bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of Severe
Streptococcus pyogenes
Disease in Europe
Authors: Lamagni Theresa L. , Darenberg Jessica , Luca-Harari Bogdan , Siljander Tuula , Efstratiou Androulla , Henriques-Normark Birgitta , Vuopio-Varkila Jaana , Bouvet Anne , Creti Roberta , Ekelund Kim , Koliou Maria , Reinert Ralf René , Stathi Angeliki , Strakova Lenka , Ungureanu Vasilica , Schalén Claes , Jasir Aftab 
Published: May 2008

ABSTRACT

The past 2 decades have brought worrying increases in severe
Streptococcus pyogenes
diseases globally. To investigate and compare the epidemiological patterns of these diseases within Europe, data were collected through a European Union FP-5-funded program (Strep-EURO). Prospective population-based surveillance of severe
S. pyogenes
infection diagnosed during 2003 and 2004 was undertaken in 11 countries across Europe (Cyprus, the Czech Republic, Denmark, Finland, France, Germany, Greece, Italy, Romania, Sweden, and the United Kingdom) using a standardized case definition. A total of 5,522 cases were identified across the 11 countries during this period. Rates of reported infection varied, reaching 3/100,000 population in the northern European countries. Seasonal patterns of infection showed remarkable congruence between countries. The risk of infection was highest among the elderly, and rates were higher in males than in females in most countries. Skin lesions/wounds were the most common predisposing factor, reported in 25% of cases; 21% had no predisposing factors reported. Skin and soft tissue were the most common foci of infection, with 32% of patients having cellulitis and 8% necrotizing fasciitis. The overall 7-day case fatality rate was 19%; it was 44% among patients who developed streptococcal toxic shock syndrome. The findings from Strep-EURO confirm a high incidence of severe
S. pyogenes
disease in Europe. Furthermore, these results have identified targets for public health intervention, as well as raising awareness of severe
S. pyogenes
disease across Europe.
Novel Chromogenic Medium for Detection of Vancomycin-Resistant
Enterococcus faecium
and
Enterococcus faecalis
Authors: Cuzon Gaëlle , Naas Thierry , Fortineau Nicolas , Nordmann Patrice 
Published: May 2008

ABSTRACT
Vancomycin-resistant enterococci (VRE) are becoming widespread worldwide, and the rapid identification of VRE carriers from surveillance cultures is crucial for the efficient control of their spread. We assessed a new selective chromogenic medium, chromID VRE (bioMérieux, France), that enhanced the isolation and presumptive identification of VRE directly from rectal swabs and reduced unnecessary confirmatory and time-consuming tests.
Comparison of Respiratory Virus Detection Rates for Infants and Toddlers by Use of Flocked Swabs, Saline Aspirates, and Saline Aspirates Mixed in Universal Transport Medium for Room Temperature Storage and Shipping
Authors: Walsh Paul , Overmyer Christina Lim , Pham Kiemanh , Michaelson Scott , Gofman Larisa , DeSalvia Lisa , Tran Ty , Gonzalez Diana , Pusavat James , Feola Melanie , Iacono Kathryn T. , Mordechai Eli , Adelson Martin E. 
Published: May 2008

ABSTRACT

A nylon flocked swab/universal transport medium collection method developed for bacterial sexually transmitted infections was adapted to detect respiratory viruses in infants and toddlers. This method significantly outperformed the traditional use of nasal aspirates in terms of PCR-based virus detection (
P
= 0.016), and the samples were easier for clinicians to evaluate, store, and transport.
Impact of
mecA
Gene Testing and Intervention by Infectious Disease Clinical Pharmacists on Time to Optimal Antimicrobial Therapy for
Staphylococcus aureus
Bacteremia at a University Hospital
Authors: Carver Peggy L. , Lin Shu-Wen , DePestel Daryl D. , Newton Duane W. 
Published: May 2008

ABSTRACT

In patients with
Staphylococcus aureus
bacteremia, intervention by infectious disease clinical pharmacists on the basis of the results of tests for
mecA
resulted in a 25.4-h reduction in the time to optimal antimicrobial therapy, from 64.7 ± 36.8 to 39.3 ± 15.5 h (
P
= 0.002), which may result in decreased mortality.
Quadruplex Real-Time PCR Assay Using Allele-Specific Scorpion Primers for Detection of Mutations Conferring Clarithromycin Resistance to
Helicobacter pylori
Authors: Burucoa Christophe , Garnier Martine , Silvain Christine , Fauchère Jean-Louis 
Published: May 2008

ABSTRACT

We developed a single-vessel multiplex real-time PCR assay that detects
Helicobacter pylori
infection and identified the four existing alleles of the 23S rRNA genes of
H. pylori
—the wild-type sequence and the three mutations conferring clarithromycin resistance—using allele-specific Scorpion primers directly on biopsy specimens. The Scorpion primers combine a primer and a probe in a single molecule and are able to distinguish single-nucleotide polymorphism. Fluorescent signals, produced when the probes are annealed, are read in four channels by a SmartCycler thermocycler. The assay was first applied successfully on 4 reference and 61 clinical strains. MICs of clarithromycin were determined by the Etest method. A perfect concordance was obtained between Etest and Scorpion PCR. Mixed populations were better detected by Scorpion PCR. We examined 259 biopsies from 229 patients by culture, PCR-restriction fragment length polymorphism (RFLP), and Scorpion PCR. One biopsy, positive for culture, exhibited inhibitors for both PCR-RFLP and Scorpion PCR. Twelve biopsies were positive for PCR-RFLP and Scorpion PCR but negative for culture with concordant determination of mutations in the 23S rRNA genes by the two PCR assays. Three biopsies were positive for Scorpion PCR only. Compared to culture, the sensitivity of Scorpion PCR was 98.3% and the specificity was 92.5%. The Scorpion PCR assay provides a highly accurate, rapid, and precise method for the detection and determination of mutations conferring clarithromycin resistance to
H. pylori.
Epstein-Barr Virus SM Protein Functions as an Alternative Splicing Factor
Authors: Verma Dinesh , Swaminathan Sankar 
Published: May 2008

ABSTRACT
Alternative splicing of RNA increases the coding potential of the genome and allows for additional regulatory control over gene expression. The full extent of alternative splicing remains to be defined but is likely to significantly expand the size of the human transcriptome. There are several examples of mammalian viruses regulating viral splicing or inhibiting cellular splicing in order to facilitate viral replication. Here, we describe a viral protein that induces alternative splicing of a cellular RNA transcript. Epstein-Barr virus (EBV) SM protein is a viral protein essential for replication that enhances EBV gene expression by enhancing RNA stability and export. SM also increases cellular STAT1 expression, a central mediator of interferon signal transduction, but disproportionately increases the abundance of the STAT1β splicing isoform, which can act as a dominant-negative suppressor of STAT1α. SM induces splicing of STAT1 at a novel 5′ splice site, resulting in a STAT1 mRNA incapable of producing STAT1α. SM-induced alternative splicing is dependent on the presence of an RNA sequence to which SM binds directly and which can confer SM-dependent splicing on heterologous RNA. The cellular splicing factor ASF/SF2 also binds to this region and inhibits SM-RNA binding and SM-induced alternative splicing. These results suggest that viruses may regulate cellular gene expression at the level of alternative mRNA splicing in order to facilitate virus replication or persistence in vivo.
Recombinant Adeno-Associated Viral Vectors Are Deficient in Provoking a DNA Damage Response
Authors: Fragkos Michalis , Breuleux Madlaina , Clément Nathalie , Beard Peter 
Published: May 2008

ABSTRACT

Adeno-associated virus type 2 (AAV2) provokes a DNA damage response that mimics a stalled replication fork. We have previously shown that this response is dependent on ataxia telangiectasia-mutated and Rad3-related kinase and involves recruitment of DNA repair proteins into foci associated with AAV2 DNA. Here, we investigated whether recombinant AAV2 (rAAV2) vectors are able to produce a similar response. Surprisingly, the results show that both single-stranded and double-stranded green fluorescent protein-expressing rAAV2 vectors are defective in producing such a response. We show that the DNA damage signaling initiated by AAV2 was not due to the virus-encoded Rep or viral capsid proteins. UV-inactivated AAV2 induced a response similar to that of untreated AAV2. This type of DNA damage response was not provoked by other DNA molecules, such as single-stranded bacteriophage M13 or plasmid DNAs. Rather, the results indicate that the ability of AAV2 to produce a DNA damage response can be attributed to the presence of
cis
-acting AAV2 DNA sequences, which are absent in rAAV2 vectors and could function as origins of replication creating stalled replication complexes. This hypothesis was tested by using a single-stranded rAAV2 vector containing the p5 AAV2 sequence that has previously been shown to enhance AAV2 replication. This vector was indeed able to trigger DNA damage signaling. These findings support the conclusion that efficient formation of AAV2 replication complexes is required for this AAV2-induced DNA damage response and provide an explanation for the poor response in rAAV2-infected cells.
Identification of the Myelin Protein Plasmolipin as the Cell Entry Receptor forMus caroliEndogenous Retrovirus
Authors: Miller A. Dusty , Bergholz Ulla , Ziegler Marion , Stocking Carol 
Published: May 2008

ABSTRACTThe Asian wild mouse speciesMus caroliharbors an endogenous retrovirus (McERV) that is closely related to but distinct from the endogenous retrovirus family defined by theMus dunniendogenous virus and theMus musculusendogenous retrovirus. McERV could infect some cell types from humans, dogs, and rats, but not all, and did not infect any mouse cell line tested. Because of its interesting host range and proposed ancestral relationship to primate retroviruses and because none of the entry receptors for this family of retroviruses had been identified, we began a search for the McERV receptor. We determined the chromosomal location of the receptor gene in the human genome by phenotypic screening of the G3 human-hamster radiation hybrid cell line panel and confirmed the localization by assaying for receptor activity conferred by bacterial artificial chromosome (BAC) clones spanning the region. We next localized the gene more precisely in one positive BAC by assaying for receptor activity following BAC digestion with several restriction enzymes that cleaved different sets of genes, and we confirmed that the final candidate gene, plasmolipin (PLLP; TM4SF11), is the novel receptor by showing that the expression of the human PLLP cDNA renders hamster and mouse cells susceptible to McERV infection. PLLP functions as a voltage-dependent potassium ion channel and is expressed primarily in kidney and brain, helping to explain the limited range of cell types that McERV can infect. Interestingly, mouse PLLP also functioned well as a receptor for McERV but was simply not expressed in the mouse cell types that we originally tested.
Small Capsid Protein pORF65 Is Essential for Assembly of Kaposi's Sarcoma-Associated Herpesvirus Capsids
Authors: Perkins Edward M. , Anacker Daniel , Davis Aaron , Sankar Vishwam , Ambinder Richard F. , Desai Prashant 
Published: May 2008

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent for KS tumors, multicentric Castleman's disease, and primary effusion lymphomas. Like other herpesvirus capsids, the KSHV capsid is an icosahedral structure composed of six proteins. The capsid shell is made up of the major capsid protein, two triplex proteins, and the small capsid protein. The scaffold protein and the protease occupy the internal space. The assembly of KSHV capsids is thought to occur in a manner similar to that determined for herpes simplex virus type 1 (HSV-1). Our goal was to assemble KSHV capsids in insect cells using the baculovirus expression vector system. Six KSHV capsid open reading frames were cloned and the proteins expressed in Sf9 cells: pORF25 (major capsid protein), pORF62 (triplex 1), pORF26 (triplex 2), pORF17 (protease), pORF17.5 (scaffold protein), and also pORF65 (small capsid protein). When insect cells were coinfected with these baculoviruses, angular capsids that contained internal core structures were readily observed by conventional electron microscopy of the infected cells. Capsids were also readily isolated from infected cells by using rate velocity sedimentation. With immuno-electron microscopy methods, these capsids were seen to be reactive to antisera to pORF65 as well as to KSHV-positive human sera, indicating the correct conformation of pORF65 in these capsids. When either virus expressing the triplex proteins was omitted from the coinfection, capsids did not assemble; similar to observations made in HSV-1-infected cells. If the virus expressing the scaffold protein was excluded, large open shells that did not attain icosahedral structure were seen in the nuclei of infected cells. The presence of pORF65 was required for capsid assembly, in that capsids did not form if this protein was absent as judged by both by ultrastructural analysis of infected cells and rate velocity sedimentation experiments. Thus, a novel outcome of this study is the finding that the small capsid protein of KSHV, like the major capsid and triplex proteins, is essential for capsid shell assembly.
A new modelling approach for unsaturated soils using independent stress variables
Authors: Sheng Daichao , Fredlund Delwyn G. , Gens Antonio 
Published: May 2008

Although a number of constitutive models for unsaturated soils exist in the literature, some fundamental questions have not been fully answered. There are questions related to (i) the change of the yield stress with soil suction, (ii) modelling slurry soils, and (iii) the smooth transition between saturated and unsaturated soil states. This paper addresses these questions by proposing an alternative modelling approach. The paper first presents a volumetric model for unsaturated soils. This volumetric model is then used to derive the yield surface in the suction – mean stress space. Hysteresis associated with soil-water characteristic curves is then formulated in the same framework of elastoplasticity. It is shown that volume collapse during wetting and plastic shrinkage during initial drying are both direct results of a suction-dependent hardening law. The proposed model seems to be more flexible in modelling different types of unsaturated soils than most models in the literature. The model can be applied to soils that are dried or loaded from initially slurry conditions, for soils that have low to high air-entry values, and for compacted soils as well.
COMPACT OPTICAL CHARACTERIZATION PLATFORM FOR DETECTION OF BIO-MOLECULES IN FLUIDIC AND AEROSOL SAMPLES
Authors: KIESEL PETER , SCHMIDT OLIVER , BASSLER MICHAEL , JOHNSON NOBLE 
Published: May 2008

An optical characterization unit based on fluorescence spectroscopy-on-a-chip is described. It comprises a compact fluidic platform that is integrated onto a chip-size spectrometer. The analyte is continuously excited within a novel waveguide. Fluorescence spectra are recorded as the analyte traverse the detection area. In order to achieve a strong interaction between excitation light and analyte we use an anti-resonant waveguide, in which the light is guided within the target-containing medium, thereby enabling a continuous excitation of a large volume. The excitation light is guided in the lower-refractive-index fluid when the light is coupled into the waveguide at an appropriate angle. Compact spectrometers can be integrated along the fluidic channel. The spectrometers are composed of a detector array which is coated with a linear variable band-pass filter. The filter converts the spectral fluorescence information into a spatially dependent signal that is analyzed by the detector array. These chip-size spectrometers are especially applicable for characterization of moving analytes.
A Negative Soil Moisture–Precipitation Relationship and Its Causes
Authors: Wei Jiangfeng , Dickinson Robert E. , Chen Haishan 
Published: May 2008

Abstract
This study examines a lagged soil moisture–precipitation (S–P) correlation for 24 yr of boreal summer (1979–2002) from the 40-yr ECMWF Re-Analysis (ERA-40), the NCEP–Department of Energy (DOE) reanalysis 2 (R-2), the North American Regional Reanalysis (NARR), 10 yr (1986–95) of data from phase 2 of the Global Soil Wetness Project (GSWP-2), and two 24-yr model simulations with the NCAR Community Atmosphere Model version 3.1 (CAM3). The different datasets and model simulations all show a similar negative-dominant S–P correlation pattern with wet areas having more significantly negative correlations than the dry areas. The experiments with CAM3 show that this correlation pattern is not caused by the soil moisture feedback. Rather, the combined effect of the precipitation variability and the memory of soil moisture is the main reason for this correlation pattern. Theoretical analysis confirms this conclusion and shows that the correlation pattern is related to both the precipitation spectrum and the time scale of soil moisture retention. This study suggests that the attribution of lagged correlations of precipitation with soil moisture or related variables should be done cautiously.
On the Upwelling of Downwelling Currents
Authors: Matano Ricardo P. , Palma Elbio D. 
Published: May 2008

Abstract
The term “downwelling currents” refers to currents with a downslope mass flux in the bottom boundary layer. Examples are the Malvinas and Southland Currents in the Southern Hemisphere and the Oyashio in the Northern Hemisphere. Although many of these currents generate the same type of highly productive ecosystems that is associated with upwelling regimes, the mechanism that may drive such upwelling remains unclear. In this article, it is postulated that the interaction between a downwelling current and the continental slope generates shelfbreak upwelling. The proposed mechanism is relatively simple. As a downwelling current flows along the continental slope, bottom friction and lateral diffusion spread it onto the neighboring shelf, thus generating along-shelf pressure gradients and a cross-shelf circulation pattern that leads to shelfbreak upwelling. At difference with previous studies of shelfbreak dynamics (e.g., Gawarkiewicz and Chapman, Chapman and Lentz, and Pickart), the shelfbreak upwelling in the proposed model is not controlled by the downslope buoyancy flux associated with the presence of a shelf current but by the along-shelf pressure gradient associated with the presence of a slope current. As these experiments demonstrate, shelfbreak upwelling will occur in flat-bottomed domains or even in the absence of a bottom boundary layer. The shelfbreak upwelling, moreover, is not evidence of the separation of the bottom boundary layer but of the downstream divergence of the slope currents, and its magnitude is proportional to the volume transport of that current. To prove this hypothesis, the results of a series of process-oriented numerical experiments are presented.
Summertime Influence of SST on Surface Wind Stress off the U.S. West Coast from the U.S. Navy COAMPS Model*
Authors: Haack Tracy , Chelton Dudley , Pullen Julie , Doyle James D. , Schlax Michael 
Published: May 2008

Abstract
High-resolution mesoscale model sea surface temperature (SST) analyses and surface wind stress forecasts off the U.S. West Coast are analyzed on monthly time scales for robust signatures of air–sea interaction as the surface winds encounter ocean surface features such as SST fronts, filaments, and eddies. This interaction is manifest by the linear relationship, or coupling coefficient, between the downwind SST gradient and wind stress divergence and between the crosswind SST gradient and wind stress curl evident from analysis of fields averaged over 29 days. This study examines fields from the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS) model, spanning the summer months, June–September, for four consecutive years, 2002–05. Relative to several models evaluated previously, coupling coefficients are much closer to those calculated from Quick Scatterometer (QuikSCAT) satellite measurements. In addition, the summertime correlation between the wind stress derivative field and its corresponding SST gradient field on monthly time scales agrees well with satellite-derived correlations. Sensible and latent heat flux fields are also analyzed for features indicative of pronounced air–sea exchange associated with SST influence.
Sequence diversity in the A domain of Staphylococcus aureusfibronectin-binding protein A
Authors: Loughman Anthony , Sweeney Tara , Keane Fiona M , Pietrocola Giampiero , Speziale Pietro , Foster Timothy J 
Published: May 2008

Abstract

Background
Fibronectin-binding protein A (FnBPA) mediates adhesion of Staphylococcus aureus to fibronectin, fibrinogen and elastin. We previously reported that S. aureus strain P1 encodes an FnBPA protein where the fibrinogen/elastin-binding domain (A domain) is substantially divergent in amino acid sequence from the archetypal FnBPA of S. aureus NCTC8325, and that these variations created differences in antigenicity. In this study strains from multilocus sequence types (MLST) that spanned the genetic diversity of S.aureus were examined to determine the extent of FnBPA A domain variation within the S. aureus population and its effect on ligand binding and immuno-crossreactivity.

Results
Seven different isotype forms (I – VII) of the FnBPA A domain were identified which were between 66 to 76% identical in amino acid sequence in any pair-wise alignment. The fnbA allelic variants in strains of different multilocus sequence type were identified by DNA hybridization using probes specific for sequences encoding the highly divergent N3 sub-domain of different isotypes. Several isotypes were not restricted to specific clones or clonal complexes but were more widely distributed. It is highly likely that certain fnbA genes have been transferred horizontally. Residues lining the putative ligand-binding trench were conserved, which is consistent with the ability of each A domain isotype to bind immobilized fibrinogen and elastin by the dock-latch-lock mechanism. Variant amino acid residues were mapped on a three-dimensional model of the FnBPA A domain and were predicted to be surface-exposed. Polyclonal antibodies raised against the recombinant isotype I A domain bound that protein with a 4 – 7 fold higher apparent affinity compared to the A domains of isotypes II – VII, while some monoclonal antibodies generated against the isotype I A domain showed reduced or no binding to the other isotypes.

Conclusion
The FnBPA A domain occurs in at least 7 different isotypes which differ antigenically and exhibit limited immuno-crossreactivity, yet retain their ligand-binding functions. Antigenic variation of the FnBPA A domain may aid S. aureus to evade the host's immune responses. These findings have implications for the development of vaccines or immunotherapeutics that target FnBPA.