SEARCH · Search PubMed

Results for “integration”

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.

SourceResearch connectionFrom yearThrough year

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

At least 721 records · Page 40Linked to original sources

PubMed1994

Signal attenuation as a function of integrator time constant and signal duration.

In some laboratories, eyeblink electromyogram is rectified and smoothed before the analog signal is digitized. The relationship among the integrator time constant, the duration of the response, and the attenuation of the data was investigated by passing a number of signals at durations of 5, 10, 20, 50, and 100 ms into a contour-following integrator (Coulbourn model S76-01), which first rectifies and then smooths (integrates) the signal. Integrator time constants of 10, 42, 70, 144, and 300 ms were used. The output of the integrator was sampled (1,000 Hz) and stored on a Macintosh SE computer. The integrator attenuated the signal, and the amount of attenuation increased as the duration of the signal decreased and as the time constant of the integrator increased. For brief inputs, the integrator does not charge fully, so only the early portion of the charge limb is present, and this early portion is the steepest part of the charge limb. Therefore, the longer the time constant, the less likely that small or brief responses will be detected.

Arousal↗

PubMed1999

Maintaining client safety and scientific integrity in research with battered women.

PURPOSE: To increase awareness of considerations of privacy and safety as well as the potential for scientific misconduct in research with battered women and other groups especially vulnerable to these concerns. Research with such vulnerable populations demands consideration of privacy and safety of participants in order to limit any potentially negative consequences while also ensuring scientific integrity. ORGANIZING FRAMEWORK: Maintaining scientific integrity and protecting vulnerable groups are important but potentially contradictory. Battered women are the examples to illustrate instances of conflict in which protecting participants may undermine scientific integrity. SOURCES: Literature on scientific integrity and misconduct, battered women, and vulnerable populations, and socially sensitive topics from nursing, other biomedical and social sciences, and the U.S. Public Health Service, 1978-1998. METHOD: Integrative literature review. FINDINGS: Conducting research with battered women in an ethically responsible manner that maintains scientific integrity without compromising advocacy or safety is possible when scientists are aware of potential conflicts and methods to ensure integrity. CONCLUSIONS: Nurses frequently do research with vulnerable groups such as battered women. Being proactive can help promote scientific integrity, avoid scientific misconduct, and decrease negative outcomes.

Battered Women↗

PubMed2003

Intergeneric conjugation in Streptomyces peucetius and Streptomyces sp. strain C5: chromosomal integration and expression of recombinant plasmids carrying the chiC gene.

Intergeneric conjugal transfer of plasmid DNA from Escherichia coli to Streptomyces circumvents problems such as host-controlled restriction and instability of foreign DNA during the transformation of Streptomyces protoplasts. The anthracycline antibiotic-producing strains Streptomyces peucetius and Streptomyces sp. strain C5 were transformed using E. coli ET12567(pUZ8002) as a conjugal donor. When this donor species, carrying pSET152, was mated with Streptomyces strains, the resident plasmid was mobilized to the recipient and the transferred DNA was also integrated into the recipient chromosome. Analysis of the exconjugants showed stable integration of the plasmid at a single chromosomal site (attB) of the Streptomyces genome. The DNA sequence of the chromosomal integration site was determined and shown to be conserved. However, the core sequence, where the crossover presumably occurred in C5 and S. peucetius, is TTC. These results also showed that the phiC31 integrative recombination is active and the phage attP site is functional in S. peucetius as well as in C5. The efficiency and specificity of phiC31-mediated site-specific integration of the plasmid in the presence of a 3.7-kb homologous DNA sequence indicates that integrative recombination is preferred under these conditions. The integration of plasmid DNA did not affect antibiotic biosynthesis or biosynthesis of essential amino acids. Integration of a single copy of a mutant chiC into the wild-type S. peucetius chromosome led to the production of 30-fold more chitinase.

Attachment Sites, Microbiological↗

PubMed1996

A novel autonomously replicating sequence (ARS) for multiple integration in the yeast Hansenula polymorpha DL-1.

Several autonomously replicating sequences of Hansenula polymorpha DL-1 (HARSs) with the characteristics of tandem integration were cloned by an enrichment procedure and analyzed for their functional elements to elucidate the mechanism of multiple integration in tandem repeats. All plasmids harboring newly cloned HARSs showed a high frequency of transformation and were maintained episomally before stabilization. After stabilization, the transforming DNA was stably integrated into the chromosome. HARS36 was selected for its high efficiency of transformation and tendency for integration. Several tandemly repeated copies of the transforming plasmid containing HARS36 (pCE36) integrated into the vicinity of the chromosomal end. Bal 31 digestion of the total DNA from the integrants followed by Southern blotting generated progressive shortening of the hybridization signal, indicating the telomeric localization of the transforming plasmids on the chromosome. The minimum region of HARS36 required for its HARS activity was analyzed by deletion analyses. Three important regions, A, B, and C, for episomal replication and integration were detected. Analysis of the DNA sequences of regions A and B required for the episomal replication revealed that region A contained several AT-rich sequences that showed sequence homology with the ARS core consensus sequence of Saccharomyces cerevisiae. Region B contained two directly repeated sequences which were predicted to form a bent DNA structure. Deletion of the AT-rich core in region A resulted in a complete loss of ARS activity, and deletion of the repeated sequences in region B greatly reduced the stability of the transforming plasmid and resulted in retarded cell growth. Region C was required for the facilitated chromosomal integration of transforming plasmids.

Base Sequence↗

PubMed1999

Bacterial conjugation protein MobA mediates integration of complex DNA structures into plant cells.

Agrobacterium tumefaciens transfers T-DNA to plant cells, where it integrates into the genome, a property that is ensured by bacterial proteins VirD2 and VirE2. Under natural conditions, the protein MobA mobilizes its encoding plasmid, RSF1010, between different bacteria. A detailed analysis of MobA-mediated DNA mobilization by Agrobacterium to plants was performed. We compared the ability of MobA to transfer DNA and integrate it into the plant genome to that of pilot protein VirD2. MobA was found to be about 100-fold less efficient than VirD2 in conducting the DNA from the pTi plasmid to the plant cell nucleus. However, interestingly, DNAs transferred by the two proteins were integrated into the plant cell genome with similar efficiencies. In contrast, most of the integrated DNA copies transferred from a MobA-containing strain were truncated at the 5' end. Isolation and analysis of the most conserved 5' ends revealed patterns which resulted from the illegitimate integration of one transferred DNA within another. These complex integration patterns indicate a specific deficiency in MobA. The data conform to a model according to which efficiency of T-DNA integration is determined by plant enzymes and integrity is determined by bacterial proteins.

Agrobacterium tumefaciens↗

PubMed1984

Random and nonrandom integration of a polyomavirus DNA molecule containing highly repetitive cellular sequences.

RmI is a circular DNA molecule that consists of a complete polyomavirus genome with an insertion (Ins) of mouse cellular DNA. This polyomavirus genome carries a mutation which renders its replication, but not its transforming ability, temperature sensitive. Ins contains both unique and repetitive cellular DNA sequences. We transfected RmI into rat cells at the permissive and nonpermissive temperatures for replication and isolated clones that had integrated RmI in their genomes. In this paper, we describe detailed mapping of the integrated RmI sequences present in 37 different cell clones. Our results indicated that transfection at the permissive temperature resulted in a random integration pattern, whereas transfection at the nonpermissive temperature resulted in a nonrandom integration pattern. The nonrandom insertions had a preferential length and preferential endpoints. We argue from these results that the nonrandom integration pattern is related to the presence of Ins and that the switch between nonrandom integration and random integration reflects a modification of the integrating substrate. When both are active, the random mechanism dominates the nonrandom mechanism.

Animals↗

PubMed1990

Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro.

Normal replication of Moloney murine leukemia virus (MoMLV) requires the integration of a DNA copy of the viral RNA genome into a chromosome of the host. In this work, we characterize the DNA sequences at the ends of the linear proviral precursor that are required for integration in the presence of MoMLV integration protein in vitro. We found that nine bases of MoMLV DNA at each end of a linear model substrate were sufficient for near-maximal levels of integration and that four bases of MoMLV DNA at each end were sufficient for low levels of correct integration. We also found that a 3'-terminal A residue was preferred for integration. We infer from the limited DNA sequence requirements for integration that factors in addition to DNA sequence direct integration protein to act at the ends of the viral DNA.

Base Sequence↗

PubMed1990

flvi-1, a common integration domain of feline leukemia virus in naturally occurring lymphomas of a particular type.

A locus in feline DNA, termed flvi-1, which may play an important role in the natural induction of lymphomas by feline leukemia virus (FeLV) was identified. Examination of a bank of 21 naturally occurring FeLV-positive feline lymphomas revealed that FeLV proviral integration occurs at flvi-1 in four independent tumors (19%). Independent integrations occurred within a 2.4-kilobase region of flvi-1, the probability of which by random chance can be estimated as 10(-16). Several lines of evidence, including sequence analysis of the long terminal repeat, demonstrated that proviruses integrated at flvi-1 are exogenously acquired and are oriented in the same transcriptional direction with respect to the locus. Molecularly cloned flvi-1 did not hybridize with probes representing several previously described proviral integration domains or with probes representing 10 oncogenes. The natural feline lymphomas examined in this study were heterogeneous with respect to tissue of origin, cell type, and number of monoclonal proviral integrations. The four tumors in which flvi-1 is interrupted were classified as members of a phenotypic subgroup containing seven lymphomas, i.e., at least four (57%) of seven lymphomas of this type contained FeLV proviral integration at flvi-1. Members of this phenotypic subgroup are non-T-cell lymphomas isolated from the spleen and contain an average of three proviruses, compared with an average of eight among all of the tumors examined. The small number of proviral integrations in tumors of this subgroup suggests that an early proviral integration event into flvi-1 can induce malignant change.

Animals↗

PubMed1991

Topoisomerase I-mediated integration of hepadnavirus DNA in vitro.

Hepadnaviruses integrate in cellular DNA via an illegitimate recombination mechanism, and clonally propagated integrations are present in most hepatocellular carcinomas which arise in hepadnavirus carriers. Although integration is not specific for any viral or cellular sequence, highly preferred integration sites have been identified near the DR1 and DR2 sequences and in the cohesive overlap region of virion DNA. We have mapped a set of preferred topoisomerase I (Topo I) cleavage sites in the region of DR1 on plus-strand DNA and in the cohesive overlap near DR2 and have tested whether Topo I is capable of mediating illegitimate recombination of woodchuck hepatitis virus (WHV) DNA with cellular DNA by developing an in vitro assay for Topo I-mediated linking. Four in vitro-generated virus-cell hybrid molecules have been cloned, and sequence analysis demonstrated that Topo I can mediate both linkage of WHV DNA to 5'OH acceptor ends of heterologous DNA fragments and linkage of WHV DNA into internal sites of a linear double-stranded cellular DNA. The in vitro integrations occurred at preferred Topo I cleavage sites in WHV DNA adjacent to the DR1 and were nearly identical to a subset of integrations cloned from hepatocellular carcinomas. The end specificity and polarity of viral sequences in the integrations allows us to propose a prototype integration mechanism for both ends of a linearized hepadnavirus DNA molecule.

Base Sequence↗

PubMed1994

In vitro integration of retrotransposon Ty1: a direct physical assay.

Retrotransposon Ty1 of Saccharomyces cerevisiae inserts a double-stranded Ty1 cDNA into the yeast genome by a reaction analogous to the integration mechanism used by retroviruses. A quantitative in vitro integration assay that directly detects integrative recombination products was developed for Ty1. Blunt-ended artificial radioactive substrates bearing Ty1 termini integrate into circular or linear target DNAs. The reaction is specific for native integrase isolated in the form of virus-like particles; virus-like particles prepared from integrase mutants were completely inactive in this assay. The products are radioactive, allowing direct detection after gel electrophoresis by autoradiography. Using this simple and amenable system, we characterized the biochemical requirements of the system and the structures of the major integration products. Two classes of products were detected: those that were the result of bona fide complete integration events (concerted reactions) and single-end joinings of substrate to target (half-reactions). Additionally, we used a genetic selection scheme to identify and characterize target sites of complete integration events into a circular target plasmid; a 5-bp target site duplication flanking the inserted DNA resembling the duplication characteristic of in vivo integration was observed.

Base Sequence↗

PubMed2005

A randomised multicentre trial of integrated versus standard treatment for patients with a first episode of psychotic illness.

OBJECTIVES: To evaluate the effects of integrated treatment for patients with a first episode of psychotic illness. DESIGN: Randomised clinical trial. SETTING: Copenhagen Hospital Corporation and Psychiatric Hospital Aarhus, Denmark. PARTICIPANTS: 547 patients with first episode of schizophrenia spectrum disorder. INTERVENTIONS: Integrated treatment and standard treatment. The integrated treatment lasted for two years and consisted of assertive community treatment with programmes for family involvement and social skills training. Standard treatment offered contact with a community mental health centre. MAIN OUTCOME MEASURES: Psychotic and negative symptoms (each scored from 0 to a maximum of 5) at one and two years' follow-up. RESULTS: At one year's follow-up, psychotic symptoms changed favourably to a mean of 1.09 (standard deviation 1.27) with an estimated mean difference between groups of -0.31 (95% confidence interval -0.55 to -0.07, P = 0.02) in favour of integrated treatment. Negative symptoms changed favourably with an estimated difference between groups of -0.36 (-0.54 to -0.17, P < 0.001) in favour of integrated treatment. At two years' follow-up the estimated mean difference between groups in psychotic symptoms was -0.32 (-0.58 to -0.06, P = 0.02) and in negative symptoms was -0.45 (-0.67 to -0.22, P < 0.001), both in favour of integrated treatment. Patients who received integrated treatment had significantly less comorbid substance misuse, better adherence to treatment, and more satisfaction with treatment. CONCLUSION: Integrated treatment improved clinical outcome and adherence to treatment. The improvement in clinical outcome was consistent at one year and two year follow-ups.

Adolescent↗

PubMed2002

Viral sequences integrated into plant genomes.

Sequences of various DNA plant viruses have been found integrated into the host genome. There are two forms of integrant, those that can form episomal viral infections and those that cannot. Integrants of three pararetroviruses, Banana streak virus (BSV), Tobacco vein clearing virus (TVCV), and Petunia vein clearing virus (PVCV), can generate episomal infections in certain hybrid plant hosts in response to stress. In the case of BSV and TVCV, one of the parents contains the integrant but is has not been seen to be activated in that parent; the other parent does not contain the integrant. The number of integrant loci is low for BSV and PVCV and high in TVCV. The structure of the integrants is complex, and it is thought that episomal virus is released by recombination and/or reverse transcription. Geminiviral and pararetroviral sequences are found in plant genomes although not so far associated with a virus disease. It appears that integration of viral sequences is widespread in the plant kingdom and has been occurring for a long period of time.

DNA Viruses↗

PubMed2000

Plasmid DNA vaccines: tissue distribution and effects of DNA sequence, adjuvants and delivery method on integration into host DNA.

A variety of factors could affect the frequency of integration of plasmid DNA vaccines into host cellular DNA, including DNA sequences within the plasmid, the expressed gene product (antigen), the formulation, delivery method, route of administration, and the type of cells exposed to the plasmid. In this report, we examined the tissue distribution and potential integration of plasmid DNA vaccines following intramuscular administration in mice and guinea pigs. We compared needle versus Biojector (needleless jet) delivery, examined the effect of aluminum phosphate adjuvants, compared the results of different plasmid DNA vaccines, and tested a gene (the human papilloma virus E7 gene) whose protein product is known to increase integration frequency in vitro. Six weeks following intramuscular injection, the vast majority of the plasmid was detected in the muscle and skin near the injection site; lower levels of plasmid were also detected in the draining lymph nodes. At early time points (1-7 days) after injection, a low level of systemic exposure could be detected. Occasionally, plasmid was detected in gonads, but it dissipated rapidly and was extrachromosomal - indicating a low risk of germline transmission. Aluminum phosphate adjuvant had no effect on the tissue distribution and did not result in a detectable increase in integration frequency. Biojector delivery, compared with needle injection, greatly increased the uptake of plasmid (particularly in skin at the injection site), but did not result in a detectable increase in integration frequency. Finally, injection of a plasmid DNA vaccine containing the human papilloma virus type 16 E7 gene, known to increase integration in vitro, did not result in detectable integration in mice. These results suggest that the risk of integration following intramuscular injection of plasmid DNA is low under a variety of experimental conditions.

Adjuvants, Immunologic↗

PubMed1985

The dependence of myocardial ultrasonic integrated backscatter on contractile performance.

We have recently shown that the cardiac cycle-dependent variation in myocardial ultrasonic integrated backscatter is blunted with regional ischemia in dogs. To determine if global and intramural regional myocardial contractile performance can be quantified by integrated backscatter, we analyzed ultrasonic responses after induction of increased and decreased contractility in five dogs. A recently developed analog data-acquisition system for measuring integrated backscatter in real time was used to sample radiofrequency signals gated from subepicardial or subendocardial regions. Base-line recordings of integrated backscatter, left ventricular pressure, left ventricular dP/dt, and wall thickness were made at 12 left ventricular sites for both intramural regions. Contractility was modified subsequently by either paired pacing or propranolol to produce significantly elevated or depressed values for maximum left ventricular dP/dt compared with baseline (1083 +/- 289 to 3001 +/- 570 mm Hg/sec; p less than .01 for all). The amplitude of the cyclic variation of integrated backscatter was 50% greater (arithmetically) in subendocardial than in subepicardial regions for all treatments (7.6 +/- 0.3 vs 6.0 +/- 0.5 dB, p less than .001). The maximum rate of change in integrated backscatter waveforms during isovolumetric contraction was faster with paired pacing and slower with propranolol than at baseline for all regions (56 +/- 6 to 74 +/- 6 to 82 +/- 5 dB/sec, p less than .005). The maximum rate of change in integrated backscatter also was greater in subendocardial than subepicardial regions (p less than .001). Thus, both regional and global differences in myocardial contractile performance are manifest quantitatively in integrated backscatter waveforms. We propose that the physiologic determinants of these differences may depend on regional and global variations in myofibril elastic characteristics.

Animals↗

PubMed1999

Clinical application of an integrated 3-phase mapping technique for localization of the site of origin of idiopathic ventricular tachycardia.

BACKGROUND: Radiofrequency (RF) catheter ablation provides curative treatment for idiopathic ventricular tachycardia (VT). METHODS AND RESULTS: Nineteen consecutive patients with an idiopathic VT underwent RF catheter ablation. An integrated 3-phase mapping approach was used, consisting of the successive application of online 62-lead body surface QRS integral mapping, directed regional paced body surface QRS integral mapping, and local activation sequence mapping. Mapping phase 1 was localization of the segment of VT origin by comparing the VT QRS integral map with a database of mean paced QRS integral maps. Mapping phase 2 was body surface pace mapping during sinus rhythm in the segment localized in phase 1 until the site at which the paced QRS integral map matched the VT QRS integral map was identified (ie, VT exit site). Mapping phase 3 was local activation sequence mapping at the circumscribed area identified in phase 2 to identify the site with the earliest local endocardial activation (ie, site of VT origin). This site became the ablation target. Ten VTs were ablated in the right ventricular outflow tract, 2 at the basal LV septum, and 7 at the midapical posterior left ventricle. A high long-term ablation success (mean follow-up duration, 14+/-9 months) was achieved in 17 of the 19 patients (89%) with a low number of RF pulses (mean, 3.3+/-2.2 pulses per patient). CONCLUSIONS: This prospective study shows that integrated 3-phase mapping for localization of the site of origin of idiopathic VT offers efficient and accurate localization of the target site for RF catheter ablation.

Adult↗

PubMed1997

Noise adaptation in integrate-and fire neurons.

The statistical spiking response of an ensemble of identically prepared stochastic integrate-and-fire neurons to a rectangular input current plus gaussian white noise is analyzed. It is shown that, on average, integrate-and-fire neurons adapt to the root-mean-square noise level of their input. This phenomenon is referred to as noise adaptation. Noise adaptation is characterized by a decrease in the average neural firing rate and an accompanying decrease in the average value of the generator potential, both of which can be attributed to noise-induced resets of the generator potential mediated by the integrate-and-fire mechanism. A quantitative theory of noise adaptation in stochastic integrate-and-fire neurons is developed. It is shown that integrate-and-fire neurons, on average, produce transient spiking activity whenever there is an increase in the level of their input noise. This transient noise response is either reduced or eliminated over time, depending on the parameters of the model neuron. Analytical methods are used to prove that nonleaky integrate-and-fire neurons totally adapt to any constant input noise level, in the sense that their asymptotic spiking rates are independent of the magnitude of their input noise. For leaky integrate-and-fire neurons, the long-run noise adaptation is not total, but the response to noise is partially eliminated. Expressions for the probability density function of the generator potential and the first two moments of the potential distribution are derived for the particular case of a nonleaky neuron driven by gaussian white noise of mean zero and constant variance. The functional significance of noise adaptation for the performance of networks comprising integrate-and-fire neurons is discussed.

Acclimatization↗

PubMed2006

Constant contour integration in peripheral vision for stimuli with good Gestalt properties.

The visual system integrates discrete but aligned local stimuli to form percept of global contours. Previous experiments using "snake" contours showed that contour integration was mainly present in foveal vision but absent or greatly weakened in peripheral vision. In this study, we demonstrated that, for contour stimuli such as circles and ellipses, which bore good Gestalt properties, contour integration for shape detection and discrimination was nearly constant from the fovea to up to 35 degrees visual periphery! Contour integration was impaired by local orientation and position jitters of contour elements, indicating that the same local contour linking mechanisms revealed with snake contour stimuli also played critical roles in integration of our good Gestalt stimuli. Contour integration was also unaffected by global position jittering up to 20% of the contour size and by dramatic shape jittering, which excluded non-contour integration processes such as detection of various local cues and template matching as alternative mechanisms for uncompromised peripheral perception of good Gestalt stimuli. Peripheral contour integration also presented an interesting upper-lower visual field symmetry after asymmetries of contrast sensitivity and shape discrimination were discounted. The constant peripheral performance might benefit from easy detection of good Gestalt stimuli, which popped out from background noise, from a boost of local contour linking by top-down influences and/or from multielement contour linking by long-range interactions.

Contrast Sensitivity↗

PubMed2005

Evaluation of integral dose in cranio-spinal axis (CSA) irradiation with conventional and helical delivery.

In cranio-spinal axis (CSA) irradiation, patients are usually treated in the prone position with junctions between cranial and spinal fields. Collimator angle and pedestal rotations are introduced to obtain coplanar alignment of the matched junction. Furthermore, daily moving junctions are commonly used to feather out the junctional dose as additional safeguards to avoid radiation myelopathy. Helical tomotherapy integrates linear accelerator and CT technology capable of delivering CSA treatment without geometric matches or feathering of junctions. The patient is treated with helical beams in the supine position. Since CSA is used mainly in the pediatric population, the potential increase in integral dose to structures or the whole body from linac- or tomotherapy-based IMRT raises concerns of increased rates of secondary malignancies. In this study, we will present an integral dose comparison between conventional CSA (3D) and helical delivery to the CSA (TOMO) utilizing the Tomotherapy Hi-ART system for three pediatric patients. Integral dose was calculated for organ at risk (OAR), two targets (PTV-BRAIN and PTV-SPINE), entire planning CT data set and to the healthy tissue (entire CT-DATA SET minus the PTV). Overall integral dose was 8% higher in the TOMO plans for Patients #1 and #3, but 2% lower in Patient #2. DVH analysis shows that TOMO plans give lower doses to larger volumes and higher doses to smaller volumes of tissue in all three cases. The advantages of the TOMO plans are minimization of matched junctions and better sparing of most OARs. With increased computational and memory power in the tomotherapy planning station, the excess integral dose to the healthy tissue can be re-distributed within the patient and in turn the total integral dose can be same or lower than in conventional delivery. The impact of a small increase in overall integral dose and the associated risks of secondary malignancies are unknown. Long-term follow-up is needed to answer this question.

Adolescent↗