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

О СОГЛАСОВАННЫХ ДВУСТОРОННИХ ОЦЕНКАХ РЕШЕНИЙ ОДНОРОДНЫХ КВАЗИЛИНЕЙНЫХ ПАРАБОЛИЧЕСКИХ УРАВНЕНИЙ И ИХ АППРОКСИМАЦИЙ

In this article, for the linearized difference scheme that approximates the Dirichlet problem for the homogeneous multidimensional quasi-linear parabolic equation with unbounded nonlinearity, two-sided point-wise estimates of the solution are established which are fully consistent with the same estimates for the differential problem. It is interesting to note that the proved two-sided estimates do not depend on diffusion coefficient. The direct application of such estimates is the proof of the convergence of the considered difference scheme in the grid norm L2 . An example of the calculation by the Crank–Nicolson difference scheme is given, showing that the violation of the consistency conditions of differential and difference estimates leads to non-monotonic numerical solutions.В настоящей работе для линеаризованной разностной схемы, аппроксимирующей задачу Дирихле для однородного многомерного квазилинейного параболического уравнения с неограниченной нелинейностью установлены поточечные двусторонние оценки решения, согласованные с аналогичными оценками для дифференциальной задачи. Любопытно отметить, что доказанные двусторонние оценки не зависят от величины коэффициента диффузии. Непосредственным применением данных оценок устанавливается сходимость исследуемой разностной схемы в сеточной норме L2 . Приводится пример расчета по схеме Кранка–Никольсона, когда нарушение условий согласованности дифференциальной и разностной оценок приводит к немонотонности численного решения.

Evaluating spatial normalization methods for the human brain

Cortical stimulation mapping (CSM) studies have shown cortical locations for language function are highly variable from one subject to the next. If individual variation can be normalized, patterns of language organization may emerge that were heretofore hidden. In order to uncover this pattern, computer-aided spatial normalization to a common atlas is required. Our problem was how to determine which spatial normalization method was best for the given research application. We developed key metrics to measure accuracy of a surface-based (Caret) and volume-based (SPM2) method. We specified that the optimal method would i) minimize variation as measured by spread reduction between CSM language sites across subjects while also ii) preserving anatomical localization of all CSM sites. Eleven subject’s structural MR data and corresponding CSM site coordinates were registered to the colin27 human brain atlas using each method. Local analysis showed that mapping error rates for both methods were highest in morphological regions with the greatest difference between source and target. Also, SPM2 mapped significantly less type 2 errors. Although our experiment did not show statistically significant global differences between the methods, our methodology provided valuable insights into the pros and cons of each

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

Distributed XQuery-based integration and visualization of multimodality data: Application to brain mapping.

This paper addresses the need for relatively small groups of collaborating investigators to integrate distributed and heterogeneous data about the brain. Although various national efforts facilitate large-scale data sharing, these approaches are generally too “heavyweight” for individual or small groups of investigators, with the result that most data sharing among collaborators continues to be ad hoc. Our approach to this problem is to create a “lightweight” distributed query architecture, in which data sources are accessible via web services that accept arbitrary query languages but return XML results. A Distributed XQuery Processor (DXQP) accepts distributed XQueries in which subqueries are shipped to the remote data sources to be executed, with the resulting XML integrated by DXQP. A web-based application called DXBrain accesses DXQP, allowing a user to create, save and execute distributed XQueries, and to view the results in various formats including a 3-D brain visualization. Example results are presented using distributed brain mapping data sources obtained in studies of language organization in the brain, but any other XML source could be included. The advantage of this approach is that it is very easy to add and query a new source, the tradeoff being that the user needs to understand XQuery and the schemata of the underlying sources. For small numbers of known sources this burden is not onerous for a knowledgeable user, leading to the conclusion that the system helps to fill the gap between ad hoc local methods and large scale but complex national data sharing efforts

On detection of narrow angle e+e- pairs from dark photon decays

A class of models of dark sectors consider new very weak interaction between the ordinary and dark matter transmitted by U'(1) gauge bosons A' (dark photons) mixing with our photons. If such A's exist, they could be searched for in a light-shining-through-a-wall experiment with a high energy electron beam from the CERN SPS. The proposed search scheme suggests detection of the e+e- pairs produced in the A' -> e+e- decay with a very small opening angle. Coordinate chambers based on the thin-wall drift tubes with a minimal material budget and a two-hit resolution for e+ and e- tracks separated by more than 0.5 mm are considered as an option for detecting such pairs

Wide-band optical field concentrator for low-index core propagation

We propose a novel chirped structure consisting of a low index polymer core bounded by modulated multilayer claddings, to realize an optical field concentrator with virtually zero propagation losses in a wide spectral range, independent of wave polarization. In spite of the absence of the total internal reflection mechanism, properly designed multilayer claddings ensure the achievement of unitary transmittance in a wide spectral range, including the widely used wavelengths for optical communications. Several cladding geometries obtained by varying the thicknesses of the cladding layers are reported and discussed.Comment: submitted to the Journal of the European Optical Societ

The Genome Portal of the Department of Energy Joint Genome Institute

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource

Alignathon: A competitive assessment of whole-genome alignment methods

© 2014 Earl et al. Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments

Tract-Based Spatial Statistical Analysis of Diffusion Tensor Imaging in Pediatric Patients with Mitochondrial Disease: Widespread Reduction in Fractional Anisotropy of White Matter Tracts

BACKGROUND AND PURPOSE: Often diagnosed at birth or in early childhood, mitochondrial disease presents with a variety of clinical symptoms, particularly in organs and tissues that require high energetic demand such as brain, heart, liver, and skeletal muscles. In a group of pediatric patients identified as having complex I or I/III deficits on muscle biopsy but with white matter tissue appearing qualitatively normal for age, we hypothesized that quantitative DTI analyses might unmask disturbance in microstructural integrity