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Results for “process mapping”

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At least 1,693 records · Page 94Linked to original sources
PubMed2003

Iodixanol development of a laboratory-scale technique to monitor the persistence of Mycobacterium avium subsp. paratuberculosis in Cheddar cheese.

Mycobacterium avium subsp. paratuberculosis (Map) is a potential human pathogen known to be present in raw milk from infected dairy herds. Current pasteurisation regimes do not totally inactivate Map resulting in the possibility of viable cells being present in pasteurised milk used for Cheddar cheese production. A laboratory-based method, ensuring strict safety precautions, was developed to manufacture 800-g Cheddar blocks, experimentally contaminated (postpasteurisation) with two different strains of Map. The composition of the model Cheddar produced was consistent with commercial product. Syneresis of the cheese curd caused a 1 log10 concentration of Map numbers from milk to cheese for a strain isolated from pasteurised milk. The type strain NCTC 8578 did not show a similar concentration effect, but did however survive the Cheddar manufacturing process. A small percentage (<5%) of the Map load for each strain was recovered in the whey fraction during the process.

Cheese↗
PubMed2001

A method for making group inferences from functional MRI data using independent component analysis.

Independent component analysis (ICA) is a promising analysis method that is being increasingly applied to fMRI data. A principal advantage of this approach is its applicability to cognitive paradigms for which detailed models of brain activity are not available. Independent component analysis has been successfully utilized to analyze single-subject fMRI data sets, and an extension of this work would be to provide for group inferences. However, unlike univariate methods (e.g., regression analysis, Kolmogorov-Smirnov statistics), ICA does not naturally generalize to a method suitable for drawing inferences about groups of subjects. We introduce a novel approach for drawing group inferences using ICA of fMRI data, and present its application to a simple visual paradigm that alternately stimulates the left or right visual field. Our group ICA analysis revealed task-related components in left and right visual cortex, a transiently task-related component in bilateral occipital/parietal cortex, and a non-task-related component in bilateral visual association cortex. We address issues involved in the use of ICA as an fMRI analysis method such as: (1) How many components should be calculated? (2) How are these components to be combined across subjects? (3) How should the final results be thresholded and/or presented? We show that the methodology we present provides answers to these questions and lay out a process for making group inferences from fMRI data using independent component analysis.

Algorithms↗
PubMed1999

Optical PCR: genomic analysis by long-range PCR and optical mapping.

Optical mapping is an approach for the rapid, automated, non-electrophoretic construction of ordered restriction maps of DNA from ensembles of single molecules. Previously, we used optical mapping to make high-resolution maps of large insert clones such as bacterial artificial chromosomes (BAC) and large genomic DNA molecules. Here, we describe a combination of optical mapping and long-range polymerase chain reaction (PCR), in a process we term optical PCR, which enables automated construction of ordered restriction maps of long-range PCR products spanning human genomic loci. Specifically, we amplified three long PCR products, each averaging 14.6 kb in length, which span the 37-kb human tissue plasminogen activator (TPA) gene. PCR products were surface mounted in gridded arrays, and samples were mapped in parallel with either ScaI, XmnI, HpaI, ClaI, or BglII. A contig of overlapping high-resolution maps was generated, which agreed closely with maps predicted from sequence data. The data demonstrate an approach to construct physical maps of genomic loci where very little prior sequence information exists, since the only sequence needed is that required to anchor PCR primers. Large segments of genomic DNA (within the practical limits imposed by long-range PCR) can be mapped quickly and to high resolution without the use of cloning vectors.

DNA Restriction Enzymes↗
PubMed1996

Brain activation induced by estimation of duration: a PET study.

Duration information about a visual stimulus requires processing as do other visual features such as size or intensity. Using positron emission tomography, iterative H215O infusions, and statistical parametric mapping, we investigated the neural correlates of time processing. Nine normal subjects underwent six serial rCBF. Three tasks were studied: (a) A temporal generalization task (D task) in which the subjects had to judge (by pressing one of two keys) whether the duration of the illumination of a green LED was equal to or different from that of a previously presented standard; (b) An intensity generalization task (I task) in which the judgment concerned the intensity of the LED; and (c) A control task (C task) in which the subjects had to press one of the two keys at random in response to LED illumination. A significant increase in rCBF during the D task, compared to that during the C task, was observed in right prefontal cortex, right inferior parietal lobule, anterior cingulate cortex, vermis, and a region corresponding to the left fusiform gyrus. A significant increase in rCBF during the I task, compared to that during the C task, was observed in right prefontal cortex, right inferior parietal lobule, right extrastriate cortex, anterior cingulate cortex, left inferior parietal lobule, vermis, and two symmetrical regions corresponding to the fusiform gyri. No significant activation was observed in the D task when compared to that in the I task. We propose that these cortical maps are best explained by the recruitment of visual attention and memory structures, which play a major role in prospective time judgements as indicated by behavioral studies. The data also suggest that the temporal dimension of a visual stimulus is processed in the same areas as other visual attributes.

Adult↗
PubMed1998

Ultrasonic mapping of the microvasculature: signal alignment.

The ultimate goal of this work was the development of a system capable of estimating the low flow velocities in the microvasculature. Estimation of low velocity flow within these vessels is challenging due to the small signal levels and the effect of cardiac and respiratory motion. Realignment of the signal from a single line-of-sight to remove physiological tissue motion is a critical part of the process of small-vessel flow mapping, and our methods for this alignment are considered in this paper. Each method involves the correlation of pulses acquired from the same line-of-sight. The first method involves the correlation of adjacent pulses (nearest-neighbor), the second involves a single reference line and the third involves averaging the correlation over a set of reference lines. We find that a nearest-neighbor strategy is suboptimal, and that strategies involving a global reference line are superior. A bound on the variance of estimates of the location of the correlation peak is presented. This bound allows us to consider our results in comparison with an absolute limit. Finally, a new algorithm allowing for alignment between lines-of-sight is described, and initial results are presented. Such an algorithm does, in fact, reduce jitter, correct for tissue motion and enables us to better visualize vessel continuity. We find that vessels as small as 40 microm can be mapped in two dimensions using a 50-MHz transducer.

Animals↗
PubMed2004

Approaches and informatics tools to assist in the integration of similar clinical research questionnaires.

OBJECTIVE: The integration of similar clinical research questionnaires is a complex process that can benefit from informatics approaches and tools that provide a systematic structure for performing mapping and integration. This systematic approach is necessary to address complex issues in integration such as data heterogeneity, differing levels of granularity of questions and responses, and other issues involving semantic differences. Informatics tools and approaches have been successfully applied to various standard clinical vocabulary integration processes but not for questionnaire integration or mapping. METHODS: A systematic approach to questionnaire integration was developed in the context of a collaboration of researchers using Trial/DB, a database designed to support clinical research. This approach was applied to the integration of questionnaires involving breast cancer risk factors from each of three research sites. RESULTS: From 375 questions on the three original questionnaires, we identified 65 concepts that were measured by two or three of the sites. An algorithm was developed and used to formalize the process of mapping questions and answers across the questionnaires. The approach was applied to previously collected data and prospective data in disparate data-base systems to import and merge the data from these three sites into Trial/DB. CONCLUSION: Informatics tools that support a systematic approach to mapping questionnaires can be used throughout the research process from questionnaire integration and creation, legacy data integration to data library maintenance and curation.

Biomedical Research↗
PubMed1988

Metabolic mapping of 2-deoxyglucose uptake in the rat piriform cortex using computerized image processing.

Using a computerized image processing method, the metabolic activity of the unfolded molecular and pyramidal layers of the piriform cortex was studied in rats during odorous stimulation. Animals were either intact or had sustained a bilateral transection of the lateral olfactory tract. 2-DG labelling was observed in corresponding areas across these two layers. No spatial pattern of 2-DG uptake could be seen in correlation with the odorant quality. These results are discussed with respect to the known anatomical and functional properties of the piriform cortex.

Animals↗
PubMed2006

An automated image-processing strategy to analyze dynamic arterial spin labeling perfusion studies. Application to human skeletal muscle under stress.

Arterial spin labeling (ASL) perfusion measurements allow the follow-up of muscle perfusion with high temporal resolution during a stress test. Automated image processing is proposed to estimate perfusion maps from ASL images. It is based on two successive analyses: at first, automated rejection of the image pairs between which a large displacement is detected is performed, followed by factor analysis of the dynamic data and cluster analysis to classify pixels with large signal variation characteristic of vessels. Then, after masking these "vascular" pixels, factor analysis and cluster analysis are further applied to separate the different muscles between low or high perfusion increase, yielding a functional map of the leg. Data from 10 subjects (five normal volunteers and five elite sportsmen) had been analyzed. Resulting time perfusion curves from a region of interest (ROI) in active muscles show a good accordance whether extracted with automated processing or with manual processing. This method of functional segmentation allows automated suppression of vessels and fast visualization of muscles with high, medium or low perfusion, without any a priori knowledge.

Adult↗
PubMed2004

An analysis of independence and interactions of brain substrates that subserve multiple attributes, memory systems, and underlying processes.

It is proposed that memory is organized into event-based, knowledge-based, and rule-based memory systems. Furthermore, each system is composed of the same set of multiple attributes and characterized by a set of process oriented operating characteristics that are mapped onto multiple neural regions and interconnected neural circuits. Based on this theoretical model of memory, it is possible to investigate the independence and interaction among brain regions between any two systems for any of the proposed attributes or processes. This applies also to the investigation of independence and interactions between any two attributes within a system and between processes associated with a system for any of the proposed attributes. In this article, research evidence is presented to suggest that there are both dissociations and interactions between the hippocampus and caudate nucleus in mediating spatial and response attributes within the event-based memory system, between the hippocampus and the parietal cortex in subserving the spatial attribute within the event-based and knowledge-based memory systems, and between the hippocampus and the prefrontal cortex in subserving the spatial attribute within the event-based and rule-based memory systems.

Animals↗
PubMed2002

Hereditary forms of intrahepatic cholestasis.

Several genes that are mutated in hereditary forms of intrahepatic cholestasis have been identified or mapped, providing new insights into the process of enterohepatic bile acid circulation in health and disease and new tools with which to study this process. Murine models of several of these disorders have been generated. Unanticipated genetic heterogeneity has been identified.

Alagille Syndrome↗
PubMed2000

Language representation in the human brain: evidence from cortical mapping.

The manner in which the human brain processes grammatical-syntactic and lexical-semantic functions has been extensively debated in neurolinguistics. The discreteness and selectivity of the representation of syntactic-morphological properties in the dominant frontal cortex and the representation of the lexical-semantics in the temporo-parietal cortex have been questioned. Three right-handed adult male neurosurgical patients undergoing left craniotomy for intractable seizures were evaluated using various grammatical and semantic tasks during cortical mapping. The sampling of language tasks consisted of trials with stimulation (experimental) and without stimulation (control) from sites in the dominant fronto-temporo-parietal cortex The sampling of language implicated a larger cortical area devoted to language (syntactic-morphological and lexical-semantic) tasks. Further, a large part of the fronto-parieto-temporal cortex was involved with syntactic-morphological functions. However, only the parieto-temporal sites were implicated with the ordering of lexicon in sentence construction. These observations suggest that the representation of language in the human brain may be columnar or multilayered.

Adult↗
PubMed2001

Mapping and expression pattern analysis of key components of the major histocompatibility complex class I antigen processing and presentation pathway in a representative human renal cell carcinoma cell line.

Renal cell carcinoma (RCC) represent approximately 5% of all cancer deaths. At the time of presentation, over 50% of the patients have already developed locally advanced or metastatic disease with five-year survival rates of less than 20%. Although relative resistant to conventional regimens, RCC are partially susceptible to T cell-based immunotherapy. To further develop this treatment modality, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was applied for both the mapping of the key components of the major histocompatibility complex (MHC) class I antigen processing and presentation machinery (APM) and the characterization of the constitutive and cytokine-regulated protein expression profiles in a representative human RCC cell line. The latter aspect is based on the fact, that the expression level of some of the APM components can be altered in response to interferon (IFN)-gamma treatment. Total cell lysates from untreated and IFN-gamma-treated tumor cells were separated on 2-D PAGE gels using broad range immobilized pH gradient (IPG) strips. Serial Western blot analyses using sets of APM-specific antibodies were performed to target the relevant protein spots. Protein verification was mostly accomplished via peptide mass finger-printing using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). To date, the majority of the APM-related components have been identified and mapped. In addition, the different protein expression profiles of untreated and IFN-gamma-treated RCC cells are under investigation.

Antigen Presentation↗
PubMed2005

Mass spectrometric contributions to the practice of phosphorylation site mapping through 2003: a literature review.

Reversible phosphorylation of proteins is among the most important post-translational modifications, and elucidation of sites of phosphorylation is essential to understanding the regulation of key cellular processes such as signal transduction. Unfortunately phosphorylation site mapping is as technically challenging as it is important. Limitations in the traditional method of Edman degradation of (32)P-labeled phosphoproteins have spurred the development of mass spectrometric methods for phosphopeptide identification and sequencing. To assess the practical contributions of the various technologies we conducted a literature search of publications using mass spectrometry to discover previously unknown phosphorylation sites. 1281 such phosphorylation sites were reported in 203 publications between 1992 and 2003. This review examines and catalogs those methods, identifies the trends that have emerged in the past decade, and presents representative examples from among these methods.

Animals↗
PubMed2002

Olfactory maps and odor images.

The understanding of neuronal processing of olfactory stimuli has been furthered by genetic studies and specialized imaging of particular neuronal populations. Selective optical imaging of odor-induced presynaptic and postsynaptic glomerular activity in the olfactory bulb/antennal lobe has visualized odorant-responsive receptor repertoires and shown a more confined odor image at the level of projection neurons compared to their olfactory receptor neuron input. Genetic tracing of projection neurons connected to particular glomeruli has revealed a somewhat dispersed spatial map of termination areas for these neurons both in insects and in vertebrates. Modifications of the glomerular odor map have resulted in altered percepts of the corresponding odors.

Animals↗
PubMed2000

Value of axillary sentinel nodal status in breast cancer.

Axillary clearance in node-negative breast cancer patients is performed only for staging and prognostic purposes. The sentinel node concept may provide an alternative conservative approach for these patients. This paper reports on the learning experience with lymphatic mapping involving the use of patent blue dye for the identification of sentinel lymph nodes (SLNs), followed by axillary dissection. The histopathology of the SLNs included serial sectioning and immunostaining for cytokeratin and epithelial membrane antigen, the remaining nodes being processed as usual. Of the 70 mapping procedures, 58 were successful; the surgical performance revealed a well defined learning period. The mean diameter of the successfully mapped tumors was 2.4 cm (ranging from in situ carcinoma to 4.8-cm invasive cancer). The mean numbers of SLNs and non-SLNs were 1.3 (range 1-3) and 19 (range 7-42), respectively. There were 36 SLN-positive cases, 21 of which had metastases only to these nodes. There were 19 node-negative cases, and 3 SLNs were falsely negative. Possible causes of the errors during lymphatic mapping are analyzed in the light of experiences published to date. SLN biopsy seems a good approach to enhancing the selectivity of axillary lymphadenectomy, but the limitations of the procedure must be evaluated and carefully considered.

Breast Neoplasms↗
PubMed2005

The effects of action video game experience on the time course of inhibition of return and the efficiency of visual search.

The ability to efficiently search the visual environment is a critical function of the visual system, and recent research has shown that experience playing action video games can influence visual selective attention. The present research examined the similarities and differences between video game players (VGPs) and non-video game players (NVGPs) in terms of the ability to inhibit attention from returning to previously attended locations, and the efficiency of visual search in easy and more demanding search environments. Both groups were equally good at inhibiting the return of attention to previously cued locations, although VGPs displayed overall faster reaction times to detect targets. VGPs also showed overall faster response time for easy and difficult visual search tasks compared to NVGPs, largely attributed to faster stimulus-response mapping. The findings suggest that relative to NVGPs, VGPs rely on similar types of visual processing strategies but possess faster stimulus-response mappings in visual attention tasks.

Adolescent↗
PubMed2006

Valence state map of iron oxide thin film obtained from electron spectroscopy imaging series.

This paper demonstrates the applicability of electron-spectroscopic imaging (ESI) for valence-state mapping of the iron oxide system. We have previously developed a set of signal-processing methods for an ESI series, to allow mapping of sp(2)/sp(3) ratio, dielectric function and energy bandgap. In this study, these methods are applied to generate a valence-state map of an iron oxide thin film (Fe/alpha-Fe(2)O(3)). Two problems, data undersampling and a convolution effect associated with extraction of the image-spectrum from the core loss image series, were overcome by using cubic-polynomial interpolation and maximum-entropy deconvolution. As a result, the reconstructed image-spectrum obtained from the ESI series images has a quality as good as that of conventional electron energy-loss spectra. The L(3)/L(2) ratio of the reconstructed ESI spectrum is determined to be 3.30+/-0.30 and 5.0+/-0.30 for Fe and alpha-Fe(2)O(3), respectively. Our L(3)/L(2) ratio mapping shows an accurate correspondence across the Cu/Fe/alpha-Fe(2)O(3) region. The effect of delocalization and chromatic aberration on the ESI resolution is discussed and estimated to be about 2 nm for the case of L(3)/L(2) ratio mapping.

Journal Article↗
PubMed1997

Cardiac memory in patients with intermittent Wolff-Parkinson-White syndrome.

This study used body surface mapping to evaluate the ventricular repolarization process in the absence of delta waves in 13 patients with the intermittent Wolff-Parkinson-White (WPW) syndrome. The findings were compared with data from 30 normal individuals and 50 patients with the overt WPW syndrome. The QRST isointegral maps of patients with the overt WPW syndrome exhibited abnormal areas and the QRST departure maps showed a peculiar distribution to each accessory pathway site. The QRST isointegral map exhibited abnormal areas in 11 of the 13 cases (85%) of the intermittent WPW syndrome in the absence of delta waves. In 8 of these 11 cases (73%), the distribution of the departure map resembled that in the overt WPW syndrome. These findings suggest that abnormal ventricular repolarization due to cardiac memory is present in patients with the intermittent WPW syndrome even in the absence of delta waves.

Adolescent↗