A set of external reference controls/probes that enable quality assurance between different microarray platforms.

RNA external standards, although important to ensure equivalence across many microarray platforms, have yet to be fully implemented in the research community. In this article, a set of unique RNA external standards (or RNA standards) and probe pairs that were added to total RNA in the samples before amplification and labeling are described. Concentration-response curves of RNA external standards were used across multiple commercial DNA microarray platforms and/or quantitative real-time polymerase chain reaction (RT-PCR) and next-generation sequencing to identify problematic assays and potential sources of variation in the analytical process. A variety of standards can be added in a range of concentrations spanning high and low abundances, thereby enabling the evaluation of assay performance across the expected range of concentrations found in a clinical sample. Using this approach, we show that we are able to confirm the dynamic range and the limit of detection for each DNA microarray platform, RT-PCR protocol, and next-generation sequencer. In addition, the combination of a series of standards and their probes was investigated on each platform, demonstrating that multiplatform calibration and validation is possible.

An iterative compensation approach without linearization of projector responses for multiple-projector system.

We aim to realize a new and simple compensation method that robustly handles multiple-projector systems without recourse to the linearization of projector response functions. We introduce state equations, which distribute arbitrary brightness among the individual projectors, and control the state equations according to the feedback from a camera. By employing the color-mixing matrix with gradient of projector responses, we compensate the controlled brightness input to each projector. Our method dispenses with cooperation among multiple projectors as well as time-consuming photometric calibration. Compared with existing methods, our method is shown to offer superior compensation performance and a more effective way of compensating multiple-projector systems.

Simple camera calibration from a single image using five points on two orthogonal 1-D objects.

We propose a simple and practical calibration technique that effectively estimates camera parameters from just five points on two orthogonal 1-D objects, each which has three collinear points, one of which is shared. We derive the basic equations needed to realize camera calibration from just five points observed on a single image that captures the objects. We describe a new camera calibration algorithm that estimates the camera parameters based on the basic equations and optimizes them by the bundle adjustment technique. Our method is validated by both computer simulated data and real images. The results show that the camera parameters yielded by our method are close to those yielded by existing methods. The tests demonstrate that our method is both effective and practical.

Motion and shape recovery based on iterative stabilization for modest deviation from planar motion.

We describe an iterative stabilization method that can simultaneously recover camera motion and 3D shape from an image sequence captured under modest deviation from planar motion. This technique iteratively applies a factorization method based on planar motion and can approximate the observed image points to the 2D points projected under planar motion by stabilizing the camera motion. We apply the proposed method to aerial images acquired by a helicopter-borne camera and show better reconstruction of both motion and shape than Christy-Horaud's perspective factorization. Moreover, we confirm that the reprojection errors calculated from the recovered camera motion and 3D shape are very similar to the optimum results yielded by bundle adjustment.

Arabidopsis 3-deoxy-D-manno-oct-2-ulosonate-8-phosphate synthase: cDNA cloning and expression analyses.

The molecular characterization of two isoforms of 3-deoxy-d-manno-oct-2-ulosonate (KDO) -8-phosphate synthase (AtkdsA1 and AtkdsA2) from Arabidopsis is reported here. First, by isolating a full-length cDNA for AtkdsA1, it was confirmed that the deduced primary structures of AtkdsA1 and AtkdsA2 proteins were 93% identical. Functional expression and purification studies demonstrated the efficient catalytic activity of the AtkdsA1 enzyme to produce KDO-8-phosphate from phosphoenolpyruvate and d-arabinose-5-phosphate. RT-PCR and RNA-gel blot analysis revealed different expression profiles for both genes; the AtkdsA1 gene was predominantly expressed in the shoots, while the AtkdsA2 transcript accumulated to a higher level in the roots, implicating differential roles of these isoforms in planta.

Purification and cDNA cloning of UDP-D-glucuronate carboxy-lyase (UDP-D-xylose synthase) from pea seedlings.

Uridine diphospho-D-glucuronate carboxy-lyase (UDP-D-xylose synthase; EC 4.1.1.35), which catalyzes the conversion of UDP-D-glucuronate to UDP-D-xylose, was purified to apparent homogenity from pea (Pisum sativum L.) seedlings. The pH optimum for enzyme activity was around 5-6, and the activity was not affected by exogeneously supplied NAD+ and NADH. The purified enzyme had a molecular weight of 250 kDa and consisted of 42 kDa polypeptides. Based on the amino acid sequence, a probe (400 bp) was prepared with degenerate primers by a reverse transcriptase-PCR. Using this probe, a clone encoding 346 amino acid residues was screened from a pea cDNA library. The recombinant protein expressed in Escherichia coli catalyzed conversion of UDP-D-glucuronate to UDP-D-xylose, confirming that the isolated clone encoded UDP-D-glucuronate carboxy-lyase.