An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim  Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.Location  World-wide.Methods  Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years.Results  Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node.Main conclusions  By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

Dual-wavelength digital holographic microscopy with sub-nanometer axial accuracy

We present dual-wavelength Digital Holographic Microscopy (DHM) measurements on a certified 8.9 nm high Chromium thin step sample and demonstrate sub-nanometer axial accuracy. We introduce a modified DHM Reference Calibrated Hologram (RCH) reconstruction algorithm taking into account amplitude contributions. By combining this with a temporal averaging procedure and a specific dual-wavelength DHM arrangement, it is shown that specimen topography can be measured with an accuracy, defined as the axial standard deviation, reduced to at least 0.9 nm. Indeed, it is reported that averaging each of the two wavefronts recorded with real-time dual-wavelength DHM can provide up to 30% spatial noise reduction for the given configuration, thanks to their non-correlated nature. ©2008 COPYRIGHT SPIE

Jeune dans sa tête. Une histoire critique du cerveau adolescent

Les recherches visant à élucider les bases neurales de l'adolescence ont émergé au cours des années 1990 pour s'imposer cette dernière décennie. Il est aujourd'hui accepté dans le champ des neurosciences cognitives et du développement que le cerveau continue à se développer après la 10eme année de vie et qu'il atteint un stade de maturation similaire à l'adulte seulement vers 25 ans. La configuration structurelle et fonctionnelle du cerveau spécifique à la période de l'adolescence impliquerait un manque de contrôle émotionnel, favorisant des comportements dits de prise de risques qui à la fois permettent l'acquisition de l'indépendance et provoquent des situations de mise en danger du jeune individu et de son entourage. Ses mêmes comportements, dans leur acception négative - consommation d'alcool et de stupéfiants, conduite en état d'ivresse, rapports sexuels non-protégés, port d'arme, etc. - mobilisent les politiques de prévention et de santé publique relatives à l'adolescence et à la jeunesse. Cette thèse qui retrace l'histoire du cerveau adolescent de la fin des années 1950 à nos jours se situe à l'intersection de ces deux thèmes d'intérêt scientifique et public. A partir d'une perspective d'histoire culturelle et sociale des sciences, elle approche les éléments expérimentaux, institutionnels et contextuels qui ont contribué à la construction d'une adolescence définie par son immaturité cérébrale, associée à des comportements dits à risque. Plus précisément, elle met en évidence, sous l'angle privilégié du genre, selon quelles modalités et quelles temporalités l'histoire des recherches scientifiques sur le développement cérébral humain à l'adolescence et celle du façonnage d'un type d'adolescent-e impulsif/ve et preneur/euse de risques - c'est-à-dire potentiellement délinquant, dépendant, invalide ou malade chronique, constitué en problème de politique et de santé publique - sont amenées à converger. L'argument développé est que le genre et le sexe sont des catégories actives dans la construction d'un cerveau adolescent idéalement unisexe. En d'autres termes, bien que le cerveau adolescent qualifie des individus en regard de leur âge, sans distinction apparente de sexe et de genre, les conditions de sa production et les critères de sa définition sont constitutivement genrés, notamment par des comportements à risque qui concernent une majorité de garçons. Il s'agit d'analyser comment du sexe et du genre peuvent produire de l'âge, a priori unisexe, et d'interroger les enjeux scientifiques, sociaux et politiques qui participent de cette invisibilisation des catégories de sexe et de genre. Le but est de considérer la manière dont l'adolescence cérébrale reconfigure la gestion des questions liées à l'adolescence et à la jeunesse, en termes de problèmes sanitaires et de délinquance, mais aussi en termes de reproduction des normes sociales, de ce qu'implique devenir un homme ou une femme.

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

Acteur et médias sur la scène

L'objet de cette étude est l'acteur dans un spectacle à composante technologique, analysé dans une perspective intermédiale qui est une pratique scénique et une approche analytique émergeante. Je place cette problématique dans le contexte du théâtre contemporain des années 1990 et du début du XXIe siècle notamment. Mon étude est organisée en trois parties. Les premiers chapitres abordent l'acteur dans sa relation avec le dispositif et l'image projetée, lors de deux périodes historiques. La première période se situe à la fin du XIXe siècle et est consacrée aux spectacles féeriques et magiques qui explorent le spectaculaire. La phase suivante se place autour des années 1920 et concerne principalement les travaux d'Erwin Piscator, de Vsevolod Meyerhold, d'Oskar Schlemmer ainsi que de Lev Koulechov. La deuxième partie de la thèse aborde la scène contemporaine imprégnée par les nouveaux médias et cela d'abord dans le contexte de la cyberculture, que je considère comme un aspect sociologique et anthropologique déterminant. Ceci me rapproche de ma définition du théâtre marqué par la technologie que je nomme un « théâtre des médias ». J'analyse les transformations et les déplacements des composantes théâtrales sous l'influence technologique en tant que re-configuration médiale de la scène. Je propose par la suite l'individuation intermédiale en tant que concept pour l'analyse de l'acteur et de la nouvelle subjectivité scénique. La troisième partie s'appuie sur deux grands axes : le dispositif et l'image, où l'acteur devient un dénominateur permanent de l'analyse permutationnelle. L'étude progresse d'abord par l'analyse des éléments suivants: écrans, moniteurs, caméras, capteurs. Ce qui est surtout ici mis en évidence, c'est la corporéité de l'acteur et son rapport spatial avec le dispositif. L'image, par contre, interroge l'interprétation et la construction du rôle. Elle apparaît dans sa fonction la plus statique ainsi que la plus complexe et dynamique, mettant en évidence la multifonction scénique de l'acteur. Il se présente sous des figures multiples (acteur cyborgisé, acteur marionnetisé), à travers ses écritures (interacteur, observateur) et ses identités scéniques nouvelles (formations hybrides). J'aborde à la fin la question de la nouvelle formation de l'interprète selon l'approche intermédiale qui émerge notamment à l'Académie de Maastricht et à l'Ecole régionale d'acteurs de Cannes. Le corpus analytique est composé d'une soixantaine de spectacles dont le noyau se concentre sur les travaux de Robert Lepage, de Jean Lambert-Wild, de LLT Videoteatr « Poza », de Komuna Otwock, du Wooster Groupe, et de Dumb Type.

On metapopulation resistance to drift and extinction.

The spatial configuration of metapopulations (numbers, sizes, and localization of patches) affects their ability to resist demographic extinction and genetic drift, but sometimes with opposite effects. Small and isolated patches, for instance, contribute marginally to demography but may play a large role in genetics by maintaining a sizeable amount of genetic variance among demes. In source-sink systems, similarly, connectivity may be beneficial in terms of effective size, but detrimental in terms of survival, by lowering the reproductive value of source populations. How to reconcile these opposite effects? Here we propose an analytical framework that integrates fixation time (ability to resist genetic drift) and extinction time (ability to resist demographic extinction) into a single index of resistance, measuring the ability of a metapopulation to maintain its demo-genetic integrity. We then illustrate with numerical examples how conflicting demands may be resolved.

Electrical neuroimaging of memory discrimination based on single-trial multisensory learning.

Multisensory experiences influence subsequent memory performance and brain responses. Studies have thus far concentrated on semantically congruent pairings, leaving unresolved the influence of stimulus pairing and memory sub-types. Here, we paired images with unique, meaningless sounds during a continuous recognition task to determine if purely episodic, single-trial multisensory experiences can incidentally impact subsequent visual object discrimination. Psychophysics and electrical neuroimaging analyses of visual evoked potentials (VEPs) compared responses to repeated images either paired or not with a meaningless sound during initial encounters. Recognition accuracy was significantly impaired for images initially presented as multisensory pairs and could not be explained in terms of differential attention or transfer of effects from encoding to retrieval. VEP modulations occurred at 100-130ms and 270-310ms and stemmed from topographic differences indicative of network configuration changes within the brain. Distributed source estimations localized the earlier effect to regions of the right posterior temporal gyrus (STG) and the later effect to regions of the middle temporal gyrus (MTG). Responses in these regions were stronger for images previously encountered as multisensory pairs. Only the later effect correlated with performance such that greater MTG activity in response to repeated visual stimuli was linked with greater performance decrements. The present findings suggest that brain networks involved in this discrimination may critically depend on whether multisensory events facilitate or impair later visual memory performance. More generally, the data support models whereby effects of multisensory interactions persist to incidentally affect subsequent behavior as well as visual processing during its initial stages.

Spontaneous pre-stimulus fluctuations in the activity of right fronto-parietal areas influence inhibitory control performance.

Inhibitory control refers to the ability to suppress planned or ongoing cognitive or motor processes. Electrophysiological indices of inhibitory control failure have been found to manifest even before the presentation of the stimuli triggering the inhibition, suggesting that pre-stimulus brain-states modulate inhibition performance. However, previous electrophysiological investigations on the state-dependency of inhibitory control were based on averaged event-related potentials (ERPs), a method eliminating the variability in the ongoing brain activity not time-locked to the event of interest. These studies thus left unresolved whether spontaneous variations in the brain-state immediately preceding unpredictable inhibition-triggering stimuli also influence inhibitory control performance. To address this question, we applied single-trial EEG topographic analyses on the time interval immediately preceding NoGo stimuli in conditions where the responses to NoGo trials were correctly inhibited [correct rejection (CR)] vs. committed [false alarms (FAs)] during an auditory spatial Go/NoGo task. We found a specific configuration of the EEG voltage field manifesting more frequently before correctly inhibited responses to NoGo stimuli than before FAs. There was no evidence for an EEG topography occurring more frequently before FAs than before CR. The visualization of distributed electrical source estimations of the EEG topography preceding successful response inhibition suggested that it resulted from the activity of a right fronto-parietal brain network. Our results suggest that the fluctuations in the ongoing brain activity immediately preceding stimulus presentation contribute to the behavioral outcomes during an inhibitory control task. Our results further suggest that the state-dependency of sensory-cognitive processing might not only concern perceptual processes, but also high-order, top-down inhibitory control mechanisms.

Abnormal cortical network activation in human amnesia: A high-resolution evoked potential study.

Little is known about how human amnesia affects the activation of cortical networks during memory processing. In this study, we recorded high-density evoked potentials in 12 healthy control subjects and 11 amnesic patients with various types of brain damage affecting the medial temporal lobes, diencephalic structures, or both. Subjects performed a continuous recognition task composed of meaningful designs. Using whole-scalp spatiotemporal mapping techniques, we found that, during the first 200 ms following picture presentation, map configuration of amnesics and controls were indistinguishable. Beyond this period, processing significantly differed. Between 200 and 350 ms, amnesic patients expressed different topographical maps than controls in response to new and repeated pictures. From 350 to 550 ms, healthy subjects showed modulation of the same maps in response to new and repeated items. In amnesics, by contrast, presentation of repeated items induced different maps, indicating distinct cortical processing of new and old information. The study indicates that cortical mechanisms underlying memory formation and re-activation in amnesia fundamentally differ from normal memory processing.

A new approach to accurate measurement of uniaxial joint angles based on a combination of accelerometers and gyroscopes.

A new method of measuring joint angle using a combination of accelerometers and gyroscopes is presented. The method proposes a minimal sensor configuration with one sensor module mounted on each segment. The model is based on estimating the acceleration of the joint center of rotation by placing a pair of virtual sensors on the adjacent segments at the center of rotation. In the proposed technique, joint angles are found without the need for integration, so absolute angles can be obtained which are free from any source of drift. The model considers anatomical aspects and is personalized for each subject prior to each measurement. The method was validated by measuring knee flexion-extension angles of eight subjects, walking at three different speeds, and comparing the results with a reference motion measurement system. The results are very close to those of the reference system presenting very small errors (rms = 1.3, mean = 0.2, SD = 1.1 deg) and excellent correlation coefficients (0.997). The algorithm is able to provide joint angles in real-time, and ready for use in gait analysis. Technically, the system is portable, easily mountable, and can be used for long term monitoring without hindrance to natural activities.

Fate of linear and supercoiled multinucleosomic templates during transcription.

Electron microscopy was used to monitor the fate of reconstituted nucleosome cores during in vitro transcription of long linear and supercoiled multinucleosomic templates by the prokaryotic T7 RNA polymerase and the eukaryotic RNA polymerase II. Transcription by T7 RNA polymerase disrupted the nucleosomal configuration in the transcribed region, while nucleosomes were preserved upstream of the transcription initiation site and in front of the polymerase. Nucleosome disruption was independent of the topology of the template, linear or supercoiled, and of the presence or absence of nucleosome positioning sequences in the transcribed region. In contrast, the nucleosomal configuration was preserved during transcription from the vitellogenin B1 promoter with RNA polymerase II in a rat liver total nuclear extract. However, the persistence of nucleosomes on the template was not RNA polymerase II-specific, but was dependent on another activity present in the nuclear extract. This was demonstrated by addition of the extract to the T7 RNA polymerase transcription reaction, which resulted in retention of the nucleosomal configuration. This nuclear activity, also found in HeLa cell nuclei, is heat sensitive and could not be substituted by nucleoplasmin, chromatin assembly factor (CAF-I) or a combination thereof. Altogether, these results identify a novel nuclear activity, called herein transcription-dependent chromatin stabilizing activity I or TCSA-I, which may be involved in a nucleosome transfer mechanism during transcription.

Plastic brain mechanisms for attaining auditory temporal order judgment proficiency.

Accurate perception of the order of occurrence of sensory information is critical for the building up of coherent representations of the external world from ongoing flows of sensory inputs. While some psychophysical evidence reports that performance on temporal perception can improve, the underlying neural mechanisms remain unresolved. Using electrical neuroimaging analyses of auditory evoked potentials (AEPs), we identified the brain dynamics and mechanism supporting improvements in auditory temporal order judgment (TOJ) during the course of the first vs. latter half of the experiment. Training-induced changes in brain activity were first evident 43-76 ms post stimulus onset and followed from topographic, rather than pure strength, AEP modulations. Improvements in auditory TOJ accuracy thus followed from changes in the configuration of the underlying brain networks during the initial stages of sensory processing. Source estimations revealed an increase in the lateralization of initially bilateral posterior sylvian region (PSR) responses at the beginning of the experiment to left-hemisphere dominance at its end. Further supporting the critical role of left and right PSR in auditory TOJ proficiency, as the experiment progressed, responses in the left and right PSR went from being correlated to un-correlated. These collective findings provide insights on the neurophysiologic mechanism and plasticity of temporal processing of sounds and are consistent with models based on spike timing dependent plasticity.

Political representation in Switzerland : democratic or plutocratic ?

Les inégalités économiques se traduisent-elles dans des inégalités politiques à travers le processus de représentation électorale? Telle est la question centrale de cette thèse qui s'attache, par ailleurs, à investiguer les mécanismes qui tendent à produire une représentation biaisée des préférences politiques des citoyens en fonction de leur statut économique. Focalisé sur le cas de la Suisse et faisant usage des données de l'enquête postélectorale Selects de 2007, ce travail démontre que sur les rares sujets qui divisent les citoyens selon des clivages économiques - la redistribution des richesses et la sécurité sociale en particulier - les élus à l'Assemblée fédérale ont des préférences qui reflètent mieux les opinions des citoyens les plus riches. Cette sous-représentation des opinions des citoyens modestes et de ceux faisant partie du centre de la distribution des revenus peut en partie être attribuée à des différences dans les taux de participation et de connaissance politiques entre ces groupes de citoyens. La thèse met également en évidence le rôle joué par la représentation descriptive - autrement dit, la similitude en termes de statut économique entre les représentants et les représentés - dans la représentation des opinions et intérêts des citoyens. Par ailleurs, la structure du système partisan en Suisse ne reflétant pas la multidimensionnalité des préférences politiques des citoyens, les électeurs ne parviennent pas à traduire la complexité de leurs préférences politiques dans un choix de vote, ce qui, dans la configuration actuelle des forces politiques, tend à favoriser l'élection de représentants aux opinions proches de la droite sur les questions économiques. Enfin, une analyse de la représentation politique au niveau cantonal tend à soutenir la thèse selon laquelle le manque de régulation en matière de financement des partis en Suisse pourrait partiellement expliquer les inégalités dans la représentation des opinions politiques des citoyens aux revenus distincts. - Do economic inequalities translate into political inequalities through electoral representation? This is the central research question of this thesis, which also investigates the mechanisms that lead to potential economically based inequalities in the representation of citizens' policy preferences. Focusing on the case of Switzerland and making use of data provided by the post- electoral survey Selects 2007, this research demonstrates that regarding the rare policy domains in which the preferences of citizens are clearly linked to economic cleavages - redistribution and social security in particular - members of the Federal Assembly have policy preferences that best reflect the policy preferences of richer citizens. The under-representation of the opinions of relatively poor citizens and of those being the in the middle of the income distribution can be to some extent be explained by differences in political participation and political information across income groups. The thesis also puts forward the role played by descriptive representation - the similarity between representatives and represented in terms of their socioeconomic status - for the representation of citizens' preferences and interests. In addition, the structure of the party system in Switzerland does not reflect the multidimensionality of policy preferences among citizens who, as a result, have a hard time translating their complex preferences into a vote choice. Given the configuration of political actors, this tends to favour the election of representatives from the right who do not represent the preferences of their voters on economic issues. Finally, an analysis of representation at the cantonal level tends to confirm that the lack of party finance regulations in Switzerland may partially explain inequalities in the representation of citizens with different levels of income.

Pi*-pi* bonding interactions generated by halogen oxidation of zirconium(IV) redox-active ligand complexes.

The new complex, [Zr(pda)2]n (1, pda2- = N,N'-bis(neo-pentyl)-ortho-phenylenediamide, n = 1 or 2), prepared by the reaction of 2 equiv of pdaLi2 with ZrCl4, reacts rapidly with halogen oxidants to afford the new product ZrX2(disq)2 (3, X = Cl, Br, I; disq- = N,N'-bis(neo-pentyl)-ortho-diiminosemiquinonate) in which each redox-active ligand has been oxidized by one electron. The oxidation products 3a-c have been structurally characterized and display an unusual parallel stacked arrangement of the disq- ligands in the solid state, with a separation of approximately 3 A. Density functional calculations show a bonding-type interaction between the SOMOs of the disq- ligands to form a unique HOMO while the antibonding linear combination forms a unique LUMO. This orbital configuration leads to a closed-shell-singlet ground-state electron configuration (S = 0). Temperature-dependent magnetism measurements indicate a low-lying triplet excited state at approximately 750 cm-1. In solution, 3a-c show strong disq--based absorption bands that are invariant across the halide series. Taken together these spectroscopic measurements provide experimental values for the one- and two-electron energies that characterize the pi-stacked bonding interaction between the two disq- ligands.

Les collectifs d'hommes autour de la condition masculine en Suisse: état des lieux

Depuis le début des années 70 en Suisse, suite aux changements de configuration entre les sexes, certains hommes se réunissent autour de problématiques en lien avec la masculinité. Qu'ils se posent en soutien, en opposition ou dans le prolongement de débats initiés par le féminisme, ils contribuent à redéfinir et à diffuser de nouveaux modèles de masculinité dans la société.Since the 70's, men in Switzerland have gathered in response to status changes and to social discourses and actions held by feminists. Either as a challenge or as a support of feminist ideas, men's movements have contributed to redefine, create and spread a wide range of representations regarding masculinity.