James R. Ellis

Analysis of emission tomographic scan data: limitations imposed by resolution and background

The proper analysis of positron emission tomographic scan data requires a careful knowledge of the limitations of the tomographic system used so that scan data can be collected and sampled in a manner consistent with those limitations. The present investigation was undertaken to clarify some of the limitations imposed by resolution. The usual imaging situation, e.g., 218FDG , C15O2, or 15O2 , involves imaging structures of limited size in all three dimensions which may appear either warm or cool in relation to some background level of activity. In emission tomography the importance of adequate data sampling within a given plane has been frequently emphasized. Little attention, however, has been given to proper z axis sampling for clinical scanning. The actual selection of regions of interest from scans can have a significant impact on the subsequent statistical analysis. Previous work on this subject has experimentally examined the relationship of object size to quantitative estimation in the hot spot-cold background situation for the one- and two-dimensional cases. Approximate three-dimensional recovery coefficients for the hot spot-cold background situation have been calculated. An examination of the factors discussed above, three-dimensional objects with varying contrast, z axis sampling, and selection of regions of interest, has not yet been addressed in the literature. The purpose of the present investigation is to examine these factors.

Weighted least squares estimation of background in EELS imaging

In quantitative Electron Energy Loss Spectrometry, a weighted least squares estimation should theoretically be used to estimate the background law below core edge energy, since the variances of the data vary. However, it is found that proper weighting makes the above edge signal‐to‐noise ratio decrease rather than increase. This result is discussed, and the influence of the bias introduced by the logarithmic transformation of the data is quantified.

Optimized acquisition parameters and statistical detection limit in quantitative EELS

Optimizing the acquisition parameters for EELS recording has to be accomplished simultaneously from the physical and the statistical points of view; the statistical aspect of the question is covered here. Approximate probability density functions of the variables of interest are derived, which provide a global measure of signal‐to‐noise ratio taking into account every step of the EELS edge area estimation process. Qualitative and quantitative advice is given regarding the critical choice of the estimation and integration energy regions. The notion of visual contrast is presented; it permits the introduction of the concept of statistical detection limit. It is found that for typical experimental conditions, when other factors are equal, the required analysis time for the sample varies approximately as the inverse square of the concentration.

Clinical heterogeneity and molecular findings in five Polish patients with glycerol kinase deficiency: investigation of two splice site mutations with computerized splice junction analysis and Xp21 gene-specific mRNA analysis.

Five cases of glycerol kinase deficiency are presented with clinical, biochemical, and genetic results. Two had the glycerol kinase deficiency as part of an Xp21 contiguous gene deletion syndrome-complex form-and three had an isolated form of the enzyme deficiency. In these we found two splice site mutations (IVS1+4A>G, IVS9-1G>T) and one insertion (1393_1394insG). In patients with the complex form, a deletion of the DAX1, GK genes and the distal part of the DMD gene was found. A computerized study was performed to predict the effects of the splice site mutations. It showed that the IVS9-1G>T mutation substantially altered and removed the wild-type site and enhanced a cryptic site seven nucleotides downstream, and that the IVS1+4A>G diminished the strength of the wild-type donor site from strong to leaky. To verify these predictions, we developed an RT-PCR system with gene-specific primers that exclusively amplifies the Xp21 glycerol kinase gene transcript. Identification of individuals at risk is motivated by a need to avoid delay in a correct diagnosis. For reliable identification of heterozygotes for isolated glycerol kinase deficiency, knowledge of the specific mutation in the proband is required. This is easily obtained with the RT-PCR analyses developed in this study.

Glycerol metabolism and the determination of triglycerides--clinical, biochemical and molecular findings in six subjects.

Abstract Recent recommendations in the National Cholesterol Education Program Expert Panel on Detection, Evaluation and Treatment of High Blood Cholesterol in Adults (ATPIII) are expected to increase the number of triglyceride (TG) determinations and consequently the risk of misinterpretation of “non-blanked” results with co-determination of free glycerol. Glycerol-kinase deficiency (GKD) is one cause of falsely elevated TG results. The natural history of isolated GKD with symptom-free cases and cases with e.g. severe episodes of hypoglycemia and/or ketoacidosis challenges the laboratories to identify cases of GKD and family members at risk. “Blanked” methods reporting both glycerol and TG concentration are therefore desirable. Molecular studies of the glycerol kinase (GK) and DAX1 genes were performed on four cases of “persistent hypertriglyceridemia” found in an Italian population and on two pediatric cases with high serum glycerol concentration. Two new missense mutations were found (C358Y, T96I). Molecular modeling on GK from E. coli, indicate that these mutations are located in parts of the enzyme important for enzyme formation or activity. One splice-site mutation, (IVS9A-1G>A), was found in two brothers. Splice-junction analysis indicates that it destroys the splice site and results in a mixture of mRNA. Deletion of the GK and DAX1 genes was found in one child with symptoms of adrenal failure. A female with glycerolemia and glyceroluria had normal GK activity but possibly slightly decreased ability to oxidize glycerol.

Effects of splicing mutations on NF2-transcripts: Transcript analysis and information theoretic predictions

This study examined the effects of 22 putative splicing mutations in the NF2 gene by means of transcript analysis and information theory based prediction. Fourteen mutations were within the dinucleotide acceptor and donor regions, often referred to as (AG/GT) sequences. Six were outside these dinucleotide regions but within the more broadly defined splicing regions used in the information theory based model. Two others were in introns and outside the broadly defined regions. Transcript analysis revealed exon skipping or activation of one or more cryptic splicing sites for 17 mutations. No alterations were found for the two intronic mutations and for three mutations in the broadly defined splicing regions. Concordance and partial concordance between the calculated predictions and the results of transcript analysis were found for 14 and 6 mutations, respectively. For two mutations, the predicted alteration was not found in the transcripts. Our results demonstrate that the effects of splicing mutations in NF2 are often complex and that information theory based analysis is helpful in elucidating the consequences of these mutations.

Application of simulated poisson statistical processes to stem imaging

The computer generation of Scanning Transmission Electron Microscope (STEM) images is one way of approximating controlled experimental conditions. These STEM images are assumed to be composed of signals derived from Poisson distributed variables; three algorithms for Poisson deviate generation are examined. Relationships between the image acquisition parameters and resulting object contrast are given. An application to evaluation of the minimum detectable elemental concentration in Electron Energy Loss Spectrometry (EELS) images is presented. It is found that for typical experimental conditions, the required analysis time for the sample varies approximately as the inverse square of the concentration (when other factors are equal).