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PubMed1995

Nonstationary vortexlike reentrant activity as a mechanism of polymorphic ventricular tachycardia in the isolated rabbit heart.

BACKGROUND: Ventricular tachycardia may result from vortexlike reentrant excitation of the myocardium. Our general hypothesis is that in the structurally normal heart, these arrhythmias are the result of one or two nonstationary three-dimensional electrical scroll waves activating the heart muscle at very high frequencies. METHODS AND RESULTS: We used a combination of high-resolution video imaging, electrocardiography, and image processing in the isolated rabbit heart, together with mathematical modeling. We characterized the dynamics of changes in transmembrane potential patterns on the epicardial surface of the ventricles using optical mapping. Image processing techniques were used to identify the surface manifestation of the reentrant organizing centers, and the location of these centers was used to determine the movement of the reentrant pathway. We also used numerical simulations incorporating Fitzhugh-Nagumo kinetics and realistic heart geometry to study how stationary and nonstationary scroll waves are manifest on the epicardial surface and in the simulated ECG. We present epicardial surface manifestations (reentrant spiral waves) and ECG patterns of nonstationary reentrant activity that are consistent with those generated by scroll waves established at the right and left ventricles. We identified the organizing centers of the reentrant circuits on the epicardial surface during polymorphic tachycardia, and these centers moved during the episodes. In addition, the arrhythmias that showed the greatest movement of the reentrant centers displayed the largest changes in QRS morphology. The numerical simulations showed that stationary scroll waves give rise to monomorphic ECG signals, but nonstationary meandering scroll waves give rise to undulating ECGs characteristic of torsade de pointes. CONCLUSIONS: Polymorphic ventricular tachycardia in the healthy, isolated rabbit heart is the result of either a single or paired ("figure-of-eight") nonstationary scroll waves. The extent of the scroll wave movement corresponds to the degree of polymorphism in the ECG. These results are consistent with our numerical simulations that showed monomorphic ECG patterns of activity for stationary scroll waves but polymorphic patterns for scroll waves that were nonstationary.

Animals↗
PubMed1994

Genetic map construction with constraints.

A pilot program, CME, is described for generating a physical genetic map from hybridization fingerprinting data. CME is implemented in the parallel constraint logic programming language ElipSys. The features of constraint logic programming are used to enable the integration of pre-existing mapping information (partial probe orders from cytogenetic maps and local physical maps) into the global map generation process, while parallelism enables the search space to be traversed more efficiently. CME was tested using data from chromosome 2 of Schizosaccharomyces pombe and was found able to generate maps as well as (and sometimes better than) a more traditional method. This paper illustrates the practical benefits of using a symbolic logic programming language and shows that the features of constraint handling and parallel execution bring the development of practical systems based on AI programming technologies nearer to being a reality.

Algorithms↗
PubMed1994

Ambiguity resolution while mapping free text to the UMLS Metathesaurus.

We propose a method for resolving ambiguities encountered when mapping free text to the UMLS Metathesaurus. Much of the research in medical informatics involves the manipulation of free text. The Metathesaurus contains extensive information which supports solutions to problems encountered while processing such text. After discussing the process of mapping free text to the Metathesaurus and describing the ambiguities which are often the result of such mapping, we provide examples of rules designed to eliminate mapping ambiguities. These rules refer to the context in which the ambiguity occurs and crucially depend on semantic types obtained from the Metathesaurus. We have conducted a preliminary test of the methodology and the results obtained indicate that the rules successfully resolve ambiguity around 80% of the time.

Abstracting and Indexing↗
PubMed1991

The extracellular domain of p185/neu is released from the surface of human breast carcinoma cells, SK-BR-3.

The human breast carcinoma cell line SK-BR-3, expresses the neu oncogene product, p185, which is a receptor tyrosine kinase. Using a double monoclonal antibody capture enzyme-linked immunosorbent assay for p185, activity was detected in conditioned media from cultures of SK-BR-3 cells. Two monoclonal antibodies specific for the extracellular domain of p185/neu immunoprecipitated a protein with a molecular mass of approximately 105 kDa. p105 was further shown to compete with p185 for binding to monoclonal antibodies and pulse-chase experiments indicate that it was generated by post-translational processing. Peptide maps showed that p105 and p185 are related polypeptides. Since p105 is close to the predicted size for the extracellular domain of p185/neu, we propose that SK-BR-3 cells specifically process and release this portion of the receptor into the medium. The release of the extracellular domain may have implications in oncogenesis and its detection could prove useful as a cancer diagnostic.

Adenocarcinoma↗
PubMed2001

Automated three-dimensional signature model for assessing brain injury in emergent stroke.

This presentation will focus on the value of established and newer MR methods that can be applied to the diagnosis and management of ischemic stroke with emphasis on future applications of MR to provide previously unmet needs of the treating clinician and clinical trials. Time alone is an inadequate indicator of the therapeutic window, especially when the time of stroke onset is uncertain. Thus, there is a need to predict the evolution of stroke in a way that more precisely and with greater resolution identifies the progression of cellular damage at the moment of investigation. This also would be of value for thrombolysis when knowledge of the degree and extent of tissue necrosis and the consequent potential for brain hemorrhage is of the utmost importance. To provide this, we perform postprocessing of diffusion-, T(1)- and T(2)-weighted images to produce the apparent diffusion coefficient of water, and T(1) and T(2) maps that are then further processed to provide maps and quantitation of the tissue signatures of ischemic histopathology. By these means, we can accomplish objective volumetric analysis of infarct size and of the proportions of potentially viable and salvageable tissue. We will show how this has the potential to predict long-term stroke outcome and facilitate decision-making in terms of safety of reperfusion strategies and the appropriateness of cytoprotective treatment. The value of our approach is to replace time as the therapeutic window and extend the opportunity of treatment to those patients presenting beyond the stringent time limits employed in current investigative clinical trials. Further, used as a surrogate marker of clinical outcome, this form of stroke analysis may speed proof of principle clinical trials in small numbers of stroke patients.

Brain↗
PubMed1998

Development of an intervention map for a parent education intervention to prevent violence among Hispanic middle school students.

This paper describes development of Padres Trabajando por la Paz, a violence prevention intervention for Hispanic parents to increase parental monitoring. The intervention was developed using an innovative new program planning process: intervention mapping. Theory and empirical evidence broadly defined performance objectives and determinants of parental monitoring. These objectives were further refined through group and individual interviews with the target parent group. Learning objectives for the intervention guided the content of the intervention that used modeling as the primary method and role model stories as a strategy delivered through newsletters. Stage-matching members of the target population for their readiness to implement the parental monitoring behaviors further refined the social cognitive message design strategies. Intervention mapping provides an explicit theory- and data-driven guide for intervention development that maximizes intervention impact for a specific target population.

Adolescent↗
PubMed1988

Developments in processing image sequences for elemental mapping.

Elemental mapping consists in searching the distribution of a given chemical species over an extended specimen area, with relation to topographical or structural features. It can be done with EELS core signals from a combination of several energy filtered images. One major problem encountered in the processing of such sequences of images lies in the extrapolation errors due to a difficult estimate of the background below the characteristic signal. The chosen method must be sufficiently reliable to avoid the risk of both "false positive" and "false negative" values: the first category may stem from spurious signals or from a non-satisfactory fit of the background. The second category is mainly due to a limited sensitivity. The EELS signal is often much weaker than the background intensity; an extrapolation error can therefore transform a negative value into a positive one, or vice versa. The purpose of the present contribution is to check the validity of the processing at different levels: i) different mathematical models of background; ii) different types of fitting procedures (one-parameter and two-parameters fits); iii) different fitting methods and several associated manipulations, such as a quasi local estimation of the involved fitting parameters. The statistical validity of those techniques is discussed through several tests on real images obtained from different specimens (Co/CeO2 catalysts, ferritin molecules, U and Tb staining clusters). Progress is made on the way of quantitative elemental mapping at a given confidence level, and towards the identification of single atoms.

Electron Probe Microanalysis↗
PubMed1995

Characterization and mapping of a highly conserved processed pseudogene and an intron-carrying gene of the heat shock cognate protein 70 (Hsc70) gene family in the rat.

A processed pseudogene of the rat Hsc70 gene, Hsc70-ps1, is described, which still presents the open reading frame of the original gene. The pseudogene does not appear to be expressed. It maps to rat Chromosome (Chr) 2. The intron-carrying Hsc70 gene localizes to Chr 8. Hsc70-specific probes detect a large number of more than 20 cross-hybridizing fragments, which show only limited length polymorphism among various inbred rat strains.

Animals↗
PubMed1989

Different anisotropies of movement direction in upper and lower layers of the cat's area 18 and their implications for global optic flow processing.

Cells in Area 18 of awake and behaving cats were tested for directional preference with a large visual noise pattern. Upper and lower layer cells were found to exhibit different anisotropies for movement direction, offset by 90 degrees. These findings could reflect different functions for the global mapping and processing of optic flow field in upper and lower layers.

Animals↗
PubMedDate not supplied

The cerebellum's role in reading: a functional MR imaging study.

BACKGROUND AND PURPOSE: Long considered to have a role limited largely to motor-related functions, the cerebellum has recently been implicated as being involved in both perceptual and cognitive processes. Our purpose was to determine whether cerebellar activation occurs during cognitive tasks that differentially engage the component processes of word identification in reading. METHODS: Forty-two neurologically normal adults underwent functional MR imaging of the cerebellum with a gradient-echo echo-planar technique while performing tasks designed to study the cognitive processing used in reading. A standard levels-of-processing paradigm was used. Participants were asked to determine whether pairs of words were written in the same case (orthographic processing), whether pairs of words and non-words rhymed with each other, respectively (phonologic assembly), and whether pairs of words belonged to the same category (semantic processing). Composite maps were generated from a general linear model based on a randomization of statistical parametric maps. RESULTS: During phonologic assembly, cerebellar activation was observed in the middle and posterior aspects of the posterior superior fissure and adjacent simple lobule and semilunar lobule bilaterally and in posterior aspects of the simple lobule, superior semilunar lobule, and inferior semilunar lobule bilaterally. Semantic processing, however, resulted in activation in the deep nuclear region on the right and in the inferior vermis, in addition to posterior areas active in phonologic assembly, including the simple, superior semilunar, and inferior semilunar lobules. CONCLUSION: The cerebellum is engaged during reading and differentially activates in response to phonologic and semantic tasks. These results indicate that the cerebellum contributes to the cognitive processes integral to reading.

Adult↗
PubMed1999

Confidence maps and confidence intervals for near infrared images in breast cancer.

This paper extends basic concepts of statistical hypothesis testing and confidence intervals to images generated by a new procedure for near infrared spectroscopic tomography being developed for use in breast cancer diagnosis. By estimating the covariance matrix of the pixels of an image from data used in the image reconstruction process, confidence maps for statistical tests on individual pixels and confidence intervals for entire images are displayed as an aid to research and clinical personnel interpreting possibly noisy images. The methods are applied to simulated and phantom-based images.

Breast Neoplasms↗
PubMed1988

Activity sharpens the regenerating retinotectal projection in goldfish: sensitive period for strobe illumination and lack of effect on synaptogenesis and on ganglion cell receptive field properties.

The regenerating optic nerve of goldfish first reestablishes a rough retinotopic map on the contralateral tectum and then sharpens it. Disruption of visual activity, either by blocking activity with intraocular tetrodotoxin (TTX; Schmidt and Edwards, 1983) or by synchronizing activity with strobe illumination (Schmidt and Eisele, 1985), disrupts the sharpening process: the map is correctly oriented but the multiunit receptive fields at each point average 25-40 degrees in diameter. In order to test whether strobe and TTX interfere with the same mechanism, we have tested whether their sensitive periods are the same, and whether strobe, like TTX treatment, does not affect either ganglion cell receptive field properties or synaptogenesis. In parallel studies, we exposed fish to 2 weeks of either strobe illumination or intraocular TTX beginning at various times after crush and determined via electrophysiological recordings that the periods of sensitivity were nearly identical. There was no effect of either treatment during the first 2 weeks (before the fibers arrive at the tectum), maximal disruption of sharpening between 14 and 50 days (the period of rapid synaptogenesis), decreasing disruption between 50 and 125 days, and no effect beyond that point or in the normal projection. In addition, long strobe exposures of up to 142 days produced no greater disruptions than shorter 2-3-week exposures, indicating no cumulative effect. The reestablishment of synaptic transmission in tectum, assayed by recording field potentials elicited by optic nerve shock, was not affected by stroboscopic illumination. Finally, individual ganglion cells, recorded intraretinally following long-term strobe exposure, had receptive fields that were normal both in size and in their characteristic responses to light-on, to light-off, or to both on and off. These findings support the hypothesis that strobe-like TTX prevents retinotopic refinement by preventing the correction of errors initially made by the ingrowing optic axons (Schmidt et al., 1988).

Animals↗
PubMed1996

Schematic maps: cognitive tools for enhancing the early stages of counseling.

The purpose of the present studies was to explore the utility of schematic maps as tools for the early stages of both peer and self-counseling. In experiment 1 (self-counseling), 42 students from undergraduate general psychology classes participated to fulfill course requirements. Participants were assigned to either a schematic map or essay group. They first extracted information about their alcohol-related behavior patterns and then analyzed the patterns from the perspective of a counselor. In experiment 2 (peer counseling), 38 students from upper-division psychology courses participated for extra credit. Participants were asked to evaluate behavior patterns, in the form of maps or essays, which were presented either in the same form as they were extracted or were transposed to the other format. In both studies, assessment consisted of questionnaires that addressed the usefulness of the tools in the counseling process. Schematic maps are potentially powerful tools for both self- and peer counseling. For self-counseling, maps were preferred over traditional essay writing. In addition, the subjective reaction to maps as tools for peer counseling was positive.

Alcohol Drinking↗
PubMed2000

From digital image processing of colour Doppler M-mode maps to noninvasive evaluation of the left ventricular diastolic function: a dedicated software package.

Noninvasive estimation of diastolic pressure gradients has recently been validated using the space-temporal velocity distribution available from colour Doppler M-mode (CDM). However, the methods currently applied for analysing CDM patterns of left ventricular (LV) filling have limitations, such as lack of automation, subjective variability and limited use of digital velocity map. For this reason, we have developed software able to acquire and process the CDM maps; thus, providing an easily interpretable graphical and numerical display. The pressure field is obtained by approximating the derivatives with centred finite differences via the incompressible Navier-Stokes equations. After digital filtering of the noise and the removal of the colour black spots, the velocity field is utilised to compute the pressure gradient field and the pressure values by spatial integration. It is concluded that automatic quantification of colour CDM patterns is feasible and will be a strategic tool in the investigation of one of the most intriguing topics in cardiology.

Blood Flow Velocity↗
PubMed1998

Comprehensive human genetic maps: individual and sex-specific variation in recombination.

Comprehensive human genetic maps were constructed on the basis of nearly 1 million genotypes from eight CEPH families; they incorporated >8,000 short tandem-repeat polymorphisms (STRPs), primarily from Généthon, the Cooperative Human Linkage Center, the Utah Marker Development Group, and the Marshfield Medical Research Foundation. As part of the map building process, 0.08% of the genotypes that resulted in tight double recombinants and that largely, if not entirely, represent genotyping errors, mutations, or gene-conversion events were removed. The total female, male, and sex-averaged lengths of the final maps were 44, 27, and 35 morgans, respectively. Numerous (267) sets of STRPs were identified that represented the exact same loci yet were developed independently and had different primer pairs. The distributions of the total number of recombination events per gamete, among the eight mothers of the CEPH families, were significantly different, and this variation was not due to maternal age. The female:male ratio of genetic distance varied across individual chromosomes in a remarkably consistent fashion, with peaks at the centromeres of all metacentric chromosomes. The new linkage maps plus much additional information, including a query system for use in the construction of reliably ordered maps for selected subsets of markers, are available from the Marshfield Website.

Chromosome Mapping↗
PubMed1994

Erythroid-specific processing of human beta spectrin I pre-mRNA.

Erythroid cells express a unique form of beta spectrin I as a result of tissue-specific alternative pre-mRNA processing. Nonerythroid cells that express the beta spectrin I gene include four additional exons at the 3' end of the mature transcript, leading to elongation of the carboxyl terminus of the protein. The nonerythroid beta spectrin I isoform is not present in the red blood cell membrane skeleton; the erythroid isoform is not detected in other cell types. Therefore, developing erythroid cells acquire this tissue-specific pre-mRNA processing activity during differentiation. In the present study, we investigated the developmental timing of erythroid-specific pre-mRNA processing in human erythroid precursors. Partially purified human peripheral blood burst forming uniterythroid (BFU-E) cells were grown in culture for 5 to 12 days. beta Spectrin I mRNA transcripts were analyzed at different time points by S1 nuclease mapping. The processing of beta spectrin I transcripts was found to be exclusively erythroid from day 5 onward, indicating that erythroid-specific processing is not linked temporally to assembly of the mature erythroid membrane skeleton. Human erythroleukemia (HEL) cells had both erythroid and nonerythroid transcripts, indicating that both processing patterns can coexist. Induction of erythroid differentiation in HEL cells using hemin resulted in a partial switch toward the erythroid processing pattern of beta spectrin I transcripts. Using a genomic S1 probe that spans the erythroid polyadenylation signal, we found that a substantial portion of the transcripts detected by the erythroid cDNA S1 probe (in both cultured BFU-E and HEL cells) is incompletely processed pre-mRNA precursors. Poly(A) RNA selection before S1 analysis showed that the unprocessed transcripts are not polyadenylated. We conclude that (1) erythroid-specific pre-mRNA processing activity is present early in erythroid differentiation; (2) beta spectrin I transcripts that are unprocessed at the 3' end accumulate, awaiting either erythroid or nonerythroid processing pathways, from which observation we infer that the regulated alternative pathways are both inefficient; and (3) HEL cells offer a human cell culture model in which to study the balance between the two pre-mRNA processing pathways. We speculate that erythroid cells evolved this tissue-specific pre-mRNA processing machinery for other erythroid genes in addition to beta spectrin I.

Base Sequence↗
PubMed2000

A bayesian analysis for spatial processes with application to disease mapping.

In epidemiology, maps of disease rates and disease risk provide a spatial perspective for researching disease aetiology. For rare diseases or when the population base is small, the rate and risk estimates may be unstable. We propose using a Bayesian analysis based on the conditional autoregressive (CAR) process that will spatially smooth disease rates or risk estimates by allowing each site to 'borrow strength' from its neighbours. Covariates may be included in the model in such a way as to establish a possible association between risk factors and disease incidence. Bayesian inferences are implemented from a direct resampling scheme where large samples are generated from the various posterior distributions. The methodology is demonstrated with a simulation that assesses the effect of sample size and the model parameters on inferences for the parameters. Our approach is also used to spatially smooth district lip cancer rates in Scotland using the CAR model with a covariate that allows for exposure to sunlight.

Bayes Theorem↗
PubMed2025

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.

Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses, often with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors…. These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac . We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC . Alevin-fry-atac is highly scalable and, when using 32 threads, is approximately 2.8 times faster than Chromap (the second fastest approach) while using approximately one third of the memory and mapping slightly more reads. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual colorenhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry ) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger . Furthermore, our modified pseudoalignment approach should be easily applicable and extendable to other genome-centric mapping-based tasks and modalities such as standard DNA-seq, DNase-seq, Chip-seq and Hi-C.

Journal Article↗