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 1,279 records · Page 71Linked to original sources

Detection and mapping of widespread intermolecular protein disulfide formation during cardiac oxidative stress using proteomics with diagonal electrophoresis.

Regulation of protein function by reversible cysteine-targeted oxidation can be achieved by multiple mechanisms, such as S-glutathiolation, S-nitrosylation, sulfenic acid, sulfinic acid, and sulfenyl amide formation, as well as intramolecular disulfide bonding of vicinal thiols. Another cysteine oxidation state with regulatory potential involves the formation of intermolecular protein disulfides. We utilized two-dimensional sequential non-reducing/reducing SDS-PAGE (diagonal electrophoresis) to investigate intermolecular protein disulfide formation in adult cardiac myocytes subjected to a series of interventions (hydrogen peroxide, S-nitroso-N-acetylpenicillamine, doxorubicin, simulated ischemia, or metabolic inhibition) that alter the redox status of the cell. More detailed experiments were undertaken with the thiol-specific oxidant diamide (5 mm), a concentration that induces a mild non-injurious oxidative stress. This increase in cellular oxidation potential caused global intermolecular protein disulfide formation in cytosolic, membrane, and myofilament/cytoskeletal compartments. A large number of proteins that undergo these associations were identified using liquid chromatography-mass spectrometry/mass spectrometry. These associations, which involve metabolic and antioxidant enzymes, structural proteins, signaling molecules, and molecular chaperones, were confirmed by assessing "shifts" on non-reducing immunoblots. The observation of widespread protein-protein disulfides indicates that these oxidative associations are likely to be fundamental in how cells respond to redox changes.

Animals↗

Diagnosing childhood acetabular dysplasia using the lateral margin of the sourcil.

The purpose of this study was to evaluate the lateral edge of the acetabulum and locate the most accurate marking point on a plain radiograph when measuring the acetabular index (AI) and the center-edge (CE) angle. We studied the radiographs of 53 patients with unilateral developmental dysplasia of the hip (DDH), all of whom were treated by closed reduction. In addition to plain radiographs, eight patients had magnetic resonance imaging (MRI) studies, 16 had three-dimensional computed tomography (3-DCT) studies, and six underwent arthrographic studies. We found that the most lateral bony margin of the acetabular roof on plain radiograph represents the anterolateral portion of the acetabulum. The lateral end of the sourcil indicates the lateral margin of the mid-superior portion of the acetabulum. To reduce intra- and interobserver errors, we suggest that when measuring the AI and the CE angle, physicians clearly indicate in the medical records which of the two marking points was used.

Acetabulum↗

Computer-assisted resection of cerebral arteriovenous malformations.

OBJECTIVE: A series of 22 patients with arteriovenous malformations (AVMs) were surgically treated using computer-assisted image guidance. The value of image guidance for nidus definition and detection of feeding arteries and draining veins was assessed. METHODS: Seven of the 22 patients presented with hemorrhage. The sizes of the AVMs ranged from 1 to 8 cm. Six patients underwent preoperative embolization. For 18 patients (81.8%), the AVMs were located in highly eloquent areas. A passive-marker-based neuronavigation system (BrainLab, Heimstetten, Germany) was used for intraoperative image guidance. Segmentation of the pathological vessels was performed preoperatively, on the basis of 2-mm helical computed tomographic angiographic slices, to obtain three-dimensional reconstructions of the AVMs. Temporary clips were initially placed on all identifiable feeding arteries, for intranidal pressure reduction before AVM dissection. Dissection of the AVMs was then performed along the main draining veins, as identified by neuronavigation. Patient follow-up monitoring ranged from 3 to 16 months (median, 7 mo). RESULTS: The computer-calculated registration accuracy ranged between 1.1 and 3.1 mm (median, 1.4 mm). Exact nidus definition was possible for all 22 patients. The principal draining veins were also identified for all patients. Feeding arteries could be detected after the segmentation process when the vessels were at least 3 mm in diameter (19 patients). Complete collapse of the AVMs was achieved with initial clip application for 3 patients; partial intranidal pressure reduction was observed for 12 patients. No significant decompression by feeder clipping was possible for pre-embolized AVMs. Perioperative mortality and morbidity rates were 0 and 14%, respectively. CONCLUSION: This image-guided technology allows observation of the relationship between AVMs and adjacent brain structures, increasing spatial orientation during surgery. Definition of an optimal surgical approach and early localization of feeding arteries for temporary occlusion minimize tissue manipulation and enhance the safety of direct dissection along the draining veins, which is necessary in eloquent areas.

Adolescent↗

Dimensional rearrangement of Escherichia coli B/r cells during a nutritional shift-down.

In a search for the mechanism underlying dimensional changes in bacteria, the glucose analogue methyl alpha-D-glucoside was used to effect a rapid reduction in the mass growth rate of Escherichia coli by competitively inhibiting glucose uptake, a so-called nutritional shift-down. The new steady-state cell mass and volume were reached after 1 h, during which the rate of cell division was maintained; rearrangement of the linear dimensions (cell length, diameter), however, required an additional 2 h and caused an undershoot in cell length, consistent with the view that E. coli is slow to modify its diameter. The results are compared with the overshoot in cell length that occurs following nutritional shift-up.

Cell Division↗

Kinetic energy driven pairing in cuprate superconductors.

Pairing occurs in conventional superconductors through a reduction of the electronic potential energy accompanied by an increase in kinetic energy. In the underdoped cuprates, optical experiments show that pairing is driven by a reduction of the electronic kinetic energy. Using the dynamical cluster approximation we study superconductivity in the two-dimensional Hubbard model. We find that pairing is indeed driven by the kinetic energy and that superconductivity evolves from an unconventional state with partial spin-charge separation, to a superconducting state with quasiparticle excitations.

Journal Article↗

Enhanced photosynthesis and redox energy production contribute to salinity tolerance in Dunaliella as revealed by homology-based proteomics.

Salinity is a major limiting factor for the proliferation of plants and inhibits central metabolic activities such as photosynthesis. The halotolerant green alga Dunaliella can adapt to hypersaline environments and is considered a model photosynthetic organism for salinity tolerance. To clarify the molecular basis for salinity tolerance, a proteomic approach has been applied for identification of salt-induced proteins in Dunaliella. Seventy-six salt-induced proteins were selected from two-dimensional gel separations of different subcellular fractions and analyzed by mass spectrometry (MS). Application of nanoelectrospray mass spectrometry, combined with sequence-similarity database-searching algorithms, MS BLAST and MultiTag, enabled identification of 80% of the salt-induced proteins. Salinity stress up-regulated key enzymes in the Calvin cycle, starch mobilization, and redox energy production; regulatory factors in protein biosynthesis and degradation; and a homolog of a bacterial Na(+)-redox transporters. The results indicate that Dunaliella responds to high salinity by enhancement of photosynthetic CO(2) assimilation and by diversion of carbon and energy resources for synthesis of glycerol, the osmotic element in Dunaliella. The ability of Dunaliella to enhance photosynthetic activity at high salinity is remarkable because, in most plants and cyanobacteria, salt stress inhibits photosynthesis. The results demonstrated the power of MS BLAST searches for the identification of proteins in organisms whose genomes are not known and paved the way for dissecting molecular mechanisms of salinity tolerance in algae and higher plants.

Algal Proteins↗

Structure of the laccase from Coprinus cinereus at 1.68 A resolution: evidence for different 'type 2 Cu-depleted' isoforms.

Laccases (E.C. 1.10.3.2; benzenediol oxygen oxidoreductases) couple the four-electron reduction of dioxygen to water to four one-electron oxidations of a reducing substrate. The three-dimensional structure of the 'blue' multi-copper oxidase laccase from the fungus Coprinus cinereus at 1.68 A reveals the structural basis for isoforms of the type 2 Cu-depleted species.

Binding Sites↗

Design-based texture feature fusion using Gabor filters and co-occurrence probabilities.

A design-based method to fuse Gabor filter and grey level co-occurrence probability (GLCP) features for improved texture recognition is presented. The fused feature set utilizes both the Gabor filter's capability of accurately capturing lower and mid-frequency texture information and the GLCP's capability in texture information relevant to higher frequency components. Evaluation methods include comparing feature space separability and comparing image segmentation classification rates. The fused feature sets are demonstrated to produce higher feature space separations, as well as higher segmentation accuracies relative to the individual feature sets. Fused feature sets also outperform individual feature sets for noisy images, across different noise magnitudes. The curse of dimensionality is demonstrated not to affect segmentation using the proposed the 48-dimensional fused feature set. Gabor magnitude responses produce higher segmentation accuracies than linearly normalized Gabor magnitude responses. Feature reduction using principal component analysis is acceptable for maintaining the segmentation performance, but feature reduction using the feature contrast method dramatically reduced the segmentation accuracy. Overall, the designed fused feature set is advocated as a means for improving texture segmentation performance.

Algorithms↗

The water crisis in the gaza strip: prospects for resolution.

Israel and the Palestinian Authority share the southern Mediterranean coastal aquifer. Long-term overexploitation in the Gaza Strip has resulted in a decreasing water table, accompanied by the degradation of its water quality. Due to high levels of salinity and nitrate and boron pollution, most of the ground water is inadequate for both domestic and agricultural consumption. The rapid rate of population growth in the Gaza Strip and dependence upon ground water as a single water source present a serious challenge for future political stability and economic development. Here, we integrate the results of geochemical studies and numerical modeling to postulate different management scenarios for joint management between Israel and the Palestinian Authority. The chemical and isotopic data show that most of the salinity phenomena in the Gaza Strip are derived from the natural flow of saline ground water from Israel toward the Gaza Strip. As a result, the southern coastal aquifer does not resemble a classic "upstream-downstream" dispute because Israel's pumping of the saline ground water reduces the salinization rates of ground water in the Gaza Strip. Simulation of different pumping scenarios using a monolayer, hydrodynamic, two-dimensional model (MARTHE) confirms the hypothesis that increasing pumping along the Gaza Strip border combined with a moderate reduction of pumping within the Gaza Strip would improve ground water quality within the Gaza Strip. We find that pumping the saline ground water for a source of reverse-osmosis desalination and then supplying the desalinated water to the Gaza Strip should be an essential component of a future joint management strategy between Israel and the Palestinian Authority.

Conservation of Natural Resources↗

Expression, secretion, and glycosylation of the 45- and 47-kDa glycoprotein of Mycobacterium tuberculosis in Streptomyces lividans.

The gene encoding the 45/47 kDa glycoprotein (Rv1860) of Mycobacterium tuberculosis was expressed in Streptomyces lividans under its own promoter and under the thiostrepton-inducible Streptomyces promoter PtipA. The recombinant protein was released into the culture medium and, like the native protein, migrated as a double band at 45 and 47 kDa in sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) gels. However, in contrast to the native protein, only the 47-kDa recombinant protein could be labeled with concanavalin A (ConA). Carbohydrate digestion with jack bean alpha-D-mannosidase resulted in a reduction in the molecular mass of the recombinant protein upper band and completely eliminated ConA binding. Two-dimensional gel electrophoresis revealed only one isoelectric point for the recombinant protein. Comparative fingerprinting analysis of the individually purified upper and lower recombinant protein bands, treated under the same conditions with specific proteases, resulted in similar peptide patterns, and the peptides had the same N-terminal sequence, suggesting that migration of the recombinant protein as two bands in SDS-PAGE gels could be due to differences in glycosylation. Mass spectrometry analysis of the recombinant protein indicated that as in native protein, both the N-terminal and C-terminal domains of the recombinant protein are glycosylated. Furthermore, it was determined that antibodies of human tuberculosis patients reacted mainly against the carbohydrate residues of the glycoprotein. Altogether, these observations show that expression of genes for mycobacterial antigens in S. lividans is very useful for elucidation of the functional role and molecular mechanisms of glycosylation in bacteria.

Amino Acid Sequence↗

Specific labeling of lens aldehyde dehydrogenase class 1 from (3)H-cholesterol or its derivatives.

We investigated the possibility that sterols could covalently modify ocular lens cell proteins. Incubation of cultured bovine lens epithelial cells (BLEC) with (3)H-cholesterol led to the labeling of a cytosolic protein of about 52 kD. Two-dimensional electrophoresis of the BLEC soluble proteins and fluorography revealed one labeled protein of 52 kD, pI = 6.6, plus a weakly labeled, slightly more acidic protein of the same size. MALDI-MS analysis of both proteins recovered from duplicate gels indicated both to be aldehyde dehydrogenase class 1 (ALDH-1). The identity was confirmed by immunoprecipitation with antiserum to ALDH-1. Alkaline hydrolysis of (3)H-labeled ALDH-1 released most of the radiolabel as compounds much more polar than cholesterol. We speculate that lens ALDH-1 can participate in the oxidation of cholesterol or its derivatives to unidentified sterol carboxylic acids and that the labeled protein reflects capture of ALDH-1 with sterol intermediates covalently bound to the enzyme in ester linkage. Lens ALDH-1 might, therefore, participate in the detoxication of polar sterols.

Aldehyde Dehydrogenase↗

Neuroanatomical digital image processing in CT-guided stereotactic operations.

In order to utilize computed tomography (CT) for functional neurosurgical procedures, a number of problems must be resolved. One such problem is the development of an appropriate technique for digital processing of neuroanatomical images. Our previous work concerned a numerical reproduction of a well-known stereotactic atlas and its three-dimensional manipulation. In order to efficiently utilize this information with CT images we propose a technique for data reduction that allows the reconstruction of anatomical structures from the atlas. The logic of implementing these data in CT-assisted stereotactic surgery is described.

Brain↗

Interaction between effects of hypoxia and hypercapnia on altering left ventricular relaxation and chamber stiffness in dogs.

Left ventricular (LV) isovolumic relaxation and chamber stiffness were examined in dogs to see how hypoxemia and hypercapnia occurring during an acute exacerbation of chronic obstructive lung disease could directly affect diastolic performance. Measurements were obtained during baseline (arterial PO2 approximately 200 mm Hg; PCO2 approximately 35 mm Hg; pH approximately 7.35), hypoxia (PO2 approximately 35 mm Hg; PCO2 approximately 35 mm Hg; pH approximately 7.35), and hypoxia-hypercapnia (PO2 approximately 35 mm Hg; PCO2 approximately 60 mm Hg; pH approximately 7.15) in an open-chest, open-pericardium preparation. Changes in LV diastolic performance during hypoxic and hypercapnic interventions were contrasted with those caused by ventricular interdependence in which pulmonary artery occlusion was used to produce a right to left ventricular septal shift. Subendocardial ultrasonic crystal transducers were placed along the three orthogonal axes of the left ventricle to measure dimensions by sonomicrometry. Along each axis, LV end-diastolic dimension-pressure relations were constructed in the various conditions; the slope of this relationship, obtained over a linear portion of the curve, was used as an index of diastolic dimensional distensibility (DD). The results showed that during hypoxia, DD appeared decreased along the three axes, with a reduction in filling primarily along the anterior-posterior and apex-base axes. The addition of hypercapnia to hypoxia completely abolished the hypoxic effect. On the other hand, during pulmonary artery occlusion, LV DD were not changed along the latter two dimensions. We conclude that during respiratory failure, LV diastolic performance may be directly affected by arterial blood gas tensions, which by altering the interaction between the contractile filaments modulate LV filling.

Animals↗

[Brain isoforms of creatine kinase in health and mental diseases: Alzheimer's disease and schizophrenia].

The paper analyzes the authors' own findings and the data available in the literature on the intensity, site, and possible causes of impairment of the creatine-creatine phosphate system of brain energy metabolism in mental diseases, such as Alzheimer's disease (AD) and schizophrenia. Examining the level of cytosolic BB creatine kinase in postmortem AD and schizophrenic's brain structures showed a significant decrease in BB creatine kinase as compared with the similar control brain structures. There was the maximum decline in AD cases. It was considerable as compared with both the control and schizophrenic groups (p < 0.01). The decrement was revealed by various techniques, including the determination of activity, immunological responsiveness and the analysis of two-dimensional protein maps. Immunocytochemical investigation indicated a decrease in responses to BB creatine kinase, mainly in astrocytes. The reduction in cytosolic BB creatine kinase levels is not a result of age, postmortem delay, or psychotic therapy. The causes of lower BB creatine kinase levels in the cell cytosol of the postmortem brain in mental pathology are discussed. The decrement in cytosolic BB creatine kinase in AD and schizophrenia occurs not only in the brain, but also in the peripheral tissues which contain BB creatine kinase. In all cases, it is greater in AD than in schizophrenia. Using immunosorbents with monoclonal antibodies to M-creatine kinase and to B-creatine kinase subunits makes it possible detect BB-creatine kinase in the extracts of human peripheral lymphocytes and platelets. A study of whether there is a relationship between the clinical data of mental patients and the level of BB creatine kinase in their blood elements is assumed to be useful in evaluating BB creatine kinase as a prognostic/diagnostic marker of mental diseases.

Alzheimer Disease↗

[CMACPAR an modified parallel neuro-controller for control processes].

CMACPAR is a Parallel Neurocontroller oriented to real time systems as for example Control Processes. Its characteristics are mainly a fast learning algorithm, a reduced number of calculations, great generalization capacity, local learning and intrinsic parallelism. This type of neurocontroller is used in real time applications required by refineries, hydroelectric centers, factories, etc. In this work we present the analysis and the parallel implementation of a modified scheme of the Cerebellar Model CMAC for the n-dimensional space projection using a mean granularity parallel neurocontroller. The proposed memory management allows for a significant memory reduction in training time and required memory size.

Algorithms↗

Community analysis of nitrifying bacteria in an advanced and compact Gappei-Johkasou by FISH and PCR-DGGE.

Fluorescent in situ hybridization (FISH) method with 16S rRNA-targeted oligonucleotide probes was used for quantitative estimation of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in a Johkasou. Although the occupation ratios of AOB and NOB increased as nitrification progressed, about one month later, the occupation ratios decreased, despite showing good nitrification ability. Furthermore, even when urea was added to the feeding wastewater to raise the amount of T-N, the occupation ratios of both nitrifying bacteria remained constant. For further investigation, denaturing gradient gel electrophoresis (DGGE) was used to study the community structure of AOB in the Johkasou. As a result, DGGE band patterns and following sequence analysis revealed that the community structure of AOB was complicated and changed during this experiment. It was suggested that even if the occupation ratio of AOB to eubacteria was constant, the majorities of AOB were changed through temperature and load fluctuation. The combination of FISH and PCR-DGGE provides new information that was not available by conventional cultivation-based methods.

Ammonia↗

Cysteine 647 in the insulin receptor is required for normal covalent interaction between alpha- and beta-subunits and signal transduction.

We have investigated the structural and functional properties of two mutant insulin receptors in which Cys647 and Cys682,683,685 have been replaced with Ser (IRS647 and IRS682,683,685, respectively). Compared with the wild-type receptor (IRWT), both mutant receptors displayed altered sensitivities to dithiothreitol with respect to insulin binding and reduction of oligomeric forms. Subunit composition of the oligomeric forms of the receptors as determined by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 125I-labeled receptors indicated that Cys682,683,685 are required for normal heterotetrameric structure and that Cys647 plays a major role in the normal covalent association of the alpha- and beta-subunits. Under nonreducing conditions, the affinity-labeled IRS647 migrated, almost exclusively, as a 230-kDa species which appeared to represent an alpha 2 form of the receptor. Furthermore, Chinese hamster ovary cells expressing IRS647 did not exhibit basal or insulin-stimulated autophosphorylation, suggesting that Cys647 is also required for signal transduction.

Affinity Labels↗

Disulfide bonding controls the processing of retroviral envelope glycoproteins.

The mitogenic membrane glycoprotein (gp55) encoded by Friend erythroleukemia virus is inefficiently processed from the rough endoplasmic reticulum (RER) and only 3-5% reaches plasma membranes. Because this processed component (gp55P) contains larger and more complex oligosaccharides, it can be separated from RER gp55. In nonreducing conditions, gp55P is a unique disulfide-bonded dimer, whereas RER gp55 consists of monomers and dimers with diverse intrachain and interchain disulfide bonds. This suggests that gp55 folds heterogeneously and that only one homodimer is competent for export from the RER. Pulse-chase analyses of gp55 components labeled with radioactive amino acids indicated that formation of diverse disulfide-bonded components occurred within minutes of polypeptide synthesis and that malfolded components did not later isomerize to generate dimers competent for export from the RER. Chemical studies suggested that all 12 cysteines of gp55 were oxidized within 5 min after synthesis of the protein. In contrast, the envelope glycoprotein precursor (gPr90) encoded by a replication-competent murine leukemia virus folds more homogeneously, and it is then processed and cleaved to form an extracellular glycoprotein gp70 plus a transmembrane protein p15E. The fully processed glycoprotein contains an unoxidized cysteine sulfhydryl that isomerizes reversibly with a disulfide bond that links gp70 to p15E. Consequently, only a proportion of gp70 and p15E is disulfide-bonded, and dissociation occurs when the environment becomes even slightly reducing. The gp55 glycoprotein appears to be an extreme example of protein malfolding associated with imprecise and irreversible disulfide bonding. We discuss evidence that folding inefficiencies are common for retroviral proteins that have newly evolving pathogenic functions.

Blotting, Western↗