Anatomical Parcellation of Cortical Language Sites

Anatomical labeling of cerebral cortical stimulation (CSM) sites is necessary for intelligent computer querying of a rich and unique experimental database examining neural substrates underlying human language production. To this end, we have developed a parcellation scheme for the lateral surface of the human cerebral cortex. We then compared results generated utilizing this approach to those generated using an alternative method implemented in the Talairach Daemon

Dissociation of Action and Object Naming: Evidence From Cortical Stimulation Mapping

This cortical stimulation mapping study investigates the neural representation of action and object naming. Data from 13 neurosurgical subjects undergoing awake cortical mapping is presented. Our findings indicate clear evidence of differential disruption of noun and verb naming in the context of this naming task. At the individual level, evidence was found for punctuate regions of perisylvian cortex subserving noun and verb function. Across subjects, however, the location of these sites varied. This finding may help explain discrepancies between lesion and functional imaging studies of noun and verb naming. In addition, an alternative coding of these data served to highlight the grammatical class vulnerability of the target response. The use of this coding scheme implicates a role for the supramarginal gyrus in verb-naming behavior. These data are discussed with respect to a functional-anatomical pathway underlying verb naming

Fast all-optical switch

An apparatus and method wherein polarization rotation in alkali vapors or other mediums is used for all-optical switching and digital logic and where the rate of operation is proportional to the amplitude of the pump field. High rates of speed are accomplished by Rabi flopping of the atomic states using a continuously operating monochromatic atomic beam as the pump

An extremal model for amorphous media plasticity

An extremal model for the plasticity of amorphous materials is studied in a simple two-dimensional anti-plane geometry. The steady-state is analyzed through numerical simulations. Long-range spatial and temporal correlations in local slip events are shown to develop, leading to non-trivial and highly anisotropic scaling laws. In particular, the plastic strain is shown to statistically concentrate over a region which tends to align perpendicular to the displacement gradient. By construction, the model can be seen as giving rise to a depinning transition, the threshold of which (i.e. the macroscopic yield stress) also reveal scaling properties reflecting the localization of the activity.Comment: 4 pages, 5 figure

Lightweight XML-based query, integration and visualization of distributed, multimodality brain imaging data

A need of many neuroimaging researchers is to integrate multimodality brain data that may be stored in separate databases. To address this need we have developed a framework that provides a uniform XML-based query interface across multiple online data sources. The development of this framework is driven by the need to integrate neurosurgical and neuroimaging data related to language. The data sources for the language studies are 1) a web-accessible relational database of neurosurgical cortical stimulation mapping data (CSM) that includes patient-specific 3-D coordinates of each stimulation site mapped to an MRI reconstruction of the patient brain surface; and 2) an XML database of fMRI and structural MRI data and analysis results, created automatically by a batch program we have embedded in SPM. To make these sources available for querying each is wrapped as an XML view embedded in a web service. A top level web application accepts distributed XQueries over the sources, which are dispatched to the underlying web services. Returned results can be displayed as XML, HTML, CSV (Excel format), a 2-D schematic of a parcellated brain, or a 3-D brain visualization. In the latter case the CSM patient-specific coordinates returned by the query are sent to a transformation web-service for conversion to normalized space, after which they are sent to our 3-D visualization program MindSeer, which is accessed via Java WebStart through a generated link. The anatomical distribution of pooled CSM sites can then be visualized using various surfaces derived from brain atlases. As this framework is further developed and generalized we believe it will have appeal for researchers who wish to query, integrate and visualize results across their own databases as well as those of collaborators

Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells.

PurposeThe RPE cell line ARPE-19 provides a dependable and widely used alternative to native RPE. However, replication of the native RPE phenotype becomes more difficult because these cells lose their specialized phenotype after multiple passages. Compounding this problem is the widespread use of ARPE-19 cells in an undifferentiated state to attempt to model RPE functions. We wished to determine whether suitable culture conditions and differentiation could restore the RPE-appropriate expression of genes and proteins to ARPE-19, along with a functional and morphological phenotype resembling native RPE. We compared the transcriptome of ARPE-19 cells kept in long-term culture with those of primary and other human RPE cells to assess the former's inherent plasticity relative to the latter.MethodsARPE-19 cells at passages 9 to 12 grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum were differentiated for up to 4 months. Immunocytochemistry was performed on ARPE-19 cells grown on filters. Total RNA extracted from ARPE-19 cells cultured for either 4 days or 4 months was used for RNA sequencing (RNA-Seq) analysis using a 2 × 50 bp paired end protocol. The RNA-Seq data were analyzed to identify the affected pathways and recognize shared ontological classification among differentially expressed genes. RPE-specific mRNAs and miRNAs were assessed with quantitative real-time (RT)-PCR, and proteins with western blotting.ResultsARPE-19 cells grown for 4 months developed the classic native RPE phenotype with heavy pigmentation. RPE-expressed genes, including RPE65, RDH5, and RDH10, as well as miR-204/211, were greatly increased in the ARPE-19 cells maintained at confluence for 4 months. The RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of the genes in the differentiated ARPE-19 cells. Of the 16,757 genes with detectable signals, nearly 1,681 genes were upregulated, and 1,629 genes were downregulated with a fold change of 2.5 or more differences between 4 months and 4 days of culture. Gene Ontology analysis showed that the upregulated genes were associated with visual cycle, phagocytosis, pigment synthesis, cell differentiation, and RPE-related transcription factors. The majority of the downregulated genes play a role in cell cycle and proliferation.ConclusionsThe ARPE-19 cells cultured for 4 months developed a phenotype characteristic of native RPE and expressed proteins, mRNAs, and miRNAs characteristic of the RPE. Comparison of the ARPE-19 RNA-Seq data set with that of primary human fetal RPE, embryonic stem cell-derived RPE, and native RPE revealed an important overall similar expression ratio among all the models and native tissue. However, none of the cultured models reached the absolute values in the native tissue. The results of this study demonstrate that low-passage ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured and differentiated

Genome-wide changes in protein translation efficiency are associated with autism

We previously proposed that changes in the efficiency of protein translation are associated with autism spectrum disorders (ASDs). This hypothesis connects environmental factors and genetic factors because each can alter translation efficiency. For genetic factors, we previously tested our hypothesis using a small set of ASD-associated genes, a small set of ASD-associated variants, and a statistic to quantify by how much a single nucleotide variant (SNV) in a protein coding region changes translation speed. In this study, we confirm and extend our hypothesis using a published set of 1,800 autism quartets (parents, one affected child and one unaffected child) and genome-wide variants. Then, we extend the test statistic to combine translation efficiency with other possibly relevant variables: ribosome profiling data, presence/absence of CpG dinucleotides, and phylogenetic conservation. The inclusion of ribosome profiling abundances strengthens our results for male–male sibling pairs. The inclusion of CpG information strengthens our results for female–female pairs, giving an insight into the significant gender differences in autism incidence. By combining the single-variant test statistic for all variants in a gene, we obtain a single gene score to evaluate how well a gene distinguishes between affected and unaffected siblings. Using statistical methods, we compute gene sets that have some power to distinguish between affected and unaffected siblings by translation efficiency of gene variants. Pathway and enrichment analysis of those gene sets suggest the importance of Wnt signaling pathways, some other pathways related to cancer, ATP binding, and ATP-ase pathways in the etiology of ASDs

Light scattering from self-affine fractal silver surfaces with nanoscale cutoff: Far-field and near-field calculations

We study the light scattered from randomly rough, one-dimensional self-affine fractal silver surfaces with nanoscale lower cutoff, illuminated by s- or p-polarized Gaussian beams a few microns wide. By means of rigorous numerical calculations based on the Green theorem integral equation formulation, we obtain both the far- and near-field scattered intensities. The influence of diminishing the fractal lower scale cutoff (from below a hundred, down to a few nanometers) is analyzed in the case of both single realizations and ensemble average magnitudes. For s polarization, variations are small in the far field, being only significant in the higher spatial frequency components of evanescent character in the near field. In the case of p polarization, however, the nanoscale cutoff has remarkable effects stemming from the roughness-induced excitation of surface-plasmon polaritons. In the far field, the effect is noticed both in the speckle pattern variation and in the decrease of the total reflected energy upon ensemble averaging, due to increased absorption. In the near field, more efficient excitation of localized optical modes is achieved with smaller cutoff, which in turn leads to huge surface electric field enhancements.Comment: REVTeX 4, 10 page

Thermodynamic aspects of materials' hardness: prediction of novel superhard high-pressure phases

In the present work we have proposed the method that allows one to easily estimate hardness and bulk modulus of known or hypothetical solid phases from the data on Gibbs energy of atomization of the elements and corresponding covalent radii. It has been shown that hardness and bulk moduli of compounds strongly correlate with their thermodynamic and structural properties. The proposed method may be used for a large number of compounds with various types of chemical bonding and structures; moreover, the temperature dependence of hardness may be calculated, that has been performed for diamond and cubic boron nitride. The correctness of this approach has been shown for the recently synthesized superhard diamond-like BC5. It has been predicted that the hypothetical forms of B2O3, diamond-like boron, BCx and COx, which could be synthesized at high pressures and temperatures, should have extreme hardness

An electromagnetic shashlik calorimeter with longitudinal segmentation

A novel technique for longitudinal segmentation of shashlik calorimeters has been tested in the CERN West Area beam facility. A 25 tower very fine samplings e.m. calorimeter has been built with vacuum photodiodes inserted in the first 8 radiation lengths to sample the initial development of the shower. Results concerning energy resolution, impact point reconstruction and electron/pion separation are reported.Comment: 13 pages, 12 figure