Visual Analysis of Biomolecular Surfaces

Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

Similarity relations in visual search predict rapid visual categorization

How do we perform rapid visual categorization?It is widely thought that categorization involves evaluating the similarity of an object to other category items, but the underlying features and similarity relations remain unknown. Here, we hypothesized that categorization performance is based on perceived similarity relations between items within and outside the category. To this end, we measured the categorization performance of human subjects on three diverse visual categories (animals, vehicles, and tools) and across three hierarchical levels (superordinate, basic, and subordinate levels among animals). For the same subjects, we measured their perceived pair-wise similarities between objects using a visual search task. Regardless of category and hierarchical level, we found that the time taken to categorize an object could be predicted using its similarity to members within and outside its category. We were able to account for several classic categorization phenomena, such as (a) the longer times required to reject category membership; (b) the longer times to categorize atypical objects; and (c) differences in performance across tasks and across hierarchical levels. These categorization times were also accounted for by a model that extracts coarse structure from an image. The striking agreement observed between categorization and visual search suggests that these two disparate tasks depend on a shared coarse object representation.

Visual ecology of Indian carpenter bees II: adaptations of eyes and ocelli to nocturnal and diurnal lifestyles

Most bees are diurnal, with behaviour that is largely visually mediated, but several groups have made evolutionary shifts to nocturnality, despite having apposition compound eyes unsuited to vision in dim light. We compared the anatomy and optics of the apposition eyes and the ocelli of the nocturnal carpenter bee, Xylocopa tranquebarica, with two sympatric species, the strictly diurnal X. leucothorax and the occasionally crepuscular X. tenuiscapa. The ocelli of the nocturnal X. tranquebarica are unusually large (diameter ca. 1 mm) and poorly focussed. Moreover, their apposition eyes show specific visual adaptations for vision in dim light, including large size, large facets and very wide rhabdoms, which together make these eyes 9 times more sensitive than those of X. tenuiscapa and 27 times more sensitive than those of X. leucothorax. These differences in optical sensitivity are surprisingly small considering that X. tranquebarica can fly on moonless nights when background luminance is as low as 10(-5) cd m(-2), implying that this bee must employ additional visual strategies to forage and find its way back to the nest. These strategies may include photoreceptors with longer integration times and higher contrast gains as well as higher neural summation mechanisms for increasing visual reliability in dim light.

Two Tools for Interprocess Communication in Distributed Data-Flow Systems

Abstract is not available.

A model for visual recognition of alphanumerics

In this paper we propose a hypothetical scheme for recognizing the alphanumerics. The scheme is based on the known physiological structure of the visual cortex and the concept of a short Lino extractor nouron (SLEN). We assumo four basic typca of such units for extracting vertical, horizontal, right and left inclined straight line segments. The patterns reconstructed from the scheme show perfect agreement with the test patterns. The model indicates that the recognition of letters T and H requires extraction of the largest number of features.

CFD tools in engineering design studies and medical sciences

In the recent time CFD tools have become increasingly useful in the engineering design studies especially in the area of aerospace vehicles. This is largely due to the advent of high speed computing platforms in addition to the development of new efficient algorithms. The algorithms based on kinetic schemes have been shown to be very robust and further meshless methods offer certain advantages over the other methods. Preliminary investigations of blood flow visualization through artery using CFD tool have shown encouraging results which further needs to be verified and validated.

Open-source tools for enhancing full-text searching of OPACs Use of Koha, Greenstone and Fedora

Purpose - There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text searching. Most of the available open-source digital library software facilitates indexing and searching of full-text documents in different formats. This paper makes an effort to enable full-text search features in the widely used open-source library automation package Koha, by integrating it with two open-source digital library software packages, Greenstone Digital Library Software (GSDL) and Fedora Generic Search Service (FGSS), independently. Design/methodology/approach - The implementation is done by making use of the Search and Retrieval by URL (SRU) feature available in Koha, GSDL and FGSS. The full-text documents are indexed both in Koha and GSDL and FGSS. Findings - Full-text searching capability in Koha is achieved by integrating either GSDL or FGSS into Koha and by passing an SRU request to GSDL or FGSS from Koha. The full-text documents are indexed both in the library automation package (Koha) and digital library software (GSDL, FGSS) Originality/value - This is the first implementation enabling the full-text search feature in a library automation software by integrating it into digital library software.

Fluorescence and visual sensing of nitroaromatic explosives using electron rich discrete fluorophores

Several pi-electron rich fluorescent aromatic compounds containing trimethylsilylethynyl functionality have been synthesized by employing Sonogashira coupling reaction and they were characterized fully by NMR (H-1, C-13)/IR spectroscopy. Incorporation of bulky trimethylsilylethynyl groups on the peripheral of the fluorophores prevents self-quenching of the initial intensity through pi-pi interaction and thereby maintains the spectroscopic stability in solution. These compounds showed fluorescence behavior in chloroform solution and were used as selective fluorescence sensors for the detection of electron deficient nitroaromatics. All these fluorophores showed the largest quenching response with high selectivity for nitroaromatics among the various electron deficient aromatic compounds tested. Quantitative analysis of the fluorescence titration profile of 9,10-bis(trimethylsilylethynyl) anthracene with picric acid provided evidence that this particular fluorophore detects picric acid even at ppb level. A sharp visual detection of 2,4,6-trinitrotoluene was observed upon subjecting 1,3,6,8-tetrakis (trimethylsilylethynyl) pyrene fluorophore to increasing quantities of 2,4,6-trinitrotoluene in chloroform. Furthermore, thin film of the fluorophores was made by spin coating of a solution of 1.0 x 10(-3) M in chloroform or dichloromethane on a quartz plate and was used for the detection of vapors of nitroaromatics at room temperature. The vapor-phase sensing experiments suggested that the sensing process is reproducible and quite selective for nitroaromatic compounds. Selective fluorescence quenching response including a sharp visual color change for nitroaromatics makes these fluorophores as promising fluorescence sensory materials for nitroaromatic compounds (NAC) with a detection limit of even ppb level as judged with picric acid.

A Gradient-Based Comparison Measure for Visual analysis of Multifield Data

We introduce a multifield comparison measure for scalar fields that helps in studying relations between them. The comparison measure is insensitive to noise in the scalar fields and to noise in their gradients. Further, it can be computed robustly and efficiently. Results from the visual analysis of various data sets from climate science and combustion applications demonstrate the effective use of the measure.

A Flexure-based Deployable Stereo Vision Mechanism and Temperature and Force Sensors for Laparoscopic Tools

This paper presents concepts, designs, and working prototypes of enhanced laparoscopic surgical tools. The enhancements are in equipping the tool with force and temperature sensing as well as image acquisition for stereo vision. Just as the pupils of our eyes are adequately spaced out and the distance between them is adjustable, two minute cameras mounted on a mechanism in our design can be moved closer or farther apart inside the inflated abdomen during the surgery. The cameras are fitted to a deployable mechanism consisting of flexural joints so that they can be inserted through a small incision and then deployed and moved as needed.A temperature sensor and a force sensor are mounted on either of the gripping faces of the surgical grasping tool to measure the temperature and gripping force, which need to be controlled for safe laparoscopic surgery. The sensors are small enough and hence they do not cause interference during surgery and insertion.Prototyping and working of the enhanced laparoscopic tool are presented with details