Standardized evaluation methodology for 2-D-3-D registration

In the past few years, a number of two-dimensional (2-D) to three-dimensional (3-D) (2-D-3-D) registration algorithms have been introduced. However, these methods have been developed and evaluated for specific applications, and have not been directly compared. Understanding and evaluating their performance is therefore an open and important issue. To address this challenge we introduce a standardized evaluation methodology, which can be used for all types of 2-D-3-D registration methods and for different applications and anatomies. Our evaluation methodology uses the calibrated geometry of a 3-D rotational X-ray (3DRX) imaging system (Philips Medical Systems, Best, The Netherlands) in combination with image-based 3-D-3-D registration for attaining a highly accurate gold standard for 2-D X-ray to 3-D MR/CT/3DRX registration. Furthermore, we propose standardized starting positions and failure criteria to allow future researchers to directly compare their methods. As an illustration, the proposed methodology has been used to evaluate the performance of two 2-D-3-D registration techniques, viz. a gradient-based and an intensity-based method, for images of the spine. The data and gold standard transformations are available on the internet (http://www.isi.uu.nl/Research/Databases/).     

Rapid forensic analysis and identification of ''lilac'' architectural finishes using Raman spectroscopy

The potential of Raman spectroscopy to discriminate between architectural finishes (household paint) has been investigated using a test set of 51 'lilac' paints and three different excitation wavelengths. The spectra obtained with visible excitation typically displayed a series of intense Raman bands on a featureless fluorescence background but the spectra of all the paints studied had essentially identical bands. With 785 nm excitation, although the same bands that dominated the 514 nm spectra were still observed, other bands with comparable intensity also appeared. The two strongest scattering constituents were identified as a dioxazine dye, Violet 23 and beta-Cu(phthalocyanine). A scatter plot of the intensities of marker bands for these constituents (normalized to the strong rutile bands that were always present) showed that, despite the fact that the sample set spanned a wide range of rutile : dioxazine dye : phthalo- cyanine ratios, many of the samples had very similar ratios and could not be discriminated. However, all the samples (even those with similar relative proportions of the main constituents) could be discriminated on the basis of their minor constituents, either by manually measuring band intensities or through the creation and searching of spectral libraries.     

Toward in-cylinder absorption tomography in a production engine

Design requirements for an 8000 frame/s dual-wavelength ratiometric chemical species tomography system, intended for hydrocarbon vapor imaging in one cylinder of a standard automobile engine, are examined. The design process is guided by spectroscopic measurements on iso-octane and by comprehensive results from laboratory phantoms and research engines, including results on temporal resolution performance. Novel image reconstruction techniques, necessary for this application, are presented. Recent progress toward implementation, including details of the optical access arrangement employed and signal-to-noise issues, is described. We present first cross-cylinder IR absorption measurements from a reduced channel-count (nontomographic) system and discuss the prospects for imaging.     

Enhanced undecylprodigiosin production from Serratia marcescens SS-1 by medium formulation and amino-acid supplementation

Serratia marcescens Simon Swift-1 (SS-1) was used to produce a prodigiosin-like pigment, undecylprodigiosin (UP), known to have antitumor activities and potential as an anticancer drug. Modified media containing components of Luria-Bertani (LB) broth and selected amino acids were used to improve UP production from S. marcescens SS-1. Optimal culture conditions (e.g., temperature, pH, agitation rate) for UP production were also identified. It was found that S. marcescens SS-1 was able to produce 690 mg l-1 of UP when it was grown with 5 g l-1 yeast extract alone (YE medium) under the optimal culture conditions of 30 degrees C, 200 rpm, and pH 8. The UP production of 690 mg l-1 is nearly 23-fold of that obtained from original LB medium. Addition of amino acids containing pyrrole-like structures further enhanced UP production. Nearly 2 and 1.4 g l-1 of UP was produced when the SS-1 strain was cultivated with YE medium supplemented with proline and histidine (5 g l-1), respectively. Moreover, the addition of aspartic acid (5 g l-1) also resulted in a high UP production of 1.4 g l-1. Optimal dosages of the three amino acids were subsequently determined and the highest UP production (2.5 g l-1) was achieved with the addition of 10 g l-1 of proline. This suggests that the supplementation of amino acids related to the formation of a UP precursor (e.g., pyrrolylpyrromethene) could enhance UP production by the SS-1 strain.     

Enhancements to GPS operations and clock evaluations using a "total" Hadamard deviation

We describe a method based on the total deviation approach whereby we improve the confidence of the estimation of the Hadamard deviation that is used primarily in global positioning system (GPS) operations. The Hadamard-total deviation described in this paper provides a significant improvement in confidence indicated by an increase of 1.3 to 3.4 times the one degree of freedom of the plain Hadamard deviation at the longest averaging time. The new Hadamard-total deviation is slightly negatively biased with respect to the usual Hadamard deviation, and tau values are restricted to less than or equal to T/3, to be consistent with the usual Hadamard's definition. We give a method of automatically removing bias by a power-law detection scheme. We review the relationship between Kalman filter parameters and the Hadamard and Allan variances, illustrate the operational problems associated with estimating these parameters, and discuss how the Hadamard-total variance can improve management of present and future GPS satellite clocks.     

Gold nanoparticles quench fluorescence by phase induced radiative rate suppression

The fluorescence quantum yield of Cy5 molecules attached to gold nanoparticles via ssDNA spacers is measured for Cy5-nanoparticle distances between 2 and 16 nm. Different numbers of ssDNA per nanoparticle allow to fine-tune the distance. The change of the radiative and nonradiative molecular decay rates with distance is determined using time-resolved photoluminescence spectroscopy. Remarkably, the distance dependent quantum efficiency is almost exclusively governed by the radiative rate.     

Structural model of the Plasmodium CDK, Pfmrk, a novel target for malaria therapeutics

Malaria, with 300-500 million clinical cases resulting in 1-3 million fatalities a year, is one of the most deadly tropical diseases. As current antimalarial therapeutics become increasingly ineffective due to parasitic resistance, there exists an urgent need to develop and pursue new therapeutic strategies. Recent genome sequencing and molecular cloning projects have identified several enzymes from Plasmodium (P.) falciparum that may represent novel drug targets, including a family of proteins that are homologous to the mammalian cyclin-dependent kinases (CDKs). CDKs are essential for the control of the mammalian cell cycle and, based on the conservation of the CDKs across species, the plasmodial CDKs are expected to play a crucial role in parasitic growth. Here we present a 3D structural model of Pfmrk, a putative human CDK activating kinase (CAK) homolog in P. falciparum. Notable features of the present structural model include: (1) parameterization of the Mg2+ hexacoordination system using ab initio quantum chemical calculations to accurately represent the ATP-kinase interaction; and (2) comparison between the docking scores and measured binding affinities for a series of oxindole-based Pfmrk inhibitors of known activity. Detailed analysis of inhibitor-Pfmrk binding interactions enabled us to identify specific residues (viz. Met66, Met75, Met91, Met94 and Phe143) within the Pfmrk binding pocket that may play an important role in inhibitor binding affinity and selectivity. The availability of this Pfmrk structural model, together with insights gained from analysis of ligand-receptor interactions, should promote the rational design of potent and selective Pfmrk inhibitors as antimalarial therapeutics.