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Biomedical subjects

M Ouali

Publications and source records attributed to M Ouali.

At least 19 recordsLinked to original sources
PubMed2003

[Bladder involvement in scleroderma: report of 3 cases].

Lower urinary tract involvement is the common manifestation of systemic sclerosis. It may represent a troublesome disturbance affecting the quality of life in systemic sclerosis patients. We report three patients with progressive systemic sclerosis who manifested pathologic abnormalities in the urinary bladder. The first patient manifested a recurrent macroscopic hematuria requiring transfusions. Both other patients developed functional and urodynamic abnormalities. With a review of the literature on this involvement of the bladder in systemic sclerosis we try to more understand urinary symptoms and urodynamics features of vesical involvement in systemic sclerosis patients.

Female↗
PubMed2001

[Unusual testicular tumor: Leydig, Sertoli, and granulosa cell mixed tumor].

We report an unusual case of a mixed granulosa-Sertoli-Leydig cell testicular tumor in a 16 year old man, who presented with bilateral gynaecomastia. A few cases have been published in the literature. Based on a case report, the authors describe the clinical, histopathological and therapeutical features of this rare affection.

Adolescent↗
PubMed2001

[Urethral diverticulosis in women. Analysis of 15 cases].

OBJECTIVE: To evaluate the aetiopathogenic, diagnostic and therapeutic aspects of urethral diverticula in women. MATERIAL AND METHODS: Over a 10-year period (January 1990 to December 1999), 15 patients with a mean age of 36 years (range: 25 to 46 years) with urethral diverticulum were included in this study. The mean parity was 2 with a history of long and difficult delivery in 6 cases. All patients presented lower urinary tract symptoms with a clinical diverticulum on gynaecological examination (14 cases) or on retrograde and voiding cystourethrography (14 cases) or intravenous urography (one case). Diverticulectomy was performed via a transvaginal approach in the dorsal position. RESULTS: There were no postoperative complications. All patients were reviewed with a mean follow-up of 3 years. The urinary symptoms had completely disappeared in 14 cases. One patient was reoperated for recurrent diverticulum. CONCLUSION: Young women with recurrent voiding disorders must be examined for the presence of urethral diverticulum that can be confirmed by cystourethrography. Transvaginal diverticulectomy in the lithotomy position is the operation which ensures the best results.

Adult↗
PubMed2001

[Transitional cell carcinoma on ureteral stump after nephrectomy for pyonephrosis].

The authors report a case of transitional cell carcinoma of the left ureteral stump in a 66-year old man treated by nephrectomy for pyonephrosis 6 years previously and cystoprostatectomy for bladder tumour 13 years previously. In the light of this case and based on a review of the literature, they essentially discuss the diagnostic and aetiopathogenic problems raised by this disease.

Aged↗
PubMed2001

[Spontaneous hematoma of the adrenal glands].

We report an uncommon case of unilateral spontaneous hematoma of the right adrenal gland in a 22-year old young man. Preoperative diagnosis was made by ultrasonography and CT-scan. A right adrenalectomy was performed. Pathological evaluation showed an isolated hematoma without adrenal abnormalities. The diagnostic and therapeutic aspects are discussed.

Adrenal Gland Diseases↗
PubMed2000

Modeling of the inhibition of retroviral integrases by styrylquinoline derivatives.

Styrylquinoline derivatives, known to be potent inhibitors of HIV-1 integrase, have been experimentally tested for their inhibitory effect on the disintegration reaction catalyzed by catalytic cores of HIV-1 and Rous sarcoma virus (RSV) integrases. A modified docking protocol, consisting of coupling a grid search method with full energy minimization, has been specially designed to study the interaction between the inhibitors and the integrases. The inhibitors consist of two moieties that have hydroxyl and/or carboxyl substituents: the first moiety is either benzene, phenol, catechol, resorcinol, or salicycilic acid; the hydroxyl substituents on the second (quinoline) moiety may be in the keto or in the enol forms. Several tautomeric forms of the drugs have been docked to the crystallographic structure of the RSV catalytic core. The computed binding energy of the keto forms correlates best with the measured inhibitory effect. The docking procedure shows that the inhibitors bind closely to the crystallographic catalytic Mg(2+) dication. Additional quantum chemistry computations show that there is no direct correlation between the binding energy of the drugs with the Mg(2+) dication and their in vitro inhibitory effect. The designed method is a leading way for identification of potent integrase inhibitors using in silico experiments.

Algorithms↗
PubMed2000

Is it better to combine predictions?

We have compared the accuracy of the individual protein secondary structure prediction methods: PHD, DSC, NNSSP and Predator against the accuracy obtained by combing the predictions of the methods. A range of ways of combing predictions were tested: voting, biased voting, linear discrimination, neural networks and decision trees. The combined methods that involve 'learning' (the non-voting methods) were trained using a set of 496 non-homologous domains; this dataset was biased as some of the secondary structure prediction methods had used them for training. We used two independent test sets to compare predictions: the first consisted of 17 non-homologous domains from CASP3 (Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction); the second set consisted of 405 domains that were selected in the same way as the training set, and were non-homologous to each other and the training set. On both test datasets the most accurate individual method was NNSSP, then PHD, DSC and the least accurate was Predator; however, it was not possible to conclusively show a significant difference between the individual methods. Comparing the accuracy of the single methods with that obtained by combing predictions it was found that it was better to use a combination of predictions. On both test datasets it was possible to obtain a approximately 3% improvement in accuracy by combing predictions. In most cases the combined methods were statistically significantly better (at P = 0.05 on the CASP3 test set, and P = 0.01 on the EBI test set). On the CASP3 test dataset there was no significant difference in accuracy between any of the combined method of prediction: on the EBI test dataset, linear discrimination and neural networks significantly outperformed voting techniques. We conclude that it is better to combine predictions.

Algorithms↗
PubMed2000

Cascaded multiple classifiers for secondary structure prediction.

We describe a new classifier for protein secondary structure prediction that is formed by cascading together different types of classifiers using neural networks and linear discrimination. The new classifier achieves an accuracy of 76.7% (assessed by a rigorous full Jack-knife procedure) on a new nonredundant dataset of 496 nonhomologous sequences (obtained from G.J. Barton and J.A. Cuff). This database was especially designed to train and test protein secondary structure prediction methods, and it uses a more stringent definition of homologous sequence than in previous studies. We show that it is possible to design classifiers that can highly discriminate the three classes (H, E, C) with an accuracy of up to 78% for beta-strands, using only a local window and resampling techniques. This indicates that the importance of long-range interactions for the prediction of beta-strands has been probably previously overestimated.

Neural Networks, Computer↗
PubMed2000

Tautomers of styrylquinoline derivatives containing a methoxy substituent: computation of their population in aqueous solution and their interaction with RSV integrase catalytic core.

8-Hydroxy-2-[2-(3-hydroxy-4-methoxyphenyl)ethenyl]-7-quinoline carboxylic acid and 8-hydroxy-2-[2-(3-methoxy-4-hydroxyphenyl)ethenyl]-7-quinoline carboxylic acid inhibit the processing and strand transfer reactions catalyzed by HIV-1 integrase with an IC50 of 2 microM. Some of their spectral properties are briefly reported. Their fluorescence is so weak that it is of no use in an experimental determination of the binding to the protein and we resorted to computer simulation. Both styrylquinoline derivatives, in their monoanionic form, have several dozens of tautomers and each of these forms has four planar rotamers. In this work computer simulations have been performed to determine which tautomer is the most abundant in aqueous solution and which binds to the Rous sarcoma virus (RSV) integrase catalytic core. As the substituents on the quinoline moiety are the same as on salicylic acid, the energies of hydroxy benzoic acid tautomers were also computed both in vacuo and embedded in a continuous medium which had the dielectric constant of bulk water, using the recent CPCM technique. The CPCM method was then applied to the two integrase inhibitors to estimate the tautomer population in water. The binding site of the compounds on the RSV integrase catalytic core was determined through a docking protocol, consisting of coupling a grid search method with full energy minimization. The designed method is a way leading to identification of potent integrase inhibitors using in silico experiments.

Avian Sarcoma Viruses↗
PubMed1999

Stability of G,A triple helices.

In this work we selected double-stranded DNA sequences capable of forming stable triplexes at 20 or 50 degrees C with corresponding 13mer purine oligonucleotides. This selection was obtained by a double aptamer approach where both the starting sequences of the oligonucleotides and the target DNA duplex were random. The results of selection were confirmed by a cold exchange method and the influence of the position of a 'mismatch' on the stability of the triplex was documented in several cases. The selected sequences obey two rules: (i) they have a high G content; (ii) for a given G content the stability of the resulting triplex is higher if the G residues lie in stretches. The computer simulation of the Mg2+, Na+and Cl-environment around three triplexes by a density scaled Monte Carlo method provides an interpretation of the experimental observations. The Mg2+cations are statistically close to the G N7 and relatively far from the A N7. The presence of an A repels the Mg2+from adjacent G residues. Therefore, the triplexes are stabilized when the Mg2+can form a continuous spine on G N7.

Base Sequence↗
PubMed1999

[Use of double-lumen umbilical vein catheters in a neonatal intensive care unit].

BACKGROUND: The aim of the study was to compare the success/failure rate and complications of insertion into the umbilical vein, of either double-lumen catheters (Charrière diameter 04, length 13 and 30 cm) or single-lumen catheters (Charrière diameter 05, length 40 cm) in a population of neonates admitted to a neonatal intensive care unit. The numbers of insertions of additional peripheral venous catheters were also compared. PATIENTS AND METHODS: The population was divided into two groups according to the severity of the respiratory failure. Group 1 (n = 52): normal hemodynamic parameters and moderate respiratory failure (FiO2 < 0.6): only single-lumen catheters were used. Group 2 (n = 56): low systemic pressure requiring vascular filling and/or inotropic drugs infusion and/or severe respiratory failure (FiO2 > 0.6): in this group, either single-lumen catheters or double-lumen catheters were inserted. RESULTS: The success rate of insertion of double-lumen catheters and of single-lumen catheters were similar (61% vs 71%: P = 0.7). Nineteen double-lumen catheters were inserted in the group 2. The average duration of double-lumen umbilical catheterization was not significantly different from simple-lumen catheterization (4.9 +/- 2.2 vs 4.6 +/- 2.2 days). Complications relating to the umbilical venous catheterization were uncommon: three catheter obstructions (two with single-lumen catheter, one with double-lumen catheters), two nosocomial infections (both with single-lumen catheter), one hydropericardium (with single-lumen catheter). In group 2, more peripheral venous catheters were required during the first 72 hours of life after insertion of single-lumen catheter than after insertion of double-lumen catheters (average number of peripheral venous catheters per infant: 1.6 +/- 0.83 vs 1 +/- 0.35 respectively; P < 0.01). CONCLUSION: Feasibility and complication rate of umbilical double-lumen catheters were similar to those of single-lumen catheters. The use of umbilical double-lumen catheters reduces the need of peripheral venous catheters.

Cardiotonic Agents↗
PubMed1999

Nitrous oxide sedation in pediatric patients undergoing gastrointestinal endoscopy.

BACKGROUND: The ideal medication to administer to children before gastrointestinal endoscopy procedures has yet to be found. The efficacy of using inhaled nitrous oxide during endoscopy in children was assessed in a pilot study. METHODS: Patients aged 5 to 17 years, referred to our hospital for diagnostic upper gastrointestinal endoscopy or rectosigmoidoscopy procedures, were eligible for enrollment in this study. All received 50% nitrous oxide in oxygen (Entonox; AGA, Rueil-Malmaison, France) before endoscopy and some of them again during endoscopy. The pediatric endoscopist and the nurse performing the procedure were separately asked to rate cooperation, emotional state, drowsiness and overall efficacy of sedation. Oxygen saturation and adverse effects were recorded throughout the procedure. After endoscopy, children scored their degree of pain during the procedures on a visual analog scale (0, no pain; 100, agony) and on a body outline (projective method). Any adverse effects were noted. RESULTS: Thirty-seven patients were enrolled in the study. Thirty patients underwent diagnostic upper gastrointestinal endoscopy and seven diagnostic rectosigmoidoscopy. The median time from administration of nitrous oxide until insertion of the endoscope was 5 minutes (range, 3-8 minutes). Good or excellent efficacy of the sedation was noted in 92% of children by the endoscopist and in 89% by the nurses. Good or excellent cooperation was noted in 92% of the children by the endoscopist and in 78% by the nurses. The children's pain score on the visual analog scale ranged from 5 to 100 (median, 20) for upper gastrointestinal endoscopy and from 0 to 30 (median, 0) for rectosigmoidoscopy. The time of discharge after endoscopy, defined as the time elapsed between the end of the endoscopy and discharge from the endoscopy suite, varied from 1 to 7 minutes (median, 1.5 minutes). CONCLUSION: Entonox provides rapid and effective analgesia without heavy sedation, leads to adequate relaxation and cooperation, and facilitates quick and efficient endoscopy. The effect of Entonox was of short duration, allowing the children to leave the endoscopy unit without need for a long recovery period. The adverse effects of Entonox appeared to be minor, and their duration was always brief. Nitrous oxide-oxygen inhalation may provide a valuable alternative to conventional sedation regimens during gastrointestinal endoscopy in children, but randomized and prospective studies comparing nitrous oxide sedation and conventional sedation regimens are necessary.

Adolescent↗
PubMed1997

Hydration of the dTn.dAn x dTn parallel triple helix: a Fourier transform infrared and gravimetric study correlated with molecular dynamics simulations.

We present a comparative analysis of the water organization around the dTn.dAn x dTn triple helix and the Watson-Crick double helix dTn.dAn respectively by means of gravimetric measurements, infrared spectroscopy and molecular dynamics simulations. The hydration per nucleotide determined by gravimetric and spectroscopic methods correlated with the molecular dynamics simulations shows that at high relative humidity (98% RH) the triple helix is less solvated than the duplex (17 +/- 2 water molecules per nucleotide instead of 21 +/-1). The experimental desorption curves are different for both structures and indicate that below 81% RH the triplex becomes more hydrated than the duplex. At this RH the FTIR spectra show the emergence of N-type sugars in the adenosine strand of the triplex. When the third strand is bound in the major groove of the Watson-Crick duplex molecular dynamics simulations show the formation of a spine of water molecules between the two thymidine strands.

DNA↗
PubMed1996

Parallel and antiparallel A*A-T intramolecular triple helices.

Intramolecular triple helices have been obtained by folding back twice oligonucleotides formed by decamers bound by non-nucleotide linkers: dA10-linker-dA10-linker-dT10 and dA10-linker-dT10-linker-dA10. We have thus prepared two triple helices with forced third strand orientation, respectively antiparallel (apA*A-T) and parallel (pA*A-T) with respect to the adenosine strand of the Watson-Crick duplex. The existence of the triple helices has been shown by FTIR, UV and fluorescence spectroscopies. Similar melting temperatures have been obtained in very different oligomer concentration conditions (micromolar solutions for thermal denaturation classically followed by UV spectroscopy, milimolar solutions in the case of melting monitored by FTIR spectroscopy) showing that the triple helices are intramolecular. The stability of the parallel triplex is found to be slightly lower than that of the antiparallel (deltaT(m) = 6 degrees C). The sugar conformations determined by FTIR are different for both triplexes. Only South-type sugars are found in the antiparallel triplex whereas both South- and North-type sugars are detected in the parallel triplex. In this case, thymidine sugars have a South-type geometry, and the adenosine strand of the Watson-Crick duplex has North-type sugars. For the antiparallel triplex the experimental results and molecular modeling data are consistent with a reverse-Hoogsteen like third-strand base pairing and South-type sugar conformation. An energetically optimized model of the parallel A*A-T triple helix with a non-uniform distribution of sugar conformations is discussed.

Carbohydrate Conformation↗
PubMed1996

A molecular mechanics and dynamics study of alternate triple-helices involving the integrase-binding site of the HIV-1 virus and oligonucleotides having a 3'-3' internucleotide junction.

Triple helix formation by oligonucleotides can be extended beyond polypurine tracts with the help of specially designed linkers. In this paper we focus our attention on the integrase-binding site of the HIV-1 virus located on the U5 LTR end which contains two adjacent purine tracts on opposite strands. Two alternate triple helices with a 3'-3' junction in the third strand are considered: 5'-GGTTTTp3'-3'pTGTGT-5' and 5'-GGAAAAp3'-3'pAGAGA-5' The structural plausibility of these triplexes is investigated using molecular mechanics and dynamics simulations, both in vacuo and in aqua. The non-isomorphism of the triplets in the GpT steps in the first sequence, gives rise to non canonical conformations in the torsion angles, hydration appears to be crucial for this triplex. Sugar puckers are predominantly South during in vacuo simulations while they turn East in aqua. In the simulation in aqua the triplexes are shrouded by an hydration shell, however, we have not been able to detect any permanent hydrogen bond bridge between DNA and water. The solvation of ions as well as their radial distribution, appear to be relatively well behaved despite the artifacts known to be generated by the simulation procedure. The experimental feasibility of these structures is discussed.

Base Sequence↗
PubMed1996

Binding of Net-Fla, a netropsin-flavin hybrid molecule, to DNA: molecular mechanics and dynamics studies in vacuo and in water solution.

We have studied the binding of the hybrid netropsin-flavin (Net-Fla) molecule onto four sequences containing four A. T base pairs. Molecular mechanics minimizations in vacuo show numerous minimal conformations separated by one base pair. 400 ps molecular dynamics simulations in vacuo have been performed using the lowest minima as the starting conformations. During these simulations, the flavin moiety of the drug makes two hydrogen bonds with an amino group of a neighboring guanine. A 200 ps molecular dynamics simulation in explicit water solution suggests that the binding of Net-Fla upon the DNA substrate is enhanced by water bridges. A water molecule bridging the amidinium of Net-Fla to the N3 atom of an adenine seems to be stuck in the drug-DNA complex during the whole simulation. The fluctuations of the DNA helical parameters and of the torsion angles of the sugar-phosphate backbone are very similar in the simulations in vacuo and in water. The time auto-correlation functions for the DNA helical parameters decrease rapidly in the picosecond range in vacuo. The same functions computed from the water solution molecular dynamics simulations seem to have two modes: the rapid mode is similar to the behavior in vacuo, and is followed by a slower mode in the 10 ps range.

Binding Sites↗
PubMed1993

Triple helix formation by alpha-oligodeoxynucleotides: a vibrational spectroscopy and molecular modeling study.

The structures of triple helices alpha dT6.beta dAn.beta dTn, alpha dT12.beta dAn.beta dTn, alpha dC12+.beta dGn.beta dCn, and alpha dC12+.beta rGn.beta rCn have been studied by Fourier transform infrared spectroscopy, Raman spectroscopy, and molecular mechanics calculations. The sugar conformations in these triplexes have been determined by vibrational spectroscopy. Our results show the existence of only S-type sugars in the alpha dT12.beta dAn.beta dTn triple helix. Both S- and N-type sugar infrared and Raman markers have been detected in the spectra of alpha dC12+.beta dGn.beta dCn. Molecular mechanics refinements taking into account vibrational spectroscopy data constraints allow us to propose third strand hydrogen-bonding schemes and third strand polarities in triple helix models. For alpha dT12.beta dA12.beta dT12 the third strand forms reverse Hoogsteen hydrogen bonds with the beta dA12 strand and therefore is parallel to the purine strand. In contrast, for alpha dC12+.beta dG12.beta dC12 calculations show that only a model in which the third strand is Hoogsteen base paired and antiparallel to the purine strand of the Watson-Crick duplex is compatible with spectroscopic data.

Hydrogen Bonding↗