A LabVIEW® based generic CT scanner control software platform

UGCT, the Centre for X-ray tomography at Ghent University (Belgium) does research on X-ray tomography and its applications. This includes the development and construction of state-of-the-art CT scanners for scientific research. Because these scanners are built for very different purposes they differ considerably in their physical implementations. However, they all share common principle functionality. In this context a generic software platform was developed using LabVIEW (R) in order to provide the same interface and functionality on all scanners. This article describes the concept and features of this software, and its potential for tomography in a research setting. The core concept is to rigorously separate the abstract operation of a CT scanner from its actual physical configuration. This separation is achieved by implementing a sender-listener architecture. The advantages are that the resulting software platform is generic, scalable, highly efficient, easy to develop and to extend, and that it can be deployed on future scanners with minimal effort

Draft crystal structure of the vault shell at 9-A resolution.

Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct of major vault protein (termed cpMVP vaults), diffracting to about 9-A resolution. The asymmetric unit contains a half vault of molecular mass 4.65 MDa. X-ray phasing was initiated by molecular replacement, using density from cryo-electron microscopy (cryo-EM). Phases were improved by density modification, including concentric 24- and 48-fold rotational symmetry averaging. From this, the continuous cryo-EM electron density separated into domain-like blocks. A draft atomic model of cpMVP was fit to this improved density from 15 domain models. Three domains were adapted from a nuclear magnetic resonance substructure. Nine domain models originated in ab initio tertiary structure prediction. Three C-terminal domains were built by fitting poly-alanine to the electron density. Locations of loops in this model provide sites to test vault functions and to exploit vaults as nanocapsules

A flexible and modular X-ray micro and sub-micron CT scanner for multi-resolution and interdisciplinary research

Several types of CT systems are commercially available, but they are typically focusing on one specific range of samples and are therefore limited in terms of resolution or sample size. They come in closed cabinets and have pre-defined acquisition routines. These restrictions are often limiting the experimental freedom necessary to apply X-ray tomography to its full extent as required when the technique is used in a very wide range of applications and imaging resolutions. UGCT has designed and built a modular micro/sub-micron CT scanner with maximal flexibility destined for multi-resolution imaging of samples from many research disciplines. Its dual source / dual detector design with eight motorized axes and in-house developed acquisition software offers the possibility to optimize acquisition depending on the type and size of sample under investigation

Aerospace medicine and biology. A continuing bibliography (supplement 231)

This bibliography lists 284 reports, articles, and other documents introduced into the NASA scientific and technical information system in March 1982

Effect of blade geometry on the aerodynamic loads produced by vertical-axis wind turbines

Accurate aerodynamic modelling of vertical-axis wind turbines poses a significant challenge. The rotation of the turbine induces large variations in the angle of attack of its blades that can manifest as dynamic stall. In addition, interactions between the blades of the turbine and the wake that they produce can result in impulsive changes to the aerodynamic loading. The Vorticity Transport Model has been used to simulate the aerodynamic performance and wake dynamics of three different vertical-axis wind turbine configurations. It is known that vertical-axis turbines with either straight or curved blades deliver torque to their shaft that fluctuates at the blade passage frequency of the rotor. In contrast, a turbine with helically twisted blades delivers a relatively steady torque to the shaft. In this article, the interactions between helically twisted blades and the vortices within their wake are shown to result in localized perturbations to the aerodynamic loading on the rotor that can disrupt the otherwise relatively smooth power output that is predicted by simplistic aerodynamic tools that do not model the wake to sufficient fidelity. Furthermore, vertical-axis wind turbines with curved blades are shown to be somewhat more susceptible to local dynamic stall than turbines with straight blades

Extracting respiratory signals from thoracic cone beam CT projections

Patient respiratory signal associated with the cone beam CT (CBCT) projections is important for lung cancer radiotherapy. In contrast to monitoring an external surrogate of respiration, such signal can be extracted directly from the CBCT projections. In this paper, we propose a novel local principle component analysis (LPCA) method to extract the respiratory signal by distinguishing the respiration motion-induced content change from the gantry rotation-induced content change in the CBCT projections. The LPCA method is evaluated by comparing with three state-of-the-art projection-based methods, namely, the Amsterdam Shroud (AS) method, the intensity analysis (IA) method, and the Fourier-transform based phase analysis (FT-p) method. The clinical CBCT projection data of eight patients, acquired under various clinical scenarios, were used to investigate the performance of each method. We found that the proposed LPCA method has demonstrated the best overall performance for cases tested and thus is a promising technique for extracting respiratory signal. We also identified the applicability of each existing method.Comment: 21 pages, 11 figures, submitted to Phys. Med. Bio

Geometric Mixing, Peristalsis, and the Geometric Phase of the Stomach

Mixing fluid in a container at low Reynolds number - in an inertialess environment - is not a trivial task. Reciprocating motions merely lead to cycles of mixing and unmixing, so continuous rotation, as used in many technological applications, would appear to be necessary. However, there is another solution: movement of the walls in a cyclical fashion to introduce a geometric phase. We show using journal-bearing flow as a model that such geometric mixing is a general tool for using deformable boundaries that return to the same position to mix fluid at low Reynolds number. We then simulate a biological example: we show that mixing in the stomach functions because of the "belly phase": peristaltic movement of the walls in a cyclical fashion introduces a geometric phase that avoids unmixing.Comment: Revised, published versio

Cilia-mediated signalling in the embryonic nodes: A computational fluid-structure-protein interaction (FSPI) model

This paper was presented at the 2nd Micro and Nano Flows Conference (MNF2009), which was held at Brunel University, West London, UK. The conference was organised by Brunel University and supported by the Institution of Mechanical Engineers, IPEM, the Italian Union of Thermofluid dynamics, the Process Intensification Network, HEXAG - the Heat Exchange Action Group and the Institute of Mathematics and its Applications.The breaking of left-right symmetry in the mammalian embryo is believed to occur in a transient embryonic structure, the node, when cilia create a leftward flow of liquid. It has been widely confirmed that this nodal flow is the first sign of left-right differentiation; however, the mechanism through which embryonic cilia produce their movement and how the leftward flow confers laterality are still requiring investigation. The ciliary motility in the embryonic node involves complex dynein activations and the handed information is transmitted to the cells by the flow produced by cilia, either mechanically and/or by advection of a chemical species. In this paper, we present a computational model of ciliary ultrastructure (protein-structure model) and discuss the scenarios that incorporate this internal microtubule-dynein system with the external fluidic environment (fluid-structure-protein interaction model, FSPI). By employing computational fluid dynamics, deformable mesh computational techniques and fluid-structure interaction analysis, and solving the three-dimensional unsteady transport equations, the protein-triggered mechanism of nodal ciliary motility has been studied, which is a primary component for the FSPI model. Future work regarding the integrative model is discussed, that will provide more accurate quantitative information on the flow rate, ciliary motion, and molecule/ particle transport in the embryonic node and support the plausibility of hypotheses regarding left-right information transmission

A high performance scanning force microscope head design

A stable and highly sensitive scanning force microscope head design is presented. The head provides an implementation of the optical lever detection method in which mechanical vibration noise has been minimized