SEARCH · PubMed Health

Results for “reference mapping”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,603 records · Page 89Linked to original sources

PubMed2000

A minimal tiling path cosmid library for functional analysis of the Pseudomonas aeruginosa PAO1 genome.

Pseudomonas aeruginosa is an important pathogenic and environmental bacterium, with the most widely studied strain being PAO1. Using the PAO1 reference cosmid library and the recently completed PAO1 genome sequence, we have mapped a minimal tiling path across the genome using a two-step strategy. First, we sequenced both ends of a set of over 500 random and previously mapped clones to create a backbone. Second, we end-sequenced a second set of cosmid clones that were identified to lie within the larger gaps using hybridization of the reference library filters with probes designed against sequences at the center of each gap. The minimal tiling path was calculated using the program Domino (http://www.bit.uq.edu.au/download/), with the overlap between adjacent clones set to 5 kb (where possible) to minimize the chance of truncating genes. This yielded a minimal tiling cosmid library (334 clones) covering 93.7% of the genome in 57 contigs. This library has reduced to a workable set the number of clones required to represent the majority of the P. aeruginosa genome and gives the precise location of each cosmid, enabling most genes of interest to be located on clones without further screening. This library should prove a useful resource to accelerate functional analysis of the P. aeruginosa genome.

Cloning, Molecular↗

PubMed2000

A stereological approach to human cortical architecture: identification and delineation of cortical areas.

Stereology offers a variety of procedures to analyze quantitatively the regional and laminar organization in cytoarchitectonically defined areas of the human cerebral cortex. Conventional anatomical atlases are of little help in localizing specific cortical areas, since most of them are based on a single brain and use highly observer-dependent criteria for the delineation of cortical areas. In consequence, numerous cortical maps exist which greatly differ with respect to number, position, size and extent of cortical areas. We describe a novel algorithm-based procedure for the delineation of cortical areas, which exploits the automated estimation of volume densities of cortical cell bodies. Spatial sampling of the laminar pattern is performed with density profiles, followed by multivariate analysis of the profiles' shape, which locates the cytoarchitectonic borders between neighboring cortical areas at sites where the laminar pattern changes significantly. The borders are then mapped to a human brain atlas system comprising tools for three dimensional reconstruction, visualization and morphometric analysis. A sample of brains with labeled cortical areas is warped into the reference brain of the atlas system in order to generate a population map of the cortical areas, which describes the intersubject variability in spatial conformation of cortical areas. These population maps provide a novel tool for the interpretation of images obtained with functional imaging techniques.

Brain Mapping↗

PubMed1985

Hemodynamic effects of a new alpha- and beta-adrenergic receptor inhibitor with calcium entry blocking effects (CGS 10078B) in WKY and SHR rats.

The immediate acute hemodynamic effects of CGS 10078B, a new agent with combined alpha- and beta-adrenergic antagonist with slow channel calcium entry blocking effects, were studied in normotensive Wistar-Kyoto (WKY) and spontaneously hypertensive (SHR) rats. Heart rate (HR), mean arterial pressure (MAP), cardiac index (CI), total peripheral resistance index (TPRI), and regional hemodynamic measurements were determined before and two hours after its administration (10 mg/kg, gavage) using the combined radioactive reference sample and microsphere techniques (85SR and 141Ce). The agent significantly reduced MAP (168 +/- 5 to 158 +/- 5 mm Hg; p less than 0.02) after 20 minutes without changing HR in SHR. After two hours MAP, HR, and Cl were significantly reduced without change in TPRI. Only Cl decreased (p less than 0.05) in WKY, presumably from its beta receptor antagonist effects. Blood flow to the major organs (eg, heart, brain, and kidneys) was maintained in both groups of rats. These hemodynamic effects reflect the combined actions of this new agent and suggest its potential value for the treatment of hypertension.

Adrenergic alpha-Antagonists↗

PubMed2001

Do patients with obstructive sleep apnea have clinically significant proteinuria?

AIM: Previous studies report a high prevalence of proteinuria in patients with obstructive sleep apnea syndrome (OSAS). This common syndrome may therefore be an important cause ofproteinuria and renal failure in the general population. This study was undertaken to assess the prevalence of proteinuria among OSAS patients, and to identify the factors associated with urine protein excretion in these patients. METHODS: Overnight polysomnography, urine protein to creatinine ratio (PTCR), body mass index (BMI), mean arterial pressure (MAP), and hematocrit were assessed prospectively in 224 patients referred for evaluation of suspected OSAS. Sleep apnea was defined as apnea-hypopnea score (AHS) > or = 5 events/hour. Proteinuria was defined as PTCR > 0.2 mg/mg. RESULTS: Sleep apnea was present in 143 subjects (63.8%), and proteinuria in 10 (4.5%). The highest PTCR was 0.677 mg/mg. PTCR and AHS were weakly correlated (r = 0.12, p = 0.08). PTCR correlated (alpha = 0.05) with lowest oxygen saturation (r = -0.18, p = < 0.01), time spent with oxygen saturation below 90% (r = 0.19, p = < 0.01), and BMI (r= 0. 17, p = < 0.01). The mean PTCR was similar in subjects with and without sleep apnea. Proteinuria was present in 7 of 143 (4.9%) subjects with AHS > or = 5 and 3 of 81 (3.7%) subjects with AHS < 5, a relative risk of 1.34, 95% CI (0.34, 5.32). Predictors of LogPTCR in multiple linear regression (model R2 - 0.104) were: AHS (< 5 or > or = 5), baseline oxygen saturation, sex, and MAP. CONCLUSIONS: Clinically significant proteinuria is uncommon in OSAS. The prevalence and severity of proteinuria are similar in both OSAS patients and patients without sleep-disordered breathing. Sleep apnea severity is weakly associated with urine protein excretion, related more to hypoxemia than to frequency of apneic events.

Analysis of Variance↗

PubMed2001

Near 10-year and longer periods modulate circadians: intersecting anti-aging and chronoastrobiological research.

Biological cycles with relatively long and some unusual periods in the range of the half-week, the half-year, years, or decades are being discovered. Their prior neglect constituted a confounder in aging and much other research, which then"flew blind" concerning the uncertainties associated with these cycles when they are not assessed. The resolution of more about 10-year and other cycles, some reported herein, replaces the admission of complete unpredictability, implied by using the label "secularity." Heretofore unaccounted-for variability becomes predictable insofar as it proves to be rhythmic and is mapped systematically to serve as a battery of useful reference values. About 10-year cycles in urinary 17-ketosteroid excretion and in heart rate and its variability, among others, are aligned with cycles of similar length in mortality from myocardial infarction. Associations accumulate between cycles of natural physical time structures, chronomes such as the 10.5-year (circadecennian) Schwabe and the 21-year (circavigintunennian) Hale cycles of solar activity, and chronomes in biota. There are about 50-year (circasemicentennian) cycles in mortality from stroke in Minnesota and in the Czech Republic and also in human morphology at birth, the latter result reducing the likelihood that these cycles are purely human made. Associations among large populations warrant long-term systematic coordinated sampling of natural physical and biological variables of interest for the design of countermeasures against already documented elevated risks of stroke, myocardial infarction, and other catastrophic diseases, notably in elderly adults. New findings will be introduced against the background of the documented value of mapping rhythms in medicine and gerontology. In both these fields, rhythms promise the seeming paradox of better care for less.

17-Ketosteroids↗

PubMed2003

Percutaneous pericardial instrumentation for endo-epicardial mapping of previously failed ablations.

BACKGROUND: The epicardial location of an arrhythmia could be responsible for unsuccessful endocardial catheter ablation. METHODS AND RESULTS: In 48 patients referred after prior unsuccessful endocardial ablation, we considered percutaneous, subxiphoid instrumentation of the pericardial space for mapping and ablation. Thirty patients had ventricular tachycardia (VT), 6 patients had a right- and 4 had a left-sided accessory pathway (AP), 4 patients had inappropriate sinus tachycardia, and 4 patients had atrial arrhythmias. Of the 30 VTs, 24 (6 with ischemic cardiomyopathy, 3 with idiopathic cardiomyopathy, and 15 with normal hearts) appeared to originate from the epicardium. Seventeen (71%) of these 24 VTs were successfully ablated with epicardial lesions. The other 7 VTs had early epicardial sites that were inaccessible, predominantly because of interference from the left atrial appendage. Six of these were successfully ablated from the left coronary cusp. In 5 of the 10 patients with an AP, the earliest activation was recorded epicardially. Three of these were right atrial appendage-to-right ventricle APs, and epicardial ablation was successful. No significant complications were observed. CONCLUSIONS: Failure of endocardial ablation could reflect the presence of an epicardial arrhythmia substrate. Epicardial instrumentation and ablation appeared feasible and safe and provided an alternative strategy for the treatment of patients with a variety of arrhythmias. This was particularly true for VT, including patients without structural heart disease.

Adolescent↗

PubMed2002

Surface atomic arrangement visualization via reference-atom-specific holography.

We demonstrate the direct reconstruction of 3D atomic images from measured low-energy electron diffraction (LEED) intensity spectra. A multiple-incident angle and multiple-energy integral are first applied to the spectra to obtain a map of interatomic vectors. From this map, a nonbulk interatomic vector is chosen that points to a desired reference atom. A second integral transformation, using the chosen interatomic vector as a filter, is applied to the LEED spectra to produce images of individual atoms in the vicinity of the selected reference atom. This two-step method overcomes the problem of multiple, nonequivalent reference atoms and is applicable to elemental or compound materials.

Journal Article↗

PubMed2006

A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome.

8-Oxoguanine (8-oxoG), a major spontaneous form of oxidative DNA damage, is considered to be a natural cause of genomic diversity in organisms because of its mutagenic potential. The steady-state level of 8-oxoG in the nuclear genome of a human cell has been estimated to be several residues per 10(6) guanines. In the present study, to clarify the genome-wide distribution of 8-oxoG in the steady state, we performed fluorescence in situ detection of 8-oxoG on human metaphase chromosomes using a monoclonal antibody. Multiple dot-like signals were observed on each metaphase chromosome. We then mapped the position of the signal at megabase resolution referring to the cytogenetically identified chromosomal band, and demonstrated that 8-oxoG is unevenly distributed in the normal human genome and that the distribution pattern is conserved among different individuals. Moreover, we found that regions with a high frequency of recombination and single nucleotide polymorphisms (SNPs) are preferentially located within chromosomal regions with a high density of 8-oxoG. Our findings suggest that 8-oxoG is one of the main causes of frequent recombinations and SNPs in the human genome, which largely contribute to the genomic diversity in human beings.

Adult↗

PubMed2003

[Lyrical and musical auditive mental imagery in functional MRI].

PURPOSE: to explore with functional MRI cerebral areas involved in musical and lyrical sounds signal processing with the mental imagery method. MATERIAL: and METHODS: nine volunteers (mean age: 27 years old) underwent functional MRI with BOLD contrast at 1.5 T. Box-car paradigms of partial recollections of musical or lyrical memories tasks were performed. Statistical correlations mappings were calculated and superimposed on previously realigned anatomical reference imaging to observe activated cerebral areas. RESULTS: all except one subjects had activation areas in primary and secondary auditive cortices in the temporal Heschl gyrus and the Planum Temporale, unilaterally (n=2) or bilaterally (n=6) during both mental tasks. Contralateral activation improvement was observed in 4 cases when the lyrical tasks were performed. Temporal and insular regions involved in language processing were observed in eight of nine subjects. CONCLUSION: auditive mental imagery can show in functional MRI cerebral areas involved in auditive functions and some of the areas involved in language processing.

Adult↗

PubMed2006

Mapping data elements to terminological resources for integrating biomedical data sources.

BACKGROUND: Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration. METHODS: We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings. RESULTS: 82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed. CONCLUSION: Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.

Abstracting and Indexing↗

PubMed1995

Paraspinal mapping. Quantified needle electromyography of the paraspinal muscles in persons without low back pain.

STUDY DESIGN: This was a case series with intervention performed by masked investigators. OBJECTIVES: To determine values for normal subjects on quantified needle electromyography of the paraspinal muscles compared with a previous sample of patients with clear evidence of radiculopathy. SUMMARY OF BACKGROUND DATA: Diagnosis of radicular back pain is difficult, even with modern imaging studies, partly due to the large percentage of imaging abnormalities in asymptomatic persons. Electromyography has been shown to be as sensitive as imaging studies in diagnosing radicular pain. An electromyographic study of the low back has never been done in normal subjects. We have previously anatomically validated and clinically demonstrated a method of quantitative needle electromyography in the paraspinal muscles called paraspinal mapping. METHODS: Thirty-five subjects free of back pain or polyneuropathy were intermixed with volunteers referred for electromyography of radicular back pain. One electrodiagnostician punctured the skin at five predetermined locations and obtained paraspinal mapping scores in one of these. An electromyographer who was masked to the study's nature then performed a complete paraspinal mapping study. A total "sensitivity" score was compared to scores of previously tested patients who had pain complaints and clear evidence for radiculopathy on either radiologic or traditional electromyographic studies. RESULTS: Mean score in normal subjects was 1.11 (SD 1.49). Mean score for abnormal subjects averaged 12.18 (SD 12.03). Differences between examiners were insignificant. CONCLUSIONS: Normal persons have few, if any electromyographic abnormalities in the paraspinal muscles. This is in contrast to computed tomography, magnetic resonance imaging, or myelographic results in normal subjects. Persons with radiculopathy have significantly different scores. Needle electromyographic examination of the paraspinal muscles is useful in distinguishing false-positive radiologic studies.

Adolescent↗

PubMed1994

A genetic linkage map of the mouse using restriction landmark genomic scanning (RLGS).

We have developed a multiplex method of genome analysis, restriction landmark genomic scanning (RLGS) that has been used to construct genetic maps in mice. Restriction landmarks are end-labeled restriction fragments of genomic DNA that are separated by using high resolution, two-dimensional gel electrophoresis identifying as many as two thousand landmark loci in a single gel. Variation for several hundred of these loci has been identified between laboratory strains and between these strains and Mus spretus. The segregation of more than 1100 RLGS loci has been analyzed in recombinant inbred (RI) strains and in two separate interspecific genetic crosses. Genetic maps have been derived that link 1045 RLGS loci to reference loci on all of the autosomes and the X chromosome of the mouse genome. The RLGS method can be applied to genome analysis in many different organisms to identify genomic loci because it uses end-labeling of restriction landmarks rather than probe hybridization. Different combinations of restriction enzymes yield different sets of RLGS loci providing expanded power for genetic mapping.

Animals↗

PubMed1995

The tetranucleotide repeat polymorphism D21S1245 demonstrates hypermutability in germline and somatic cells.

Six novel polymorphic short sequence repeats were identified and localized on the linkage map of human chromosome 21 by genotyping the CEPH reference pedigrees. One of these markers, the tetrameric (AAAG)n repeat D21S1245, was found to be hypermutable. In the DNAs from lymphoblastoid cell lines of members of the 40 CEPH families a total of 18 new alleles were detected. These new alleles, sometimes appearing in mosaic forms, arose equally in paternal and maternal DNAs, and could be equally larger or smaller than the alleles from which they were derived. The larger alleles of D21S1245 are more prone to be converted to new alleles. None of the new alleles with mosaicism were present in the corresponding genomic blood DNA, and therefore originated during or after the establishment of the lymphoblastoid cell lines; half of the new alleles without mosaicism were also found in genomic blood DNA of the appropriate CEPH individuals. The range of germline mutation rate observed in the 716 meioses examined was 0.56-1.4 x 10(-2); the range of somatic mutations observed in the 405 cell lines examined was 1.96-3.46 x 10(-2). This is one of the most hypermutable microsatellite repeat polymorphism in the human genome detected to date. D21S1245, is highly polymorphic (heterozygosity of 0.96) and maps between D21S231 and D21S198.

Alleles↗

PubMed2000

Homozygosity mapping identifies an additional locus for Wolfram syndrome on chromosome 4q.

Wolfram syndrome, which is sometimes referred to as "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness), is an autosomal recessive neurodegenerative disorder for which only insulin-dependent diabetes mellitus and optic atrophy are necessary to make the diagnosis. Researchers have mapped Wolfram syndrome to chromosome 4p16.1, and, recently, a gene encoding a putative transmembrane protein has been cloned and mutations have been identified in patients. To pursue the possibility of locus heterogeneity, 16 patients from four different families were recruited. These patients, who have the Wolfram syndrome phenotype, also have additional features that have not previously been reported. There is an absence of diabetes insipidus in all affected family members. In addition, several patients have profound upper gastrointestinal ulceration and bleeding. With the use of three microsatellite markers (D4S432, D4S3023, and D4S2366) reported to be linked to the chromosome 4p16.1 locus, we significantly excluded linkage in three of the four families. The two affected individuals in one family showed homozygosity for all three markers from the region of linkage on chromosome 4p16.1. For the other three families, genetic heterogeneity for Wolfram syndrome was verified by demonstration of linkage to chromosome 4q22-24. In conclusion, we report the unique clinical findings and linkage-analysis results of 16 patients with Wolfram syndrome and provide further evidence for the genetic heterogeneity of this disorder. We also provide data on a new locus that plays a role in the etiology of insulin-dependent diabetes mellitus.

Adolescent↗

PubMed1994

Squirrel monkey lateral thalamus. II. Viscerosomatic convergent representation of urinary bladder, colon, and esophagus.

The response properties of 106 visceroceptive lateral thalamic neurons were investigated in anesthetized squirrel monkeys. Most neurons were located in the ventral posterior lateral nucleus (VPL), and a smaller number of cells was also found in a variety of thalamic nuclei around VPL. Ninety (85%) of these cells responded to distension of the urinary bladder, the distal colon, and/or the lower esophagus. The majority of the visceral-responsive cells also had convergent somatic and multivisceral responses (71% of the 85%). A small population (6%) was visceral specific; that is, these neurons were not activated with somatic stimuli. Visceral responses were excitatory, inhibitory, or mixed, and most were either visceral nociceptive specific (65%) or visceral wide-dynamic-range type (34%). Very few visceral responses (1%) could be classified as low threshold. The incidence of these response types were highly dependent on the specific viscus stimulated. Most visceral responses were able to code stimulus duration and intensity. The majority (69%) of the visceroceptive neurons had somatic low-threshold convergent input mainly from the surface of the lower body. The somatic receptive field locations and the somatic response properties seem unrelated to the convergent visceral input and the visceral response properties, although there were some exceptions. No obvious viscerotopical organization was found in VPL. The results lead us to propose two different modes of representation for processing of and distinguishing between visceral and somatic inputs: a distributed population code for visceral inputs, and a local code for somatic inputs. Based on these codes, we discuss a new hypothesis for referred pain.

Animals↗

PubMed1999

The isolation and mapping of 19 tetranucleotide microsatellite markers in the chicken.

Microsatellites consisting of tetranucleotide repeats are more easily, and consequently efficiently, scored than loci consisting of dinucleotides. However, they are much less frequent in the genome. A hybridisation selection protocol was therefore employed to generate a chicken genomic library enriched for inserts containing the tetranucleotide repeat motif (TTTC)n. Forty-five new microsatellite sequences were isolated that mainly consisted of perfect repeats of the tetranucleotide (TTTC) motif. Nineteen markers were mapped in one or both of the East Lansing and Compton international chicken reference populations.

Animals↗

PubMed2000

NCBI genetic resources supporting immunogenetic research.

The NCBI creates and maintains a set of integrated bibliographic, sequence, map, structure and other database resources to promote the efficient retrieval of information and the discovery of novel relationships. The connections made between elements of these resources permit researchers to start a search from a wide spectrum of entry points. These multiple dimensions of data can be roughly categorized by primary content as text or bibliographic (PubMed, PubMedCentral, OMIM, LocusLink), sequence (GenBank, Reference Sequence Project (RefSeq), dbSNP, MMDB), protein structure (MMDB) or map position (MapView). They can also becategorized by level of expert curation, which may range from validation of submissions from external groups (GenBank, PubMed, PubMedCentral,), to automatic computation (HomoloGene, UniGene), and to highly reviewed and corrected (LocusLink, MMDB, OMIM, RefSeq). Searches can be made by words (in an article title, key words, sequence annotation, database value, author) by sequence (BLAST or e-PCR against multiple sequence databases), or by map coordinates. By computing or curating bi-directional links between related objects, NCBI can represent content on the genetics, molecular biology, and clinical considerations of interest to immunogeneticists. There is also an emerging resource developed by the NCBI in collaboration with the IHWG devoted to the presentation of MHC data (dbMHC). How dbMHC will augment existing resources at the NCBI is described.

Computational Biology↗

PubMed2001

Formation of a direction map by projection learning using Kohonen's self-organization map.

In this paper, we propose a modification of Kohonen's self-organization map (SOM) algorithm. When the input signal space is not convex, some reference vectors of SOM can protrude from it. The input signal space must be convex to keep all the reference vectors fixed on it for any updates. Thus, we introduce a projection learning method that fixes the reference vectors onto the input signal space. This version of SOM can be applied to a non-convex input signal space. We applied SOM with projection learning to a direction map observed in the primary visual cortex of area 17 of ferrets, and area 18 of cats. Neurons in those areas responded selectively to the orientation of edges or line segments, and their directions of motion. Some iso-orientation domains were subdivided into selective regions for the opposite direction of motion. The abstract input signal space of the direction map described in the manner proposed by Obermayer and Blasdel [(1993) J Neurosci 13: 4114-4129] is not convex. We successfully used SOM with projection learning to reproduce a direction-orientation joint map.

Algorithms↗