been shown to occur by clathrin-dependent endocytosis, a pathway that involves the formation of clathrin-coated pits and fusion to early endosomes. Recently, it has been demonstrated that the closely related JC virus can enter cells in clathrin-coated vesicles and subsequently traffic to caveolae, the organelle where vesicles of the caveolin-dependent pathway deliver their cargo. In this study, we use immunofluorescence staining of BPV1 pseudovirions to show that BPV1 overlaps with the endosome marker EEA1 early during infection and later colocalizes with caveolin-1. We provide evidence through the colocalization of BPV1 with transferrin and cholera toxin B that BPVl trafficking may not be restricted to the clathrin-dependent pathway. Disrupting the entry of caveolar vesicles did not affect BPV1 infection; however, we show that blocking the caveolar pathway postentry results in a loss of BPV1 infection. These data indicate that BPV1 may enter by clathrin-mediated endocytosis and then utilize the caveolar pathway for infection, a pattern of trafficking that may explain the slow kinetics of BPV1 infection.
Infection with Vpr-Positive Human Immunodeficiency Virus Type 1 Impairs NK Cell Function Indirectly through Cytokine Dysregulation of Infected Target Cells
Authors: Majumder Biswanath , Venkatachari Narasimhan J. , O'Leary Shaylee , Ayyavoo Velpandi 
Published: April 2008

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) infection has been implicated in impairing various aspects of NK cell function in viremic condition, and several viral factors contribute to these defects. Here, we evaluated the effect of HIV-1 Vpr on NK cell cytolytic function and cytokine (gamma interferon [IFN-γ]) production in the context of infection and exposure. Our data indicate that NK cells derived from a peripheral blood mononuclear cell culture infected in vitro with HIV-1 vpr(+) virus or exposed to recombinant Vpr protein exhibited reduced target cell killing in conjunction with diminished expression of CD107a and reduced IFN-γ production compared to their Vpr-negative counterparts. This Vpr-induced NK cell defect is in part through differential regulation of interleukin-12 and transforming growth factor β production by the infected target cells and concomitant activation of Smad3 signaling pathway. Collectively, these results illustrate the ability of Vpr to impair NK cell-mediated innate immune functions indirectly by dysregulating multiple cytokines in the infected target cells, thus increasing disease severity and affecting the final outcome in HIV-1 infection.
Cell-Type-Specific Tyrosine Phosphorylation of the Herpes Simplex Virus Tegument Protein VP11/12 Encoded by Gene UL46
Authors: Zahariadis George , Wagner Melany J. , Doepker Rosalyn C. , Maciejko Jessica M. , Crider Carly M. , Jerome Keith R. , Smiley James R. 
Published: April 2008

ABSTRACTCytotoxic T lymphocytes (CTL) and natural killer (NK) cells play key roles in limiting herpesvirus infections; consequently, many herpesviruses, including herpes simplex virus (HSV), have evolved diverse strategies to evade and/or disarm these killer lymphocytes. Previous studies have shown that CTL and NK cells are functionally inactivated following contact with HSV-infected fibroblasts. During studies of the mechanisms involved, we discovered that HSV-inactivated NK-92 NK cells and Jurkat T cells contain a strikingly prominent, novel, ca. 90-kDa tyrosine-phosphorylated protein that we identified as the HSV tegument protein VP11/12. Inasmuch as VP11/12 produced in fibroblasts and epithelial cells is not obviously tyrosine phosphorylated, these data suggested that VP11/12 serves as the substrate of a cell-type-specific protein tyrosine kinase. Consistent with this hypothesis, VP11/12 was also tyrosine phosphorylated in B lymphocytes, and this modification was severely reduced in Jurkat T cells lacking the lymphocyte-specific Src family kinase Lck. These findings demonstrate that HSV tegument proteins can be differentially modified depending on the cell type infected. Our data also raise the possibility that VP11/12 may modulate one or more lymphocyte-specific signaling pathways or serve another lymphocyte-specific function. However, HSV type 1 mutants lacking the UL46 gene retained the ability to block signaling through the T-cell receptor in Jurkat cells and remained competent to functionally inactivate the NK-92 NK cell line, indicating that VP11/12 is not essential for lymphocyte inactivation. Further studies are therefore required to determine the biological function of tyrosine-phosphorylated VP11/12.
Length Requirements for Membrane Fusion of Influenza Virus Hemagglutinin Peptide Linkers to Transmembrane or Fusion Peptide Domains
Authors: Li Zhu-Nan , Lee Byeong-Jae , Langley William A. , Bradley Konrad C. , Russell Rupert J. , Steinhauer David A. 
Published: April 2008

ABSTRACT
During membrane fusion, the influenza A virus hemagglutinin (HA) adopts an extended helical structure that contains the viral transmembrane and fusion peptide domains at the same end of the molecule. The peptide segments that link the end of this rod-like structure to the membrane-associating domains are approximately 10 amino acids in each case, and their structure at the pH of fusion is currently unknown. Here, we examine mutant HAs and influenza viruses containing such HAs to determine whether these peptide linkers are subject to specific length requirements for the proper folding of native HA and for membrane fusion function. Using pairwise deletions and insertions, we show that the region flanking the fusion peptide appears to be important for the folding of the native HA structure but that mutant proteins with small insertions can be expressed on the cell surface and are functional for membrane fusion. HA mutants with deletions of up to 10 residues and insertions of as many as 12 amino acids were generated for the peptide linker to the viral transmembrane domain, and all folded properly and were expressed on the cell surface. For these mutants, it was possible to designate length restrictions for efficient membrane fusion, as functional activity was observed only for mutants containing linkers with insertions or deletions of eight residues or less. The linker peptide mutants are discussed with respect to requirements for the folding of native HAs and length restrictions for membrane fusion activity.
Sindbis Virus Conformational Changes Induced by a Neutralizing Anti-E1 Monoclonal Antibody
Authors: Hernandez Raquel , Paredes Angel , Brown Dennis T. 
Published: April 2008

ABSTRACT
A rare Sindbis virus anti-E1 neutralizing monoclonal antibody, Sin-33, was investigated to determine the mechanism of in vitro neutralization. A cryoelectron microscopic reconstruction of Sindbis virus (SVHR) neutralized with FAb from Sin-33 (FAb-33) revealed conformational changes on the surface of the virion at a resolution of 24 Å. FAb-33 was found to bind E1 in less than 1:1 molar ratios, as shown by the absence of FAb density in the reconstruction and stoichiometric measurements using radiolabeled FAb-33, which determined that about 60 molecules of FAb-33 bound to the 240 possible sites in a single virus particle. FAb-33-neutralized virus particles became sensitive to digestion by endoproteinase Glu-C, providing further evidence of antibody-induced structural changes within the virus particle. The treatment of FAb-33-neutralized or Sin-33-neutralized SVHR with low pH did not induce the conformational rearrangements required for virus membrane-cell membrane fusion. Exposure to low pH, however, increased the amount of Sin-33 or FAb-33 that bound to the virus particles, indicating the exposure of additional epitopes. The neutralization of SVHR infection by FAb-33 or Sin-33 did not prevent the association of virus with host cells. These data are in agreement with the results of previous studies that demonstrated that specific antibodies can inactivate the infectious state of a metastable virus in vitro by the induction of conformational changes to produce an inactive structure. A model is proposed which postulates that the induction of conformational changes in the infectious state of a metastable enveloped virus may be a general mechanism of antibody inactivation of virus infectivity.
Vaccinia Virus DNA Ligase Recruits Cellular Topoisomerase II to Sites of Viral Replication and Assembly
Authors: Lin Y.-C. James , Li Jianhong , Irwin Chad R. , Jenkins Heather , DeLange Luke , Evans David H. 
Published: April 2008

ABSTRACT

Vaccinia virus replication is inhibited by etoposide and mitoxantrone even though poxviruses do not encode the type II topoisomerases that are the specific targets of these drugs. Furthermore, one can isolate drug-resistant virus carrying mutations in the viral DNA ligase and yet the ligase is not known to exhibit sensitivity to these drugs. A yeast two-hybrid screen was used to search for proteins binding to vaccinia ligase, and one of the nine proteins identified comprised a portion (residue 901 to end) of human topoisomerase IIβ. One can prevent the interaction by introducing a C
11
-to-Y substitution mutation into the N terminus of the ligase bait protein, which is one of the mutations conferring etoposide and mitoxantrone resistance. Coimmunoprecipitation methods showed that the native ligase and a Flag-tagged recombinant protein form complexes with human topoisomerase IIα/β in infected cells and that this interaction can also be disrupted by mutations in the A50R (ligase) gene. Immunofluorescence microscopy showed that both topoisomerase IIα and IIβ antigens are recruited to cytoplasmic sites of virus replication and that less topoisomerase was recruited to these sites in cells infected with mutant virus than in cells infected with wild-type virus. Immunoelectron microscopy confirmed the presence of topoisomerases IIα/β in virosomes, but the enzyme could not be detected in mature virus particles. We propose that the genetics of etoposide and mitoxantrone resistance can be explained by vaccinia ligase binding to cellular topoisomerase II and recruiting this nuclear enzyme to sites of virus biogenesis. Although other nuclear DNA binding proteins have been detected in virosomes, this appears to be the first demonstration of an enzyme being selectively recruited to sites of poxvirus DNA synthesis and assembly.
Authentic Replication and Recombination of
Tomato Bushy Stunt Virus
RNA in a Cell-Free Extract from Yeast
Authors: Pogany Judit , Nagy Peter D. 
Published: April 2008

ABSTRACT

To study the replication of
Tomato bushy stunt virus
(TBSV), a small tombusvirus of plants, we have developed a cell-free system based on a
Saccharomyces cerevisiae
extract. The cell-free system was capable of performing a complete replication cycle on added plus-stranded TBSV replicon RNA (repRNA) that led to the production of ∼30-fold-more plus-stranded progeny RNAs than the minus-stranded replication intermediate. The cell-free system also replicated the full-length TBSV genomic RNA, which resulted in production of subgenomic RNAs as well. The cell-free system showed high template specificity, since a mutated repRNA, minus-stranded repRNA, or a heterologous viral RNA could not be used as templates by the tombusvirus replicase. Similar to the in vivo situation, replication of the TBSV replicon RNA took place in a membraneous fraction, in which the viral replicase-RNA complex was RNase and protease resistant but sensitive to detergents. In addition to faithfully replicating the TBSV replicon RNA, the cell-free system was also capable of generating TBSV RNA recombinants with high efficiency. Altogether, tombusvirus replicase in the cell-free system showed features remarkably similar to those of the in vivo replicase, including carrying out a complete cycle of replication, high template specificity, and the ability to recombine efficiently.