ProteinShader: illustrative rendering of macromolecules

<p>Abstract</p> <p>Background</p> <p>Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings.</p> <p>Results</p> <p>The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline.</p> <p>Conclusion</p> <p>By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images.</p

Dark matter, neutron stars and strange quark matter

We show that self-annihilating neutralino WIMP dark matter accreted onto neutron stars may provide a mechanism to seed compact objects with long-lived lumps of strange quark matter, or strangelets, for WIMP masses above a few GeV. This effect may trigger a conversion of most of the star into a strange star. We use an energy estimate for the long-lived strangelet based on the Fermi gas model combined with the MIT bag model to set a new limit on the possible values of the WIMP mass that can be especially relevant for subdominant species of massive neutralinos.Comment: 5 pages, 2 figures, accepted for publication in Phys. Rev. Let

Proteomic Analysis of a Poplar Cell Suspension Culture Suggests a Major Role of Protein S-Acylation in Diverse Cellular Processes

S-acylation is a reversible post-translational modification (PTM) of proteins known to be involved in membrane targeting, subcellular trafficking and the determination of a great variety of functional properties of proteins. The aim of this work was to identify S-acylated proteins in poplar. Th use of an acyl-biotin exchange method and mass spectrometry allowed the identification of around 450 S-acylated proteins, which were subdivided into three major groups of proteins involved in transport, signal transduction and response to stress, respectively. The largest group of S-acylated proteins was the protein kinase superfamily. Soluble N-ethylmaleimide-sensitive factor-activating protein receptors (SNAREs), band 7 family proteins and tetraspanins, all primarily related to intracellular trafficking, were also identified. In addition, cell wall related proteins, including cellulose synthases and other glucan synthases, were found to be S-acylated. Twenty four of the identified S-acylated proteins were also enriched in detergent-resistant membrane microdomains, suggesting S-acylation plays a key role in the localization of proteins to specialized plasma membrane subdomains. This dataset promises to enhance our current understanding of the various functions of S-acylated proteins in plants

Ariel - Volume 4 Number 6

Editors David A. Jacoby Eugenia Miller Tom Williams Associate Editors Paul Bialas Terry Burt Michael Leo Gail Tenikat Editor Emeritus and Business Manager Richard J. Bonnano Movie Editor Robert Breckenridge Staff Richard Blutstein Mary F. Buechler J.D. Kanofsky Rocket Weber David Maye

Gravitational waves and dragging effects

Linear and rotational dragging effects of gravitational waves on local inertial frames are studied in purely vacuum spacetimes. First the linear dragging caused by a simple cylindrical pulse is investigated. Surprisingly strong transversal effects of the pulse are exhibited. The angular momentum in cylindrically symmetric spacetimes is then defined and confronted with some results in literature. In the main part, the general procedure is developed for studying weak gravitational waves with translational but not axial symmetry which can carry angular momentum. After a suitable averaging the rotation of local inertial frames due to such rotating waves can be calculated explicitly and illustrated graphically. This is done in detail in the accompanying paper. Finally, the rotational dragging is given for strong cylindrical waves interacting with a rotating cosmic string with a small angular momentum.Comment: Scheduled to appear in Class. Quantum Grav. July 200

Intelligent Transportation Systems Strategic Plan (Phase I Report)

This interim report on an Intelligent Transportation Systems Strategic (ITS) Plan has been developed as documentation of the process of offering a vision for ITS and recommending an outline for organizational structure, infrastructure, and long-term planning for ITS in Kentucky. This plan provides an overview of the broad scope of ITS and relationships between various Intelligent Vehicle Highway Systems (IVHS) functional areas and ITS user service areas. Three of the functional areas of ITS have been addressed in this interim report with sections devoted to mission, vision, goals, and potential technology applications. Within each of the three areas, recommendations have been made for applications and technologies for deployment. A more formalized business plan for will be developed to recommend specific projects for implementation. Those three functional areas are 1) Advanced Rural Transportation Systems (ARTS), 2) Advanced Traveler Information Systems (ATIS), and 3) Commercial Vehicle Operations (CVO). A survey of other states was conducted to determine the status of the development of ITS strategic plans. Information received from the 11 states that had completed strategic plans was used to determine the overall approach taken in development of the plans and to evaluate the essential contents of the reports for application in Kentucky. Kentucky\u27s ITS Strategic Plan evolved from an early decision by representatives of the Kentucky Transportation Cabinet (KyTC) to formalize the procedure by requesting the Kentucky Transportation Center to prepare a work plan outlining the proposed tasks. Following several introductory meetings of the Study Advisory Committee, additional focus group meetings were held with various transportation representatives to identify ITS issues of importance. Results from these meetings were compiled and used as input to the planning process for development of the Strategic Plan components of ARTS and ATIS. The development of a strategic plan for Commercial Vehicle Operations originated from a different procedure than did the other functional areas of ITS. As part of well-developed commercial vehicle activities through the ITS-related programs of Advantage I-75 and CVISN, Kentucky has become a national leader in this area and has developed a strategic plan of advanced technology applications to commercial vehicles. The strategic plan for Commercial Vehicle Operations was developed out of the convergence of several parallel processes in Kentucky. Empower Kentucky work teams had met over a two-year period to develop improved and more efficient processes for CVO in Kentucky. Their conclusions and recommendations encouraged the further activities of the Kentucky ITS/CVO working group that first convened in the summer of 1996. In an effort to conceptually organize the various ITS/CVO activities in Kentucky, and as a commitment to the CVISN Mainstreaming plan, an inclusive visioning exercise was held in early 1997. Out of this exercise emerged the six critical vision elements that guided the CVO strategic plan. The remaining functional areas to be included in the ITS Strategic Plan will be addressed in the second phase of this study. Those areas are Advanced Traffic Management Systems (ATMS), Advanced Vehicle Control Systems (AVCS), and Advanced Public Transportation Systems (APTS). It is anticipated that a process similar to that developed for the first phase of this study will continue

The epidemiology of fighting in group-housed laboratory mice

Injurious home-cage aggression (fighting) in mice affects both animal welfare and scientific validity. It is arguably the most common potentially preventable morbidity in mouse facilities. Existing literature on mouse aggression almost exclusively examines territorial aggression induced by introducing a stimulus mouse into the home-cage of a singly housed mouse (i.e. the resident/intruder test). However, fighting occurring in mice living together in long-term groups under standard laboratory housing conditions has barely been studied. We performed a point-prevalence epidemiological survey of fighting at a research institution with an approximate 60,000 cage census. A subset of cages was sampled over the course of a year and factors potentially influencing home-cage fighting were recorded. Fighting was almost exclusively seen in group-housed male mice. Approximately 14% of group-housed male cages were observed with fighting animals in brief behavioral observations, but only 14% of those cages with fighting had skin injuries observable from cage-side. Thus simple cage-side checks may be missing the majority of fighting mice. Housing system (the combination of cage ventilation and bedding type), genetic background, time of year, cage location on the rack, and rack orientation in the room were significant risk factors predicting fighting. Of these predictors, only bedding type is easily manipulated to mitigate fighting. Cage ventilation and rack orientation often cannot be changed in modern vivaria, as they are baked in by cookie-cutter architectural approaches to facility design. This study emphasizes the need to invest in assessing the welfare costs of new housing and husbandry systems before implementing them

Order parameter for two-dimensional critical systems with boundaries

Conformal transformations can be used to obtain the order parameter for two-dimensional systems at criticality in finite geometries with fixed boundary conditions on a connected boundary. To the known examples of this class (such as the disk and the infinite strip) we contribute the case of a rectangle. We show that the order parameter profile for simply connected boundaries can be represented as a universal function (independent of the criticality model) raised to the power eta/2. The universal function can be determined from the Gaussian model or equivalently a problem in two-dimensional electrostatics. We show that fitting the order parameter profile to the theoretical form gives an accurate route to the determination of eta. We perform numerical simulations for the Ising model and percolation for comparison with these analytic predictions, and apply this approach to the study of the planar rotor model.Comment: 10 pages, 14 figures. Revisions: Removed many typos, improved presentation of most of the figure

Where constructionism and critical realism converge: interrogating the domain of epistemological relativism

The paper interrogates the status, nature and significance of epistemological relativism as a key element of constructionism and critical realism. It finds that epistemological relativism is espoused by authorities in critical realism and marginalized or displaced in the field of management and organization studies, resulting in forms of analysis that are empirically, but not fully critically, realist. This evaluation prompts reflection on the question of whether, how and with what implications epistemological relativism might be recast at the heart of critical realist studies of management and organization