DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Summary: We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (?, G) and population differentiation statistics (D, GST ', ? test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis. © 2013 British Ecological Society.

Experimental investigation of hole boring and light sail regimes of RPA by varying laser and target parameters

Temporal evolution of plasma jets from micrometre-scale thick foils following the interaction of intense (3 × 10 W cm ) laser pulses is studied systematically by time resolved optical interferometry. The fluid velocity in the plasma jets is determined by comparing the data with 2D hydrodynamic simulation, which agrees with the expected hole-boring (HB) velocity due to the laser radiation pressure. The homogeneity of the plasma density across the jets has been found to be improved substantially when irradiating the laser at circular polarization compared to linear polarization. While overdense plasma jets were formed efficiently for micrometre thick targets, decreasing the target areal density and/or increasing the irradiance on the target have provided indication of transition from the 'HB' to the 'light sail (LS)' regime of RPA, characterized by the appearance of narrow-band spectral features at several MeV/nucleon in proton and carbon spectra.

Measuring specific parameters in pretensioned concrete members using a single testing technique

Pretensioned concrete members are designed and manufactured by using at least two materials: concrete and prestressing reinforcement. Also, two main stages must be considered: prestress transfer and member loading. Hence, the behavior of these members depends strongly on the reinforcement-to-concrete bond performance and prestress losses. In this paper, a testing technique to measure the specific parameters related with the involved phenomena is presented. The testing technique is based on the analysis of series of specimens varying in embedment length to simulate several cross sections at only one end of a pretensioned concrete member. Each specimen is characterized by means of the sequential release of the prestress transfer (detensioning) and the pull-out (loading) operation. The test provides data on prestressing force, transmission length (initial and long-term), anchorage length (without and with slip), reinforcement slips, bond stresses, longitudinal concrete strains, concrete modulus of elasticity, and prestress losses (instantaneous and time-dependent).

Effect of the crown design and interface lute parameters on the stress-state of a machined crown-tooth system: A finite element analysis

The effect of preparation design and the physical properties of the interface lute on the restored machined ceramic crown-tooth complex are poorly understood. The aim of this work was to determine, by means of three-dimensional finite element analysis (3D FEA) the effect of the tooth preparation design and the elastic modulus of the cement on the stress state of the cemented machined ceramic crown-tooth complex. The three-dimensional structure of human premolar teeth, restored with adhesively cemented machined ceramic crowns, was digitized with a micro-CT scanner. An accurate, high resolution, digital replica model of a restored tooth was created. Two preparation designs, with different occlusal morphologies, were modeled with cements of 3 different elastic moduli. Interactive medical image processing software (mimics and professional CAD modeling software) was used to create sophisticated digital models that included the supporting structures; periodontal ligament and alveolar bone. The generated models were imported into an FEA software program (hypermesh version 10.0, Altair Engineering Inc.) with all degrees of freedom constrained at the outer surface of the supporting cortical bone of the crown-tooth complex. Five different elastic moduli values were given to the adhesive cement interface 1.8 GPa, 4 GPa, 8 GPa, 18.3 GPa and 40 GPa; the four lower values are representative of currently used cementing lutes and 40 GPa is set as an extreme high value. The stress distribution under simulated applied loads was determined. The preparation design demonstrated an effect on the stress state of the restored tooth system. The cement elastic modulus affected the stress state in the cement and dentin structures but not in the crown, the pulp, the periodontal ligament or the cancellous and cortical bone. The results of this study suggest that both the choice of the preparation design and the cement elastic modulus can affect the stress state within the restored crown-tooth complex.

Simulation of three-dimension cutting force and tool deflection in the end milling operation based on finite element method

This paper presents a 3D simulation system which is employed in order to predict cutting forces and tool deflection during end-milling operation. In order to verify the accuracy of 3D simulation, results (cutting forces and tool deflection) were compared with those based on the theoretical relationships, in terms of agreement with experiments. The results obtained indicate that the simulation is capable of predicting the cutting forces and tool deflection.

Changes in modal parameters of a steel truss bridge due to artificial damage

This study investigated how damage changes the modal parameters of a real bridge by means of a field experiment which was conducted on a real steel truss bridge consecutively subjected to four artificial damage scenarios. In the experiment, both the forced and free vibrations of the bridge were recorded, the former for identifying higher modes available exclusively and the latter for lower modes with higher resolution. Results show that modal parameters are little affected by damage causing low stress redistribution. Modal frequencies decrease as damage causing high stress redistribution is applied; such a change can be observed if the damage is at the non-nodal point of the corresponding mode shape. Mode shapes are distorted due to asymmetric damage; they show an amplification in the damaged side as damage is applied at the non-nodal point. Torsion modes become more dominant as damage is applied either asymmetrically or on an element against large design loads. © 2013 Taylor & Francis Group, London.

Identification of the Dynamic Parameters of a Real Bridge under Different Damage Conditions in a Field Experiment

This paper presents the results of a real bridge field experiment in which damage was applied artificially to a steel truss bridge. The aim of this paper is to identify the dynamic parameters of this bridge using conventional techniques and investigate the effect of various damage conditions on those parameters. In the field experiment, acceleration measurements were recorded at a number of locations on the bridge deck. To excite the bridge, a two-axle van was driven across the bridge at constant speed. Dynamic parameters, such as the bridge mode shape, natural frequency and damping constant, are identified from the acceleration signals using existing techniques such as the fast Fourier transform, logarithmic decrement and frequency domain decomposition. The variation of these parameters under the influence of artificially applied damage conditions is investigated in order to evaluate their sensitivity to the bridge damage.

Theoretical investigation of the use of a moving vehicle to identify bridge dynamic parameters

Pavements and bridges are subject to a continuous degradation due to traffic aggressiveness, ageing and environmental factors. A rational transport policy requires the monitoring of this transport infrastructure in order to provide adequate maintenance and guarantee the required levels of transport service and safety. This paper investigates the use of an instrumented vehicle fitted with accelerometers on its axles to monitor the dynamics of bridges. A simplified quarter carbridge interaction model is used in theoretical simulations and the natural frequency of the bridge is extracted from the spectra of the vehicle accelerations. The accuracy is better at lower speeds and for smooth road profiles. The structural damping of the bridge was also monitored for smooth and rough road profiles. The magnitude of peaks in the power spectral density of the vehicle accelerations decreased with increasing bridge damping and this decrease was easier to detect the smoother the road profile.

Mask assisted fabrication of nanoislands of BiFeO3 by ion beam milling

We report on a low-damage method for direct and rapid fabrication of arrays of epitaxial BiFeO3(BFO) nanoislands. An array of aluminium dots is evaporated through a stencil mask on top of an epitaxial BiFeO3 thin film. Low energy focused ion beam milling of an area several microns wide containing the array-covered film leads to removal of the bismuth ferrite in between the aluminium-masked dots. By chemical etching of the remaining aluminium, nanoscale epitaxial bismuth ferrite islands with diameter ∼250 nm were obtained. Piezoresponse force microscopy showed that as-fabricated structures exhibited good piezoelectric and ferroelectric properties, with polarization state retention of several days.

Ferroelectric nanostructures fabricated by focused-ion-beam milling in epitaxial BiFeO3 thin films

We studied a suitable route to fabricate ferroelectric islands by focused-ion-beam milling in bismuth ferrite epitaxial thin films. Piezoresponse force microscopy shows that the damage induced by the milling process is extended to 1 mu m away from the edge of the focused-ion-beam patterned islands. After a combined vacuum and oxygen atmosphere annealing procedure, ferroelectricity is fully recovered in structures with sizes down to 500 nm, while for 250 nm islands the defects at the interfaces induce polarization direction pinning.

Tidally Distorted Exoplanets: Density Corrections for Short-period Hot-Jupiters Based Solely on Observable Parameters

The close proximity of short-period hot-Jupiters to their parent star means they are subject to extreme tidal forces. This has a profound effect on their structure and, as a result, density measurements that assume that the planet is spherical can be incorrect. We have simulated the tidally distorted surface for 34 known short-period hot-Jupiters, assuming surfaces of constant gravitational equipotential for the planet, and the resulting densities have been calculated based only on observed parameters of the exoplanet systems. Comparing these results to the density values, assuming the planets are spherical, shows that there is an appreciable change in the measured density for planets with very short periods (typically less than two days). For one of the shortest-period systems, WASP-19b, we determine a decrease in bulk density of 12% from the spherical case and, for the majority of systems in this study, this value is in the range of 1%-5%. On the other hand, we also find cases where the distortion is negligible (relative to the measurement errors on the planetary parameters) even in the cases of some very short period systems, depending on the mass ratio and planetary radius. For high-density gas planets requiring apparently anomalously large core masses, density corrections due to tidal deformation could become important for the shortest-period systems.

Investigation of Finish-cut of Microelectrodischarge Milling for Nano Surface Finish

In this article, the machining conditions to achieve nanometric surface roughness in finish cut microelectrodischarge milling were investigated. For a constant gap voltage, the effect of feed rate and capacitance was studied on average surface roughness (Ra) and maximum peak-to-valley roughness height (Ry). Statistical models were developed using a three-level, two-factor experimental design. The developed models minimized Ra and Ry by desirability function approach. Maximum desirability was found to be more than 98%. The minimum values of Ra and Ry were 23 and 173 nm, respectively, for 1.00 μm s-1 feed rate and 0.01 nF capacitance. Verification experiments were conducted to check the accuracy of the models, where the responses were found to be very close to the predicted values. Thus, the developed models can be used to generate nanometric level surface finish, which are useful for many applications in microelectromechanical systems.