MissForest - nonparametric missing value imputation for mixed-type data

Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a nonparametric method which can cope with different types of variables simultaneously. We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple data sets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in data sets including different types of variables. In our comparative study missForest outperforms other methods of imputation especially in data settings where complex interactions and nonlinear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data.Comment: Submitted to Oxford Journal's Bioinformatics on 3rd of May 201

Modeling of a Segmented Electrode for Desynchronizing Deep Brain Stimulation

Deep brain stimulation (DBS) is an effective therapy for medically refractory movement disorders like Parkinson’s disease. The electrodes, implanted in the target area within the human brain, generate an electric field which activates nerve fibers and cell bodies in the vicinity. Even though the different target nuclei display considerable differences in their anatomical structure, only few types of electrodes are currently commercially available. It is desirable to adjust the electric field and in particular the volume of tissue activated around the electrode with respect to the corresponding target nucleus in a such way that side effects can be reduced. Furthermore, a more selective and partial activation of the target structure is desirable for an optimal application of novel stimulation strategies, e.g., coordinated reset neuromodulation. Hence we designed a DBS electrode with a segmented design allowing a more selective activation of the target structure. We created a finite element model (FEM) of the electrode and analyzed the volume of tissue activated for this electrode design. The segmented electrode activated an area in a targeted manner, of which the dimension and position relative to the electrode could be controlled by adjusting the stimulation parameters for each electrode contact. According to our computational analysis, this directed stimulation might be superior with respect to the occurrence of side effects and it enables the application of coordinated reset neuromodulation under optimal conditions

Tissue Distribution and Maternal Transfer of Mercury in Diamondback Terrapins with Implications for Human Health

2010 S.C. Water Resources Conferences - Science and Policy Challenges for a Sustainable Futur

Interaction of Gold Nanoparticles in Barium Titanate Thin Films

A novel approach to control the grain size of oxide thin film materials has been investigated. Perovskite BaTiO3 shows interesting grain structures when deposited on gold predeposited, (111)-oriented, singlecrystal SrTiO3 substrates. Solid oxide films grow epitaxially on patterned seed layers and show variations in grain size relative to the films deposited on SrTiO3 directly.Comment: 14 pages, 4 figure

Blue lasing at room temperature in high quality factor GaN/AlInN microdisks with InGaN quantum wells

The authors report on the achievement of optically pumped III-V nitride blue microdisk lasers operating at room temperature. Controlled wet chemical etching of an AlInN interlayer lattice matched to GaN allows forming inverted cone pedestals. Whispering gallery modes are observed in the photoluminescence spectra of InGaN∕GaN quantum wells embedded in the GaN microdisks. Typical quality factors of several thousands are found (Q>4000). Laser action at ∼420nm is achieved under pulsed excitation at room temperature for a peak power density of 400kW/cm2. The lasing emission linewidth is down to 0.033nm

Egg and clutch sizes of western chicken turtles (Deirochelys reticularia miaria)

Chicken turtles (Deirochelys reticularia) are generally characterized as having atypical reproductive characteristics relative to other sympatric emydids. However, the comparatively understudied western chicken turtle (D. r. miaria) has been shown to exhibit some reproductive characteristics that differ from the other subspecies. Therefore, we examined clutch and egg sizes from six D. r. miaria (13 clutches) in Oklahoma and compared the results to values that have been reported for the other two subspecies. Females nested up to three times per year, with clutches ranging from 8-13 eggs per clutch (mean = 10.9). The eggs were 19.4-25.3 mm wide (mean = 22.2 mm). These values are greater than the means reported for the other subspecies, but the differences were not statistically significant

The giant planet orbiting the cataclysmic binary DP Leonis

Planets orbiting post-common envelope binaries provide fundamental information on planet formation and evolution, especially for the yet nearly unexplored class of circumbinary planets. We searched for such planets in \odp, an eclipsing short-period binary, which shows long-term eclipse-time variations. Using published, reanalysed, and new mid-eclipse times of the white dwarf in DP\,Leo, obtained between 1979 and 2010, we find agreement with the light-travel-time effect produced by a third body in an elliptical orbit. In particular, the measured binary period in 2009/2010 and the implied radial velocity coincide with the values predicted for the motion of the binary and the third body around the common center of mass. The orbital period, semi-major axis, and eccentricity of the third body are P_c = 28.0 +/- 2.0 yrs, a_c = 8.2 +/- 0.4 AU, and e_c = 0.39 +/- 0.13. Its mass of M_c sin(i_c) = 6.1 +/- 0.5 M_J qualifies it as a giant planet. It formed either as a first generation object in a protoplanetary disk around the original binary or as a second generation object in a disk formed in the common envelope shed by the progenitor of the white dwarf. Even a third generation origin in matter lost from the present accreting binary can not be entirely excluded. We searched for, but found no evidence for a fourth body.Comment: Accepted by A&

The global decline of reptiles, deja’ vu amphibians

Reptile species are declining on a global scale. Six significant threats to reptile populations are habitat loss and degradation, introduced invasive species, environmental pollution, disease, unsustainable use, and global climate change

Diamond deposition on modified silicon substrates: Making diamond atomic force microscopy tips for nanofriction experiments

Fine-crystalline diamond particles are grown on standard Si atomic force microscopy tips, using hot filament-assisted chemical vapor deposition. To optimize the conditions for diamond deposition, first a series of experiments is carried out using silicon substrates covered by point-topped pyramids as obtained by wet chemical etching. The apexes and the edges of the silicon pyramids provide favorable sites for diamond nucleation and growth. The investigation of the deposited polycrystallites is done by means of optical microscopy, scanning electron microscopy and micro-Raman spectroscopy. The resulting diamond-terminated tips are tested in ultra high vacuum using contact-mode atomic force microscope on a stepped surface of sapphire showing high stability, sharpness, and hardnes