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 1,639 records · Page 91Linked to original sources

PubMed1990

[Mapping the spontaneous EEG in focal disorders].

It will be reported about 142 EEG spectral analytic mappings in 100 patients with focal EEG findings which were recorded already in routine EEG examinations. Drawings of the visually analysed paper recordings have been compared with the maps. We found in about 30 per cent a true gain of information. It is based on a more precise demarcation of focal findings or a better display of points of most severe dysfunction within extended disturbances. Beyond that the pictorial presentation of topographic features is a general advantage of EEG mapping. On the other side there are limits and disadvantages of topographic EEG analysis. With special reference to the analysis of circumscribed dysfunctions they will be demonstrated. Problems are related to the type of reference, to the choice of analysis time, or to "spatial aliasing effects" which are introduced by the interpolation procedure of mapping analysis. Beside the neuroradiological imaging methods the EEG mapping maintains special significance because it displays the functional aspect of cerebral processes.

Brain Diseases↗

PubMed1997

Fine genetic mapping of LCN1/D9S1826 within 9q34.

LCN1 gene encodes the tear lipocalin; the lipocalins are a large and growing family of proteins characterized by their ability to bind small hydrophobic molecules. We report here the location of a dinucleotide repeat microsatellite marker (D9S1826) close to LCN1 gene. Using the CEPH reference families, the position of LCN1 is located within the 9q34 genetic map between D9S23 and D9S158.

Carrier Proteins↗

PubMed2004

Removal of EPI Nyquist ghost artifacts with two-dimensional phase correction.

Odd-even echo inconsistencies result in Nyquist ghost artifacts in the reconstructed EPI images. The ghost artifacts reduce the image signal-to-noise ratio and make it difficult to correctly interpret the EPI data. In this article a new 2D phase mapping protocol and a postprocessing algorithm are presented for an effective Nyquist ghost artifacts removal. After an appropriate k-space data regrouping, a 2D map accurately encoding low- and high-order phase errors is derived from two phase-encoded reference scans, which were originally proposed by Hu and Le (Magn Reson Med 36:166-171;1996) for their 1D nonlinear correction method. The measured phase map can be used in the postprocessing algorithm developed to remove ghost artifacts in subsequent EPI experiments. Experimental results from phantom, animal, and human studies suggest that the new technique is more effective than previously reported methods and has a better tolerance to signal intensity differences between reference and actual EPI scans. The proposed method may potentially be applied to repeated EPI measurements without subject movements, such as functional MRI and diffusion coefficient mapping.

Animals↗

PubMed2003

Properties of MEG tomographic maps obtained with spatial filtering.

Magnetoencephalography (MEG) has, in comparison with other functional imaging modalities, unique properties which makes it the prime candidate for the noninvasive investigation of long-range oscillatory interactions in the human brain. Recent methodological developments based on spatial filtering introduced the computation of functional tomographic maps covering the entire brain and representing the distribution of coherence to a given reference signal or the distribution of power. Because of the spatially inhomogeneous sensitivity profile of the MEG sensors, the spatial resolution of the resulting functional maps is not isotropic across the brain. Here, we introduce a convenient analytic expression for the computation of the spatial resolution at any given point in the brain. We derive the dependence of the resolution on the signal-to-noise ratio and on the changes of the leadfields. The resolution map can be displayed on anatomical MRI in the same way as the functional maps. In addition, we establish a procedure for computing a confidence volume of local maxima which is based on a bootstrap method. The confidence volume is a measure for the uncertainty of the localization. It is important for assigning local maxima of activation to specific anatomical structures and may be used to test for differences in localization between different experimental conditions.

Artifacts↗

PubMed1992

Complexity of sea urchin embryo nuclear proteins that contain basic domains.

We describe a quantitative two-dimensional gel electrophoretic analysis of nuclear extract from 24-hr sea urchin embryos. The extract was fractionated by using a weak cation-exchange resin, and eight known DNA-binding proteins were shown to be entirely included in a salt eluate that releases proteins containing basic domains. This fraction and a lower-salt fraction containing the majority of the protein species were mapped two-dimensionally by using new algorithms that permit reproducible spot identification, storage of intensity and map-position data, and subtractive comparison of one pattern with respect to another. By reference to a previously characterized DNA-binding factor, spot intensity could be interpreted in terms of the number of molecules per embryo nucleus. A map was constructed displaying all nuclear proteins containing basic domains that are present within the concentration range per nucleus of a set of known DNA-binding factors of the sea urchin embryo. The map includes 265 spots that fulfill both of these criteria, probably representing about 100 different protein species.

Animals↗

PubMed1984

Strategies for multilocus linkage analysis in humans.

The increasing number of DNA polymorphisms characterized in humans will soon allow the construction of fine genetic maps of human chromosomes. This advance calls for a reexamination of current methodologies for linkage analysis by the family method. We have investigated the relative efficiency of two-point and three-point linkage tests for the detection of linkage and the estimation of recombination in a variety of situations. This led us to develop the computer program LINKAGE to perform multilocus linkage analysis. The investigation also enables us to propose a method of location scores for the efficient detection of linkage between a disease locus, or a new genetic marker, and a linkage group previously established from a reference panel of families. The method is illustrated by an application to simulated pedigree data in a situation akin to Duchenne muscular dystrophy. These results show that considerable economy and efficiency can be brought to the mapping endeavor by resorting to appropriate strategies of detecting linkage and by constructing the human genetic map on a common reference panel of families.

Chromosome Mapping↗

PubMed1999

First chromosomal restriction map of Actinobacillus pleuropneumoniae and localization of putative virulence-associated genes.

Combined physical and genetic maps of the genomes of Actinobacillus pleuropneumoniae AP76 (serotype 7 clinical isolate) and of A. pleuropneumoniae ATCC 27088 (serotype 1 reference strain) were constructed by using the restriction endonucleases ApaI, AscI, NotI, and SalI. The chromosome sizes as determined by the addition of estimated fragment sizes were 2.4 Mbp, and both maps had a resolution of approximately 100 kbp. The linkages between the ApaI, AscI, NotI, and SalI fragments and their relative positions were determined by (i) fragment excision and redigestion and (ii) partial digests of defined fragments and Southern blot using end-standing probes. The single SalI site within the chromosome of strain A. pleuropneumoniae AP76 was defined as position 1 of the map; for the map of A. pleuropneumoniae ATCC 27088, the corresponding SalI site was chosen. Putative virulence-associated genes (apx, omlA, sodA, tbpBA, ureC, and a repeat element) and housekeeping genes (glyA, metJ, recA, and rhoAP) were positioned on the physical maps and located on the ApaI and NotI fragments of A. pleuropneumoniae serotype reference strains.

Actinobacillus pleuropneumoniae↗

PubMed2005

Proteome analysis of chicken embryonic gonads: identification of major proteins from cultured gonadal primordial germ cells.

The domestic chicken (Gallus gallus) is an important model for research in developmental biology because its embryonic development occurs in ovo. To examine the mechanism of embryonic germ cell development, we constructed proteome map of gonadal primordial germ cells (gPGCs) from chicken embryonic gonads. Embryonic gonads were collected from 500 embryos at 6 days of incubation, and the gPGCs were cultured in vitro until colony formed. After 7-10 days in culture, gPGC colonies were separated from gonadal stroma cells (GSCs). Soluble extracts of cultured gPGCs were then fractionated by two-dimensional gel electrophoresis (pH 4-7). A number of protein spots, including those that displayed significant expression levels, were then identified by use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry and LC-MS/MS. Of the 89 gPGC spots examined, 50 yielded mass spectra that matched avian proteins found in on-line databases. Proteome map of this type will serve as an important reference for germ cell biology and transgenic research.

Animals↗

PubMed2006

Quantitative study of changes in oxidative metabolism during visual stimulation using absolute relaxation rates.

In the context of quantitative functional MRI (fMRI), deoxyhemoglobin (dHb) content is the essential physiological parameter for calibrating the blood oxygenation level-dependent (BOLD) signal. In studies on humans, the baseline dHb content or its equivalent has been evaluated indirectly by means of carbon dioxide breathing as a physiological reference condition. In this study with normal volunteers, quantitative mapping of baseline dHb content was performed in a direct manner by measuring the reversible contribution of the effective transverse relaxation rate. The BOLD signal change in the visual cortex during 8 Hz flicker visual stimulation was calibrated based on the quantitative map of baseline dHb content. The calibrated relaxation rate change that represents the stimulation-induced fractional change of dHb content decreased by 14% within the activated visual cortex. Simultaneous measurement of cerebral blood flow (CBF) with BOLD showed an increase of 59%. From the calibrated relaxation rate and CBF changes, the cerebral metabolic rate of oxygen (CMRO2) was calculated to increase by 19-28% within the activated visual cortex. The ratio of the CBF increase to the CMRO2 increase was 2-3:1, which agreed well with results of similar quantitative fMRI studies for humans. The method proposed here for quantitative evaluation of the BOLD signal may be applicable not only to fMRI for normal human subjects, but also to physiologically altered or diseased states, because it requires no physiological perturbation.

Adult↗

PubMed1998

A New Method for Estimating Model Parameters for Multinomial Data.

A new procedure for estimating the parameters of a scientific model is described, and the method is applied and illustrated for the class of experiments with multinominal data structure. The procedure is referred to as the method of population-parameter mapping, and it has a number of novel and advantageous features. The method is a variation of a standard Bayesian analysis. However, instead of directly developing a posterior distribution for the model parameters, this procedure first characterizes the population proportions for the multinomial cells. Random samples are then drawn from the posterior distribution for these proportions, and these samples are mapped to the parameters of the scientific model. This method leads naturally to a definition of model identifiability, and leads to a direct probability estimate of the coherence of the scientific model. Moreover, the new procedure can circumvent the problem of dealing with computationally difficult integrals that frequently occur with Bayesian analyses of complex multinomial models. The method is illustrated by means of several memory measurement models as well as a signal-detection model. Copyright 1998 Academic Press.

Journal Article↗

PubMed1981

A T7 amber mutant defective in DNA-binding protein.

A T7 amber mutant, UP-2, in the gene for T7 DNA-binding protein was isolated from mutants that could not grow on sup+ ssb-1 bacteria but could grow on glnU ssb-1 and sup+ ssb+ bacteria. The mutant phage synthesized a smaller amber polypeptide (28,000 daltons) than T7 wild-type DNA-binding protein (32,000 daltons). DNA synthesis of the UP-2 mutant in sup+ ssb-1 cells was severely inhibited and the first round of replication was found to be repressed. The abilities for genetic recombination and DNA repair were also low even in permissive hosts compared with those of wild-type phage. Moreover, recombination intermediate T7 DNA molecules were not formed in UP-2 infected nonpermissive cells. The gene that codes for DNA-binding protein is referred to as gene 2.5 since the mutation was mapped between gene 2 and gene 3.

Carrier Proteins↗

PubMed1992

Isolation of a Drosophila gene encoding glutathione S-transferase.

We have isolated a Drosophila gene, DmGST-2, that encodes glutathione S-transferase, a homo- or heterodimeric enzyme thought to be involved in detoxification of xenobiotics, including known carcinogens. The encoded protein has a primary sequence that is more similar to mammalian placental and nematode GSTs than that of a previously described Drosophila GST gene, herein referred to as DmGST-1. We provide a physical map of the gene and show that it specifies at least two mRNAs, measuring 1.9 and 1.6 kb, which differ only in the lengths of their 3' untranslated regions. Both of the mRNAs are present during all developmental stages. In situ hybridization of the DmGST-2 gene to larval polytene chromosomes places it within the 53F subdivision of chromosome 2, and Southern blotting to chromosomal DNA indicates that the gene has no close relatives within the Drosophila genome. Our results make possible molecular genetic approaches for further elaborating the function of glutathione S-transferases in insect development and physiology, in the metabolism of plant toxins, and in conferring insecticide resistance.

Amino Acid Sequence↗

PubMed1998

AUTO-SMASH: a self-calibrating technique for SMASH imaging. SiMultaneous Acquisition of Spatial Harmonics.

Recently a new fast magnetic resonance imaging strategy, SMASH, has been described, which is based on partially parallel imaging with radiofrequency coil arrays. In this paper, an internal sensitivity calibration technique for the SMASH imaging method using self-calibration signals is described. Coil sensitivity information required for SMASH imaging is obtained during the actual scan using correlations between undersampled SMASH signal data and additionally sampled calibration signals with appropriate offsets in k-space. The advantages of this sensitivity reference method are that no extra coil array sensitivity maps have to be acquired and that it provides coil sensitivity information in areas of highly non-uniform spin-density. This auto-calibrating approach can be easily implemented with only a small sacrifice of the overall time savings afforded by SMASH imaging. The results obtained from phantom imaging experiments and from cardiac studies in nine volunteers indicate that the self-calibrating approach is an effective method to increase the potential and the flexibility of rapid imaging with SMASH.

Adult↗

PubMed1987

Surface distribution of flash-evoked and pattern reversal-evoked potentials in hooded rats.

Simultaneous recording from 21 electrode sites in a 4 X 4 mm area over the posterior cortex was used to determine the surface distribution of all major peaks which constitute flash-evoked potentials (FEPs) and pattern reversal evoked-potentials (PREPs) in hooded rats. Topographical maps were constructed with respect to Bregma and midline reference points. The data indicate that not all of the peaks which constitute either evoked potential have their greatest amplitude within the classically defined primary visual cortex. Further, since the FEPs were produced by uniform stimulation, the data suggest that surface regions of the rat visual cortex differ in ways other than simply the portion of the visual field from which information is received.

Animals↗

PubMed1990

Correlation analysis of gap junction lattice images.

Fourier averages of connexon images computed from low-irradiation electron micrographs of isolated negatively stained gap junction domains exhibited differences in stain distribution and connexon orientation. To analyze these polymorphic structures, correlation averaging methods were applied to images from negatively stained and frozen-hydrated specimens. For the negatively stained specimens, separate averages over two subsets of connexons with differing degrees of stain accumulation in the axial channel were obtained. Two populations of connexons with opposite skew orientations were distinguishable within a single junctional domain of a frozen-hydrated specimen. Correlation maps calculated using the left- and right-skewed references showed that the selected connexons tend to locally cluster. Using correlation methods to analyze packing disorder in a typical connexon lattice, we estimated the root-mean-square variation in the nearest neighbor pair separation to be approximately 11% of the lattice constant. Displacements of the connexons relative to each other increased with increasing pair separation in the lattice, rather like a liquid, although long-range orientation order was conserved as in a crystal. These results support the hypothesis that the hexagonal ordering of the connexons results from short-range repulsive forces.

Biophysical Phenomena↗

PubMedDate not supplied

Trends in comparative genetics and their potential impacts on wheat and barley research.

We review some general points about comparative mapping, the evolution of gene families and recent advances in the understanding of angiosperm phylogeny. These are considered in relation to studies of large-genome cereals, particularly barley (Hordeum vulgare) and wheat (Triticum aestivum), with reference to methods of gene isolation. The relative merits of direct map-based cloning in barley and wheat, utilization of the smaller genome of rice (Oryza sativa) and gene homology methods that utilize information from model species such as Arabidopsis thaliana are briefly discussed.

Chromosome Mapping↗

PubMed2000

The three-dimensional structure of halorhodopsin to 5 A by electron crystallography: A new unbending procedure for two-dimensional crystals by using a global reference structure.

Electron microscopy does not, in principle, require highly ordered crystals to determine a high-resolution structure. Nevertheless, crystals of any type help to constrain the molecules into a more limited range of orientations and positions, from which it is easier to carry out structure determination. We describe an improved procedure for determination of crystalline disorder, which we have applied to poorly ordered two-dimensional crystals of the chloride pump halorhodopsin from Halobacterium salinarum. The new image analysis procedure involves the use of a reference projection calculated from a global three-dimensional map to carry out the initial cross-correlation analysis. Coupled with a greater number of images taken with field emission gun microscopes, this has allowed us to calculate a three-dimensional structure for halorhodopsin, in which the seven transmembrane helices and certain molecular features, such as the beta-ionone ring of retinal, are now resolved.

Bacteriorhodopsins↗

PubMed2007

Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells.

NDRG1 is known to play important roles in both androgen-induced cell differentiation and inhibition of prostate cancer metastasis. However, the proteins associated with NDRG1 function are not fully enumerated. Using coimmunoprecipitation and mass spectrometry analysis, we identified 58 proteins that interact with NDRG1 in prostate cancer cells. These proteins include nuclear proteins, adhesion molecules, endoplasmic reticulum (ER) chaperons, proteasome subunits, and signaling proteins. Integration of our data with protein-protein interaction data from the Human Proteome Reference Database allowed us to build a comprehensive interactome map of NDRG1. This interactome map consists of several modules such as a nuclear module and a cell membrane module; these modules explain the reported versatile functions of NDRG1. We also determined that serine 330 and threonine 366 of NDRG1 were phosphorylated and demonstrated that the phosphorylation of NDRG1 was prominently mediated by protein kinase A (PKA). Further, we showed that NDRG1 directly binds to beta-catenin and E-cadherin. However, the phosphorylation of NDRG1 did not interrupt the binding of NDRG1 to E-cadherin and beta-catenin. Finally, we showed that the inhibition of NDRG1 expression by RNA interference decreased the ER inducible chaperon GRP94 expression, directly proving that NDRG1 is involved in the ER stress response. Intriguingly, we observed that many members of the NDRG1 interactome are androgen-regulated and that the NDRG1 interactome links to the androgen response network through common interactions with beta-catenin and heat shock protein 90. Therefore we overlaid the transcriptomic expression changes in the NDRG1 interactome in response to androgen treatment and built a dual dynamic picture of the NDRG1 interactome in response to androgen. This interactome map provides the first road map for understanding the functions of NDRG1 in cells and its roles in human diseases, such as prostate cancer, which can progress from androgen-dependent curable stages to androgen-independent incurable stages.

Androgens↗