Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Dimensionality Reduction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 595 records · Page 33Linked to original sources

A novel frameshift mutation of the mtDNA COIII gene leads to impaired assembly of cytochrome c oxidase in a patient affected by Leigh-like syndrome.

We report on a novel frameshift mutation in the mtDNA gene encoding cytochrome c oxidase (COX) subunit III. The proband is an 11-year-old girl with a negative family history and an apparently healthy younger brother. Since 4 years of age, she has developed a progressive spastic paraparesis associated with ophthalmoparesis and moderate mental retardation. The presence of severe lactic acidosis and Leigh-like lesions of putamina prompted us to perform muscle and skin biopsies. In both, a profound, isolated defect of COX was found by histochemical and biochemical assays. Sequence analysis of muscle mtDNA resulted in the identification of a virtually homoplasmic frameshift mutation in the COIII gene, due to the insertion of an extra C at nucleotide position 9537 of mtDNA. Although the 9537C(ins) does not impair transcription of COIII, no full-length COX III protein was detected in mtDNA translation assays in vivo. Western blot analysis of two-dimensional blue-native electrophoresis showed a reduction of specific crossreacting material and the accumulation of early-assembly intermediates of COX, whereas the fully assembled complex was absent. One of these intermediates had an electrophoretic mobility different from those seen in controls, suggesting the presence of a qualitative abnormality of COX assembly. Immunostaining with specific antibodies failed to detect the presence of several smaller subunits in the complex lacking COX III, in spite of the demonstration that these subunits were present in the crude mitochondrial fraction of patient's cultured fibroblasts. Taken together, the data indicate a role for COX III in the incorporation and maintenance of smaller COX subunits within the complex.

Base Sequence↗

Analysis of Escherichia coli ribosomal proteins by an improved two dimensional gel electrophoresis. II. Characterization of four new proteins.

Four new proteins, A, B, C, and D, found in Escherichia coli ribosomes by an improved two dimensional gel electrophoresis were characterized by oxidation, reduction, and carboxymethylation of cysteine residues, and CsCl fractionation. The cysteine contents of proteins A, B, C, and D were determined to be 1 +/- 0, 3 +/- 1, 5 +/- 1, and 0 +/- 0 by carboxymethylation with iodoacetic acid. The components of protein complexes, which formed numerously under non-reducing conditions, were analyzed. Including protein A, B, and C, every ribosomal protein (r-protein) having cysteine residue(s) except unconfirmed S1 was proved to form such complexes with various combinations. The cysteine residue in protein A, in particular, was highly reactive to make intermolecular S-S bridges so that spot A almost disappeared on the second dimension gel under the non-reducing conditions. Proteins B and C shifted their spots by reduction towards upper left side as do all known r-proteins having plural cysteine residues except S1. This suggests that proteins B and C change their conformation by intramolecular S-S bridges. The CsCl density gradient centrifugation of high salt washed 70S ribosomes showed that protein A belonged to the insoluble split proteins, proteins B and C to the core particles, and protein D and a small population of B to the soluble split proteins. The electrophoretic behaviors, CsCl fractionation and stoichiometry of the four new proteins suggested strongly that they were intrinsic ribosomal constituents different from known ribosomal proteins or factors.

Bacterial Proteins↗

Denoising human speech signals using chaoslike features.

A local projective noise reduction scheme, originally developed for low-dimensional stationary deterministic chaotic signals, is successfully applied to human speech. This is possible by exploiting properties of the speech signal which resemble structure exhibited by deterministic dynamical systems. In high-dimensional embedding spaces, the strong inherent nonstationarity is resolved as a sequence of many different dynamical regimes of moderate complexity.

Humans↗

Chemical Cross-linking of Neighboring Thylakoid Membrane Polypeptides.

Cross-linking between protein components of whole spinach (Spinacia oleracea var. Nobel) thylakoids and of photosystem I- and II-enriched thylakoid fractions has been produced by reaction with the bifunctional imidoester dimethyl-3,3'-dithiobispropionimidate dihydrochloride as well as by the oxidation of intrinsic sulfydryl groups with an orthophenanthrolinecupric ion complex. The mixture of membrane proteins and their cross-linked products has been analyzed by two-dimensional sodium dodecyl sulfate electrophoresis, with a reductive cleavage step of the cross-linkages before the second dimension. Cross-linked aggregates up to a molecular weight of about 130 kilodaltons (kD) were analyzed, and it was inferred that the polypeptides appearing together in the same aggregates were neighbors within the membrane.In thylakoids as well as in isolated photosystem fractions, oligomers were formed by cross-linking polypeptides of the 60 to 90 kD range, among them the polypeptides of the chlorophyll-protein complex I. Polypeptides of 46, 19, and 12 kD were cross-linked to these complexes. Polypeptides of 25 and 22 kD, which are related to the chlorophyll-protein complex II, were cross-linked in thylakoids as well as in photosystem II fractions, suggesting that in the membrane these molecules are close together. In photosystem II fractions an oligomer having a molecular weight of about 60 kD was formed by cross-linking several polypeptides of different molecular weights: 40, 25, and 22 kD.Our cross-linking experiments show that protein interactions in the thylakoid membrane occurred mainly among the polypeptides of the two chlorophyll-protein complexes, thus suggesting an oligomeric nature of these apoproteins.

Journal Article↗

Characterization of novel sequence motifs within N- and C-terminal extensions of p26, a small heat shock protein from Artemia franciscana.

The small heat shock proteins function as molecular chaperones, an activity often requiring reversible oligomerization and which protects against irreversible protein denaturation. An abundantly produced small heat shock protein termed p26 is thought to contribute to the remarkable stress resistance exhibited by encysted embryos of the crustacean, Artemia franciscana. Three novel sequence motifs termed G, R and TS were individually deleted from p26 by site-directed mutagenesis. G encompasses residues G8-G29, a glycine-enriched region, and R includes residues R36-R45, an arginine-enhanced sequence, both in the amino terminus. TS, composed of residues T169-T186, resides in the carboxy-extension and is augmented in threonine and serine. Deletion of R had more influence than removal of G on p26 oligomerization and chaperoning, the latter determined by thermotolerance induction in Escherichia coli, protection of insulin and citrate synthase from dithiothreitol- and heat-induced aggregation, respectively, and preservation of citrate synthase activity upon heating. Oligomerization of the TS and R variants was similar, but the TS deletion was slightly more effective than R as a chaperone. The extent of p26 structural perturbation introduced by internal deletions, including modification of intrinsic fluorescence, 1-anilino-8-naphthalene-sulphonate binding and secondary structure, paralleled reductions in oligomerization and chaperoning. Three-dimensional modeling of p26 based on wheat Hsp16.9 crystal structure indicated many similarities between the two proteins, including peptide loops associated with secondary structure elements. Loop 1 of p26 was deleted in the G variant with minimal effect on oligomerization and chaperoning, whereas loop 3, containing beta-strand 6 was smaller than the corresponding loop in Hsp16.9, which may influence p26 function.

Amino Acid Motifs↗

Absorptive capacity of the transplanted small bowel.

Small bowel transplantation (SBT) has been carried out in man in several cases without success, because immunologic problems were unsolved. In experimental SBT a 'two step' model was developed, which enables long term observation of immunologic phenomena. In this model the graft is in a heterotopic position to the recipient's own small bowel. After 35 days the recipient's own bowel is removed and replaced by the graft, now in orthotopic position and again in contact with luminal chymus. To investigate functional and morphological changes, which result from the procedure, the resorption of glucose and water was measured in syngeneic transplanted rats by an in vivo recirculation system and the mucosa was evaluated three dimensionally. The graft mucosa showed a significant reduction in villus height, crypt length and villus surface and a corresponding decrease in glucose and water absorption during heterotopic position. If the graft came into the orthotopic position, the mucosa did regenerate which was expressed by the significant longer crypts of the graft compared with those of the controls, although the graft's villus height and surface are still smaller. Glucose and water absorption increased and were higher in orthotopic transplanted animals, when absorption was expressed per unit intestinal length. The results indicate that in the 'two step' model of SBT the absorption of water and glucose is influenced to such an extent, that recovery is possible after three weeks, thus enabling orthotopic SBT. This almost complete recovery of the mucosa is further evidence of the regeneratory capacity of the small bowel, which enables clinical small bowel transplantation.

Animals↗

Quantitative coronary angiography: measurement of the "critical" stenosis in patients with unstable angina and single-vessel disease without collaterals.

Quantitative angiographic assessment of proximal coronary artery stenosis was performed in 15 patients with consecutive presentations in two categories defined by clinical and angiographic criteria. Group 1 consisted of 10 patients who had new onset of refractory rest angina and ischemic ST-T changes, but no infarction, single-vessel coronary disease without collateralization, and normal left ventricular (LV) angiograms. Group 2 consisted of five patients who were similar to patients in group 1, but had subendocardial infarction (SEI). Quantitative coronary arteriography, using paired perpendicular angiographic views and digital computation, yielded statistically different lesion dimensions and hemodynamic predictions for the two groups. Minimum stenosis diameters were 0.88 +/- 0.14 (SD) and 0.64 +/- 0.08 mm, respectively, for groups 1 and 2. This corresponded to 72% and 78% diameter reduction and 92% and 95% cross-sectional area reduction for the two groups. These small dimensional differences among lesions in the two groups resulted in large differences in their hemodynamic impact as predicted from classic fluid mechanics theory. We conclude that there are characteristic lesion dimensions for the isolated "critical" stenosis in these selected patients with rest angina. Further small increases in lesions severity result in SEI. Certain practical applications and limitations of these observations are discussed.

Angina Pectoris↗

Dimension selection for feature selection and dimension reduction with principal and independent component analysis.

This letter is concerned with the problem of selecting the best or most informative dimension for dimension reduction and feature extraction in high-dimensional data. The dimension of the data is reduced by principal component analysis; subsequent application of independent component analysis to the principal component scores determines the most nongaussian directions in the lower-dimensional space. A criterion for choosing the optimal dimension based on bias-adjusted skewness and kurtosis is proposed. This new dimension selector is applied to real data sets and compared to existing methods. Simulation studies for a range of densities show that the proposed method performs well and is more appropriate for nongaussian data than existing methods.

Algorithms↗

Intensity-modulated radiotherapy in the standard management of head and neck cancer: promises and pitfalls.

The purpose of this article is to review the role of intensity-modulated radiotherapy (IMRT) in the standard management of patients with head and neck cancer through a critical review of the pertinent literature. IMRT may result in a dose distribution that is more conformal than that achieved with three-dimensional conformal radiotherapy (3D CRT), allowing dose reduction to normal structures and thus decreasing toxicity and possibly enhancing locoregional control through dose escalation. Disadvantages associated with IMRT include increased risk of a marginal miss, decreased dose homogeneity, increased total body dose, and increased labor and expense. Outcomes data after IMRT are limited, and follow-up is relatively short. Locoregional control rates appear to be comparable to those achieved with 3D CRT and, depending on the location and extent of the tumor, late toxicity may be lower. Despite limited data on clinical outcomes, IMRT has been widely adopted as a standard technique in routine practice and clinical trials. The use of IMRT involves a learning curve for the practitioner and will continue to evolve, requiring continuing education and monitoring of outcomes from routine practice. Additional standards pertaining to a variety of issues, including target definitions and dose specification, need to be developed. Phase III trials will better define the role of IMRT in coming years.

Antineoplastic Agents↗

Superresolution of ultrasound images using the first and second harmonic signal.

This paper presents a new method of blind two-dimensional (2-D) homomorphic deconvolution and speckle reduction applied to medical ultrasound images. The deconvolution technique is based on an improved 2-D phase unwrapping scheme for pulse estimation. The input images are decomposed into minimum-phase and allpass components. The 2-D phase unwrapping is applied only to the allpass component. The 2-D phase of the minimum-phase component is derived by a Hilbert transform. The accuracy of 2-D phase unwrapping is also improved by processing small (16 x 16 pixels) overlapping subimages separately. This takes the spatial variance of the ultrasound pulse into account. The deconvolution algorithm is applied separately to the first and second harmonic images, producing much sharper images of approximately the same resolution and different speckle patterns. Speckle reduction is made by adding the envelope images of the deconvolved first and second harmonic images. Neither the spatial resolution nor the frame rate decreases, as the common compounding speckle reduction techniques do. The method is tested on sequences of clinical ultrasound images, resulting in high-resolution ultrasound images with reduced speckle noise.

Algorithms↗

Variation in labial shoulder geometry of metal ceramic crown preparations: a finite element analysis.

Recent studies have highlighted variations in the geometry of teeth prepared to receive metal ceramic crowns, particularly in the region of the labial shoulder, where shoulder designs have often involved less reduction than is recommended. Using two-dimensional finite element analysis, this study subjected crowns, superimposed upon preparations with clinically common labial margin designs, to loads of 200N in three different directions. The resultant stress distribution within the labial marginal porcelain was examined. Results imply that variations in the marginal preparation geometry of metal ceramic crowns influenced the stress response of the finished crown. Within the limits of this study, a crown constructed a 1.3mm chamfer preparation appeared to have the best response to a simulated load applied to the palatal/incisal surface, at 45 degrees to the long axis.

Crowns↗

Doppler color flow images of iliofemoral graft end-to-side distal anastomotic models.

Hemodynamics within the distal anastomoses of iliofemoral bypass grafts were simulated using Plexiglas models (2.5 cm ID) within a pulsatile flow loop system (Re(mean) = 92, Re(peak) = 459 and alpha = 3.56). End-to-side distal anastomoses were constructed with angles of 30 degrees, 45 degrees and 60 degrees to bypass proximal artery segments with stenoses of 60% and 100% diameter reduction. Velocities were obtained over a two-dimensional field within the artery using an ultrasonic Doppler color flow imager operating at 5 MHz at positions from 1.5 diameters upstream to 3 diameters downstream of the anastomosis. Flow patterns downstream of an occlusion demonstrated definite skewing effects toward the outer wall with resultant flow separation along the inner wall. Presence of a partial (60% diameter reduction) arterial stenosis upstream of the anastomosis produced flow separation along both artery walls and a more symmetric profile downstream. Measurement of a separation area index (SAI) along each arterial wall demonstrated a minimum area exposed to low velocities for the 30 degrees anastomotic angle compared to the 45 degrees and 60 degrees anastomotic angles and for the occluded proximal artery cases compared to corresponding stenotic artery cases. The SAI values were minimal at peak systole compared to successive quarter cycle intervals. The findings of this study provide further information regarding the relationship between local fluid mechanics and predominant sites for intimal hyperplasia formation.

Anastomosis, Surgical↗

Phosphorylation of purified rat brain Na+ channel reconstituted into phospholipid vesicles by protein kinase C.

Phosphorylation of voltage-sensitive Na+ channels in neurons by protein kinase C slows Na+ channel inactivation and reduces peak Na+ currents. Na+ channels purified from rat brain and reconstituted into phospholipid vesicles under conditions that restore Na+ channel function were rapidly phosphorylated by protein kinase C on their 260-kDa alpha subunit. The phosphorylation reaction required Ca2+, diolein, and phosphatidylserine for activation of protein kinase C, and the rate of phosphorylation of reconstituted Na+ channels was 3- to 4-fold faster than for Na+ channels in detergent solution. Phosphorylation was on serine residues in three distinct tryptic phosphopeptides designated A, B, and C. Up to 2.5 mol of phosphate were incorporated per mol of Na+ channel. Following maximum phosphorylation by protein kinase C, cAMP-dependent protein kinase was able to incorporate more than 2.25 mol of phosphate per mol of Na+ channel indicating that these two kinases phosphorylate distinct sites. However, prior phosphorylation by cAMP-dependent protein kinase prevented phosphorylation of phosphopeptide B indicating that both kinases phosphorylate the site in this peptide. Phosphopeptide B shown here to be phosphorylated by protein kinase C and phosphopeptide 7 previously shown to be phosphorylated by cAMP-dependent protein kinase co-migrate on two-dimensional phosphopeptide maps and evidently are identical. The reduction in peak Na+ currents caused by both protein kinase C and cAMP-dependent protein kinase may result from phosphorylation of this single common site.

Animals↗

Micro-CT of carotid arteries: a tool for experimental studies.

Micro-computed tomography (micro-CT) is a high-resolution, non-destructive tool for two- and three-dimensional imaging and quantification. The ability of this technique to assess atherosclerosis of the carotid artery was evaluated in three human cadaver samples based on the original axial acquisitions, multiplanar reconstructions and volume rendering techniques. Quantitative analysis included the calculation of: (1) the original lumen perimeter, original lumen area, plaque area, residual lumen area, calcified area and gross sectional area reduction of the vascular lumen from two-dimensional slices; (2) the total tissue volume, soft tissue volume and calcified tissue volume from the three-dimensional data set. This preliminary study demonstrates the potential of micro-CT as a supplementary method for the two- and three-dimensional ex vivo evaluation of carotid atherosclerosis.

Aged↗

Infragenual cuff-compression reduces venous contamination in contrast-enhanced MR angiography of the calf.

PURPOSE: To reduce venous contamination at the calf level in three-dimensional contrast-enhanced MR angiography (CE-MRA) by applying continuous infragenual cuff-compression. MATERIALS AND METHODS: Ten patients with clinically relevant peripheral arterial occlusive disease (PAOD) underwent dynamic three-dimensional CE-MRA of the calf. Six consecutive measurements were acquired with the first measurement serving as mask. Cuff-compression of 50 mmHg was attached below the knee. To allow intra-individual comparison, compression was applied unilaterally. The cuff was inflated three minutes before scanning and was continued throughout the MRA session. Venous contamination and arterial visualization scores were ranked using a five-point rating scale. Contrast-to-noise ratios (CNRs) of superficial enhancing calf-veins on the uncompressed and compressed calf sides were evaluated. An asymmetry index (AI) defined by CNR(mean) (uncompressed)/CNR(mean) (compressed) was introduced to describe the ratio in venous contrast agent supply between both sides quantitatively. RESULTS: Three-dimensional CE-MRA of the calves demonstrated significantly lower superficial venous contamination scores (P < 0.004) and clearly improved arterial visualization (P < 0.009) on the compressed side. Additionally, AI values were larger than 1 (P < 0.02), indicating a higher contrast agent supply in the superficial veins on the uncompressed side. CONCLUSION: Infragenual cuff-compression minimizes venous overlay in three-dimensional CE-MRA at calf level by reduction of contrast agent supply in the superficial veins.

Aged↗

Two-dimensional mapping of three-dimensional SPECT data: a preliminary step to the quantitation of thallium myocardial perfusion single photon emission tomography.

A method is presented by which tomographic myocardial perfusion data are prepared for quantitative analysis. The method is characterized by an interrogation of the original data, which results in a size and shape normalization. The method is analogous to the circumferential profile methods used in planar scintigraphy but requires a polar-to-cartesian transformation from three to two dimensions. As was the case in the planar situation, centering and reorientation are explicit. The degree of data reduction is evaluated by reconstructing "idealized" three-dimensional data from the two-dimensional sampling vectors. The method differs from previously described approaches by the absence in the resulting vector of a coordinate reflecting cartesian coordinate in the original data (slice number).

Coronary Circulation↗

PLS dimension reduction for classification with microarray data.

Partial Least Squares (PLS) dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, the classification procedure consisting of PLS dimension reduction and linear discriminant analysis on the new components is compared with some of the best state-of-the-art classification methods. Moreover, a boosting algorithm is applied to this classification method. In addition, a simple procedure to choose the number of PLS components is suggested. The connection between PLS dimension reduction and gene selection is examined and a property of the first PLS component for binary classification is proved. In addition, we show how PLS can be used for data visualization using real data. The whole study is based on 9 real microarray cancer data sets.

Journal Article↗

Striated flagellar roots: isolation and partial characterization of a calcium-modulated contractile organelle.

We report the isolation of striated flagellar roots from the Prasinophycean green alga Tetraselmis striata using sedimentation in gradients of sucrose and flotation on gradients of colloidal silica. PAGE in the presence of 0.1% SDS demonstrates that striated flagellar roots are composed of a number of polypeptides, the most predominant one being a protein of 20,000 Mr. The 20,000 Mr protein band represents approximately 63% of the Coomassie Brilliant Blue staining of gels of isolated flagellar roots. Two-dimensional gel electrophoresis (isoelectric focusing and SDS PAGE) resolves the major 20,000 Mr flagellar root protein into two components of nearly identical Mr, but of differing isoelectric points (i.e., pl's of 4.9 and 4.8), which we have designated 20,000-Mr-alpha and 20,000-Mr-beta, respectively. Densitometric scans of two-dimensional gels of cell extracts indicate that the 20,000-Mr-alpha and -beta polypeptides vary, in their stoichiometry, between 2:1 and 1:1. This variability appears to be related to the state of contraction or extension of the striated flagellar roots at the time of cell lysis. Incubation of cells with 32PO4 followed by analysis of cell extracts by two-dimensional gel electrophoresis and autoradiography reveals that the more acidic 20,000-Mr-beta component is phosphorylated and the 20,000-Mr-alpha component contains no detectable label. These results suggest that the 20,000-Mr-alpha component is converted to the more acidic 20,000-Mr-beta form by phosphorylation. Both the 20,000-Mr-alpha and -beta flagellar root components exhibit a calcium-induced reduction in relative electrophoretic mobilities in two-dimensional alkaline urea gels. Antiserum raised in rabbits against the 20,000-Mr protein binds to both the 20,000-Mr-alpha and 20,000-Mr-beta forms of the flagellar root protein when analyzed by electrophoretic immunoblot techniques. Indirect immunofluorescence on vegetative or interphase cells demonstrate that the antibodies bind to two cyclindrical organelles located in the anterior region of the cell. Immunocytochemical investigations at ultrastructural resolution using this antiserum and a colloidal gold-conjugated antirabbit-IgG reveals immunospecific labeling of striated flagellar roots and their extensions. We conclude that striated flagellar roots are simple ion-sensitive contractile organelles composed predominantly of a 20,000 Mr calcium-binding phosphoprotein, and that this protein is largely responsible for the motile behavior of these organelles.

Calcium↗