bluuebunny/crossref_metadata_2025_split huggingface dataset:
1987 Compilation of Elemental Concentration Data for USGS BHVO‐1, MAG‐1, QLO‐1, RGM‐1, SCo‐1, SDC‐1, SGR‐1 and STM‐1
Authors: GLADNEY Ernest S. , ROELANDTS Iwan 
Published: May 2007

Elemental concentration data on up to 84 individual constituents in BHVO‐1, MAG‐1, QLO‐1, RGM‐1, SCo‐1, SDC‐1, SGR‐1 and STM‐1 have been collected from 311 journal articles and technical reports. These data are summarized in consensus (mean) values with uncertainties expressed as one standard deviation. Mean values are also calculated as a function of analytical procedure and all raw data are given in the tables.Ce rapport rassemble des données analytiques parues dans 311 articles scientifiques ou rapports techniques sur 84 éléments dans huit échantillons du Service Géologique des Etats‐Unis: BHVO‐1, MAG‐1, QLO‐1, RGM‐1, SCo‐1, SDC‐1, SGR‐1 et STM‐1. Quand cela a été possible, les valeurs de consensus (moyenne) sont présentées pour chaque élément avec l'incertitude exprimée en un écart‐type. Des valeurs moyennes en fonction des procédures analytiques sont également présentées.
NEW REFERENCE MATERIALS FOR NITROGEN‐ISOTOPE‐RATIO MEASUREMENTS
Authors: BOHLKE J.K. , GWINN C.J. , COPLEN T.B. 
Published: May 2007

Three new reference materials were manufactured for calibration of relative stable nitrogen‐isotope‐ratio measurements:USGS25 (ammonium sulfate) δ615″=−30 per milUSGS26 (ammonium sulfate) δ615″=+54 per milUSGS32 (potassium nitrate) δ615″=+180 per milwhere δN′, relative to atmospheric nitrogen, is an approximate value subject to change following interlaboratory comparisons. These materials are isotopically homogeneous in aliquots at least as small as 10 pot N, (or about 1‐2 mg of salt). The new reference materials greatly extend the range of δ15N values of internationally distributed standards, and they allow normalization of δ15N measurements over almost the full range of known natural isotope variation on Earth. The methods used to produce these materials may be adapted to produce homogeneous local laboratory standards for routine use.
Epitope Length, Genospecies Dependency, and Serum Panel Effect in the IR6 Enzyme-Linked Immunosorbent Assay for Detection of Antibodies toBorrelia burgdorferi
Authors: Gomes-Solecki Maria J. C. , Meirelles Luciana , Glass John , Dattwyler Raymond J. 
Published: May 2007

ABSTRACTIn the absence of erythema migrans, the basis for diagnosis of Lyme disease is the demonstration of an antibody response againstBorrelia burgdorferiin an appropriate clinical setting. The C6 enzyme-linked immunosorbent assay, based on the IR6 region of VlsE, has become widely used in both the United States and Europe. We mapped the antigenic epitopes of IR6 to a shorter sequence that is equivalent in sensitivity and specificity to the full-length IR6 25-residue peptide. In addition, we observed significant differences in sensitivity between serum panels (60 to 100%), indicating that the selection of the serum panels can shape the apparent overall sensitivity of the assay. Contrary to prior reports, the assay sensitivity is greater when the IR6 peptide is derived from the sequence of the same infectingBorreliagenospecies. Using our North American panels and the two panels obtained from European Lyme disease patients, we determined that the IR6 assay that is based on a single genospecies ofBorreliaspp. is not optimal for use as a universal diagnostic assay for Lyme disease.
Delayed Processing of Blood Samples Influences Time to Positivity of Blood Cultures and Results of Gram Stain-Acridine Orange Leukocyte Cytospin Test
Authors: Schwetz I. , Hinrichs G. , Reisinger E. C. , Krejs G. J. , Olschewski H. , Krause R. 
Published: May 2007

ABSTRACT
We investigated in vitro whether storage of blood samples influences the time to positivity used for the calculation of the differential time to positivity (DTP) and the results of the Gram stain-acridine orange leukocyte Cytospin (AOLC) test. A 24-hour storage of blood samples at room temperature may lead to false-negative DTP and false-positive Gram stain-AOLC test results, whereas storage at 4°C does not.
Host Genetic Resistance to Symptomatic Norovirus (GGII.4) Infections in Denmark
Authors: Kindberg Elin , Åkerlind Britt , Johnsen Christina , Knudsen Jenny Dahl , Heltberg Ole , Larson Göran , Böttiger Blenda , Svensson Lennart 
Published: May 2007

ABSTRACT

A total of 61 individuals involved in five norovirus outbreaks in Denmark were genotyped at nucleotides 428 and 571 of the
FUT2
gene, determining secretor status, i.e., the presence of ABH antigens in secretions and on mucosa. A strong correlation (
P
= 0.003) was found between the secretor phenotype and symptomatic disease, extending previous knowledge and confirming that nonsense mutations in the
FUT2
gene provide protection against symptomatic norovirus (GGII.4) infections.
Drug Susceptibility Testing of
Mycobacterium tuberculosis
Complex by Use of a High-Throughput, Reproducible, Absolute Concentration Method
Authors: van Klingeren Bert , Dessens-Kroon Mirjam , van der Laan Tridia , Kremer Kristin , van Soolingen Dick 
Published: May 2007

ABSTRACT

Accurate drug susceptibility testing (DST) for
Mycobacterium tuberculosis
is highly important for both therapy guidance and surveillance of drug resistance. Although liquid medium DST methods are used increasingly and seem most efficient and fast, the high costs hamper widespread implementation. In addition, an inability to check the colony morphology of the growing bacteria is a disadvantage of these methods. Moreover, these methods discriminate only between susceptibility and resistance and do not determine the MIC. In this paper, we describe a low-cost, reproducible, high-throughput, proportional absolute concentration DST method. The method uses a concentration series of antituberculosis drugs, including pyrazinamide in 7H10 medium, distributed semiautomatically in 25-well plates. The performance of this 25-well DST method was evaluated by the World Health Organization and the International Union against Tuberculosis and Lung Disease in 10 rounds of proficiency testing regarding sensitivity, specificity, efficiency, reproducibility, and predictive value for resistance and susceptibility. The performance of the method for these characteristics was 100% for isoniazid and from 96 to 100% for rifampin, 91 to 100% for streptomycin, and 85 to 100% for ethambutol. The method was 100% reproducible for all four drugs. The levels of drug resistance and the MIC distributions for the first-line antituberculosis drugs were determined for all 7,956
M. tuberculosis
strains isolated in The Netherlands from 1998 to 2005 and amounted to 7.5% for isoniazid, 1.4% for rifampin, 8.5% for streptomycin, and 1.0% for ethambutol. Pyrazinamide testing was successful for 7,026 (88.3%) of the isolates and showed a resistance level of 0.8%.
Vaginal
Staphylococcus aureus
Superantigen Profile Shift from 1980 and 1981 to 2003, 2004, and 2005
Authors: Schlievert Patrick M. , Case Laura C. , Strandberg Kristi L. , Tripp Timothy J. , Lin Ying-Chi , Peterson Marnie L. 
Published: May 2007

ABSTRACT

We determined vaginal
Staphylococcus aureus
superantigens. Staphylococci were quantified from tampons/diaphragms in 2003 to 2005, with counts compared to those determined in 1980 and 1981. In 2003 to 2005, more women were colonized than in 1980 and 1981 (23 versus 12%). Enterotoxins G and I and enterotoxin-like superantigens M and N declined, but enterotoxin-like superantigens K, L, and Q increased.
Factors Affecting Serum Concentrations of Hepatitis C Virus (HCV) RNA in HCV Genotype 1-Infected Patients with Chronic Hepatitis
Authors: Ticehurst John R. , Hamzeh Fayez M. , Thomas David L. 
Published: May 2007

ABSTRACTThe serum concentration of hepatitis C virus (HCV) RNA is usually stable (4 to 8 log10IU/ml) in untreated patients with chronic hepatitis C. While this baseline HCV RNA concentration ([HCV RNA]BL) is predictive of a sustained virologic response to treatment, its determinants are only partially identified. We therefore analyzed the baseline characteristics of 2,472 HCV genotype 1-infected patients to identify correlations with gender, age, race, weight, body mass index (BMI), HCV acquisition mode, HCV subtype, alanine aminotransferase concentration, or histopathologic changes in the liver. After separation of the data according to four [HCV RNA]BLgroups (≤5.0, >5.0 to 5.6, >5.6 to 5.9, and >5.9 log10IU/ml), we determined that increasing [HCV RNA]BLcorrelated (P< 0.05) with increasing proportions of patients who were male, >40 years of age, or heavier (a weight of >85 kg or a BMI of >27 kg/m2). Histologic activity index (HAI) data were available for 1,304 of these patients: increasing [HCV RNA]BLcorrelated with higher fibrosis and necrosis-inflammation scores. As a continuous variable, [HCV RNA]BLcorrelated with age, gender, weight (continuous or ≤85 versus >85 kg), BMI (continuous or ≤27 versus >27 kg/m2), subtype, fibrosis score, and necrosis-inflammation score; however, multiple-regression analysis yieldedPvalues of <0.1 only for age, gender, BMI (≤27 versus >27 kg/m2), and fibrosis score. While our findings are suggestive of a role for these factors in maintenance of the pretreatment state of HCV infection, the multiple-regression model accounted for only ≤4.6% of the [HCV RNA]BLdifferences between individuals (R2= 0.046 for 1,304 patients with HAI scores; 0.043 for all 2,472 patients).
Evaluation and Improvement of Real-Time PCR Assays Targeting
lytA
,
ply
, and
psaA
Genes for Detection of Pneumococcal DNA
Authors: Carvalho Maria da Gloria S. , Tondella Maria Lucia , McCaustland Karen , Weidlich Luciana , McGee Lesley , Mayer Leonard W. , Steigerwalt Arnold , Whaley Melissa , Facklam Richard R. , Fields Barry , Carlone George , Ades Edwin W. , Dagan Ron , Sampson Jacquelyn S. 
Published: May 2007

ABSTRACT

The accurate diagnosis of pneumococcal disease has frequently been hampered not only by the difficulties in obtaining isolates of the organism from patient specimens but also by the misidentification of pneumococcus-like viridans group streptococci (P-LVS) as
Streptococcus pneumoniae
. This is especially critical when the specimen comes from the respiratory tract. In this study, three novel real-time PCR assays designed for the detection of specific sequence regions of the
lytA
,
ply
, and
psaA
genes were developed (
lytA
-CDC,
ply
-CDC, and
psaA
, respectively). These assays showed high sensitivity (<10 copies for
lytA
-CDC and
ply
-CDC and an approximately twofold less sensitivity for
psaA
). Two additional real-time PCR assays for
lytA
and
ply
described previously for pneumococcal DNA detection were also evaluated. A panel of isolates consisting of 67
S. pneumoniae
isolates (44 different serotypes and 3 nonencapsulated
S. pneumoniae
isolates from conjunctivitis outbreaks) and 104 nonpneumococcal isolates was used. The 67
S. pneumoniae
isolates were reactive in all five assays. The new real-time detection assays targeting the
lytA
and
psaA
genes were the most specific for the detection of isolates confirmed to be
S. pneumoniae
, with
lytA
-CDC showing the greatest specificity. Both
ply
PCRs were positive for all isolates of
S. pseudopneumoniae
, along with 13 other isolates of other P-LVS isolates confirmed to be non-
S. pneumoniae
by DNA-DNA reassociation. Thus, the use of the
ply
gene for the detection of pneumococci can lead to false-positive reactions in the presence of P-LVS. The five assays were applied to 15 culture-positive cerebrospinal fluid specimens with 100% sensitivity; and serum and ear fluid specimens were also evaluated. Both the
lytA
-CDC and
psaA
assays, particularly the
lytA
-CDC assay, have improved specificities compared with those of currently available assays and should therefore be considered the assays of choice for the detection of pneumococcal DNA, particularly when upper respiratory P-LVS might be present in the clinical specimen.
High-Throughput, Sensitive, and Accurate Multiplex PCR-Microsphere Flow Cytometry System for Large-Scale Comprehensive Detection of Respiratory Viruses
Authors: Lee Wai-Ming , Grindle Kris , Pappas Tressa , Marshall David J. , Moser Michael J. , Beaty Edward L. , Shult Peter A. , Prudent James R. , Gern James E. 
Published: May 2007

ABSTRACT
Human respiratory viruses are a diverse group of pathogens composed of hundreds of virus strains, and this presents a major challenge for diagnostic laboratories. To efficiently detect numerous viruses in a large epidemiologic study, we developed a fast, multitarget, sensitive, and specific assay named the Respiratory MultiCode-PLx Assay (RMA). The RMA utilizes improved multiplex PCR chemistry (EraGen MultiCode-PLx technology) coupled with high-throughput microsphere flow cytometry (Luminex). Eighteen sets of virus-specific multiplex PCR primers were developed based on the conserved sequences of all available respiratory-virus sequences for eight distinct groups: human rhinovirus (HRV), respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza virus (InfV), metapneumovirus, adenovirus (Ad), coronavirus, and enterovirus. Each primer set detected 20 cDNA copies of the intended target per sample and had no reaction with 60,000 copies of human genomic DNA. The accuracy and sensitivity of the RMA for detecting respiratory viruses in human samples were tested with two sets of clinical specimens. First, 101 nasal-wash specimens that were positive for HRV, RSV, InfV, PIV, or Ad by traditional techniques were reanalyzed by RMA, and all target viruses were detected with an overall sensitivity of 94% and specificity of 99%. Second, 103 nasal-wash samples from 5-year-old children with asthma and respiratory symptoms were analyzed; RMA detected viruses in 74 specimens (71.8%) compared to only 24 (23.3%) by traditional culture and immunofluorescent-staining techniques. These results show that RMA is an accurate, sensitive, and practical test for respiratory-virus infections.
Natural Recombination Event within the Capsid Genomic Region Leading to a Chimeric Strain of Human Enterovirus B
Authors: Bouslama Lamjed , Nasri Dorsaf , Chollet Lionel , Belguith Khaoula , Bourlet Thomas , Aouni Mahjoub , Pozzetto Bruno , Pillet Sylvie 
Published: May 2007

ABSTRACT
Recombination between two strains is a known phenomenon for enteroviruses replicating within a single cell. We describe a recombinant strain recovered from human stools, typed as coxsackievirus B4 (CV-B4) and CV-B3 after partial sequencing of the VP1 and VP2 coding regions, respectively. The strain was neutralized by a polyclonal CV-B3-specific antiserum but not by a CV-B4-specific antiserum. The nucleotide sequence analysis of the whole structural genomic region showed the occurrence of a recombination event at position 1950 within the VP3 capsid gene, in a region coding for the 2b antigenic site previously described for CV-B3. This observation evidences for the first time the occurrence of an interserotypic recombination within the VP2-VP3-VP1 capsid region between two nonpoliovirus enterovirus strains. The neutralization pattern suggests that the major antigenic site is located within the VP2 protein.
Direct Interactions of Kaposi's Sarcoma-Associated Herpesvirus/Human Herpesvirus 8 ORF50/Rta Protein with the Cellular Protein Octamer-1 and DNA Are Critical for Specifying Transactivation of a Delayed-Early Promoter and Stimulating Viral Reactivation
Authors: Carroll Kyla Driscoll , Khadim Farah , Spadavecchia Sophia , Palmeri Diana , Lukac David M. 
Published: May 2007

ABSTRACT
The Kaposi's sarcoma-associated herpesvirus (KSHV) delayed-early K-bZIP promoter contains an ORF50/Rta binding site whose sequence is conserved with the ORF57 promoter. Mutation of the site in the full-length K-bZIP promoter reduced Rta-mediated transactivation by greater than 80%. The K-bZIP element contains an octamer (Oct) binding site that overlaps the Rta site and is well conserved with Oct elements found in the immediate-early promoters of herpes simplex virus type 1(HSV-1). The cellular protein Oct-1, but not Oct-2, binds to the K-bZIP element in a sequence-specific fashion in vitro and in vivo and stimulates Rta binding to the promoter DNA. The coexpression of Oct-1 enhances Rta-mediated transactivation of the wild type but not the mutant K-bZIP promoter, and Oct-1 and Rta proteins bind to each other directly in vitro. Mutations of Rta within an amino acid sequence conserved with HSV-1 virion protein 16 eliminate Rta's interactions with Oct-1 and K-bZIP promoter DNA but not RBP-Jk. The binding of Rta to both Oct-1 and DNA contributes to the transactivation of the K-bZIP promoter and viral reactivation, and Rta mutants deficient for both interactions are completely debilitated. Our data suggest that the Rta/Oct-1 interaction is essential for optimal KSHV reactivation. Transfections of mouse embryo fibroblasts and an endothelial cell line suggest cell-specific differences in the requirement for Oct-1 or RBP-Jk in Rta-mediated transactivation of the K-bZIP promoter. We propose a model in which Rta transactivation of the promoter is specified by the combination of DNA binding and interactions with several cellular DNA binding proteins including Oct-1.
De Novo Initiation of RNA Synthesis by the Arterivirus RNA-Dependent RNA Polymerase
Authors: Beerens Nancy , Selisko Barbara , Ricagno Stefano , Imbert Isabelle , van der Zanden Linda , Snijder Eric J. , Canard Bruno 
Published: May 2007

ABSTRACT

All plus-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that functions as the catalytic subunit of the viral replication/transcription complex, directing viral RNA synthesis in concert with other viral proteins and, sometimes, host proteins. RNA synthesis essentially can be initiated by two different mechanisms, de novo initiation and primer-dependent initiation. Most viral RdRps have been identified solely on the basis of comparative sequence analysis, and for many viruses the mechanism of initiation is unknown. In this study, using the family prototype equine arteritis virus (EAV), we address the mechanism of initiation of RNA synthesis in arteriviruses. The RdRp domains of the members of the arterivirus family, which are part of replicase subunit nsp9, were compared to coronavirus RdRps that belong to the same order of
Nidovirales
, as well as to other RdRps with known initiation mechanisms and three-dimensional structures. We report here the first successful expression and purification of an arterivirus RdRp that is catalytically active in the absence of other viral or cellular proteins. The EAV nsp9/RdRp initiates RNA synthesis by a de novo mechanism on homopolymeric templates in a template-specific manner. In addition, the requirements for initiation of RNA synthesis from the 3′ end of the viral genome were studied in vivo using a reverse genetics approach. These studies suggest that the 3′-terminal nucleotides of the EAV genome play a critical role in viral RNA synthesis.
Hepatitis C Virus p7 and NS2 Proteins Are Essential for Production of Infectious Virus
Authors: Jones Christopher T. , Murray Catherine L. , Eastman Dawnnica K. , Tassello Jodie , Rice Charles M. 
Published: May 2007

ABSTRACT
Hepatitis C virus (HCV) infection is a global health concern affecting an estimated 3% of the world's population. Recently, cell culture systems have been established, allowing recapitulation of the complete virus life cycle for the first time. Since the HCV proteins p7 and NS2 are not predicted to be major components of the virion, nor are they required for RNA replication, we investigated whether they might have other roles in the viral life cycle. Here we utilize the recently described infectious J6/JFH chimera to establish that the p7 and NS2 proteins are essential for HCV infectivity. Furthermore, unprocessed forms of p7 and NS2 were not required for this activity. Mutation of two conserved basic residues, previously shown to be important for the ion channel activity of p7 in vitro, drastically impaired infectious virus production. The protease domain of NS2 was required for infectivity, whereas its catalytic active site was dispensable. We conclude that p7 and NS2 function at an early stage of virion morphogenesis, prior to the assembly of infectious virus.
Mamu-B*08-Positive Macaques Control Simian Immunodeficiency Virus Replication
Authors: Loffredo John T. , Maxwell Jess , Qi Ying , Glidden Chrystal E. , Borchardt Gretta J. , Soma Taeko , Bean Alex T. , Beal Dominic R. , Wilson Nancy A. , Rehrauer William M. , Lifson Jeffrey D. , Carrington Mary , Watkins David I. 
Published: May 2007

ABSTRACTCertain major histocompatibility complex (MHC) class I alleles are associated with the control of human immunodeficiency virus and simian immunodeficiency virus (SIV) replication. We have designed sequence-specific primers for detection of the rhesus macaque MHC class I alleleMamu-B*08by PCR and screened a cohort of SIV-infected macaques for this allele. Analysis of 196 SIVmac239-infected Indian rhesus macaques revealed thatMamu-B*08was significantly overrepresented in elite controllers; 38% of elite controllers wereMamu-B*08positive compared to 3% of progressors (P= 0.00001).Mamu-B*08was also associated with a 7.34-fold decrease in chronic phase viremia (P= 0.002).Mamu-B*08-positive macaques may, therefore, provide a good model to understand the correlates of MHC class I allele-associated immune protection and viral containment in human elite controllers.
Characterization of Fusion Determinants Points to the Involvement of Three Discrete Regions of Both E1 and E2 Glycoproteins in the Membrane Fusion Process of Hepatitis C Virus
Authors: Lavillette Dimitri , Pécheur Eve-Isabelle , Donot Peggy , Fresquet Judith , Molle Jennifer , Corbau Romuald , Dreux Marlène , Penin François , Cosset François-Loïc 
Published: May 2007

ABSTRACT

Infection of eukaryotic cells by enveloped viruses requires the merging of viral and cellular membranes. Highly specific viral surface glycoproteins, named fusion proteins, catalyze this reaction by overcoming inherent energy barriers. Hepatitis C virus (HCV) is an enveloped virus that belongs to the genus
Hepacivirus
of the family
Flaviviridae
. Little is known about the molecular events that mediate cell entry and membrane fusion for HCV, although significant progress has been made due to recent developments in infection assays. Here, using infectious HCV pseudoparticles (HCVpp), we investigated the molecular basis of HCV membrane fusion. By searching for classical features of fusion peptides through the alignment of sequences from various HCV genotypes, we identified six regions of HCV E1 and E2 glycoproteins that present such characteristics. We introduced conserved and nonconserved amino acid substitutions in these regions and analyzed the phenotype of HCVpp generated with mutant E1E2 glycoproteins. This was achieved by (i) quantifying the infectivity of the pseudoparticles, (ii) studying the incorporation of E1E2 and their capacity to mediate receptor binding, and (iii) determining their fusion capacity in cell-cell and liposome/HCVpp fusion assays. We propose that at least three of these regions (i.e., at positions 270 to 284, 416 to 430, and 600 to 620) play a role in the membrane fusion process. These regions may contribute to the merging of viral and cellular membranes either by interacting directly with lipid membranes or by assisting the fusion process through their involvement in the conformational changes of the E1E2 complex at low pH.