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Results for “reference mapping”

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PubMed1993

Experimental validation of a new quantitative method for the analysis of infarct size by cardiac perfusion tomography (SPECT).

Using global constraints and dynamic programming, a new model-based segmentation algorithm was developed to determine myocardial borders and basal plane. The segmented image is transformed to a countrate polar map and the infarct size (I.S.) is determined by comparison with a reference polar map. In order to evaluate our method the algorithm was applied to heart phantoms, to software simulations and to animal studies. In the last experiments, Tc-99m Sestamibi was used as a perfusion agent. The total myocardial volume and infarct size of a Jasczack phantom were overestimated, especially when I.S. was expressed in absolute rather than relative values. It was proven by software simulations of cardiac Spect studies that those errors were mainly due to finite resolution effects causing a clear overestimation of myocardial thickness. Implementation of a constant thickness in the algorithm resulted in a much better correlation with actual values. In a dog experiment the size of total myocardial volume of the area at risk during occlusion and of the final infarct size after thrombolysis was correlated with the histologic values obtained by planimetry after TTC staining. In 8 studies, an excellent correlation between the histologic area at risk versus the estimated perfusion defects was obtained (r = 0.97). The automatic delineation of myocardial borders and valve plane was excellent even when perfusion defects were present. Manual intervention was only necessary in certain slices where a clear overlap between liver and myocardium was present in the dog studies. Segmental polar maps expressing count rate and volume information provided a visual and quantitative tool to evaluate the influence of thrombolysis in acute ligation experiments. It is concluded that the new algorithm is ready to be used in a clinical environment for the quantitative evaluation of perfusion defects after acute myocardial infarction and for the follow-up of the therapeutic strategy.

Animals↗

PubMed2006

MR measurement of articular cartilage thickness distribution in the hip.

OBJECTIVE: To develop a method to determine the distribution of articular cartilage in the hip and to evaluate the potential of the method in a study of normal weight-bearing effects in asymptomatic young volunteers. DESIGN: Six volunteers were scanned after periods of standing and lying supine, using 3D gradient-echo magnetic resonance imaging (MRI). The protocol was repeated for two successive weeks to determine reproducibility. The femoral and acetabular cartilage layers were segmented as a single unit and thickness distribution maps were calculated using a spherical bone model as a frame of reference. Thickness maps were combined over the population using the bone model and post-weight-bearing and post-resting maps were compared. RESULTS: Mean thickness values were compared using an analysis of variance and a significant increase in cartilage thickness of 0.05 mm (P=0.02) was observed. The reproducibility of the method, assessed using test-retest coefficient of variation was 2.5%. CONCLUSIONS: The technique is reproducible, sensitive to sub-millimetre changes in thickness and may be useful in monitoring changes due to disease progression in patients with arthritis of the hip.

Adult↗

PubMed2002

Comparison of independent component analysis and conventional hypothesis-driven analysis for clinical functional MR image processing.

BACKGROUND AND PURPOSE: With independent component analysis (ICA), regions of activation can be identified on functional MR (fMR) images without a priori knowledge of expected hemodynamic responses. The purpose of this study was to compare the results of fMR imaging data processed with spatial ICA with results obtained with conventional hypothesis-driven analysis. METHODS: Eleven patients with focal cerebral lesions and one with agenesis of the corpus callosum were enrolled. Each patient performed text-listening, finger-tapping, and word-generation tasks. Conventional activation maps were generated by fitting time courses of each voxel to a boxcar reference function. Maps were created from the same image data with ICA techniques. To compare the maps, a concurrence ratio (CR) (number of voxels activated on both maps to number of voxels activated on either map) was calculated. RESULTS: In the ICA analysis, maps with appropriate spatial and temporal features for auditory, sensorimotor, or language cortices were identified in most patients. Images processed with ICA resembled images processed with conventional means. In patients who moved or performed the task incorrectly, ICA produced a map that resembled the expected activation pattern but differed from the conventional image. CRs averaged 70% for all comparisons in the 12 patients. CONCLUSION: fMR imaging maps for auditory, sensorimotor, and language tasks produced with ICA and conventional techniques were similar in most cases. Differences were consistent with the particular characteristics of the method. In data sets corrupted by motion or incorrect task performance, ICA may produce more accurate maps.

Arousal↗

PubMedDate not supplied

Plasma protein map: an update by microsequencing.

The reference plasma protein map, obtained with immobilized pH gradients in the first dimension of two-dimensional electrophoresis, is presented. By microsequencing, more than 40 polypeptide chains were identified. The new polypeptides and previously known proteins are listed in a table and labeled on the protein map, thus providing an update of the human plasma two-dimensional gel database.

Amino Acid Sequence↗

PubMedDate not supplied

An autosomal genetic linkage map of the chicken.

We have developed an autosomal genetic linkage map of the chicken genome using a subpanel of 52 DNAs from a previously described reference backcross mapping population. The population derived from a cross of an inbred Red Jungle Fowl male and a highly inbred White Leghorn female. The backcross subpanel used was made up of offspring of a single F1 male with four White Leghorn females. Ninety-eight markers consisting of classical and erythrocyte antigen genes, restriction fragment length polymorphisms, random amplified polymorphic DNA, and chicken CR1 repeat-element polymorphisms were typed. Seventy-two of these markers were resolved into 19 linkage groups. Four of the linkage groups were assigned to chromosomes 1, 4, and 17. Four linkage groups were associated with linkage groups published earlier. Linkages within approximately 27 cM can be detected with a lod score of 3 with the panel used. The preliminary map contains approximately 590 cM within the linkage groups, and approximately 70% of the randomly selected markers fell in one of the groups; however, a considerable portion of the genome may remain outside of the existing linkage groups. These markers greatly expand the existing linkage map of the chicken genome.

Animals↗

PubMedDate not supplied

A case map reduces time to administration of thrombolytic therapy in patients experiencing an acute myocardial infarction.

As one of the first hospitals in northwest Arkansas to begin administering thrombolytic therapy to patients with heart attack, or acute myocardial infarction (AMI), Crawford Memorial Hospital (CMH) first administered streptokinase to a patient experiencing an AMI on April 26, 1984. A national standard in lytic therapy was set in 1992 by the National Heart Attack Alert Program Coordinating Committee. The committee set a benchmark of having every appropriate AMI patient receive thrombolytic therapy within 30 minutes of hospital arrival. To monitor quality in lytic therapy administration, CMH began to participate in the National Registry for Myocardial Infarction (NRMI), in January 1995. The first quarter of data revealed a median door-to-drug time (time from arrival at hospital to administration of drug) of 67 minutes. As a quality improvement project, a research experiment was conducted to assess the effect of a case map, also referred to as a clinical pathway, on time to administration of thrombolytic therapy. A case map is a written management plan that provides the ideal sequence and timing of health care staff actions to achieve optimal patient outcomes with minimal variation in care. The researcher developed a case map designed to increase efficiency in delivery of thrombolytic agents. The research was conducted throughout an 18-month period from July 1995 until December 1996. Median time to administration of thrombolytic therapy was reduced from 64 minutes to 25 minutes as a result of case map use (p = 0.028). In this article, research findings are presented regarding the use of case maps in thrombolytic therapy, as well as implications for practice.

Case Management↗

PubMed1994

Characterization of microsatellites from flow-sorted porcine chromosome 13.

Porcine flow-sorted Chromosome (Chr) 13 was PCR amplified with primers based on porcine short interspersed element (SINE) sequences. The product was cloned, gridded in microtiter plates, and screened with a [GT]10 oligonucleotide which gave 45 positive clones. Sequencing of these clones showed that 36 were unique, and 26 [GT]n microsatellites were characterized. Six other simple repeat sequences, the majority of which were associated with the 3' end of the SINE sequence, were also detected. Twenty-one primers sets were selected, and 13 of these detected useful polymorphisms in the grandparents (n = 26) of the European porcine mapping collaboration (PiGMaP) reference families. These 13 markers were mapped in the "PiGMaP" reference families, and a two-point linkage analysis was performed. The Lod scores indicated that three of the markers were not linked and the remaining 11 formed two linkage groups of two and nine markers respectively. The larger linkage group was also linked to the transferrin locus, permitting assignment of nine markers to porcine Chr 13.

Animals↗

PubMedDate not supplied

Temporal phase unwrapping for CINE velocity imaging.

A simple algorithm named temporal phase unwrapping (TPU) is introduced to address the phase aliasing problem in time-dependent phase contrast (CINE-PC) velocity imaging. The method exploits the temporal continuity of velocity field and unwraps the phase along time. TPU only involves a one-dimensional (1D) temporal integration; therefore, many complications in 2D or 3D spatial phase unwrapping are avoided. Differential velocity maps (DVM) between adjacent movie frames are first calculated from the complex MR images. The DVMs have no phase aliasing as the differential velocities are much smaller than the absolute velocities. Aliasing-free velocity maps are obtained by integrating the DVMs along the time direction provided an aliasing-free reference velocity map (RVM) is found as a starting point of the integration. Typically, such RVMs are always available within the cardiac cycle, especially in diastole where the blood flow is the lowest. In vivo results from fully automated processing and detailed discussion on noise behavior are presented.

Algorithms↗

PubMed1993

Anchored reference loci for comparative genome mapping in mammals.

Recent advances in gene mapping technologies have led to increased emphasis in developing representative genetic maps for several species, particularly domestic plants and animals. These maps are being compiled with two distinct goals: to provide a resource for genetic analysis, and to help dissect the evolution of genome organization by comparing linkage relationships of homologous genes. We propose here a list of 321 reference anchor loci suitable for comparative gene mapping in mammals and other vertebrate classes. We selected cloned mouse and human functional genes spaced an average of 5-10 centiMorgans throughout their respective genomes. We also attempted to include loci that are evolutionarily conserved and represented in comparative gene maps in other mammalian orders, particularly cattle and the domestic cat. We believe that the map may provide the basis for a unified approach to comparative analysis of mammalian species genomes.

Animals↗

PubMed1997

Correlating cytoarchitecture and function in cat primary somatosensory cortex: the challenge of individual differences.

Principles of organization for the primary somatosensory cortex are generalizations derived by examining data obtained in different individuals. The manner in which these data are combined influences the conclusions derived. We found the line representing the widest anteroposterior distance across the sigmoid gyrus to be a useful reference in the cat somatosensory cortex for combining and comparing electrophysiological and cytoarchitectonic data from different individuals when we constructed cytoarchitectonic and functional maps of the bank of the medial ansate sulcus; maps prepared from combined data sets had boundaries similar to those found among individuals. Nevertheless, we argue that, for reasons inherent to the nature of the cerebral hemispheres and cortical maps, such references will never allow combinations of data capable of defining a unique high resolution prototypical map of individual body parts; the somatotopic order of body representations is, as are certain other attributes of somatosensory cortex, idiosyncratic. The genetic, developmental and use-dependent reasons for this situation are discussed.

Acetylcholinesterase↗

PubMed1999

Factors affecting and computation of myocardial perfusion reference images.

Many quantitative analysis methods for myocardial perfusion studies require as a central step a comparison with a 'normal' or average density distribution map or reference image. It has been recognized, however, that the normal distribution can be affected by patient attributes, including sex and weight or body habitus, and by acquisition attributes, including the choice of tracer and the position of the patient during imaging. Some authors have proposed separate reference images for the sexes and the tracer. This approach fails if a large number of binary attributes have to be considered, since one would need 2" reference images for each attribute. The problem is compounded when continuous attributes (e.g. age and weight) are included, especially if the approach is to average separate homogeneous groups for each attribute. We propose to create case-specific reference images for the interpretation of myocardial perfusion studies by creating a model based on the influence of each attribute. From a non-homogeneous population of normal cases, or cases presumed to be normal on the basis of the Diamond and Forrester stratification, the effect of patient and study attributes on the density distribution in the stress image and the density differences between rest and stress images were computed. The effects are computed by multi-linear regression, to account for cross-correlation. Significance is assigned on the basis of a partial Fisher test. The data are myocardial perfusion images matched in 3D to a template by an elastic transformation. Even though there was some cross-correlation in the data, we were able to show independent effects of sex, position (prone or supine), age, weight, tracer combination and stress method (exercise, persantine and adenosine). Taken as a whole, the multi-linear regression demonstrated a significant effect in 72% of the pixels within the myocardial volume. In addition, the distribution predicted by the model was equivalent to average images from homogeneous matched groups. In conclusion, our approach makes it possible to produce case-specific reference images without the need for multiple homogeneous large groups to produce averages for each possible patient or study attribute.

Adenosine↗

PubMed2003

Assessment of SAGE in transcript identification.

An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mapping are incomplete, and thus do not allow assessment of the efficacy of SAGE in transcript identification. A method of tag mapping is described here and applied to the Drosophila melanogaster and Caenorhabditis elegans genomes, which permits detailed SAGE assessment and provides tag-mapping resources that were unavailable previously for these organisms. In our method, a conceptual transcriptome is constructed using genomic sequence and annotation by extending predicted coding regions to include UTRs on the basis of EST and cDNA alignments, UTR length distributions, and polyadenylation signals. Analysis of extracted tags suggests that, using the standard SAGE procedure, expression of 8% of D. melanogaster and 15% of C. elegans genes cannot be detected unambiguously by SAGE due to shared sequence or lack of NlaIII-anchoring enzyme sites. Both increasing tag length by 2-3 bp and using Sau3A instead of NlaIII as the anchoring enzyme increases potential for transcript detection. This work identifies and quantifies genes not amenable to SAGE analysis, in addition to providing tag-to-gene mappings for two model organisms.

Animals↗

PubMedDate not supplied

Expressed sequence tags for the chicken genome from a normalized 10-day-old White Leghorn whole embryo cDNA library: 1. DNA sequence characterization and linkage analysis.

Expressed sequence tags (ESTs) provide a rapid and reliable method for gene discovery as well as a resource for the large-scale analysis of gene expression of known and unknown genes. Here we describe a normalized cDNA library developed from a 10-day-old White Leghorn chicken whole embryo. The utility of the library was evaluated by partial sequencing of 99 randomly selected insert-containing clones and the analysis of EST-targeted genomic regions for single nucleotide polymorphisms (SNPs) in the East Lansing chicken reference DNA mapping panel. Using stringent match criteria of percent identity of 80 or higher across a length of 50 or more bases, 46 ESTs matched database sequences including previously reported Gallus gallus genes. Thirty-seven of the 50 primer pairs developed from 50 unique ESTs amplified a single fragment. The size of the 37 amplicons ranged from 276 to 693 bp for a total of 17,508 and an average of 473. About 70% of the SNPs detected were either G-->A or C-->T transition. The number of SNPs detected within the amplicons from EST-targeted genomic regions ranged from 0 to 4 for a total of 65 and a frequency of about 1 every 470 bases. About 35% of the amplicons contained only 1 SNP, while 19% had 4 SNPs. Using the SNPs that were informative in the East Lansing reference panel, 17 ESTs were mapped on the East Lansing chicken genetic map. The ESTs described, as well as the nucleotide variants identified within the EST-targeted genomic regions, represent significant resources for genome analysis in the chicken.

Animals↗

PubMed2005

Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families.

A genetic linkage map of the horse consisting of 742 markers, which comprises a single linkage group for each of the autosomes and the X chromosome, is presented. The map has been generated from two three-generation full-sibling reference families, sired by the same stallion, in which there are 61 individuals in the F2 generation. Each linkage group has been assigned to a chromosome and oriented with reference to markers mapped by fluorescence in situ hybridization. The average interval between markers is 3.7 cM and the linkage groups collectively span 2772 cM. The 742 markers comprise 734 microsatellite and 8 gene-based markers. The utility of the microsatellite markers for comparative mapping has been significantly enhanced by comparing their flanking sequences with the human genome sequence; this enabled conserved segments between human and horse to be identified. The new map provides a valuable resource for genetically mapping traits of interest in the horse.

Animals↗

PubMed1996

Assignment of Rfp-Y to the chicken major histocompatibility complex/NOR microchromosome and evidence for high-frequency recombination associated with the nucleolar organizer region.

Rfp-Y is a second region in the genome of the chicken containing major histocompatibility complex (MHC) class I and II genes. Haplotypes of Rfp-Y assort independently from haplotypes of the B system, a region known to function as a MHC and to be located on chromosome 16 (a microchromosome) with the single nucleolar organizer region (NOR) in the chicken genome. Linkage mapping with reference populations failed to reveal the location of Rfp-Y, leaving Rfp-Y unlinked in a map containing >400 markers. A possible location of Rfp-Y became apparent in studies of chickens trisomic for chromosome 16 when it was noted that the intensity of restriction fragments associated with Rfp-Y increased with increasing copy number of chromosome 16. Further evidence that Rfp-Y might be located on chromosome 16 was obtained when individuals trisomic for chromosome 16 were found to transmit three Rfp-Y haplotypes. Finally, mapping of cosmid cluster III of the molecular map of chicken MHC genes (containing a MHC class II gene and two rRNA genes) to Rfp-Y validated the assignment of Rfp-Y to the MHC/NOR microchromosome. A genetic map can now be drawn for a portion of chicken chromosome 16 with Rfp-Y, encompassing two MHC class I and three MHC class II genes, separated from the B system by a region containing the NOR and exhibiting highly frequent recombination.

Animals↗

PubMed2003

Comparative proteomic profiling of murine skin.

Mammalian skin is regularly exposed to different environmental stresses, each of which results in specific compensatory changes in protein expression that can be assessed by proteomic analysis. We have established a reference proteome map of BALB/c murine skin allowing the resolution of greater than 500 protein spots in a single two-dimensional polyacrylamide gel. Forty-four protein spots, corresponding to 28 different cutaneous proteins, were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and the Mascot online database searching algorithm. Twenty-five proteins were expressed at higher levels in the epidermis, whereas only nine were found predominantly in the subepidermal tissues. A subset of protein spots exhibited strain-specific expression. Proteins of diverse function were identified, including those involved in stress response, apoptosis, growth inhibition, the maintenance of structural integrity, translational control, energy metabolism, calcium binding, cholesterol transport, and the scavenging of free radicals. Prohibitin expression was detected cutaneously, with more abundant protein and mRNA levels in the epidermis. Five molecular chaperones including protein di-sulfide isomerase, 78 kDa glucose-regulated protein precursor, heat shock protein 60 (HSP60), HSP70, and HSP27 were also identified. Of these, HSP27 expression was confined mainly to the epidermis, and expression of protein disulfide isomerase was found primarily in the subepidermal tissues. Proteomic analysis of skin following heat or cold shock resulted in increased levels of HSP27, HSP60, and HSP70 suggesting involvement of these chaperones in the cutaneous response mechanism to temperature stress. These data establish numerous reference markers within the proteome map of murine skin and provide an important framework for future efforts aimed at characterization of the epidermal and subepidermal responses to environmental changes.

Abdomen↗

PubMed2006

Cardiac anisotropy: is it negligible regarding noninvasive activation time imaging?

The aim of this study was to quantify the effect of cardiac anisotropy in the activation-based inverse problem of electrocardiography. Differences of the patterns of simulated body surface potential maps for isotropic and anisotropic conditions were investigated with regard to activation time (AT) imaging of ventricular depolarization. AT maps were estimated by solving the nonlinear inverse ill-posed problem employing spatio-temporal regularization. Four different reference AT maps (sinus rhythm, right-ventricular and septal pacing, accessory pathway) were calculated with a bidomain theory based anisotropic finite-element heart model in combination with a cellular automaton. In this heart model a realistic fiber architecture and conduction system was implemented. Although the anisotropy has some effects on forward solutions, effects on inverse solutions are small indicating that cardiac anisotropy might be negligible for some clinical applications (e.g., imaging of focal events) of our AT imaging approach. The main characteristic events of the AT maps were estimated despite neglected electrical anisotropy in the inverse formulation. The worst correlation coefficient of the estimated AT maps was 0.810 in case of sinus rhythm. However, all characteristic events of the activation pattern were found. The results of this study confirm our clinical validation studies of noninvasive AT imaging in which cardiac anisotropy was neglected.

Action Potentials↗

PubMedDate not supplied

Automatic segmentation of medical images using image registration: diagnostic and simulation applications.

Automatic identification of the boundaries of significant structure (segmentation) within a medical image is an are of ongoing research. Various approaches have been proposed but only two methods have achieved widespread use: manual delineation of boundaries and segmentation using intensity values. In this paper we describe an approach based on image registration. A reference image is prepared and segmented, by hand or otherwise. A patient image is registered to the reference image and the mapping then applied to ther reference segmentation to map it back to the patient image. In general a high-resolution nonlinear mapping is required to achieve accurate segmentation. This paper describes an algorithm that can efficiently generate such mappings, and outlines the uses of this tool in two relevant applications. An important feature of the approach described in this paper is that the algorithm is independent of the segmentation problem being addresses. All knowledge about the problem at hand is contained in files of reference data. A secondary benefit is that the continuous three-dimensional mapping generated is well suited to the generation of patient-specific numerical models (e.g. finite element meshes) from the library models. Smoothness constraints in the morphing algorithm tend to maintain the geometric quality of the reference mesh.

Algorithms↗