Use of Remote Surface Based Tools for Visualizing Integrated Brain Imaging Data

We describe a surface-based approach to 3D visualization of integrated neuroimaging data. Our web-enabled software allows researchers to use these visualization tools over the Internet. We present examples of brain imaging studies where such remote surface-based visualization techniques have proven to be quite effective

Brain Visualization in Java3D

BrainJ3D is a cross-platform Java/Java3D software toolkit for processing and visualizing brain imaging data, which 1) contains general purpose tools for reconstructing, mapping and visualizing integrated structural and functional images and 2) leverages Java's Remote Method Invocation to provide both a standalone and a client/server mode

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

Modes of faulting at mid-ocean ridges

Abyssal-hill-bounding faults that pervade the oceanic crust are the most common tectonic feature on the surface of the Earth. The recognition that these faults form at plate spreading centres came with the plate tectonic revolution. Recent observations reveal a large range of fault sizes and orientations; numerical models of plate separation, dyke intrusion and faulting require at least two distinct mechanisms of fault formation at ridges to explain these observations. Plate unbending with distance from the top of an axial high reproduces the observed dip directions and offsets of faults formed at fast-spreading centres. Conversely, plate stretching, with differing amounts of constant-rate magmatic dyke intrusion, can explain the great variety of fault offset seen at slow-spreading ridges. Very-large-offset normal faults only form when about half the plate separation at a ridge is accommodated by dyke intrusion

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

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine

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

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.

Regularly log-periodic functions and some applications

We prove a Tauberian theorem for the Laplace--Stieltjes transform and Karamata-type theorems in the framework of regularly log-periodic functions. As an application we determine the exact tail behavior of fixed points of certain type smoothing transforms

Unobtrusive Integration of Data Management With fMRI Analysis

This note describes a software utility, called X-batch which addresses two pressing issues typically faced by functional magnetic resonance imaging (fMRI) neuroimaging laboratories (1) analysis automation and (2) data management. The first issue is addressed by providing a simple batch mode processing tool for the popular SPM software package (http://www.fil.ion. ucl.ac.uk/spm/; Welcome Department of Imaging Neuroscience, London, UK). The second is addressed by transparently recording metadata describing all aspects of the batch job e.g., subject demographics, analysis parameters, locations and names of created files, date and time of analysis, and so on). These metadata are recorded as instances of an extended version of the Protégé-based Experiment Lab Book ontology created by the Dartmouth fMRI Data Center. The resulting instantiated ontology provides a detailed record of all fMRI analyses performed, and as such can be part of larger systems for neuroimaging data management, sharing, and visualization. The X-batch system is in use in our own fMRI research, and is available for download at http://X-batch.sourceforge.net/