Gremlin: an interactive visualization model for analyzing genomic rearrangements

In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously scaled from the high-level, complete genome perspective, down to the low-level, structural rearrangement view, while preserving global context at all times. We have implemented these techniques in Gremlin, a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.     

基于MapX的高速公路动态拓扑结构的构建

最优路径分析是地理信息系统(GIS,Geographic Information System)网络分析的基础,而道路网络拓扑结构的构建又是最优路径分析的关键.结合高速公路网和MapX组件的特点,将MapX控件与Visual C++ 6.0开发平台相结合,采用数据结构中的邻接表来表示高速公路网络的拓扑结构.仿真结果表明,对高速公路电子地图中任意选定的某条道路或某些区域,系统都能形成所选区域中道路之间的拓扑关系,并将提取出的相关道路的路网信息自动存储到数据库中,从而为后续的道路交通仿真及事故救援时进行最优路径搜索提供必要的信息.     

Magnetic compound refractive lens for focusing and polarizing cold neutron beams

Biconcave cylindrical lenses are used to focus beams of x rays or neutrons using the refractive properties of matter. In the case of neutrons, the refractive properties of magnetic induction can similarly focus and simultaneously polarize the neutron beam without the concomitant attenuation of matter. This concept of a magnetic refractive lens was tested using a compound lens consisting of 99 pairs of cylindrical permanent magnets. The assembly successfully focused the intensity of a white beam of cold neutrons of one spin state at the detector, while defocusing the other. This experiment confirmed that a lens of this nature may boost the intensity locally by almost an order of magnitude and create a polarized beam. An estimate of the performance of a more practically dimensioned device suitable for incorporation in reflectometers and slit-geometry small angle scattering instruments is given.     

Practical considerations for high spatial and temporal resolution dynamic transmission electron microscopy

Although recent years have seen significant advances in the spatial resolution possible in the transmission electron microscope (TEM), the temporal resolution of most microscopes is limited to video rate at best. This lack of temporal resolution means that our understanding of dynamic processes in materials is extremely limited. High temporal resolution in the TEM can be achieved, however, by replacing the normal thermionic or field emission source with a photoemission source. In this case the temporal resolution is limited only by the ability to create a short pulse of photoexcited electrons in the source, and this can be as short as a few femtoseconds. The operation of the photo-emission source and the control of the subsequent pulse of electrons (containing as many as 5 x 10(7) electrons) create significant challenges for a standard microscope column that is designed to operate with a single electron in the column at any one time. In this paper, the generation and control of electron pulses in the TEM to obtain a temporal resolution <10(-6)s will be described and the effect of the pulse duration and current density on the spatial resolution of the instrument will be examined. The potential of these levels of temporal and spatial resolution for the study of dynamic materials processes will also be discussed.     

ProteinParser--a community based tool for the generation of a detailed protein consensus and FASTA output

Comparison of bioinformatic data is a common application in the life sciences and beyond. In this communication, a novel Java based software tool, ProteinParser, is outlined. This software tool calculates a detailed consensus, or most common, amino acid at a given position in an aligned protein set, whilst also generating a full consensus protein FASTA output. A second application of this software tool, computing a consensus amino acid given a tolerance threshold, is also demonstrated. The phytase and the common bacterial beta-lactamase proteins are analysed as 'proof of concept' examples. Consensus proteins, as generated by ProteinParser, are regularly utilised in the selection of residues for protein stabilisation mutagenesis; however, this widely applicable software tool will find many alternative applications in areas such as protein homology modelling.     

Perceptual issues in the use of head-mounted visual displays

OBJECTIVE: We provide a review and analysis of much of the published literature on visual perception issues that impact the design and use of head-mounted displays (HMDs). BACKGROUND: Unlike the previous literature on HMDs, this review draws heavily from the basic vision literature in order to help provide insight for future design solutions for HMDs. METHOD: Included in this review are articles and books found cited in other works as well as articles and books obtained from an Internet search. RESULTS: Issues discussed include the effect of brightness and contrast on depth of field, dark focus, dark vergence, and perceptual constancy; the effect of accommodation-vergence synergy on perceptual constancy, eyestrain, and discomfort; the relationship of field of view to the functioning of different visual pathways and the types of visual-motor tasks mediated by them; the relationship of binocular input to visual suppression; and the importance of head movements, head tracking, and display update lag. CONCLUSION: This paper offers a set of recommendations for the design and use of HMDs. APPLICATION: Consideration of the basic vision literature will provide insight for future design solutions for HMDs.     

A memory-based model for planning target reach postures in the presence of obstructions

Existing posture prediction and motion simulation models generally lack the capability of simulating human obstruction avoidance during target reach. This compromises the utility of digital human models for ergonomics, as many design problems involve interactions between humans and obstructions. To address this problem, this paper presents a novel memory-based posture planning (MBPP) model, which plans reach postures that avoid obstructions. In this model, the task space is partitioned into small regions called cells. For a given human figure, each cell is linked to a memory that stores various alternative postures for reaching the cell. When a posture planning problem is given in terms of a target and an obstruction configuration, the model examines postures belonging to the relevant cell, selects collision-free ones and modifies them to exactly meet the hand target acquisition constraint. Simulation results showed that the MBPP model is capable of rapidly and robustly planning reach postures for various scenarios.     

Receptive field structures for recognition

Localized operators, like Gabor wavelets and difference-of-gaussian filters, are considered useful tools for image representation. This is due to their ability to form a sparse code that can serve as a basis set for high-fidelity reconstruction of natural images. However, for many visual tasks, the more appropriate criterion of representational efficacy is recognition rather than reconstruction. It is unclear whether simple local features provide the stability necessary to subserve robust recognition of complex objects. In this article, we search the space of two-lobed differential operators for those that constitute a good representational code under recognition and discrimination criteria. We find that a novel operator, which we call the dissociated dipole, displays useful properties in this regard. We describe simple computational experiments to assess the merits of such dipoles relative to the more traditional local operators. The results suggest that nonlocal operators constitute a vocabulary that is stable across a range of image transformations.