PENALIZED LIKELIHOOD AND BAYESIAN METHODS FOR SPARSE CONTINGENCY TABLES: AN ANALYSIS OF ALTERNATIVE SPLICING IN FULL-LENGTH cDNA LIBRARIES

We develop methods to perform model selection and parameter estimation in loglinear models for the analysis of sparse contingency tables to study the interaction of two or more factors. Typically, datasets arising from so-called full-length cDNA libraries, in the context of alternatively spliced genes, lead to such sparse contingency tables. Maximum Likelihood estimation of log-linear model coefficients fails to work because of zero cell entries. Therefore new methods are required to estimate the coefficients and to perform model selection. Our suggestions include computationally efficient penalization (Lasso-type) approaches as well as Bayesian methods using MCMC. We compare these procedures in a simulation study and we apply the proposed methods to full-length cDNA libraries, yielding valuable insight into the biological process of alternative splicing

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

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

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

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

RETRACTED: Autoimmunity as the Consequence of a Spontaneous Mutation in Rasgrp1

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of the Authors.The authors have agreed to retract the paper because of the falsification of the Western blot in Figure 6A. The figure shows a defect in Ras activation, labeled as RasGTP, following TCR engagement, in thymocytes isolated from a RasGRP1 lag mutant mouse strain. This data set is one of several that show signaling and functional deficiencies identified for cells with lost of function of RasGRP. The authors stand by the validity of the other figures, results and interpretation in this paper. This matter was investigated by the Massachusetts Institute of Technology and the Office of Research Integrity at the United States Department of Health & Human Services, which found the figure was falsified by Luk Van Parijs, who is solely responsible. The authors deeply regret any inconvenience resulting from the publication of this data

Embryonic Death Is Linked to Maternal Identity in the Leatherback Turtle (Dermochelys coriacea)

Leatherback turtles have an average global hatching success rate of ∼50%, lower than other marine turtle species. Embryonic death has been linked to environmental factors such as precipitation and temperature, although, there is still a lot of variability that remains to be explained. We examined how nesting season, the time of nesting each season, the relative position of each clutch laid by each female each season, maternal identity and associated factors such as reproductive experience of the female (new nester versus remigrant) and period of egg retention between clutches (interclutch interval) affected hatching success and stage of embryonic death in failed eggs of leatherback turtles nesting at Playa Grande, Costa Rica. Data were collected during five nesting seasons from 2004/05 to 2008/09. Mean hatching success was 50.4%. Nesting season significantly influenced hatching success in addition to early and late stage embryonic death. Neither clutch position nor nesting time during the season had a significant affect on hatching success or the stage of embryonic death. Some leatherback females consistently produced nests with higher hatching success rates than others. Remigrant females arrived earlier to nest, produced more clutches and had higher rates of hatching success than new nesters. Reproductive experience did not affect stage of death or the duration of the interclutch interval. The length of interclutch interval had a significant affect on the proportion of eggs that failed in each clutch and the developmental stage they died at. Intrinsic factors such as maternal identity are playing a role in affecting embryonic death in the leatherback turtle