bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skin testing with raw egg does not predict tolerance to baked egg in egg‐allergic children
Authors: Turner P. J. , Kumar K. , Fox A. T. 
Published: October 2014

AbstractBackgroundMost children with egg allergy tolerate egg in baked foods, such as cake, but tolerance cannot be predicted with conventional allergy testing. We hypothesized that the skin prick test (SPT) wheal to unprocessed raw egg might predict tolerance of baked egg at formal oral food challenge (OFC).MethodsWe conducted a retrospective chart review to assess the utility of SPT wheal to egg extract (EE), raw egg (RE), and the ratio of EE:RE in predicting outcome of baked‐egg OFC in children presenting to our tertiary referral centers with a physician diagnosis of egg allergy and following complete egg avoidance in their diet, between 2009 and 2013. OFC were performed following a standardized protocol using baked egg in cake, to a total dose equivalent to 3g egg protein.ResultsData were analyzed from 186 completed challenges: OFC was positive in 64 (34%) children and negative in 122 (66%). Six children experienced anaphylaxis at OFC. Children tolerant to baked egg were more likely to have a lower SPT to egg extract/raw egg and EE:RE (median 0.56) than their allergic counterparts (0.70, p < 0.05). However, ROC curve analysis demonstrated poor predictivity of challenge outcome, with AUC for SPT to egg extract, raw egg and EE:ER equal to 0.71, 0.63 and 0.60, respectively.ConclusionEE:RE was not helpful in predicting outcome of baked‐egg OFC. Indeed, SPT to egg extract was slightly better at predicting outcome than either SPT to raw egg or EE:RE. Unfortunately, tolerance to baked egg can only be predicted from previous history or through controlled exposure.
Biofilm formation and motility of Xanthomonas strains with different citrus host range
Authors: Sena‐Vélez M. , Redondo C. , Gell I. , Ferragud E. , Johnson E. , Graham J. H. , Cubero J. 
Published: October 2014

Xanthomonas citri subsp. citri (Xcc) strain A is the causal agent of citrus bacterial canker (CBC) on most Citrus spp. and close relatives. Two restricted host range strains of CBC, Aw and A*, from Florida and southwest Asia, respectively, infect Mexican lime. Several studies have linked biofilm formation by Xcc to bacterial colonization prior to and after plant ingress, but none have evaluated connections between biofilm formation and the behaviour of different strains of Xcc on citrus hosts and non‐hosts. In this study biofilm formation and swimming motility were evaluated for citrus pathogenic xanthomonads including wide and restricted host range strains of Xcc, X. alfalfae subsp. citrumelonis (Xac) (the causal agent of citrus bacterial spot) and X. campestris pv. campestris (Xc). Differential biofilm formation was observed in vitro and in planta among the Xanthomonas strains assayed. Minimal medium XVM2 increased biofilm formation, especially for those strains with a host range restricted to Mexican lime. In planta, strains produced more biofilm on leaves or fruits of their host than on non‐hosts. Scanning electron microscopy of biofilms on leaf and fruit surfaces revealed differences in structure of bacterial aggregates with respect to the strain's host range. In addition, swimming motility varied widely depending on the host range of the strain. It was concluded that biofilm formation in vitro and in planta for strains of Xcc and Xac was related to their host range, as these processes affect colonization at the early stages of the infection process.
Inference for Quantiles of a Finite Population: Asymptotic versus Resampling Results
Authors: Conti Pier Luigi , Marella Daniela 
Published: October 2014

AbstractThe aim of the paper is to study the problem of estimating the quantile function of a finite population. Attention is first focused on point estimation, and asymptotic results are obtained. Confidence intervals are then constructed, based on both the following: (i) asymptotic results and (ii) a resampling technique based on rescaling the ‘usual’ bootstrap. A simulation study to compare asymptotic and resampling‐based results, as well as an application to a real population, is finally performed.
The Late Carboniferous Triplosoba pulchella is not a fly in the ointment but a stem‐mayfly
Authors: BÉTHOUX OLIVIER 
Published: October 2014

AbstractThe Late Carboniferous Triplosoba pulchella (Brongniart, 1893) was regarded by most authors as a stem‐mayfly. Contrary to this, it was related to the extinct ‘palaeopteran’ order Diaphanopterodea in the most recent revision of the species. The only available specimen of the species is re‐investigated using various manual and computer‐assisted optical techniques. New data are presented and compared with previous data. The reasoning underlying the ‘Diaphanopterodea hypothesis’ is found to be deficient due to incomplete observations. Moreover, this hypothesis requires multiple character conflicts within Diaphanopterodea. Instead, the ‘(stem‐)Ephemeroptera hypothesis’ is favoured. The occurrence of a forked RP2, observed in one hindwing of T. pulchella (RP2 is simple in the other hindwing, and incompletely preserved in forewings) is a strict apomorphy of the group. It is also shown that the species possessed what is interpreted as an early state of the costal brace. Other observations do not contradict this placement, which is overall more consistent than an assignment to the Diaphanopterodea. This contribution demonstrates the importance of long‐term conservation of natural history collections, allowing new investigation techniques to be applied in the future.
Post‐transplant lymphoproliferative disorders are not associated with IgG4 sclerosing disease
Authors: Cathro H.P. , Bullock G.C. , Bonatti H. , Meriden Z. , Cook S. , Aguilera N. 
Published: October 2014

AbstractBackgroundAlthough the majority of post‐transplant lymphoproliferative disorder (PTLD) cases are associated with Epstein–Barr virus (EBV), 20–42% of cases are EBV negative (EBV‐N). The antigenic stimulus that drives EBV‐N PTLD is unknown, but is likely heterogeneous. A common feature of PTLD, regardless of EBV status, is an abnormal polytypic lymphoplasmacytic infiltrate. Immunglobulin‐G4 (IgG4) syndrome is also characterized by a polytypic lymphoplasmacytic infiltrate with a predominance of IgG4‐positive (IgG4‐P) plasma cells.MethodsWe investigated the possibility of an association between EBV‐N PTLD and IgG4 syndrome. Of 33 evaluated PTLD cases, 9 (27%) were EBV‐N. EBV‐N PTLD cases showed longer transplantation‐to‐diagnosis times than EBV‐positive cases.ResultsA single patient had a preceding benign duodenal biopsy with focally prominent IgG4‐P plasma cells; however, no clinical data supported IgG4 syndrome, precluding an association between IgG4 syndrome and subsequent EBV‐N PTLD in this patient.ConclusionAs none of 29 evaluable cases of PTLD (including all 9 EBV‐N cases) were associated with an increase in IgG4‐P plasma cells, IgG4 syndrome does not appear to play a role in the etiology of EBV‐N PTLD. The significance of these findings and the current understanding of the etiology of EBV‐N PTLD are discussed.
Products of twists, geodesic lengths and Thurston shears
Authors: Wolpert Scott A. 
Published: October 2014

AbstractThurston introduced shear deformations (cataclysms) on geodesic laminations–deformations including left and right displacements along geodesics. For hyperbolic surfaces with cusps, we consider shear deformations on disjoint unions of ideal geodesics. The length of a balanced weighted sum of ideal geodesics is defined and the Weil–Petersson (WP) duality of shears and the defined length is established. The Poisson bracket of a pair of balanced weight systems on a set of disjoint ideal geodesics is given in terms of an elementary$2$-form. The symplectic geometry of balanced weight systems on ideal geodesics is developed. Equality of the Fock shear coordinate algebra and the WP Poisson algebra is established. The formula for the WP Riemannian pairing of shears is also presented.
Dosimetry of cone‐defined stereotactic radiosurgery fields with a commercial synthetic diamond detector
Authors: Morales Johnny E. , Crowe Scott B. , Hill Robin , Freeman Nigel , Trapp J. V. 
Published: October 2014

Purpose:Small field x‐ray beam dosimetry is difficult due to lack of lateral electronic equilibrium, source occlusion, high dose gradients, and detector volume averaging. Currently, there is no single definitive detector recommended for small field dosimetry. The objective of this work was to evaluate the performance of a new commercial synthetic diamond detector, namely, the PTW 60019 microDiamond, for the dosimetry of small x‐ray fields as used in stereotactic radiosurgery (SRS).Methods:Small field sizes were defined by BrainLAB circular cones (4–30 mm diameter) on a Novalis Trilogy linear accelerator and using the 6 MV SRS x‐ray beam mode for all measurements. Percentage depth doses (PDDs) were measured and compared to an IBA SFD and a PTW 60012 E diode. Cross profiles were measured and compared to an IBA SFD diode. Field factors, , were calculated by Monte Carlo methods using BEAMnrc and correction factors, , were derived for the PTW 60019 microDiamond detector.Results:For the small fields of 4–30 mm diameter, there were dose differences in the PDDs of up to 1.5% when compared to an IBA SFD and PTW 60012 E diode detector. For the cross profile measurements the penumbra values varied, depending upon the orientation of the detector. The field factors, , were calculated for these field diameters at a depth of 1.4 cm in water and they were within 2.7% of published values for a similar linear accelerator. The corrections factors, , were derived for the PTW 60019 microDiamond detector.Conclusions:The authors conclude that the new PTW 60019 microDiamond detector is generally suitable for relative dosimetry in small 6 MV SRS beams for a Novalis Trilogy linear equipped with circular cones.
Exomes and the Clinical Research Conundrum: New Approaches to Enhancing the Value of Genomic Data
Authors: Miller David , Milos Patrice 
Published: October 2014

Clinical research providers who investigate unknown genetic disorders have an unprecedented opportunity to gather and examine large-scale genetic information to seek the underlying variation that could potentially explain a given condition. The use of exome sequencing to inform disease characterization and treatment in the future, while not yet very widely accessible, is increasing. However, the availability of exome and genome scale data have presented the broader community with questions about reproducibility and scalability of DNA sequencing and interpretation processes, the importance of integrating relevant phenotypic information, and the ability to provide statements about “significance” in an environment where new knowledge about variants is being acquired on a daily basis.
In this webinar, our expert speakers will highlight both the opportunities and the questions that powerful NGS technologies raise, and how best to address them with new approaches that have been developed based on the needs of the clinical research community, including but not limited to the use of orthogonal platforms and focused interpretation to provide the most relevant results quickly.
Immunologic Characterization of a Rhesus Macaque H1N1 Challenge Model for Candidate Influenza Virus Vaccine Assessment
Authors: Skinner Jason A. , Zurawski Sandra M. , Sugimoto Chie , Vinet-Oliphant Heather , Vinod Parvathi , Xue Yaming , Russell-Lodrigue Kasi , Albrecht Randy A. , García-Sastre Adolfo , Salazar Andres M. , Roy Chad J. , Kuroda Marcelo J. , Oh SangKon , Zurawski Gerard 
Published: October 2014

ABSTRACTDespite the availability of annually formulated vaccines, influenza virus infection remains a worldwide public health burden. Therefore, it is important to develop preclinical challenge models that enable the evaluation of vaccine candidates while elucidating mechanisms of protection. Here, we report that naive rhesus macaques challenged with 2009 pandemic H1N1 (pH1N1) influenza virus do not develop observable clinical symptoms of disease but develop a subclinical biphasic fever on days 1 and 5 to 6 postchallenge. Whole blood microarray analysis further revealed that interferon activity was associated with fever. We then tested whether type I interferon activity in the blood is a correlate of vaccine efficacy. The animals immunized with candidate vaccines carrying hemagglutinin (HA) or nucleoprotein (NP) exhibited significantly reduced interferon activity on days 5 to 6 postchallenge. Supported by cellular and serological data, we conclude that blood interferon activity is a prominent marker that provides a convenient metric of influenza virus vaccine efficacy in the subclinical rhesus macaque model.
Genetic Diversity and Dynamic Distribution of Mycobacterium tuberculosis Isolates Causing Pulmonary and Extrapulmonary Tuberculosis in Thailand
Authors: Srilohasin Prapaporn , Chaiprasert Angkana , Tokunaga Katsushi , Nishida Nao , Prammananan Therdsak , Smittipat Nat , Mahasirimongkol Surakameth , Chaiyasirinroje Boonchai , Yanai Hideki , Palittapongarnpim Prasit 
Published: October 2014

ABSTRACT

This study examined the genetic diversity and dynamicity of circulating
Mycobacterium tuberculosis
strains in Thailand using nearly neutral molecular markers. The single nucleotide polymorphism (SNP)-based genotypes of 1,414 culture-positive
M. tuberculosis
isolates from 1,282 pulmonary tuberculosis (PTB) and 132 extrapulmonary TB (EPTB) patients collected from 1995 to 2011 were characterized. Among the eight SNP cluster groups (SCG), SCG2 (44.1%), which included the Beijing (BJ) genotype, and SCG1 (39.4%), an East African Indian genotype, were dominant. Comparisons between the genotypes of
M. tuberculosis
isolates causing PTB and EPTB in HIV-negative cases revealed similar prevalence trends although genetic diversity was higher in the PTB patients. The identification of 10 reported sequence types (STs) and three novel STs was hypothesized to indicate preferential expansion of the SCG2 genotype, especially the modern BJ ST10 (15.6%) and ancestral BJ ST19 (13.1%). An association between SCG2 and SCG1 genotypes and particular patient age groups implies the existence of different genetic advantages among the bacterial populations. The results revealed that increasing numbers of young patients were infected with
M. tuberculosis
SCGs 2 and 5, which contrasts with the reduction of the SCG1 genotype. Our results indicate the selection and dissemination of potent
M. tuberculosis
genotypes in this population. The determination of heterogeneity and dynamic population changes of circulating
M. tuberculosis
strains in countries using the
Mycobacterium bovis
BCG (bacillus Calmette-Guérin) vaccine are beneficial for vaccine development and control strategies.
External Quality Assessments for Microbiologic Diagnosis of Diphtheria in Europe
Authors: Both Leonard , Neal Shona , De Zoysa Aruni , Mann Ginder , Czumbel Ida , Efstratiou Androulla 
Published: October 2014

ABSTRACT
The European Diphtheria Surveillance Network (EDSN) ensures the reliable epidemiological and microbiologic assessment of disease prevalence in the European Union. Here, we describe a survey of current diagnostic techniques for diphtheria surveillance conducted across the European Union and report the results from three external quality assessment (EQA) schemes performed between 2010 and 2014.
Comparing Whole-Genome Sequencing with Sanger Sequencing for
spa
Typing of Methicillin-Resistant Staphylococcus aureus
Authors: Bartels Mette Damkjær , Petersen Andreas , Worning Peder , Nielsen Jesper Boye , Larner-Svensson Hanna , Johansen Helle Krogh , Andersen Leif Percival , Jarløv Jens Otto , Boye Kit , Larsen Anders Rhod , Westh Henrik 
Published: October 2014

ABSTRACT

spa
typing of methicillin-resistant
Staphylococcus aureus
(MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the
spa
repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an in-house analysis pipeline determines the
spa
types. Due to national surveillance, all MRSA isolates are sent to Statens Serum Institut, where the
spa
type is determined by PCR and Sanger sequencing. The purpose of this study was to evaluate the reliability of the
spa
types obtained by 150-bp paired-end Illumina WGS. MRSA isolates from new MRSA patients in 2013 (
n
= 699) in the capital region of Denmark were included. We found a 97% agreement between
spa
types obtained by the two methods. All isolates achieved a
spa
type by both methods. Nineteen isolates differed in
spa
types by the two methods, in most cases due to the lack of 24-bp repeats in the whole-genome-sequenced isolates. These related but incorrect
spa
types should have no consequence in outbreak investigations, since all epidemiologically linked isolates, regardless of
spa
type, will be included in the single nucleotide polymorphism (SNP) analysis. This will reveal the close relatedness of the
spa
types. In conclusion, our data show that WGS is a reliable method to determine the
spa
type of MRSA.
Toward Standardization of BK Virus Monitoring: Evaluation of the BK Virus R-gene Kit for Quantification of BK Viral Load in Urine, Whole-Blood, and Plasma Specimens
Authors: Sueur Charlotte , Solis Morgane , Meddeb Mariam , Soulier Eric , Domingo-Calap Pilar , Lepiller Quentin , Freitag Rachel , Bahram Seiamak , Caillard Sophie , Barth Heidi , Stoll-Keller Françoise , Fafi-Kremer Samira 
Published: October 2014

ABSTRACT

Screening of BK virus (BKV) replication is recommended to identify patients at increased risk of BKV-associated diseases. However, the heterogeneity of molecular techniques hinders the establishment of universal guidelines for BKV monitoring. Here we aimed to compare the performance of the CE-marked BK virus R-gene kit (R-gene) to the performance of our in-house assay for quantification of BKV DNA loads (BKVL). A 12-specimen panel from the Quality Control for Molecular Diagnostics (QCMD) organization, 163 urine samples, and 88 paired specimens of plasma and whole blood (WB) from transplant recipients were tested. Both the R-gene and in-house assays showed a good correlation within the QCMD panel (
r
= 0.995 and
r
= 0.989, respectively). BKVL were highly correlated between assays, although positive biases were observed with the in-house assay in analysis of urine (0.72 ± 0.83 log
10
copies/ml), plasma (1.17 ± 0.63 log
10
copies/ml), and WB (1.28 ± 0.37 log
10
copies/ml). Recalibration with a common calibrator significantly reduced the bias in comparisons between assays. In contrast, BKVL was underestimated with the in-house PCR in eight samples containing BKV genotype II, presenting point mutations at primer-annealing sites. Using the R-gene assay, plasma and WB specimens were found to be equally suitable for quantification of BKVL, as indicated by the high correlation coefficient (
r
= 0.965,
P
< 0.0001). In conclusion, the R-gene assay demonstrated reliable performance and higher accuracy than the in-house assay for quantification of BKVL in urine and blood specimens. Screening of BKV replication by a well-validated commercial kit may enable clinical laboratories to assess viral loads with greater reproducibility and precision.
Laboratory Evaluation of Three Rapid Diagnostic Tests for Dual Detection of HIV and Treponema pallidum Antibodies
Authors: Humphries Romney M. , Woo Jennifer S. , Chung Jun Ho , Sokovic Anita , Bristow Claire C. , Klausner Jeffrey D. 
Published: October 2014

ABSTRACT

The performance of three research-use-only, dual HIV and syphilis rapid diagnostic tests (RDTs) was evaluated for 150 patient serum samples and compared to reference HIV and
Treponema pallidum
antibody detection methods. The RDTs performed comparably, with sensitivities of 93 to 99% and specificities of 97 to 100%. The kappa statistic between the RDTs was 0.95.
The VP40 Protein of Marburg Virus Exhibits Impaired Budding and Increased Sensitivity to Human Tetherin following Mouse Adaptation
Authors: Feagins Alicia R. , Basler Christopher F. 
Published: October 2014

ABSTRACT
The Marburg virus VP40 protein is a viral matrix protein that spontaneously buds from cells. It also functions as an interferon (IFN) signaling antagonist by targeting Janus kinase 1 (JAK1). A previous study demonstrated that the VP40 protein of the Ravn strain of Marburg virus (Ravn virus [RAVV]) failed to block IFN signaling in mouse cells, whereas the mouse-adapted RAVV (maRAVV) VP40 acquired the ability to inhibit IFN responses in mouse cells. The increased IFN antagonist function of maRAVV VP40 mapped to residues 57 and 165, which were mutated during the mouse adaptation process. In the present study, we demonstrate that maRAVV VP40 lost the capacity to efficiently bud from human cell lines, despite the fact that both parental and maRAVV VP40s bud efficiently from mouse cell lines. The impaired budding in human cells corresponds with the appearance of protrusions on the surface of maRAVV VP40-expressing Huh7 cells and with an increased sensitivity of maRAVV VP40 to restriction by human tetherin but not mouse tetherin. However, transfer of the human tetherin cytoplasmic tail to mouse tetherin restored restriction of maRAVV VP40. Residues 57 and 165 were demonstrated to contribute to the failure of maRAVV VP40 to bud from human cells, and residue 57 was demonstrated to alter VP40 oligomerization, as assessed by coprecipitation assay, and to determine sensitivity to human tetherin. This suggests that RAVV VP40 acquired, during adaptation to mice, changes in its oligomerization potential that enhanced IFN antagonist function. However, this new capacity impaired RAVV VP40 budding from human cells.

IMPORTANCE
Filoviruses, which include Marburg viruses and Ebola viruses, are zoonotic pathogens that cause severe disease in humans and nonhuman primates but do not cause similar disease in wild-type laboratory strains of mice unless first adapted to these animals. Although mouse adaptation has been used as a method to develop small animal models of pathogenesis, the molecular determinants associated with filovirus mouse adaptation are poorly understood. Our study demonstrates how genetic changes that accrued during mouse adaptation of the Ravn strain of Marburg virus have impacted the budding function of the viral VP40 matrix protein. Strikingly, we find impairment of mouse-adapted VP40 budding function in human but not mouse cell lines, and we correlate the impairment with an increased sensitivity of VP40 to restriction by human but not mouse tetherin and with changes in VP40 oligomerization. These data suggest that there are functional costs associated with filovirus adaptation to new hosts and implicate tetherin as a filovirus host restriction factor.