Biomedical subjects

Y Moreau

Publications and source records attributed to Y Moreau.

At least 19 recordsLinked to original sources

PubMed2006

Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors.

Interpretation of Human Immunodeficiency Virus 1 (HIV-1) genotypic drug resistance is still a major challenge in the follow-up of antiviral therapy in infected patients. Because of the high degree of HIV-1 natural variation, complex interactions and stochastic behaviour of evolution, the role of resistance mutations is in many cases not well understood. Using Bayesian network learning of HIV-1 sequence data from diverse subtypes (A, B, C, F and G), we could determine the specific role of many resistance mutations against the protease inhibitors (PIs) nelfinavir (NFV), indinavir (IDV), and saquinavir (SQV). Such networks visualize relationships between treatment, selection of resistance mutations and presence of polymorphisms in a graphical way. The analysis identified 30N, 88S, and 90M for nelfinavir, 90M for saquinavir, and 82A/T and 46I/L for indinavir as most probable major resistance mutations. Moreover we found striking similarities for the role of many mutations against all of these drugs. For example, for all three inhibitors, we found that the novel mutation 89I was minor and associated with mutations at positions 90 and 71. Bayesian network learning provides an autonomous method to gain insight in the role of resistance mutations and the influence of HIV-1 natural variation. We successfully applied the method to three protease inhibitors. The analysis shows differences with current knowledge especially concerning resistance development in several non-B subtypes.

Bayes Theorem↗

PubMed2006

Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance.

Human Immunodeficiency Virus-1 (HIV-1) antiviral resistance is a major cause of antiviral therapy failure and compromises future treatment options. As a consequence, resistance testing is the standard of care. Because of the high degree of HIV-1 natural variation and complex interactions, the role of resistance mutations is in many cases insufficiently understood. We applied a probabilistic model, Bayesian networks, to analyze direct influences between protein residues and exposure to treatment in clinical HIV-1 protease sequences from diverse subtypes. We can determine the specific role of many resistance mutations against the protease inhibitor nelfinavir, and determine relationships between resistance mutations and polymorphisms. We can show for example that in addition to the well-known major mutations 90M and 30N for nelfinavir resistance, 88S should not be treated as 88D but instead considered as a major mutation and explain the subtype-dependent prevalence of the 30N resistance pathway.

Amino Acid Sequence↗

PubMed2006

Predicting the outcome of pregnancies of unknown location: Bayesian networks with expert prior information compared to logistic regression.

BACKGROUND: As women present at earlier gestations to early pregnancy units (EPUs), the number of women diagnosed with a pregnancy of unknown location (PUL) increases. Some of these women will have an ectopic pregnancy (EP), and it is this group in the PUL population that poses the greatest concern. The aim of this study was to develop Bayesian networks to predict EPs in the PUL population. METHODS: Data were gathered in a single EPU from all women with a PUL. This data set was divided into a model-building (599 women with 44 EPs) and a validation (257 women with 22 EPs) data set and consisted of the following variables: vaginal bleeding, fluid in the pouch of Douglas, midline echo, lower abdominal pain, age, endometrial thickness, gestation days, the ratio of HCG at 48 and 0 h, progesterone levels (0 and 48 h) and the clinical outcome of the PUL. We developed Bayesian networks with expert information using this data set to predict EPs. RESULTS: The best Bayesian network used the gestational age, HCG ratio and the progesterone level at 48 h and had an area under the receiver operator characteristic curve (AUC) of 0.88 for predicting EPs when tested prospectively. CONCLUSIONS: Discrete-valued Bayesian networks are more complex to build than, for example, logistic regression. Nevertheless, we have demonstrated that such models can be used to predict EPs in a PUL population. Prospective interventional multicentre studies are needed to validate the use of such models in clinical practice.

Adolescent↗

PubMed2006

Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports.

BACKGROUND: Chromosomal abnormalities are a major cause of mental retardation and multiple congenital anomalies (MCA/MR). Screening for these chromosomal imbalances has mainly been done by standard karyotyping. Previous array CGH studies on selected patients with chromosomal phenotypes and normal karyotypes suggested an incidence of 10-15% of previously unnoticed de novo chromosomal imbalances. OBJECTIVE: To report array CGH screening of a series of 140 patients (the largest published so far) with idiopathic MCA/MR but normal karyotype. RESULTS: Submicroscopic chromosomal imbalances were detected in 28 of the 140 patients (20%) and included 18 deletions, seven duplications, and three unbalanced translocations. Seventeen of 24 imbalances were confirmed de novo and 19 were assumed to be causal. Excluding subtelomeric imbalances, our study identified 11 clinically relevant interstitial submicroscopic imbalances (8%). Taking this and previously reported studies into consideration, array CGH screening with a resolution of at least 1 Mb has been undertaken on 432 patients with MCA/MR. Most imbalances are non-recurrent and spread across the genome. In at least 8.8% of these patients (38 of 432) de novo intrachromosomal alterations have been identified. CONCLUSIONS: Array CGH should be considered an essential aspect of the genetic analysis of patients with MCA/MR. In addition, in the present study three patients were mosaic for a structural chromosome rearrangement. One of these patients had monosomy 7 in as few as 8% of the cells, showing that array CGH allows detection of low grade mosaicisims.

Abnormalities, Multiple↗

PubMed2004

Balancing false positives and false negatives for the detection of differential expression in malignancies.

A basic problem of microarray data analysis is to identify genes whose expression is affected by the distinction between malignancies with different properties. These genes are said to be differentially expressed. Differential expression can be detected by selecting the genes with P-values (derived using an appropriate hypothesis test) below a certain rejection level. This selection, however, is not possible without accepting some false positives and negatives since the two sets of P-values, associated with the genes whose expression is and is not affected by the distinction between the different malignancies, overlap. We describe a procedure for the study of differential expression in microarray data based on receiver-operating characteristic curves. This approach can be useful to select a rejection level that balances the number of false positives and negatives and to assess the degree of overlap between the two sets of P-values. Since this degree of overlap characterises the balance that can be reached between the number of false positives and negatives, this quantity can be seen as a quality measure of microarray data with respect to the detection of differential expression. As an example, we apply our method to data sets studying acute leukaemia.

False Negative Reactions↗

PubMed2003

Evaluation of the vector space representation in text-based gene clustering.

Thanks to its increasing availability, electronic literature can now be a major source of information when developing complex statistical models where data is scarce or contains much noise. This raises the question of how to deeply integrate information from domain literature with experimental data. Evaluating what kind of statistical text representations can integrate literature knowledge in clustering still remains an unsufficiently explored topic. In this work we discuss how the bag-of-words representation can be used successfully to represent genetic annotation and free-text information coming from different databases. We demonstrate the effect of various weighting schemes and information sources in a functional clustering setup. As a quantitative evaluation, we contrast for different parameter settings the functional groupings obtained from text with those obtained from expert assessments and link each of the results to a biological discussion.

Artificial Intelligence↗

PubMed2003

Probabilistic graphical models for computational biomedicine.

BACKGROUND: As genomics becomes increasingly relevant to medicine, medical informatics and bioinformatics are gradually converging into a larger field that we call computational biomedicine. OBJECTIVES: Developing a computational framework that is common to the different disciplines that compose computational biomedicine will be a major enabler of the further development and integration of this research domain. METHODS: Probabilistic graphical models such as Hidden Markov Models, belief networks, and missing-data models together with computational methods such as dynamic programming, Expectation-Maximization, data-augmentation Gibbs sampling, and the Metropolis-Hastings algorithm provide the tools for an integrated probabilistic approach to computational biomedicine. RESULTS AND CONCLUSIONS: We show how graphical models have already found a broad application in different fields composing computational biomedicine. We also indicate several challenges that lie at the interface between medical informatics, statistical genomics, and bioinformatics. We also argue that graphical models offer a unified framework making it possible to integrate in a statistically meaningful way multiple models ranging from the molecular level to cellular and to clinical levels. Because of their versatility and firm statistical underpinning, we assert that probabilistic graphical models can serve as the lingua franca for many computationally intensive approaches to biology and medicine. As such, graphical models should be a foundation of the curriculum of students in these fields. From such a foundation, students could then build towards specific computational methods in medical informatics, medical image analysis, statistical genetics, or bioinformatics while keeping the communication open between these areas.

Computational Biology↗

PubMed2002

Isolation, characterization and inhibition by acarbose of the alpha-amylase from Lactobacillus fermentum: comparison with Lb. manihotivorans and Lb. plantarum amylases.

Extracellular alpha-amylase from Lactobacillus fermentum (FERMENTA) was purified by glycogen precipitation and ion exchange chromatography. The purification was approximately 28-fold with a 27% yield. The FERMENTA molecular mass (106,000 Da) is in the same range as the ones determined for L. amylovorus (AMYLOA), L. plantarum (PLANTAA) and L. manihotivorans (MANIHOA) alpha-amylases. The amino acid composition of FERMENTA differs from the other lactobacilli considered here, but however, indicates that the peptidic sequence contains two equal parts: the N-terminal catalytic part; and the C-terminal repeats. The isoelectric point of FERMENTA, PLANTAA, MANIHOA are approximately the same (3.6). The FERMENTA optimum pH (5.0) is slightly more acidic and the optimum temperature is lower (40 degrees C). Raw starch hydrolysis catalyzed by all three amylases liberates maltotriose and maltotretaose. Maltose is also produced by FERMENTA and MANIHOA. Maltohexaose FERMENTA catalyzed hydrolysis produces maltose and maltotriose. Finally, kinetics of FERMENTA, PLANTAA and MANIHOA using amylose as a substrate and acarbose as an inhibitor, were carried out. Statistical analysis of kinetic data, expressed using a general velocity equation and assuming rapid equilibrium, showed that: (1) in the absence of inhibitor k(cat)/Km are, respectively, 1x10(9), 12.6x10(9) and 3.2x10(9) s(-1) M(-1); and (2) the inhibition of FERMENTA is of the mixed non-competitive type (K(1i)=5.27 microM; L(1i)=1.73 microM) while the inhibition of PLANTAA and MANIHOA is of the uncompetitive type (L(1i)=1.93 microM and 1.52 microM, respectively). Whatever the inhibition type, acarbose is a strong inhibitor of these Lactobacillus amylases. These results indicate that, as found in porcine and barley amylases, Lactobacillus amylases contain in addition to the active site, a soluble carbohydrate (substrate or product) binding site.

Acarbose↗

PubMed2002

Efficacy and tolerance of calcium alginate versus vaseline gauze dressings in the treatment of diabetic foot lesions.

BACKGROUND: The study aimed at comparing the efficacy and tolerance of an alginate wound dressing with a vaseline gauze dressing in the treatment of diabetic foot lesions. METHODS: This open-label randomized multicenter controlled study was designed to assess the effect of an up to 6-week treatment with either calcium alginate or vaseline gauze dressings. Lesions were either acute or chronic, under cleansing, and with a surface area of 1-50 cm(2); osteomyelitis and severe hypovascularization were non-inclusion criteria. Dressings were changed every day then, once granulation had occurred, every 2 to 3 days. Primary outcome was the proportion of patients with granulation tissue over 75% of the wound area and having a 40% decrease in wound surface area; secondary outcomes were pain on dressing changes, the number of dressing changes, and adverse events. RESULTS: Seventy-seven patients were enrolled. Due to the premature cessation of treatment in 13 patients, it was decided to reduce the period of the efficacy analysis to 4 weeks (without revising the criteria of efficacy). The success rate was of 42.8% in the calcium alginate group and of 28.5% in the vaseline gauze group (not significant difference). A subsequent analysis of granulation tissue surfaces covering the wounds at week 4 (all surfaces taken together) showed a superiority of calcium alginate (p=0.04). Pain on dressing change was lower in the calcium alginate group (p=0.047) and the total number of dressing changes tended also to be lower (p=0.07). Adverse events, which occurred 4 times in the calcium alginate group and 6 times in the other, were judged independent of the treatments. CONCLUSIONS: As compared with vaseline gauze, calcium alginate appears to be more appropriate for topical treatment of diabetic foot lesions in terms of both healing and tolerance.

Age of Onset↗

PubMed2001

Starch digestion in tropical fishes: isolation, structural studies and inhibition kinetics of alpha-amylases from two tilapias Oreochromis niloticus and Sarotherodon melanotheron.

alpha-Amylases from the intestinal cavity of two tilapia species, Oreochromis niloticus (ONI-AMY) and Sarotherodon melanotheron (SME-AMY), were purified using ammonium sulfate precipitation, affinity chromatography and chromatofocusing procedures. The purification was approximately 100-fold. The amylolytic activity, specific activity, product distribution, pH and temperature profile of ONI-AMY and SME-AMY are quite similar. The molecular mass differs slightly: 56600 (ONI-AMY) vs. 55500 (SME-AMY). As shown by isoelectric focusing analysis, both amylases contain two isoforms A and B with distinct pI: 7.2 (A) and 7.8 (B), vs. 8.3 (A) and 8.8 (B), respectively. It was not possible to isolate B, since B converts into A with time. The kinetics of the inhibition of ONI-AMY and SME-AMY activity by alpha-, beta- and gamma-cyclodextrin (alpha-, beta- and gamma-CD) were investigated using amylose as the substrate. Statistical analysis of the kinetic data expressed using a general velocity equation and assuming rapid equilibrium showed that the inhibition is of the mixed noncompetitive type. Similar results were obtained with ONI-AMY and SME-AMY. beta- and gamma-CD are stronger inhibitors than alpha-CD. ONI-AMY and SME-AMY are then closely related and show the general features common to the members of the alpha-amylase class (family 13). They enable ONI and SME tilapias to digest starch in food.

Amino Acids↗

PubMed2001

Mechanism of porcine pancreatic alpha-amylase. Inhibition of amylose and maltopentaose hydrolysis by alpha-, beta- and gamma-cyclodextrins.

The effects of alpha-, beta- and gamma-cyclodextrins on the amylose and maltopentaose hydrolysis catalysed by porcine pancreatic alpha-amylase (PPA) were investigated. The results of the statistical analysis performed on the kinetic data using the general initial velocity equation of a one-substrate reaction in the presence of one inhibitor indicate that the type of inhibition involved depends on the substrate used: the inhibition of amylose hydrolysis by alpha-, beta- and gamma-cyclodextrin is of the competitive type, while the inhibition of maltopentaose hydrolysis is of the mixed noncompetitive type. Consistently, the Lineweaver-Burk plots intersect on the vertical axis when amylose is used as the substrate, while in the case of maltopentaose, the intersection occurs at a point located in the second quadrant. The inhibition of the hydrolysis therefore involves only one abortive complex, PPA-cyclodextrin, when amylose is used as the substrate, while two abortive complexes, PPA-cyclodextrin and PPA-maltopentaose-cyclodextrin, are involved with maltopentaose. The mixed noncompetitive inhibition thus shows the existence of one accessory binding site. In any case, only one molecule of inhibitor binds to PPA. In line with these findings, the difference spectra of PPA produced by alpha-, beta- and gamma-cyclodextrin indicate that binding occurs at a tryptophan and a tyrosine residue. The corresponding dissociation constants and the inhibition constants obtained using the kinetic approach are in the same range (1.2-7 mM). The results obtained here on the inhibition of maltopentaose hydrolysis by cyclodextrin are similar to those previously obtained with acarbose as the inhibitor [Alkazaz, M., Desseaux, V., Marchis-Mouren, G., Prodanov, E. & Santimone, M. (1998) Eur. J. Biochem. 252, 100-107], but differ from those obtained with amylose as the substrate and acarbose as inhibitor [Alkazaz, M., Desseaux, V., Marchis-Mouren, G., Payan, F., Forest, E. & Santimone, M. (1996) Eur. J. Biochem. 241, 787-796]. It is concluded that the hydrolysis of both long and short chain substrates requires at least one secondary binding site, including a tryptophan residue.

Amylose↗

PubMed2001

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

MOTIVATION: Transcriptome analysis allows detection and clustering of genes that are coexpressed under various biological circumstances. Under the assumption that coregulated genes share cis-acting regulatory elements, it is important to investigate the upstream sequences controlling the transcription of these genes. To improve the robustness of the Gibbs sampling algorithm to noisy data sets we propose an extension of this algorithm for motif finding with a higher-order background model. RESULTS: Simulated data and real biological data sets with well-described regulatory elements are used to test the influence of the different background models on the performance of the motif detection algorithm. We show that the use of a higher-order model considerably enhances the performance of our motif finding algorithm in the presence of noisy data. For Arabidopsis thaliana, a reliable background model based on a set of carefully selected intergenic sequences was constructed. AVAILABILITY: Our implementation of the Gibbs sampler called the Motif Sampler can be used through a web interface: http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html. CONTACT: gert.thijs@esat.kuleuven.ac.be; yves.moreau@esat.kuleuven.ac.be

Algorithms↗

PubMed1999

Mechanism of porcine pancreatic alpha-amylase inhibition of amylose and maltopentaose hydrolysis by kidney bean (Phaseolus vulgaris) inhibitor and comparison with that by acarbose.

The effects of Phaseolus vulgaris inhibitor (alpha-AI) on the amylose and maltopentaose hydrolysis catalysed by porcine pancreatic alpha-amylase (PPA) were investigated. Based on a statistical analysis of the kinetic data and using the general velocity equation, which is valid at equilibrium for all types of inhibition in a single-substrate reaction, it was concluded that the inhibitory mode is of the mixed noncompetitive type involving two molecules of inhibitor. In line with this conclusion, the Lineweaver-Burk primary plots intersect in the second quadrant and the secondary plots of the slopes and the intercepts versus the inhibitor concentrations are parabolic curves, whether the substrate used was amylose or maltopentaose. A specific inhibition model of the mixed noncompetitive type applies here. This model differs from those previously proposed for acarbose [Al Kazaz, M., Desseaux, V., Marchis-Mouren, G., Payan, F., Forest, E. & Santimone, M. (1996) Eur. J. Biochem. 241, 787-796 and Al Kazaz, M., Desseaux, V., Marchis-Mouren, G., Prodanov, E. & Santimone, M. (1998) Eur. J. Biochem. 252, 100-107]. In particular, with alpha-AI, the inhibition takes place only when PPA and alpha-AI are preincubated together before the substrate is added. This shows that the inhibitory PPA-alphaAI complex is formed during the preincubation period. Secondly, other inhibitory complexes are formed, in which two molecules of inhibitor are bound to either the free enzyme or the enzyme-substrate complex. The catalytic efficiency was determined both with and without inhibitor. Using the same molar concentration of inhibitor, alpha-AI was found to be a much stronger inhibitor than acarbose. However, when the inhibitor amount is expressed on a weight basis (mg x L-1), the opposite conclusion is drawn. In addition, limited proteolysis was performed on PPA alone and on the alpha-AI-PPA complex. The results show that, in the complex, PPA is more sensitive to subtilisin attack, and shorter fragments are obtained. These data reflect the conformational changes undergone by PPA as the result of the protein inhibitor binding, which differ from those previously observed with acarbose.

Acarbose↗

PubMed1995

Risk analysis in the manufacture of veterinary biologicals.

"Primum non nocere' must be the first quality of veterinary immunological medicinal products. Throughout the manufacturing process, stage by stage, various ingredients and/or operations could be responsible for safety problems observed when the product is administered. During the preliminary stages, various ingredients--e.g. master seed strains (virus, bacteria or parasite), cell substrates (cell-lines or primary cells) and substances of animal origin--could be contaminated by extraneous agents. These represent the most important risks. During the process--i.e. preliminary stages, microorganism growth, downstream processing (harvest, purification, concentration, inactivation, etc.), formulation, filling, freeze-drying and finally packaging--environmental conditions (working areas, equipment, etc.) might also be defective and responsible for product contamination. The author examines all aspects of risks and their assessments through consideration of "good manufacturing practice' based on quality assurance and quality control systems.

Animals↗

PubMed1992

Babesia divergens vaccine.

A vaccine strategy against Babesia divergens bovine babesiosis was successfully developed after perfecting of an efficient in vitro culture. Crude supernatants and purified fractions were able to induce a vaccine protection in gerbils against B. divergens infection. More, supernatants induced an effective vaccine protection in cattle. The role of B. divergens exoantigens of 17, 37, 46, 70 and 90 kDa in the development of the immune response was clearly demonstrated in gerbils, cattle, and man.

Animals↗

PubMed1991

Analysis of immune responses of different hosts to Babesia divergens isolates from different geographic areas and capacity of culture-derived exoantigens to induce efficient cross-protection.

The immunoprecipitation of [35S]methionine-radiolabelled antigens from different Babesia divergens isolates by using bovine, gerbil, and human immune sera has shown that many B. divergens proteins contain epitopes shared between isolates. The cross-protective capacity of culture-derived soluble immunogens from the B. divergens Rouen 1987 isolate was tested against different B. divergens isolates. Results showed complete protection against the 7107b French isolate and substantial protection against the Weybridge 8843 English isolate (80% protection) and the Munich 87 German isolate (60% protection). In order to explain these vaccination results and to assess both the common and variable antigenicity of B. divergens, the antigenic patterns of the challenge isolates (Rouen 1987, 7107b, Weybridge 8843, and Munich 87) were compared by immunoprecipitation, using gerbil antisera raised against the Rouen 1987 vaccine isolate. Differences in the antigenic patterns and in the cross-protection of gerbils in these heterologous challenges were examined by studying the virulence and the antigenic status of each isolate.

Animals↗

PubMed1989

Vaccination against canine babesiosis: an overview of field observations.

Pirodog (ND) is a novel vaccine against canine babesiosis. It is commercially distributed and has been used in France since May 1988. More than 150,000 dogs have now been vaccinated and the results of the immunization have been contradictory. Many things remain to be understood concerning individual susceptibility, the immunosuppressive effect of the disease, and the incidence of concomitant infections.

Animals↗

PubMed1986

Resistance and immunity of dogs against Babesia canis in an endemic area.

Canine babesiosis is increasing in incidence and prevalence in some areas in France and is now a major problem for dogs. Sex and age do not have any influence on the animals' susceptibility to the disease. Some breeds are more resistant (Beagle, Fox terrier, Porcelain, Teckel, mongrel dogs) and others are more susceptible (Spaniel, Cocker, Griffon, Yorkshire terrier, Doberman, Pekinese); however, none of them is completely resistant. Dogs which live in endemic areas can synthesize antibodies against Babesia canis, sometimes at high levels, without any sign of disease.

Age Factors↗