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At least 1,171 records · Page 65Linked to original sources
PubMed2006

Additional value of integrated PET-CT in the detection and characterization of lung metastases: correlation with CT alone and PET alone.

The purpose was evaluating retrospectively the additional value of integrated positron emission tomography (PET) and computed tomography (CT) in the detection of pulmonary metastases in comparison with CT and PET alone. Fifty-six lung nodules, divided into three groups according their size, detected in 24 consecutive patients with a known primary tumor were retrospectively evaluated with integrated PET-CT, CT and PET. The nature of these nodules was determined by either histopathology or a follow-up of at least 6 months. The CT and PET images of the integrated PET-CT were evaluated separately by a radiologist and a nuclear medicine physician, the integrated PET-CT images were evaluated by a chest radiologist and nuclear medicine physician in consensus. The investigators were asked to search lung nodules and to determine whether these nodules were metastases or not. Sensitivity and accuracy for CT, PET and integrated PET-CT for characterization of all pulmonary nodules were, respectively: 100%, 90%, 100% and 57%, 55%, 55%. There was no significant difference in the characterization of pulmonary nodules between integrated PET-CT and CT alone (P=1.000) and PET alone (P=0.1306). An accurate evaluation is only possible for lesions larger than 1 cm.

Adult↗
PubMed2004

Integrated visual fields: a new approach to measuring the binocular field of view and visual disability.

BACKGROUND: We have developed a method of quantifying the central binocular visual field by merging results from monocular fields (Integrated visual field). This study aims to compare the new measure with the binocular Esterman visual field test in identifying patients with self-reported visual disability. METHODS: Forty-eight patients with glaucoma each recorded Humphrey 24-2 fields for both eyes and an Esterman on the same day, and each completed a binary forced-choice questionnaire relating to perceived visual disability. Computer software merged sensitivity values from monocular fields to generate an integrated visual field and a related score of the number of defects at the <10 dB and <20 dB level. Receiver operating characteristic (ROC) analysis was used to compare the integrated visual field score and the Esterman disability score with individual responses to the questions on perceived difficulty with visual tasks. RESULTS: Comparison of areas under ROC curves revealed that a score based on the integrated visual field was generally better (median area: 0.79) than Esterman scores (median area: 0.70) in classifying patients with or without a self-reported perceived difficulty with visual tasks. CONCLUSIONS: The integrated visual field offers a rapid assessment of a glaucoma patient's binocular visual field without extra perimetric testing. As compared to an actual binocular field test (Esterman), the integrated visual field provides a better prediction of a glaucoma patient's perceived inability to perform certain visual tasks.

Adult↗
PubMed2005

Computational modeling and exploration of contour integration for visual saliency.

We propose a computational model of contour integration for visual saliency. The model uses biologically plausible devices to simulate how the representations of elements aligned collinearly along a contour in an image are enhanced. Our model adds such devices as a dopamine-like fast plasticity, local GABAergic inhibition and multi-scale processing of images. The fast plasticity addresses the problem of how neurons in visual cortex seem to be able to influence neurons they are not directly connected to, for instance, as observed in contour closure effect. Local GABAergic inhibition is used to control gain in the system without using global mechanisms which may be non-plausible given the limited reach of axonal arbors in visual cortex. The model is then used to explore not only its validity in real and artificial images, but to discover some of the mechanisms involved in processing of complex visual features such as junctions and end-stops as well as contours. We present evidence for the validity of our model in several phases, starting with local enhancement of only a few collinear elements. We then test our model on more complex contour integration images with a large number of Gabor elements. Sections of the model are also extracted and used to discover how the model might relate contour integration neurons to neurons that process end-stops and junctions. Finally, we present results from real world images. Results from the model suggest that it is a good current approximation of contour integration in human vision. As well, it suggests that contour integration mechanisms may be strongly related to mechanisms for detecting end-stops and junction points. Additionally, a contour integration mechanism may be involved in finding features for objects such as faces. This suggests that visual cortex may be more information efficient and that neural regions may have multiple roles.

Form Perception↗
PubMed2004

Targeted DNA integration within different functional gene domains in yeast reveals ORF sequences as recombinational cold-spots.

The efficiency of gene targeting within different segments of genes in yeast was estimated by transforming yeast cells with double-stranded integrative plasmids, bearing functional gene domains [promoter (P), ORF (O) and terminator (T)] derived from the common genetic markers HIS3, LEU2, TRP1 and URA3. Transformation experiments with circular plasmids carrying a single gene domain demonstrated that the 5' and 3' flanking DNA regions (P and T) of the HIS3 and URA3 genes are preferred as sites for plasmid integration by several fold over the corresponding ORFs. Moreover, when plasmids bearing combinations of two or three regions were linearized to target them to a specific site of integration, three of the ORFs were found to be less preferred as sites for plasmid integration than their corresponding flanking regions. Surprisingly, in up to 50% of the transformants obtained with plasmids that had been linearized within coding sequences, the DNA actually integrated into neighbouring regions. Almost the same frequencies of ORF mis-targeting were obtained with plasmid vectors containing only two functional domains ("PO" or "OT") of the gene URA3, demonstrating that this event is not the consequence of competition between homologous DNA regions distal to the ORF. Therefore, we suggest that coding sequences could be considered to be "cold spots" for plasmid integration in yeast.

Aldose-Ketose Isomerases↗
PubMed1997

Restriction enzyme-mediated DNA integration in Coprinus cinereus.

Restriction enzyme-mediated DNA integration (REMI) has recently received attention as a new technique for the generation of mutants by transformation in fungi. Here we analyse this method in the basidiomycete Coprinus cinereus using the homologous pabI gene as a selectable marker and the restriction enzymes BamHI, EcoRI and PstI. Addition of restriction enzymes to transformation mixtures results in an earlier appearance of transformants and influences transformation rates in an enzyme- and concentration-dependent manner. Low concentrations of restriction enzyme result in increased numbers of transformation rates decrease with higher enzyme concentrations. If protoplasts are made from cells stored in the cold, the transformation rates drop drastically even in the presence of low amounts of enzyme. In several transformants, plasmid integration directly correlated with the action of restriction enzyme at random chromosomal restriction sites. In some cases, restriction enzymes appear to reduce the number of integration events per transformant. Simultaneously, mutation rates can be enhanced due to the presence of restriction enzymes. Although restriction enzymes clearly promote plasmid integration into the host genome they also have cytotoxic and possibly mutagenic effects that result from processes other than plasmid integration. In consequence, for any given enzyme used in REMI mutagenesis, the enzyme concentration that gives the highest number of transformants must be defined experimentally. Such optimal transformation conditions should give the highest probability of obtaining mutations caused by a single restriction enzyme-mediated integration of the selection marker.

Blotting, Southern↗
PubMed2006

Sparse cerebellar innervation can morph the dynamics of a model oculomotor neural integrator.

The oculomotor integrator is a brainstem neural network that converts velocity signals into the position commands necessary for eye-movement control. The cerebellum can independently adjust the amplitude of eye-movement commands and the temporal characteristics of neural integration, but the percentage of integrator neurons that receive cerebellar input is very small. Adaptive dynamic systems models, configured using the genetic algorithm, show how sparse cerebellar inputs could morph the dynamics of the oculomotor integrator and independently adjust its overall response amplitude and time course. Dynamic morphing involves an interplay of opposites, in which some model Purkinje cells exert positive feedback on the network, while others exert negative feedback. Positive feedback can be increased to prolong the integrator time course at virtually any level of negative feedback. The more these two influences oppose each other, the larger become the response amplitudes of the individual units and of the overall integrator network.

Algorithms↗
PubMed1990

Studies on the sedimentation behavior of the Neurospora crassa plasma membrane H(+)-ATPase synthesized in vitro and integrated into homologous microsomal membranes.

RNA transcripts that encoded the Neurospora crassa plasma membrane H(+)-ATPase (pma+), a polytopic integral membrane protein, and the pma+344, a truncated pma+ with the amino terminal 344 amino acids, were translated in a N. crassa in vitro system. The microsomal membranes integrated products were insensitive to extraction by Na2CO3 (pH 11.5). The velocity sedimentation behavior of the in vitro synthesized pma+ were examined under various conditions. The pma+ migrated on linear sucrose gradients as aggregates which were heterogeneous in size, in the regions of 9-13 S; whereas, these values were reduced when Triton X-100 was presence in the gradients. The formation of these aggregates is interpreted to suggest a mechanism that maintains this polytopic integral membrane protein in a soluble form until it is targeted to the membranes. The sedimentation coefficient of the Triton X-100 solubilized microsomal membranes integrated pma+ corresponded roughly to a monomer of the pma+. Furthermore, a comparison of the trypsin cleavage patterns of the in vitro synthesized pma+ and of the microsomal membranes integrated pma+ suggest that they have different tertiary, or quaternary, structures. The latter did not give the characteristic trypsin cleavage patterns that have been observed for the native pma+ in the presence of its ligands MgATP and vanadate (Addison, R. and Scarborough, G.A. (1982) J. Biol. Chem. 257, 10421-10426). This was interpreted to suggest that the microsomal membranes integrated pma+ cannot interact with its substrate, suggesting that it is catalytically inactive.

Cell Membrane↗
PubMed1984

Integrated electrical activity and number of zero crossings during a gradual increase in muscle force in patients with neuromuscular diseases.

In the brachial biceps muscle of 17 patients with myopathy and of 14 patients with neurogenic disorders the integrated electrical activity and number of zero crossings per unit time were analysed in 3 sites of each muscle every 100 msec during a gradual increase in force from zero to maximum within 10 sec. The analysis of integrated electrical activity could not discriminate between patients with myopathy and patients with neurogenic disorders. The slope of the linear relation between the square root of integrated electrical activity and force expressed in kilograms was increased in 44% of the patients with myopathy and in 64% of the patients with neurogenic disorders. The increase in slope may be due to increase in the ratio of electrical activity and force of individual motor units. The integrated electrical activity related to a force of 40% of maximum was decreased in about two-thirds of patients with myopathy and in about half of the patients with neurogenic disorders. This decrease in integrated electrical activity may be due to random loss of muscle fibres or to loss of whole motor units respectively. The integrated electrical activity was linearly related to mean amplitude between potential reversals per unit time (turns). The number of zero crossings was increased in 29% of the patients with myopathy and decreased in 70% of the patients with neurogenic disorders at a force of 30% of maximum. The number of zero crossings was linearly related to turns.(ABSTRACT TRUNCATED AT 250 WORDS)

Action Potentials↗
PubMed1987

Integration of human papillomavirus type 16 into cellular DNA of cervical carcinoma: preferential deletion of the E2 gene and invariable retention of the long control region and the E6/E7 open reading frames.

The integration patterns of human papillomavirus (HPV) type 16 in the cellular DNA of six cervical carcinoma samples were analyzed by the Southern blot procedure. None of the HPV integrants retained the entire viral genome. Double HPV integration was found in one case while all other cases were single integrants. In some samples, internal deletion and selective amplification of the viral sequences were observed. On integration, the E2 open reading frame (ORF) was invariably lost but the E6/E7 ORFs and the long control region of the HPV-16 genome were retained in all seven integrations analyzed and may play a role in cellular transformation and/or maintenance of the transformed phenotype.

Base Sequence↗
PubMed1994

An analysis of the temporal integration mechanism in human motion perception.

We present a model for the temporal integration of apparent motion information. The model is constructed by considering psychophysical and neurophysiological data, and consists of the leaky integration of pulsatile motion detector responses to apparent motion stimuli. Each pulse represents a motion detector populational response to a discrete spatial displacement of the spatial pattern. Temporal contrast sensitivity determines the shape of constant-stimulus-duration threshold curves for image frame exposure durations less than about 133 msec. The shape of the threshold curve for image frame exposure durations greater than about 133 msec is determined by the leaky integrator time constant and the shape of the pulses emitted by the motion detectors. The leaky integrator model exhibits threshold saturation behaviour (the reaching of a maximum sensitivity or minimum threshold) seen in psychophysical data as well as dependence of saturation time on the frame rate of the apparent motion stimulus. A low frame rate results in a longer time-to-saturation because the leaky integrator discharges more between detector output pulses. When the motion detector output pulses are far enough apart there is effectively no temporal integration and therefore no threshold improvement over time. Finally, the behaviour of the psychophysical threshold curves across spatial displacement sizes is consistent with a populational-response threshold mechanism combined with spatial summation over a non-uniform distribution of detector types across the visual field.

Adaptation, Ocular↗
PubMed1984

An electronic device for accurate quantification of neuronal mass activity based on a digital integration method.

Quantification of different kinds of neuronal mass activity was performed using an integrative method. For this purpose an electronic device was designed and constructed which is based on a fully digital approach. High precision of the method and an easy way to interface with a digital computer are the advantages of this strategy when compared to other techniques. Performance of quantification and the possibility of the universal use of the device are demonstrated by two examples. (1) Quantitative analysis of whole nerve bundle activity is demonstrated in the case of phrenic nerve mass activity. (2) The usefulness of the digital integrator is further verified in quantification of theta waves of the human EEG as a rather different field of application. In addition, the device is valuable as a tool for the analysis of EMGs. The described digital integrator has many advantages compared to conventional analog integrators, such as autorange feature, very high dynamic range, excellent long-term stability, in principle unlimited integration times and interface capability to a digital computer; it avoids all problems associated with the application of high-impedance integrator operational amplifiers.

Electroencephalography↗
PubMed1988

Regional chromosome localization of human papillomavirus integration sites near fragile sites, oncogenes, and cancer chromosome breakpoints.

The integration sites of human papillomavirus (HPV) DNA within the cervical carcinoma cell line C4-I and a primary cervical tumor were mapped by in situ hybridization. Cloned cellular sequences flanking the integrated viral DNA were used as probes. For the cell line, the viral integration site was mapped to chromosome region 8q21-q22.3, while in the primary tumor chromosome band 3p21 was the target for integration. The HPV DNA integration appears to occur in the vicinity of fragile sites, oncogenes, and chromosome breakpoints that are characteristic of hematologic malignancies and solid tumors. The integration of HPV may thus promote chromosome changes in cancer cells.

Cells, Cultured↗
PubMed1988

Identification of a chromosomal aberration associated with a hepatitis B DNA integration site in human cells.

Hepatitis B virus (HBV) DNA integrates into human cellular DNA during long-term persistent infections, implicating integration as one of the steps leading to hepatocarcinogenesis. The present study demonstrates that the integration of HBV DNA can result in or be accompanied by interchromosomal exchange of genomic material containing the integrated DNA. Unique cellular DNA to the left of an HBV DNA integration site cloned from a primary tumor mapped to chromosome 18q (18q11.1-q11.2); right hand flanking DNA mapped to chromosome #17 at a near-terminal region. The presence of chromosomal rearrangements in association with HBV integration may play a role in multistage hepatocarcinogenesis.

Carcinoma, Hepatocellular↗
PubMed1983

Stable integration of foreign DNA into the chromosome of the cyanobacterium Synechococcus R2.

The blue-green alga, Synechococcus R2, is transformed to antibiotic resistance by chimeric DNA molecules consisting of Synechococcus R2 chromosomal DNA linked to antibiotic-resistance genes from Escherichia coli. Chimeric DNA integrates into the Synechococcus R2 chromosome by homologous recombination. The efficiency of transformation, as well as the stability of integrated foreign DNA, depends on the position of the foreign genes relative to Synechococcus R2 DNA in the chimeric molecule. When the Synechococcus R2 DNA fragment is interrupted by foreign DNA, integration occurs through replacement of chromosomal DNA by homologous chimeric DNA containing the foreign insert; transformation is efficient and the foreign gene is stable. Mutagenesis in some cases attends integration, depending on the site of insertion. Foreign DNA linked to the ends of Synechococcus R2 DNA in a circular molecule, however, integrates less efficiently. Integration results in duplicate copies of Synechococcus R2 DNA flanking the foreign gene and the foreign DNA is unstable. Transformation in Synechococcus R2 can be exploited to modify precisely and extensively the genome of this photosynthetic microorganism.

Cyanobacteria↗
PubMed1984

Length of foreign DNA in chimeric plasmids determines the efficiency of its integration into the chromosome of the cyanobacterium Synechococcus R2.

The photosynthetic cyanobacterium Synechococcus R2 is efficiently transformed by DNA molecules that contain antibiotic genes from Escherichia coli linked to a segment of Synechococcus R2 chromosomal DNA. Antibiotic-resistant transformants result from integration of donor DNA into the cyanobacterial chromosome by homologous recombination. Foreign DNA interrupting the cyanobacterial sequence in the donor molecule integrates by replacement of homologous recipient DNA with donor DNA containing the foreign insert. Foreign DNA linked to the ends of the cyanobacterial fragment in a circular donor molecule integrates by a reciprocal cross-over between donor and recipient sequences. Using donor molecules that contain different lengths of foreign DNA in both of the above positions, we have determined that the probability of integration decreases by half for each increase of 2 to 3 kb in length of a foreign segment, regardless of its position in the donor molecule. The length of one of the two foreign segments has no effect on the integration of the other. Foreign DNA 20 kb in length is completely stable when it has integrated by the replacement mechanism. The ability to stably introduce large pieces of foreign DNA makes Synechococcus R2 an attractive organism in which to study and modify both native and heterologous genes involved in oxygenic photosynthesis.

Cyanobacteria↗
PubMed1990

Genomic integration system based on pBR322 sequences for the cyanobacterium Synechococcus sp. PCC7942: transfer of genes encoding plastocyanin and ferredoxin.

Synechococcus sp. PCC7942 recipient strains were constructed for the chromosomal integration of DNA fragments cloned in any pBR322-derived vector, which carries the ampicillin resistance (ApR) marker. The construction was based on the incorporation of specific recombination targets, the so-called 'integration platforms', into the chromosomal metF gene. These platforms consist of an incomplete bla gene (ApS) and the pBR322 ori separated from each other by a gene encoding an antibiotic (streptomycin or kanamycin) resistance (SmR or KmR). Recombination between a pBR322-derived donor plasmid and such a chromosomal platform results with high frequency in restoration of the bla gene and replacement of the chromosomal marker (SmR or KmR) by the insert of the donor plasmid. The integration into the platform depends on recombination between pBR322 ori and bla sequences only and is therefore independent of the DNA insert to be transferred. The desired recombinants are found by selection for a functional bla gene (ApR) and subsequent screening for absence of the chromosomal antibiotic marker. Gene transfer with this integration system was found to occur efficiently and reliably. Furthermore, the presence of the pBR322 ori in the platform allowed for 'plasmid rescue' of integrated sequences. The system was applied successfully for the transfer of the gene encoding plastocyanin (petE1) from Anabaena sp. PCC7937 and for the integration of an extra copy of the gene encoding ferredoxin I (petF1) from Synechococcus sp. PCC7942 itself.

Blotting, Northern↗
PubMed1992

Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector.

An integration vector for gene analysis in Streptomyces has been constructed. This vector replicates in Escherichia coli, and integrates into Streptomyces by homologous recombination between a cloned fragment and the genome. To overcome methylation-specific restriction barriers, an E. coli mutant triply defective in DNA methylation was constructed as a source for the integration plasmids. The frequency of integration of pVE616 derivatives into the Streptomyces avermitilis genome was proportional to the size of the cloned DNA. Derivatives of pVE616, containing fragments from pVE650, a plasmid with a 24-kb insert of S. avermitilis DNA, were used in complementation analyses of seven S. avermitilis mutants defective in glycosylation of avermectin (Av). Three complementation groups, located in a 7-kb region, were identified. Derivatives of pVE616, containing fragments from the 18-kb of DNA adjacent to the glycosylation region, were integrated into an Av producer. Av produced from the integrants was substantially reduced, indicating that the 18 kb also encodes gene products which are involved in Av biosynthesis.

Base Sequence↗
PubMed1992

Enhancer trap integrations in mouse embryonic stem cells give rise to staining patterns in chimaeric embryos with a high frequency and detect endogenous genes.

We have generated mouse embryonic stem cell lines that carry lacZ enhancer trap constructs integrated in their genome. Fifty-nine cell lines were analysed for lacZ expression in undifferentiated stem cells and at day 7.5, 8.5 and 12.5 of development in chimaeric embryos obtained after blastocyst injection. In 13 cell lines the lacZ reporter gene was expressed in undifferentiated stem cells ('blue', lines) as monitored by beta-galactosidase activity; 46 cell lines did not show detectable beta-galactosidase activity ('white', lines). In chimaeric embryos one-third of the analysed 59 embryonic stem cell lines gave rise to a variety of patterns. Six out of the 13 'blue' lines and 14 out of the 46 'white' lines showed spatially and temporally regulated patterns of beta-galactosidase expression and were additionally analysed on day 9.5. The majority of patterns showed staining exclusively or predominantly in structures of the developing nervous system, three patterns were observed only or predominantly in non-neuronal structures and five patterns were found exclusively in extraembryonic tissues. The analysis of DNA from cell lines that gave rise to staining patterns in chimaeric embryos showed that in 11 out of 15 cases simple integrations had occurred at a single site while in the remaining four cell lines multiple copies had integrated either at a single or at multiple sites. Flanking sequences from five reporter gene integrations have been cloned. At present, three integration sites have been analysed further and in all three cases we have identified transcribed sequences in the flanking DNA and isolated corresponding cDNA clones. The expression patterns of two of these genes were analysed by RNA in situ hybridisation. In both cases, expression of the endogenous genes was more widespread than the corresponding beta-galactosidase staining, suggesting that the reporter gene responded to only a subset of the regulatory elements of the endogenous gene. Our results demonstrate that enhancer trap integrations in embryonic stem cells can be used to efficiently identify transcriptional activation patterns during mouse embryogenesis and to isolate endogenous genes expressed in spatially and temporally regulated patterns.

Animals↗