bluuebunny/crossref_metadata_2025_split huggingface dataset:
PspA Family Distribution, unlike Capsular Serotype, Remains Unaltered following Introduction of the Heptavalent Pneumococcal Conjugate Vaccine
Authors: Croney Christina M. , Coats Mamie T. , Nahm Moon H. , Briles David E. , Crain Marilyn J. 
Published: April 2012

ABSTRACT
Pneumococcal conjugate vaccines (PCVs) are recommended for the prevention of invasive pneumococcal disease (IPD) in young children. Since the introduction of the heptavalent pneumococcal vaccine (PCV7) in 2000, IPD caused by serotypes in the vaccine has almost been eliminated, and previously uncommon capsular serotypes now cause most cases of pediatric IPD in the United States. One way to protect against these strains would be to add cross-reactive protein antigens to new vaccines. One such protein is pneumococcal surface protein A (PspA). Prior to 2000, PspA families 1 and 2 were expressed by 94% of isolates. Because PCV7 vaccine pressure has resulted in IPD caused by capsular serotypes that were previously uncommon and unstudied for PspA expression, it was possible that many of the new strains expressed different PspA antigens or even lacked PspA. Of 157 pediatric invasive pneumococcal isolates collected at a large pediatric hospital in Alabama between 2002 and 2010, only 60.5% had capsular serotypes included in PCV13, which came into general use in Alabama after our strains were collected. These isolates included 17 serotypes that were not covered by PCV13. Nonetheless, pneumococcal capsular serotype replacement was not associated with changes in PspA expression; 96% of strains in this collection expressed PspA family 1 or 2. Continued surveillance will be critical to vaccine strategies to further reduce IPD.
Does Tetanus-Diphtheria-Acellular Pertussis Vaccination Interfere with Serodiagnosis of Pertussis Infection?
Authors: Pawloski Lucia C. , Kirkland Kathryn B. , Baughman Andrew L. , Martin Monte D. , Talbot Elizabeth A. , Messonnier Nancy E. , Tondella Maria Lucia 
Published: April 2012

ABSTRACT
An anti-pertussis toxin (PT) IgG enzyme-linked immunosorbent assay (ELISA) was analytically validated for the diagnosis of pertussis at a cutoff of 94 ELISA units (EU)/ml. Little was known about the performance of this ELISA in the diagnosis of adults recently vaccinated with tetanus-diphtheria-acellular pertussis (Tdap) vaccine, which contains PT. The goal of this study was to determine when the assay can be used following Tdap vaccination. A cohort of 102 asymptomatic health care personnel (HCP) vaccinated with Tdap (Adacel; Sanofi Pasteur) were aged 19 to 79 years (median, 47 years) at vaccination. For each HCP, specimens were available for evaluation at 2 to 10 time points (prevaccination to 24 months postvaccination), and geometric mean concentrations (GMC) for the cohort were calculated at each time point. Among 97 HCP who responded to vaccination, a mixed-model analysis with prediction and tolerance intervals was performed to estimate the time at which serodiagnosis can be used following vaccination. The GMCs were 8, 21, and 9 EU/ml at prevaccination and 4 and 12 months postvaccination, respectively. Eight (8%) of the 102 HCP reached antibody titers of ≥94 EU/ml during their peak response, but none had these titers by 6 months postvaccination. The calculated prediction and tolerance intervals were <94 EU/ml by 45 and 75 days postvaccination, respectively. Tdap vaccination 6 months prior to testing did not confound result interpretation. This seroassay remains a valuable diagnostic tool for adult pertussis.
Draft Genome Sequence of Daldinia eschscholzii Isolated from Blood Culture
Authors: Ng Kee Peng , Ngeow Yun Fong , Yew Su Mei , Hassan Hamimah , Soo-Hoo Tuck Soon , Na Shiang Ling , Chan Chai Ling , Hoh Chee-Choong , Lee Kok-Wei , Yee Wai-Yan 
Published: April 2012

ABSTRACT

Daldinia eschscholzii
is an invasive endophyte that is most commonly found in plant tissues rich in secondary metabolites. We report the draft genome sequence of
D. eschscholzii
isolated from blood culture. The draft genome is 35,494,957 bp in length, with 42,898,665 reads, 61,449 contigs, and a G+C content of 46.8%. The genome was found to contain a high abundance of genes associated with plant cell wall degradation enzymes, mycotoxin production, and antifungal drug resistance.
Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Caspofungin Susceptibility Testing of Candida and Aspergillus Species
Authors: De Carolis Elena , Vella Antonietta , Florio Ada R. , Posteraro Patrizia , Perlin David S. , Sanguinetti Maurizio , Posteraro Brunella 
Published: April 2012

ABSTRACT

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was evaluated for testing susceptibility to caspofungin of wild-type and
fks
mutant isolates of
Candida
and
Aspergillus
. Complete essential agreement was observed with the CLSI reference method, with categorical agreement for 94.1% of the
Candida
isolates tested. Thus, MALDI-TOF MS is a reliable and accurate method to detect fungal isolates with reduced caspofungin susceptibility.
Accurate Identification of Candida parapsilosis (Sensu Lato) by Use of Mitochondrial DNA and Real-Time PCR
Authors: Souza Ana Carolina R. , Ferreira Renata C. , Gonçalves Sarah S. , Quindós Guillermo , Eraso Elena , Bizerra Fernando C. , Briones Marcelo R. S. , Colombo Arnaldo L. 
Published: April 2012

ABSTRACT

Candida parapsilosis
is the
Candida
species isolated the second most frequently from blood cultures in South America and some European countries, such as Spain. Since 2005, this species has been considered a complex of 3 closely related species:
C. parapsilosis
,
Candida metapsilosis
, and
Candida orthopsilosis
. Here, we describe a real-time TaqMan-MGB PCR assay, using mitochondrial DNA (mtDNA) as the target, which readily distinguishes these 3 species. We first used comparative genomics to locate syntenic regions between these 3 mitochondrial genomes and then selected
NADH5
as the target for the real-time PCR assay. Probes were designed to include a combination of different single-nucleotide polymorphisms that are able to differentiate each species within the
C. parapsilosis
complex. This new methodology was first tested using mtDNA and then genomic DNA from 4 reference and 5 clinical strains. For assay validation, a total of 96 clinical isolates and 4 American Type Culture Collection (ATCC) isolates previously identified by internal transcribed spacer (
ITS
) ribosomal DNA (rDNA) sequencing were tested. Real-time PCR using genomic DNA was able to differentiate the 3 species with 100% accuracy. No amplification was observed when DNA from other species was used as the template. We observed 100% congruence with
ITS
rDNA sequencing identification, including for 30 strains used in blind testing. This novel method allows a quick and accurate intracomplex identification of
C. parapsilosis
and saves time compared with sequencing, which so far has been considered the “gold standard” for
Candida
yeast identification. In addition, this assay provides a useful tool for epidemiological and clinical studies of these emergent species.
Development and Validation of a Semiquantitative, Multitarget PCR Assay for Diagnosis of Bacterial Vaginosis
Authors: Cartwright Charles P. , Lembke Bryndon D. , Ramachandran Kalpana , Body Barbara A. , Nye Melinda B. , Rivers Charles A. , Schwebke Jane R. 
Published: April 2012

ABSTRACT

Quantitative PCR assays were developed for 4 organisms reported previously to be useful positive indicators for the diagnosis of bacterial vaginosis (BV)—
Atopobium vaginae
, Bacterial Vaginosis-Associated Bacterium 2 (BVAB-2),
Gardnerella vaginalis
, and
Megasphaera-
1—and a single organism (
Lactobacillus crispatus
) that has been implicated as a negative indicator for BV. Vaginal samples (
n
= 169), classified as positive (
n
= 108) or negative (
n
= 61) for BV based on a combination of the Nugent Gram stain score and Amsel clinical criteria, were analyzed for the presence and quantity of each of the marker organisms, and the results were used to construct a semiquantitative, multiplex PCR assay for BV based on detection of 3 positive indicator organisms (
A. vaginae
, BVAB-2, and
Megasphaera
-1) and classification of samples using a combinatorial scoring system. The prototype BV PCR assay was then used to analyze the 169-member developmental sample set and, in a prospective, blinded manner, an additional 227 BV-classified vaginal samples (110 BV-positive samples and 117 BV-negative samples). The BV PCR assay demonstrated a sensitivity of 96.7% (202/209), a specificity of 92.2% (153/166), a positive predictive value of 94.0%, and a negative predictive value of 95.6%, with 21 samples (5.3%) classified as indeterminate for BV. This assay provides a reproducible and objective means of evaluating critical components of the vaginal microflora in women with signs and symptoms of vaginitis and is comparable in diagnostic accuracy to the conventional gold standard for diagnosis of BV.
Seronegative Hepatitis C Virus Infection in a Child Infected via Mother-to-Child Transmission
Authors: Larouche Ariane , Gaëtan Geneviève , El-Bilali Nabil , Quesnel-Vallières Mathieu , Martin Steven R. , Alvarez Fernando , Shoukry Naglaa H. , Soudeyns Hugo 
Published: April 2012

ABSTRACT
Hepatitis C virus (HCV) infection typically leads to antibody response within weeks after primary infection. Here, we describe the case of a child infected with HCV by mother-to-child transmission who remained persistently seronegative despite the presence of high levels of circulating HCV RNA.
Comparison of Three Roche Hepatitis B Virus Viral Load Assay Formats
Authors: Pyne Michael T. , Vest Lauren , Clement Jennifer , Lee Jessica , Rosvall Jessica R. , Luk Kevin , Rossi Michael , Cobb Bryan , Hillyard David R. 
Published: April 2012

ABSTRACT

Two FDA-approved (
in vitro
diagnostic [IVD]) hepatitis B virus (HBV) viral load assays, the manual Cobas TaqMan HBV Test for use with the High Pure System (HP) and the automated Cobas AmpliPrep/Cobas TaqMan HBV Test v2.0 (CAP/CTM), were compared to a modified (not FDA-approved) version of the HP assay by automating the DNA extraction using the Total Nucleic Acid Isolation (TNAI) kit on the Cobas AmpliPrep. On average, CAP/CTM measurements were 0.08 log IU/ml higher than HP results (
n
= 206), and TNAI results were 0.17 log IU/ml higher than HP results (
n
= 166). The limit of detection (LOD), as determined by probit analysis using dilutions of the 2nd HBV international standard, was 10.2 IU/ml for CAP/CTM. The data sets for HP and TNAI were insufficient for probit analysis; however, there was 100% detection at ≥5 or ≥10 IU/ml for TNAI and HP, respectively. Linearity was demonstrated between 60 and 2,000,000 IU/ml, with slopes between 0.95 and 0.99 and
R
2
values of >0.99 for all assays. Total precision (log percent coefficient of variance [CV]) was between 0.8% and 2.1% at 4.3 log IU/ml and between 1.4% and 4.9% at 2.3 log IU/ml. Correlation of samples, reproducibility, linearity, and LOD were acceptable and similar in all assays. The CAP/CTM assay and, to a lesser extent, the TNAI assay reduced hands-on time due to automation. There were no instances of contamination detected in negative samples during the course of the study, despite testing several samples up to 9.6 log IU/ml. The incidence of false-positive negative controls in HP and CAP/CTM clinical testing was <0.5% over 6 to 7 months of testing.
Comparison of Dimethyl Sulfoxide and Water as Solvents for Echinocandin Susceptibility Testing by the EUCAST Methodology
Authors: Alastruey-Izquierdo Ana , Gómez-López Alicia , Arendrup Maiken C. , Lass-Florl Cornelia , Hope William W. , Perlin David S. , Rodriguez-Tudela Juan L. , Cuenca-Estrella Manuel 
Published: April 2012

ABSTRACT

Ninety-six strains of
Candida
, including 29 resistant and 67 susceptible isolates with mutations in the
FKS1
and
FKS2
genes were tested by the European Committee on Antibiotic Susceptibility Testing EDef 7.1 and 7.2 methodologies to determine the impact on the MIC when water was replaced with dimethyl sulfoxide (DMSO) as the solvent for caspofungin and micafungin. The MICs were significantly lower and the MIC ranges were narrower when DMSO was used as the solvent. The use of DMSO may help to better discriminate between susceptible and resistant populations.
Head, neck, and brain tumor embolization guidelines
Authors: Duffis E Jesus , Gandhi Chirag D , Prestigiacomo Charles Joseph , Abruzzo Todd , Albuquerque Felipe , Bulsara Ketan R , Derdeyn Colin P , Fraser Justin F , Hirsch Joshua A , Hussain Muhammad Shazam , Do Huy M , Jayaraman Mahesh V , Meyers Philip M , Narayanan Sandra 
Published: April 2012

BackgroundManagement of vascular tumors of the head, neck, and brain is often complex and requires a multidisciplinary approach. Peri-operative embolization of vascular tumors may help to reduce intra-operative bleeding and operative times and have thus become an integral part of the management of these tumors. Advances in catheter and non-catheter based techniques in conjunction with the growing field of neurointerventional surgery is likely to expand the number of peri-operative embolizations performed. The goal of this article is to provide consensus reporting standards and guidelines for embolization treatment of vascular head, neck, and brain tumors.SummaryThis article was produced by a writing group comprised of members of the Society of Neurointerventional Surgery. A computerized literature search using the National Library of Medicine database (Pubmed) was conducted for relevant articles published between 1 January 1990 and 31 December 2010. The article summarizes the effectiveness and safety of peri-operative vascular tumor embolization. In addition, this document provides consensus definitions and reporting standards as well as guidelines not intended to represent the standard of care, but rather to provide uniformity in subsequent trials and studies involving embolization of vascular head and neck as well as brain tumors.ConclusionsPeri-operative embolization of vascular head, neck, and brain tumors is an effective and safe adjuvant to surgical resection. Major complications reported in the literature are rare when these procedures are performed by operators with appropriate training and knowledge of the relevant vascular and surgical anatomy. These standards may help to standardize reporting and publication in future studies.
Fishing power and standardized catch rates: implications of missing vessel-characteristic data from the Australian eastern king prawn (Melicertus plebejus) fishery
Authors: Braccini J.M. , O’Neill M.F. , Campbell A.B. , Leigh G.M. , Courtney A.J. 
Published: April 2012

Standardized time series of fishery catch rates require collations of fishing power data on vessel characteristics. Linear mixed models were used to quantify fishing power trends and study the effect of missing data encountered when relying on commercial logbooks. For this, Australian eastern king prawn ( Melicertus plebejus ) harvests were analysed with historical (from vessel surveys) and current (from commercial logbooks) vessel data. Between 1989 and 2010, fishing power increased up to 76%. To date, both forward-filling and, alternatively, omitting records with missing vessel information from commercial logbooks produce broadly similar fishing power increases and standardized catch rates, owing to the strong influence of years with complete vessel data (16 out of 23 years of data). However, if gaps in vessel information had not originated randomly and skippers from the most efficient vessels were the most diligent at filling in logbooks, considerable errors would be introduced. Also, the buffering effect of complete years would be short-lived as years with missing data accumulate. Given ongoing changes in fleet profile with high-catching vessels fishing proportionately more of the fleet’s effort, compliance with logbook completion, or alternatively ongoing vessel gear surveys, is required for generating accurate estimates of fishing power and standardized catch rates.
Will environmental calcium declines hinderBythotrephesestablishment success in Canadian Shield lakes?
Authors: Kim Natalie , Walseng Bjørn , Yan Norman David 
Published: April 2012

Recently, calcium-rich daphniids have declined on the Canadian Shield in response to falling lake-water calcium concentrations, or [Ca]. Meanwhile the invader Bythotrephes longimanus , a predator that feeds on Daphnia , continues to spread. Our goal was to determine if ongoing calcium declines might directly or indirectly affect Bythotrephes ’ establishment success. To address direct effects, we provide the first quantification of Bythotrephes’ calcium content, which is very low (0.03% as dry mass) compared with other Cladocera. We also examined the effects of differing [Ca] (0.1–2.6 mg·L–1) on Bythotrephes’ performance in the laboratory. For all [Ca], population growth rates remained positive, indicating that Bythotrephes has great tolerance of low [Ca]. Finally, we examined Bythotrephes’ distribution in relation to [Ca] on the Shield where is it relatively new, alongside its distribution in Norway where it is endemic and found that Bythotrephes inhabits very low calcium environments in Norway (minimum = 0.2 mg·L–1). These results suggest that Bythotrephes establishment in Canada is currently not — and in the future will likely not — be limited by falling calcium. Rather, as Bythotrephes is more tolerant of low [Ca] than are its daphniid prey, we propose that both calcium decline and Bythotrephes invasions may contribute to Daphnia decline.
Critical swim speed and fast-start response in the African cichlidPseudocrenilabrus multicolor victoriae: convergent performance in divergent oxygen regimes
Authors: Gotanda K.M. , Reardon E.E. , Murphy S.M.C. , Chapman L.J. 
Published: April 2012

Dissolved oxygen (DO) can be a strong predictor of intraspecific variation in morphology and physiology in fishes. In the African cichlid Pseudocrenilabrus multicolor victoriae Seegers, 1990, fish reared under low DO develop larger gills, deeper bodies, and larger, wider heads than full siblings reared under high DO, which could influence swim performance. In this study, we compared critical swim speed (Ucrit) and fast-start swimming in F1-generation fish from two field populations (one high and one low DO) of P. m. victoriae reared under high or low DO. There was no difference in Ucritbetween populations or rearing treatments. However, females exhibited a lower Ucritthan males. In fast-start trials, low-DO-reared fish reacted faster (lower response latency) and used double bends more often than high-DO-reared fish, but there was no difference in maximum velocity or acceleration. Low-DO-reared fish might compensate for morphological differences by using double bends to achieve similar performance as high-DO siblings. These results suggest that divergent morphotypes of P. m. victoriae are capable of achieving the same level of performance under their home DO condition and highlights the importance of developmental plasticity in facilitating adaptive response to alternative environments.
The cybrid invasion: widespread postglacial dispersal byPhoxinus(Pisces: Cyprinidae) cytoplasmic hybrids
Authors: Mee J.A. , Taylor E.B. 
Published: April 2012

Peculiar reproductive processes that arise during sperm-dependent asexual reproduction may have important roles in allowing coexistence of sperm-dependent asexuals and their sexually reproducing hosts. Though typically clonal, nonclonal reproduction in the hybrid gynogenetic species Phoxinus eos–neogaeus can reestablish sexual northern redbelly dace ( Phoxinus eos (Cope, 1861)) nuclear genomes. These hybrid-derived P. eos biotypes, known as cybrids, have finescale dace ( Phoxinus neogaeus Cope, 1867) mitochondria but are otherwise indistinguishable from “pure” P. eos. Our goal was to determine the extent of the cybrids’ distribution, and hence to evaluate their role in mechanisms of asexual–sexual coexistence. We also set out to determine the geographic origins of P. eos–neogaeus and cybrids. Our sampling revealed that all Phoxinus species and biotypes are widely distributed in North America, but that cybrids have replaced pure P. eos, or preempted postglacial colonization by pure P. eos, in the northern portion of their distribution. Also, all P. eos–neogaeus and cybrids had mitochondrial DNA (mtDNA) sequences closely related to a lineage originating from a Mississippi glacial refugium. No P. eos–neogaeus or cybrids were derived from a divergent P. neogaeus lineage discovered in Atlantic Canada. It is therefore unlikely that P. eos–neogaeus or cybrids originated in any Atlantic glacial refugia. If P. neogaeus mitochondria are better adapted to northern environments, widespread mtDNA introgression may facilitate coexistence in northern areas by reducing the disparity in fitness between P. eos–neogaeus and its sexual hosts.
Population subdivision and peripheral isolation in American badgers (Taxidea taxus) and implications for conservation planning in Canada
Authors: Ethier D.M. , Laflèche A. , Swanson B.J. , Nocera J.J. , Kyle C.J. 
Published: April 2012

In Canada, three subspecies of American badgers ( Taxidea taxus (Schreber, 1777)) traditionally are identified; two of which are listed as endangered because of their restricted geographic range and low population sizes. To verify their subspecific designations and genetic insularity, we analyzed mitochondrial control region sequences within and among badger subspecies ( Taxidea taxus jacksoni Schantz, 1946, Taxidea taxus jeffersonii (Harlan, 1825), and Taxidea taxus taxus (Schreber, 1777)) from nine locations in Canada and bordering United States. Although subspecies designations were supported (a priori subspecific designations, n = 3, AMOVA: FST = 0.40, p < 0.001), insular populations also were found within subspecific ranges as shown by spatial analysis of molecular variation, which suggested that our sample set consisted of five genetic groups (FST = 0.39, p < 0.001). These five distinct groupings included the subdivision of T. t. jeffersonii on either side of the Selkirk Mountains, and of T. t. jacksoni in the western part of its range grouping more closely with T. t. taxus of Manitoba. These results indicate that endangered populations of badgers may be more segregated than previously identified using morphological characteristics as proxies for subspecific designation. These results have important implications for the conservation of badgers in Canada, particularly of the two endangered subspecies.
Effects of male ejaculate on female reproductive output and longevity in Photinus fireflies
Authors: South A. , Lewis S.M. 
Published: April 2012

In many insects, nuptial gifts in the form of spermatophores have been shown to increase female fecundity and to contribute to female somatic maintenance. Examining how variation in male spermatophore size affects female fitness components can provide insight into the evolution of nuptial gifts, as well as insight into potential conflicts between the sexes. Here we present an experimental study on the firefly Photinus obscurellus LeConte, 1851 in which we altered spermatophore size by manipulating male mating history and examined effects on female offspring production and longevity. Females were randomly allocated to one of two mating treatments in which they mated once with a male producing either a large or a small spermatophore. We found that male spermatophore size had no significant effect on lifetime fecundity or daily reproductive rates of female P. obscurellus, but females that received a larger spermatophore showed a tendency toward longer postmating life spans. These results suggest a direct benefit to females from nuptial gifts and also reveal the potential for synergistic effects on multiple facets of female fitness.