A Kolmogorov-Smirnov test for the molecular clock on Bayesian ensembles of phylogenies

Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter $\lambda$ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides again of power.Comment: 14 pages, 9 figures, 8 tables. Minor revision, additin of a new example and new title. Software: https://github.com/FernandoMarcon/PKS_Test.gi

Vortex state microwave resistivity in Tl-2212 thin films

We present measurements of the field induced changes in the 47 GHz complex resistivity, $\Delta \tilde \rho(H,T)$, in Tl$_{2}$Ba$_{2}$CaCu$_{2}$O$_{8+x}$ (TBCCO) thin films with $T_{c}\simeq$ 105 K, prepared on CeO$_{2}$ buffered sapphire substrates. At low fields ($\mu_{0}H<$10 mT) a very small irreversible feature is present, suggesting a little role of intergranular phenomena. Above that level $\Delta \tilde \rho(H,T)$ exhibits a superlinear dependence with the field, as opposed to the expected (at high frequencies) quasilinear behaviour. We observe a crossover between predominantly imaginary to predominantly real (dissipative) response with increasing temperature and/or field. In addition, we find the clear scaling property $\Delta \tilde \rho(H,T)=\Delta \tilde \rho[H/H^{*}(T)]$, where the scaling field $H^{*}(T)$ maps closely the melting field measured in single crystals. We discuss our microwave results in terms of loss of flux lines rigidity.Comment: 8 pages, 3 figures, proceedings of 9th HTSHFF, accepted for publication on J. Supercon

Anisotropic renormalized fluctuations in the microwave resistivity in YBCO

We discuss the excess conductivity above Tc due to renormalized order-parameter fluctuations in YBCO at microwave frequencies. We calculate the effects of the uniaxial anisotropy on the renormalized fluctuations in the Hartree approximation, extending the isotropic theory developed by Dorsey [Phys. Rev. B 43, 7575 (1991)]. Measurements of the real part of the microwave resistivity at 24 and 48 GHz and of the dc resistivity are performed on different YBCO films. The onset of the superconducting transition and the deviation from the linear temperature behavior above Tc can be fully accounted for by the extended theory. According to the theoretical calculation here presented, a departure from gaussian toward renormalized fluctuations is observed. Very consistent values of the fundamental parameters (critical temperature, coherence lenghts, penetration depth) of the superconducting state are obtained.Comment: RevTex, 8 pages with 5 figures included, to be published in Physical Review

Mixed-state microwave response in superconducting cuprates

We report measurements of the magnetic-field induced microwave complex resistivity in REBa$_{2}$Cu$_{3}$O$_{7-\delta}$ thin films, with RE = Y, Sm. Measurements are performed at 48 GHz by means of a resonant cavity in the end-wall-replacement configuration. The magnetic field dependence is investigated by applying a moderate (0.8 T) magnetic field along the c-axis. The measured vortex state complex resistivity in YBa$_{2}$Cu$_{3}$O$_{7-\delta}$ and SmBa$_{2}$Cu$_{3}$O$_{7-\delta}$ is analyzed within the well-known models for vortex dynamics. It is shown that attributing the observed response to vortex motion alone leads to inconsistencies in the as-determined vortex parameters (such as the vortex viscosity and the pinning constant). By contrast, attributing the entire response to field-induced pair breaking leads to a nearly quantitative description of the data.Comment: 6 pages, 4 figures, to be published in J. Supercond. as proceedings of 8th HTSHFF (May 26th-29th, 2004, Begur, Spain

Scaling of the microwave magneto-impedance in Tl2_2Ba2_2CaCu2_2O8+δ_{8+\delta} thin films

We present measurements of the magnetic field-induced microwave complex resistivity changes at 47 GHz in Tl$_2$Ba$_2$CaCu$_2$O$_{8+\delta}$ (TBCCO) thin films, in the ranges 58 K$<T<T_{c}$ and 0$<\mu_{0}H<$0.8 T. The large imaginary part $\Delta\rho_{2}(H)$ points to strong elastic response, but the data are not easily reconciled with a rigid vortex model. We find that, over a wide range of temperatures, all the pairs of curves $\Delta\rho_{1}(H)$ and $\Delta\rho_{2}(H)$ can be collapsed on a pair of scaling curves $\Delta\rho_{1}[H/H^{*}(T)]$, $\Delta\rho_{2}[H/H^{*}(T)]$, with the same scaling field $H^{*}(T)$. We argue that $H^{*}(T)$ is related to the loss of vortex rigidity due to a vortex transformation.Comment: Two printed pages, Proceedings of M2S (Dresden, 2006), to appear in Physica

Association of mid-infrared solar plages with Calcium K line emissions and magnetic structures

Solar mid-IR observations in the 8-15 micrometer band continuum with moderate angular resolution (18 arcseconds) reveal the presence of bright structures surrounding sunspots. These plage-like features present good association with calcium CaII K1v plages and active region magnetograms. We describe a new optical setup with reflecting mirrors to produce solar images on the focal plane array of uncooled bolometers of a commercial camera preceded by germanium optics. First observations of a sunspot on September 11, 2006 show a mid-IR continuum plage exhibiting spatial distribution closely associated with CaII K1v line plage and magnetogram structures. The mid-IR continuum bright plage is about 140 K hotter than the neighboring photospheric regions, consistent with hot plasma confined by the magnetic spatial structures in and above the active regionComment: 5 pages, 4 figures. Accepted by PAS

Reducing the anxiety of patients undergoing an oral biopsy by means of graphic novels: an open-label randomized clinical trial

Background: The use of graphic novels is a trending topic in health communication as a new form of visual storytelling which explores narratives of health care, cancer, healing, and disability. The objective of the present study was to evaluate - for the first time in the literature - the effect of graphic novels in reducing the anxiety of patients waiting for an incisional biopsy in an oral oncology setting. Material and methods: This open-label randomized clinical trial comprised 50 patients with a clinical suspicion of oral potentially malignant disorders. Twenty-five patients were randomly allocated to the test group, and a colourful graphic novel was provided. Subsequently, the Beck Depression Inventory and the Depression Anxiety Stress Scales-21 were administered to all 50 recruited patients, after which a biopsy was performed on each patient. Results: No statistically significant difference was observed between the test and control groups for the variables regarding the demographic data (p&gt;0.2). There was a significant difference after the introduction of the graphic novel, regardless of which questionnaire was used. The graphic novel demonstrated an improvement in the ability of the test group to tolerate anxiety while waiting for an oral biopsy in both psychological tests (p&lt;0.05). Conclusions: In light of these initial positive results, the authors of this study would like to suggest the use of graphic novels in oral oncology, dentistry, and medicine with the aim of reducing patient anxiety