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At least 559 records · Page 31Linked to original sources
PubMed2003

Scatter correction on its own increases image contrast in Tl-201 myocardium perfusion scintigraphy, but does it also improve diagnostic accuracy?

UNLABELLED: Poor and variable spatial resolution of the gamma camera, the movement of the heart and, above all, the inclusion of scattered photons in the acquisition data contribute to the deterioration of image contrast in 201Tl myocardium perfusion studies. Scatter correction algorithms may correct for the latter factor by removing (most of) the scattered photons from the acquisition data. METHODS: In this study we investigated the contrast changes induced by the Triple Energy Window scatter correction method (TEW) applied to clinical 201Tl myocardium perfusion studies and its influence on the reading of the images. Stress and rest studies of 30 consecutive patients were used for this study. Maximum image contrasts were measured between the myocardium and the left ventricular cavity in four mid-ventricular short axis slices, as well as between normally and abnormally perfused myocardium using bull's-eye displays of the activity within the myocardium. To assess image quality and perfusion abnormalities, an experienced nuclear medicine physician, blind to patient characteristics, visually reviewed all studies. RESULTS: In all individual measurements, the maximum contrast after scatter correction was higher than without correction (p < 0.001). The average increase in contrast between the myocardium and the left ventricular cavity was 43% and 48% for stress and rest studies respectively. The contrast within the myocardium increased by 25% and 32% respectively. After TEW, image quality was rated lower in almost half of the studies, while in only one study the quality was rated higher. In stress studies 11 additional perfusion defects were observed, with rest studies revealing 15 more defects after TEW, but this difference was not significant. Cohen's kappa indicated a moderate agreement of the image reading between studies with and without scatter correction. CONCLUSION: We conclude that image contrast improves significantly by scatter correction. However, image quality decreased as a result of an unfavorable signal-to-noise ratio. As an overall result, no significant change in the clinical outcome of the studies could be shown. Additional training of the readers may be required to obtain optimal results.

Adult↗
PubMed2001

SoxR-dependent response to oxidative stress and virulence of Erwinia chrysanthemi: the key role of SufC, an orphan ABC ATPase.

Erwinia chrysanthemi causes soft-rot disease in a great variety of plants. In addition to the depolymerizing activity of plant cell wall-degrading enzymes, iron acquisition and resistance to oxidative stress contribute greatly to the virulence of this pathogen. Here, we studied the pin10 locus originally thought to encode new virulence factors. The sequence analysis revealed six open reading frames that were homologous to the Escherichia coli sufA, sufB, sufC, sufD, sufS and sufE genes. Sequence similarity searching predicted that (i) SufA, SufB, SufD, SufS and SufE proteins are involved in iron metabolism and possibly in Fe-S cluster assembly; and (ii) SufC is an ATPase of an ABC transporter. The reverse transcription-polymerase chain reaction procedure showed that the sufABCDSE genes constitute an operon. Expression of a sufB:uidA fusion was found to be induced in iron-deficient growth conditions and to be repressed by the iron-sensing Fur repressor. Each of the six suf genes was inactivated by the insertion of a cassette generating a non-polar mutation. The intracellular iron level in the sufA, sufB, sufC, sufS and sufE mutants was higher than in the wild type, as assessed by increased sensitivity to the iron-activated antibiotic streptonigrin. In addition, inactivation of sufC and sufD led to increased sensitivity to paraquat. Virulence tests showed that sufA and sufC mutants exhibited reduced ability to cause maceration of chicory leaves, whereas a functional sufC gene was necessary for the bacteria to cause systemic invasion of Saintpaulia ionantha. The E. coli sufC homologue was inactivated by reverse genetic. This mutation was found to modify the soxR-dependent induction of soxS gene expression. We discuss the possibility that SufC is a versatile ATPase that can associate either with the other Suf proteins to form a Fe-S cluster-assembling machinery or with membrane proteins encoded elsewhere in the chromosome to form an Fe-S ABC exporter. Overall, these results stress the importance of the connection between iron metabolism and oxidative stress during the early steps of infection by E. chrysanthemi.

ATP-Binding Cassette Transporters↗
PubMed2004

A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high-pathogenicity island.

Diversification of bacterial species and pathotypes is largely caused by horizontal transfer of diverse DNA elements such as plasmids, phages and genomic islands (e.g. pathogenicity islands, PAIs). A PAI called high-pathogenicity island (HPI) carrying genes involved in siderophore-mediated iron acquisition (yersiniabactin system) has previously been identified in Yersinia pestis, Y. pseudotuberculosis and Y. enterocolitica IB strains, and has been characterized as an essential virulence factor in these species. Strikingly, an orthologous HPI is a widely distributed virulence determinant among Escherichia coli and other Enterobacteriaceae which cause extraintestinal infections. Here we report on the HPI of E. coli strain ECOR31 which is distinct from all other HPIs described to date because the ECOR31 HPI comprises an additional 35 kb fragment at the right border compared to the HPI of other E. coli and Yersinia species. This part encodes for both a functional mating pair formation system and a DNA-processing region related to plasmid CloDF13 of Enterobacter cloacae. Upon induction of the P4-like integrase, the entire HPI of ECOR31 is precisely excised and circularised. The HPI of ECOR31 presented here resembles integrative and conjugative elements termed ICE. It may represent the progenitor of the HPI found in Y. pestis and E. coli, revealing a missing link in the horizontal transfer of an element that contributes to microbial pathogenicity upon acquisition.

Base Sequence↗
PubMed2005

An fMRI study of verbal self-monitoring: neural correlates of auditory verbal feedback.

The ability to recognize one's own inner speech is essential for a sense of self. The verbal self-monitoring model proposes that this process entails a communication from neural regions involved in speech production to areas of speech perception. According to the model, if the expected verbal feedback matches the perceived feedback, then there would be no change in activation in the lateral temporal cortices. We investigated the neural correlates of verbal self-monitoring in a functional magnetic resonance (fMRI) study. Thirteen healthy male volunteers read aloud presented adjectives and heard their auditory feedback which was experimentally modified. Decisions about the source of the feedback were made with a button-press response. We used a 'clustered' fMRI acquisition sequence, consisting of periods of relative silence in which subjects could speak aloud and hear the feedback in the absence of scanner noise, and an event-related design which allowed separate analysis of trials associated with correct attributions and misattributions. Subjects made more misattribution responses when the feedback was a distorted version of their voice. This condition showed increased superior temporal activation relative to the conditions of hearing their own voice undistorted and hearing another person's voice. Furthermore, correct attributions during this condition were associated with greater temporal activation than misattributions. These findings support the self-monitoring model as mismatches between expected and actual auditory feedback were associated with greater temporal activation.

Adult↗
PubMed2006

A computer simulated phantom study of tomotherapy dose optimization based on probability density functions (PDF) and potential errors caused by low reproducibility of PDF.

Lung tumor motion trajectories measured by four-dimensional CT or dynamic MRI can be converted to a probability density function (PDF), which describes the probability of the tumor at a certain position, for PDF based treatment planning. Using this method in simulated sequential tomotherapy, we study the dose reduction of normal tissues and more important, the effect of PDF reproducibility on the accuracy of dosimetry. For these purposes, realistic PDFs were obtained from two dynamic MRI scans of a healthy volunteer within a 2 week interval. The first PDF was accumulated from a 300 s scan and the second PDF was calculated from variable scan times from 5 s (one breathing cycle) to 300 s. Optimized beam fluences based on the second PDF were delivered to the hypothetical gross target volume (GTV) of a lung phantom that moved following the first PDF The reproducibility between two PDFs varied from low (78%) to high (94.8%) when the second scan time increased from 5 s to 300 s. When a highly reproducible PDF was used in optimization, the dose coverage of GTV was maintained; phantom lung receiving 10%-20% prescription dose was reduced by 40%-50% and the mean phantom lung dose was reduced by 9.6%. However, optimization based on PDF with low reproducibility resulted in a 50% underdosed GTV. The dosimetric error increased nearly exponentially as the PDF error increased. Therefore, although the dose of the tumor surrounding tissue can be theoretically reduced by PDF based treatment planning, the reliability and applicability of this method highly depend on if a reproducible PDF exists and is measurable. By correlating the dosimetric error and PDF error together, a useful guideline for PDF data acquisition and patient qualification for PDF based planning can be derived.

Artifacts↗
PubMed2003

Implementation of a fast 16-Bit dynamic clamp using LabVIEW-RT.

The dynamic-clamp method provides a powerful electrophysiological tool for creating virtual ionic conductances in living cells and studying their influence on membrane potential. Here we describe G-clamp, a new way to implement a dynamic clamp using the real-time version of the Lab-VIEW programming environment together with a Windows host, an embedded microprocessor that runs a real-time operating system and a multifunction data-acquisition board. The software includes descriptions of a fast voltage-dependent sodium conductance, delayed rectifier, M-type and A-type potassium conductances, and a leak conductance. The system can also read synaptic conductance waveforms from preassembled data files. These virtual conductances can be reliably implemented at speeds < or =43 kHz while simultaneously saving two channels of data with 16-bit precision. G-clamp also includes utilities for measuring current-voltage relations, synaptic strength, and synaptic gain. Taking an approach built on a commercially available software/hardware platform has resulted in a system that is easy to assemble and upgrade. In addition, the graphical programming structure of LabVIEW should make it relatively easy for others to adapt G-clamp for new experimental applications.

Analog-Digital Conversion↗
PubMed2002

Variables affecting naming latency for Japanese Kanji: a re-analysis of Yamazaki, et al. (1997).

Yamazaki, Ellis, Morrison, and Lambon Ralph in 1997 demonstrated that written and spoken age-of-acquisitions had a stronger effect on the naming latency of single Kanji words than any other variable including familiarity. The present study was designed to reanalyze Yamazaki, et al.'s data, using the ratings of written and spoken age-of-acquisitions and visual and auditory familiarities taken from the NTT lexical database. This analysis showed that visual familiarity exerted a stronger independent effect on naming latency than two types of age-of-acquisitions.

Adolescent↗
PubMed1976

The development and functional control of reading-comprehension behavior.

Reading comprehension, indicated by motor behavior and multiple-choice picture selection called for in written instructions, was taught to an autistic child using verbal prompts, modelling, and physical guidance. The child was rewarded for correct behaviors to training items; nonrewarded probes were used to assess generalization. Probable maintaining events were assessed through their sequential removal in a reversal design. Results showed: (a) following acquisition, performance was maintained at a near-100% level when candy, praise, attention, and training were removed, (b) absence of other persons was correlated with a marked decrease in performance, whereas their presence was associated with performance at near 100%, and (c) performance generalized to probes and across experimenters. Rewards, which may have been reinforcing during acquisition, did not appear necessary to maintain later performance. Instead, presence of others (a setting event) was demonstrated to have control over maintained performance.

Autistic Disorder↗
PubMed2006

Direct detector radiography versus dual reading computed radiography: feasibility of dose reduction in chest radiography.

The image quality of dual-reading computed radiography and dose-reduced direct radiography of the chest was compared in a clinical setting. The study group consisted of 50 patients that underwent three posteroanterior chest radiographs within minutes, one image obtained with a dual read-out computed radiography system (CR; Fuji 5501) at regular dose and two images with a flat panel direct detector unit (DR; Diagnost, Philips). The DR images were obtained with the same and with 50% of the dose used for the CR images. Images were evaluated in a blinded side-by-side comparison. Eight radiologists ranked the visually perceivable difference in image quality using a three-point scale. Then, three radiologists scored the visibility of anatomic landmarks in low and high attenuation areas and image noise. Statistical analysis was based on Friedman tests and Wilcoxon rank sum tests at a significance level of P<0.05. DR was judged superior to CR for the delineation of structures in high attenuation areas of the mediastinum even when obtained with 50% less dose (P<0.001). The visibility of most pulmonary structures was judged equivalent with both techniques, regardless of acquisition dose and speed level. Scores for image noise were lower for DR compared with CR, with the exception of DR obtained at a reduced dose. Thus, in this clinical preference study, DR was equivalent or even superior to the most modern dual read-out CR, even when obtained with 50% dose. A further dose reduction does not appear to be feasible for DR without significant loss of image quality.

Adult↗
PubMed1987

Distribution of mitochondrial introns in the species Schizosaccharomyces pombe and the origin of the group II intron in the gene encoding apocytochrome b.

The mitochondrial genome size of 26 different Schizosaccharomyces pombe strains varies between 17.6 and 24.6 kilobase pairs due to the presence or absence of introns. One of these is the group II intron in the gene encoding apocytochrome b (cob: intron cobI1). Partial DNA sequences of continuous cob genes from six strains (including strain EF1: Trinkl et al. 1985) revealed identical nucleotide sequence in the region where the group II intron is inserted in the mosaic form of the gene. In contrast, analysis of the mosaic cob gene in strain UCD-FstI revealed several base pair changes in the exon regions flanking the splice point, compared with the continuous genes and with the mosaic cob gene in strain 50 (Lang et al. 1985). The base pair differences between the exons of the two mosaic cob genes and the identity of exons in all continuous cob genes argue in favour of the two cob introns in strains 50 and UCD-FstI as independent later acquisitions of the genes, rather than loss of the intron from a common mosaic ancestor of all strains. Other introns present in some but not all strain include two group I introns without open reading frame in the gene encoding subunit 1 of cytochrome c oxidase (cox1: introns cox1I2a and cox1I3), and two group I introns with open reading frames in the same gene (introns cox1I1 and cox1I2b).

Apoproteins↗
PubMed1999

Impact of electronic imaging on clinician behavior in the urgent care setting.

Although it is intuitively valuable that more expedient delivery of radiographic images and reports to clinicians would improve patient care, it is important to document these outcomes to validate further advances in these areas. We evaluated the care of 215 patients seen at a walk-in clinic to determine what benefit digital imaging is to the patient. Cohorts consisted of all patients for whom specified radiology examinations were ordered during a 7-day period. The first cohort was recruited when analog films were used. The second cohort received examinations performed with computed radiography (CR) acquisition and computer display, which had been in use for 2 years. Patients were categorized as to the type of study they received, as well as whether a staff radiologist was immediately available to read the study. Clinical behavior was characterized by outcome measures of time to final diagnosis, time to final treatment, and need for follow-up. Our analysis demonstrated a reduction in time to final diagnosis that was better appreciated during the times when a staff radiologist was not immediately available. It also suggested that greater time reductions were seen for patients who received extremity examinations than those who received chest, sinus, or rib films. These data suggest that digital imaging is a useful tool to improve clinical outcome of patients seen in the acute care setting.

Adult↗
PubMed2005

Highly polymorphic vitelline-coat protein HaVC80 from the ascidian, Halocynthia aurantium: structural analysis and involvement in self/nonself recognition during fertilization.

Ascidians release sperm and eggs simultaneously, but self-fertilization is effectively blocked by unknown mechanisms. We previously reported that a 70-kDa sperm receptor HrVC70 on the egg vitelline coat (VC) consisting of 12 EGF-like repeats is a candidate self/nonself recognition molecule during fertilization of the ascidian, Halocynthia roretzi. Here, we report that Halocynthia aurantium also utilizes a homolog (HaVC80) of HrVC70 as an allorecognizable sperm receptor. HaVC80 is attached to the VC during the acquisition of self-sterility and is detached from the VC by acid treatment, allowing self-fertilization. A cDNA clone of the HaVC80 precursor, HaVC130, consists of 3726 nucleotides and encodes an open reading frame of 1208 amino acids. The structure of HaVC130 is very similar to the HrVC70 precursor HrVC120, but the number of EGF-like repeats of HaVC130/VC80 is one repeat larger than that of HrVC120/VC70. There are several amino acid substitutions between different individuals, and two alleles of the HaVC80 sequence were detected in each individual. Genomic DNA sequence analysis reveals that each EGF-like domain corresponds to a specific exon, and HaVC130 may have been evolutionarily generated from HrVC120 by duplication of the 8th EGF-like repeat. The data support the hypothesis that HaVC80 is a highly polymorphic protein responsible for self-sterility in H. aurantium.

Animals↗
PubMed2000

Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications.

A compact time-resolved near-IR fluorescence imager was constructed to obtain lifetime and intensity images of DNA sequencing slab gels. The scanner consisted of a microscope body with f/1.2 relay optics onto which was mounted a pulsed diode laser (repetition rate 80 MHz, lasing wavelength 680 nm, average power 5 mW), filtering optics, and a large photoactive area (diameter 500 microns) single-photon avalanche diode that was actively quenched to provide a large dynamic operating range. The time-resolved data were processed using electronics configured in a conventional time-correlated single-photon-counting format with all of the counting hardware situated on a PC card resident on the computer bus. The microscope head produced a timing response of 450 ps (fwhm) in a scanning mode, allowing the measurement of subnano-second lifetimes. The time-resolved microscope head was placed in an automated DNA sequencer and translated across a 21-cm-wide gel plate in approximately 6 s (scan rate 3.5 cm/s) with an accumulation time per pixel of 10 ms. The sampling frequency was 0.17 Hz (duty cycle 0.0017), sufficient to prevent signal aliasing during the electrophoresis separation. Software (written in Visual Basic) allowed acquisition of both the intensity image and lifetime analysis of DNA bands migrating through the gel in real time. Using a dual-labeling (IRD700 and Cy5.5 labeling dyes)/two-lane sequencing strategy, we successfully read 670 bases of a control M13mp18 ssDNA template using lifetime identification. Comparison of the reconstructed sequence with the known sequence of the phage indicated the number of miscalls was only 2, producing an error rate of approximately 0.3% (identification accuracy 99.7%). The lifetimes were calculated using maximum likelihood estimators and allowed on-line determinations with high precision, even when short integration times were used to construct the decay profiles. Comparison of the lifetime base calling to a single-dye/four-lane sequencing strategy indicated similar results in terms of miscalls, but reduced insertion and deletion errors using lifetime identification methods, improving the overall read accuracy.

DNA↗
PubMed2002

The 3'-untranslated region of the dystrophin gene - conservation and consequences of loss.

The 3'-untranslated region (3'UTR) of some vertebrate dystrophin genes shows an extraordinary degree and extent of conservation (better than that of many coding regions), a phenomenon that remains unexplained. We examine novel sequence and mutational data to explore the possible reasons for this. We show that loss of the human dystrophin 3'UTR is sufficient to cause Becker muscular dystrophy with pronounced reduction in dystrophin protein levels. The acquisition of dystrophin 3'UTR sequence from an amphibian and a cartilaginous fish allows us to refine previously identified functionally constrained regions which might account for the observed phenotype. These comprise (a) the open reading frame encoding the ancestral 'alternative' amphipathic C-terminal alpha-helix, normally removed from adult dystrophin by inclusion of a poorly conserved frameshifting penultimate exon, and (b) two highly conserved untranslated regions ('Lemaire A', 350 nucleotides and 'Lemaire D', 250 nucleotides) separated by a non-conserved 700-2000-nucleotide spacer. We consider the possibility that the 3'UTR may represent a significant target for pathogenic mutations.

3' Untranslated Regions↗
PubMed2003

Advances in EELS spectroscopy by using new detector and new specimen preparation technologies.

First results obtained with a Gatan UHV Enfina system, which was attached to a VG HB 501 UX dedicated STEM, are reported. The Enfina system is based on a CCD detector and offers, compared to the previously used photodiode array, a narrower point-spread function, higher sensitivity, and faster read-out capabilities. These improvements are demonstrated with electron energy-loss measurements on various oxides, such as Al2O3, TiO2 and SrTiO3. It is shown that a better energy resolution is achieved and that acquisition of high-energy absorption edges with a reasonable signal-to-noise ratio becomes possible. Furthermore, we report on the influence of the TEM specimen quality on the energy-loss spectra. Thin amorphous layers at the specimen surfaces, which are induced by ion-milling processes, can modify specific electron energy-loss near-edge structure features. We found that for the investigated ceramics the use of low-energy ion-milling systems is highly recommended, since the loss of energy-loss near-edge structure details by the presence of the amorphous layers is considerably reduced. This is especially true for very thin specimens.

Journal Article↗
PubMed2002

Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing.

A "gene-island" sequencing strategy has been developed that expedites the targeted acquisition of orthologous gene sequences from related species for comparative genome analysis. A 152-kb bacterial artificial chromosome (BAC) clone from sorghum (Sorghum bicolor) encoding phytochrome A (PHYA) was fully sequenced, revealing 16 open reading frames with a gene density similar to many regions of the rice (Oryza sativa) genome. The sequences of genes in the orthologous region of the maize (Zea mays) and rice genomes were obtained using the gene-island sequencing method. BAC clones containing the orthologous maize and rice PHYA genes were identified, sheared, subcloned, and probed with the sorghum PHYA-containing BAC DNA. Sequence analysis revealed that approximately 75% of the cross-hybridizing subclones contained sequences orthologous to those within the sorghum PHYA BAC and less than 25% contained repetitive and/or BAC vector DNA sequences. The complete sequence of four genes, including up to 1 kb of their promoter regions, was identified in the maize PHYA BAC. Nine orthologous gene sequences were identified in the rice PHYA BAC. Sequence comparison of the orthologous sorghum and maize genes aided in the identification of exons and conserved regulatory sequences flanking each open reading frame. Within genomic regions where micro-colinearity of genes is absolutely conserved, gene-island sequencing is a particularly useful tool for comparative analysis of genomes between related species.

Base Sequence↗
PubMed1995

Purification, characterization, and genetic analysis of Mycobacterium tuberculosis urease, a potentially critical determinant of host-pathogen interaction.

Mycobacterium tuberculosis urease (urea amidohydrolase [EC 3.5.1.5]) was purified and shown to contain three subunits: two small subunits, each approximately 11,000 Da, and a large subunit of 62,000 Da. The N-terminal sequences of the three subunits were homologous to those of the A, B, and C subunits, respectively, of other bacterial ureases. M. tuberculosis urease was specific for urea, with a Km of 0.3 mM, and did not hydrolyze thiourea, hydroxyurea, arginine, or asparagine. The enzyme was active over a broad pH range (optimal activity at pH 7.2) and was remarkably stable against heating to 60 degrees C and resistant to denaturation with urea. The enzyme was not inhibited by 1 mM EDTA but was inhibited by N-ethylmaleimide, hydroxyurea, acetohydroxamate, and phenylphosphorodiamidate. Urease activity was readily detectable in M. tuberculosis growing in nitrogen-rich broth, but expression increased 10-fold upon nitrogen deprivation, which is consistent with a role for the enzyme in nitrogen acquisition by the bacterium. The gene cluster encoding urease was shown to have organizational similarities to urease gene clusters of other bacteria. The nucleotide sequence of the M. tuberculosis urease gene cluster revealed open reading frames corresponding to the urease A, B, and C subunits, as well as to the urease accessory molecules F and G.

Amino Acid Sequence↗