Fractional dynamics in DNA

This paper addresses the DNA code analysis in the perspective of dynamics and fractional calculus. Several mathematical tools are selected to establish a quantitative method without distorting the alphabet represented by the sequence of DNA bases. The association of Gray code, Fourier transform and fractional calculus leads to a categorical representation of species and chromosomes.

Analysis and visualization of chromosome information

This paper analyzes the DNA code of several species in the perspective of information content. For that purpose several concepts and mathematical tools are selected towards establishing a quantitative method without a priori distorting the alphabet represented by the sequence of DNA bases. The synergies of associating Gray code, histogram characterization and multidimensional scaling visualization lead to a collection of plots with a categorical representation of species and chromosomes.

La controverse autour du code des personnes et de la famille au Mali : enjeux et stratégies des acteurs

L’objectif de cette thèse est d’analyser et de comprendre la dynamique de la controverse autour de l’adoption en 2009 du code des personnes et de la famille au Mali. Elle s’intéresse particulièrement aux principaux enjeux, c'est-à-dire aux questions à l’origine de cette controverse ainsi qu’aux stratégies mises en place par les différents acteurs sociaux (les organisations islamiques et leurs alliés, d’une part, et d’autre part, les organisations féminines et les leurs) afin d’infléchir le processus. En plus du pourquoi et du comment de cette controverse, notre recherche visait à comprendre le bilan du processus tiré par les acteurs eux-mêmes, le sentiment qui les anime à l’issu de ce long processus, leur appréciation de leur expérience, et leur vision de l’avenir. Pour étudier cette problématique, nous avons choisi l’approche de l’action collective protestataire, laquelle s’inspire à la fois des théories de l’action collective, et de celles des mouvements sociaux et des dynamiques contestataires. Afin d’analyser les enjeux au cœur de cette controverse, les stratégies utilisées par les acteurs ainsi que leur bilan du processus, nous avons opté pour une démarche qualitative. En plus de la littérature grise, des articles de presse, documents audio et audiovisuels sur le sujet, notre travail de terrain de quatre mois dans la capitale malienne nous a permis de réaliser plusieurs entrevues auprès des acteurs impliqués dans ce processus. S’étendant de 1996 à 2011, soit seize ans, l’élaboration du code des personnes et de la famille au Mali fut un processus long, complexe, inhabituel et controversé. Les résultats de notre recherche révèlent que plusieurs enjeux, notamment sociaux, étaient au cœur de cette controverse : le «devoir d’obéissance » de la femme à son mari, la légalisation du mariage religieux, l’« égalité » entre fille et garçon en matière d’héritage et de succession et la reconnaissance de l’enfant naturel ont été les questions qui ont suscité le plus de débats. Si durant tout le processus, les questions relatives à l’égalité de genre, au respect des droits de la femme et de l’enfant, étaient les arguments défendus par les organisations féminines et leurs alliés, celles relatives au respect des valeurs religieuses (islamiques), sociétales ou socioculturelles maliennes étaient, par contre, mises de l’avant par les organisations islamiques et leurs alliés. Ainsi, si le discours des OSC féminines portait essentiellement sur le « respect de l’égalité des sexes » conformément aux engagements internationaux signés par le Mali, celui des OSC islamiques s’est, en revanche, centré sur le « respect des valeurs islamiques et socioculturelles » du Mali. Quant aux canaux de communication, les OSC féminines se sont focalisées sur les canaux classiques comme la presse, les radios, les conférences, entre autres. Les OSC islamiques ont également utilisé ces canaux, mais elles se sont distinguées des OSC féminines en utilisant aussi les prêches. Organisés généralement dans les mosquées et autres espaces désignés à cet effet, ces prêches ont consacré la victoire des OSC islamiques. Les radios islamiques ont joué elles aussi un rôle important dans la transmission de leurs messages. Pour ce qui est des stratégies d’actions, l’action collective qui a changé la donne en faveur des OSC islamiques (renvoi du code en seconde lecture, prise en compte de leurs idées), a été le meeting du 22 août 2009 à Bamako, précédé de marches de protestation dans la capitale nationale et toutes les capitales régionales du pays. Quant aux OSC féminines, elles n’ont mené que quelques actions classiques (ou habituelle) comme les pétitions, le plaidoyer-lobbying, les conférences-débats, au point que certains observateurs ont parlé de « stratégie d’inaction » chez elles. L’analyse a également révélé l’utilisation de stratégies inusitées de menaces et d’intimidation par certains acteurs du camp des OSC islamiques à l’endroit des partisans du code. Si chaque groupe d’acteurs a noué des alliances avec des acteurs locaux, les OSC féminines sont les seules à reconnaitre des alliances avec les acteurs extérieurs. Aujourd’hui, si la plupart des membres des OSC islamiques ne cachent pas leur satisfaction face à leur « victoire » et se présentent en « sauveur de la nation malienne », la plupart des membres des OSC féminines se disent, quant à elles, très « déçues » et « indignées » face à l’adoption du code actuel. Elles ne comprennent pas pourquoi d’un « code progressiste », le Mali s’est retrouvé avec un « code rétrograde et discriminatoire » envers les femmes. La thèse confirme non seulement la difficile conciliation entre droit coutumier, loi islamique et droit « moderne », mais également l’idée que le droit demeure l’expression des rapports de pouvoir et de domination. Enfin, notre recherche confirme la désormais incontournable influence des acteurs religieux sur le processus d’élaboration des politiques publiques au Mali.

MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Gray market vehicle program: extension warranted, but improvements in vehicle identification are needed.

Mode of access: Internet.

Infratentorial Gray Matter Atrophy And Excess In Primary Craniocervical Dystonia.

Primary craniocervical dystonia (CCD) is generally attributed to functional abnormalities in the cortico-striato-pallido-thalamocortical loops, but cerebellar pathways have also been implicated in neuroimaging studies. Hence, our purpose was to perform a volumetric evaluation of the infratentorial structures in CCD. We compared 35 DYT1/DYT6 negative patients with CCD and 35 healthy controls. Cerebellar volume was evaluated using manual volumetry (DISPLAY software) and infratentorial volume by voxel based morphometry of gray matter (GM) segments derived from T1 weighted 3 T MRI using the SUIT tool (SPM8/Dartel). We used t-tests to compare infratentorial volumes between groups. Cerebellar volume was (1.14 ± 0.17) × 10(2) cm(3) for controls and (1.13 ± 0.14) × 10(2) cm(3) for patients; p = 0.74. VBM demonstrated GM increase in the left I-IV cerebellar lobules and GM decrease in the left lobules VI and Crus I and in the right lobules VI, Crus I and VIIIb. In a secondary analysis, VBM demonstrated GM increase also in the brainstem, mostly in the pons. While gray matter increase is observed in the anterior lobe of the cerebellum and in the brainstem, the atrophy is concentrated in the posterior lobe of the cerebellum, demonstrating a differential pattern of infratentorial involvement in CCD. This study shows subtle structural abnormalities of the cerebellum and brainstem in primary CCD.

Morphine infusions into the rostrolateral periaqueductal gray affect maternal behaviors

It is well established that morphine inhibits maternal behaviors. Previous studies by our group have shown activation of the rostrolateral periaqueductal gray (rlPAG) upon inhibition-intended subcutaneous injections of morphine. In this context, we demonstrated that a single naloxone infusion into the rlPAG, following this opioid-induced inhibition, reactivated maternal behaviors. Since these data were obtained by using peripheral morphine injections, the present study was designed to test whether morphine injected directly into the rlPAG would affect maternal behaviors. Our hypothesis that morphine acting through the rlPAG would disrupt maternal behaviors was confirmed with a local infusion of morphine. The mothers showed shorter latency for locomotor behavior to explore the home cage (P = 0.049). Inhibition was especially evident regarding retrieving (P = 0.002), nest building (P = 0.05) and full maternal behavior (P = 0.023). These results support the view that opioidergic transmission plays a behaviorally meaningful inhibitory role in the rostrolateral PAG.

Effect of Alloying Elements on Thermal Diffusivity of Gray Cast Iron Used in Automotive Brake Disks

The purpose of this work was to experimentally investigate the thermal diffusivity of four different gray cast iron alloys, regularly used to produce brake disks for automotive vehicles. Thermal diffusivity measurements were performed at temperatures ranging from room temperature to 600 A degrees C. The influence of the thermal conductivity on the thermomechanical fatigue life is also briefly presented. The measurements were sensitive to the influence of the carbon equivalent and alloying elements, such as molybdenum, copper and chromium. Molybdenum, unlike copper, lowered the thermal diffusivity of the gray cast iron, and alloy E (without molybdenum), besides presenting a relatively low carbon equivalent content and an increase in the values of the thermal diffusivity, presented the best performance during the thermomechanical fatigue. The molybdenum present in alloys B and C did not fulfill the expectations of providing the best thermomechanical fatigue behavior. Consequently, its elimination in the gray cast iron alloy for this application will result in a significant economy.

Afferent Connections to the Rostrolateral Part of the Periaqueductal Gray: A Critical Region Influencing the Motivation Drive to Hunt and Forage

Previous studies have shown that a particular site in the periaqueductal gray (PAG), the rostrolateral PAG, influences the motivation drive to forage or hunt. To have a deeper understanding on the putative paths involved in the decision-making process between foraging, hunting, and other behavioral responses, in the present investigation, we carried out a systematic analysis of the neural inputs to the rostrolateral PAG (rlPAG), using Fluorogold as a retrograde tracer. According to the present findings, the rlPAG appears to be importantly driven by medial prefrontal cortical areas involved in controlling attention-related and decision-making processes. Moreover, the rlPAG also receives a wealth of information from different amygdalar, hypothalamic, and brainstem sites related to feeding, drinking, or hunting behavioral responses. Therefore, this unique combination of afferent connections puts the rlPAG in a privileged position to influence the motivation drive to choose whether hunting and foraging would be the most appropriate adaptive responses. Copyright (C) 2009 Sandra Regina Mota-Ortiz et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reliability-based evaluation of design code provisions for circular concrete-filled steel columns

This paper presents an investigation of design code provisions for steel-concrete composite columns. The study covers the national building codes of United States, Canada and Brazil, and the transnational EUROCODE. The study is based on experimental results of 93 axially loaded concrete-filled tubular steel columns. This includes 36 unpublished, full scale experimental results by the authors and 57 results from the literature. The error of resistance models is determined by comparing experimental results for ultimate loads with code-predicted column resistances. Regression analysis is used to describe the variation of model error with column slenderness and to describe model uncertainty. The paper shows that Canadian and European codes are able to predict mean column resistance, since resistance models of these codes present detailed formulations for concrete confinement by a steel tube. ANSI/AISC and Brazilian codes have limited allowance for concrete confinement, and become very conservative for short columns. Reliability analysis is used to evaluate the safety level of code provisions. Reliability analysis includes model error and other random problem parameters like steel and concrete strengths, and dead and live loads. Design code provisions are evaluated in terms of sufficient and uniform reliability criteria. Results show that the four design codes studied provide uniform reliability, with the Canadian code being best in achieving this goal. This is a result of a well balanced code, both in terms of load combinations and resistance model. The European code is less successful in providing uniform reliability, a consequence of the partial factors used in load combinations. The paper also shows that reliability indexes of columns designed according to European code can be as low as 2.2, which is quite below target reliability levels of EUROCODE. (C) 2009 Elsevier Ltd. All rights reserved.

Verification of a mixed high-order accurate DNS code for laminar turbulent transition by the method of manufactured solutions

This paper presents results on a verification test of a Direct Numerical Simulation code of mixed high-order of accuracy using the method of manufactured solutions (MMS). This test is based on the formulation of an analytical solution for the Navier-Stokes equations modified by the addition of a source term. The present numerical code was aimed at simulating the temporal evolution of instability waves in a plane Poiseuille flow. The governing equations were solved in a vorticity-velocity formulation for a two-dimensional incompressible flow. The code employed two different numerical schemes. One used mixed high-order compact and non-compact finite-differences from fourth-order to sixth-order of accuracy. The other scheme used spectral methods instead of finite-difference methods for the streamwise direction, which was periodic. In the present test, particular attention was paid to the boundary conditions of the physical problem of interest. Indeed, the verification procedure using MMS can be more demanding than the often used comparison with Linear Stability Theory. That is particularly because in the latter test no attention is paid to the nonlinear terms. For the present verification test, it was possible to manufacture an analytical solution that reproduced some aspects of an instability wave in a nonlinear stage. Although the results of the verification by MMS for this mixed-order numerical scheme had to be interpreted with care, the test was very useful as it gave confidence that the code was free of programming errors. Copyright (C) 2009 John Wiley & Sons, Ltd.

Alprazolam potentiates the antiaversive effect induced by the activation of 5-HT(1A) and 5-HT(2A) receptors in the rat dorsal periaqueductal gray

Rationale Serotonin in the dorsal periaqueductal gray (DPAG) through the activation of 5-HT(1A) and 5-HT(2A) receptors inhibits escape, a defensive behavior associated with panic attacks. Long-term treatment with antipanic drugs that nonselectively or selectively blocks the reuptake of serotonin (e.g., imipramine and fluoxetine, respectively) enhances the inhibitory effect on escape caused by intra-DPAG injection of 5-HT(1A) and 5-HT(2A) receptor agonists. It has been proposed that these compounds exert their effect on panic by facilitating 5-HT-mediated neurotransmission in the DPAG. Objectives The objective of this study was to investigate whether facilitation of 5-HT neurotransmission in the DPAG is also observed after treatment with alprazolam, a pharmacologically distinct antipanic drug that acts primarily as a high potency benzodiazepine receptor agonist. Materials and methods Male Wistar rats, subchronically (3-6 days) or chronically (14-17 days) treated with alprazolam (2 and 4 mg/kg, i.p.) were intra-DPAG injected with (+/-)-8-hydroxy-2-(di-n-propylamino)tetralin hydrobromide (8-OH-DPAT), (+/-)-1-(2,5-dimethoxy-4-iodophenyl) piperazine dihydrochloride (DOI), and midazolam, respectively, 5-HT(1A), 5-HT(2A/2C), and benzodiazepine receptor agonists. The intensity of electrical current that needed to be applied to the DPAG to evoke escape behavior was measured before and after the microinjection of these agonists. Results Intra-DPAG injection of the 5-HT agonists and midazolam increased the escape threshold in all groups of animals tested, indicating a panicolytic-like effect. The inhibitory effect of 8-OH-DPAT and DOI, but not midazolam, was significantly higher in animals receiving long-, but not short-term treatment with alprazolam. Conclusions Alprazolam as antidepressants compounds facilitates 5-HT(1A)- and 5-HT(2A)-receptor-mediated neurotransmission in the DPAG, implicating this effect in the mode of action of different classes of antipanic drugs.

Theory manual to OctVCE – a cartesian cell CFD code with special application to blast wave problems, Department of Mechanical Engineering Report 2007/12

OctVCE is a cartesian cell CFD code produced especially for numerical simulations of shock and blast wave interactions with complex geometries, in particular, from explosions. Virtual Cell Embedding (VCE) was chosen as its cartesian cell kernel for its simplicity and sufficiency for practical engineering design problems. The code uses a finite-volume formulation of the unsteady Euler equations with a second order explicit Runge-Kutta Godonov (MUSCL) scheme. Gradients are calculated using a least-squares method with a minmod limiter. Flux solvers used are AUSM, AUSMDV and EFM. No fluid-structure coupling or chemical reactions are allowed, but gas models can be perfect gas and JWL or JWLB for the explosive products. This report also describes the code’s ‘octree’ mesh adaptive capability and point-inclusion query procedures for the VCE geometry engine. Finally, some space will also be devoted to describing code parallelization using the shared-memory OpenMP paradigm. The user manual to the code is to be found in the companion report 2007/13.