Generation of a flat-top laser beam for gravitational wave detectors by means of a nonspherical Fabry-Perot resonator

We have tested a new kind of Fabry-Perot long-baseline optical resonator proposed to reduce the thermal noise sensitivity of gravitational wave interferometric detectors--the "mesa beam" cavity--whose flat top beam shape is achieved by means of an aspherical end mirror. We present the fundamental mode intensity pattern for this cavity and its distortion due to surface imperfections and tilt misalignments, and contrast the higher order mode patterns to the Gauss-Laguerre modes of a spherical mirror cavity. We discuss the effects of mirror tilts on cavity alignment and locking and present measurements of the mesa beam tilt sensitivity

Self-repair ability of evolved self-assembling systems in cellular automata

Self-repairing systems are those that are able to reconfigure themselves following disruptions to bring them back into a defined normal state. In this paper we explore the self-repair ability of some cellular automata-like systems, which differ from classical cellular automata by the introduction of a local diffusion process inspired by chemical signalling processes in biological development. The update rules in these systems are evolved using genetic programming to self-assemble towards a target pattern. In particular, we demonstrate that once the update rules have been evolved for self-assembly, many of those update rules also provide a self-repair ability without any additional evolutionary process aimed specifically at self-repair

The York map as a Shanmugadhasan canonical transformation in tetrad gravity and the role of non-inertial frames in the geometrical view of the gravitational field

A new parametrization of the 3-metric allows to find explicitly a York map in canonical ADM tetrad gravity, the two pairs of physical tidal degrees of freedom and 14 gauge variables. These gauge quantities (generalized inertial effects) are all configurational except the trace ${}^3K(\tau ,\vec \sigma)$ of the extrinsic curvature of the instantaneous 3-spaces $\Sigma_{\tau}$ (clock synchronization convention) of a non-inertial frame. The Dirac hamiltonian is the sum of the weak ADM energy $E_{ADM} = \int d^3\sigma {\cal E}_{ADM}(\tau ,\vec \sigma)$ (whose density is coordinate-dependent due to the inertial potentials) and of the first-class constraints. Then: i) The explicit form of the Hamilton equations for the two tidal degrees of freedom in an arbitrary gauge: a deterministic evolution can be defined only in a completely fixed gauge, i.e. in a non-inertial frame with its pattern of inertial forces. ii) A general solution of the super-momentum constraints, which shows the existence of a generalized Gribov ambiguity associated to the 3-diffeomorphism gauge group. It influences: a) the explicit form of the weak ADM energy and of the super-momentum constraint; b) the determination of the shift functions and then of the lapse one. iii) The dependence of the Hamilton equations for the two pairs of dynamical gravitational degrees of freedom (the generalized tidal effects) and for the matter, written in a completely fixed 3-orthogonal Schwinger time gauge, upon the gauge variable ${}^3K(\tau ,\vec \sigma)$, determining the convention of clock synchronization. Therefore it should be possible (for instance in the weak field limit but with relativistic motion) to try to check whether in Einstein's theory the {\it dark matter} is a gauge relativistic inertial effect induced by ${}^3K(\tau ,\vec \sigma)$.Comment: 90 page

Evaluation of the diagnostic accuracy of prototype rapid tests for human African trypanosomiasis

Peer reviewedPublisher PD

Distribution of Fe3+ and H in Minerals During Partial Melting and Metasomatism of Spinel Peridotite

Oxygen fugacity and water content are crucial parameters for many chemical and physical properties of the Earth's mantle, for example bearing on fluid type, melting initiation, and deformation. However, the exact behaviour of Fe3+ and H during melting and metasomatism is still under debate. Here, the Fe3+/Fe ratio (Mssbauer and EMP) and water content (FTIR) of peridotite minerals are examined in mantle xenoliths from Kilbourne Hole (KH), NM, and Dish Hill (DH), CA (USA). These spinel peridotites have compositions consistent with partial melting with variable degrees of metasomatism (undetectable to cryptic to modal). Pyroxenites also allow to examine melt-rock reactions. Bulk-rock Fe2O3 content of the KH peridotites correlates with indices of melting (positive with bulk-rock Al2O3 and Cpx Yb contents, and negative with spinel Cr#) confirming that Fe3+ behaves as an incompatible element during melting. Correlations of the Fe3+/Fe ratio of minerals with these indices, however, indicates that Fe3+ is incompatible in Cpx but compatible in Opx and spinel during melting. Water contents in olivine, Cpx and Opx from most KH peridotites can be explained by partial melting and correlate negatively with the Fe3+/Fe ratio of spinel and Opx but positively with that of Cpx. This indicates partial control of Fe3+ on the incorporation of H in pyroxene, but not related to a redox equilibrium in Cpx. The higher Fe3+/Fe ratio of spinel in the metasomatized KH and DH peridotites, and in the pyroxenites confirms that oxidation characterizes modal metasomatism. Metasomatism, however, is not necessarily accompanied by water addition

Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

A simple graphical way of evaluating coverage and directional non-coverages

Evaluation of the coverage probability and, more recently, of the intervalar location of con dence intervals, is a useful procedure if exact and asymptotic methods for constructing con dence intervals are used for some populacional parameter. In this paper, a simple graphical procedure is presented to execute this kind of evaluation in con dence methods for linear combinations of k independent binomial proportions. Our proposal is based on the representation of the mesial and distal non-coverage probabilities on a plane. We carry out a simulation study to show how this graphical representation can be interpreted and used as a basis for the evaluation of intervalar location of con dence interval methods

Power estimation of tests in log-linear non-uniform association models for ordinal agreement

<p>Abstract</p> <p>Background</p> <p>Log-linear association models have been extensively used to investigate the pattern of agreement between ordinal ratings. In 2007, log-linear non-uniform association models were introduced to estimate, from a cross-classification of two independent raters using an ordinal scale, varying degrees of distinguishability between distant and adjacent categories of the scale.</p> <p>Methods</p> <p>In this paper, a simple method based on simulations was proposed to estimate the power of non-uniform association models to detect heterogeneities across distinguishabilities between adjacent categories of an ordinal scale, illustrating some possible scale defects.</p> <p>Results</p> <p>Different scenarios of distinguishability patterns were investigated, as well as different scenarios of marginal heterogeneity within rater. For sample size of N = 50, the probabilities of detecting heterogeneities within the tables are lower than .80, whatever the number of categories. In additition, even for large samples, marginal heterogeneities within raters led to a decrease in power estimates.</p> <p>Conclusion</p> <p>This paper provided some issues about how many objects had to be classified by two independent observers (or by the same observer at two different times) to be able to detect a given scale structure defect. Our results also highlighted the importance of marginal homogeneity within raters, to ensure optimal power when using non-uniform association models.</p

Using ordinal logistic regression to evaluate the performance of laser-Doppler predictions of burn-healing time

Background Laser-Doppler imaging (LDI) of cutaneous blood flow is beginning to be used by burn surgeons to predict the healing time of burn wounds; predicted healing time is used to determine wound treatment as either dressings or surgery. In this paper, we do a statistical analysis of the performance of the technique. Methods We used data from a study carried out by five burn centers: LDI was done once between days 2 to 5 post burn, and healing was assessed at both 14 days and 21 days post burn. Random-effects ordinal logistic regression and other models such as the continuation ratio model were used to model healing-time as a function of the LDI data, and of demographic and wound history variables. Statistical methods were also used to study the false-color palette, which enables the laser-Doppler imager to be used by clinicians as a decision-support tool. Results Overall performance is that diagnoses are over 90% correct. Related questions addressed were what was the best blood flow summary statistic and whether, given the blood flow measurements, demographic and observational variables had any additional predictive power (age, sex, race, % total body surface area burned (%TBSA), site and cause of burn, day of LDI scan, burn center). It was found that mean laser-Doppler flux over a wound area was the best statistic, and that, given the same mean flux, women recover slightly more slowly than men. Further, the likely degradation in predictive performance on moving to a patient group with larger %TBSA than those in the data sample was studied, and shown to be small. Conclusion Modeling healing time is a complex statistical problem, with random effects due to multiple burn areas per individual, and censoring caused by patients missing hospital visits and undergoing surgery. This analysis applies state-of-the art statistical methods such as the bootstrap and permutation tests to a medical problem of topical interest. New medical findings are that age and %TBSA are not important predictors of healing time when the LDI results are known, whereas gender does influence recovery time, even when blood flow is controlled for. The conclusion regarding the palette is that an optimum three-color palette can be chosen 'automatically', but the optimum choice of a 5-color palette cannot be made solely by optimizing the percentage of correct diagnoses