Using graphical probability analysis (Bayes Nets) to evaluate a conditional DNA inclusion

This paper discusses the analysis of cases in which the inclusion or exclusion of a particular suspect, as a possible contributor to a DNA mixture, depends on the value of a variable (the number of contributors) that cannot be determined with certainty. It offers alternative ways to deal with such cases, including sensitivity analysis and object-oriented Bayesian networks, that separate uncertainty about the inclusion of the suspect from uncertainty about other variables. The paper presents a case study in which the value of DNA evidence varies radically depending on the number of contributors to a DNA mixture: if there are two contributors, the suspect is excluded; if there are three or more, the suspect is included; but the number of contributors cannot be determined with certainty. It shows how an object-oriented Bayesian network can accommodate and integrate varying perspectives on the unknown variable and how it can reduce the potential for bias by directing attention to relevant considerations and distinguishing different sources of uncertainty. It also discusses the challenge of presenting such evidence to lay audiences.

The adaptive dynamics of niche constructing traits in spatially subdivided populations: evolving posthumous extended phenotypes.

Niche construction, by which organisms modify the environment in which they live, has been proposed to affect the evolution of many phenotypic traits. But what about the evolution of a niche constructing trait itself, whose expression changes the pattern of natural selection to which the trait is exposed in subsequent generations? This article provides an inclusive fitness analysis of selection on niche constructing phenotypes, which can affect their environment from local to global scales in arbitrarily spatially subdivided populations. The model shows that phenotypic effects of genes extending far beyond the life span of the actor can be affected by natural selection, provided they modify the fitness of those individuals living in the future that are likely to have inherited the niche construction lineage of the actor. Present benefits of behaviors are thus traded off against future indirect costs. The future costs will generally result from a complicated interplay of phenotypic effects, population demography and environmental dynamics. To illustrate these points, I derive the adaptive dynamics of a trait involved in the consumption of an abiotic resource, where resource abundance in future generations feeds back to the evolutionary dynamics of the trait.

Accurate memory for object location by individuals with intellectual disability: Absolute spatial tagging instead of configural processing?

Using head-mounted eye tracker material, we assessed spatial recognition abilities (e.g., reaction to object permutation, removal or replacement with a new object) in participants with intellectual disabilities. The "Intellectual Disabilities (ID)" group (n=40) obtained a score totalling a 93.7% success rate, whereas the "Normal Control" group (n=40) scored 55.6% and took longer to fix their attention on the displaced object. The participants with an intellectual disability thus had a more accurate perception of spatial changes than controls. Interestingly, the ID participants were more reactive to object displacement than to removal of the object. In the specific test of novelty detection, however, the scores were similar, the two groups approaching 100% detection. Analysis of the strategies expressed by the ID group revealed that they engaged in more systematic object checking and were more sensitive than the control group to changes in the structure of the environment. Indeed, during the familiarisation phase, the "ID" group explored the collection of objects more slowly, and fixed their gaze for a longer time upon a significantly lower number of fixation points during visual sweeping.

Population density and optimal body size.

The population density of an organism is one of the main aspects of its environment, and shoud therefore strongly influence its adaptive strategy. The r/K theory, based on the logistic model, was developed to formalize this influence. K-selectioon is classically thought to favour large body sizes. This prediction, however, cannot be directly derived from the logistic model: some auxiliary hypotheses are therefor implicit. These are to be made explicit if the theory is to be tested. An alternative approach, based on the Euler-Lotka equation, shows that density itself is irrelevant, but that the relative effect of density on adult and juvenile features is crucial. For instance, increasing population will select for a smaller body size if the density affects mainly juvenile growth and/or survival. In this case, density shoud indeed favour large body sizes. The theory appears nevertheless inconsistent, since a probable consequence of increasing body size will be a decrease in the carrying capacity

Evaluation of the potential use of trabecular bone score to complement bone mineral density in the diagnosis of osteoporosis: a preliminary spine BMD-matched, case-control study.

The trabecular bone score (TBS) is a new parameter that is determined from gray-level analysis of dual-energy X-ray absorptiometry (DXA) images. It relies on the mean thickness and volume fraction of trabecular bone microarchitecture. This was a preliminary case-control study to evaluate the potential diagnostic value of TBS as a complement to bone mineral density (BMD), by comparing postmenopausal women with and without fractures. The sample consisted of 45 women with osteoporotic fractures (5 hip fractures, 20 vertebral fractures, and 20 other types of fracture) and 155 women without a fracture. Stratification was performed, taking into account each type of fracture (except hip), and women with and without fractures were matched for age and spine BMD. BMD and TBS were measured at the total spine. TBS measured at the total spine revealed a significant difference between the fracture and age- and spine BMD-matched nonfracture group, when considering all types of fractures and vertebral fractures. In these cases, the diagnostic value of the combination of BMD and TBS likely will be higher compared with that of BMD alone. TBS, as evaluated from standard DXA scans directly, potentially complements BMD in the detection of osteoporotic fractures. Prospective studies are necessary to fully evaluate the potential role of TBS as a complementary risk factor for fracture.

Spatially and genetically distinct control of seed germination by phytochromes A and B.

Phytochromes phyB and phyA mediate a remarkable developmental switch whereby, early upon seed imbibition, canopy light prevents phyB-dependent germination, whereas later on, it stimulates phyA-dependent germination. Using a seed coat bedding assay where the growth of dissected embryos is monitored under the influence of dissected endosperm, allowing combinatorial use of mutant embryos and endosperm, we show that canopy light specifically inactivates phyB activity in the endosperm to override phyA-dependent signaling in the embryo. This interference involves abscisic acid (ABA) release from the endosperm and distinct spatial activities of phytochrome signaling components. Under the canopy, endospermic ABA opposes phyA signaling through the transcription factor (TF) ABI5, which shares with the TF PIF1 several target genes that negatively regulate germination in the embryo. ABI5 enhances the expression of phytochrome signaling genes PIF1, SOMNUS, GAI, and RGA, but also of ABA and gibberellic acid (GA) metabolic genes. Over time, weaker ABA-dependent responses eventually enable phyA-dependent germination, a distinct type of germination driven solely by embryonic growth.

Predictors of developmental dyslexia in European orthographies with varying complexity.

Background:  The relationship between phoneme awareness, rapid automatized naming (RAN), verbal short-term/working memory (ST/WM) and diagnostic category is investigated in control and dyslexic children, and the extent to which this depends on orthographic complexity. Methods:  General cognitive, phonological and literacy skills were tested in 1,138 control and 1,114 dyslexic children speaking six different languages spanning a large range of orthographic complexity (Finnish, Hungarian, German, Dutch, French, English). Results:  Phoneme deletion and RAN were strong concurrent predictors of developmental dyslexia, while verbal ST/WM and general verbal abilities played a comparatively minor role. In logistic regression models, more participants were classified correctly when orthography was more complex. The impact of phoneme deletion and RAN-digits was stronger in complex than in less complex orthographies. Conclusions:  Findings are largely consistent with the literature on predictors of dyslexia and literacy skills, while uniquely demonstrating how orthographic complexity exacerbates some symptoms of dyslexia.

On the use of spatially discrete data to compute energy and mass balance

In many practical applications the state of field soils is monitored by recording the evolution of temperature and soil moisture at discrete depths. We theoretically investigate the systematic errors that arise when mass and energy balances are computed directly from these measurements. We show that, even with no measurement or model errors, large residuals might result when finite difference approximations are used to compute fluxes and storage term. To calculate the limits set by the use of spatially discrete measurements on the accuracy of balance closure, we derive an analytical solution to estimate the residual on the basis of the two key parameters: the penetration depth and the distance between the measurements. When the thickness of the control layer for which the balance is computed is comparable to the penetration depth of the forcing (which depends on the thermal diffusivity and on the forcing period) large residuals arise. The residual is also very sensitive to the distance between the measurements, which requires accurately controlling the position of the sensors in field experiments. We also demonstrate that, for the same experimental setup, mass residuals are sensitively larger than the energy residuals due to the nonlinearity of the moisture transport equation. Our analysis suggests that a careful assessment of the systematic mass error introduced by the use of spatially discrete data is required before using fluxes and residuals computed directly from field measurements.

Effects of Exemestane and Tamoxifen Treatment on Bone Texture Analysis Assessed by TBS in Comparison With Bone Mineral Density Assessed by DXA in Women With Breast Cancer.

We performed an analysis of a substudy of the randomized Tamoxifen Exemestane Adjuvant Multinational trial to determine the effects of exemestane (EXE) and tamoxifen (TAM) adjuvant treatment on bone mineral density (BMD) measured by dual-energy X-ray absorptiometry compared with the trabecular bone score, a novel grey-level texture measurement that correlates with 3-dimensional parameters of bone texture in postmenopausal women with hormone receptor-positive breast cancer for the first time. In total, 36 women were randomized to receive TAM (n = 17) or EXE (n = 19). Patients receiving TAM showed a mean increase of BMD in lumbar spine from baseline of 1.0%, 1.5%, and 1.9% and in trabecular bone score of 2.2%, 3.5%, and 3.3% at 6-, 12-, and 24-mo treatment, respectively. Conversely, patients receiving EXE showed a mean decrease from baseline in lumbar spine BMD of -2.3%, -3.6%, and -5.3% and in trabecular bone score of -0.9%, -1.7%, and -2.3% at 6-, 12-, and 24-mo treatment, respectively. Changes in trabecular bone score from baseline at spine were also significantly different between EXE and TAM: p = 0.05, 0.007, and 0.006 at 6, 12, and 24mo, respectively. TAM induced an increase in BMD and bone texture analysis, whereas EXE resulted in decreases. The results were independent from each other.

Landscape structure affects dispersal in the greater white-toothed shrew: inference between genetic and simulated ecological distances

Animal dispersal in a fragmented landscape depends on the complex interaction between landscape structure and animal behavior. To better understand how individuals disperse, it is important to explicitly represent the properties of organisms and the landscape in which they move. A common approach to modelling dispersal includes representing the landscape as a grid of equal sized cells and then simulating individual movement as a correlated random walk. This approach uses a priori scale of resolution, which limits the representation of all landscape features and how different dispersal abilities are modelled. We develop a vector-based landscape model coupled with an object-oriented model for animal dispersal. In this spatially explicit dispersal model, landscape features are defined based on their geographic and thematic properties and dispersal is modelled through consideration of an organism's behavior, movement rules and searching strategies (such as visual cues). We present the model's underlying concepts, its ability to adequately represent landscape features and provide simulation of dispersal according to different dispersal abilities. We demonstrate the potential of the model by simulating two virtual species in a real Swiss landscape. This illustrates the model's ability to simulate complex dispersal processes and provides information about dispersal such as colonization probability and spatial distribution of the organism's path

A temporal hierarchy for conspecific vocalization discrimination in humans.

The ability to discriminate conspecific vocalizations is observed across species and early during development. However, its neurophysiologic mechanism remains controversial, particularly regarding whether it involves specialized processes with dedicated neural machinery. We identified spatiotemporal brain mechanisms for conspecific vocalization discrimination in humans by applying electrical neuroimaging analyses to auditory evoked potentials (AEPs) in response to acoustically and psychophysically controlled nonverbal human and animal vocalizations as well as sounds of man-made objects. AEP strength modulations in the absence of topographic modulations are suggestive of statistically indistinguishable brain networks. First, responses were significantly stronger, but topographically indistinguishable to human versus animal vocalizations starting at 169-219 ms after stimulus onset and within regions of the right superior temporal sulcus and superior temporal gyrus. This effect correlated with another AEP strength modulation occurring at 291-357 ms that was localized within the left inferior prefrontal and precentral gyri. Temporally segregated and spatially distributed stages of vocalization discrimination are thus functionally coupled and demonstrate how conventional views of functional specialization must incorporate network dynamics. Second, vocalization discrimination is not subject to facilitated processing in time, but instead lags more general categorization by approximately 100 ms, indicative of hierarchical processing during object discrimination. Third, although differences between human and animal vocalizations persisted when analyses were performed at a single-object level or extended to include additional (man-made) sound categories, at no latency were responses to human vocalizations stronger than those to all other categories. Vocalization discrimination transpires at times synchronous with that of face discrimination but is not functionally specialized.

Preserved capillary density of dorsal finger skin in treated hypertensive patients with or without type 2 diabetes.

OBJECTIVES: Capillary rarefaction is a hallmark of untreated hypertension. Recent data indicate that rarefaction may be reversed by antihypertensive treatment in nondiabetic hypertensive patients. Despite the frequent association of diabetes with hypertension, nothing is known on the capillary density of treated diabetic patients with hypertension. METHODS: We enrolled 21 normotensive healthy, 25 hypertensive only, and 21 diabetic (type 2) hypertensive subjects. All hypertensive patients were treated with a blocker of the renin-angiotensin system, and a majority had a home blood pressure ≤135/85 mmHg. Capillary density was assessed with videomicroscopy on dorsal finger skin and with laser Doppler imaging on forearm skin (maximal vasodilation elicited by local heating). RESULTS: There was no difference between any of the study groups in either dorsal finger skin capillary density (controls 101 ± 11 capillaries/mm(2) , nondiabetic hypertensive 99 ± 16, diabetic hypertensive 96 ± 18, p > 0.5) or maximal blood flow in forearm skin (controls 666 ± 114 perfusion units, nondiabetic hypertensive 612 ± 126, diabetic hypertensive 620 ± 103, p > 0.5). CONCLUSIONS: Irrespective of the presence or not of type 2 diabetes, capillary density is normal in hypertensive patients with reasonable control of blood pressure achieved with a blocker of the renin-angiotensin system.

Multiscale descriptions of density-driven flow instabilities in porous media

Les instabilités engendrées par des gradients de densité interviennent dans une variété d'écoulements. Un exemple est celui de la séquestration géologique du dioxyde de carbone en milieux poreux. Ce gaz est injecté à haute pression dans des aquifères salines et profondes. La différence de densité entre la saumure saturée en CO2 dissous et la saumure environnante induit des courants favorables qui le transportent vers les couches géologiques profondes. Les gradients de densité peuvent aussi être la cause du transport indésirable de matières toxiques, ce qui peut éventuellement conduire à la pollution des sols et des eaux. La gamme d'échelles intervenant dans ce type de phénomènes est très large. Elle s'étend de l'échelle poreuse où les phénomènes de croissance des instabilités s'opèrent, jusqu'à l'échelle des aquifères à laquelle interviennent les phénomènes à temps long. Une reproduction fiable de la physique par la simulation numérique demeure donc un défi en raison du caractère multi-échelles aussi bien au niveau spatial et temporel de ces phénomènes. Il requiert donc le développement d'algorithmes performants et l'utilisation d'outils de calculs modernes. En conjugaison avec les méthodes de résolution itératives, les méthodes multi-échelles permettent de résoudre les grands systèmes d'équations algébriques de manière efficace. Ces méthodes ont été introduites comme méthodes d'upscaling et de downscaling pour la simulation d'écoulements en milieux poreux afin de traiter de fortes hétérogénéités du champ de perméabilité. Le principe repose sur l'utilisation parallèle de deux maillages, le premier est choisi en fonction de la résolution du champ de perméabilité (grille fine), alors que le second (grille grossière) est utilisé pour approximer le problème fin à moindre coût. La qualité de la solution multi-échelles peut être améliorée de manière itérative pour empêcher des erreurs trop importantes si le champ de perméabilité est complexe. Les méthodes adaptatives qui restreignent les procédures de mise à jour aux régions à forts gradients permettent de limiter les coûts de calculs additionnels. Dans le cas d'instabilités induites par des gradients de densité, l'échelle des phénomènes varie au cours du temps. En conséquence, des méthodes multi-échelles adaptatives sont requises pour tenir compte de cette dynamique. L'objectif de cette thèse est de développer des algorithmes multi-échelles adaptatifs et efficaces pour la simulation des instabilités induites par des gradients de densité. Pour cela, nous nous basons sur la méthode des volumes finis multi-échelles (MsFV) qui offre l'avantage de résoudre les phénomènes de transport tout en conservant la masse de manière exacte. Dans la première partie, nous pouvons démontrer que les approximations de la méthode MsFV engendrent des phénomènes de digitation non-physiques dont la suppression requiert des opérations de correction itératives. Les coûts de calculs additionnels de ces opérations peuvent toutefois être compensés par des méthodes adaptatives. Nous proposons aussi l'utilisation de la méthode MsFV comme méthode de downscaling: la grille grossière étant utilisée dans les zones où l'écoulement est relativement homogène alors que la grille plus fine est utilisée pour résoudre les forts gradients. Dans la seconde partie, la méthode multi-échelle est étendue à un nombre arbitraire de niveaux. Nous prouvons que la méthode généralisée est performante pour la résolution de grands systèmes d'équations algébriques. Dans la dernière partie, nous focalisons notre étude sur les échelles qui déterminent l'évolution des instabilités engendrées par des gradients de densité. L'identification de la structure locale ainsi que globale de l'écoulement permet de procéder à un upscaling des instabilités à temps long alors que les structures à petite échelle sont conservées lors du déclenchement de l'instabilité. Les résultats présentés dans ce travail permettent d'étendre les connaissances des méthodes MsFV et offrent des formulations multi-échelles efficaces pour la simulation des instabilités engendrées par des gradients de densité. - Density-driven instabilities in porous media are of interest for a wide range of applications, for instance, for geological sequestration of CO2, during which CO2 is injected at high pressure into deep saline aquifers. Due to the density difference between the C02-saturated brine and the surrounding brine, a downward migration of CO2 into deeper regions, where the risk of leakage is reduced, takes place. Similarly, undesired spontaneous mobilization of potentially hazardous substances that might endanger groundwater quality can be triggered by density differences. Over the last years, these effects have been investigated with the help of numerical groundwater models. Major challenges in simulating density-driven instabilities arise from the different scales of interest involved, i.e., the scale at which instabilities are triggered and the aquifer scale over which long-term processes take place. An accurate numerical reproduction is possible, only if the finest scale is captured. For large aquifers, this leads to problems with a large number of unknowns. Advanced numerical methods are required to efficiently solve these problems with today's available computational resources. Beside efficient iterative solvers, multiscale methods are available to solve large numerical systems. Originally, multiscale methods have been developed as upscaling-downscaling techniques to resolve strong permeability contrasts. In this case, two static grids are used: one is chosen with respect to the resolution of the permeability field (fine grid); the other (coarse grid) is used to approximate the fine-scale problem at low computational costs. The quality of the multiscale solution can be iteratively improved to avoid large errors in case of complex permeability structures. Adaptive formulations, which restrict the iterative update to domains with large gradients, enable limiting the additional computational costs of the iterations. In case of density-driven instabilities, additional spatial scales appear which change with time. Flexible adaptive methods are required to account for these emerging dynamic scales. The objective of this work is to develop an adaptive multiscale formulation for the efficient and accurate simulation of density-driven instabilities. We consider the Multiscale Finite-Volume (MsFV) method, which is well suited for simulations including the solution of transport problems as it guarantees a conservative velocity field. In the first part of this thesis, we investigate the applicability of the standard MsFV method to density- driven flow problems. We demonstrate that approximations in MsFV may trigger unphysical fingers and iterative corrections are necessary. Adaptive formulations (e.g., limiting a refined solution to domains with large concentration gradients where fingers form) can be used to balance the extra costs. We also propose to use the MsFV method as downscaling technique: the coarse discretization is used in areas without significant change in the flow field whereas the problem is refined in the zones of interest. This enables accounting for the dynamic change in scales of density-driven instabilities. In the second part of the thesis the MsFV algorithm, which originally employs one coarse level, is extended to an arbitrary number of coarse levels. We prove that this keeps the MsFV method efficient for problems with a large number of unknowns. In the last part of this thesis, we focus on the scales that control the evolution of density fingers. The identification of local and global flow patterns allows a coarse description at late times while conserving fine-scale details during onset stage. Results presented in this work advance the understanding of the Multiscale Finite-Volume method and offer efficient dynamic multiscale formulations to simulate density-driven instabilities. - Les nappes phréatiques caractérisées par des structures poreuses et des fractures très perméables représentent un intérêt particulier pour les hydrogéologues et ingénieurs environnementaux. Dans ces milieux, une large variété d'écoulements peut être observée. Les plus communs sont le transport de contaminants par les eaux souterraines, le transport réactif ou l'écoulement simultané de plusieurs phases non miscibles, comme le pétrole et l'eau. L'échelle qui caractérise ces écoulements est définie par l'interaction de l'hétérogénéité géologique et des processus physiques. Un fluide au repos dans l'espace interstitiel d'un milieu poreux peut être déstabilisé par des gradients de densité. Ils peuvent être induits par des changements locaux de température ou par dissolution d'un composé chimique. Les instabilités engendrées par des gradients de densité revêtent un intérêt particulier puisque qu'elles peuvent éventuellement compromettre la qualité des eaux. Un exemple frappant est la salinisation de l'eau douce dans les nappes phréatiques par pénétration d'eau salée plus dense dans les régions profondes. Dans le cas des écoulements gouvernés par les gradients de densité, les échelles caractéristiques de l'écoulement s'étendent de l'échelle poreuse où les phénomènes de croissance des instabilités s'opèrent, jusqu'à l'échelle des aquifères sur laquelle interviennent les phénomènes à temps long. Etant donné que les investigations in-situ sont pratiquement impossibles, les modèles numériques sont utilisés pour prédire et évaluer les risques liés aux instabilités engendrées par les gradients de densité. Une description correcte de ces phénomènes repose sur la description de toutes les échelles de l'écoulement dont la gamme peut s'étendre sur huit à dix ordres de grandeur dans le cas de grands aquifères. Il en résulte des problèmes numériques de grande taille qui sont très couteux à résoudre. Des schémas numériques sophistiqués sont donc nécessaires pour effectuer des simulations précises d'instabilités hydro-dynamiques à grande échelle. Dans ce travail, nous présentons différentes méthodes numériques qui permettent de simuler efficacement et avec précision les instabilités dues aux gradients de densité. Ces nouvelles méthodes sont basées sur les volumes finis multi-échelles. L'idée est de projeter le problème original à une échelle plus grande où il est moins coûteux à résoudre puis de relever la solution grossière vers l'échelle de départ. Cette technique est particulièrement adaptée pour résoudre des problèmes où une large gamme d'échelle intervient et évolue de manière spatio-temporelle. Ceci permet de réduire les coûts de calculs en limitant la description détaillée du problème aux régions qui contiennent un front de concentration mobile. Les aboutissements sont illustrés par la simulation de phénomènes tels que l'intrusion d'eau salée ou la séquestration de dioxyde de carbone.