Detecting epistasis with restricted response patterns in pairs of biallelic loci.

Well-established examples of genetic epistasis between a pair of loci typically show characteristic patterns of phenotypic distributions in joint genotype tables. However, inferring epistasis given such data is difficult due to the lack of power in commonly used approaches, which decompose the epistatic patterns into main plus interaction effects followed by testing the interaction term. Testing additive-only or all terms may have more power, but they are sensitive to nonepistatic patterns. Alternatively, the epistatic patterns of interest can be enumerated and the best matching one is found by searching through the possibilities. Although this approach requires multiple testing correction over possible patterns, each pattern can be fitted with a regression model with just one degree of freedom and thus the overall power can still be high, if the number of possible patterns is limited. Here we compare the power of the linear decomposition and pattern search methods, by applying them to simulated data generated under several patterns of joint genotype effects with simple biological interpretations. Interaction-only tests are the least powerful; while pattern search approach is the most powerful if the range of possibilities is restricted, but still includes the true pattern.

RP 59500 prophylaxis of experimental endocarditis due to erythromycin-susceptible and -resistant isogenic pairs of viridans group streptococci.

RP 59500 is a new injectable streptogramin composed of two synergistic components (quinupristin and dalfopristin) which are active against a number of erythromycin-susceptible and -resistant gram-positive bacteria. The following experiments investigate the ability of RP 59500 to prevent experimental endocarditis due to either of two erythromycin-susceptible streptococcal isolates or their constitutively erythromycin-resistant Tn916 delta E transconjugants. RP 59500 had low MICs (0.125 to 0.5 mg/liter) for all four test organisms and was substantially bactericidal in vitro. Rats with catheter-induced aortic vegetations were given single-dose antibiotic prophylaxis 30 to 60 min before bacterial inoculation through a computerized pump system which permitted the simulation of drug kinetics for humans produced by either 7 mg of RP 59500 per kg of body weight or 1 g of vancomycin. Single-dose RP 59500 prophylaxis successfully prevented endocarditis due to both the erythromycin-susceptible parent strains and their erythromycin-resistant derivatives in rats challenged with the minimal inoculum infecting 90% of controls. In addition, RP 59500 also prevented infection in animals challenged with fivefold-larger inocula of the erythromycin-susceptible parent strains. Vancomycin successfully prevented endocarditis due to any of the four test organisms. These results underline the in vivo efficacy of RP 59500 against both erythromycin-susceptible and -resistant streptococci. Such good results against the resistant strains would not be expected with erythromycin or clindamycin, which are the standard macrolidelincosamide-streptogramin antibiotics used for endocarditis prophylaxis in humans. An oral form of RP 59500 which might advantageously replace some of the older prophylactic regimens is currently being developed.

Adaptation en français et en allemand d'une échelle de pression des pairs pour jeunes adultes : le Peer Pressure Inventory [Adaptation of a peer pressure scale in French and German: the Peer Pressure Inventory].

BACKGROUND: Peer pressure is regarded as an important determinant of substance use, sexual behavior and juvenile delinquency. However, few peer pressure scales are validated, especially in French or German. Little is known about the factor structure of such scales or the kind of scale needed: some scales takes into account both peer pressure to do and peer pressure not to do, while others consider only peer pressure to do. The aim of the present study was to adapt French and German versions of the Peer Pressure Inventory, which is one of the most widely used scales in this field. We considered its factor structure and concurrent validity. METHODS: Five thousand eight hundred and sixty-seven young Swiss men filled in a questionnaire on peer pressure, substance use, and other variables (conformity, involvement) in a cohort study. RESULTS: We identified a four-factor structure, with the three factors of the initial Peer Pressure Inventory (involvement, conformity, misconduct) and adding a new one (relationship with girls). A non-valued scale (from no peer pressure to peer pressure to do only) showed stronger psychometric qualities than a valued scale (from peer pressure not to do to peer pressure to do). Concurrent validity was also good. Each behavior or attitude was significantly associated with peer pressure. CONCLUSION: Peer pressure seems to be a multidimensional concept. In this study, peer pressure to do showed the strongest influence on participants. Indeed, peer pressure not to do did not add anything useful. Only peer pressure to do affected young Swiss men's behaviors and attitudes and was reliable.

Molecular characterization of HLA-C incompatibilities in HLA-ABDR-matched unrelated bone marrow donor-recipient pairs. Sequence of two new Cw alleles (Cw*02023 and Cw*0707) and recognition by cytotoxic T lymphocytes.

While the influence of HLA-AB and -DRB1 matching on the outcome of bone marrow transplantation (BMT) with unrelated donors is clear, the evaluation of HLA-C has been hampered by its poor serological definition. Because the low resolution of standard HLA-C typing could explain the significant number of positive cytotoxic T lymphocyte precursor frequency (CTLpf) tests found among HLA-AB-subtype, DRB1/B3/B5-subtype matched patient/donor pairs, we have identified by sequencing the incompatibilities recognized by CD8+ CTL clones obtained from such positive CTLpf tests. In most cases the target molecules were HLA-C antigens that had escaped detection by serology (e.g. Cw*1601, 1502 or 0702). Direct recognition of HLA-C by a CTL clone was demonstrated by lysis of the HLA class I-negative 721.221 cell line transfected with Cw*1601 cDNA. Because of the functional importance of Cw polymorphism, a PCR-SSO oligotyping procedure was set up allowing the resolution of 29 Cw alleles. Oligotyping of a panel of 382 individuals (including 101 patients and their 272 potential unrelated donors, 5 related donors and 4 platelet donors) allowed to determine HLA-C and HLA A-B-Cw-DRB1 allelic frequencies, as well as a number of A-Cw, B-Cw, and DRB1-Cw associations. Two new HLA-Cw alleles (Cw*02023 and Cw*0707) were identified by DNA sequencing of PCR-amplified exon 2-intron 2-exon 3 amplicons. Furthermore, we determined the degree of HLA-C compatibility in 287 matched pairs that could be formed from 73 patients and their 184 potential unrelated donors compatible for HLA-AB by serology and for HLA-DRB1/ B3/B5 by oligotyping. Cw mismatches were identified in 42.1% of these pairs, and AB-subtype oligotyping showed that 30% of these Cw-incompatible pairs were also mismatched for A or B-locus subtype. The degree of HLA-C incompatibility was strongly influenced by the linkage with B alleles and by the ABDR haplotypes. Cw alleles linked with B*4403, B*5101, B18, and B62 haplotypes were frequently mismatched. Apparently high resolution DNA typing for HLA-AB does not result in full matching at locus C. Since HLA-C polymorphism is recognized by alloreactive CTLs, such incompatibilities might be as relevant as AB-subtype mismatches in clinical transplantation.

Voluntary Explicit versus Involuntary Conceptual Memory Are Associated with Dissociable fMRI Responses in Hippocampus, Amygdala, and Parietal Cortex for Emotional and Neutral Word Pairs.

Although functional neuroimaging studies have supported the distinction between explicit and implicit forms of memory, few have matched explicit and implicit tests closely, and most of these tested perceptual rather than conceptual implicit memory. We compared event-related fMRI responses during an intentional test, in which a group of participants used a cue word to recall its associate from a prior study phase, with those in an incidental test, in which a different group of participants used the same cue to produce the first associate that came to mind. Both semantic relative to phonemic processing at study, and emotional relative to neutral word pairs, increased target completions in the intentional test, but not in the incidental test, suggesting that behavioral performance in the incidental test was not contaminated by voluntary explicit retrieval. We isolated the neural correlates of successful retrieval by contrasting fMRI responses to studied versus unstudied cues for which the equivalent "target" associate was produced. By comparing the difference in this repetition-related contrast across the intentional and incidental tests, we could identify the correlates of voluntary explicit retrieval. This contrast revealed increased bilateral hippocampal responses in the intentional test, but decreased hippocampal responses in the incidental test. A similar pattern in the bilateral amygdale was further modulated by the emotionality of the word pairs, although surprisingly only in the incidental test. Parietal regions, however, showed increased repetition-related responses in both tests. These results suggest that the neural correlates of successful voluntary explicit memory differ in directionality, even if not in location, from the neural correlates of successful involuntary implicit (or explicit) memory, even when the incidental test taps conceptual processes.

One hundred base pairs of 5' flanking sequence of a vaccinia virus late gene are sufficient to temporally regulate late transcription.

A vaccinia virus late gene coding for a major structural polypeptide of 11 kDa was sequenced. Although the 5' flanking gene region is very A+T rich, it shows little homology either to the corresponding region of vaccinia early genes or to consensus sequences characteristic of most eukaryotic genes. Three DNA fragments (100, 200, and 500 base pairs, respectively), derived from the flanking region and including the late gene mRNA start site, were inserted into the coding sequence of the vaccinia virus thymidine kinase (TK) early gene by homologous in vivo recombination. Recombinants were selected on the basis of their TK- phenotype. Cells were infected with the recombinant viruses and RNA was isolated at 1-hr intervals. Transcripts initiating either from the TK early promoter, or from the late gene promoter at its authentic position, or from the translocated late gene promoters within the early gene were detected by nuclease S1 mapping. Early after infection, only transcripts from the TK early promoter were detected. Later in infection, however, transcripts were also initiated from the translocated late promoters. This RNA appeared at the same time and in similar quantities as the RNA from the late promoter at its authentic position. No quantitative differences in promoter efficiency between the 100-, 200-, and 500-base-pair insertions were observed. We conclude that all necessary signals for correct regulation of late-gene expression reside within only 100 base pairs of 5' flanking sequence.

Rgtsp: a generalized top scoring pairs package for class prediction.

SUMMARY: A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe a parallel implementation of this classifier which significantly reduces the training time, and a number of extensions, including a multi-class approach, which has the potential of improving the classification performance. AVAILABILITY AND IMPLEMENTATION: Full C++ source code and R package Rgtsp are freely available from http://lausanne.isb-sib.ch/~vpopovic/research/. The implementation relies on existing OpenMP libraries.

Penser la médecine communautaire s'apprend avec les pairs. [The spirit of community medicine: students learning from students].

At the University of Lausanne third-year medical students are given the task of spending a month investigating a question of community medicine. In 2009, four students evaluated the legitimacy of health insurers intervening in the management of depression. They found that health insurers put pressure on public authorities during the development of legislation governing the health system and reimbursement for treatment. This fact emerged during the scientific investigation led jointly by the team in the course of the "module of immersion in community medicine." This paper presents each step of their study. The example chosen illustrates the learning objectives covered by the module.

Light-induced racemization: artifacts in the analysis of the diastereoisomeric pairs of thioridazine 5-sulfoxide in the plasma and urine of patients treated with thioridazine.

The ring sulfoxidation of thioridazine (THD), a widely used neuroleptic agent, yields two diastereoisomeric pairs, fast- and slow-eluting (FE and SE) thioridazine 5-sulfoxide (THD 5-SO). Until now, studies in which concentrations of these metabolites were measured in THD-treated patients have revealed no significant differences in their concentrations. Preliminary experiments in our laboratory had shown that sunlight and, to a lesser extent, dim daylight led to racemization and probably also to photolysis of the diastereoisomeric pairs as measured by high-performance liquid chromatography. Similar results were also obtained with direct UV light (UV lamp). In appropriate light-protected conditions, THD, northioridazine, mesoridazine, sulforidazine, and FE and SE THD 5-SO were measured in 11 patients treated with various doses of THD for at least 1 week. Significantly higher concentrations of the FE stereoisomeric pair were found. The concentration ratios THD 5-SO (FE)/THD 5-SO (SE) ranged from 0.89 to 1.75 in plasma and from 1.15 to 2.05 in urine. Because it is known that the ring sulfoxide contributes to the cardiotoxicity of the drug even more potently than the parent compound does, these results justify further studies to determine whether there is stereoselectivity in the cardiotoxicity of THD 5-SO.

Determination of the enantiomers of thioridazine, thioridazine 2-sulfone, and of the isomeric pairs of thioridazine 2-sulfoxide and thioridazine 5-sulfoxide in human plasma.

Thioridazine is a commonly prescribed phenothiazine drug administered as a racemate and it is believed that its antipsychotic effect is mainly associated with (R)-thioridazine. A method based on high-performance liquid chromatography has been developed for the determination of the enantiomers of thioridazine and thioridazine 2-sulfone (THD 2-SO2 or sulforidazine) and of the enantiomers of the diastereoisomeric pairs of thioridazine 2-sulfoxide (THD 2-SO or mesoridazine) and thioridazine 5-sulfoxide (THD 5-SO) in the plasma of thioridazine-treated patients. The method involves sequential achiral and chiral HPLC. The limits of quantitation for total (R) + (S) concentrations were found to be 15 ng/ml for thioridazine and 5 ng/ml for its metabolites. The limits for the determination of the (R)/(S) ratios were found to be 60 ng/ml for racemic THD and 10 ng/ml for racemic THD 2-SO, THD 2-SO2, THD 5-SO (FE) and THD 5-SO (SE). The method has been used to determine the concentrations of the enantiomers of thioridazine and of its metabolites in the plasma of a patient treated with 100 mg of racemic thioridazine hydrochloride per os per day for 14 days. The results show a high enantioselectivity in the metabolism of this drug: the (R)/(S) ratios for THD, THD 2-SO (FE), THD 2-SO (SE), THD 2-SO2, THD 5-SO (FE) and THD 5-SO (SE) were found to be 3.90, 1.22, 6.10, 4.10, 0.09 and 28.0, respectively.

BoBo mixing meseasurement at Belle using dilepton events tagged with a soft pion

L'expérience Belle, située dans le centre de recherche du KEK, au Japon, est consacrée principalement à l'étude de la violation de CP dans le système des mésons B. Elle est placée sur le collisionneur KEKB, qui produit des paires Banti-B. KEKB, l'une des deux « usines à B » actuellement en fonction, détient le record du nombre d'événements produits avec plus de 150 millions de paires. Cet échantillon permet des mesures d'une grande précision dans le domaine de la physique du méson B. C'est dans le cadre de ces mesures de précision que s'inscrit cette analyse. L'un des phénomènes remarquables de la physique des hautes énergies est la faculté qu'a l'interaction faible de coupler un méson neutre avec son anti-méson. Dans le présent travail, nous nous intéressons au méson B neutre couplé à l'anti-méson B neutre, avec une fréquence d'oscillation _md mesurable précisément. Outre la beauté de ce phénomène lui-même, une telle mesure trouve sa place dans la quête de l'origine de la violation de CP. Cette dernière n'est incluse que d'une façon peu satisfaisante dans le modèle standard des interactions électro-faibles. C'est donc la recherche de phénomènes physiques encore inexpliqués qui motive en premier lieu la collaboration Belle. Il existe déjà de nombreuses mesures de _md antérieures. Celle que nous présentons ici est cependant d'une précision encore jamais atteinte grâce, d'une part, à l'excellente performance de KEKB et, d'autre part, à une approche originale qui permet de réduire considérablement la contamination de la mesure par des événements indésirés. Cette approche fut déjà mise à profit par d'autres expériences, dans des conditions quelque peu différentes de celles de Belle. La méthode utilisée consiste à reconstruire partiellement l'un des mésons dans le canal ___D*(D0_)l_l, en n'utilisant que les informations relatives au lepton l et au pion _. L'information concernant l'autre méson de la paire Banti-B initiale n'est tirée que d'un seul lepton de haute énergie. Ainsi, l'échantillon à disposition ne souffre pas de grandes réductions dues à une reconstruction complète, tandis que la contamination due aux mésons B chargés, produits par KEKB en quantité égale aux B0, est fortement diminuée en comparaison d'une analyse inclusive. Nous obtenons finalement le résultat suivant : _md = 0.513±0.006±0.008 ps^-1, la première erreur étant l'erreur statistique et la deuxième, l'erreur systématique.<br/><br/>The Belle experiment is located in the KEK research centre (Japan) and is primarily devoted to the study of CP violation in the B meson sector. Belle is placed on the KEKB collider, one of the two currently running "B-meson factories", which produce Banti-B pairs. KEKB has created more than 150 million pairs in total, a world record for this kind of colliders. This large sample allows very precise measurements in the physics of beauty mesons. The present analysis falls within the framework of these precise measurements. One of the most remarkable phenomena in high-energy physics is the ability of weak interactions to couple a neutral meson to its anti-meson. In this work, we study the coupling of neutral B with neutral anti-B meson, which induces an oscillation of frequency _md we can measure accurately. Besides the interest of this phenomenon itself, this measurement plays an important role in the quest for the origin of CP violation. The standard model of electro-weak interactions does not include CP violation in a fully satisfactory way. The search for yet unexplained physical phenomena is, therefore, the main motivation of the Belle collaboration. Many measurements of _md have previously been performed. The present work, however, leads to a precision on _md that was never reached before. This is the result of the excellent performance of KEKB, and of an original approach that allows to considerably reduce background contamination of pertinent events. This approach was already successfully used by other collaborations, in slightly different conditions as here. The method we employed consists in the partial reconstruction of one of the B mesons through the decay channel ___D*(D0_)l_l, where only the information on the lepton l and the pion _ are used. The information on the other B meson of the initial Banti-B pair is extracted from a single high-energy lepton. The available sample of Banti-B pairs thus does not suffer from large reductions due to complete reconstruction, nor does it suffer of high charged B meson background, as in inclusive analyses. We finally obtain the following result: _md = 0.513±0.006±0.008 ps^-1, where the first error is statistical, and the second, systematical.<br/><br/>De quoi la matière est-elle constituée ? Comment tient-elle ensemble ? Ce sont là les questions auxquelles la recherche en physique des hautes énergies tente de répondre. Cette recherche est conduite à deux niveaux en constante interaction. D?une part, des modèles théoriques sont élaborés pour tenter de comprendre et de décrire les observations. Ces dernières, d?autre part, sont réalisées au moyen de collisions à haute énergie de particules élémentaires. C?est ainsi que l?on a pu mettre en évidence l?existence de quatre forces fondamentales et de 24 constituants élémentaires, classés en « quarks » et « leptons ». Il s?agit là de l?une des plus belles réussites du modèle en usage aujourd?hui, appelé « Modèle Standard ». Il est une observation fondamentale que le Modèle Standard peine cependant à expliquer, c?est la disparition quasi complète de l?anti-matière (le « négatif » de la matière). Au niveau fondamental, cela doit correspondre à une asymétrie entre particules (constituants de la matière) et antiparticules (constituants de l?anti-matière). On l?appelle l?asymétrie (ou violation) CP. Bien qu?incluse dans le Modèle Standard, cette asymétrie n?est que partiellement prise en compte, semble-t-il. En outre, son origine est inconnue. D?intenses recherches sont donc aujourd?hui entreprises pour mettre en lumière cette asymétrie. L?expérience Belle, au Japon, en est une des pionnières. Belle étudie en effet les phénomènes physiques liés à une famille de particules appelées les « mésons B », dont on sait qu?elles sont liées de près à l?asymétrie CP. C?est dans le cadre de cette recherche que se place cette thèse. Nous avons étudié une propriété remarquable du méson B neutre : l?oscillation de ce méson avec son anti-méson. Cette particule est de se désintégrer pour donner l?antiparticule associée. Il est clair que cette oscillation est rattachée à l?asymétrie CP. Nous avons ici déterminé avec une précision encore inégalée la fréquence de cette oscillation. La méthode utilisée consiste à caractériser une paire de mésons B à l?aide de leur désintégration comprenant un lepton chacun. Une plus grande précision est obtenue en recherchant également une particule appelée le pion, et qui provient de la désintégration d?un des mésons. Outre l?intérêt de ce phénomène oscillatoire en lui-même, cette mesure permet d?affiner, directement ou indirectement, le Modèle Standard. Elle pourra aussi, à terme, aider à élucider le mystère de l?asymétrie entre matière et anti-matière.