bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interlaboratory Standardization of the Sandwich Enzyme-Linked Immunosorbent Assay Designed for MATS, a Rapid, Reproducible Method for Estimating the Strain Coverage of Investigational Vaccines
Authors: Plikaytis Brian D. , Stella Maria , Boccadifuoco Giuseppe , DeTora Lisa M. , Agnusdei Mauro , Santini Laura , Brunelli Brunella , Orlandi Luca , Simmini Isabella , Giuliani Marzia , Ledroit Morgan , Hong Eva , Taha Muhamed-Kheir , Ellie Kim , Rajam Gowrisankar , Carlone George M. , Claus Heike , Vogel Ulrich , Borrow Ray , Findlow Jamie , Gilchrist Stefanie , Stefanelli Paola , Fazio Cecilia , Carannante Anna , Oksnes Jan , Fritzsønn Elisabeth , Klem Anne-Marie , Caugant Dominique A. , Abad Raquel , Vázquez Julio A. , Rappuoli Rino , Pizza Mariagrazia , Donnelly John J. , Medini Duccio 
Published: August 2012

ABSTRACTThe meningococcal antigen typing system (MATS) sandwich enzyme-linked immunosorbent assay (ELISA) was designed to measure the immunologic cross-reactivity and quantity of antigens in target strains of a pathogen. It was first used to measure the factor H-binding protein (fHbp), neisserial adhesin A (NadA), and neisserial heparin-binding antigen (NHBA) content of serogroup B meningococcal (MenB) isolates relative to a reference strain, or “relative potency” (RP). With the PorA genotype, the RPs were then used to assess strain coverage by 4CMenB, a multicomponent MenB vaccine. In preliminary studies, MATS accurately predicted killing in the serum bactericidal assay using human complement, an accepted correlate of protection for meningococcal vaccines. A study across seven laboratories assessed the reproducibility of RPs for fHbp, NadA, and NHBA and established qualification parameters for new laboratories. RPs were determined in replicate for 17 MenB reference strains at laboratories A to G. The reproducibility of RPs among laboratories and against consensus values across laboratories was evaluated using a mixed-model analysis of variance. Interlaboratory agreement was very good; the Pearson correlation coefficients, coefficients of accuracy, and concordance correlation coefficients exceeded 99%. The summary measures of reproducibility, expressed as between-laboratory coefficients of variation, were 7.85% (fHbp), 16.51% (NadA), and 12.60% (NHBA). The overall within-laboratory measures of variation adjusted for strain and laboratory were 19.8% (fHbp), 28.8% (NHBA), and 38.3% (NadA). The MATS ELISA was successfully transferred to six laboratories, and a further laboratory was successfully qualified.
Relapse of Systemic Juvenile Idiopathic Arthritis after Influenza Vaccination in a Patient Receiving Tocilizumab
Authors: Shimizu Masaki , Ueno Kazuyuki , Yachie Akihiro 
Published: August 2012

ABSTRACTWe report the case of a patient with systemic juvenile idiopathic arthritis (s-JIA) receiving tocilizumab (TCZ) who experienced relapses of s-JIA after receiving influenza vaccination. Systemic symptoms of s-JIA might be masked during TCZ therapy. Careful observation with the monitoring of serum interleukin (IL)-18 and IL-6 levels may be useful.
Microsatellite Genotyping Clarified Conspicuous Accumulation of Candida parapsilosis at a Cardiothoracic Surgery Intensive Care Unit
Authors: Diab-Elschahawi Magda , Forstner Christina , Hagen Ferry , Meis Jacques F. , Lassnig Andrea M. , Presterl Elisabeth , Klaassen Corné H. W. 
Published: August 2012

ABSTRACT

Candida parapsilosis
has become a significant cause of invasive fungal infections in seriously ill patients. Nosocomial outbreaks through direct and indirect contact have been described. The aim of this study was the molecular characterization of what appeared to be an ongoing
C. parapsilosis
outbreak at the cardiothoracic intensive care unit of the University Hospital of Vienna between January 2007 and December 2008. Using two different molecular typing methods—automated repetitive sequence-based PCR (DiversiLab; bioMérieux) and microsatellite genotyping—we investigated the genetic relationship of 99
C. parapsilosis
isolates. Eighty-three isolates originated from the cardiothoracic intensive care unit, while 16 isolates were random control isolates from other intensive care units and a different Austrian hospital. The 99
C. parapsilosis
isolates analyzed by repetitive-element PCR all showed identical genotypes, suggesting an ongoing outbreak. In contrast, microsatellite genotyping showed a total of 56 different genotypes. Two major genotypes were observed in 10 and 15 isolates, respectively, whereas another 13 genotypes were observed in 2 to 4 isolates each. Forty-one genotypes were observed only once. Closely related genotypes that differed in only a single microsatellite marker were grouped into clonal complexes. When it comes to
C. parapsilosis
, microsatellite genotyping is a more discriminative method than repetitive-element PCR genotyping to investigate outbreaks.
Clonal Distribution of Common Pneumococcal Serotypes Not Included in the 7-Valent Conjugate Vaccine (PCV7): Marked Differences between Two Ethnic Populations in Southern Israel
Authors: Porat Nurith , Benisty Rachel , Trefler Ronit , Givon-Lavi Noga , Dagan Ron 
Published: August 2012

ABSTRACT
This study aimed to compare the clonal distribution of common pneumococcal strains not included in the 7-valent pneumococcal conjugate vaccine (PCV7) that were isolated from cases of acute otitis media (AOM) and invasive pneumococcal disease (IPD) in two distinct ethnic populations in southern Israel during the decade (1999 to 2008) preceding PCV7 implementation. Isolates recovered from Jewish and Bedouin children <5 years old were characterized by antibiotic resistance and molecular epidemiology using pulsed-field gel electrophoresis and multilocus sequence typing. Of 5,236 AOM and 425 IPD isolates, 43% and 57% were from Jewish and Bedouin children, respectively. PCV7 accounted for 54% and 45% of the AOM and IPD episodes, respectively. Eleven major non-PCV7 serotypes (1, 3, 5, 6A, 7F, 12F, 15B/C, 19A, 21, 33F, and 35B) constituted 31% and 42% of the AOM and IPD episodes, respectively. The clonal distributions of the 11 non-PCV7 serotypes and their antibiotic susceptibilities were significantly different among the two ethnic populations in both the AOM and IPD groups. About half of the AOM and IPD cases resulted from non-PCV7 pneumococci, even before PCV7 implementation. The significant differences between the two ethnic populations suggest that lifestyle and microenvironment are major determinants in the clonal distribution of disease-causing pneumococci. Post-PCV7 surveillance is important in understanding non-PCV7 clonal expansion in the two distinct populations.
A PCR-Based Intergenic Spacer Region-Capillary Gel Electrophoresis Typing Method for Identification and Subtyping of Nocardia Species
Authors: Wehrhahn M. C. , Xiao M. , Kong F. , Xu Y.-C. , Chen S.C.-A. 
Published: August 2012

ABSTRACT

While 16S rRNA sequence-based identification of
Nocardia
species has become the gold standard, it is not without its limitations. We evaluated a novel approach encompassing the amplification of the
Nocardia
16S-23S rRNA intergenic spacer (IGS) region followed by fragment analysis by capillary gel electrophoresis (CGE) of the amplified product for species identification of
Nocardia
. One hundred forty-five
Nocardia
isolates (19 species) and four non-
Nocardia
aerobic actinomycetes were studied. Reproducibility testing was performed in a subset (21%) of isolates. Ninety-five different electropherograms were identified, with heterogeneity within species being a general observation. Among common
Nocardia
species (e.g.,
Nocardia cyriacigeorgica
,
N. nova
,
N. farcinica
), 2 or 3 dominant electropherogram subgroups were typical. While only a minority (8/19; 42%) of the different
Nocardia
species contained isolates displaying unique fragment sizes that were predictive of a particular species, virtually all isolates (142/145; 98%) could be assigned to the correct species using IGS-CGE typing based on the number and size of amplified fragments. The median number of fragments for each isolate was 2 (range, 1 to 5) with only a minority (17%) having a single fragment detected. The majority (93%) of amplified fragments were between 408 and 461 bp. The technique was also non-operator dependent, highly reproducible, and quicker and less expensive than 16S sequencing. In summary, PCR-based IGS-CGE typing is relatively simple, accurate, reproducible, and cost-effective and offers a potential alternative to 16S rRNA sequencing for identifying and subtyping
Nocardia
isolates.
Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children
Authors: Pierce Virginia M. , Hodinka Richard L. 
Published: August 2012

ABSTRACTA novel eSensor respiratory viral panel (eSensor RVP) multiplexed nucleic acid amplification test (GenMark Diagnostics, Inc., Carlsbad, CA) was compared to laboratory-developed real-time PCR assays for the detection of various respiratory viruses. A total of 250 frozen archived pediatric respiratory specimens previously characterized as either negative or positive for one or more viruses by real-time PCR were examined using the eSensor RVP. Overall agreement between the eSensor RVP and corresponding real-time PCR assays for shared analytes was 99.2% (kappa = 0.96 [95% confidence interval {CI}, 0.94 to 0.98]). The combined positive percent agreement was 95.4% (95% CI, 92.5 to 97.3); the negative percent agreement was 99.7% (95% CI, 99.4 to 99.8). The mean real-time PCR threshold cycle (CT) value for specimens with discordant results was 39.73 (95% CI, 38.03 to 41.43). Detection of coinfections and correct identification of influenza A virus subtypes were comparable between methods. Of note, the eSensor RVP rhinovirus assay was found to be more sensitive and specific than the corresponding rhinovirus real-time PCR. In contrast, the eSensor RVP adenovirus B, C, and E assays demonstrated some cross-reactivity when tested against known adenovirus serotypes representing groups A through F. The eSensor RVP is robust and relatively easy to perform, it involves a unique biosensor technology for target detection, and its multiplexed design allows for efficient and simultaneous interrogation of a single specimen for multiple viruses. Potential drawbacks include a slower turnaround time and the need to manipulate amplified product during the protocol, increasing the possibility of contamination.
Identification of Blood Culture Isolates Directly from Positive Blood Cultures by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and a Commercial Extraction System: Analysis of Performance, Cost, and Turnaround Time
Authors: Lagacé-Wiens Philippe R. S. , Adam Heather J. , Karlowsky James A. , Nichol Kimberly A. , Pang Paulette F. , Guenther Jodi , Webb Amanda A. , Miller Crystal , Alfa Michelle J. 
Published: August 2012

ABSTRACT

Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry represents a revolution in the rapid identification of bacterial and fungal pathogens in the clinical microbiology laboratory. Recently, MALDI-TOF has been applied directly to positive blood culture bottles for the rapid identification of pathogens, leading to reductions in turnaround time and potentially beneficial patient impacts. The development of a commercially available extraction kit (Bruker Sepsityper) for use with the Bruker MALDI BioTyper has facilitated the processing required for identification of pathogens directly from positive from blood cultures. We report the results of an evaluation of the accuracy, cost, and turnaround time of this method for 61 positive monomicrobial and 2 polymicrobial cultures representing 26 species. The Bruker MALDI BioTyper with the Sepsityper gave a valid (score, >1.7) identification for 85.2% of positive blood cultures with no misidentifications. The mean reduction in turnaround time to identification was 34.3 h (
P
< 0.0001) in the ideal situation where MALDI-TOF was used for all blood cultures and 26.5 h in a more practical setting where conventional identification or identification from subcultures was required for isolates that could not be directly identified by MALDI-TOF. Implementation of a MALDI-TOF-based identification system for direct identification of pathogens from blood cultures is expected to be associated with a marginal increase in operating costs for most laboratories. However, the use of MALDI-TOF for direct identification is accurate and should result in reduced turnaround time to identification.
Complete Genome Sequence of Pseudomonas aeruginosa Siphophage MP1412
Authors: Bae Hee-Won , Chung In-Young , Sim Nuri , Cho You-Hee 
Published: August 2012

ABSTRACT

We report the complete genome sequence of
Pseudomonas aeruginosa
siphophage MP1412, which displays synteny to those of
P. aeruginosa
phages M6 and YuA. However, the presence of two homing endonucleases of the GIY-YIG family is unique to MP1412, suggesting their unique role in the phage life cycle of the bacterial host.
Complete Genome Sequence of Bacteriophage BC-611 Specifically Infecting Enterococcus faecalis Strain NP-10011
Authors: Horiuchi Tomohiro , Sakka Makiko , Hayashi Atsushi , Shimada Takashi , Kimura Tetsuya , Sakka Kazuo 
Published: August 2012

ABSTRACT

Enterococcus faecalis
is an opportunistic pathogen that causes serious infections in humans and animals and is also an important bacterium for dairy and probiotic supplement production. Therefore, bacteriophages infecting
E. faecalis
may be useful for phage therapy against multidrug-resistant strains or may threaten industrial fermentation. We isolated a virulent
Siphoviridae
bacteriophage, BC-611, specifically infecting
E. faecalis
strain NP-10011 but not infecting other
E. faecalis
strains or other enterococci. Although the genome sequence of BC-611 resembled that of enterococcal bacteriophage SAP6, BC-611 was marked by its narrow host specificity.
Complete Genome Sequence of a Novel Pararetrovirus Isolated from Soybean
Authors: Han Junping , Domier Leslie L. , Dorrance Anne , Qu Feng 
Published: August 2012

ABSTRACT

We report the complete genome sequence of soybean Putnam virus (SPuV), a new pararetrovirus isolated from a soybean field in Putnam County, OH. Comparison of SPuV with other plant-infecting pararetroviruses places it in the genus
Caulimovirus
of the family
Caulimoviridae
.
Arenavirus Infection Induces Discrete Cytosolic Structures for RNA Replication
Authors: Baird Nicholas L. , York Joanne , Nunberg Jack H. 
Published: August 2012

ABSTRACT
Arenaviruses are responsible for acute hemorrhagic fevers with high mortality and pose significant threats to public health and biodefense. These enveloped negative-sense RNA viruses replicate in the cell cytoplasm and express four proteins. To better understand how these proteins insinuate themselves into cellular processes to orchestrate productive viral replication, we have identified and characterized novel cytosolic structures involved in arenavirus replication and transcription. In cells infected with the nonpathogenic Tacaribe virus or the attenuated Candid#1 strain of Junín virus, we find that newly synthesized viral RNAs localize to cytosolic puncta containing the nucleoprotein (N) of the virus. Density gradient centrifugation studies reveal that these replication-transcription complexes (RTCs) are associated with cellular membranes and contain full-length genomic- and antigenomic-sense RNAs. Viral mRNAs segregate at a higher buoyant density and are likewise scant in immunopurified RTCs, consistent with their translation on bulk cellular ribosomes. In addition, confocal microscopy analysis reveals that RTCs contain the lipid phosphatidylinositol-4-phosphate and proteins involved in cellular mRNA metabolism, including the large and small ribosomal subunit proteins L10a and S6, the stress granule protein G3BP1, and a subset of translation initiation factors. Elucidating the structure and function of RTCs will enhance our understanding of virus-cell interactions that promote arenavirus replication and mitigate against host cell immunity. This knowledge may lead to novel intervention strategies to limit viral virulence and pathogenesis.
Composition of Dithyrea wislizenii fruit extract and free-radical scavenging activity of its constituents
Authors: Montaut Sabine , Grandbois Julie , Rossi Laura S. , Kamal Sonia , Khouri James , Ménard Melissa G. , Joly Hélène A. 
Published: August 2012

Glucolesquerellin (2), glucohesperin (3), quercetin 3-O-sophoroside (4), and quercetin 3-O-sophoroside-7-O-glucoside (5), isolated from the fruit of Dithyrea wislizenii , were quantified by HPLC. The fruit extract and flavonoids were not found to be toxic by using a brine shrimp lethality assay. The fruit extract and the flavonoids and glucosinolates were submitted to a free-radical scavenging activity assay with the diphenylpicrylhydrazyl radical (DPPH•). The concentration of quercetin (6) (a positive control for the flavonoids) able to scavenge 50% of DPPH• (SC50) was 32 ± 2 µmol/L (or 4 ± 1 µg/mL), which was about 27 times more potent than the crude extract. Compounds 4 and 5 had a SC50, the concentration of the compound required to scavenge 50% of the DPPH•, of 78 ± 1 µmol/L and 113 ± 10 µmol/L, respectively. The positive control for the glucosinolates, glucoraphasatin, (1) had a SC50 of 1768 ± 60 µmol/L. The glucosinolates 2 and 3 had a SC50 of 7819 ± 1968 and 970 ± 63 µmol/L, respectively.
Evidence for non-Andersonian faulting above evaporites in the Nile Delta
Authors: Tingay Mark , Bentham Peter , De Feyter Arnoud , Kellner Axel 
Published: August 2012

Abstract

This study examines present-day stress orientations from borehole breakout and drilling-induced fractures in 57 boreholes in the Nile Delta. A total of 588 breakouts and 68 drilling-induced fractures from 50 wells reveal sharply contrasting present-day maximum horizontal stress (
S
Hmax
) orientations across the Nile Delta. A typical deltaic margin-parallel
S
Hmax
exists in parts of the Nile Delta that are below or absent from evaporites (NNE–SSW in the west, east–west in the central Nile, ESE–WNW in the east). However, a largely margin-normal (NNE–SSW)
S
Hmax
is observed in sequences underlain by evaporites in the eastern Nile Delta. The margin-normal supra-salt
S
Hmax
orientations are often subperpendicular to the strike of nearby active extensional faults, rather than being parallel to the faults as predicted by Andersonian criteria. The high angle between
S
Hmax
and strike of these extensional faults represents a new type of non-Andersonian faulting that is even less-suitably oriented for shear failure than previously described anomalous faulting such as low-angle normal faults and highly oblique strike-slip faults (e.g. San Andreas). While the mechanics of these non-Andersonian faults remains uncertain, it is suggested that the margin-normal supra-salt orientation generated by basal forces imparted upon rafted blocks sliding down seawards-dipping evaporites.
Reverse fault rupturing: competition between non-optimal and optimal fault orientations
Authors: Sibson R. H. 
Published: August 2012

Abstract

A dip histogram for intracontinental
M
>5.5 reverse-slip ruptures reveals a trimodal distribution with a dominant Andersonian peak (fault dip,
δ
=30±5°) flanked by subsidiary clusters at
δ
=10±5° and 50±5°, and no dips greater than 60°. For a simple compressional regime (
σ
v
=
σ
3
), the dominant peak is in accord with the reshear of optimally oriented faults with a friction coefficient of
μ
s
=0.6±0.2, implying frictional lock-up at
δ
=60±10° consistent with the observed upper dip bound. The low-dip cluster (
δ
=10±5°) is dominated by thrusting in the frontal Himalaya and may incorporate staircase thrust systems in cover sequences with deflections along bedding anisotropy. The cluster of moderate-to-steep reverse fault ruptures (
δ
=50±5°) is likely dominated by compressional inversion of inherited normal faults. In both circumstances, however, there appears to be competition between Andersonian thrusts in various stages of development and non-optimal failure planes dipping at either high or low angles. A delicate balance between levels of differential stress and fluid-pressure determines whether or not a poorly oriented thrust or reverse fault reactivates in preference to the development of new, favourably oriented Andersonian thrusts.
The complexity of 3D stress-state changes during compressional tectonic inversion at the onset of orogeny
Authors: Van Noten Koen , Van Baelen Hervé , Sintubin Manuel 
Published: August 2012

Abstract

Compressional tectonic inversions are classically represented in 2D brittle failure mode (BFM) plots that illustrate the change in differential stress (
σ
1
−
σ
3
) versus the pore-fluid pressure during orogenic shortening. In these BFM plots, the tectonic switch between extension and compression occurs at a differential stress state of zero. However, mostly anisotropic conditions are present in the Earth's crust, making isotropic stress conditions highly questionable. In this study, theoretical 3D stress-state reconstructions are proposed to illustrate the complexity of triaxial stress transitions during compressional inversion of Andersonian stress regimes. These reconstructions are based on successive late burial and early tectonic quartz veins which reflect early Variscan tectonic inversion in the Rhenohercynian foreland fold-and-thrust belt (High-Ardenne Slate Belt, Belgium, Germany). This theoretical exercise predicts that, no matter the geometry of the basin or the orientation of shortening, a transitional ‘wrench’ tectonic regime should always occur between extension and compression. To date, this intermediate regime has never been observed in structures in a shortened basin affected by tectonic inversion. Our study implies that stress transitions are therefore more complex than classically represented in 2D. Ideally, a transitional ‘wrench’ regime should be implemented in BFM plots at the switch between the extensional and compressional regimes.