bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved Methylation Patterns of Human Papillomavirus Type 16 DNA in Asymptomatic Infection and Cervical Neoplasia
Authors: Kalantari Mina , Calleja-Macias Itzel E. , Tewari Devansu , Hagmar Bjørn , Lie Kathrine , Barrera-Saldana Hugo A. , Wiley Dorothy J. , Bernard Hans-Ulrich 
Published: November 2004

ABSTRACTDNA methylation contributes to the chromatin conformation that represses transcription of human papillomavirus type16 (HPV-16), which is prevalent in the etiology of cervical carcinoma. In an effort to clarify the role of this phenomenon in the regulation and carcinogenicity of HPV-16, 115 clinical samples were studied to establish the methylation patterns of the 19 CpG dinucleotides within the long control region and part of the L1 gene by bisulfite modification, PCR amplification, DNA cloning, and sequencing. We observed major heterogeneities between clones from different samples as well as between clones from individual samples. The methylation frequency of CpGs was measured at 14.5%. In addition, 0.21 and 0.23%, respectively, of the CpA and CpT sites, indicators of de novo methylation, were methylated. Methylation frequencies exceeded 30% in the CpGs overlapping with the L1 gene and were about 10% for most other positions. A CpG site located in the linker between two nucleosomes positioned over the enhancer and promoter of HPV-16 had minimal methylation. This region forms part of the HPV replication origin and is close to binding sites of master-regulators of transcription during epithelial differentiation. Methylation of most sites was highest in carcinomas, possibly due to tandem repetition and chromosomal integration of HPV-16 DNA. Methylation was lowest in dysplasia, likely reflecting the transcriptional activity in these infections. Our data document the efficient targeting of HPV genomes by the epithelial methylation machinery, possibly as a cellular defense mechanism, and suggest involvement of methylation in HPV oncogene expression and the early-late switch.
Role of the Proximal Enhancer of the Major Immediate-Early Promoter in Human Cytomegalovirus Replication
Authors: Isomura Hiroki , Tsurumi Tatsuya , Stinski Mark F. 
Published: November 2004

ABSTRACT
The human cytomegalovirus (CMV) enhancer has a distal component (positions −550 to −300) and a proximal component (−300 to −39) relative to the transcription start site (+1) of the major immediate-early (MIE) promoter. Without the distal enhancer, human CMV replicates slower and has a small-plaque phenotype. We determined the sequence requirements of the proximal enhancer by making 5′-end deletions to positions −223, −173, −116, −67, and −39. Even though recombinant virus with the proximal enhancer deleted to −39 has the minimal TATA box-containing MIE promoter element, it cannot replicate independently in human fibroblast cells. Recombinant virus with a deletion to −67 has an Sp-1 transcription factor binding site which may represent a minimal enhancer element for recombinant virus replication in human fibroblast cells. Although recombinant virus with a deletion to −223 replicates to titers at least 100-fold less than that of the wild-type virus, it replicates to titers 8-fold higher than that of recombinant virus with a deletion to −173 and 20-fold higher than that of virus with a deletion to −67. Recombinant virus with a deletion to −173 replicates more efficiently than that with a deletion to −116. There was a direct correlation between the level of infectious virus replication and time after infection, amount of MIE gene transcription, MIE and early viral protein synthesis, and viral DNA synthesis. The extent of the proximal enhancer determines the efficiency of viral replication.
SYNCRIP, a Member of the Heterogeneous Nuclear Ribonucleoprotein Family, Is Involved in Mouse Hepatitis Virus RNA Synthesis
Authors: Choi Keum S. , Mizutani Akihiro , Lai Michael M. C. 
Published: November 2004

ABSTRACT
Several cellular proteins, including several heterogeneous nuclear ribonucleoproteins (hnRNPs), have been shown to function as regulatory factors for mouse hepatitis virus (MHV) RNA synthesis as a result of their binding to the 5′ and 3′ untranslated regions (UTRs) of the viral RNA. Here, we identified another cellular protein, p70, which has been shown by UV cross-linking to bind both the positive- and negative-strand UTRs of MHV RNA specifically. We purified p70 with a a one-step RNA affinity purification procedure with the biotin-labeled 5′-UTR. Matrix-assisted laser desorption ionization (MALDI)-mass spectrometry identified it as synaptotagmin-binding cytoplasmic RNA-interacting protein (SYNCRIP). SYNCRIP is a member of the hnRNP family and localizes largely in the cytoplasm. The p70 was cross-linked to the MHV positive- or negative-strand UTR in vitro and in vivo. The bacterially expressed SYNCRIP was also able to bind to the 5′-UTR of both strands. The SYNCRIP-binding site was mapped to the leader sequence of the 5′-UTR, requiring the UCUAA repeat sequence. To investigate the functional significance of SYNCRIP in MHV replication, we expressed a full-length or a C-terminally truncated form of SYNCRIP in mammalian cells expressing the MHV receptor. The overexpression of either form of SYNCRIP inhibited syncytium formation induced by MHV infection. Furthermore, downregulation of the endogenous SYNCRIP with a specific short interfering RNA delayed MHV RNA synthesis; in contrast, overexpression or downregulation of SYNCRIP did not affect MHV translation. These results suggest that SYNCRIP may be directly involved in MHV RNA replication as a positive regulator. This study identified an additional cellular hnRNP as an MHV RNA-binding protein potentially involved in viral RNA synthesis.
Comparative Analysis of Signal Transduction by CD40 and the Epstein-Barr Virus Oncoprotein LMP1 In Vivo
Authors: Panagopoulos Dimitris , Victoratos Panayiotis , Alexiou Maria , Kollias George , Mosialos George 
Published: November 2004

ABSTRACTThere is much evidence, based primarily on in vitro studies, indicating that the Epstein-Barr virus oncoprotein latent membrane protein 1 (LMP1) mimics an activated CD40 receptor. In order to investigate the extent of similarity between LMP1 and CD40 functions in vivo, we analyzed the cytoplasmic signaling properties of LMP1 and CD40 in B cells in a directly comparable manner. For this purpose, we generated transgenic mice expressing either LMP1 or a chimeric LMP1CD40 molecule, which constitutively activates the CD40 pathway, under the control of the CD19 promoter. LMP1 and LMP1CD40 were expressed at similar levels in a B-lymphocyte-specific manner. Similar to LMP1, LMP1CD40 suppressed germinal center (GC) formation and antibody production in response to thymus-dependent antigens, albeit to a greater extent than LMP1. Furthermore, the avidity of the antibodies produced against thymus-dependent antigens was lower for LMP1CD40 transgenic mice than for wild-type and LMP1 transgenic mice. GC suppression was linked to the ability of LMP1CD40 and LMP1 to downregulate mRNA and protein levels of BCL6 and to suppress the activity of the BCL6 promoter. In contrast to LMP1, LMP1CD40 caused an upregulation of CD69, CD80, and CD86 in B cells and a dramatic increase in serum immunoglobulin M. In addition, LMP1CD40 but not LMP1 transgenic mice had elevated numbers of marginal-zone B cells and increased populations of polymorphonuclear cells and/or neutrophils. Consistent with these findings, LMP1CD40 but not LMP1 transgenic mice showed signs of spontaneous inflammatory reactions and the potential for autoimmunity.
Effects of Mutations in the G Tract of the Human Immunodeficiency Virus Type 1 Polypurine Tract on Virus Replication and RNase H Cleavage
Authors: Julias John G. , McWilliams Mary Jane , Sarafianos Stefan G. , Alvord W. Gregory , Arnold Eddy , Hughes Stephen H. 
Published: November 2004

ABSTRACT
The RNase H cleavages that generate and remove the polypurine tract (PPT) primer during retroviral reverse transcription must be specific in order to create a linear viral DNA that is suitable for integration. Lentiviruses contain a highly conserved sequence consisting of six guanine residues at the 3′ end of the PPT (hereafter referred to as the G tract). We introduced mutations into the G tract of a human immunodeficiency virus type 1-based vector and determined the effects on the virus titer and RNase H cleavage specificity. Most mutations in the G tract had little or no effect on the virus titer. Mutations at the second and fifth positions of the G tract increased the proportion of two-long-terminal-repeat (2-LTR) circle junctions with one or two nucleotide insertions. The second and fifth positions of the G tract make specific contacts with amino acids in the RNase H domain that are important for RNase H cleavage specificity. These complementary data define protein-nucleic acid interactions that help control the specificity of RNase H cleavage. When the G-tract mutants were analyzed in a viral background that was deficient in integrase, in most cases the proportion of consensus 2-LTR circle junctions increased. However, in the case of a mutant with Ts at the second and fifth positions of the G tract, the proportion of 2-LTR circle junctions containing the one-nucleotide insertion increased, suggesting that linear viral DNAs containing an extra base are substrates for integration. This result is consistent with the idea that the 3′ end-processing reactions of retroviral integrases may help to generate defined ends from a heterogenous population of linear viral DNAs.
Characterization of Murine Gammaherpesvirus 68 Glycoprotein B
Authors: Lopes Filipa B. , Colaco Susanna , May Janet S. , Stevenson Philip G. 
Published: November 2004

ABSTRACT
Murine gammaherpesvirus 68 (MHV-68) glycoprotein B (gB) was identified in purified virions by immunoblotting, immunoprecipitation, and immunoelectron microscopy. It was synthesized as a 120-kDa precursor in infected cells and cleaved into 65-kDa and 55-kDa disulfide-linked subunits close to the time of virion release. The N-linked glycans on the cleaved, virion gB remained partially endoglycosidase H sensitive. The processing of MHV-68 gB therefore appears similar to that of Kaposi's sarcoma-associated herpesvirus gB and human cytomegalovirus gB.
ON THE FUNDAMENTAL GROUP OF AN ABELIAN COVER
Authors: PARDINI RITA , TOVENA FRANCESCA 
Published: November 2004

Let X, Y be smooth complex projective varieties of dimension n≥2 and let f: Y→X be a totally ramified abelian cover. Assume that the components of the branch divisor of f are ample. Then the map f*: π1(Y)→π1(X) is surjective and gives rise to a central extension: [Formula: see text] where K is a finite group. Here we show how the kernel K and the cohomology class c(f) ∈ H2(π1(X), K) of (1) can be computed in terms of the Chern classes of the components of the branch divisor of f and of the eigensheaves of [Formula: see text] under the action of the Galois group. Using this result, for any integer m>0, we construct m varieties X1,…, Xm no two of which are homeomorphic, even though they have the same numerical invariants and they are realized as covers of the same projective variety X with the same Galois group, branch locus and inertia subgroups.
AUTOMATIC EXTRACTION OF CHARACTERS IN COMPLEX SCENE IMAGES
Authors: LEE CHUNG-MONG , KANKANHALLI ATREYI 
Published: November 2004

We have developed a generalized alphanumeric character extraction algorithm that can efficiently and accurately locate and extract characters from complex scene images. A scene image may be complex due to the following reasons: (1) the characters are embedded in an image with other objects, such as structural bars, company logos and smears; (2) the characters may be painted or printed in any color including white, and the background color may differ only slightly from that of the characters; (3) the font, size and format of the characters may be different; and (4) the lighting may be uneven. The main contribution of this research is that it permits the quick and accurate extraction of characters in a complex scene. A coarse search technique is used to locate potential characters, and then a fine grouping technique is used to extract characters accurately. Several additional techniques in the postprocessing phase eliminate spurious as well as overlapping characters. Experimental results of segmenting characters written on cargo container surfaces show that the system is feasible under real-life constraints. The program has been installed as part of a vision system which verifies container codes on vehicles passing through the Port of Singapore.
3-D OBJECT RECOGNITION THROUGH IMPLICIT MODEL MATCHING
Authors: DAWSON-HOWE KENNETH M. , VERNON DAVID 
Published: November 2004

A new approach to object recognition is presented, in which secondary representations of 3-D models are synthesized/derived (in various forms) and subsequently compared in order to invoke views of models, tune model pose and verify recognition hypotheses. The use of these secondary representations allows complex models (e.g. surface-based or volumetric models) to be compared implicitly (rather than explicitly comparing the component primitives of the models). This in turn overcomes the problem of the stability of the model primitives, and provides independence between the complex 3-D representations and the recognition strategy (i.e. the invocation, matching and verification techniques). The secondary representations employed are Extended Gaussian Images, directional histograms, needle diagrams, depth maps and boundary curvature signatures. The technique is demonstrated using models, of reasonably complex objects, derived from actively sensed range data.
SNUBBER BEHAVIOR AND DESIGN IN FLYBACK CONVERTERS FOR ISOLATED IGBT DRIVERS
Authors: BRAMBILLA ANGELO 
Published: November 2004

When flyback converters are connected to floating loads, voltage swings at the output can give rise to spikes which pass through the flyback transformer stray capacitor. This happens when flyback converters supply IGBT floating gate drivers. These voltage spikes can interfere with the correct behavior of the gate driver. In order to reduce the transformer stray capacitance, the two windings must be wound on the opposite sides of the core. However, this reduces the coupling factor of the transformer by increasing its leakage inductance and snubbers must be employed in some cases. This paper deals with snubber design and behavior for flyback converter applications. Since it is shown that snubbers transfer the energy through the flyback transformer, they should be designed in a different way with respect to conventional applications.
EFFECTS OF FORMAL PLANNING AND CONTROL ON GROWTH: A CASE STUDY APPROACH
Authors: ROMANO CLAUDIO A. , RATNATUNGA JANEK 
Published: November 2004

While planning and control and their impact on small firm growth are implicit in many academic discussions, much of our understanding of these phenomena are based on speculation and opinion. Thus, they seem neglected areas of small business research. This paper seeks to improve the understanding of formal planning and control systems and their relationship to the growth of small business in Australian manufacturing. First, a framework is developed which incorporates the main contextual variables which independently and simultaneously have been shown to have a major relationship with growth. Second, the study provides empirically-based qualitative evidence to further the understanding of causality in the growth of small business by focusing on how formal planning and control systems are embedded within the external or internal contextual variables of small business and the characteristics of their management. Evidence is also provided as to the conditions and circumstances under which formal planning and control are likely to be most effective in controlling the effects of contextual variables, and to the differences between high growth and low growth firms in the use of formal planning and control. The findings of this study are important for two principal reasons. First, it has provided the opportunity to conduct exploratory research into how a small business is managed within the context in which the processes are applied. Second, it has provided the opportunity to identify factors which encourage or discourage small firms to plan, thus providing a better understanding of the planning and control process adopted by small firms.
Tropospheric Ozone in Louisiana and Synoptic Circulation
Authors: Rohli Robert V. , Russo Michelle M. , Vega Anthony J. , Cole John B. 
Published: November 2004

Abstract
Tropospheric ozone (O3) is a pollutant of increasing concern in many urban areas in the United States. There is an increasing need to understand the geographical and meteorological properties associated with O3, particularly because of the changing criteria that are being implemented by the U.S. Environmental Protection Agency to monitor O3. This research examines the relationship between O3 mixing ratios in Louisiana and surface and low-tropospheric synoptic circulation patterns. Results suggest that local conditions and synoptic influences are both important in determining the behavior of observed O3 in Louisiana during this period in which “exceedance” frequencies decreased until 2000–01, at which time they increased again. Furthermore, the expected pattern of surface anticyclonic activity, low-tropospheric ridging, weak pressure gradients, and subsidence from the lower troposphere is found to be associated with anomalously high O3, both at most local sites in the state and on days with anomalously high O3 statewide. More surprising, however, is the tendency for high O3 to be associated with low surface pressure in the Great Plains, perhaps in advance of a midlatitude wave cyclone to the north. This and other surface patterns may be linked to advection from the southeastern Texas urban–industrial corridor. A temporally increasing tendency for surface and lower-tropospheric ridging over the 1994–2001 study period provides at least a partial explanation for the absence of a frequency decline in statewide anomalously high ozone days during a time of increasing public awareness and concern for meeting the O3 standard.
Large-Eddy Simulation of Flow and Pollutant Transport in Street Canyons of Different Building-Height-to-Street-Width Ratios
Authors: Liu Chun-Ho , Barth Mary C. , Leung Dennis Y. C. 
Published: November 2004

Abstract
This study employs a large-eddy simulation technique to investigate the flow, turbulence structure, and pollutant transport in street canyons of building-height-to-street-width (aspect) ratios of 0.5, 1.0, and 2.0 at a Reynolds number of 12 000 and a Schmidt number of 0.72. When the approaching wind is perpendicular to the street axis, a single primary recirculation is calculated for the street canyons of aspect ratios 0.5 and 1.0, and two vertically aligned, counterrotating primary recirculations are found for the street canyon of aspect ratio 2.0. Two to three secondary recirculations are also calculated at the corners of the street canyons. A ground-level passive pollutant line source is used to simulate vehicular emission. The turbulence intensities, pollutant concentration variance, and pollutant fluxes are analyzed to show that the pollutant removal by turbulent transport occurs at the leeward roof level for all aspect ratios. Whereas the ground-level pollutant concentration is greatest at the leeward corner of the street canyons of aspect ratios 0.5 and 1.0, the ground-level pollutant concentration in a street canyon of aspect ratio 2.0 occurs at the windward corner and is greater than the peak concentrations of the other two cases. Because of the smaller ground-level wind speed and the domination of turbulent pollutant transport between the vertically aligned recirculations, the ground-level air quality is poor in street canyons of large aspect ratios. The retention of pollutant in the street canyons is calculated to be 95%, 97%, and 99% for aspect ratios of 0.5, 1.0, and 2.0, respectively.
Numerical Estimations of Horizontal Advection inside Canopies
Authors: Park Young-San , Paw U Kyaw Tha 
Published: November 2004

Abstract
Local advection of scalar quantities such as heat, moisture, or carbon dioxide occurs not only above inhomogeneous surfaces but also within roughness elements on these surfaces. A two-dimensional advection–diffusion equation is applied to examine the fractionation of scalar exchange into horizontal advection within a canopy and vertical turbulent eddy transport at the canopy top. Simulations were executed with combinations of various wind speeds, eddy diffusivities, canopy heights, and source strengths. The results show that the vertical turbulent fluxes at the canopy top increase along the fetch and approach a limit at some downstream distance. The horizontal advection in the canopy is maximum at the edge of canopy and decreases exponentially along the fetch. All cases have the same features, except the absolute quantities depend on the environmental conditions. When the horizontal axis is normalized by using the dimensionless variable xK/uh2, horizontal diffusion is negligible, and the upwind concentration profile is constant, the curves of horizontal advection and vertical flux collapse into single, unique lines, respectively (x is the horizontal distance from the canopy edge, K is the eddy diffusivity, u is the wind speed, and h is the canopy height). The ratios of horizontal advection to the vertical turbulent flux also collapse into one universal curve when plotted against the dimensionless variable xK/uh2, irrespective of source strength. The ratio R shows a power-law relation to the dimensionless distance [R = a(xK/uh2)−b, where a and b are constant].
Phase Alignment of the Tropical Stratospheric QBO in the Annual Cycle
Authors: Hampson John , Haynes Peter 
Published: November 2004

Abstract
This paper investigates the occurrence of phase alignment of the tropical stratospheric quasi-biennial oscillation (QBO) with the annual cycle. First, updating previous studies, observational results are shown for NCEP reanalysis data and Singapore radiosondes: both datasets show strong phase alignment of the QBO at 24.5 km. Phase alignment is investigated in a 3D mechanistic stratospheric model including explicit large-scale planetary waves, forced by a lower boundary geopotential anomaly, and a simple equatorial wave parameterization. The model simulates a QBO-like oscillation, with the period depending on the lower boundary momentum flux of the parameterized waves. Phase alignment is manifested in two different ways. First, simulated oscillations of both integer and noninteger year periods are shown to lock on to a certain phase of the annual cycle. Second, when the magnitude of the lower boundary momentum flux is varied about a range implying oscillation period close to 2 yr, the period of the resulting oscillation is exactly 2 yr for a finite range of such magnitude. Analysis of the 3D model results suggest that the the phase alignment is due largely to the annual cycle in tropical upwelling. This hypothesis is supported by simulations with a 1D equatorial model including both parameterized waves and seasonally varying upwelling. The oscillations in this model show significant phase alignment when the upwelling parameters are tuned to correspond to the 3D model, although the phase alignment is weaker than that seen in the 3D model.