T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Quantitative morphometry analysis of the fetal brain using clinical MR imaging

In vivo fetal magnetic resonance imaging provides aunique approach for the study of early human braindevelopment [1]. In utero cerebral morphometry couldpotentially be used as a marker of the cerebralmaturation and help to distinguish between normal andabnormal development in ambiguous situations. However,this quantitative approach is a major challenge becauseof the movement of the fetus inside the amniotic cavity,the poor spatial resolution provided by very fast MRIsequences and the partial volume effect. Extensiveefforts are made to deal with the reconstruction ofhigh-resolution 3D fetal volumes based on severalacquisitions with lower resolution [2,3,4]. Frameworkswere developed for the segmentation of specific regionsof the fetal brain such as posterior fossa, brainstem orgerminal matrix [5,6], or for the entire brain tissue[7,8], applying the Expectation-Maximization MarkovRandom Field (EM-MRF) framework. However, many of theseprevious works focused on the young fetus (i.e. before 24weeks) and use anatomical atlas priors to segment thedifferent tissue or regions. As most of the gyraldevelopment takes place after the 24th week, acomprehensive and clinically meaningful study of thefetal brain should not dismiss the third trimester ofgestation. To cope with the rapidly changing appearanceof the developing brain, some authors proposed a dynamicatlas [8]. To our opinion, this approach however faces arisk of circularity: each brain will be analyzed /deformed using the template of its biological age,potentially biasing the effective developmental delay.Here, we expand our previous work [9] to proposepost-processing pipeline without prior that allow acomprehensive set of morphometric measurement devoted toclinical application. Data set & Methods: Prenatal MRimaging was performed with a 1-T system (GE MedicalSystems, Milwaukee) using single shot fast spin echo(ssFSE) sequences (TR 7000 ms, TE 180 ms, FOV 40 x 40 cm,slice thickness 5.4mm, in plane spatial resolution1.09mm). For each fetus, 6 axial volumes shifted by 1 mmwere acquired under motherâeuro?s sedation (about 1min pervolume). First, each volume is segmentedsemi-automatically using region-growing algorithms toextract fetal brain from surrounding maternal tissues.Inhomogeneity intensity correction [10] and linearintensity normalization are then performed. Brain tissues(CSF, GM and WM) are then segmented based on thelow-resolution volumes as presented in [9]. Ahigh-resolution image with isotropic voxel size of 1.09mm is created as proposed in [2] and using B-splines forthe scattered data interpolation [11]. Basal gangliasegmentation is performed using a levet setimplementation on the high-resolution volume [12]. Theresulting white matter image is then binarized and givenas an input in FreeSurfer software(http://surfer.nmr.mgh.harvard.edu) to providetopologically accurate three-dimensional reconstructionsof the fetal brain according to the local intensitygradient. References: [1] Guibaud, Prenatal Diagnosis29(4) (2009). [2] Rousseau, Acad. Rad. 13(9), 2006. [3]Jiang, IEEE TMI 2007. [4] Warfield IADB, MICCAI 2009. [5]Claude, IEEE Trans. Bio. Eng. 51(4) 2004. [6] Habas,MICCAI 2008. [7] Bertelsen, ISMRM 2009. [8] Habas,Neuroimage 53(2) 2010. [9] Bach Cuadra, IADB, MICCAI2009. [10] Styner, IEEE TMI 19(39 (2000). [11] Lee, IEEETrans. Visual. And Comp. Graph. 3(3), 1997. [12] BachCuadra, ISMRM 2010.

Nestmate recognition and levels of aggression are not altered by changes in genetic diversity in a socially polymorphic ant

The ability to distinguish nestmates from foreign individuals is central to the functioning of insect societies. In ants, workers from multiple-queen colonies are often less aggressive than workers from single-queen ones. In line with this observation, it has been hypothesized that workers from multiple-queen colonies have less precise recognition abilities than workers from single-queen ones because their colonies contain genetically more diverse individuals, which results in a broader template of recognition cues. Here, we assessed the impact of social structure ( queen number) variation on nestmate recognition and aggression in a large population of the socially polymorphic ant Formica selysi. We staged unilateral aggression tests on the nest surface. Workers from single-and multiple-queen colonies had good nestmate recognition ability and did not differ significantly in their level of aggression towards foreign, immobilized workers ( cue-bearers). In particular, workers from multiple-queen colonies efficiently recognized non-nestmates despite the higher genetic diversity in their colony. Cue-bearers from single- and multiple-queen colonies elicited similar reactions. However, the level of aggression was higher between than within social forms, suggesting that workers detect a signal that is specific to the colony social structure. Finally, the level of aggression was not correlated with the genetic distance between colonies. Overall, we found no evidence for the hypothesis that the presence of multiple breeders in the same colony decreases recognition abilities and found no simple relationship between genetic diversity and aggression level. (c) 2007 The Association for the Study of Animal Behaviou

Liver-specific loss of lipin-1-mediated phosphatidic acid phosphatase activity does not mitigate intrahepatic TG accumulation in mice.

Lipin proteins (lipin 1, 2, and 3) regulate glycerolipid homeostasis by acting as phosphatidic acid phosphohydrolase (PAP) enzymes in the TG synthesis pathway and by regulating DNA-bound transcription factors to control gene transcription. Hepatic PAP activity could contribute to hepatic fat accumulation in response to physiological and pathophysiological stimuli. To examine the role of lipin 1 in regulating hepatic lipid metabolism, we generated mice that are deficient in lipin-1-encoded PAP activity in a liver-specific manner (Alb-Lpin1(-/-) mice). This allele of lipin 1 was still able to transcriptionally regulate the expression of its target genes encoding fatty acid oxidation enzymes, and the expression of these genes was not affected in Alb-Lpin1(-/-) mouse liver. Hepatic PAP activity was significantly reduced in mice with liver-specific lipin 1 deficiency. However, hepatocytes from Alb-Lpin1(-/-) mice had normal rates of TG synthesis, and steady-state hepatic TG levels were unaffected under fed and fasted conditions. Furthermore, Alb-Lpin1(-/-) mice were not protected from intrahepatic accumulation of diacylglyerol and TG after chronic feeding of a diet rich in fat and fructose. Collectively, these data demonstrate that marked deficits in hepatic PAP activity do not impair TG synthesis and accumulation under acute or chronic conditions of lipid overload.

Derivation of an observer model adapted to irregular signals based on convolution channels.

Anthropomorphic model observers are mathe- matical algorithms which are applied to images with the ultimate goal of predicting human signal detection and classification accuracy across varieties of backgrounds, image acquisitions and display conditions. A limitation of current channelized model observers is their inability to handle irregularly-shaped signals, which are common in clinical images, without a high number of directional channels. Here, we derive a new linear model observer based on convolution channels which we refer to as the "Filtered Channel observer" (FCO), as an extension of the channelized Hotelling observer (CHO) and the nonprewhitening with an eye filter (NPWE) observer. In analogy to the CHO, this linear model observer can take the form of a single template with an external noise term. To compare with human observers, we tested signals with irregular and asymmetrical shapes spanning the size of lesions down to those of microcalfications in 4-AFC breast tomosynthesis detection tasks, with three different contrasts for each case. Whereas humans uniformly outperformed conventional CHOs, the FCO observer outperformed humans for every signal with only one exception. Additive internal noise in the models allowed us to degrade model performance and match human performance. We could not match all the human performances with a model with a single internal noise component for all signal shape, size and contrast conditions. This suggests that either the internal noise might vary across signals or that the model cannot entirely capture the human detection strategy. However, the FCO model offers an efficient way to apprehend human observer performance for a non-symmetric signal.

Territorialisation des politiques énergétiques dans l'agglomération franco-valdo-genevoise : la planification énergétique comme opportunité de réaménagement des zones frontières ?

La présente recherche traite des défis posés à l'action publique territoriale par la transition énergétique, transition désormais érigée au rang de priorité par les autorités françaises et suisses, comme plus globalement européennes. Elle prend pour cela appui sur une analyse des démarches de planification énergétique territoriale menées entre 2007 et 2014 sur le territoire franco-valdo-genevois (agglomération du « Grand-Genève »). Considérées comme des laboratoires d'expérimentation de la territorialisation des politiques énergétiques, ces démarches sont ici examinées selon une perspective institutionnaliste et pragmatiste visant à mettre lumière les éléments qui interviennent dans la délimitation du champ des possibles en matière d'action publique énergétique et territoriale. Ce positionnement découle des évolutions observées sur le territoire franco-valdo-genevois durant la période d'étude (chapitre 1). Il découle plus précisément du constat de récurrence de certains points de blocage rencontrés aussi bien dans les démarches de planification énergétique elles-mêmes que dans les travaux méthodologiques qui ont pu être réalisés parallèlement à ces démarches, dans le but d'en affiner les outils techniques et organisationnels de mise en oeuvre. Ainsi, le point de départ de la présente recherche est le constat selon lequel on peine tout autant à construire des solutions énergétiques appropriables et réalisables par les acteurs des territoires concernés qu'à reconfigurer les outils de production de ces solutions. De ce constat découle l'intérêt porté aux cadres institutionnels qui régissent ces planifications énergétiques territoriales. Définis comme l'ensemble des repères - formels et informels - qui rendent possibles en même temps qu'ils contraignent les interactions territorialisées entre les acteurs, ces cadres institutionnels sont placés au coeur de la grille de (re)lecture des expériences de planification énergétique territoriale établie au chapitre 2 de la thèse. En référence aux concepts institutionnalistes et pragmatistes sur lesquels elle prend appui, cette grille conduit à appréhender ces expériences comme autant d'enquêtes contribuant, à travers le travail de mobilisation et construction de représentations territoriales auquel elles donnent lieu, à l'équipement sociocognitif d'un champ d'intervention territorial spécifique. Partant de l'hypothèse selon laquelle les potentialités comme les limites associées à l'équipement sociocognitif de ce champ orientent les possibilités d'action collective, la réflexion consiste en une application de cette grille à une trentaine d'expériences de planification énergétique territoriale. Cette application s'effectue en deux temps, correspondant à deux niveaux de lecture de ces démarches. Le premier porte sur les dispositifs organisationnels et les modalités d'interactions entre les cultures d'action qu'elles réunissent (chapitre 3). Le second se concentre davantage sur les supports cognitifs (représentations territoriales) autour desquels se structurent ces interactions (chapitre 4). Présentés dans le dernier chapitre de la thèse (chapitre 5), les enseignements tirés de ce travail de réexamen des démarches franco-valdo-genevoises de planification énergétique territoriale sont de deux ordres. Ils portent d'abord sur les caractéristiques des cadres institutionnels existants, la manière dont ils orientent ces démarches et délimitent les évolutions possibles dans les modes d'action collective et plus particulièrement d'action publique qui y sont associés. Mais ils portent aussi sur les potentiels de changement associés à ces démarches, et sur les pistes envisageables pour mieux valoriser es potentiels, dont l'activation passe par des évolutions profondes des systèmes institutionnels en place. -- In France as in Switzerland, local authorities stand out as leading players of energy transition, a transition that requires an important renewal of public intervention instruments. It is the stakes and the conditions of such a renewal that the present work aims to examine, based on the experiments of territorial energy planning led on the franco-valdo-genevan cross-border territory. Conceived as initiatives of relocation of the energy supply system, these energy planning initiatives are examined through an institutionalist and pragmatic « reading template ». This « reading template » consists of seeing these energy planning initiatives as pragmatist inquiries aiming, through a collective work of cognitive equipment of the territorial franco-valdo-genevan field of intervention, at the reconstruction of the means of coordination between people about their material, organizational and political territory. It opens towards a double reading of the energy planning initiatives. The first one concentrates on the organizational dimension of these inquiries - i.e. on the cultures of action which they gather and the modalities of interaction between them - whereas the second focuses on the cognitive substance which represents the medium of the interactions. This double reading provides insights at various levels. The first one concerns the (cognitive) territorial field of intervention that these energy-planning experiments contribute to draw. A field which, although better and better characterized in its technical dimensions, remains at the same time limited and " deformed " so that it values more the fossil energy systems, from which we want to release ourselves, than the renewable ones, which we would like to replace them with. The second level of teaching concerns the processes of production of territorial knowledge (PPTK) which presides over the demarcation and « equipment » of the territorial field of intervention. Examined through the institutional norms and the culture of action at stake in them, this PPTK turns out to create a sociocognitive "cross-border" area, the kind of area that could shelter the desired reconfigurations...on the condition that they are beforehand correctly "equipped", in cognitive and also in organizational terms. The determining factor for the quality of this equipment is concentrated in the third category of teaching. Starting with the opportunities created by these energy planning experiments concerning the renewal of public intervention instruments, these elements also allow us to take a new look at the urban area project under construction in this cross-border territory, a project th t shows itself closely linked to the energy experiments through a common challenge of territorialisation.

Emergent geomorphic-vegetation interactions on a subalpine alluvial fan

Following perturbation, an ecosystem (flora, fauna, soil) should evolve as a function of time at a rate conditioned by external variables (relief, climate, geology). More recently, biogeomorphologists have focused upon the notion of co-development of geomorphic processes with ecosystems over very short through to very long (evolutionary) timescales. Alpine environments have been a particular focus of this co-development. However, work in this field has tended to adopt a simplified view of the relationship between perturbation and succession, including: how the landform and ecosystem itself conditions the impact of a perturbation to create a complex spatial response impact; and how perturbations are not simply ecosystem destroyers but can be a significant source of ecosystem resources. What this means is that at the within landform scale, there may well be a complex and dynamic topographic and sedimentological template that co-develops with soil, flora and fauna. Here, we present and test a conceptual model of this template for a subalpine alluvial fan. We combine detailed floristic inventory with soil inventory, determination of edaphic variables and analysis of historical aerial imagery. Spatial variation in the probability of perturbation of sites on the fan surface was associated with down fan variability in the across-fan distribution of fan ages, fan surface channel characteristics and fan surface sedimentology. Floristic survey confirmed that these edaphic factors distinguished site floristic richness and plant communities up until the point that the soil-vegetation system was sufficiently developed to sustain plant communities regardless of edaphic conditions. Thus, the primary explanatory variable was the estimated age of each site, which could be tied back into perturbation history and its spatial expression due to the geometry of the fan: distinct plant communities were emergent both across fan and down fan, a distribution maintained by the way in which the fan dissipates potentially perturbing events.

Stabbing simulations and DNA transfer

Technical developments have made it possible to analyze very low amounts of DNA. This has many advantages, but the drawback of this technological progress is that interpretation of the results becomes increasingly complex: the number of mixed DNA profiles increased relatively to single source DNA profiles and stochastic effects in the DNA profile, such as drop-in and drop-out, are more frequently observed. Moreover, the relevance of low template DNA material regarding the activities alleged is not as straightforward as it was a few years ago, when for example large quantities of blood were recovered. The possibility of secondary and tertiary transfer is now becoming an issue. The purpose of this research is twofold: first, to study the transfer of DNA from the handler and secondly, to observe if handlers would transfer DNA from persons closely connected to them. We chose to mimic cases where the offender would attack a person with a knife. As a first approach, we envisaged that the defense would not give an alternative explanation for the origin of the DNA. In our transfer experiments (4 donors, 16 experiments each, 64 traces), 3% of the traces were single DNA profiles. Most of the time, the DNA profile of the person handling the knife was present as the major profile: in 83% of the traces the major contributor profile corresponded to the stabber's DNA profile (in single stains and mixtures). Mixture with no clear major/minor fraction (12%) were observed. 5% of the traces were considered of insufficient quality (more than 3 contributors, presence of a few minor peaks). In that case, we considered that the stabber's DNA was absent. In our experiments, no traces allowed excluding the stabber, however it must be noted that precautions were taken to minimize background DNA as knives were cleaned before the experiments. DNA profiles of the stabber's colleagues were not observed. We hope that this study will allow for a better understanding of the transfer mechanism and of how to assess and describe results given activity level propositions. In this preliminary research, we have focused on the transfer of DNA on the hand of the person. Besides, more research is needed to assign the probability of the results given an alternative activity proposed by the defense, for instance when the source of the DNA is not contested, but that the activities are.

Automatic Brain Extraction in Fetal MRI using Multi-Atlas-based Segmentation

In fetal brain MRI, most of the high-resolution reconstruction algorithms rely on brain segmentation as a preprocessing step. Manual brain segmentation is however highly time-consuming and therefore not a realistic solution. In this work, we assess on a large dataset the performance of Multiple Atlas Fusion (MAF) strategies to automatically address this problem. Firstly, we show that MAF significantly increase the accuracy of brain segmentation as regards single-atlas strategy. Secondly, we show that MAF compares favorably with the most recent approach (Dice above 0.90). Finally, we show that MAF could in turn provide an enhancement in terms of reconstruction quality.

Biopsies de la prostate en 2015: quelle biopsie pour quel patient [Prostate biopsy: which strategy for which patient?].

L'adoption de l'IRM dans le parcours diagnostique a déterminé la transition des biopsies aléatoires aux biopsies ciblées vers les lésions visibles à l'imagerie. L'utilisation de logiciels rendant possible la fusion d'images IRM et échographiques permet d'améliorer significativement la précision diagnostique de ces biopsies. De plus, pour déterminer l'éligibilité d'un patient à une thérapie focale, davantage de précision diagnostique est requise au niveau de toute la glande ; par conséquent, des biopsies avec une densité d'échantillonnage plus élevée par voie transpérinéale peuvent être proposées.Les nouvelles techniques de biopsie de la prostate permettent une prise en charge personnalisée grâce à une meilleure caractérisation de l'agressivité et de l'extension locale du cancer de la prostate. The adoption of multiparametric MRI within the diagnostic pathway has allowed urologists to move from random biopsy to targeted biopsy directed towards MR-visible lesions. The use of software for MR to TRUS fusion may enhance the diagnostic accuracy of targeted biopsy. To determine the eligibility for tissue-preserving approaches, further precision is required, and template prostate mapping biopsy may be offered. The employment of novel biopsy techniques provide better characterisation of the disease, and allows a tailored approach to a single subject.