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At least 1,603 records · Page 89Linked to original sources
PubMed1997

Normalisation of metabolite images in 1H NMR spectroscopic imaging.

Single slice proton magnetic resonance spectroscopic images were taken from a volume of interest (VOI), which was localised using the point resolved spectroscopy (PRESS) sequence. Non-uniformities in the excitation profile of the VOI within the image plane were accounted for using a uniformity correction image. Metabolite images were divided on a voxel-by-voxel basis with a water image obtained from a VOI of the same spatial dimensions from a phantom acquisition. Normalisation procedures carried out on phantom metabolite images were needed to account for the spatial shift in the excitation profile of the VOI, which varies linearly with the chemical shift of the metabolite. Patient metabolite images were then normalised using a VOI water image from a phantom acquisition, which was spatially shifted according to the metabolite chemical shift. In a study of 14 stroke patients, metabolite maps of the distribution of choline, creatine and N-acetyl aspartate (NAA) were constructed. The spectral signal intensities from these metabolites in the infarcted and in the contralateral region were calculated using the raw maps and secondly with the same maps after the B1 normalisation process. In the initial analysis only the metabolite NAA showed a significant decrease, whilst all three metabolites showed a significant reduction in the normalised analysis. These results confirm that normalisation of PRESS localised images does have a significant bearing upon any quantitative measurements made using such images.

Algorithms↗
PubMed1986

Determination of the earliest site of ventricular activation in Wolff-Parkinson-White syndrome: application of digital continuous loop two-dimensional echocardiography.

Surgical and transcatheter ablation of accessory atrioventricular (AV) connections (Wolff-Parkinson-White syndrome) requires accurate localization of the accessory pathway. In a canine model of endocardial pacing, a continuous loop two-dimensional echocardiographic technique was developed for determining the earliest site of ventricular activation. This technique was then used to localize accessory AV connections in patients. Echocardiographic images were acquired on videotape and converted to a digital continuous loop format, from which the earliest site of systolic motion was determined. In six dogs, using six distinct endocardial sites, two blinded observers accurately identified the earliest site of ventricular activation in 31 (86%) of 36 and 32 (89%) of 36 locations. Determination of the earliest site of ventricular activation with the continuous loop digital technique was superior to standard analog analysis in overall accuracy (p less than 0.02) and in intraobserver variability (p less than 0.004). After validation of this technique, 21 patients with 22 accessory AV connections with anterograde conduction were studied. The earliest site of mechanical activity was determined during sinus (10 patients) or atrial paced (11 patients) rhythms by two blinded observers and compared with electrophysiologic mapping and surface electrocardiograms. Digitally processed echocardiograms correctly localized the earliest site of ventricular activation in 18 of 22 connections and predicted an adjacent location in the remaining 4.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed1995

Molecular biology of bovine viral diarrhea virus and its interactions with the host.

The contributions of pestivirus molecular biology research to our understanding of Bovine Viral Diarrhea Virus (BVDV) biology and disease have been remarkable. Completion of nucleotide sequence information for genomes of NCP and CP-BVDV isolates was an important milestone. Subsequent work on the protein map of BVDV and polyprotein processing pathways paved the way for the interpretation of many other virologic and immunologic studies. Discovery of a correlation between genotype II and virulence (hemorrhagic syndrome) will help to clarify previously controversial data and to improve disease control. Description of multiple pathways of p80 expression in CP-BVDV offered insight into the pathogenesis of mucosal disease. Identification of gp53/ E2 as the target of neutralizing antibodies and source of antigenic hypervariability helped us to understand immunity to BVDV. Collectively, the advances described contribute to the implementation of improved diagnostic and control strategies to reduce losses inflicted by the bovine pestivirus.

Animals↗
PubMed2002

Both carboxy-terminal tails of alpha- and beta-tubulin are essential, but either one will suffice.

Microtubules (MTs) are organized into distinct systems essential for cell shape, movement, intracellular transport, and division. Electron crystallographic analyses provide little information about how MTs produce diverse structures and functions, perhaps because they failed to visualize the last 10 residues of the alpha- and the last 18 of the beta-tubulin C-terminal tails (CTTs), which likely play a role in MT diversity. CTTs define conserved, nonallelic isotypes in mammals, are major sites of posttranslational modifications (PTMs), are binding sites for microtubule-associated proteins (MAPs), and determine MT motor processivity. Using mutagenesis and homologous gene replacement in Tetrahymena thermophila, we analyzed mutations, deletions, tail switches, and tail duplications of alpha- and beta-tubulin CTTs. We demonstrate that a tail is required for the essential function of both alpha- and beta-tubulin. However, the two tails are interchangeable, and cells grow normally with either an alpha or a beta tail on both tubulins. In addition, an alpha gene containing a duplicated alpha C terminus rescues a lethal mutant lacking all known posttranslational modification sites on the beta C terminus but cannot rescue deletion of the beta tail. Thus, tubulin tails have a second essential function that is not associated with posttranslational modification.

Amino Acid Motifs↗
PubMed1999

Lateralized ultradian rhythms of the right and left brain: temporal variations of tactile discrimination tested in German subjects.

Endogenous ultradian rhythms with a periodicity of 2-3 hours operate separately in the right and left hemispheres of the human brain and modulate physiological functions, perception and cognition. Since sensory pathways from either hand terminate in the contralateral hemisphere, ultradian rhythms of the right and left brain can be monitored by variations in the tactile discrimination of the left and right hand, respectively. Thirteen right-handed German males were tested every 15 minutes for 8 hours. Time series of the tactile error rate determined for the right and left hands oscillate with significantly different ultradian periodicities. Whereas cycles in tactile discrimination of the right hand (left hemisphere) have a periodicity of about 2 hours, tactile discrimination of the left hand (right hemisphere) is modulated by longer periods of about 3 hours. This is interpreted in terms of the overall functional asymmetry of the human brain. Since the left brain is the specialized locus for verbal processing and the right brain for visual-spatial processing, lateralized ultradian rhythms operating in the hemispheres may provide a distinct frame for long-term timing of neuronal processes underlying semantic and spatial mapping of the environment. This is particularly important for interpreting biosocial behavioural rhythms seen in humans living under natural conditions.

Adult↗
PubMed2003

Sorption versus biomineralization of Pb(II) within Burkholderia cepacia biofilms.

X-ray spectroscopy measurements have been combined with macroscopic uptake data and transmission electron microscopy (TEM) results to show that Pb(II) uptake by Burkholderia cepacia is due to simultaneous sorption and biomineralization processes. X-ray microprobe mapping of B. cepacia biofilms formed on alpha-Al2O3 surfaces shows that Pb(II) is distributed heterogeneously throughout the biofilms because of the formation of Pb "hot spots". EXAFS data and TEM observations show that the enhanced Pb accumulation is due to the formation of nanoscale crystals of pyromorphite (Pb5(PO4)3(OH)) adjacent to the outer-membrane of a fraction of the total population of B. cepacia cells. In contrast, B. cepacia cell suspensions or biofilms that were heat-killed or pretreated with X-rays do not form pyromorphite, which suggests that metabolic activity is required. Precipitation of pyromorphite occurs over several orders of magnitude in [H-] and [Pb] and accounts for approximately 90% of the total Pb uptake below pH 4.5 but only 45-60% at near-neutral pH because of the formation of additional Pb(II) adsorption complexes. Structural fits of Pb L(III) EXAFS data collected for heat-treated cells at near-neutral pH suggest that Pb(II) forms inner-sphere adsorption complexes with carboxyl functional groups in the biofilms.

Adsorption↗
PubMed2003

Comparative molecular surface analysis: a novel tool for drug design and molecular diversity studies.

The application of the SOM network in drug design and molecular diversity is discussed. In particular, examples of the applications of the Comparative Molecular Surface Analysis (CoMSA) are reviewed. Molecular surface is a fuzzy category, inspired by the macroscopic world, which has no unique equivalent in the molecular scale. However, it is somewhere near the area where the molecular recognition processes are taking place. Consequently, the methods that analyze this region promise better efficiency than procedures that are based on uniform grids. An important advantage of the CoMSA method is the possibility for the generation of fuzzy molecular representations together with its ability to discover such aspects of molecular similarity that can be easily overlooked by a chemist. The ability for data compression is a further advantage. It has also been shown that the fast processing of the comparative Kohonen mapping enables one to implement this method in the field of molecular diversity.

Anti-HIV Agents↗
PubMed1982

Form and texture in hierarchically constructed patterns.

Perceived organization of hierarchically constructed patterns was investigated through similarity judgments and a verbal description task. The number of elements and their sizes relative to the configuration were varied in a series of five experiments. The results show that in patterns composed of a few relatively large elements, the elements are perceived as individual parts of the overall form and are perceptually salient. Increasing the number of elements and/or decreasing their size results in a perceived unified form associated with texture, representing the structural properties of the elements as a group. In the latter case, the perceptual salience of the individual element decreases and the global form (or sometimes the texture) dominates perception. These findings suggest that the perceptual levels arising from global configuration of local elements may not correspond directly to these two geometrical levels in the stimulus domain as much previous work on "global versus local" processing has assumed. Rather, the mapping of the two independent geometrical levels into meaningful perceptual levels depends critically on the number and relative size of the elements, thus changing the perceived organization of the whole pattern.

Adult↗
PubMed1999

Expression and activation of RAS and mitogen-activated protein kinases in macrophages treated in vitro with cisplatin: regulation by kinases, phosphatases and Ca2+/calmodulin.

Cisplatin (cis-dichlorodiammineplatinum II), a potent antitumour compound, stimulates immune responses by activating monocytes/macrophages and other cells of the immune system. However, the exact mechanism by which cisplatin activates these cells is poorly characterized and attempts are being made to understand this mechanism. Previous studies from this laboratory have shown that Lyn, a protein tyrosine kinase of the src family, and nuclear factor (NF)-kappaB are involved in cisplatin-induced macrophage activation. Recent studies suggest that the RAS and mitogen-activated protein (MAP) kinases function as a connecting link between activated lyn and NF-kB, which raises the possibility of their involvement in cisplatin-induced macrophage activation. Therefore, this study was undertaken to investigate the effect of cisplatin treatment on the expression/activation of RAS (a low molecular weight GTP-binding protein) and MAP kinases in murine peritoneal macrophages. The underlying mechanism of expression/activation of RAS and MAP kinases in cisplatin-treated macrophages was also investigated. Immunoblotting and immune-complex kinase assays revealed that cisplatin treatment of macrophages leads to increased expression/activation of RAS and MAP kinases, with optimal expression/activation at 15 min of treatment. Using a battery of specific inhibitor/modulators of different signalling molecules, this study shows that expression and activation of MAP kinases are two unrelated processes. It was also observed that kinase (protein tyrosine and protein kinase C) inhibitor and Ca2+/calmodulin antagonist inhibit expression/activation of RAS/MAP kinases in macrophages, whereas phosphatases (protein tyrosine and serine/threonine) inhibitor up-regulate these kinases.

Animals↗
PubMed2003

The influence of gender and emotional valence of visual cues on FMRI activation in humans.

Emotional neuroscience maps neurocircuits associated with the processing of affective stimuli. To assess gender differences in brain activation elicited by affective stimuli, we used pictures from the International Affective Picture System in a functional magnetic resonance imaging (fMRI) study. Ten male and ten female age-matched healthy volunteers were included and viewed affectively negative versus positive pictures, which were presented in an event related design. There was a significant interaction between valence of emotional stimuli and gender in the sublenticular extended amygdala (SLEA) and the rostral anterior cingulate. fMRI activation in these regions was stronger for negative compared to positive cues in women. In men fMRI activation was independent of stimulus valence. These results suggest to take gender differences into account when emotional paradigms are tested in functional brain imaging.

Adult↗
PubMed2006

Sleep after spatial learning promotes covert reorganization of brain activity.

Sleep promotes the integration of recently acquired spatial memories into cerebral networks for the long term. In this study, we examined how sleep deprivation hinders this consolidation process. Using functional MRI, we mapped regional cerebral activity during place-finding navigation in a virtual town, immediately after learning and 3 days later, in subjects either allowed regular sleep (RS) or totally sleep-deprived (TSD) on the first posttraining night. At immediate and delayed retrieval, place-finding navigation elicited increased brain activity in an extended hippocampo-neocortical network in both RS and TSD subjects. Behavioral performance was equivalent between groups. However, striatal navigation-related activity increased more at delayed retrieval in RS than in TSD subjects. Furthermore, correlations between striatal response and behavioral performance, as well as functional connectivity between the striatum and the hippocampus, were modulated by posttraining sleep. These data suggest that brain activity is restructured during sleep in such a way that navigation in the virtual environment, initially related to a hippocampus-dependent spatial strategy, becomes progressively contingent in part on a response-based strategy mediated by the striatum. Both neural strategies eventually relate to equivalent performance levels, indicating that covert reorganization of brain patterns underlying navigation after sleep is not necessarily accompanied by overt changes in behavior.

Adult↗
PubMed2002

The effect of activation of Mammalian oocytes on remodeling of donor nuclei after nuclear transfer.

Activation of bovine oocytes by experimental procedures that closely mimic normal fertilization is essential both for intracytoplasmic sperm injection and for nuclear transfer (NT). Therefore, with the goal of producing haploid activated oocytes, we evaluated whether butyrolactone I and bohemine, either alone or in combination with ionomycin, are able to activate young matured mammalian oocytes. Furthermore, the effect on the patterns of DNA synthesis after pronuclear formation as well as changes in histone H1 kinase and MAP kinase activities during the process of activation were studied. Our results with bohemine show that the specific inhibition of cyclin-dependent kinases (CDKs) in metaphase II bovine oocytes induces parthenogenetic activation in a dose dependent manner (25, 50, and 100 microM, respectively), either alone (3%, 30%, and 50%) or in combination with ionomycin (30%, 70%, and 87.5%). The effect of two activation protocols on nuclear remodeling, DNA synthesis during the first cell cycle, chromosome segregation after first mitosis, and development to blastocyst of embryos produced by somatic nuclear transfer were studied. Pronuclear formation was significantly higher when activation lasted 5 h compared to 3 h for both ethanol-cycloheximide and ionomycin-bohemine treatment. Initiation of DNA synthesis was delayed in ethanol-cycloheximide group, however, after 12-h labeling 100% of embryos synthesized DNA in both groups. Analysis of two-cell embryos with DNA probes for chromosome 6, 7, and 15 by fluorescence in situ hybridization showed that at least 50% of NT embryos were of normal ploidy, independent of the activation protocol.

Animals↗
PubMed1999

A p90(rsk) mutant constitutively interacting with MAP kinase uncouples MAP kinase from p34(cdc2)/cyclin B activation in Xenopus oocytes.

The efficient activation of p90(rsk) by MAP kinase requires their interaction through a docking site located at the C-terminal end of p90(rsk). The MAP kinase p42(mpk1) can associate with p90(rsk) in G(2)-arrested but not in mature Xenopus oocytes. In contrast, an N-terminally truncated p90(rsk) mutant named D2 constitutively interacts with p42(mpk1). In this report we show that expression of D2 inhibits Xenopus oocyte maturation. The inhibition requires the p42(mpk1) docking site. D2 expression uncouples the activation of p42(mpk1) and p34(cdc2)/cyclin B in response to progesterone but does not prevent signaling through p90(rsk). Instead, D2 interferes with a p42(mpk1)-triggered pathway, which regulates the phosphorylation and activation of Plx1, a potential activator of the Cdc25 phosphatase. This new pathway that links the activation of p42(mpk1) and Plx1 during oocyte maturation is independent of p34(cdc2)/cyclin B activity but requires protein synthesis. Using D2, we also provide evidence that the sustained activation of p42(mpk1) can trigger nuclear migration in oocytes. Our results indicate that D2 is a useful tool to study MAP kinase function(s) during oocyte maturation. Truncated substrates such as D2, which constitutively interact with MAP kinases, may also be helpful to study signal transduction by MAP kinases in other cellular processes.

Animals↗
PubMed1995

ALIGNMENT SERVICE: creation and processing of alignments of sequences of unlimited length.

A package for the creation and processing of multiple sequence alignment is described. There is no limit on the lengths of the processed nucleotide or amino acid sequences, and the number of sequences in the alignment is also unlimited. The main groups of functions are: a semiautomatic alignment editor; a wide set of functions for technical processing of alignments; nucleotide alignment mapping and translation; and similarity search functions. A user-friendly interface and a set of generally used file actions provide a special operational subsystem for everyday tasks.

Amino Acid Sequence↗
PubMed2025

nf-core/pacvar: a pipeline for analyzing long-read PacBio whole genome and repeat expansion sequencing data.

MOTIVATION: Pacific Biosciences (PacBio) single-molecule, long-read sequencing enables whole genome annotation and the characterization of 20 complex repetitive repeat regions, especially relevant to neurodegenerative diseases, through their PureTarget panel. Long-read whole-genome sequencing (WGS) also allows for the detection of structural variants that would be difficult to detect with traditional short-read sequencing. However, the raw unaligned Binary Alignment Map data need to be processed before analysis. There is a need for an intuitive comprehensive bioinformatic pipeline that can analyze these data. RESULTS: We present nf-core/pacvar, a comprehensive pipeline for analyzing both PacBio single-molecule PureTarget and WGS data that demultiplexes and parallelizes pre-processing, variant calling and repeat characterization. nf-core/pacvar is compatible with little configuration and has few dependencies. This pipeline enables rapid end-to-end, parallel processing of PacBio single-molecule whole genome and targeted repeat expansion sequencing. AVAILABILITY AND IMPLEMENTATION: nf-core/pacvar is available on nf-core website (https://nf-co.re/pacvar/) and on github (https://github.com/nf-core/pacvar) under MIT License (DOI: 10.5281/zenodo.14813048).

Software↗
PubMed1996

Mutations in the Drosophila pushover gene confer increased neuronal excitability and spontaneous synaptic vesicle fusion.

We describe the identification of a gene called pushover (push), which affects both behavior and synaptic transmission at the neuromuscular junction. Adults carrying either of two mutations in push exhibit sluggishness, uncoordination, a defective escape response, and male sterility. Larvae defective in push exhibit increased release of transmitter at the neuromuscular junction. In particular, the frequency of spontaneous transmitter release and the amount of transmitter release evoked by nerve stimulation are each increased two- to threefold in push mutants at the lowest external [Ca2+] tested (0.15 mM). Furthermore, these mutants are more sensitive than wild type to application of the potassium channel-blocking drug quinidine: following quinidine application, push mutants, but not wild-type, display repetitive firing of the motor axon, leading to repetitive muscle postsynaptic potentials. The push gene thus might affect both neuronal excitability and the transmitter release process. Complementation tests and recombinational mapping suggest that the push mutations are allelic to a previously identified P-element-induced mutation, which also causes behavioral abnormalities and male sterility.

Animals↗
PubMed1994

Alternate pathways for processing in the internal transcribed spacer 1 in pre-rRNA of Saccharomyces cerevisiae.

We have extended the system of Nogi et al. (Proc. Natl. Acad. Sci. USA 88, 1991, 3962-3966) for transcription of rRNA from an RNA polymerase II promoter in strains lacking functional RNA polymerase I. In our strains two differentially marked rRNA transcription units can be expressed alternately. Using this system we have shown that the A2 processing site in the internal transcribed spacer 1 (ITS1) of the pre-rRNA is dispensable. According to the accepted processing scheme, the A2 site serves to separate the parts of the primary rRNA transcript that are destined for incorporation into the two ribosomal subunits. However, we have found that, when A2 is impaired, separation of the small and large subunit rRNAs occurs at a processing site further downstream in ITS1, indicating that alternate pathways for ITS1 processing exist. Short deletions in the A2 region still allow residual processing at the A2 site. Mapping of the cleavage sites in such deletion transcripts suggests that sequences downstream of the A2 site are used for determining the position of the cleavage.

Alternative Splicing↗
PubMed2002

euGenes: a eukaryote genome information system.

euGenes is a genome information system and database that provides a common summary of eukaryote genes and genomes, at http://iubio.bio.indiana.edu/eugenes/. Seven popular genomes are included: human, mouse, fruitfly, Caenorhabditis elegans worm, Saccharomyces yeast, Arabidopsis mustard weed and zebrafish, with more planned. This information, automatically extracted and updated from several source databases, offers features not readily available through other genome databases to bioscientists looking for gene relationships across organisms. The database describes 150 000 known, predicted and orphan genes, using consistent gene names along with their homologies and associations with a standard vocabulary of molecular functions, cell locations and biological processes. Usable whole-genome maps including features, chromosome locations and molecular data integration are available, as are options to retrieve sequences from these genomes. Search and retrieval methods for these data are easy to use and efficient, allowing one to ask combined questions of sequence features, protein functions and other gene attributes, and fetch results in reports, computable tabular outputs or bulk database forms. These summarized data are useful for integration in other projects, such as gene expression databases. euGenes provides an extensible, flexible genome information system for many organisms.

Animals↗