Informatics methods to enable sharing of quantitative imaging research data

Introduction

The National Cancer Institute Quantitative Research Network (QIN) is a collaborative research network whose goal is to share data, algorithms and research tools to accelerate quantitative imaging research. A challenge is the variability in tools and analysis platforms used in quantitative imaging. Our goal was to understand the extent of this variation and to develop an approach to enable sharing data and to promote reuse of quantitative imaging data in the community.

Methods

We performed a survey of the current tools in use by the QIN member sites for representation and storage of their QIN research data including images, image meta-data and clinical data. We identified existing systems and standards for data sharing and their gaps for the QIN use case. We then proposed a system architecture to enable data sharing and collaborative experimentation within the QIN.

Results

There are a variety of tools currently used by each QIN institution. We developed a general information system architecture to support the QIN goals. We also describe the remaining architecture gaps we are developing to enable members to share research images and image meta-data across the network.

Conclusions

As a research network, the QIN will stimulate quantitative imaging research by pooling data, algorithms and research tools. However, there are gaps in current functional requirements that will need to be met by future informatics development. Special attention must be given to the technical requirements needed to translate these methods into the clinical research workflow to enable validation and qualification of these novel imaging biomarkers.     

Use of a temperature‐programmable injector coupled to gas chromatography–combustion–isotope ratio mass spectrometry for compound‐specific carbon isotopic analysis of polycyclic aromatic hydrocarbons

Compound‐specific isotopic analysis (CSIA) can provide information about the origin of analysed compounds; for instance, polycyclic aromatic hydrocarbons (PAHs) in aerosols. This could be a valuable tool in source apportionment of particulate matter (PM) air pollution. Because gas chromatography–combustion–isotope ratio mass spectrometry (GC‐C‐IRMS) analysis requires an amount of at least 10 ng of an individual PAH, a high concentration of PAHs in the injected extract is needed. When the concentration is low a large volume injector creates the possibility of introducing a satisfactory amount of individual PAHs. In this study a temperature‐programmable injector was coupled to GC‐C‐IRMS and injection parameters (solvent level, transfer column flow, transfers time) were optimised using six solid aromatic compounds (anthracene, fluoranthene, pyrene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene) dissolved in n‐pentane and EPA 610 reference mixture. CSIA results for solid PAHs were compared with results obtained for the single components analysed by elemental analysis–isotope ratio mass spectrometry. The injection method was validated for two sample injection volumes, 50 and 100 µL. This method was also compared with commonly used splitless injection. To be included in the study, measurements had to have an uncertainty lower than 0.5‰ for and a minimum peak height of 200 mV. The lower concentration limits at which these criteria were fulfilled for PAHs were 30 mg/L for 1 µL in splitless injection and 0.3 and 0.2 mg/L for 50 and 100 µL, respectively, in large volume injection. Copyright © 2009 John Wiley & Sons, Ltd.     

Determination of loads applied perpendicularly to the outer boundary of a ring using coefficients of influence

A procedure is explained to determined the amount of several pairs of diametrical loads applied to the outside boundary of a ring when stresses at selected points of the inside or outside boundaries are known. Coefficients of influence are used, following an approach similar to the one presented in a previous paper. Examples of application are given and the possible increase in precision is shown when the number of points of measurements is larger than the number of loads to be determined.     

Accommodation of oxygen loss in WO3 equilibrated with CO + CO2 buffers

Tungsten trioxide reduced at about 1270 K by means of controlled atmospheres (P₀₂ = 3.7 · 10^?8 to 1.7 · 10^?13 atm) was studied by high resolution transmission electron microscopy, electron diffraction, and X-ray powder diffraction. The accommodation of oxygen loss in the parent WO₃ lattice in the range WO₃ to WO_2.72 was clarified. The results indicate a solid state mechanism. Intergrowth has been found to take place between several of the structural types that occur in this composition range. The intergrowth features include directional changes in shear plane arrays (“swinging shear planes”). Details of the structural variation with the oxygen content are reported. Ordered shear planes on {102} directions were found to stabilize the orthorhombic WO₃ parent lattice at room temperature. W₂₄O₆₈ has been prepared in a fairly well-defined state.     

Fast carbon-carbon bond formation by a promiscuous lipase

Lipase B from Candida antarctica was redesigned to catalyze the promiscuous reaction of carbon-carbon bond formation. Mutation of the catalytic serine to alanine afforded a mutant that catalyzed Michael additions of 1,3-dicarbonyls to alpha,beta-unsaturated carbonyl compounds at high specific rates, such as 4000 s-1. The enzyme-catalyzed Michael addition reaction followed saturation kinetics and showed substrate inhibition. The designed enzyme showed high rate enhancements with a catalytic proficiency higher than 108, which is on the same level as that observed for enzymes with native substrates.     

Impact of azaproline on amide cis-trans isomerism: conformational analyses and NMR studies of model peptides including TRH analogues

The beta-turn is a well-studied motif in both proteins and peptides. Four residues, making almost a complete 180 degree-turn in the direction of the peptide chain, define the beta-turn. Several types of the beta-turn are defined according to Phi and Psi torsional angles of the backbone for residues i + 1 and i + 2. One special type of beta-turn, the type VI-turn, usually contains a proline with a cis-amide bond at residue i + 2. In an aza-amino acid, the alpha-carbon of the amino acid is changed to nitrogen. Peptides containing azaproline (azPro) have been shown to prefer the type VI beta-turn both in crystals and in organic solvents by NMR studies. MC/MD simulations using the GB/SA solvation model for water explored the conformational preferences of azPro-containing peptides in aqueous systems. An increase in the conformational preference for the cis-amide conformer of azPro was clearly seen, but the increased stability was relatively minor with respect to the trans-conformer as compared to previous suggestions. To test the validity of the calculations in view of the experimental data from crystal structures and NMR in organic solvents, [azPro(3)]-TRH and [Phe(2), azPro(3)]-TRH were synthesized, and their conformational preferences were determined by NMR in polar solvents as well as the impact of the azPro substitution on their biological activities.