False-positive PCR results linked to administration of seasonal influenza vaccine

False-positive PCR results usually occur as a consequence of specimen-to-specimen or amplicon-to-specimen contamination within the laboratory. Evidence of contamination at time of specimen collection linked to influenza vaccine administration in the same location as influenza sampling is described. Clinical, circumstantial and laboratory evidence was gathered for each of five cases of influenza-like illness (ILI) with unusual patterns of PCR reactivity for seasonal H1N1, H3N2, H1N1 (2009) and influenza B viruses. Two 2010 trivalent influenza vaccines and environmental swabs of a hospital influenza vaccination room were also tested for influenza RNA. Sequencing of influenza A matrix (M) gene amplicons from the five cases and vaccines was undertaken. Four 2009 general practitioner (GP) specimens were seasonal H1N1, H3N2 and influenza B PCR positive. One 2010 GP specimen was H1N1 (2009), H3N2 and influenza B positive. PCR of 2010 trivalent vaccines showed high loads of detectable influenza A and B RNA. Sequencing of the five specimens and vaccines showed greatest homology with the M gene sequence of Influenza A/Puerto Rico/8/1934 H1N1 virus (used in generation of influenza vaccine strains). Environmental swabs had detectable influenza A and B RNA. RNA detection studies demonstrated vaccine RNA still detectable for at least 66 days. Administration of influenza vaccines and clinical sampling in the same room resulted in the contamination with vaccine strains of surveillance swabs collected from patients with ILI. Vaccine contamination should therefore be considered, particularly where multiple influenza virus RNA PCR positive signals (e.g. H1N1, H3N2 and influenza B) are detected in the same specimen.

Optimizing the balance between false positive and false negative error probabilities of confirmatory methods for the detection of veterinary drug residues

GC-MS data on veterinary drug residues in bovine urine are used for controlling the illegal practice of fattening cattle. According to current detection criteria, peak patterns of preferably four ions should agree within 10 or 20% from a corresponding standard pattern. These criteria are rigid, rather arbitrary and do not match daily practice. A new model, based on multivariate modeling of log peak abundance ratios, provides a theoretical basis for the identification of analytes and optimizes the balance between the avoidance of false positives and false negatives. The performance of the model is demonstrated on data provided by five laboratories, each supplying GC-MS measurements on the detection of clenbuterol, dienestrol and 19 beta-nortestosterone in urine. The proposed model shows a better performance than confirmation by using the current criteria and provides a statistical basis for inspection criteria in terms of error probabilities.

Dark room provocative test and extent of angle closure: an anterior segment OCT study.

PURPOSE: To clarify the risk parameters measured by anterior segment optical coherence tomography (AS-OCT) for elevated intraocular pressures (IOP) provoked by the darkroom test and to provide recommendations for its clinical usage. METHODS: Subjects aged >40 years and whose peripheral anterior chambers were ≤1/4 corneal thickness were recruited. The anterior segment of the eye was imaged in sitting position and under both light and dark conditions and biometry was performed using anterior segment optical coherence tomography. The analyzed parameters were: (1) central anterior chamber depth (ACD); (2) anterior chamber width; (3) pupil diameter; (4) iris curvature; (5) lens thickness; and (6) number of meridians with closed angles (NCA). Then the darkroom test was performed and a positive provocative test result was defined as a rise in IOP ≥8 mm Hg after the test. Statistical analyses included: (1) the difference in parameters between positive and negative eyes; (2) the association between posttest IOP and the parameters; and (3) the difference in parameters between the 2 eyes in subjects with the asymmetric results. RESULTS: A total of 70 subjects were recruited. ACD (P=0.022), NCA in light (P<0.001), and NCA in dark (P<0.001) were different significantly between eyes with positive and negative results. There was a strong association between NCA in dark (r=0.755, P<0.001) and the posttest IOP. Among subjects with asymmetric results between the 2 eyes, the ACD was shallower and the lens thickness was larger in the positive eye. CONCLUSIONS: The posttest IOP is determined by the extent of functionally closed angles in the dark. The test may be useful in the early diagnosis of primary angle closure. At the same time, angle configuration should be evaluated to remove false positive result.

A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours.

BACKGROUND: Although most gastrointestinal stromal tumours (GIST) carry oncogenic mutations in KIT exons 9, 11, 13 and 17, or in platelet-derived growth factor receptor alpha (PDGFRA) exons 12, 14 and 18, around 10% of GIST are free of these mutations. Genotyping and accurate detection of KIT/PDGFRA mutations in GIST are becoming increasingly useful for clinicians in the management of the disease. METHOD: To evaluate and improve laboratory practice in GIST mutation detection, we developed a mutational screening quality control program. Eleven laboratories were enrolled in this program and 50 DNA samples were analysed, each of them by four different laboratories, giving 200 mutational reports. RESULTS: In total, eight mutations were not detected by at least one laboratory. One false positive result was reported in one sample. Thus, the mean global rate of error with clinical implication based on 200 reports was 4.5%. Concerning specific polymorphisms detection, the rate varied from 0 to 100%, depending on the laboratory. The way mutations were reported was very heterogeneous, and some errors were detected. CONCLUSION: This study demonstrated that such a program was necessary for laboratories to improve the quality of the analysis, because an error rate of 4.5% may have clinical consequences for the patient.

Economic modelling of antenatal screening and ultrasound scanning programmes for identification of fetal abnormalities

Objective Within the framework of a health technology assessment and using an economic model, to determine the most clinically and cost effective policy of scanning and screening for fetal abnormalities in early pregnancy. Design A discrete event simulation model of 50,000 singleton pregnancies. Setting Maternity services in Scotland. Population Women during the first 24 weeks of their pregnancy. Methods The mathematical model was populated with data on uptake of screening, prevalence, detection and false positive rates for eight fetal abnormalities and with costs for ultrasound scanning and serum screening. Inclusion of abnormalities was based on the relative prevalence and clinical importance of conditions and the availability of data. Six strategies for the identification of abnormalities prenatally including combinations of first and second trimester ultrasound scanning and first and second trimester screening for chromosomal abnormalities were compared. Main outcome measures The number of abnormalities detected and missed, the number of iatrogenic losses resulting from invasive tests, the total cost of strategies and the cost per abnormality detected were compared between strategies. Results First trimester screening for chromosomal abnormalities costs more than second trimester screening but results in fewer iatrogenic losses. Strategies which include a second trimester ultrasound scan result in more abnormalities being detected and have lower costs per anomaly detected. Conclusions The preferred strategy includes both first and second trimester ultrasound scans and a first trimester screening test for chromosomal abnormalities. It has been recommended that this policy is offered to all women in Scotland.

The management of radial scars of the breast - does core biopsy help?

Purpose: To compare the effectiveness of fine needle aspiration cytology (FNAC) with core biopsy (CB) in the pre-operative diagnosis of radial scar (RS) of the breast.

Patients and methods: A retrospective analysis was made of all radial scars diagnosed on surgical histology over an 8-year period. Comparison was made between the results of different preoperative needle biopsy techniques and surgical histology findings.

Results: Forty of 47 patients with a preoperative radiological diagnosis of radial scar were included in this analysis. Thirty-eight patients had impalpable lesions diagnosed on mammography and two presented with a palpable lump. FNAC (n=17) was inadequate in 47% of patients, missed two co-existing carcinomas found in this group, and gave a false positive or suspicious result for malignancy in 4 patients. CB (n=23) suggested a RS in 15 patients, but only diagnosed 4 out of 7 co-existing carcinomas found in this group.

Conclusion: CB is more accurate than FNAC in the diagnosis of RS. However, these data demonstrate that CB may offer little to assist in the management of patients with RS. In summary, this paper advocates the use of CB in any lesion with a radiological suspicion of carcinoma and diagnostic excision of all lesions thought to be typical of RS on mammography.

Repeated measures screening for down's syndrome

Objective To demonstrate the potential value of screening for Down's Syndrome using highly correlated repeated measures of serum markers taken in the first and second trimesters of pregnancy. Design A Monte Carlo simulation study. Population Detection rates and false positive rates relating to the maternal age distribution of England and Wales for the period 1996 to 1998 were obtained using marker distributions from the SURUSS study. Results Screening using first trimester nuchal translucency and repeated measures of uE3 and PAPP-A in the first and second trimester has an estimated false positive rate of 0.3% for an 85% detection rate. This should be compared with the integrated test with an estimated false positive rate of 1.2% for the same detection rate. Conclusionsâ?? The performance of repeated measures screening tests, and their acceptability to women, should be assessed in further prospective studies.

Contingent screening for down syndrome is an efficient alternative to non-disclosure sequential screening

Objective To present a first and second trimester Down syndrome screening strategy, whereby second-trimester marker determination is contingent on the first-trimester results. Unlike non-disclosure sequential screening (the Integrated test), which requires all women to have markers in both trimesters, this allows a large proportion of the women to complete screening in the first trimester. Methods Two first-trimester risk cut-offs defined three types of results: positive and referred for early diagnosis; negative with screening complete; and intermediate, needing second-trimester markers. Multivariate Gaussian modelling with Monte Carlo simulation was used to estimate the false-positive rate for a fixed 85% detection rate. The false-positive rate was evaluated for various early detection rates and early test completion rates. Model parameters were taken from the SURUSS trial. Results Completion of screening in the first trimester for 75% of women resulted in a 30% early detection rate and a 55% second trimester detected rate (net 85%) with a false-positive rate only 0.1% above that achievable by the Integrated test. The screen-positive rate was 0.1% in the first trimester and 4.7% for those continuing to be tested in the second trimester. If the early detection rate were to be increased to 45% or the early completion rate were to be increased to 80%, there would be a further 0.1% increase in the false-positive rate. Conclusion Contingent screening can achieve results comparable with the Integrated test but with earlier completion of screening for most women. Both strategies need to be evaluated in large-scale prospective studies particularly in relation to psychological impact and practicability.

Three-stage contingent screening for down syndrome

Objective To demonstrate the potential value of three-stage sequential screening for Down syndrome. Methods Protocols were considered in which maternal serum pregnancy associated plasma protein-A (PAPP-A) and free -human chorionic gonadotropin (hCG) measurements were taken on all women in the first trimester. Those women with very low Down syndrome risks were screened negative at that stage and nuchal translucency (NT) was measured on the remainder and the risk reassessed. Those with very low risk were then screened negative and those with very high risk were offered early diagnostic testing. Those with intermediate risks received second-trimester maternal serum -fetoprotein, free -hCG, unconjugated estriol and inhibin-A. Risk was then reassessed and those with high risk were offered diagnosis. Detection rates and false-positive rates were estimated by multivariate Gaussian modelling using Monte-Carlo simulation. Results The modelling suggests that, with full adherence to a three-stage policy, overall detection rates of nearly 90% and false-positive rates below 2.0% can be achieved. Approximately two-thirds of pregnancies are screened on the basis of first-trimester biochemistry alone, five out of six women complete their screening in the first trimester, and the first-trimester detection rate is over 60%. Conclusion Three-stage contingent sequential screening is potentially highly effective for Down syndrome screening. The acceptability of this protocol and its performance in practice, should be tested in prospective studies. Copyright © 2006 John Wiley & Sons, Ltd.

Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics

The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/- 0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly-with the positive result that for ionic charges of +/- 0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/- 1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems-especially when looking at properties beyond liquid structure-thus providing on alternative to computationally expensive polarisable force fields.

Multimodal Biometric Human Recognition for Perceptual Human-Computer Interaction

In this paper, a novel video-based multimodal biometric verification scheme using the subspace-based low-level feature fusion of face and speech is developed for specific speaker recognition for perceptual human--computer interaction (HCI). In the proposed scheme, human face is tracked and face pose is estimated to weight the detected facelike regions in successive frames, where ill-posed faces and false-positive detections are assigned with lower credit to enhance the accuracy. In the audio modality, mel-frequency cepstral coefficients are extracted for voice-based biometric verification. In the fusion step, features from both modalities are projected into nonlinear Laplacian Eigenmap subspace for multimodal speaker recognition and combined at low level. The proposed approach is tested on the video database of ten human subjects, and the results show that the proposed scheme can attain better accuracy in comparison with the conventional multimodal fusion using latent semantic analysis as well as the single-modality verifications. The experiment on MATLAB shows the potential of the proposed scheme to attain the real-time performance for perceptual HCI applications.

Ireland's Innovation Performance: 1991-2005

In this paper we use data from the five waves of the Irish Innovation Panel (IIP) to profile the innovation performance of manufacturing plants in Ireland and Northern Ireland over the period 1991 to 2005. Despite considerable public sector investment on both sides of the border levels of innovation activity have remained broadly similar throughout this period although somewhat different trends are evident in Ireland and Northern Ireland. In terms of product innovation for example, the proportion of manufacturing plants making product changes has increased 5 per cent in Ireland and just over 7 per cent in Northern Ireland. In terms of process innovation a decline of almost 7 per cent in Ireland has been accompanied by a 7 per cent increase in Northern Ireland. These trends provide some evidence of convergence in innovation performance over the 1991 to 2005 period. This is evident in the narrowing gap between the proportion of product innovators in Ireland and Northern Ireland, convergence in the proportion of plants undertaking process innovation and in terms of the increasingly similar proportions of sales derived from innovative products. Looking in more detail at the determinants of manufacturing innovation emphasises the importance of R&D and backwards supply chain linkages as sources of new knowledge for innovation. Other external linkages prove less important suggesting the value of policy initiatives designed to promote knowledge sharing. We also find a significant negative innovation effect from legislative restrictions on plants’ product innovation. Public support for both product and process innovation are having positive effects on innovation outputs at the level of the individual plant. Future research interest centres on the contrast between this strong positive result at firm level and the more modest increases in innovation among the population of firms in Ireland and Northern Ireland.

Comparison of porcine urine and bile as matrices to screen for the residues of two sulfonamides using a semi-automated enzyme immunoassay.

Porcine urine enzyme immunoassays for sulfamethazine and sulfadiazine have previously been employed as screening tests to predict the concentrations of the drugs in the corresponding tissues (kidneys), If a urine was found positive (> 800 ng ml(-1)) the corresponding kidney was then analysed by an enzyme immunoassay and, if found positive, a confirmatory analysis by HPLC was performed. Urine was chosen as the screening matrix since sulfonamides are mainly eliminated through this body fluid, However, after obtaining a number of false positive predictions, an investigation was carried out to assess the possibility of using an alternative body fluid which would act as a superior indicator of the presence of sulfonamides in porcine kidney, An initial study indicated that serum, plasma and bile could all be used as screening matrices. From these, bile was chosen as the preferred sample matrix and an extensive study followed to compare the efficiencies of sulfonamide positive bile and urine at predicting sulphonamide positive kidneys, Bile was found to be 17 times more efficient than urine at predicting a sulfamethazine positive kidney and 11 times more efficient at predicting a sulfadiazine positive kidney, With this enhanced performance of the initial screening test, the need for the costly and time consuming kidney enzyme immunoassay, prior to HPLC analysis, was eliminated