Discussion of "EQUI-energy sampler" by Kou, Zhou and Wong

Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of a protein chain given the sequence of its amino acid building blocks. The complexity of the problem strongly depends on the protein representation and its energy function. The more detailed the model, the more complex its corresponding energy function and the more challenge it sets for sampling algorithms. Kou, Zhou and Wong [math.ST/0507080] have introduced a novel sampling method, which could contribute significantly to the field of structural prediction.Comment: Published at http://dx.doi.org/10.1214/009053606000000470 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences

We introduce and study a set of training-free methods of information-theoretic and algorithmic complexity nature applied to DNA sequences to identify their potential capabilities to determine nucleosomal binding sites. We test our measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint (high) nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that complexity indices are informative of nucleosome occupancy. We compare against the gold standard (Kaplan model) and find similar and complementary results with the main difference that our sequence complexity approach. For example, for high occupancy, complexity-based scores outperform the Kaplan model for predicting binding representing a significant advancement in predicting the highest nucleosome occupancy following a training-free approach.Comment: 8 pages main text (4 figures), 12 total with Supplementary (1 figure

HLA-DM Stabilizes the Empty MHCII Binding Groove:A Model Using Customized Natural Move Monte Carlo

MHC class II molecules bind peptides derived from extracellular proteins that have been ingested by antigen-presenting cells and display them to the immune system. Peptide loading occurs within the antigen-presenting cell and is facilitated by HLA-DM. HLA-DM stabilises the open conformation of the MHCII binding groove when no peptide is bound. While a structure of the MHCII/HLA-DM complex exists, the mechanism of stabilisation is still largely unknown. Here, we applied customised Natural Move Monte Carlo to investigate this interaction. We found a possible long range mechanism that implicates the configuration of the membrane-proximal globular domains in stabilising the open state of the empty MHCII binding groove

L’analyse de pratiques professionnelles en IUFM

Le texte que nous présentons ici concerne la description et l’analyse d’un ensemble de dispositifs d’analyse de pratiques mis en place dans plusieurs IUFM. Il tente d’en abstraire les principaux organisateurs en analysant finement les orientations théoriques sous-jacentes, le cadre retenu ainsi que les principaux éléments du contexte institutionnel. Ce travail insiste particulièrement sur deux aspects jugés essentiels : les différents niveaux d’inscription institutionnelle des dispositifs et l’analyse des dimensions groupales en tant qu’espace théorique spécifique à l’analyse

Dimensions of the Complexity of Health Interventions: What Are We Talking about? A Review

Many recommendations and innovative approaches are available for the development and evaluation of complex health interventions. We investigated the dimensions of complexity described in health research and how these descriptions may affect the adopted research methodology (e.g., the choice of designs and methods). We used a mixed method approach to review the scientific literature evaluating complex interventions in the health field. Of 438 articles identified, 179 were subjected to descriptive analysis and 48 to content analysis. The three principal dimensions of complexity were: stakeholder characteristics, intervention multimodality and context. Recognition of such dimensions influenced the methodological choices made during evaluation of the interventions with their use of designs and methods, which aimed to address the complexity. We analysed not only how researchers view complexity but also the effects of such views on researcher practices. Our results highlight the need for clarification of what complexity means and to consider complexity when deciding how to evaluate research interventions

Nanoscale characterization of isolated individual type I collagen fibrils: polarization and piezoelectricity

Abstract Piezoresponse force microscopy was applied to directly study individual type I collagen fibrils with diameters of ∼100 nm isolated from bovine Achilles tendon. It was revealed that single collagen fibrils behave predominantly as shear piezoelectric materials with a piezoelectric coefficient on the order of 1 pm V −1 , and have unipolar axial polarization throughout their entire length. It was estimated that, under reasonable shear load conditions, the fibrils were capable of generating an electric potential up to tens of millivolts. The result substantiates the nanoscale origin of piezoelectricity in bone and tendons, and implies also the potential importance of the shear load-transfer mechanism, which has been the principle basis of the nanoscale mechanics model of collagen, in mechanoelectric transduction in bone

La bioadsorption sur amidon réticulé pour enlever des métaux des effluents industriels

L’industrie de traitement de surface utilise de nombreux produits chimiques, en particulier des métaux toxiques et des substances organiques, qui sont connus pour être nocifs vis-à-vis des humains et de l’environnement. En raison d’une réglementation de plus en plus stricte, les effluents contenant des métaux lourds doivent être traités. Il existe une grande variété de procédés de traitement des eaux usées provenant de la filière traitement de surface. En général, les systèmes conventionnels de détoxification se composent principalement d’un ajustement de pH, d’une oxydation des cyanures et d’une réduction des chromes, suivi d’une précipitation sous forme d’hydroxydes et d’une clarification, et parfois d’une étape d’adsorption sur charbon. Cependant, la technologie sur charbon actif présente plusieurs problèmes tels que la saturation rapide et des problèmes de colmatage des réacteurs. Comme les résines d'échange d’ions, leur utilisation est restreinte due au coût élevé. Pour ces raisons, la plupart des petites et moyennes entreprises ne peuvent pas utiliser de tels traitements. Ainsi, afin de répondre à ces problématiques, de nombreuses études sont menées pour trouver des alternatives peu coûteuses, qui soient efficaces et acceptables pour un usage industriel. Dans cette étude, la bioadsorption sur un adsorbant d’amidon réticulé a été utilisée pour retenir les métaux contenus dans des effluents industriels. L’adsorption a été étudiée en fonction du temps de contact, de la masse d’adsorbant et de la charge polluante. L’influence de ces paramètres sur l’efficacité d’adsorption a été évaluée en utilisant une méthode conventionnelle en mode cuvée. Les résultats ont montré que le matériau présente des capacités d’adsorption élevées vis-à-vis des ions métalliques, ce qui permet de diminuer les concentrations métalliques en dessous des valeurs réglementaires. Des mesures de taux de germination sur des graines de Lactuca sativa, utilisé comme test de phytotoxicité, ont été réalisées sur les rejets industriels avant et après adsorption. Ces tests ont confirmé l’efficacité du procédé pour diminuer fortement la toxicité du rejet. L’abattement chimique et la réduction de la toxicité ont montré que la bioadsorption sur un matériau non conventionnel peut être une étape de finition intéressante pour la détoxification des rejets industriels.The surface-treatment industry consumes and discharges an important range of chemicals, in particular toxic metals and organics, that are known to be harmful to humans and the environment. Because of more and more stringent regulations, effluents polluted with heavy metals must be treated. There are a variety of treatment processes for wastewater from the surface-treatment industry. In general, conventional treatment and detoxification systems consist mainly of pH adjustments, oxidation of cyanide and reduction of chromium bearing wastewaters, followed by hydroxide precipitation, clarification, and sometimes carbon sorption. However, active carbon technology presents several problems such as rapid saturation and clogging of the reactors. Like ion-exchange resins, their widespread use is restricted due to high cost. For these reasons, most small and medium-size enterprises cannot employ such treatments. Thus, in order to overcome these problems, many attempts have been made to find inexpensive alternative sorbents, which are both effective and acceptable for industrial use. In this study, biosorption with a starch-based cross-linked adsorbent was used for the removal of heavy metals from industrial effluents. The adsorption of metals was studied as a function of contact time, adsorbent mass and pollutant load. The influence of these parameters on the adsorption efficiency was evaluated using a conventional batch method. Batch experiments showed that the material exhibited high sorption capacities toward metal ions, leading to concentrations that were below current regulatory values. Measurements of the germination rate of Lactuca sativa seeds, used as a phytotoxicity test, were carried out on discharged industrial waters before and after the finishing sorption treatment. Germination tests confirmed the ability of the sorption step to radically decrease the effluent toxicity. Both the chemical abatement and toxicity mitigation of waste water showed that biosorption onto a non-conventional sorbent may constitute an interesting additional treatment step for the detoxification of industrial wastewater

Grid-based density functional calculation of many-electron systems

Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many-electron systems in the 3D cartesian coordinate grid (CCG). The atom-centered localized gaussian basis set, electronic density and the two-body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange-correlation potential, while Hay-Wadt-type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom-centered grid as well as the grid-free calculation. Results for 3 atoms are also given. Combination of CCG and the convolution procedure used for classical Coulomb potential can provide reasonably accurate and reliable results for many-electron systems.Comment: 17 pages, 1 figure, 6 tables, 34 reference

Jeunes en difficulté et auteurs de violences sexuelles : comment les aider sans violence ?

Les violences sexuelles commises par les mineurs sur d'autres enfants généralement plus jeunes qu'eux sont prises en charge en France conjointement par les services de Justice et de Santé. Après avoir rappelé quelques-uns des questionnements partagés par les chercheurs et les praticiens sur cette problématique, l'article s'interroge sur les enjeux et les effets de la prise en charge des jeunes auteurs au sein d'un groupe thérapeutique d'inspiration cognitivo-comportementale, constitué spécifiquement dans cette intention. Les données sur lesquelles il s'appuie proviennent d'une recherche-action engagée dans le cadre d'un partenariat entre institution judiciaire et institution de soin ; elles portent sur les retentissements du dispositif sur les jeunes eux-mêmes et sur la qualité des pratiques professionnelles des acteurs engagés.Sexual violence committed by adolescents on younger children are usually supported in France by Justice and Health services. First, this article presents the most important questions shared by judicial and health professionals about this issue. Second, we develop the main effects of a therapeutic group for minor sex offenders. This group is based both on cognitive behavioral inspiration and psychodynamic approach and propose a new psychological care for this adolescents. Through action research, the study data were collected from youg people and health and judicial professionals. The analysis focuses on how the adolescents have experienced the therapeutic group, and on the implications of professional practice.En Francia, las violencias sexuales cometidas por los menores de edad sobre otros niños generalmente mas jóvenes que ellos mismos, son a cargo conjuntamente de los departamentos de justicia y de salud. Tras haber evocado unas de las interrogaciones compartidas entre los investigadores y los profesionales sobre esta problemática, el artículo se pregunta sobre los objectivos y los efectos del trabajo realizado con jovenes autores dentro de un grupo terapéutico de obediencia cognitivo-conductista, especificamente constituido con esta fin. Los datos utilizados en el artículo proceden de una investigación-actión empezada en el marco de una colaboración entre la institución judicial y la de salud ; tratan de las repercuciones del dispositivo sobre los propios jóvenes y sobre la cualidad de las prácticas profesionales de los actores comprometidos