Dismantling the Mantel tests

The simple and partial Mantel tests are routinely used in many areas of evolutionary biology to assess the significance of the association between two or more matrices of distances relative to the same pairs of individuals or demes. Partial Mantel tests rather than simple Mantel tests are widely used to assess the relationship between two variables displaying some form of structure. We show that contrarily to a widely shared belief, partial Mantel tests are not valid in this case, and their bias remains close to that of the simple Mantel test. We confirm that strong biases are expected under a sampling design and spatial correlation parameter drawn from an actual study. The Mantel tests should not be used in case auto-correlation is suspected in both variables compared under the null hypothesis. We outline alternative strategies. The R code used for our computer simulations is distributed as supporting material

Resampling: an improvement of Importance Sampling in varying population size models

Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic situations. In this work, we modify a previous sequential importance sampling algorithm to improve the efficiency of the likelihood estimation. Our procedure is still based on features of the model with constant size, but uses a resampling technique with a new resampling probability distribution depending on the pairwise composite likelihood. We tested our algorithm, called sequential importance sampling with resampling (SISR) on simulated data sets under different demographic cases. In most cases, we divided the computational cost by two for the same accuracy of inference, in some cases even by one hundred. This study provides the first assessment of the impact of such resampling techniques on parameter inference using sequential importance sampling, and extends the range of situations where likelihood inferences can be easily performed

Two-Finger 3D Rotations for Novice Users: Surjective and Integral Interactions

International audienceNow that 3D interaction is available on tablets and smart phones, it becomes critical to provide efficient 3D interaction techniques for novice users. This paper investigates interaction techniques for 3D rotation with two fingers of a single hand, on multitouch mobile devices. We introduce two new rotation techniques that allow integral control of the 3 axes of rotation. These techniques also satisfy a new criterion that we introduce: surjection. We ran a study to compare the new techniques with two widely used rotation techniques from the literature. Results indicate that surjection and integration lead to a performance improvement of a group of participants who had no prior experience in 3D interaction. Qualitative results also indicate participants' preference for the new interaction techniques

Measuring many-body effects in carbon nanotubes with a scanning tunneling microscope

Electron-electron interactions and excitons in carbon nanotubes are locally measured by combining Scanning tunneling spectroscopy and optical absorption in bundles of nanotubes. The largest gap deduced from measurements at the top of the bundle is found to be related to the intrinsic quasi-particle gap. From the difference with optical transitions, we deduced exciton binding energies of 0.4 eV for the gap and 0.7 eV for the second Van Hove singularity. This provides the first experimental evidence of substrate-induced gap renormalization on SWNTs

Fitness, inclusive fitness, and optimization

Individual-as-maximizing agent analogies result in a simple understanding of the functioning of the biological world. Identifying the conditions under which individuals can be regarded as fitness maximizing agents is thus of considerable interest to biologists. Here, we compare different concepts of fitness maximization, and discuss within a single framework the relationship between Hamilton's (J Theor Biol 7:1-16, 1964) model of social interactions, Grafen's (J Evol Biol 20:1243-1254,2007a) formal Darwinism project, and the idea of evolutionary stable strategies. We distinguish cases where phenotypic effects are additive separable or not, the latter not being covered by Grafen's analysis. In both cases it is possible to define a maximand, in the form of an objective function ϕ(z), whose argument is the phenotype of an individual and whose derivative is proportional to Hamilton's inclusive fitness effect. However, this maximand can be identified with the expression for fecundity or fitness only in the case of additive separable phenotypic effects, making individual-as-maximizing agent analogies unattractive (although formally correct) under general situations of social interactions. We also feel that there is an inconsistency in Grafen's characterization of the solution of his maximization program by use of inclusive fitness arguments. His results are in conflict with those on evolutionary stable strategies obtained by applying inclusive fitness theory, and can be repaired only by changing the definition of the problem

Visualization in cryogenic environment: Application to two-phase studies

11 pagesInternational audienceThis paper reviews recent technical developments devoted to the study of cryogenic two-phase fluids. These techniques span from simple flow visualization to quantitative measurements of light scattering. It is shown that simple flow pattern configurations are obtained using classical optical tools (CCD cam- eras, endoscopes), even in most severe environments (high vacuum, high magnetic field). Quantitative measurements include laser velocimetry, particle sizing, and light scattering analysis. In the case of mag- netically compensated gravity boiling oxygen, optical access is used to control the poistioning of a bubble subject to buoyancy forces in an experimental cell. Flow visualization on a two-phase superfluid helium pipe-flow, performed as a support of LHC cooldown studies, leads to flow pattern characterization. Visu- alization includes stratified and atomized flows. Thanks to the low refractive index contrast between the liquid and its vapor, quantitative results on droplet densities can be obtained even in a multiple scatter- ing regime

SomeRDFS in the Semantic Web

The Semantic Web envisions a world-wide distributed architecture where computational resources will easily inter-operate to coordinate complex tasks such as query answering. Semantic marking up of web resources using ontologies is expected to provide the necessary glue for making this vision work. Using ontology languages, (communities of) users will build their own ontologies in order to describe their own data. Adding semantic mappings between those ontologies, in order to semantically relate the data to share, gives rise to the Semantic Web: data on the web that are annotated by ontologies networked together by mappings. In this vision, the Semantic Web is a huge semantic peer data management system. In this paper, we describe the SomeRDFS peer data management systems that promote a "simple is beautiful" vision of the Semantic Web based on data annotated by RDFS ontologies