Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also eliminates the problem of arbitrary threshold selection inherent in any binary membership based pathway enrichment approach. We demonstrate the marked increase in power by analyzing summary statistics from dozens of large meta-studies for various traits. Our extensive testing indicates that our method not only excels in rigorous type I error control, but also results in more biologically meaningful discoveries.

Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.

Metabolic problems lead to numerous failures during clinical trials, and much effort is now devoted to developing in silico models predicting metabolic stability and metabolites. Such models are well known for cytochromes P450 and some transferases, whereas less has been done to predict the activity of human hydrolases. The present study was undertaken to develop a computational approach able to predict the hydrolysis of novel esters by human carboxylesterase hCES2. The study involved first a homology modeling of the hCES2 protein based on the model of hCES1 since the two proteins share a high degree of homology (congruent with 73%). A set of 40 known substrates of hCES2 was taken from the literature; the ligands were docked in both their neutral and ionized forms using GriDock, a parallel tool based on the AutoDock4.0 engine which can perform efficient and easy virtual screening analyses of large molecular databases exploiting multi-core architectures. Useful statistical models (e.g., r (2) = 0.91 for substrates in their unprotonated state) were calculated by correlating experimental pK(m) values with distance between the carbon atom of the substrate's ester group and the hydroxy function of Ser228. Additional parameters in the equations accounted for hydrophobic and electrostatic interactions between substrates and contributing residues. The negatively charged residues in the hCES2 cavity explained the preference of the enzyme for neutral substrates and, more generally, suggested that ligands which interact too strongly by ionic bonds (e.g., ACE inhibitors) cannot be good CES2 substrates because they are trapped in the cavity in unproductive modes and behave as inhibitors. The effects of protonation on substrate recognition and the contrasting behavior of substrates and products were finally investigated by MD simulations of some CES2 complexes.

The Smartcanula: a new tool for remote access perfusion in limited access cardiac surgery.

Devices for venous cannulation have seen significant progress over time: the original, rigid steel cannulas have evolved toward flexible plastic cannulas with wire support that prevents kinking, very thin walled wire wound cannulas allowing for percutaneous application, and all sorts of combinations. In contrast to all these rectilinear venous cannula designs, which present the same cross-sectional area over their entire intravascular path, the smartcanula concept of "collapsed insertion and expansion in situ" is the logical next step for venous access. Automatically adjusting cross-sectional area up to a pre-determined diameter or the vessel lumen provides optimal flow and ease of use for both, insertion and removal. Smartcanula performance was assessed in a small series of patients (76 +/- 17 kg) undergoing redo procedures. The calculated target pump flow (2.4 L/min/m2) was 4.42 +/- 61 L/ min. Mean pump flow achieved during cardiopulmonary bypass was 4.84 +/- 87 L/min or 110% of the target. Reduced atrial chatter, kink resistance in situ, and improved blood drainage despite smaller access orifice size, are the most striking advantages of this new device. The benefits of smart cannulation are obvious in remote cannulation for limited access cardiac surgery, but there are many other cannula applications where space is an issue, and that is where smart cannulation is most effective.

Improvement of the specificity of cancer detection by autofluorescence imaging in the tracheo-bronchial tree using backscattered violet light.

BACKGROUND: Autofluorescence bronchoscopy (AFB) is a highly sensitive tool for the detection of early bronchial cancers. However, its specificity remains limited due to primarily false positive results induced by hyperplasia, metaplasia and inflammation. We have investigated the potential of blue-violet backscattered light to eliminate false positive results during AFB in a clinical pilot study. METHODS: The diagnostic autofluorescence endoscopy (DAFE) system was equipped with a variable band pass filter in the imaging detection path. The backscattering properties of normal and abnormal bronchial mucosae were assessed by computing the contrast between the two tissue types for blue-violet wavelengths ranging between 410 and 490 nm in 12 patients undergoing routine DAFE examination. In a second study including 6 patients we used a variable long pass (LP) filter to determine the spectral design of the emission filter dedicated to the detection of this blue-violet light with the DAFE system. RESULTS: (Pre-)neoplastic mucosa showed a clear wavelength dependence of the backscattering properties of blue-violet light while the reflectivity of normal, metaplastic and hyperplastic autofluorescence positive mucosa was wavelength independent. CONCLUSIONS: Our results showed that the detection of blue-violet light has the potential to reduce the number of false positive results in AFB. In addition we determined the spectral design of the emission filter dedicated to the detection of this blue-violet light with the DAFE system.

Relative and absolute reliability of the clinical version of the Narrow Path Walking Test (NPWT) under single and dual task conditions.

Decline in gait stability has been associated with increased fall risk in older adults. Reliable and clinically feasible methods of gait instability assessment are needed. This study evaluated the relative and absolute reliability and concurrent validity of the testing procedure of the clinical version of the Narrow Path Walking Test (NPWT) under single task (ST) and dual task (DT) conditions. Thirty independent community-dwelling older adults (65-87 years) were tested twice. Participants were instructed to walk within the 6-m narrow path without stepping out. Trial time, number of steps, trial velocity, number of step errors, and number of cognitive task errors were determined. Intraclass correlation coefficients (ICCs) were calculated as indices of agreement, and a graphic approach called "mountain plot" was applied to help interpret the direction and magnitude of disagreements between testing procedures. Smallest detectable change and smallest real difference (SRD) were computed to determine clinically relevant improvement at group and individual levels, respectively. Concurrent validity was assessed using Performance Oriented Mobility Assessment Tool (POMA) and the Short Physical Performance Battery (SPPB). Test-retest agreement (ICC1,2) varied from 0.77 to 0.92 in ST and from 0.78 to 0.92 in DT conditions, with no apparent systematic differences between testing procedures demonstrated by the mountain plot graphs. Smallest detectable change and smallest real change were small for motor task performance and larger for cognitive errors. Significant correlations were observed for trial velocity and trial time with POMA and SPPB. The present results indicate that the NPWT testing procedure is highly reliable and reproducible.

Morphological Study of Intracardiac Signals as a New Tool to Track the Efficiency of Stepwise Ablation of Persistent Atrial Fibrillation

Intracardiac organization indices such as atrial fibrillation (AF) cycle length (AFCL) have been used to track the efficiency of stepwise catheter ablation (step-CA) of longstanding persistent AF, however with limited success. The morphology of AF activation waves reflects the underlying activation patterns. Its temporal evolution is a local organization indicator that could be potentially used for tracking the efficiency of step-CA. We report a new method for characterizing the structure of the temporal evolution of activation wave morphology. Using recurrence plots, novel organization indices are proposed. By computing their relative evolution during the first step of ablation vs baseline, we found that these new parameters are superior to AFCL to track the effect of step-CA "en route" to AF termination.

Accessory phases as a tool to investigate magmatic underplating in polymetamorphic metasediments : an example from a fossil lower crust : Ivrea Verbano zne, NW Italy

The Ivrea and the Strona-Ceneri zones, NW italy and S Switzerland, offer the possibility to study the continental crust of the Southern Alps. Because of its high metamorphic degree and the abundant Permo- Carboniferous mafic intrusions, the Ivrea Zone is classically interpreted an exposed section trough the Permian lower crust. The present work is focused here on metasedimentary slices (septa) intercalated within Permian gabbro (mafic complex). In particular I studied the evolution of accessory phases such as rutile and zircon and the chemistry of the metasediments. The septa build an irregular and discontinuous band that cut obliquely the mafic complex from its deepest part (N) to its roof (S). The chemistry of the metasediments evolves along the band and the chemical evolution can be compared with that observed in the country-rock surrounding the mafic intrusion to the NE and overprinted by a main regional metamorphic event. This suggests that the degree of chemical depletion of the septa was mainly established during the same regional metamorphic event. Moreover it suggests that incorporation of the septa within the gabbro did not modify their original stratigraphie distribution within the crust. It implies that the mafic complex has been emplaced following a dynamic substantially different from the classic model of « gabbro glacier » (Quick et al., 1992; Quick et al., 1994). It is more likely that it has been emplaced by repeated injections of sills at different depths during a protracted period of time. Zircon trace elements and U-Pb ages suggest that regional metamorphism occurred 330-320Ma, the first sills in the deepest part of the Mafic Complex are injected at ~300Ma, the mafic magmas reached higher levels in the crust at 285Ma and the magmatic activity continued locally until 275Ma. The ages of detrital cores in zircons fix the maximal sedimentation age at ~370Ma, this age corresponds therefore with the maximal age of the incorporation of the Ivrea zone within the lower crust. I propose that the Ivrea zone has been accreted to the lower crust during the Hercynian orogeny sensu lato. The analysis of detrital ages suggests that the source terrains for the Ivrea zone and those for the Strona-Ceneri zone have a completely different Palaeozoic history. The systematic analysis of rutile in partially molten metasediments of the Ivrea zone reveals the occurrence of two generations. The two generations are characterized by a different chemistry and textural distribution. A first generation is formed during pro-grade metamorphism in the restitic counterpart. The second generation is formed in the melts during cooling at the same time that part of the first generation re-equilibrate. Re-equilibration of the first generation seems to be spatially controlled by the presence of fluids. Locally the second generation forms overgrowths on the first generation. Considered the different diffusivity of U and Pb in rutile, U heterogeneities have important implication for U-Pb dating of rutile. ID-TIMS and LA-ICPMS dating coupled with a careful textural investigation (SEM) suggest that rutile grains are characterized by multiple path along which Pb diffusion can occur: volume diffusion is an important process, but intragrain and subgrain boundaries provide additional high diffusivity pathways for Pb escape and reduce drastically the effective diffusion length. -- La zone d'Ivrea et la zone de Strona-Ceneri, en Italie nord-occidentale et Suisse méridionale, offrent la possibilité d'étudier la croûte continentale des Alpes du Sud. En raison du haut degré métamorphique et l'abondance d'intrusions mafiques d'âge Permo-Carbonifère [complexe mafique), la zone d'Ivrea est interprétée classiquement comme de la croûte inférieure permienne. Ce travail ce concentre sur des bandes metasédimentaires (septa) incorporées dans les magmas mafiques lors de l'intrusion. Les septa forment une bande irrégulière qui coupe obliquement le complexe mafique du bas (N) vers le haut (S). La chimie des septa évolue du bas vers le haut et l'évolution chimique se rapproche de l'évolution observé dans la roche encaissante l'intrusion affecté par un événement métamorphique régionale. Cette relation suggère que le degré d'appauvrissement chimique des septa a été établit principalement lors de l'événement métamorphique régional. De plus l'incorporation dans les gabbros n'a pas perturbée la distribution stratigraphique originelle des septa. Ces deux observations impliquent que le métamorphisme dans la roche encaissante précède la mise en place du gabbro et que cette dernière ne se fait pas selon le modèle classique (« gabbro glacier » de Quick et al., 1992, 1994), mais se fait plutôt par injections répétées de sills a différentes profondeurs. Les âges U-Pb et les éléments traces des zircons suggèrent que le métamorphisme régionale a eu lieu 330-320Ma, alors que les premiers sills dans la partie profonde du Mafic Complex s'injectent à ~300Ma, le magmatisme mafique atteigne des niveaux supérieurs à 285Ma et continue localement jusqu'à 270Ma. Les âges des coeurs détritiques des zircons permettent de fixer l'âge maximale de sédimentation à ~370Ma ce qui correspond donc à l'âge maximale de l'incorporation de la zone d'Ivrea dans la croûte inférieur. L'analyse systématique des rutiles, nous a permit de montrer l'existence de plusieurs générations qui ont une répartition texturale et une chimie différente. Une génération se forme lors de l'événement UHT dans les restites, une autre génération se forme dans les liquides lors du refroidissement, au même temps qu'une partie de la première génération se rééquilibre au niveau du Zr. Localement la deuxième génération peut former des surcroissances autour de la première génération. Dans ces cas, des fortes différences en uranium entre les deux générations ont des importantes implications pour la datation U-Pb sur rutile. Classiquement les ratios Pb/U dans le rutile sont interprétés comme indiquant l'âges du refroidissement du minéral sous une température à la quelle la diffusion du Pb dans le minéral n'est plus détectable et la diffusion à plus hautes températures est assumée se faire par «volume diffusion» dans le grain (Mezger et al., 1989). Par des datations ID-TIMS (sur grain entier) et LA-ICPMS (in-situ) et une analyse texturale (MEB) approfondie nous montrons que cette supposition est trop simpliste et que le rutile est repartie en sous-domaines. Chacun de ces domaines a ça propre longueur ou chemin de diffusion spécifique. Nous proposons donc une nouvelle approche plus cohérente pour l'interprétation des âges U-Pb sur rutile.

"Vie et Passion de Jésus-Christ" (Pathé, 1902-1905): hétérogénéité des "tableaux", déclinaison des motifs

Cette étude examine deux copies de la "Vie et Passion de Jésus Christ" conservées par la Cinémathèque suisse avec une première préoccupation de type philologique qui conduit à prendre la mesure de l'autonomisation de chacun des "tableaux" composant le film et de l'hétérogénéité de ce dernier. Puis les constats émis à propos du support matériel sont articulés avec une réflexion d'ordre esthétique qui dégage l'importance de l'"effet-tableau" inscrivant cette production filmique dans une généalogie plus large. Le cinéma étant alors le lieu de convergences entre diverses séries culturelles, l'article envisage les liens entre la production Pathé et une pratique jusqu'ici peu discutée dans ce contexte, celle du tableau vivant. This article is a study of two copies of the "Life and Passion of Jesus Christ" held at the Cinemathèque suisse. Our first, broadly philological, concern is to recognise the degree of autonomy of each of the "tableaus" that make up the film, thus establishing the latter's heterogeneous composition. Secondly, adopting a more aesthetic approach, we discuss the importance of the tableau-effect, placing this kind of film production in a wider genealogical context. Given that cinema was at the time a meeting place for different cultural sequences, this article the examines the links between Pathe films and the "tableau vivant", a practice that until now has been rarely discussed in this regard.

Benchmarking therapeutic drug monitoring software: A review of available computer tools

Therapeutic drug monitoring (TDM) aims to optimize treatments by individualizing dosage regimens based on the measurement of blood concentrations. Dosage individualization to maintain concentrations within a target range requires pharmacokinetic and clinical capabilities. Bayesian calculations currently represent the gold standard TDM approach but require computation assistance. In recent decades computer programs have been developed to assist clinicians in this assignment. The aim of this survey was to assess and compare computer tools designed to support TDM clinical activities. The literature and the Internet were searched to identify software. All programs were tested on personal computers. Each program was scored against a standardized grid covering pharmacokinetic relevance, user friendliness, computing aspects, interfacing and storage. A weighting factor was applied to each criterion of the grid to account for its relative importance. To assess the robustness of the software, six representative clinical vignettes were processed through each of them. Altogether, 12 software tools were identified, tested and ranked, representing a comprehensive review of the available software. Numbers of drugs handled by the software vary widely (from two to 180), and eight programs offer users the possibility of adding new drug models based on population pharmacokinetic analyses. Bayesian computation to predict dosage adaptation from blood concentration (a posteriori adjustment) is performed by ten tools, while nine are also able to propose a priori dosage regimens, based only on individual patient covariates such as age, sex and bodyweight. Among those applying Bayesian calculation, MM-USC*PACK© uses the non-parametric approach. The top two programs emerging from this benchmark were MwPharm© and TCIWorks. Most other programs evaluated had good potential while being less sophisticated or less user friendly. Programs vary in complexity and might not fit all healthcare settings. Each software tool must therefore be regarded with respect to the individual needs of hospitals or clinicians. Programs should be easy and fast for routine activities, including for non-experienced users. Computer-assisted TDM is gaining growing interest and should further improve, especially in terms of information system interfacing, user friendliness, data storage capability and report generation.

A new chemical tool (C0036E08) supports the role of adenosine A(2B) receptors in mediating human mast cell activation.

Asthma is a chronic inflammatory disease of the airways that involves many cell types, amongst which mast cells are known to be important. Adenosine, a potent bronchoconstricting agent, exerts its ability to modulate adenosine receptors of mast cells thereby potentiating derived mediator release, histamine being one of the first mediators to be released. The heterogeneity of sources of mast cells and the lack of highly potent ligands selective for the different adenosine receptor subtypes have been important hurdles in this area of research. In the present study we describe compound C0036E08, a novel ligand that has high affinity (pK(i) 8.46) for adenosine A(2B) receptors, being 9 times, 1412 times and 3090 times more selective for A(2B) receptors than for A(1), A(2A) and A(3) receptors, respectively. Compound C0036E08 showed antagonist activity at recombinant and native adenosine receptors, and it was able to fully block NECA-induced histamine release in freshly isolated mast cells from human bronchoalveolar fluid. C0036E08 has been shown to be a valuable tool for the identification of adenosine A(2B) receptors as the adenosine receptors responsible for the NECA-induced response in human mast cells. Considering the increasing interest of A(2B) receptors as a therapeutic target in asthma, this chemical tool might provide a base for the development of new anti-asthmatic drugs.

The management of iron deficiency in inflammatory bowel disease--an online tool developed by the RAND/UCLA appropriateness method.

BACKGROUND: Iron deficiency is a common and undertreated problem in inflammatory bowel disease (IBD). AIM: To develop an online tool to support treatment choice at the patient-specific level. METHODS: Using the RAND/UCLA Appropriateness Method (RUAM), a European expert panel assessed the appropriateness of treatment regimens for a variety of clinical scenarios in patients with non-anaemic iron deficiency (NAID) and iron deficiency anaemia (IDA). Treatment options included adjustment of IBD medication only, oral iron supplementation, high-/low-dose intravenous (IV) regimens, IV iron plus erythropoietin-stimulating agent (ESA), and blood transfusion. The panel process consisted of two individual rating rounds (1148 treatment indications; 9-point scale) and three plenary discussion meetings. RESULTS: The panel reached agreement on 71% of treatment indications. 'No treatment' was never considered appropriate, and repeat treatment after previous failure was generally discouraged. For 98% of scenarios, at least one treatment was appropriate. Adjustment of IBD medication was deemed appropriate in all patients with active disease. Use of oral iron was mainly considered an option in NAID and mildly anaemic patients without disease activity. IV regimens were often judged appropriate, with high-dose IV iron being the preferred option in 77% of IDA scenarios. Blood transfusion and IV+ESA were indicated in exceptional cases only. CONCLUSIONS: The RUAM revealed high agreement amongst experts on the management of iron deficiency in patients with IBD. High-dose IV iron was more often considered appropriate than other options. To facilitate dissemination of the recommendations, panel outcomes were embedded in an online tool, accessible via http://ferroscope.com/.

The application of chemometrics on Infrared and Raman spectra as a tool for the forensic analysis of paints

The aim of this work is to evaluate the capabilities and limitations of chemometric methods and other mathematical treatments applied on spectroscopic data and more specifically on paint samples. The uniqueness of the spectroscopic data comes from the fact that they are multivariate - a few thousands variables - and highly correlated. Statistical methods are used to study and discriminate samples. A collection of 34 red paint samples was measured by Infrared and Raman spectroscopy. Data pretreatment and variable selection demonstrated that the use of Standard Normal Variate (SNV), together with removal of the noisy variables by a selection of the wavelengths from 650 to 1830 cm−1 and 2730-3600 cm−1, provided the optimal results for infrared analysis. Principal component analysis (PCA) and hierarchical clusters analysis (HCA) were then used as exploratory techniques to provide evidence of structure in the data, cluster, or detect outliers. With the FTIR spectra, the Principal Components (PCs) correspond to binder types and the presence/absence of calcium carbonate. 83% of the total variance is explained by the four first PCs. As for the Raman spectra, we observe six different clusters corresponding to the different pigment compositions when plotting the first two PCs, which account for 37% and 20% respectively of the total variance. In conclusion, the use of chemometrics for the forensic analysis of paints provides a valuable tool for objective decision-making, a reduction of the possible classification errors, and a better efficiency, having robust results with time saving data treatments.