A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

Generation and nonlinear evolution of shore-oblique/transverse sand bars

The coupling between topography, waves and currents in the surf zone may selforganize to produce the formation of shore-transverse or shore-oblique sand bars on an otherwise alongshore uniform beach. In the absence of shore-parallel bars, this has been shown by previous studies of linear stability analysis, but is now extended to the finite-amplitude regime. To this end, a nonlinear model coupling wave transformation and breaking, a shallow-water equations solver, sediment transport and bed updating is developed. The sediment flux consists of a stirring factor multiplied by the depthaveraged current plus a downslope correction. It is found that the cross-shore profile of the ratio of stirring factor to water depth together with the wave incidence angle primarily determine the shape and the type of bars, either transverse or oblique to the shore. In the latter case, they can open an acute angle against the current (upcurrent oriented) or with the current (down-current oriented). At the initial stages of development, both the intensity of the instability which is responsible for the formation of the bars and the damping due to downslope transport grow at a similar rate with bar amplitude, the former being somewhat stronger. As bars keep on growing, their finite-amplitude shape either enhances downslope transport or weakens the instability mechanism so that an equilibrium between both opposing tendencies occurs, leading to a final saturated amplitude. The overall shape of the saturated bars in plan view is similar to that of the small-amplitude ones. However, the final spacings may be up to a factor of 2 larger and final celerities can also be about a factor of 2 smaller or larger. In the case of alongshore migrating bars, the asymmetry of the longshore sections, the lee being steeper than the stoss, is well reproduced. Complex dynamics with merging and splitting of individual bars sometimes occur. Finally, in the case of shore-normal incidence the rip currents in the troughs between the bars are jet-like while the onshore return flow is wider and weaker as is observed in nature.

Iowa Historic Property Study: Iowana Farms Milk Company, 1416 State Street, City of Bettendorf, Scott County, Iowa, 2012

The Iowana Farms Milk Company factory building was considered to retain sufficient integrity and possess sufficient significance to be considered eligible for the National Register of Historic Places under Criteria A and C for its historical and architectural significance in the Bettendorf community. The Iowana Farms Milk Company was an important early to mid-twentieth-century business in Bettendorf, and was among the few that was not owned or operated by the Bettendorf Company. It was a strong and thriving business for many years, and its products were well known in the Quad Cities region. The importance of this property becomes even more significant when one considers that most of the buildings once associated with the actual Bettendorf Company, which was undeniably the most important business and industry in town, are now gone. As a result, the Iowana Farms Milk Company factory building was a physical vestige of the once-thriving commercial industries that made Bettendorf into a city in the twentieth century. This property was further significant for its representation of the evolution of the dairy industry in the twentieth century from farm to factory production. It also reflected the changes to the industry based on scientific discoveries, mechanical innovations, and governmental regulations related to improved sanitation and the pure milk movement. The Iowana Farms Milk Company represented a model plant for the time, and the marketing strategies it employed followed the trends of the industry. The Iowana Farms Milk Company plant had to be removed to make room for a new I-74 bridge over the Mississippi River at Bettendorf. The construction of the new bridge also required removal of the historic Iowa-Illinois Memorial Bridge. The documentation reported herein and for that of the Iowa-Illinois Memorial Bridge fulfills the requirements of the Memorandum of Agreement regarding the removal of these historic properties.

Blind channel deconvolution of real world signals using source separation techniques

In this paper we present a method for blind deconvolution of linear channels based on source separation techniques, for real word signals. This technique applied to blind deconvolution problems is based in exploiting not the spatial independence between signals but the temporal independence between samples of the signal. Our objective is to minimize the mutual information between samples of the output in order to retrieve the original signal. In order to make use of use this idea the input signal must be a non-Gaussian i.i.d. signal. Because most real world signals do not have this i.i.d. nature, we will need to preprocess the original signal before the transmission into the channel. Likewise we should assure that the transmitted signal has non-Gaussian statistics in order to achieve the correct function of the algorithm. The strategy used for this preprocessing will be presented in this paper. If the receiver has the inverse of the preprocess, the original signal can be reconstructed without the convolutive distortion.

Pluralité des corps. 1. Les corps de La medicine [Multifaceted body. I. The bodies of medicine].

Le corps humain est l'objet privilégié d'action de la médecine, mais aussi réalité vécue, image, symbole, représentation et l'objet d'interprétation et de théorisation. Tous ces éléments constitutifs du corps influencent la façon dont la médecine le traite. Dans cette série de trois articles, nous abordons le corps sous différentes perspectives : médicale (1), phénoménologique (2), psychosomatique et socio-anthropologique (3). Ce premier article traite des représentations du corps en médecine, dont nous décrivons quatre types distincts, qui renvoient à autant de démarches scientifiques spécifiques et de formes de légitimité clinique : le corps-objet de l'anatomie, le corps-machine de la physiologie, le corps cybernétique de la biologie et le corps statistique de l'épidémiologie. The human body is the object upon which medicine is acting, but also lived reality, image, symbol, representation and the object of elaboration and theory. All these elements which constitute the body influence the way medicine is treating it. In this series of three articles, we address the human body from various perspectives: medical (1), phenomenological (2), psychosomatic and socio-anthropological (3). This first article discusses four distinct types of representation of the body within medicine, each related to a specific epistemology and shaping a distinct kind of clinical legitimacy: the body-object of anatomy, the body-machine of physiology, the cybernetic body of biology, the statistical body of epidemiology.

Organization and plasticity of auditory spatial representations

Spatial hearing refers to a set of abilities enabling us to determine the location of sound sources, redirect our attention toward relevant acoustic events, and recognize separate sound sources in noisy environments. Determining the location of sound sources plays a key role in the way in which humans perceive and interact with their environment. Deficits in sound localization abilities are observed after lesions to the neural tissues supporting these functions and can result in serious handicaps in everyday life. These deficits can, however, be remediated (at least to a certain degree) by the surprising capacity of reorganization that the human brain possesses following damage and/or learning, namely, the brain plasticity. In this thesis, our aim was to investigate the functional organization of auditory spatial functions and the learning-induced plasticity of these functions. Overall, we describe the results of three studies. The first study entitled "The role of the right parietal cortex in sound localization: A chronometric single pulse transcranial magnetic stimulation study" (At et al., 2011), study A, investigated the role of the right parietal cortex in spatial functions and its chronometry (i.e. the critical time window of its contribution to sound localizations). We concentrated on the behavioral changes produced by the temporarily inactivation of the parietal cortex with transcranial magnetic stimulation (TMS). We found that the integrity of the right parietal cortex is crucial for localizing sounds in the space and determined a critical time window of its involvement, suggesting a right parietal dominance for auditory spatial discrimination in both hemispaces. In "Distributed coding of the auditory space in man: evidence from training-induced plasticity" (At et al., 2013a), study B, we investigated the neurophysiological correlates and changes of the different sub-parties of the right auditory hemispace induced by a multi-day auditory spatial training in healthy subjects with electroencephalography (EEG). We report a distributed coding for sound locations over numerous auditory regions, particular auditory areas code specifically for precise parts of the auditory space, and this specificity for a distinct region is enhanced with training. In the third study "Training-induced changes in auditory spatial mismatch negativity" (At et al., 2013b), study C, we investigated the pre-attentive neurophysiological changes induced with a training over 4 days in healthy subjects with a passive mismatch negativity (MMN) paradigm. We showed that training changed the mechanisms for the relative representation of sound positions and not the specific lateralization themselves and that it changed the coding in right parahippocampal regions. - L'audition spatiale désigne notre capacité à localiser des sources sonores dans l'espace, de diriger notre attention vers les événements acoustiques pertinents et de reconnaître des sources sonores appartenant à des objets distincts dans un environnement bruyant. La localisation des sources sonores joue un rôle important dans la façon dont les humains perçoivent et interagissent avec leur environnement. Des déficits dans la localisation de sons sont souvent observés quand les réseaux neuronaux impliqués dans cette fonction sont endommagés. Ces déficits peuvent handicaper sévèrement les patients dans leur vie de tous les jours. Cependant, ces déficits peuvent (au moins à un certain degré) être réhabilités grâce à la plasticité cérébrale, la capacité du cerveau humain à se réorganiser après des lésions ou un apprentissage. L'objectif de cette thèse était d'étudier l'organisation fonctionnelle de l'audition spatiale et la plasticité induite par l'apprentissage de ces fonctions. Dans la première étude intitulé « The role of the right parietal cortex in sound localization : A chronometric single pulse study » (At et al., 2011), étude A, nous avons examiné le rôle du cortex pariétal droit dans l'audition spatiale et sa chronométrie, c'est-à- dire le moment critique de son intervention dans la localisation de sons. Nous nous sommes concentrés sur les changements comportementaux induits par l'inactivation temporaire du cortex pariétal droit par le biais de la Stimulation Transcrânienne Magnétique (TMS). Nous avons démontré que l'intégrité du cortex pariétal droit est cruciale pour localiser des sons dans l'espace. Nous avons aussi défini le moment critique de l'intervention de cette structure. Dans « Distributed coding of the auditory space : evidence from training-induced plasticity » (At et al., 2013a), étude B, nous avons examiné la plasticité cérébrale induite par un entraînement des capacités de discrimination auditive spatiale de plusieurs jours. Nous avons montré que le codage des positions spatiales est distribué dans de nombreuses régions auditives, que des aires auditives spécifiques codent pour des parties données de l'espace et que cette spécificité pour des régions distinctes est augmentée par l'entraînement. Dans « Training-induced changes in auditory spatial mismatch negativity » (At et al., 2013b), étude C, nous avons examiné les changements neurophysiologiques pré- attentionnels induits par un entraînement de quatre jours. Nous avons montré que l'entraînement modifie la représentation des positions spatiales entraînées et non-entrainées, et que le codage de ces positions est modifié dans des régions parahippocampales.

Statistical mechanics of multi-edge networks

Statistical properties of binary complex networks are well understood and recently many attempts have been made to extend this knowledge to weighted ones. There are, however, subtle yet important considerations to be made regarding the nature of the weights used in this generalization. Weights can be either continuous or discrete magnitudes, and in the latter case, they can additionally have undistinguishable or distinguishable nature. This fact has not been addressed in the literature insofar and has deep implications on the network statistics. In this work we face this problem introducing multiedge networks as graphs where multiple (distinguishable) connections between nodes are considered. We develop a statistical mechanics framework where it is possible to get information about the most relevant observables given a large spectrum of linear and nonlinear constraints including those depending both on the number of multiedges per link and their binary projection. The latter case is particularly interesting as we show that binary projections can be understood from multiedge processes. The implications of these results are important as many real-agent-based problems mapped onto graphs require this treatment for a proper characterization of their collective behavior.

Evaluation of Hot Mix Asphalt Moisture Sensitivity Using the Nottingham Asphalt Test Equipment, TR-555, 2010

Pavements are subjected to different stresses during their design lives. A properly designed pavement will perform adequately during its design life, and the distresses will not exceed the allowable limits; however, there are several factors that can lead to premature pavement failure. One such factor is moisture sensitivity. AASHTO T 283 is the standard test used in the moisture susceptibility evaluation of asphalt mixtures, but the results of the test are not very representative of the expected behavior of asphalt mixtures. The dynamic modulus test measures a fundamental property of the mixture. The results of the dynamic modulus test can be used directly in the Mechanistic-Empirical Pavement Design Guide (MEPDG) and are considered a very good representation of the expected field performance of the mixture. Further research is still needed to study how the dynamic modulus results are affected by moisture. The flow number test was studied in previous research as a candidate test for moisture-susceptibility evaluation, but the results of that research were not favorable. This research has four main objectives. The first objective of this research is to evaluate the usefulness of the dynamic modulus and flow number tests in moisture-susceptibility evaluation. The second objective is to compare the results to those achieved using the AASHTO T 283 test. The third objective is to study the effect of different methods of sample conditioning and testing conditions. The fourth objective of the research is to study the variability in the test results.

Classification of very high spatial resolution imagery using mathematical morphology and support vector machines

We investigate the relevance of morphological operators for the classification of land use in urban scenes using submetric panchromatic imagery. A support vector machine is used for the classification. Six types of filters have been employed: opening and closing, opening and closing by reconstruction, and opening and closing top hat. The type and scale of the filters are discussed, and a feature selection algorithm called recursive feature elimination is applied to decrease the dimensionality of the input data. The analysis performed on two QuickBird panchromatic images showed that simple opening and closing operators are the most relevant for classification at such a high spatial resolution. Moreover, mixed sets combining simple and reconstruction filters provided the best performance. Tests performed on both images, having areas characterized by different architectural styles, yielded similar results for both feature selection and classification accuracy, suggesting the generalization of the feature sets highlighted.

Spatial visualization of DNA in solution.

An image analysis method is presented which allows for the reconstruction of the three-dimensional path of filamentous objects from two of their projections. Starting with stereo pairs, this method is used to trace the trajectory of DNA molecules embedded in vitreous ice and leads to a faithful representation of their three-dimensional shape in solution. This computer-aided reconstruction is superior to the subjective three-dimensional impression generated by observation of stereo pairs of micrographs because it enables one to look at the reconstructed molecules from any chosen direction and distance and allows quantitative analysis such as determination of distances, curvature, persistence length, and writhe of DNA molecules in solution.