bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serological Reactivity and Biochemical Characterization of Methylated and Unmethylated Forms of a Recombinant Protein Fragment Derived from Outer Membrane Protein B of
Rickettsia typhi
Authors: Chao Chien-Chung , Zhang Zhiwen , Wang Hui , Alkhalil Abdulnaser , Ching Wei-Mei 
Published: February 2008

ABSTRACT

Rickettsia typhi
, an obligate intracellular bacterium that causes murine typhus, possesses a heavily methylated outer membrane protein B (OmpB) antigen. This immunodominant antigen is responsible for serological reactions and is capable of eliciting protective immune responses with a guinea pig model. Western blot analysis of partially digested OmpB with patient sera revealed that most of the reactive fragments are larger than 20 kDa. One of these fragments, which is located at the N terminus (amino acids 33 to 273), fragment A (At), has been expressed in
Escherichia coli
. The expressed protein (rAt) was purified by chromatography and properly refolded by sequential dialysis. The refolded rAt protein was recognized by at least 87% of the typhus group patient sera as determined by enzyme-linked immunosorbent assay (ELISA). However, the titers were lower than those obtained with OmpB of
R. typhi
. Since native OmpB is hypermethylated at lysine residues, we chemically methylated the lysine residues in rAt. The methylation was confirmed by amino acid composition analysis, and the methylation pattern of the methylated rAt (mrAt) protein was similar to that of native At from OmpB, as revealed by liquid chromatography-mass spectrometry analysis. Both rAt and mrAt were evaluated in an ELISA for their serological reactivity with patient sera. Among patient sera tested, 83% exhibited higher titers with mrAt than with rAt. These results suggest that rAt, with or without methylation, can potentially replace rickettsia-derived OmpB or whole-cell antigen for the diagnosis of
R. typhi
infection.
Comparative Analysis of Human and Canine
Campylobacter upsaliensis
Isolates by Amplified Fragment Length Polymorphism
Authors: Damborg Peter , Guardabassi Luca , Pedersen Karl , Kokotovic Branko 
Published: February 2008

ABSTRACT

Human (
n
= 33) and canine (
n
= 53)
Campylobacter upsaliensis
isolates from seven countries were genotyped by a new amplified fragment length polymorphism method. We observed 100% typeability and high overall diversity. The majority of human strains (23/33) clustered separately from canine strains, indicating that dogs may not be the main source of human infection.
Comparison of Reverse Hybridization, Microarray, and Sequence Analysis for Genotyping Hepatitis B Virus
Authors: Pas Suzan D. , Tran Nathalie , de Man Robert A. , Burghoorn-Maas C. , Vernet Guy , Niesters Hubert G. M. 
Published: February 2008

ABSTRACT
Hepatitis B virus (HBV) genotyping has become important in epidemiological and clinical diagnoses, given the relationship between the viral genotype and the progression of disease or the appearance of antiviral resistance. Since genotyping by sequence and phylogenetic analyses is not convenient in the clinical setting, we evaluated InnoLipa HBV genotyping (Innogenetics, Belgium) and an HBV DNA-Chip (bioMerieux, France) prototype assay and compared their sequencing of the gold standard S gene, using a cohort of 275 individual patient samples. All but two samples, belonging to distant and individual subgroups within a single genotype, were detected by InnoLipa HBV assay. Four samples with dual infections belonging to genotypes A and G were identified only by InnoLipa HBV assay. Using an HBV DNA-Chip assay, one sample could not be amplified due to a low viral load. Four samples were identified as genotype C and two as genotype D by sequencing but were classified as genotype A (two samples) and D (two samples) and as A (one sample) and G (one sample) by the DNA-Chip assay. In conclusion, the InnoLipa HBV genotyping strip assay detected dual infections and was an easy and quick tool for genotyping, with a sensitivity of 99.3% and a specificity of 100% compared to sequence analysis. HBV DNA-Chip assay showed a sensitivity and specificity of 97.5 and 97.8%, respectively.
Population Structure of Invasive and Colonizing Strains of
Streptococcus agalactiae
from Neonates of Six U.S. Academic Centers from 1995 to 1999
Authors: Bohnsack John F. , Whiting April , Gottschalk Marcelo , Dunn Diane Marie , Weiss Robert , Azimi Parvin H. , Philips Joseph B. , Weisman Leonard E. , Rhoads George G. , Lin Feng-Ying C. 
Published: February 2008

ABSTRACT
The purpose of this study was to describe the population structure of group B streptococci (GBS) isolated from infected and colonized neonates during a prospective active-surveillance study of early-onset disease in six centers in the United States from July 1995 to June 1999 and to examine its relationship to bovine strains of GBS. The phylogenetic lineage of each GBS isolate was determined by multilocus sequence typing, and isolates were clustered into clonal complexes (CCs) using the eBURST software program. A total of 899 neonatal GBS isolates were studied, of which 129 were associated with invasive disease. Serotype Ia, Ib, and V isolates were highly clonal, with 92% to 96% of serotype Ia, Ib, and V isolates being confined to single clonal clusters. In contrast, serotype II and III isolates were each comprised of two major clones, with 39% of serotype II and 41% of serotype III isolates in CC 17 and 41% of serotype II and 54% of serotype III isolates in CC 19. Further analysis demonstrates that the CC 17 serotype II and III GBS are closely related to a previously described “ancestral” lineage of bovine GBS. While 120 (93%) of invasive GBS were confined to the same lineages that colonized neonates, 9 (7%) of the invasive GBS isolates were from rare lineages that comprised only 2.7% of colonizing lineages. These results are consistent with those for other geographic regions that demonstrate the highly clonal nature of GBS infecting and colonizing human neonates.
Impact of Human Bocavirus on Children and Their Families
Authors: Esposito Susanna , Bosis Samantha , Niesters Hubert G. M. , Tremolati Elena , Sabatini Caterina , Porta Alessandro , Fossali Emilio , Osterhaus Albert D. M. E. , Principi Nicola 
Published: February 2008

ABSTRACT

This study was planned to investigate the prevalence and clinical features of the illnesses associated with human bocavirus (hBoV) in children with acute disease. We prospectively enrolled all subjects aged less than 15 years attending an emergency room in Milan, Italy, on Wednesdays and Sundays between 1 November 2004 and 31 March 2005 for any acute medical reason, excluding surgical diseases and trauma. Nasopharyngeal swabs were collected at admission to detect hBoV; influenza A and B viruses; respiratory syncytial virus; human metapneumovirus; parainfluenza viruses 1, 2, 3, and 4; rhinovirus; adenovirus; and coronaviruses 229E, OC43, NL63, and HKU1 by real-time PCR. Among the 1,332 enrolled children, hBoV was the fifth most frequently detected virus (7.4%). The rate of hBoV coinfections with other viruses was significantly higher than for the other viruses (50.5% versus 27.5%;
P
< 0.0001). Eighty-nine of the 99 hBoV-positive children (89.9%) had a respiratory tract infection, and 10 (10.1%) had gastroenteritis. hBoV coinfections had a significantly greater clinical and socioeconomic impact on the infected children and their households than hBoV infection alone. In conclusion, these findings show that the role of hBoV infection alone seems marginal in children attending an emergency room for acute disease; its clinical and socioeconomic importance becomes relevant only when it is associated with other viruses.
High-Capacity Adenovirus Vector-Mediated Anti-Glioma Gene Therapy in the Presence of Systemic Antiadenovirus Immunity
Authors: King Gwendalyn D. , Muhammad A. K. M. Ghulam , Xiong Weidong , Kroeger Kurt M. , Puntel Mariana , Larocque Daniel , Palmer Donna , Ng Philip , Lowenstein Pedro R. , Castro Maria G. 
Published: February 2008

ABSTRACT
Gene therapy is proposed as a novel therapeutic strategy for treating glioblastoma multiforme (GBM), a devastating brain cancer. In the clinic, antivector immune responses pose formidable challenges. Herein we demonstrate that high-capacity adenovirus vectors (HC-Ads) carrying the conditional cytotoxic gene herpes simplex virus type 1-thymidine kinase (TK) induce tumor regression and long-term survival in an intracranial glioma model, even in the presence of systemic antiadenovirus immunity, as could be encountered in patients. First-generation Ad-TK failed to elicit tumor regression in this model. These results pave the way for implementing HC-Ad-TK-mediated gene therapy as a powerful adjuvant for treating GBM.
Inhibition of CD1 Antigen Presentation by Human Cytomegalovirus
Authors: Raftery Martin J. , Hitzler Manuel , Winau Florian , Giese Thomas , Plachter Bodo , Kaufmann Stefan H. E. , Schönrich Günther 
Published: February 2008

ABSTRACTThe betaherpesvirus human cytomegalovirus (HCMV) encodes several molecules that block antigen presentation by the major histocompatibility complex (MHC) proteins. Humans also possess one other family of antigen-presenting molecules, the CD1 family; however, the effect of HCMV on CD1 expression is unknown. The majority of CD1 molecules are classified on the basis of homology as group 1 CD1 and are present almost exclusively on professional antigen-presenting cells such as dendritic cells, which are a major target for HCMV infection and latency. We have determined that HCMV encodes multiple blocking strategies targeting group 1 CD1 molecules. CD1 transcription is strongly inhibited by the HCMV interleukin-10 homologue cmvIL-10. HCMV also blocks CD1 antigen presentation posttranscriptionally by the inhibition of CD1 localization to the cell surface. This function is not performed by a known HCMV MHC class I-blocking molecule and is substantially stronger than the blockage induced by herpes simplex virus type 1. Antigen presentation by CD1 is important for the development of the antiviral immune response and the generation of mature antigen-presenting cells. HCMV present in antigen-presenting cells thus blunts the immune response by the blockage of CD1 molecules.
The GLN Family of Murine Endogenous Retroviruses Contains an Element Competent for Infectious Viral Particle Formation
Authors: Ribet David , Harper Francis , Esnault Cécile , Pierron Gérard , Heidmann Thierry 
Published: February 2008

ABSTRACT

Several families of endogenous retroviruses (ERVs) have been identified in the mouse genome, in several instances by in silico searches, but for many of them it remains to be determined whether there are elements that can still encode functional retroviral particles. Here, we identify, within the GLN family of highly reiterated ERVs, one, and only one, copy that encodes retroviral particles prone to infection of mouse cells. We show that its envelope protein confers an ecotropic host range and recognizes a receptor different from mCAT1 and mSMIT1, the two previously identified receptors for other ecotropic mouse retroviruses. Electron microscopy disclosed viral particle assembly and budding at the cell membrane, as well as release of mature particles into the extracellular space. These particles are closely related to murine leukemia virus (MLV) particles, with which they have most probably been confused in the past. This study, therefore, identifies a new class of infectious mouse ERVs belonging to the family
Gammaretroviridae
, with one family member still functional today. This family is in addition to the two MLV and mouse mammary tumor virus families of active mouse ERVs with an extracellular life cycle.
Theiler's Virus-Induced Intrinsic Apoptosis in M1-D Macrophages Is Bax Mediated and Restricts Virus Infectivity: a Mechanism for Persistence of a Cytolytic Virus
Authors: Son Kyung-No , Becker Robert P. , Kallio Patricia , Lipton Howard L. 
Published: February 2008

ABSTRACTTheiler's murine encephalomyelitis virus (TMEV), a member of theCardiovirusgenus in the familyPicornaviridae, is a highly cytolytic virus that produces necrotic death in rodent cells except for macrophages, which undergo apoptosis. In the present study we have analyzed the kinetics of BeAn virus infection in M1-D cells, in order to temporally relate virus replication to the apoptotic signaling events. Apoptosis was associated with early exponential virus growth from 1 to 12 h postinfection (p.i.); however, ≥80% of peak infectivity was lost by 16 to 24 h p.i. The pan-caspase inhibitor qVD-OPh led to significantly higher virus yields, while zVAD-fmk completely inhibited virus replication until 10 h p.i., precluding its assessment in apoptosis. In contrast, while zVAD-fmk significantly inhibited BeAn virus replication in BHK-21 cells at 12 and 16 h p.i., virus replication at these time points was not altered by qVD-OPh. Bax translocation into mitochondria, efflux of cytochromecinto the cytoplasm, and activation of caspases 9 and 3 between ∼8 and 12 h p.i. (all hallmarks of the intrinsic apoptotic pathway) were transiently inhibited by expression of Bcl-2, which is not expressed in M1-D cells. Thus, BeAn virus infection in M1-D macrophages, which restricts virus replication, provides a potential mechanism for modulating TMEV neurovirulence during persistence in the mouse central nervous system.
Measles Virus Infects both Polarized Epithelial and Immune Cells by Using Distinctive Receptor-Binding Sites on Its Hemagglutinin
Authors: Tahara Maino , Takeda Makoto , Shirogane Yuta , Hashiguchi Takao , Ohno Shinji , Yanagi Yusuke 
Published: February 2008

ABSTRACT
Measles is one of the most contagious human infectious diseases and remains a major cause of childhood morbidity and mortality worldwide. The signaling lymphocyte activation molecule (SLAM), also called CD150, is a cellular receptor for measles virus (MV), presumably accounting for its tropism for immune cells and its immunosuppressive properties. On the other hand, pathological studies have shown that MV also infects epithelial cells at a later stage of infection, although its mechanism has so far been unknown. In this study, we show that wild-type MV can infect and produce syncytia in human polarized epithelial cell lines independently of SLAM and CD46 (a receptor for the vaccine strains of MV). Progeny viral particles are released exclusively from the apical surface of these polarized epithelial cell lines. We have also identified amino acid residues on the MV attachment protein that are likely to interact with a putative receptor on epithelial cells. All of these residues have aromatic side chains and may form a receptor-binding pocket located in a different position from the putative SLAM- and CD46-binding sites on the MV attachment protein. Thus, our results indicate that MV has an intrinsic ability to infect both polarized epithelial and immune cells by using distinctive receptor-binding sites on the attachment protein corresponding to each of their respective receptors. The ability of MV to infect polarized epithelial cells and its exclusive release from the apical surface may facilitate its efficient transmission via aerosol droplets, resulting in its highly contagious nature.
Periodic Orbits with Least Period Three on the Circle
Authors: Zhao Xuezhi 
Published: February 2008

AbstractThe self-maps on the circle having periodic orbits with least period 3 are classified into relative homotopy-conjugacy classes. We will show that except for the maps in one exceptional class, all these kinds of maps have periodic orbits with all least periods but 2. Thus, a kind of Sharkovskii's type theorem on the circle is obtained.
Multisensor Estimation of Mixing Heights over a Coastal City
Authors: Nielsen-Gammon John W. , Powell Christina L. , Mahoney M. J. , Angevine Wayne M. , Senff Christoph , White Allen , Berkowitz Carl , Doran Christopher , Knupp Kevin 
Published: February 2008

AbstractAn airborne microwave temperature profiler (MTP) was deployed during the Texas 2000 Air Quality Study (TexAQS-2000) to make measurements of boundary layer thermal structure. An objective technique was developed and tested for estimating the mixed layer (ML) height from the MTP vertical temperature profiles. The technique identifies the ML height as a threshold increase of potential temperature from its minimum value within the boundary layer. To calibrate the technique and evaluate the usefulness of this approach, coincident estimates from radiosondes, radar wind profilers, an aerosol backscatter lidar, and in situ aircraft measurements were compared with each other and with the MTP. Relative biases among all instruments were generally less than 50 m, and the agreement between MTP ML height estimates and other estimates was at least as good as the agreement among the other estimates. The ML height estimates from the MTP and other instruments are utilized to determine the spatial and temporal evolution of ML height in the Houston, Texas, area on 1 September 2000. An elevated temperature inversion was present, so ML growth was inhibited until early afternoon. In the afternoon, large spatial variations in ML height developed across the Houston area. The highest ML heights, well over 2 km, were observed to the north of Houston, while downwind of Galveston Bay and within the late afternoon sea breeze ML heights were much lower. The spatial variations that were found away from the immediate influence of coastal circulations were unexpected, and multiple independent ML height estimates were essential for documenting this feature.
Assessing Predictability of Cotton Yields in the Southeastern United States Based on Regional Atmospheric Circulation and Surface Temperatures
Authors: Baigorria Guillermo A. , Hansen James W. , Ward Neil , Jones James W. , O’Brien James J. 
Published: February 2008

AbstractThe potential to predict cotton yields up to one month before planting in the southeastern United States is assessed in this research. To do this, regional atmospheric variables that are related to historic summer rainfall and cotton yields were identified. The use of simulations of those variables from a global circulation model (GCM) for estimating cotton yields was evaluated. The authors analyzed detrended cotton yields (1970–2004) from 48 counties in Alabama and Georgia, monthly rainfall from 53 weather stations, monthly reanalysis data of 850- and 200-hPa winds and surface temperatures over the southeast U.S. region, and monthly predictions of the same variables from the ECHAM 4.5 GCM. Using the reanalysis climate data, it was found that meridional wind fields and surface temperatures around the Southeast were significantly correlated with county cotton yields (explaining up to 52% of the interannual variability of observed yields), and with rainfall over most of the region, especially during April and July. The tendency for cotton yields to be lower during years with atmospheric circulation patterns that favor higher humidity and rainfall is consistent with increased incidence of disease in cotton during flowering and harvest periods under wet conditions. Cross-validated yield estimations based on ECHAM retrospective simulations of wind and temperature fields forced by observed SSTs showed significant predictability skill (up to 55% and 60% hit skill scores based on terciles and averages, respectively). It is concluded that there is potential to predict cotton yields in the Southeast by using variables that are forecast by numerical climate models.
Retrieval of Raindrop Size Distribution from Simulated Dual-Frequency Radar Measurements
Authors: Munchak S. Joseph , Tokay Ali 
Published: February 2008

Abstract
Observations of raindrop size distributions (DSDs) have validated the use of three-parameter distribution functions in representing the observed spectra. However, dual-frequency radar measurements are limited to retrieving two independent parameters of the DSD, thus requiring a constraint on a three-parameter distribution. In this study, disdrometer observations from a variety of climate regions are employed to develop constraints on the gamma distribution that are optimized for dual-frequency radar rainfall retrievals. These observations are composited by reflectivity, and then gamma parameters are fit to the composites. The results show considerable variability in shape parameter between regions and within a region at different reflectivities. Most notable is that oceanic regions exhibit maxima in shape parameter at 13.6-GHz reflectivities between 40 and 50 dBZ, in contrast to continental regions. The shape parameter and slope parameter of all composite DSDs are poorly correlated. Thus, constraints of a constant shape parameter or shape parameter–slope parameter relationship are inadequate to represent the observed variability. However, the shape and slope parameters are highly correlated at a given reflectivity. Constraints of a fixed shape parameter and relationships between a shape parameter m and slope parameter Λ, both of which are given as functions of 13.6-GHz reflectivity, are applied to retrieve rain rate, liquid water content, and mean mass diameter from the composites. The m–Λ relationships perform best at high reflectivity (dBZ13.6 &gt; 35), whereas the fixed shape parameter generally results in lower error at medium and low reflectivities (dBZ13.6 &lt; 35). All calculations have been made under the assumption that the reflectivity measurements have been corrected for attenuation.
Turbulent Flux Transfer over Bare-Soil Surfaces: Characteristics and Parameterization
Authors: Yang Kun , Koike Toshio , Ishikawa Hirohiko , Kim Joon , Li Xin , Liu Huizhi , Liu Shaomin , Ma Yaoming , Wang Jieming 
Published: February 2008

AbstractParameterization of turbulent flux from bare-soil and undercanopy surfaces is imperative for modeling land–atmosphere interactions in arid and semiarid regions, where flux from the ground is dominant or comparable to canopy-sourced flux. This paper presents the major characteristics of turbulent flux transfers over seven bare-soil surfaces. These sites are located in arid, semiarid, and semihumid regions in Asia and represent a variety of conditions for aerodynamic roughness length (z0m; from &lt;1 to 10 mm) and sensible heat flux (from −50 to 400 W m−2). For each site, parameter kB−1 [=ln(z0m/z0h), where z0h is the thermal roughness length] exhibits clear diurnal variations with higher values during the day and lower values at night. Mean values of z0h for the individual sites do not change significantly with z0m, resulting in kB−1 increasing with z0m, and thus the momentum transfer coefficient increases faster than the heat transfer coefficient with z0m. The term kB−1 often becomes negative at night for relatively smooth surfaces (z0m ∼ 1 mm), indicating that the widely accepted excess resistance for heat transfer can be negative, which cannot be explained by current theories for aerodynamically rough surfaces. Last, several kB−1 schemes are evaluated using the same datasets. The results indicate that a scheme that can reproduce the diurnal variation of kB−1 generally performs better than schemes that cannot.