Robustness of correlations between PCA of FDG-PET scans and biological variables in healthy and demented subjects.

In neuroimaging it is helpful and useful to obtain robust and accurate estimates of relationships between the image derived data and separately derived covariates such as clinical and demographic measures. Due to the high dimensionality of brain images, complex image analysis is typically used to extract certain image features, which may or may not relate to the covariates. These correlations which explain variance within the image data are frequently of interest. Principal component analysis (PCA) is used to extract image features from a sample of 42 FDG PET brain images (19 normal controls (NCs), 23 Alzheimer's disease (AD) patients). For the first three most robust PCs, the correlation of the PC scores with: i) the Mini Mental Status Exam (MMSE) score and ii) age is examined. The key aspects of this work is the assessment of: i) the robustness and significance of the correlations using bootstrap resampling; ii) the influence of the PCA on the robustness of the correlations; iii) the impact of two intensity normalization methods (global and cerebellum). Results show that: i) Pearson's statistics can lead to overoptimistic results. ii) The robustness of the correlations deteriorate with the number of PCs. iii) The correlations are hugely influenced by the method of intensity normalization: the correlation of cognitive impairment with PC1 are stronger and more significant for global normalization; whereas the correlations with age were strongest and more robust with PC2 and cerebellar normalization.

Verification of predicted robustness and accuracy of multivariate analysis.

The assessment of accuracy and robustness of multivariate analysis of FDG-PET brain images as presented in [Markiewicz, P.J., Matthews, J.C., Declerck, J., Herholz, K., 2009. Robustness of multivariate image analysis assessed by resampling techniques and applied to FDG-PET scans of patients with Alzheimer's disease. Neuroimage 46, 472-485.] using a homogeneous sample (from one centre) of small size is here verified using a heterogeneous sample (from multiple centres) of much larger size. Originally the analysis, which included principal component analysis (PCA) and Fisher discriminant analysis (FDA), was established using a sample of 42 subjects (19 Normal Controls (NCs) and 23 Alzheimer's disease (AD) patients) and here the analysis is verified using an independent sample of 166 subjects (86 NCs and 80 ADs) obtained from the ADNI database. It is shown that bootstrap resampling combined with the metric of the largest principal angle between PCA subspaces as well as the deliberate clinical misdiagnosis simulation can predict robustness of the multivariate analysis when used with new datasets. Cross-validation (CV) and the .632 bootstrap overestimated the predictive accuracy encouraging less robust solutions. Also, it is shown that the type of PET scanner and image reconstruction method has an impact on such analysis and affects the accuracy of the verification sample.

Robustness of multivariate image analysis assessed by resampling techniques and applied to FDG-PET scans of patients with Alzheimer's disease.

For finite and noisy samples extraction of robust features or patterns which are representative of the population is a formidable task in which over-interpretation is not uncommon. In this work, resampling techniques have been applied to a sample of 42 FDG PET brain images of 19 healthy volunteers (HVs) and 23 Alzheimer's disease (AD) patients to assess the robustness of image features extracted through principal component analysis (PCA) and Fisher discriminant analysis (FDA). The objective of this work is to: 1) determine the relative variance described by the PCA to the population variance; 2) assess the robustness of the PCA to the population sample using the largest principal angle between PCA subspaces; 3) assess the robustness and accuracy of the FDA. Since the sample does not have histopathological data the impact of possible clinical misdiagnosis on the discrimination analysis is investigated. The PCA can describe up to 40% of the total population variability. Not more than the first three or four PCs can be regarded as robust on which a robust FDA can be build. Standard error images showed that regions close to the falx and around ventricles are less stable. Using the first three PCs, sensitivity and specificity were 90.5% and 96.9% respectively. The use of resampling techniques in the evaluation of the robustness of many multivariate image analysis methods enables researchers to avoid over-analysis when using these methods applied to many different neuroimaging studies often with small sample sizes.

Lac repressor genetic map in real space.

Here, we present a graphic display of the phenotypes of more than 4000 single amino acid substitution mutations on the three-dimensional structure of the lac repressor tetramer bound to DNA. The genetic data and the X-ray diffraction studies contribute to define an allosteric mechanism and yield a visual demonstration of the importance of core or buried residues in protein structure.

CSF total and phosphorylated tau protein, regional glucose metabolism and dementia severity in Alzheimer's disease.

BACKGROUND AND PURPOSE: We investigated associations between severity of cognitive impairment, cerebrospinal fluid (CSF) concentrations of total-tau (t-tau) protein and tau phosphorylated at threonin 181 (p-tau(181)) and regional glucose metabolism measured with 18F-fluorodeoxyglucose-positron emission tomography (18F-FDG-PET) in patients with probable Alzheimer's disease (AD). METHODS: In 38 patients (mean age 66.5 +/- 8.0 years) with AD, Mini-Mental State Examination (MMSE) scores were evaluated and CSF levels of t-tau and p-tau(181) measured. All patients underwent an 18F-FDG-PET scan. Image analysis including correlation analysis and principal component analysis (PCA) were performed using SPM5 and VINCI. RESULTS: Dementia severity (MMSE 21.2 +/- 4.9) correlated well with metabolic impairment especially in left hemisphere association areas that are typically affected in patients with AD (e.g. inferior parietal lobule, r = 0.512; medial temporal gyrus, r = 0.478; inferior temporal gyrus, r = 0.488; precuneus, r = 0.468; PCA: r = 0.639, F = 7.751; all P < 0.001). There were no associations between t-tau and p-tau(181) with dementia severity and only weak correlations between t-tau and cerebral glucose metabolism (superior parietal gyrus, r = -0.325, P < 0.05; precentral gyrus r = -0.418, P < 0.01; amygdala r = -0.362, P < 0.05). No correlations were found between p-tau(181) and regional hypometabolism in FDG-PET. CONCLUSION: MMSE and CSF t-tau represent different aspects of disease severity. Whilst MMSE is closely related to impaired cerebral glucose metabolism, CSF t-tau is less closely related and appears to be less well suited for assessment of disease progression.

High accuracy multiple scatter modelling for 3D whole body PET.

A new technique for modelling multiple-order Compton scatter which uses the absolute probabilities relating the image space to the projection space in 3D whole body PET is presented. The details considered in this work give a valuable insight into the scatter problem, particularly for multiple scatter. Such modelling is advantageous for large attenuating media where scatter is a dominant component of the measured data, and where multiple scatter may dominate the total scatter depending on the energy threshold and object size. The model offers distinct features setting it apart from previous research: (1) specification of the scatter distribution for each voxel based on the transmission data, the physics of Compton scattering and the specification of a given PET system; (2) independence from the true activity distribution; (3) in principle no scaling or iterative process is required to find the distribution; (4) explicit multiple scatter modelling; (5) no scatter subtraction or addition to the forward model when included in the system matrix used with statistical image reconstruction methods; (6) adaptability to many different scatter compensation methods from simple and fast to more sophisticated and therefore slower methods; (7) accuracy equivalent to that of a Monte Carlo model. The scatter model has been validated using Monte Carlo simulation (SimSET).

Rapid processing of PET list-mode data for efficient uncertainty estimation and data analysis.

In this technical note we propose a rapid and scalable software solution for the processing of PET list-mode data, which allows the efficient integration of list mode data processing into the workflow of image reconstruction and analysis. All processing is performed on the graphics processing unit (GPU), making use of streamed and concurrent kernel execution together with data transfers between disk and CPU memory as well as CPU and GPU memory. This approach leads to fast generation of multiple bootstrap realisations, and when combined with fast image reconstruction and analysis, it enables assessment of uncertainties of any image statistic and of any component of the image generation process (e.g. random correction, image processing) within reasonable time frames (e.g. within five minutes per realisation). This is of particular value when handling complex chains of image generation and processing. The software outputs the following: (1) estimate of expected random event data for noise reduction; (2) dynamic prompt and random sinograms of span-1 and span-11 and (3) variance estimates based on multiple bootstrap realisations of (1) and (2) assuming reasonable count levels for acceptable accuracy. In addition, the software produces statistics and visualisations for immediate quality control and crude motion detection, such as: (1) count rate curves; (2) centre of mass plots of the radiodistribution for motion detection; (3) video of dynamic projection views for fast visual list-mode skimming and inspection; (4) full normalisation factor sinograms. To demonstrate the software, we present an example of the above processing for fast uncertainty estimation of regional SUVR (standard uptake value ratio) calculation for a single PET scan of (18)F-florbetapir using the Siemens Biograph mMR scanner.

Studies of the hyperthermophile Thermotoga maritima by random sequencing of cDNA and genomic libraries. Identification and sequencing of the trpEG (D) operon.

Random sequencing of cDNA and genomic libraries has been used to study the genome of the hyperthermophile Thermotoga maritima. To date, 175 unique clones have been analyzed by comparing short sequence tags with known proteins in the PIR and GenBank databases. We find that a significant proportion of sequences can be matched to previously identified protein from non-Thermotoga sources. A high match rate was obtained from an oligo(dT)-primed cDNA library, where one-third of all unique sequences analyzed (21/65) shared high amino acid sequence similarity with proteins in the PIR and GenBank databases. Also, approximately one-third of the unique sequences from a second cDNA library (28/89), constructed with random oligo primers, could be matched to sequences in PIR and GenBank. Identification of genes from the oligo(dT)-primed cDNA library indicates that some Thermotoga mRNAs are polyadenylated. Genes have also been identified from a 1 to 2 kb genomic DNA library. Here, (3/21) of genomic sequences analyzed could be matched to protein in PIR and GenBank. One of the genomic clones had high sequence similarity to the tryptophan synthesis gene anthranilate synthase component I (trpE). Using this sequence tag, the Thermotoga trp operon was isolated and sequenced. The Thermotoga maritima trp operon is arranged with trpE forming an overlapping transcript with a second protein consisting of a fusion of anthranilate synthase component II (trpG) and anthranilate phosphoribosyltransferse (trpD). With regard to the fusion, the operon organization is similar to Escherichia coli and Salmonella typhimurium, but lacks the classic attenuation system of enteric bacteria. Amino acid sequence comparison with 19 trpE, 18 trpG and 14 trpD genes from other organisms suggest that the Thermotoga trp genes resemble corresponding genes from other thermophiles more closely than expected.

Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence.

Amber mutations have been constructed at 328 positions, corresponding to residues 2 to 329 in the E. coli lac repressor protein. Synthetic and naturally occurring nonsense suppressors have been used to insert, in series, 12-13 amino acids at positions specified by an amber (UAG) codon in the lacI mRNA. The resulting set of over 4000 single amino acid replacements in the lac repressor protein allows a detailed analysis of its substitution tolerance along the linear array of residues, and reveals structure-function relationships in lac repressor and in proteins in general. (1) There are two main regions in the repressor which are extremely sensitive to amino acid replacements. One, the amino-terminal 59 residues, has been implicated in DNA and operator binding by a large body of work. The second, extending from approximately residues 239 to 289/292, forms the repressor core and shares the most homology with other repressor and DNA binding proteins. (2) Throughout the rest of the protein, segments of 6 to 14 amino acids, which are highly tolerant to single amino acid replacements, appear to act as "spacers" between one or several hydrophobic residues that are relatively intolerant to substitutions. (3) We have replaced the amino acids in these tolerant regions with spans of alanine residues, from 5 to 13 amino acids. In all five of the regions tested, alanine replacements, sometimes of up to 8 amino acids, still allowed functional repressor, while deletion of the same residues destroyed repressor function. This reinforces the view that many regions of a protein do not require a specific sequence to serve as spacers between more important residues. (4) A distinct pattern of substitutions leading to the I(s) phenotype suggests the location of residues involved in inducer binding. (5) A number of general substitution patterns can be recognized. For instance, proline is not tolerated at over 40 sites which tolerate all the other amino acid replacements. Another set of sites tolerates only non-polar amino acids, whereas a third set tolerates a subset of the smallest amino acids, (serine, alanine, glycine and cysteine, and sometimes threonine and valine). (5) Overall, 93 of 328 sites (28%) tolerate all 13 amino acids tested, and 144 of 328 (44%) tolerate 12/13 or all 13 substitutions. We judge that 192 of 328 sites (59%) are generally tolerant to substitutions.

Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure.

Each amino acid from position 2 to 329 of Lac repressor was replaced by 12 or 13 of the 20 natural occurring amino acids. The resulting phenotypes are discussed on the basis of (1) the recently published structure of the Lac repressor core complexed with the inducer IPTG and (2) a model of the dimeric Lac repressor built by homology modelling from the X-ray structure of the purine repressor-corepressor-operator complex. This phenotype analysis, based on 4000 well-defined mutants, yields a functional description of each amino acid position of Lac repressor. In most cases, mutant effects can be directly correlated with the structure and function of the protein. This connection between the amino acid position and the structure and function of the protein is in most cases direct and not complicated: amino acids which are directly involved in sugar binding are affected in Lac repressor mutants of the Is type; small amino acids which can only be replaced by other small acids are located in the core of the protein; positions at which nearly all amino acids are tolerated are in most cases located on the surface of the protein. Amino acids which are highly conserved throughout the LacI family of repressors, and not directly involved in specific functions of the protein like DNA recognition or sugar binding, form a network of contacts with other amino acids. Such amino acids are either located inside one subunit, mostly at the interface between secondary structure elements, or are involved in the dimerisation interface.

Assessment of bootstrap resampling performance for PET data.

Bootstrap resampling has been successfully used for estimation of statistical uncertainty of parameters such as tissue metabolism, blood flow or displacement fields for image registration. The performance of bootstrap resampling as applied to PET list-mode data of the human brain and dedicated phantoms is assessed in a novel and systematic way such that: (1) the assessment is carried out in two resampling stages: the 'real world' stage where multiple reference datasets of varying statistical level are generated and the 'bootstrap world' stage where corresponding bootstrap replicates are generated from the reference datasets. (2) All resampled datasets were reconstructed yielding images from which multiple voxel and regions of interest (ROI) values were extracted to form corresponding distributions between the two stages. (3) The difference between the distributions from both stages was quantified using the Jensen-Shannon divergence and the first four moments. It was found that the bootstrap distributions are consistently different to the real world distributions across the statistical levels. The difference was explained by a shift in the mean (up to 33% for voxels and 14% for ROIs) being proportional to the inverse square root of the statistical level (number of counts). Other moments were well replicated by the bootstrap although for very low statistical levels the estimation of the variance was poor. Therefore, the bootstrap method should be used with care when estimating systematic errors (bias) and variance when very low statistical levels are present such as in early time frames of dynamic acquisitions, when the underlying population may not be sufficiently represented.

The sequence of a subtilisin-type protease (aerolysin) from the hyperthermophilic archaeum Pyrobaculum aerophilum reveals sites important to thermostability.

The hyperthermophilic archaeum Pyrobaculum aerophilum grows optimally at 100 degrees C and pH 7.0. Cell homogenates exhibit strong proteolytic activity within a temperature range of 80-130 degrees C. During an analysis of cDNA and genomic sequence tags, a genomic clone was recovered showing strong sequence homology to alkaline subtilisins of Bacillus sp. The total DNA sequence of the gene encoding the protease (named "aerolysin") was determined. Multiple sequence alignment with 15 different serine-type proteases showed greatest homology with subtilisins from gram-positive bacteria rather than archaeal or eukaryal serine proteases. Models of secondary and tertiary structure based on sequence alignments and the tertiary structures of subtilisin Carlsberg, BPN', thermitase, and protease K were generated for P. aerophilum subtilisin. This allowed identification of sites potentially contributing to the thermostability of the protein. One common transition put alanines at the beginning and end of surface alpha-helices. Aspartic acids were found at the N-terminus of several surface helices, possibly increasing stability by interacting with the helix dipole. Several of the substitutions in regions expected to form surface loops were adjacent to each other in the tertiary structure model.

Paired helical filaments are twisted ribbons composed of two parallel and aligned components: image reconstruction and modeling of filament structure using atomic force microscopy.

To study the structure of Alzheimer paired helical filaments (PHF) we examined isolated detergent-insoluble PHF using atomic force microscopy with image reconstruction. The reconstructed AFM images of Alzheimer PHF most closely resembled ribbon-like helices with thin edges. The presence of a conspicuous furrow in the PHF midline indicated that PHF were composed of two distinctive strands. Our present conception of the overall configuration of PHF is consistent with that proposed by Crowther and Wischik in 1985 but includes an essential component of the prevailing model: the presence of two strands. Thus, our new model of PHF structure, based on atomic force microscopy-derived data, indicates that the true structure of PHF is actually a hybrid of the prevailing PHF model and a thin helical ribbon.

Identification and sequencing of the Thermotoga maritima lacZ gene, part of a divergently transcribed operon.

The lacZ gene encoding a beta-galactosidase (beta Gal) from the hyperthermophile Thermotoga maritima was cloned on an 11-kb fragment by complementation of an Escherichia coli lacZ deletion stain. The nucleotide sequence of the structural gene and two other ORFs found within a 6317-bp region were determined. The deduced amino acid (aa) sequence of the Tt. maritima beta Gal predicts a 1037-aa polypeptide with a calculated M(r) of 122,312. The translated sequence is 30% similar to nine other beta Gal sequences from bacteria and one yeast. Alignment of the Tt. maritima beta Gal with these other sequences reveals that the residues responsible for Mg2+ binding, catalysis and substrate recognition are conserved in the thermophilic enzyme. Sequence analysis also revealed the presence of a divergently transcribed operon containing at least two other genes 5' to lacZ. These ORFs encode proteins homologous to a second family of beta Gal found in Bacillus species and to an ATP-dependent family of bacterial oligopeptide transport proteins.

Quality of survival of patients with brain gliomas treated with postoperative CCNU and radiation therapy.

This prospective randomized clinical trial compared the effectiveness of combined treatment with CCNU and radiation therapy to the use of radiation therapy alone for the postoperative management of supratentorial brain gliomas (67% anaplastic) in 198 patients. The results were evaluated with the aid of a specially developed weighted neuropsychological test battery providing single-value estimation of "life quality" of patients, as well as with a clinical performance scale. Based on these methods, it was established that patients improved within 6 months following therapy. This improvement was maintained in surviving patients during the 2-year follow-up period. The patients led a relatively normal life, but when their condition deteriorated their decline was rapid. The median survival time of patients treated with radiotherapy did not differ significantly from that of patients receiving chemotherapy in addition. Nor did the analysis of life quality and of changes in clinical performance show any benefit in supplementing surgery and radiation therapy with CCNU chemotherapy at the dosage used.

[Level of dopamine beta-hydroxylase activity in subarachnoid hemorrhage treated conservatively and surgically]. / Poziom aktywnosci beta-hydroksylazy dopaminy u chorych po krwawieniu podpajeczynówkowym leczonych zachowawczo i operacyjnie.

The activity of the catecholaminergic system was studied by analysis of changes in the activity of dopamine beta-hydroxylase (DBH) in patients after subarachnoid haemorrhage treated conservatively or surgically. The activity of DBH was analysed in a group of 20 conservatively treated patients and 41 treated surgically, with comparison to 50 controls. DBH activity was determined on days 1-3 after subarachnoid haemorrhage, in the second week, and before and after operation. In the period of the investigations changes were noted in DBH activity depending on the clinical state of the patients, and no direct effect of the operation was noted on DBH activity in the serum.

[The application and evaluation of TachoComb in repair of lacerations of dural sac]. / Zastosowanie i ocena przydatnosci Tachocombu w operacyjnym zaopatrywaniu uszkodzen worka oponowego.

The opening of dural sac (deliberate or accidental) during operation of the spine should be watertightly closed because of the risk of cerebro-spinal fluid leakage and infectious complications. Suturing the dural sac is sometimes difficult and time-consuming in cases of dural sac lacerations in a narrow confined space or in the proximity of radices. This occurs particularly in the case of reoperation in presence of scar involving the dural sac, that increases the risk of laceration. The aim of this paper is to asses the usefulness of a new sealing and haemostatic material--TachoComb in a watertight closure of the dural sac during spinal operation. We compared the frequency of complications related to closing of the dural sac in patients operated before and after introduction of TachoComb. The results indicate that the rate of liquorrhoea and infections is lower in the postoperative period with addition of TachoComb. Addition of TachoComb allows to shorten the time of operation, while its application is relatively easy.

[The influence of radiation doses on the results of radiosurgery of brain arteriovenous malformations]. / Wplyw dawki promieniowania na wyniki radiochirurgicznego leczenia naczyniaków mózgu.

Stereotactic radiosurgery as a method of treatment of inoperable brain angiomas has been in use in the Neurosurgery Department, Medical Academy in Lublin since 1990. The patients receive radiation from a Neptune 10P linear accelerator of 9 MeV photon energy (X radiation). The Laitinen stereoadapter used by us makes possible precise targeting and radiation application in time suitable for the patient and the whole treatment team. This frame produces no disturbances of CT image and is not covering the target. Non-invasive head immobilization in the frame is highly stable, although it requires good communication with the patient and his full cooperation. The purpose of the study was a comparison of the results of radiosurgery applied in the treatment of inoperable brain angiomas of various size with radiation doses 4000 cGy and 3000 cGy. The material comprises 40 first cases out of over 120 patients treated in this way for inoperable angiomas. The first group of 20 patients received 4000 cGy and the second group of 20 patients received 3000 cGy doses. Complete obliteration of angiomas was achieved in 16 (80%) cases treated with the 4000 cGy dose, and in 17 (85%) cases treated with the 3000 cGy dose. Late postradiation reactions developed in 15 (75%) patients in the first group with permanent changes in 5 (25%) patients. In the second group late postradiation reactions developed in only 6 (30%) cases and regressed in all. Treatment effectiveness (complete obliteration) after doses of 3000 and 4000 cGy was similar, and it decreased with greater size of angiomas. The per cent of postradiation complications after lower doses was much smaller, and permanent neurological changes were seen only after higher doses. The obtained results of the method are comparable with those of the authors using invasive methods of fixation of stereotactic frames.

[Results of the treatment of idiopathic hydrocephalus by shunt implantation after computerized cisternography]. / Wyniki leczenia wodoglowia idiopatycznego wszczepieniem zastawki po tomocysternografii komputerowej.

A retrospective study was reported of 19 patients (10 males and 9 females aged from 11 to 65 years) with idiopathic hydrocephalus treated by shunt implantation after qualification for this treatment based on computed tomocisternography. Clinical improvement was noted in 16 patients (84%), and after 2 months the therapeutic results by Black's scale were good in 13 patients (65%).

[Vasoactive neuropeptides CGRP (calcitonin gene-related peptide) and vasospasm during subarachnoid hemorrhage from ruptured intracranial aneurysm]. / Naczynioaktywne neuropeptydy CGRP (calcitonin gene-related peptide) i VIP (vasoactive intestinal polypeptide) a skurcz naczyniowy w przebiegu krwawienia podpajeczynówkowego z peknietego tetniaka wewnatrzczaszkowego.

The authors discuss the role of active neuropeptides Calcitonin Gene-Related Peptide (CGRP) and Vasoactive Intestinal Polypeptide (VIP) in the arterial spasm caused by haemorrhage from ruptured intracranial aneurysm. These substances act as vasodilators on brain vessels. Between the first and the second week after subarachnoid haemorrhage their concentration in the periarterial nerve fibres of the big vessels is significantly low. According to the experiments, the erythrocytes are this component of the blood which causes the decrease of the number of nerve fibres containing CGRP and VIP. The clinical tests of CGRP and VIP in the treatment of the vascular spasm after subarachnoid haemorrhage are being continued.