Clustering files of chemical structures using the Szekely-Rizzo generalization of Ward's method

Ward's method is extensively used for clustering chemical structures represented by 2D fingerprints. This paper compares Ward clusterings of 14 datasets (containing between 278 and 4332 molecules) with those obtained using the Szekely–Rizzo clustering method, a generalization of Ward's method. The clusters resulting from these two methods were evaluated by the extent to which the various classifications were able to group active molecules together, using a novel criterion of clustering effectiveness. Analysis of a total of 1400 classifications (Ward and Székely–Rizzo clustering methods, 14 different datasets, 5 different fingerprints and 10 different distance coefficients) demonstrated the general superiority of the Székely–Rizzo method. The distance coefficient first described by Soergel performed extremely well in these experiments, and this was also the case when it was used in simulated virtual screening experiments

Evaluation du Respect des Bonnes Pratiques de Sondage Vesical a Demeure Chez L’adulte par les Soignants : Utilisation de « Vignettes Cliniques »

Le sondage urinaire ou vésical est une technique utilisée depuis l’antiquité qui repose sur l’utilisation de dispositifs médicaux invasifs pour le patient. Cet acte de soin doit se faire de façon sécurisée et s’appuyer sur des référentiels. Les objectifs ont été l’évaluation durespect des recommandations du protocole institutionnel sur la pose d’une sonde urinaire à demeure chez l'adulte, le respect de l’hygiène et de l’asepsie et l’évaluation des conduites à tenir lors d’une fuite urinaire sur sonde. Dans le cadre d’une démarche d’évaluation des pratiques professionnelles, une enquête prospective basée sur le concept des « vignettes cliniques » a été menée, avec des mises en situations des soignants du CHU Charles Nicolle, Bois-Guillaume et Oissel en 2011. L’enquête révèle un suivi des recommandations sur certains points comme le respect de l’asepsie et du système clos. Des divergences ont été mises en évidence concernant notamment l’usage de la bandelette urinaire chez le patient sondé, le choix du type de sonde et les couples de produits à utiliser pour la détersion et l’antisepsie. Des axes d’améliorations sont proposés comme la sensibilisation des équipes soignantes mais également médicales par le biais notammentd’une plaquette simple et illustrée de support d’information sur les bonnes pratiques de sondage vésical à demeure chez l’adulte et des kits « prêts à l’emploi » de produits pour la détersion et l’antisepsie.Since antiquity, the urinary or bladder catheter is a technique that relies on the use of invasive medical devices for the patient. This care act must be done in a secure manner and rely on standards. First, the evaluation of the respect of the recommendations of the institutional protocol on hanging an indwelling urinary catheter in adult, the respect of the hygiene and finally, the asepsis and the evaluation of the behaviors to be maintained during a urinary leak on probe were the objectives. As part of an evaluation of professional practices, a prospective survey based on the concept of "clinical vignettes" was conducted, with situations from nurses from CHU Charles Nicolle, BoisGuillaume and Oissel in 2011. The survey reveals a follow-up of the recommendations like the respect of the asepsis and the closed system. Discrepancies have been identified about the use of the urine strip in the patient being probed, the choice of the type of probe and the pairs of products to be used for the debridement and antisepsis. Different areas for improvement are proposed, first of all, raising the awareness of health care teams, but also medical ones, in particular through a simple plaque illustrated with information support on good practice of adult bladder catheterization and then use the packaging “ready to use” for debridement and antisepsis

Plausibility functions and exact frequentist inference

In the frequentist program, inferential methods with exact control on error rates are a primary focus. The standard approach, however, is to rely on asymptotic approximations, which may not be suitable. This paper presents a general framework for the construction of exact frequentist procedures based on plausibility functions. It is shown that the plausibility function-based tests and confidence regions have the desired frequentist properties in finite samples---no large-sample justification needed. An extension of the proposed method is also given for problems involving nuisance parameters. Examples demonstrate that the plausibility function-based method is both exact and efficient in a wide variety of problems.Comment: 21 pages, 5 figures, 3 table

Bayesian Exponential Random Graph Models with Nodal Random Effects

We extend the well-known and widely used Exponential Random Graph Model (ERGM) by including nodal random effects to compensate for heterogeneity in the nodes of a network. The Bayesian framework for ERGMs proposed by Caimo and Friel (2011) yields the basis of our modelling algorithm. A central question in network models is the question of model selection and following the Bayesian paradigm we focus on estimating Bayes factors. To do so we develop an approximate but feasible calculation of the Bayes factor which allows one to pursue model selection. Two data examples and a small simulation study illustrate our mixed model approach and the corresponding model selection.Comment: 23 pages, 9 figures, 3 table

Naturalness and theoretical constraints on the Higgs boson mass

Arbitrary regularization dependent parameters in Quantum Field Theory are usually fixed on symmetry or phenomenology grounds. We verify that the quadratically divergent behavior responsible for the lack of naturalness in the Standard Model (SM) is intrinsically arbitrary and regularization dependent. While quadratic divergences are welcome for instance in effective models of low energy QCD, they pose a problem in the SM treated as an effective theory in the Higgs sector. Being the very existence of quadratic divergences a matter of debate, a plausible scenario is to search for a symmetry requirement that could fix the arbitrary coefficient of the leading quadratic behavior to the Higgs boson mass to zero. We show that this is possible employing consistency of scale symmetry breaking by quantum corrections. Besides eliminating a fine-tuning problem and restoring validity of perturbation theory, this requirement allows to construct bounds for the Higgs boson mass in terms of $\delta m^2/m^2_H$ (where $m_H$ is the renormalized Higgs mass and $\delta m^2$ is the 1-loop Higgs mass correction). Whereas $\delta m^2/m^2_H<1$ (perturbative regime) in this scenario allows the Higgs boson mass around the current accepted value, the inclusion of the quadratic divergence demands $\delta m^2/m^2_H$ arbitrarily large to reach that experimental value.Comment: 6 pages, 4 figure

Halogen species record Antarctic sea ice extent over glacial–interglacial periods

Abstract. Sea ice is an integral part of the earth's climate system because it affects planetary albedo, sea-surface salinity, and the atmosphere–ocean exchange of reactive gases and aerosols. Bromine and iodine chemistry is active at polar sea ice margins with the occurrence of bromine explosions and the biological production of organoiodine from sea ice algae. Satellite measurements demonstrate that concentrations of bromine oxide (BrO) and iodine oxide (IO) decrease over sea ice toward the Antarctic interior. Here we present speciation measurements of bromine and iodine in the TALDICE (TALos Dome Ice CorE) ice core (159°11' E, 72°49' S; 2315 m a.s.l.) spanning the last 215 ky. The Talos Dome ice core is located 250 km inland and is sensitive to marine air masses intruding onto the Antarctic Plateau. Talos Dome bromide (Br−) is positively correlated with temperature and negatively correlated with sodium (Na). Based on the Br−/Na seawater ratio, bromide is depleted in the ice during glacial periods and enriched during interglacial periods. Total iodine, consisting of iodide (I−) and iodate (IO3−), peaks during glacials with lower values during interglacial periods. Although IO3− is considered the most stable iodine species in the atmosphere it was only observed in the TALDICE record during glacial maxima. Sea ice dynamics are arguably the primary driver of halogen fluxes over glacial–interglacial timescales, by altering the distance between the sea ice edge and the Antarctic plateau and by altering the surface area of sea ice available to algal colonization. Based on our results we propose the use of both halogens for examining Antarctic variability of past sea ice extent

The Making of a Mobile Caliphate State in the African Sahel

The goal of this chapter is to thoroughly understand the context of the dominant jihadist narratives and the nature of their appeal in the Sahelian region. All these jihadist ideologies are based on a peculiar Salafi Radicalism that aimed to transform the state and society by methods of preaching and violence. Therefore, studying and analyzing the principles of the Salafist discourse as a political project helps us to understand its points of strengths and weaknesses. In addition, we can be better look at the future trends and prospects of violent jihadist groups in the African Sahel. The roots of this Islamic discourse as a political project may be attributed to what Lunay and Suarez call the “Islamic domain.” The rise of violent radical Islamism represents drive from the internal political and socioeconomic dynamics evolving in each Sahelian state. However, the struggle and rivalry of jihadist ideologies after the military defeat of Daesh in Mosul is important at a time when thousands of fighters who have survived the civil wars in Iraq, Syria, and Libya are looking for new jihadist fields

Symmetry preserving regularization with a cutoff

A Lorentz and gauge symmetry preserving regularization method is proposed in 4 dimension based on momentum cutoff. We use the conditions of gauge invariance or freedom of shift of the loop-momentum to define the evaluation of the terms carrying Lorentz indices, e.g. proportional to k_{\mu}k_{\nu}. The remaining scalar integrals are calculated with a four dimensional momentum cutoff. The finite terms (independent of the cutoff) are unambiguous and agree with the result of dimensional regularization.Comment: 12 pages, 1 figure, v2 references adde