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 1,441 records · Page 80Linked to original sources
PubMed1993

Identification of p42 mitogen-activated protein kinase as a tyrosine kinase substrate activated by maximal electroconvulsive shock in hippocampus.

Recent studies have demonstrated that administration of an electroconvulsive shock produces a rapid and transient increase in tyrosyl phosphorylation of a approximately 40-kDa protein in rat brain. Initial characterization of this protein's chromatographic properties indicated that it might be a member of a recently identified family of kinases, referred to as mitogen-activated protein (MAP) kinases, that are activated by tyrosyl phosphorylation. In the present study, we have used MAP kinase antisera to assess the identity of this protein. We have found that the approximately 40-kDa phosphotyrosine-containing protein comigrates with p42 MAP kinase (p42mapk) and not with two other 44-kDa MAP kinase family members detected by these antisera. Western blots of proteins immunoprecipitated with MAP kinase antibodies confirm that p42mapk displays increased tyrosyl phosphorylation after an electroconvulsive stimulus. Chromatographic separation of hippocampal extracts indicates that MAP kinase activity elutes in parallel with p42mapk. Accordingly, these studies identify p42mapk as a tyrosyl kinase substrate that is activated by this stimulus and suggest that this form of MAP kinase may be selectively regulated by neuronal stimulation.

Amino Acid Sequence↗
PubMed1983

Genomic structure of human polyoma virus JC: nucleotide sequence of the region containing replication origin and small-T-antigen gene.

The nucleotide sequence of the region of human polyoma virus JC DNA between 0.5 and 0.7 map units from a unique EcoRI cleavage site was determined and compared with those of the corresponding regions of another human polyoma virus, BK, and simian virus 40 DNAs. Within this region consisting of 945 base pairs, we located the origin of DNA replication near 0.7 map units, the entire coding region for small T antigen, and the splice junctions for large-T-antigen mRNA. The deduced amino acid sequences for small T antigen and the part of large T antigen markedly resembled those of polyoma virus BK and simian virus 40. The results strongly suggest that polyoma virus JC has the same organization of early genome as polyoma virus BK and simian virus 40 on the physical map, with the EcoRI site as a reference point.

Amino Acid Sequence↗
PubMed1999

Zoo-FISH analysis of dog chromosome 5: identification of conserved synteny with human and cat chromosomes.

Conserved segments of synteny between the human genome and chromosome 5 (CFA 5) of the domestic dog (Canis familiaris) have been identified by reciprocal chromosome painting analysis. A CFA 5 paint probe was applied to human metaphase spreads, revealing distinct hybridisation sites on human (HSA) chromosomes 1, 11, 16, and 17. Paint probes for these human chromosomes were then hybridised to dog metaphase spreads, identifying the regions of CFA 5 with which homology is shared with the corresponding human chromosome. Application of the CFA 5 paint probe to metaphase spreads of the domestic cat (Felis catus, FCA) demonstrated hybridisation to cat chromosomes C1, D1, E1, and E2. Dog PCR primers for type 1 markers known to lie in the corresponding regions of HSA 11, 16, and 17 were used to isolate dog BAC clones representing four genes. Fluorescence in situ hybridisation analysis confirmed their localisation to CFA 5 and suggested that two of the conserved segments lie in opposing orientations on CFA 5, compared to the human chromosome concerned. A third segment appears to lie in the same orientation on both human and dog chromosomes. No suitable gene markers were available for analysis of the fourth segment. The significance of these findings is discussed with reference to current and future dog genome mapping efforts.

Animals↗
PubMed1985

Hemodynamic effects of prolonged treatment with diltiazem in conscious normotensive and spontaneously hypertensive rats.

To determine systemic and regional hemodynamic effects of prolonged treatment with the calcium antagonist diltiazem (30 mg/kg twice daily by gastric gavage, for 3 weeks), data from 12 Wistar-Kyoto (WKY) and 10 spontaneously hypertensive (SHR) rats were compared with those obtained from 11 WKY and 10 SHR controls treated with the vehicle. Systemic and regional hemodynamics were determined in the conscious, unrestrained state using the reference sample microsphere method. Mean arterial pressure (MAP) decreased in SHR by 9% (183 +/- 4 to 167 +/- 4 mm Hg; p less than 0.05) but remained unchanged in WKY, while cardiac index (CI) tended to decrease in both strains; heart rate fell by 15% only in WKY (481 +/- 10 to 354 +/- 13 beats/min; p less than 0.05). Total peripheral resistance index (TPRI) tended to decrease in SHR but to increase in WKY. Organ blood flow in SHR decreased in skin and splanchnic organs, while organ vascular resistance decreased in brain and increased in splanchnic organs. In contrast, organ blood flow increased in heart and decreased in kidneys and skin of the WKY, while organ vascular resistance decreased in heart and increased in kidneys and skin. Thus, diltiazem produced nonuniform and different hemodynamic effects in the two strains. Further, diltiazem did not alter the cardiac mass in either rat strain. We therefore conclude that diltiazem demonstrated a mild hypotensive effect in SHR that was associated with slight reductions in CI and TPRI, the latter being nonuniformly distributed in the component organ circulations.

Animals↗
PubMed2006

Amplification of D22S283 as a favorable prognostic indicator in liver fluke related cholangiocarcinoma.

AIM: To analyze the DNA copy number of target genes NF2, TIMP3, ST13, TOB2, BIK, and TP and the reference microsatellite markers D22S283, D22S423, and D22S274 mapped on 22q12-qter in liver fluke related cholangiocarcinoma (CCA) and define its correlation with clinical parameters. METHODS: Quantitative real time PCR (qPCR) was used for determining allelic imbalances in 65 liver fluke related CCA tissues. Statistical correlations between allelic imbalances and clinicopathological parameters, i.e. age, sex, tumor stage, histological type, blood vessel invasion, nerve invasion and lymphatic invasion were evaluated by means of the chi2 test. Cox regression analysis was used for determining patient's survival. RESULTS: Amplifications of the TP (22q13.33), TOB2 (22q13.2-13.31), D22S283 (22q12.3), TIMP3 (22q12.3) and NF2 (22q12.2) were found in 35 (53.8%), 28 (43.1%), 27 (41.5%), 24 (36.9%), and 24 (36.9%), respectively. Losses at the D22S423 (22q13.1-13.2) and BIK (22q13.31) were detected in 26 (40%) and 23 (35.4%), respectively. Significant correlations were observed between lymphatic invasion and allelic losses of BIK (P = 0.025) and D22S283 (P = 0.041). Univariate and multivariate Cox regression analysis revealed D22S283 amplification as an independent predictor of good prognosis (P = 0.006, death hazard ratio = 0.411, 95% CI = 0.217-0.779) and blood vessel invasion as an independent poor prognostic factor (P = 0.042, death hazard ratio = 1.911, 95% CI = 1.022-3.571) in CCA patients. CONCLUSION: This study provides evidence for the involvement of gene amplification and deletion on chromosome 22q in liver fluke related CCA. This is the first report of D22S283 amplification as an independent indicator of favorable prognosis in liver fluke related CCA.

Adult↗
PubMed1992

Structure and strategy in encoding simplified graphs.

Tversky and Schiano (1989) found a systematic bias toward the 45 degrees line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal "axes" are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as "graphs" only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

Bias↗
PubMed1996

[Not Available].

This article starts with the description of a medical case: the removal of a brain tumor carried out in 1886 in London at the National Hospital for the Paralysed and Epileptic. This medical case is recorded in the Casebooks that today can be found in the archive of the hospital. Firstly, there is the description of the patient's state of health and of the intracranical surgery performed by Victor Horsley who referred himself to David Ferrier's cortical maps. Secondly, there is the reconstruction of the theoretical path that led Ferrier, in the 1870s, to prove on an experimental basis the existence of different localised cerebral functions in specific cortical areas. These cerebral localizations are then compared with the model that, at the beginning of the century, contained their first theoretical seed: the Organology of Franz Joseph Gall.

Brain↗
PubMedDate not supplied

Reference fields in phantom tooth pain as a marker for remapping in the facial territory.

Six patients with chronic phantom tooth pain were studied for the presence of reference fields for their phantom sensation. In five of them, pain or dysesthesia in the affected oral structures was elicited by thermal or mechanical stimulation of areas that were well separate from these structures. However, a relation of topographical proximity between the stimulated areas and the areas of reference could be traced in the sensory maps. Therefore, denervation of small structures with coarse sensitivity can yield the plastic changes that have previously been described for larger deafferentations of areas endowed with finer discriminative capacity.

Adult↗
PubMed1991

[Cardiac rehabilitation in patients with acute myocardial infarction: assessments with T1-201 myocardial scintigraphy].

The effects of exercise training on myocardial perfusion during the first 3 months after acute myocardial infarction (AMI) were assessed by exercise myocardial scintigraphy and fibrinolytic examinations. Symptom-limited treadmill exercise with thallium-201 myocardial single photon emission CT (SPECT) and fibrinolytic examinations (tissue plasminogen activator antigen: tPA, plasminogen activator inhibitor-1 antigen : PAI-1) were performed 2 and 14 weeks after AMI in 13 patients with exercise training and in 12 patients without exercise training. For quantitative analysis, counts of region of interest in the infarct area and normal reference area were calculated on a polar map obtained from myocardial SPECT. Severity of the hypoperfused myocardium was determined as an initial percent uptake (%IU) and a delayed percent uptake (%DU). The difference (%DU-%IU) was defined as a parameter of residual ischemia in the infarct area (%redistribution : %RD). Total treadmill exercise duration according to the Bruce protocol increased significantly in the training group (351 +/- 89 to 431 +/- 118 sec, p < 0.01); whereas, there was no significant change in the non-training group (340 +/- 95 to 356 +/- 123 sec). In the training group the pressure-rate product and %DU increased significantly (225 +/- 55 to 259 +/- 58 mmHg.beats/min x 100, 59 +/- 19 to 65 +/- 20%, p < 0.01, respectively), and %RD decreased significantly (8.8 +/- 6.7 to 4.8 +/- 4.5%, p < 0.01), but there was no significant change in the non-training group (231 +/- 89 to 240 +/- 86 mmHg.beats/min x 100, 56 +/- 17 to 57 +/- 12% and 7.4 +/- 5.5 to 6.2 +/- 6.5%, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)

Coronary Circulation↗
PubMed1993

Overexpression of mitogen-activated protein kinase (ERK1) enhances T-cell cytokine gene expression: role of AP1, NF-AT, and NF-KB.

Transfected Jurkat cells overexpressing extracellular signal-regulated kinase (ERK1), also referred to as mitogen-activated protein (MAP) kinase, were selected by Western blotting assay using anti-ERK1 and antiphosphotyrosine antibodies in combination with a functional MAP kinase assay. We then asked whether enhanced ERK1 expression had any effect on induction of T-cell cytokine genes. The results show that overexpression of ERK1 enhances expression of T-cell interleukin-2 (IL-2), IL-3, and granulocyte-macrophage colony-stimulating factor mRNA; no change was seen in expression of the alpha-actin gene. DNA-binding activities of the transcription factors AP1, NF-AT, and NF-kB were specifically increased twofold to fourfold in ERK1-overexpressing clones relative to nontransformed or vector-transformed cells, whereas no enhancement of CK1-CK2 protein DNA binding activity was detected after ERK1 overexpression. Additionally, increased NF-AT DNA binding activity was associated with functional enhancement of NF-AT transactivating activity in ERK1-overexpressing cells. These results provide direct evidence for the role of MAP kinase in the regulation of cytokine gene expression and indicate that such regulation is likely mediated through the enhanced DNA binding activity of specific nuclear transcription factors.

Base Sequence↗
PubMed1998

[Diagnosis of sentinel lymph node in malignant melanoma: preoperative lymphoscintigraphy and intraoperative gamma probe guidance].

AIM: The sentinel lymph node (SLN) has shown to reflect the histologic features of the remainder of the lymphatic basin in patients with melanoma and is of considerable prognostic relevance. Aim of the study was to localize the SLN pre and intraoperatively by means of lymphoscintigraphy and gamma probe guidance. METHODS: 38 patients with histologically proven malignant melanoma (tumor thickness > 0.75 mm) were preoperatively examined by injecting 40 MBq 99mTc-Nanocoll intradermally around the lesion. The first lymph node identified was marked on the skin. Immediately after scintigraphy patients were referred to the operation room and intraoperatively mapped using a handheld gamma probe. Activity of the SLN and of the adjacent nodes was measured ex vivo. After excision of the SLN, the lymphatic basin was re-checked for radioactivity and activity of the SLN and of the adjacent nodes was re-measured after removal. RESULTS: The hottest reading was found in all patients in vivo and ex vivo in the preoperatively marked lymph node. Morphologically (macroscopically, ultrasound, CT) all nodes were unsuspicious. Histologically, in 8 patients metastatic involvement of the lymph node was found which led to a wide exploration of the lymphatic basin with consecutive lymph node excision in 7 patients. CONCLUSION: The findings suggest that combined preoperative lymphoscintigraphy and intraoperative mapping with a gamma probe is a powerful approach for exact localization of the SLN. Diagnostic detection of the SLN may have considerable impact for patient management, since extended lymph node dissection may be confined to patients presenting with positive SLN.

Adult↗
PubMed1996

Cyclin D1 amplification as a new predictive classification for squamous cell carcinoma of the esophagus, adding gene information.

The cyclin D1, referred to as PRAD-1, has been mapped to the 11q13 region, and its expression has been detected in squamous cell lines and several primary esophageal carcinomas. We assessed cyclin D1 amplification in 122 squamous cell carcinomas of the esophagus. Samples for DNA extraction were obtained from formalin-fixed paraffin-embedded specimens, and 10 microgram of each DNA sample were subjected to slot blot analysis. The presence of more than three gene copies was considered evidence of gene amplification. Amplification of cyclin D1 was detected in 28 (23%) of 122 cases of squamous cell carcinoma of the esophagus. There were no significant differences between the clinicopathological background factors in groups positive and negative for cyclin D1 amplification, but the survival rate of patients exhibiting amplification was significantly lower (P < 0.001). The groups were stratified according to the pN (pathological N category) factor and pT (pathological T category) factor in the TNM classification, and the cumulative survival rates in the amplification groups were always significantly lower. Amplification of cyclin D1 was correlated with distant organ metastasis after curative operations, but there was no significant difference in lymph node recurrence rates of patients with or without amplification. Cyclin D1 amplification had the second highest partial regression coefficient in the multivariate analysis, after the pN factor. Amplification of cyclin D1 was independent of the TNM classification as a prognostic factor, and was a useful marker for predicting outcome and distant organ metastasis in patients with squamous cell carcinoma of the esophagus. It appears that appropriate treatment can be selected by evaluating both TNM factors and cyclin D1 amplification.

Adult↗
PubMed1998

[Application of a semi-automatic ROI setting system for brain PET images to animal PET studies].

ProASSIST, a semi-automatic ROI (region of interest) setting system for human brain PET images, has been modified for use with the canine brain, and the performance of the obtained system was evaluated by comparing the operational simplicity for ROI setting and the consistency of ROI values obtained with those by a conventional manual procedure. Namely, we created segment maps for the canine brain by making reference to the coronal section atlas of the canine brain by Lim et al., and incorporated them into the ProASSIST system. For the performance test, CBF (cerebral blood flow) and CMRglc (cerebral metabolic rate in glucose) images in dogs with or without focal cerebral ischemia were used. In ProASSIST, brain contours were defined semiautomatically. In the ROI analysis of the test image, manual modification of the contour was necessary in half cases examined (8/16). However, the operation was rather simple so that the operation time per one brain section was significantly shorter than that in the manual operation. The ROI values determined by the system were comparable with those by the manual procedure, confirming the applicability of the system to these animal studies. The use of the system like the present one would also merit the more objective data acquisition for the quantitative ROI analysis, because no manual procedure except for some specifications of the anatomical features is required for ROI setting.

Animals↗
PubMed1998

Protein affinity map of chemical space.

Affinity fingerprinting is a quantitative method for mapping chemical space based on binding preferences of compounds for a reference panel of proteins. An effective reference panel of <20 proteins can be empirically selected which shows differential interaction with nearly all compounds. By using this map to iteratively sample the chemical space, identification of active ligands from a library of 30,000 candidate compounds has been accomplished for a wide spectrum of specific protein targets. In each case, <200 compounds were directly assayed against the target. Further, analysis of the fingerprint database suggests a strategy for effective selection of affinity chromatography ligands and scaffolds for combinatorial chemistry. With such a system, the large numbers of potential therapeutic targets emerging from genome research can be categorized according to ligand binding properties, complementing sequence based classification.

Chromatography, Affinity↗
PubMed2006

Direct classification of high-dimensional data in low-dimensional projected feature spaces--comparison of several classification methodologies.

Previously, we introduced a distance (similarity)-based mapping for the visualization of high-dimensional patterns and their relative relationships. The mapping preserves exactly the original distances from all points to any two reference patterns in a special two-dimensional coordinate system, the relative distance plane (RDP). We extend the RDP mapping's applicability from visualization to classification. Several of the classifiers use the RDP directly. These include the standard linear discriminant analysis (LDA), nearest neighbor classifiers, and a transvariation probabilities-based classification method that is natural in the RDP. Several reference directions can also be combined to create new coordinate systems in which arbitrary classifiers can be developed. We obtain increased confidence in the classification results by cycling through all possible reference pairs and computing a misclassification-based weighted accuracy. The classification results on several high-dimensional biomedical datasets are compared.

Algorithms↗