The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.

Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.

Extension of ultrasound Fourier slice Imaging theory to sectorial acquisition

Ultrasound image reconstruction from the echoes received by an ultrasound probe after the transmission of diverging waves is an active area of research because of its capacity to insonify at ultra-high frame rate with large regions of interest using small phased arrays as the ones used in echocardiography. Current state-of-the-art techniques are based on the emission of diverging waves and the use of delay and sum strategies applied on the received signals to reconstruct the desired image (DW/DAS). Recently, we have introduced the concept of Ultrasound Fourier Slice Imaging (UFSI) theory for the reconstruction of ultrafast imaging for linear acquisition. In this study, we extend this theory to sectorial acquisition thanks to the introduction of an explicit and invertible spatial transform. Starting from a diverging wave, we show that the direct use of UFSI theory along with the application of the proposed spatial transform allows reconstructing the insonified medium in the conventional Cartesian space. Simulations and experiments reveal the capacity of this new approach in obtaining competitive quality of ultrafast imaging when compared with the current reference method.

Seismic characterization of heterogeneous sedimentary and fractured rocks based on Biot's theory of poroelasticity

Understanding and quantifying seismic energy dissipation, which manifests itself in terms of velocity dispersion and attenuation, in fluid-saturated porous rocks is of considerable interest, since it offers the perspective of extracting information with regard to the elastic and hydraulic rock properties. There is increasing evidence to suggest that wave-induced fluid flow, or simply WIFF, is the dominant underlying physical mechanism governing these phenomena throughout the seismic, sonic, and ultrasonic frequency ranges. This mechanism, which can prevail at the microscopic, mesoscopic, and macroscopic scale ranges, operates through viscous energy dissipation in response to fluid pressure gradients and inertial effects induced by the passing wavefield. In the first part of this thesis, we present an analysis of broad-band multi-frequency sonic log data from a borehole penetrating water-saturated unconsolidated glacio-fluvial sediments. An inherent complication arising in the interpretation of the observed P-wave attenuation and velocity dispersion is, however, that the relative importance of WIFF at the various scales is unknown and difficult to unravel. An important generic result of our work is that the levels of attenuation and velocity dispersion due to the presence of mesoscopic heterogeneities in water-saturated unconsolidated clastic sediments are expected to be largely negligible. Conversely, WIFF at the macroscopic scale allows for explaining most of the considered data while refinements provided by including WIFF at the microscopic scale in the analysis are locally meaningful. Using a Monte-Carlo-type inversion approach, we compare the capability of the different models describing WIFF at the macroscopic and microscopic scales with regard to their ability to constrain the dry frame elastic moduli and the permeability as well as their local probability distribution. In the second part of this thesis, we explore the issue of determining the size of a representative elementary volume (REV) arising in the numerical upscaling procedures of effective seismic velocity dispersion and attenuation of heterogeneous media. To this end, we focus on a set of idealized synthetic rock samples characterized by the presence of layers, fractures or patchy saturation in the mesocopic scale range. These scenarios are highly pertinent because they tend to be associated with very high levels of velocity dispersion and attenuation caused by WIFF in the mesoscopic scale range. The problem of determining the REV size for generic heterogeneous rocks is extremely complex and entirely unexplored in the given context. In this pilot study, we have therefore focused on periodic media, which assures the inherent self- similarity of the considered samples regardless of their size and thus simplifies the problem to a systematic analysis of the dependence of the REV size on the applied boundary conditions in the numerical simulations. Our results demonstrate that boundary condition effects are absent for layered media and negligible in the presence of patchy saturation, thus resulting in minimum REV sizes. Conversely, strong boundary condition effects arise in the presence of a periodic distribution of finite-length fractures, thus leading to large REV sizes. In the third part of the thesis, we propose a novel effective poroelastic model for periodic media characterized by mesoscopic layering, which accounts for WIFF at both the macroscopic and mesoscopic scales as well as for the anisotropy associated with the layering. Correspondingly, this model correctly predicts the existence of the fast and slow P-waves as well as quasi and pure S-waves for any direction of wave propagation as long as the corresponding wavelengths are much larger than the layer thicknesses. The primary motivation for this work is that, for formations of intermediate to high permeability, such as, for example, unconsolidated sediments, clean sandstones, or fractured rocks, these two WIFF mechanisms may prevail at similar frequencies. This scenario, which can be expected rather common, cannot be accounted for by existing models for layered porous media. Comparisons of analytical solutions of the P- and S-wave phase velocities and inverse quality factors for wave propagation perpendicular to the layering with those obtained from numerical simulations based on a ID finite-element solution of the poroelastic equations of motion show very good agreement as long as the assumption of long wavelengths remains valid. A limitation of the proposed model is its inability to account for inertial effects in mesoscopic WIFF when both WIFF mechanisms prevail at similar frequencies. Our results do, however, also indicate that the associated error is likely to be relatively small, as, even at frequencies at which both inertial and scattering effects are expected to be at play, the proposed model provides a solution that is remarkably close to its numerical benchmark. -- Comprendre et pouvoir quantifier la dissipation d'énergie sismique qui se traduit par la dispersion et l'atténuation des vitesses dans les roches poreuses et saturées en fluide est un intérêt primordial pour obtenir des informations à propos des propriétés élastique et hydraulique des roches en question. De plus en plus d'études montrent que le déplacement relatif du fluide par rapport au solide induit par le passage de l'onde (wave induced fluid flow en anglais, dont on gardera ici l'abréviation largement utilisée, WIFF), représente le principal mécanisme physique qui régit ces phénomènes, pour la gamme des fréquences sismiques, sonique et jusqu'à l'ultrasonique. Ce mécanisme, qui prédomine aux échelles microscopique, mésoscopique et macroscopique, est lié à la dissipation d'énergie visqueuse résultant des gradients de pression de fluide et des effets inertiels induits par le passage du champ d'onde. Dans la première partie de cette thèse, nous présentons une analyse de données de diagraphie acoustique à large bande et multifréquences, issues d'un forage réalisé dans des sédiments glaciaux-fluviaux, non-consolidés et saturés en eau. La difficulté inhérente à l'interprétation de l'atténuation et de la dispersion des vitesses des ondes P observées, est que l'importance des WIFF aux différentes échelles est inconnue et difficile à quantifier. Notre étude montre que l'on peut négliger le taux d'atténuation et de dispersion des vitesses dû à la présence d'hétérogénéités à l'échelle mésoscopique dans des sédiments clastiques, non- consolidés et saturés en eau. A l'inverse, les WIFF à l'échelle macroscopique expliquent la plupart des données, tandis que les précisions apportées par les WIFF à l'échelle microscopique sont localement significatives. En utilisant une méthode d'inversion du type Monte-Carlo, nous avons comparé, pour les deux modèles WIFF aux échelles macroscopique et microscopique, leur capacité à contraindre les modules élastiques de la matrice sèche et la perméabilité ainsi que leur distribution de probabilité locale. Dans une seconde partie de cette thèse, nous cherchons une solution pour déterminer la dimension d'un volume élémentaire représentatif (noté VER). Cette problématique se pose dans les procédures numériques de changement d'échelle pour déterminer l'atténuation effective et la dispersion effective de la vitesse sismique dans un milieu hétérogène. Pour ce faire, nous nous concentrons sur un ensemble d'échantillons de roches synthétiques idéalisés incluant des strates, des fissures, ou une saturation partielle à l'échelle mésoscopique. Ces scénarios sont hautement pertinents, car ils sont associés à un taux très élevé d'atténuation et de dispersion des vitesses causé par les WIFF à l'échelle mésoscopique. L'enjeu de déterminer la dimension d'un VER pour une roche hétérogène est très complexe et encore inexploré dans le contexte actuel. Dans cette étude-pilote, nous nous focalisons sur des milieux périodiques, qui assurent l'autosimilarité des échantillons considérés indépendamment de leur taille. Ainsi, nous simplifions le problème à une analyse systématique de la dépendance de la dimension des VER aux conditions aux limites appliquées. Nos résultats indiquent que les effets des conditions aux limites sont absents pour un milieu stratifié, et négligeables pour un milieu à saturation partielle : cela résultant à des dimensions petites des VER. Au contraire, de forts effets des conditions aux limites apparaissent dans les milieux présentant une distribution périodique de fissures de taille finie : cela conduisant à de grandes dimensions des VER. Dans la troisième partie de cette thèse, nous proposons un nouveau modèle poro- élastique effectif, pour les milieux périodiques caractérisés par une stratification mésoscopique, qui prendra en compte les WIFF à la fois aux échelles mésoscopique et macroscopique, ainsi que l'anisotropie associée à ces strates. Ce modèle prédit alors avec exactitude l'existence des ondes P rapides et lentes ainsi que les quasis et pures ondes S, pour toutes les directions de propagation de l'onde, tant que la longueur d'onde correspondante est bien plus grande que l'épaisseur de la strate. L'intérêt principal de ce travail est que, pour les formations à perméabilité moyenne à élevée, comme, par exemple, les sédiments non- consolidés, les grès ou encore les roches fissurées, ces deux mécanismes d'WIFF peuvent avoir lieu à des fréquences similaires. Or, ce scénario, qui est assez commun, n'est pas décrit par les modèles existants pour les milieux poreux stratifiés. Les comparaisons des solutions analytiques des vitesses des ondes P et S et de l'atténuation de la propagation des ondes perpendiculaires à la stratification, avec les solutions obtenues à partir de simulations numériques en éléments finis, fondées sur une solution obtenue en 1D des équations poro- élastiques, montrent un très bon accord, tant que l'hypothèse des grandes longueurs d'onde reste valable. Il y a cependant une limitation de ce modèle qui est liée à son incapacité à prendre en compte les effets inertiels dans les WIFF mésoscopiques quand les deux mécanismes d'WIFF prédominent à des fréquences similaires. Néanmoins, nos résultats montrent aussi que l'erreur associée est relativement faible, même à des fréquences à laquelle sont attendus les deux effets d'inertie et de diffusion, indiquant que le modèle proposé fournit une solution qui est remarquablement proche de sa référence numérique.

A feed-forward spiking model of shape-coding by IT cells

The ability to recognize a shape is linked to figure-ground (FG) organization. Cell preferences appear to be correlated across contrast-polarity reversals and mirror reversals of polygon displays, but not so much across FG reversals. Here we present a network structure which explains both shape-coding by simulated IT cells and suppression of responses to FG reversed stimuli. In our model FG segregation is achieved before shape discrimination, which is itself evidenced by the difference in spiking onsets of a pair of output cells. The studied example also includes feature extraction and illustrates a classification of binary images depending on the dominance of vertical or horizontal borders.

Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae.

Accurate perception of taste information is crucial for animal survival. In adult Drosophila, gustatory receptor neurons (GRNs) perceive chemical stimuli of one specific gustatory modality associated with a stereotyped behavioural response, such as aversion or attraction. We show that GRNs of Drosophila larvae employ a surprisingly different mode of gustatory information coding. Using a novel method for calcium imaging in the larval gustatory system, we identify a multimodal GRN that responds to chemicals of different taste modalities with opposing valence, such as sweet sucrose and bitter denatonium, reliant on different sensory receptors. This multimodal neuron is essential for bitter compound avoidance, and its artificial activation is sufficient to mediate aversion. However, the neuron is also essential for the integration of taste blends. Our findings support a model for taste coding in larvae, in which distinct receptor proteins mediate different responses within the same, multimodal GRN.

A Write-Based Solver for SAT Modulo the Theory of Arrays

The extensional theory of arrays is one of the most important ones for applications of SAT Modulo Theories (SMT) to hardware and software verification. Here we present a new T-solver for arrays in the context of the DPLL(T) approach to SMT. The main characteristics of our solver are: (i) no translation of writes into reads is needed, (ii) there is no axiom instantiation, and (iii) the T-solver interacts with the Boolean engine by asking to split on equality literals between indices. As far as we know, this is the first accurate description of an array solver integrated in a state-of-the-art SMT solver and, unlike most state-of-the-art solvers, it is not based on a lazy instantiation of the array axioms. Moreover, it is very competitive in practice, specially on problems that require heavy reasoning on array literals

Under what conditions? Therapist and client characteristics moderate the role of change talk in brief motivational intervention.

OBJECTIVE: Client change talk has been proposed as a mechanism of change in motivational interviewing (MI) by mediating the link between therapist MI-consistent behaviors (MICO) and client behavioral outcomes. We tested under what circumstances this mechanism was supported in the context of a clinical trial of brief MI for heavy drinking among nontreatment seeking young men. METHOD: We conducted psycholinguistic coding of 174 sessions using the MI Skill Code 2.1 and derived the frequency of MICO and the strength of change talk (CTS) averaged over the session. CTS was examined as a mediator of the relationship between MICO and a drinking composite score measured at 3-month follow-up, controlling for the composite measure at baseline. Finally, we tested therapist gender and MI experience as well as client readiness to change and alcohol problem severity as moderators of this mediation model. RESULTS: CTS significantly predicted outcome (higher strength related to less drinking), but MICO did not predict CTS. However, CTS mediated the relationship between MICO and drinking outcomes when therapists had more experience in MI and when clients had more severe alcohol problems (i.e., significant conditional indirect effects). CONCLUSIONS: The mechanism hypothesized by MI theory was operative in our brief MI with heavy drinking young men, but only under particular conditions. Our results suggest that attention should be paid to therapist selection, training, and/or supervision until they reach a certain level of competence, and that MI might not be appropriate for nontreatment seeking clients drinking at a lower level of risk. (PsycINFO Database Record

Concepts and Reference. Defending a Dual Theory of Natural Kind Concepts

In this thesis I argue that the psychological study of concepts and categorisation, and the philosophical study of reference are deeply intertwined. I propose that semantic intuitions are a variety of categorisation judgements, determined by concepts, and that because of this, concepts determine reference. I defend a dual theory of natural kind concepts, according to which natural kind concepts have distinct semantic cores and non-semantic identification procedures. Drawing on psychological essentialism, I suggest that the cores consist of externalistic placeholder essence beliefs. The identification procedures, in turn, consist of prototypes, sets of exemplars, or possibly also theory-structured beliefs. I argue that the dual theory is motivated both by experimental data and theoretical considerations. The thesis consists of three interrelated articles. Article I examines philosophical causal and description theories of natural kind term reference, and argues that they involve, or need to involve, certain psychological elements. I propose a unified theory of natural kind term reference, built on the psychology of concepts. Article II presents two semantic adaptations of psychological essentialism, one of which is a strict externalistic Kripkean-Putnamian theory, while the other is a hybrid account, according to which natural kind terms are ambiguous between internalistic and externalistic senses. We present two experiments, the results of which support the strict externalistic theory. Article III examines Fodor’s influential atomistic theory of concepts, according to which no psychological capacities associated with concepts constitute them, or are necessary for reference. I argue, contra Fodor, that the psychological mechanisms are necessary for reference.

Statistical Inversion Theory in X-ray Tomography

In this thesis the X-ray tomography is discussed from the Bayesian statistical viewpoint. The unknown parameters are assumed random variables and as opposite to traditional methods the solution is obtained as a large sample of the distribution of all possible solutions. As an introduction to tomography an inversion formula for Radon transform is presented on a plane. The vastly used filtered backprojection algorithm is derived. The traditional regularization methods are presented sufficiently to ground the Bayesian approach. The measurements are foton counts at the detector pixels. Thus the assumption of a Poisson distributed measurement error is justified. Often the error is assumed Gaussian, altough the electronic noise caused by the measurement device can change the error structure. The assumption of Gaussian measurement error is discussed. In the thesis the use of different prior distributions in X-ray tomography is discussed. Especially in severely ill-posed problems the use of a suitable prior is the main part of the whole solution process. In the empirical part the presented prior distributions are tested using simulated measurements. The effect of different prior distributions produce are shown in the empirical part of the thesis. The use of prior is shown obligatory in case of severely ill-posed problem.