Biomedical subjects

Eric Dubois

Publications and source records attributed to Eric Dubois.

7 recordsLinked to original sources

PubMed2006

Intra-laboratory validation of a concentration method adapted for the enumeration of infectious F-specific RNA coliphage, enterovirus, and hepatitis A virus from inoculated leaves of salad vegetables.

Salad vegetables exposed to fecal contamination may cause outbreaks of hepatitis or gastro-enteritis if they are eaten raw. A procedure, based on elution with phosphate-buffered saline and concentration by filtration through membrane filters, was developed for the recovery of enteric viruses from salad leaves. The method was evaluated using lettuce leaves inoculated with hepatitis A virus (HAV), poliovirus, and MS2 bacteriophage. In addition, this method was validated by an intra-laboratory study using leaves of various salad vegetables inoculated with MS2 phage. The French standard NF V 03-110 was used to establish the general principle and the technical protocol of the validation procedure. Linear regression models describing the quantitative reactions were good fits to data in the whole range of viral concentrations tested, which was from about 1 to 4 log plaque-forming units (PFU) per 25 g of lettuce. The fractions of inoculated viruses recovered were estimated to be about 64% for HAV, 18% for poliovirus, and 29% for MS2. No significant effect of the food matrix was found using various types of salad vegetable (butter lettuce, iceberg lettuce, romaine lettuce, witloof chicory, curly endive, corn salad, rocket and watercress). Moreover, the variance of the results was constant for all levels of virus contamination within the experimental range. Intermediate reproducibility experiments were also performed to allow calculation of the uncertainty factor, which was found to be 0.58 log PFU/25 g. When used in association with phage enumeration, this validated procedure is rapid enough to be used for screening salad vegetables for evaluation of the efficacy of processes for control of pathogenic microorganisms on such foods.

Clinical Laboratory Techniques↗

PubMed2005

Specification of the observation model for regularized image up-sampling.

Regularization is one of the most promising methods for image up-sampling, which is an ill-posed inverse problem. A key element of such a regularization approach is the observation model relating the observed lower resolution (LR) image to the desired higher resolution (HR) up-sampled image, used in the data-fidelity term of the regularization cost function. This paper presents an algorithm to determine this observation model based on a model of the physical acquisition process for the LR image, and the ideal acquisition process for the desired HR image, both from the same underlying continuous image. The method is illustrated with typical scenarios corresponding to LR and HR cameras modeled by either Gaussian or rectangular apertures. Experiments with some regularized image up-samplers demonstrate the importance of using the correct, adapted observation model as determined by our algorithm. Index Terms-Camera aperture, data fidelity, image up-sampling, interpolation, multidimensional signal processing, observation model, power spectral density (PSD), super-resolution.

Algorithms↗

PubMed2005

Reconstruction of nonuniformly sampled images in spline spaces.

This paper presents a novel approach to the reconstruction of images from nonuniformly spaced samples. This problem is often encountered in digital image processing applications. Nonrecursive video coding with motion compensation, spatiotemporal interpolation of video sequences, and generation of new views in multicamera systems are three possible applications. We propose a new reconstruction algorithm based on a spline model for images. We use regularization, since this is an ill-posed inverse problem. We minimize a cost function composed of two terms: one related to the approximation error and the other related to the smoothness of the modeling function. All the processing is carried out in the space of spline coefficients; this space is discrete, although the problem itself is of a continuous nature. The coefficients of regularization and approximation filters are computed exactly by using the explicit expressions of B-spline functions in the time domain. The regularization is carried out locally, while the computation of the regularization factor accounts for the structure of the nonuniform sampling grid. The linear system of equations obtained is solved iteratively. Our results show a very good performance in motion-compensated interpolation applications.

Algorithms↗

PubMed2005

Image up-sampling using total-variation regularization with a new observation model.

This paper presents a new formulation of the regularized image up-sampling problem that incorporates models of the image acquisition and display processes. We give a new analytic perspective that justifies the use of total-variation regularization from a signal processing perspective, based on an analysis that specifies the requirements of edge-directed filtering. This approach leads to a new data fidelity term that has been coupled with a total-variation regularizer to yield our objective function. This objective function is minimized using a level-sets motion that is based on the level-set method, with two types of motion that interact simultaneously. A new choice of these motions leads to a stable solution scheme that has a unique minimum. One aspect of the human visual system, perceptual uniformity, is treated in accordance with the linear nature of the data fidelity term. The method was implemented and has been verified to provide improved results, yielding crisp edges without introducing ringing or other artifacts.

Algorithms↗

PubMed2004

Diversity of enterovirus sequences detected in oysters by RT-heminested PCR.

Oysters harvested in western France, from five sites associated with outbreaks of food-borne norovirus gastroenteritis between February 2000 and March 2001, were assayed for enterovirus RNA by reverse transcriptase-heminested polymerase chain reaction (RT-heminested PCR). Forty percent (21/52) of shellfish samples (pool of seven oysters) were contaminated by enteroviruses. Infectious coxsackieviruses serotype A21 were isolated from three of these positive samples. Amplicons corresponding to 65 base sequences in the 5' untranslated region of the enteroviral genome were analyzed by direct sequencing. Interpretable results were obtained from 18 amplicons, but mixtures of sequences confused the results from 3 samples. Sequences isolated from samples from the different sites were different but similarities were observed between sequences detected in shellfish from two sites at different dates. Sequences were also compared to sequences of human, bovine and porcine enteroviruses. Both human and animal origins of enterovirus contamination of shellfish seemed likely.

Animals↗

PubMed2003

A semiquantitative approach to estimate Norwalk-like virus contamination of oysters implicated in an outbreak.

Gastroenteritis outbreaks linked to shellfish consumption are numerous and Norwalk-like viruses (NLVs) are frequently the responsible causative agents. However, molecular data linking shellfish and clinical samples are still rare despite the availability of diagnostic methods. In a recent outbreak we found the same NLV sequence in stool and shellfish samples (100% identity over 313 bp in the capsid region), supporting the epidemiological data implicating the shellfish as the source of infection. A semiquantitative approach using most-probable-number-RT-PCR (MPN-RT-PCR) demonstrated the presence of a hundred of RT-PCR units per oyster. Follow-up of the oysters in the harvest area, for approximately 2 months, showed persistence of NLV contamination of the shellfish at levels up to a thousand RT-PCR units per oyster prior to depuration of the shellfish. This finding is useful in beginning to understand shellfish contamination and depuration for use in future hazard analyses.

Animals↗

PubMed2002

Modified concentration method for the detection of enteric viruses on fruits and vegetables by reverse transcriptase-polymerase chain reaction or cell culture.

Fruits and vegetables may act as a vehicle of human enteric virus if they are irrigated with sewage-contaminated water or prepared by infected food handlers. An elution-concentration method was modified to efficiently detect, by reverse transcriptase-polymerase chain reaction (RT-PCR) or by cell culture, contamination by poliovirus, hepatitis A virus (HAV), and Norwalk-like virus (NLV) of various fresh and frozen berries and fresh vegetables. The protocol included washing the fruit or vegetable surface with 100 mM Tris-HCl, 50 mM glycine, and 3% beef extract, pH 9.5 buffer, which favors viral elution from acid-releasing berries, supplemented with 50 mM MgCl2 to reduce the decrease in viral infectivity during the process. The viral concentration method was based on polyethylene glycol precipitation. Copurified RT-PCR inhibitors and cytotoxic compounds were removed from viral concentrates by chloroform-butanol extraction. Viruses from 100 g of vegetal products could be recovered in volumes of 3 to 5 ml. Viral RNAs were isolated by a spin column method before molecular detection or concentrates were filtered (0.22-microm porosity) and inoculated on cell culture for infectious virus detection. About 15% of infectious poliovirus and 20% of infectious HAV were recovered from frozen raspberry surfaces. The percentage of viral RNA recovery was estimated by RT-PCR to be about 13% for NLV, 17% for HAV, and 45 to 100% for poliovirus. By this method, poliovirus and HAV RNA were detected on products inoculated with a titer of about 5 x 10(1) 50% tissue culture infectious dose per 100 g. NLV RNA was detected at an initial inoculum of 1.2 x 10(3) RT-PCR amplifiable units. This method would be useful for the viral analysis of fruits or vegetables during an epidemiological investigation of foodborne diseases.

Cells, Cultured↗