PubMed Health⌕ Search

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 1,549 records · Page 86Linked to original sources

Crystallization, X-ray characterization and selenomethionine phasing of Mlc1p bound to IQ motifs from myosin V.

Mlc1p is a calmodulin-like protein from the budding yeast Saccharomyces cerevisiae, where it has been identified as a subunit of a class V myosin, Myo2p, and a binding partner of an IQGAP-like protein, Iqg1p. Through its interactions with these two proteins, Mlc1p plays a role in polarized growth and cytokinesis. Mlc1p has been crystallized in complexes with four different IQ target motifs from the neck region of Myo2p: IQ2, IQ3, IQ4 and IQ2-IQ3 (referred to as IQ2,3). Electron-density maps for two of the complexes (Mlc1p-IQ4 and Mlc1p-IQ2,3) were obtained from multiple anomalous dispersion (MAD) experiments based on selenomethionine derivatives. The other two structures (Mlc1p-IQ2 and Mlc1p-IQ3) were determined by molecular replacement using the partially refined structure of Mlc1p-IQ2,3 as a search model.

Amino Acid Sequence↗

A pseudo-cell based approach to efficient crystallographic refinement of viruses.

Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several strains of poliovirus, focus on an arbitrary-sized parallelepiped (termed the 'protomer' box) containing a single complete averaged copy of the structural motif which forms the protein capsid, together with the fragments of other symmetry-related copies of the motif which are located in its immediate neighborhood. The Fourier transform of the protomer box provides reference structure factors for stereochemically restrained crystallographic refinement of the atomic model parameters. The phases of the reference structure factors are based on the averaged map, and are not permitted to change during the refinement. It is demonstrated that models refined using the protomer box methods do not differ significantly from models refined by more expensive full-cell calculations.

Journal Article↗

Accurate template-based correction of brain MRI intensity distortion with application to dementia and aging.

This paper examines an alternative approach to separating magnetic resonance imaging (MRI) intensity inhomogeneity from underlying tissue-intensity structure using a direct template-based paradigm. This permits the explicit spatial modeling of subtle intensity variations present in normal anatomy which may confound common retrospective correction techniques using criteria derived from a global intensity model. A fine-scale entropy driven spatial normalisation procedure is employed to map intensity distorted MR images to a tissue reference template. This allows a direct estimation of the relative bias field between template and subject MR images, from the ratio of their low-pass filtered intensity values. A tissue template for an aging individual is constructed and used to correct distortion in a set of data acquired as part of a study on dementia. A careful validation based on manual segmentation and correction of nine datasets with a range of anatomies and distortion levels is carried out. This reveals a consistent improvement in the removal of global intensity variation in terms of the agreement with a global manual bias estimate, and in the reduction in the coefficient of intensity variation in manually delineated regions of white matter.

Aging↗

Enhancement of steady-state auditory evoked magnetic fields in tinnitus.

The steady-state auditory evoked magnetic field and the Pbm, the magnetic counterpart of the second frontocentrally positive middle latency component of the transitory auditory evoked potential, were measured in ten tinnitus patients using a 122-channel gradiometer system. The patients had varying degrees of hearing loss. In all patients, the tinnitus frequency was located above the frequency of the audiometric edge, i.e. the location on the frequency axis above which hearing loss increases more rapidly. Stimuli were amplitude-modulated sinusoids with carrier frequencies at the tinnitus frequency, the audiometric edge, two frequencies below the audiometric edge, and two frequencies between the audiometric edge and the tinnitus frequency. Below the audiometric edge, the root-mean-square field amplitude of the steady-state response computed across the whole head as well as the contralateral and the ipsilateral dipole moment decreased as a function of carrier frequency. With carrier frequency above the audiometric edge, the steady-state response increased again. The amplitudes of the transitory Pbm component were patterned in a qualitatively similar way, but without the differences being significant. For the steady-state response, both whole-head root-mean-square field amplitude and the dipole moment of the sources at the tinnitus frequency showed significant positive correlations with subjective ratings of tinnitus intensity and intrusiveness. These correlations remained significant when the influence of hearing loss was partialled out. The observed steady-state response amplitude pattern likely reflects an enhanced state of excitability of the frequency region in primary auditory cortex above the audiometric edge. The relationship of tinnitus to auditory cortex hyperexcitability and its independence of hearing loss is discussed with reference to loss of surround inhibition in and map reorganization of primary auditory cortex.

Acoustic Stimulation↗

Repeated reserpine increases striatal dopamine receptor and guanine nucleotide binding protein RNA.

In the present study the effects of repeated administration of reserpine on striatal dopamine receptor and guanine nucleotide binding protein mRNAs were determined. Twenty-four hours after seven consecutive daily injections of reserpine--a treatment that is known to produce functional sensitization of D1 and D2 dopamine receptors--the level of striatal D1 dopamine receptor mRNA was unchanged. However, the level of mRNA for the G protein Gs alpha was increased by 127%. After extended reserpine treatment for 14 days, levels of both striatal D1 DA receptor and Gs alpha mRNAs were elevated by 99 and 78%, respectively. Seven days of reserpine treatment also increased levels of mRNA of the striatal D2 dopamine receptor and of G proteins Gi2 alpha and Go alpha by 200, 79, and 32%, respectively. After 14 days of reserpine treatment the level of striatal D2 dopamine receptor mRNA was increased by twofold. In contrast, levels of the mRNAs coding for the G proteins Gi2 alpha and Go alpha were unchanged. These data suggest that dopamine receptors and their respective G proteins play important roles in the development of sensitization of striatal dopamine receptors during repeated reserpine treatment. Furthermore, the persistent increase in level of striatal Gs alpha mRNA suggests that this G protein is necessary to maintain supersensitivity of the striatal D1 dopamine receptor system following long-term dopamine depletion.

Animals↗

Characterization of lambda Escherichia coli hybrids carrying chemotaxis genes.

Molecular cloning techniques were used to construct hybrid Escherichia coli lambda phage and isolate Col E1 factors that carried the cheB region of the E. coli genome. The products of these genes were examined by using a series of deletions in the phage to stimulate specific polypeptide synthesis in ultraviolet-irradiated cells and by using Col factor to program protein synthesis in minicells. Seven flagellar related polypeptides were synthesized. Three of these with apparent molecular weights of 38,000, 28,000, and 8,000 were associated with the cheB region; three polypeptides 63,000, 61,000, and 60,000 were associated with the region that maps between cheB and cheA. These bands were referred to as the triplet group. We suggest that these polypeptides are the same as the methyl-accepting chemotaxis protein described by Kort et al. (Proc. Natl. Acad. Sci. U.S.A. 72:3939-3943, 1975). Another polypeptide with a molecular weight of 12,000 is associated with the cheA region which also produces at least three gene products. We conclude that the cheA-cheB region in E. coli is complex. Further genetic and biochemical analyses are required to describe all of these products.

Bacterial Proteins↗

Cloning of genes from mucoid Pseudomonas aeruginosa which control spontaneous conversion to the alginate production phenotype.

Strains of Pseudomonas aeruginosa causing chronic pulmonary infections in patients with cystic fibrosis are known to convert to a mucoid form in vivo characterized by the production of the exopolysaccharide alginate. The alginate production trait is not stable, and mucoid strains frequently convert back to the nonmucoid form in vitro. The DNA involved in these spontaneous alginate conversions, referred to as algS, was shown here to map near hisI and pru markers on the chromosome of strain FRD, an isolate from a cystic fibrosis patient. Although cloning algS+ by trans-complementation was not possible, a clone (pJF5) was isolated that caused algS mutants to convert to the Alg+ phenotype at detectable frequencies (approximately 0.1%) in vitro. Gene replacement with transposon-marked pJF5 followed by mapping studies showed that pJF5 contained DNA transducibly close to algS in the chromosome. Another clone was identified called pJF15 which did contain algS+ from mucoid P. aeruginosa. The plasmid-borne algS+ locus could not complement spontaneous algS mutations in trans, but its cis-acting activity was readily observed after gene replacement with the algS mutant chromosome by using an adjacent transposon as the selectable marker. pJF15 also contained a trans-active gene called algT+ in addition to the cis-active gene algS+. The algT gene was localized on pJF15 by using deletion mapping and transposon mutagenesis. By using gene replacement, algT::Tn501 mutants of P. aeruginosa were constructed which were shown to be complemented in trans by pJF15. Both algS and algT were located on a DNA fragment approximately 3 kilobases in size. The algS gene may be a genetic switch which regulates the process of alginate conversion.

Alginates↗

PEBP2 alpha B/mouse AML1 consists of multiple isoforms that possess differential transactivation potentials.

A murine transcription factor, PEBP2, is composed of two subunits, alpha and beta. There are two genes in the mouse genome, PEBP2 alpha A and PEBP2 alpha B, which encode the alpha subunit. Two types of the alpha B cDNA clones, alpha B1 and alpha B2, were isolated from mouse fibroblasts and characterized. They were found to represent 3.8- and 7.9-kb transcripts, respectively. The 3.8-kb RNA encodes the previously described alpha B protein referred to as alpha B1, while the 7.9-kb RNA encodes a 387-amino-acid protein, termed alpha B2, which is identical to alpha B1 except that it has an internal deletion of 64 amino acid residues. Both alpha B1 and alpha B2 associate with PEBP2 beta and form a heterodimer. The alpha B2/beta complex binds to the PEBP2 binding site two- to threefold more strongly than the alpha B1/beta complex does. alpha B1 stimulates transcription through the PEBP2 site about 40-fold, while alpha B2 is only about 25 to 45% as active as alpha B1. Transactivation domain is located downstream of the 128-amino-acid runt homology region, referred to as the Runt domain. Mouse chromosome mapping studies revealed that alpha A, alpha B, and beta genes are mapped to chromosomes 17, 16, and 8, respectively. The last two genes are syntenic with the human AML1 on chromosome 21q22 and PEBP2 beta/CBF beta on 16q22 detected at the breakpoints of characteristic chromosome translocations of the two different subtypes of acute myeloid leukemia. These results suggest that previously described chimeric gene products, AML1/MTG8(ETO) and AML1-EAP generated by t(8;21) and t(3;21), respectively, lack the transactivation domain of AML1.

Amino Acid Sequence↗

Myocardial perfusion and intracapillary blood volume in rats at rest and with coronary dilatation: MR imaging in vivo with use of a spin-labeling technique.

PURPOSE: To validate a magnetic resonance (MR) imaging technique that is not first pass and that reveals perfusion and regional blood volume (RBV) in the intact rat. MATERIALS AND METHODS: Measurement of perfusion was based on the perfusion-sensitive T1 relaxation after magnetic spin labeling of water protons. RBV was determined from steady-state measurements of T1 before and after administration of an intravascular contrast agent. The colored microsphere technique was used as a reference method for perfusion measurement. RBV and perfusion maps were obtained with the rats at rest and during administration of 3 mg of adenosine phosphate per kilogram of body weight per minute. RESULTS: At MR imaging, perfusion during resting conditions was 3.5 mL/g/min +/- 0.1 (SEM), and RBV was 11.6% +/- 0.6 (SEM). Adenosine phosphate significantly increased perfusion to 4.5 mL/g/min +/- 0.3 (SEM) and decreased mean arterial pressure from 120 mm Hg to 65 mm Hg, which implies a reduction of coronary resistance to 40% of baseline. RBV increased consistently to 23.8% +/- 0.6 (SEM). CONCLUSION: The study results show that quantitative mapping of perfusion and RBV may be performed noninvasively by means of MR imaging in the intact animal. The presented method allows determination of vasodilative and perfusion reserve, which reflects the in vivo regulation of coronary microcirculation for a given stimulus.

Adenosine↗

Abnormal functional activation during a simple word repetition task: A PET study of adult dyslexics.

Eight dyslexic subjects, impaired on a range of tasks requiring phonological processing, were matched for age and general ability with six control subjects. Participants were scanned using positron emission tomography (PET) during three conditions: repeating real words, repeating pseudowords, and rest. In both groups, speech repetition relative to rest elicited widespread bilateral activation in areas associated with auditory processing of speech; there were no significant differences between words and pseudowords. However, irrespective of word type, the dyslexic group showed less activation than the control group in the right superior temporal and right post-central gyri and also in the left cerebellum. Notably, the right anterior superior temporal cortex (Brodmann's area 22 [BA 22]) was less activated in each of the eight dyslexic subjects, compared to each of the six control subjects. This deficit appears to be specific to auditory repetition as it was not detected in a previous study of reading which used the same sets of stimuli (Brunswick, N., McCrory, E., Price, C., Frith, C.D., & Frith, U. [1999]. Explicit and implicit processing of words and pseudowords by adult developmental dyslexics: A search for Wernicke's Wortschatz? Brain, 122, 1901-1917). This implies that the observed neural manifestation of developmental dyslexia is task-specific (i.e., functional rather than structural). Other studies of normal subjects indicate that attending to the phonetic structure of speech leads to a decrease in right-hemisphere processing. Lower right hemisphere activation in the dyslexic group may therefore indicate less processing of non-phonetic aspects of speech, allowing greater salience to be accorded to phonological aspects of attended speech.

Adult↗

Colorectal cancer metastasis: in the surgeon's hands?

BACKGROUND: Lymphovascular ligation before tumour manipulation during colorectal cancer resection is termed the 'no-touch isolation' technique. It aims to reduce the intra-operative dissemination of colorectal cancer cells. Recently, the detection of circulating tumour cells has been enhanced by molecular biology techniques. This paper reviews the evidence for the no-touch isolation technique in light of the recent developments in circulating tumour cell detection. METHODS: Studies investigating the effect of colorectal cancer surgery on circulating tumour cells were identified by a Medline search using the subject headings colorectal neoplasms and neoplasm circulating cells together with the map term 'no-touch isolation technique'. Further references were obtained from key articles. RESULTS: Molecular biological techniques have improved the detection of circulating colorectal cancer cells. There is a trend towards reduced tumour cell dissemination with the no-touch technique compared with the conventional method. However the benefit in terms of improved patient survival remains unproven. CONCLUSION: The no-touch isolation technique reduces circulating tumour cell dissemination but further work is needed to determine the significance of this with regards to patient survival.

Journal Article↗

Color constancy at a pixel.

In computational terms we can solve the color constancy problem if device red, green, and blue sensor responses, or RGB's, for surfaces seen under an unknown illuminant can be mapped to corresponding RGB's under a known reference light. In recent years almost all authors have argued that this three-dimensional problem is too hard. It is argued that because a bright light striking a dark surface results in the same physical spectra as those of a dim light incident on a light surface, the magnitude of RGB's cannot be recovered. Consequently, modern color constancy algorithms attempt only to recover image chromaticities under the reference light: They solve a two-dimensional problem. While significant progress has been made toward achieving chromaticity constancy, recent work has shown that the most advanced algorithms are unable to render chromaticity stable enough so that it can be used as a cue for object recognition [B. V. Funt, K. Bernard, and L. Martin, in Proceedings of the Fifth European Conference on Computer Vision (European Vision Society, Springer-Verlag, Berlin, 1998), Vol. II, p. 445.] We take this reductionist approach a little further and look at the one-dimensional color constancy problem. We ask, Is there a single color coordinate, a function of image chromaticities, for which the color constancy problem can be solved? Our answer is an emphatic yes. We show that there exists a single invariant color coordinate, a function of R, G, and B, that depends only on surface reflectance. Two corollaries follow. First, given an RGB image of a scene viewed under any illuminant, we can trivially synthesize the same gray-scale image (we simply code the invariant coordinate as a gray scale). Second, this result implies that we can solve the one-dimensional color constancy problem at a pixel (in scenes with no color diversity whatsoever). We present experiments that show that invariant gray-scale histograms are a stable feature for object recognition. Indexing on invariant distributions supports almost perfect recognition for a dataset of 11 objects viewed under five colored lights. In contrast, object recognition based on chromaticity histograms (post-color constancy preprocessing) delivers much poorer recognition.

Artificial Intelligence↗

The impact of genotype on outcome in oligodendroglioma: validation of the loss of chromosome arm 1p as an important factor in clinical decision making.

OBJECT: Oligodendrogliomas are rare primary brain tumors. They comprise approximately 5 to 33% of all glial tumors but differ from astrocytomas by being associated with a more favorable prognosis, making their correct identification important. Allelic loss of chromosome arms 1p and 19q is found in a substantial subpopulation of tumors with an oligodendroglioma phenotype. Anaplastic oligodendrogliomas with allelic loss of 1p have been associated with chemosensitivity and a longer patient survival period. METHODS: Oligodendroglial neoplasms were studied using fluorescence in situ hybridization of formalin-fixed, paraffin-embedded tissue specimens; reference and target probe sets were used to map the telomeric regions of 1p and 19q. The results were correlated with the clinical characteristics of patients treated at our institution between 1993 and 2003. Data obtained in 96 patients were analyzed. This included 63 patients (65.6%) with World Health Organization (WHO) Grade II oligodendroglioma, 22 (23%) with Grade III oligodendroglioma, and 11 (11.4%) with mixed oligoastrocytoma. Analysis of 1p in patients with pure oligodendroglioma revealed a loss of 1p in 42 patients (49.4%). In 46 of these patients 19q was lost and in 70 (82.3%) there was concordance for combined loss or retention of both 1p and 19q (p < 0.0001). Patients with oligodendroglioma in whom a loss of 1p was present fared significantly better, and this outcome was unrelated to the treatment modality or WHO grade, compared with patients in whom 1p was intact (p < 0.05). CONCLUSIONS: To the authors' knowledge, this study includes the largest published series of WHO Grade II oligodendroglioma and 1p analysis. The results suggest that the association between long-term survival and 1p loss in oligodendroglioma is unrelated to treatment. The authors of further prospective studies may better determine the true value of the allelic loss of 1p and its implication for clinical decision making.

Adolescent↗

[Isolated pontine infarction: vascular anatomy helps understand clinical signs].

Clinical findings of pontine infarcts are more frequently described as classical crossed-syndrome. The aim of this study was to analyse clinical presentation of isolated pontine infarcts. From the Besancon Stroke Registry, we retrospectively studied 34 patients with isolated pontine infarcts documented on MRI with a strict centro-bicommissural plane as the reference. MRI were analyzed using an arterial territories mapping of brainstem. Among our 34 pts, none developed a classical crossed-syndrome. A thorough knowledge of vascular anatomy of brainstem is necessary to understand clinical findings. Moreover, this knowledge allow to explain the rare occurrence of pontine crossed-syndrome.

Adult↗

[The spatial structure of the alpha rhythm in the healthy human being studied by EEG mapping].

EEG study was conducted in the state of relative rest in 15 healthy subjects with predominance of the alpha rhythm. Data processing was performed on neuromapper ("Neuroscience", Great Britain). Principal attention was paid to the dynamics of spatial-temporal relations of the alpha rhythm. Cyclic changes were shown of the alpha-rhythm amplitude, proceeding with change of high and low amplitudes during seconds, varying in time in various individuals. Three types of spatial distribution of the alpha rhythm over the cortex at the relative rest were obtained: 1) generalized distribution over the cortex with the wavy shift of the frequency fields; 2) formation of delimited local zones of the alpha rhythm, differing by the frequency from the rhythm in other cortical areas; 3) local zone of the low-frequency alpha rhythm in the visual projection zone (18 and 19 fields). Change of the distribution types of the alpha rhythm in the state of rest takes place in the seconds of time intervals, corresponding, according to the literature data, to the proceeding of elementary mental processes.

Adult↗

[Experimental study of laser ablation on lethal arrhythmias--features and effectiveness of epicardial mapping].

To find the exact location of the ventricular arrhythmogenic myocardium, we mapped activation times of local epicardial electrograms (ATLE: 16 bipolar electrodes, 2 x 2 cm2) aided by an on-line computer and guided laser ablation of lethal ventricular arrhythmias induced by aconitine. Thirty-six tests involved 12 dog hearts. Nd:YAG laser application converted ventricular tachycardias and fibrillation to sinus rhythm in all tests. Epicardial mapping results showed: Taking ECG lead II as reference, the differences among all ATLE were within 15ms, and there was no obvious conduct slow zone before drugging and after resuming sinus rhythm, even though 298 +/- 157 mm2 photocoagulation areas (n = 36) resulted from laser irradiation; During VT, the majority of ATLE were preexcited from 90 to 30 ms, and more than one breakthrough point existed, with one predominating; ATLE changed significantly after laser. The ectopic foci were located exactly by using ATLE for laser treatment.

Aconitine↗

Optimization of reversed-phase peptide liquid chromatography ultraviolet mass spectrometry analyses using an automated blending methodology.

The balance between chromatographic performance and mass spectrometric response has been evaluated using an automated series of experiments where separations are produced by the real-time automated blending of water with organic and acidic modifiers. In this work, the concentration effects of two acidic modifiers (formic acid and trifluoroacetic acid) were studied on the separation selectivity, ultraviolet, and mass spectrometry detector response, using a complex peptide mixture. Peptide retention selectivity differences were apparent between the two modifiers, and under the conditions studied, trifluoroacetic acid produced slightly narrower (more concentrated) peaks, but significantly higher electrospray mass spectrometry suppression. Trifluoroacetic acid suppression of electrospray signal and influence on peptide retention and selectivity was dominant when mixtures of the two modifiers were analyzed. Our experimental results indicate that in analyses where the analyzed components are roughly equimolar (e.g., a peptide map of a recombinant protein), the selectivity of peptide separations can be optimized by choice and concentration of acidic modifier, without compromising the ability to obtain effective sequence coverage of a protein. In some cases, these selectivity differences were explored further, and a rational basis for differentiating acidic modifier effects from the underlying peptide sequences is described.

Acetonitriles↗

Examination of X chromosome markers in Rett syndrome: exclusion mapping with a novel variation on multilocus linkage analysis.

Rett syndrome is a neurologic disorder characterized by early normal development followed by regression, acquired deceleration of head growth, autism, ataxia, and stereotypic hand movements. The exclusive occurrence of the syndrome in females and the occurrence of a few familial cases with inheritance through maternal lines suggest that this disorder is most likely secondary to a mutation on the X chromosome. To address this hypothesis and to identify candidate regions for the Rett syndrome gene locus, genotypic analysis was performed in two families with maternally related affected half-sisters by using 63 DNA markers from the X chromosome. Maternal and paternal X chromosomes from the affected sisters were separated in somatic cell hybrids and were examined for concordance/discordance of maternal alleles at the tested loci. Thirty-six markers were informative in at least one of the two families, and 25 markers were informative in both families. Twenty loci were excluded as candidates for the Rett syndrome gene, on the basis of discordance for maternal alleles in the half-sisters. Nineteen of the loci studied were chosen for multipoint linkage analysis because they have been previously genetically mapped using a large number of meioses from reference families. Using the exclusion criterion of a lod score less than -2, we were able to exclude the region between the Duchenne muscular dystrophy locus and the DXS456 locus. This region extends from Xp21.2 to Xq21-q23. The use of the multipoint linkage analysis approach outlined in this study should allow the exclusion of additional regions of the X chromosome as new markers are analyzed. This in turn will result in a defined region of the X chromosome that should be searched for candidate sequences for the Rett syndrome gene in both familial and sporadic cases.

Alleles↗