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PubMed2006

Treatment integrity in a home-based pre-reading intervention programme.

Treatment integrity is an underexposed issue in the phonological awareness intervention research. The current study assessed the integrity of treatment of the families (N = 32) participating in the experimental condition of a home-based pre-reading intervention study. The participating kindergartners were all genetically at risk for developing dyslexia. Two aspects of treatment integrity, the number of lessons completed (quantity) and the quality of the administration of the programme (observed in a videotaped session), were investigated. The level of treatment integrity turned out to be 66% when completion of all lessons was taken as quantitative criterion, and about 74% when quality of the parent-child interaction was assessed. The two measures could predict the pre-reading skills at the end of kindergarten. Together they accounted for 43% of the variance in this dependent variable. Together with pre-reading scores at the pre-test the total predicted variance was 87%. The number of lessons completed still contributed 12% to the prediction after controlling for pre-test scores. The results indicated that treatment integrity indeed appears to be an important aspect of treatment outcome and should therefore be included in intervention studies.

Dyslexia↗
PubMed2004

Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration.

Nuclear mitochondrial DNA sequences (NUMTs) are common in eukaryotes. However, the mechanism by which they integrate into the nuclear genome remains a riddle. We analyzed 247 NUMTs in the human nuclear DNA (nDNA), along with their flanking regions. This analysis revealed that some NUMTs have accumulated many changes, and thus have resided in the nucleus a long time, while others are >94% similar to the reference human mitochondrial DNA (mtDNA), and thus must be recent. Among the latter, two NUMTs, encompassing the COI gene, carry a set of transitions characteristic of the extant African-specific L macrohaplogroup mtDNAs and are more homologous to human mtDNA than to chimp. Screening for one of these NUMTs revealed its presence in all human samples tested, confirming that the African macrohaplogroup L mtDNAs were present in the earliest modern humans and thus were the first human mtDNAs. An analysis of flanking sequences of the NUMTs revealed that 59% were within 150 bp of repetitive elements, with 26% being within 15 bp of and 33% being within 15-150 bp of repetitive elements. Only 14% were integrated into a repetitive element. This association of NUMTs with repetitive elements is highly nonrandom (p<0.001). These data suggest that the vicinity of transposable elements influences the ongoing integration of mtDNA sequences and their subsequent duplication within the nDNA. Finally, NUMTs appear to preferentially integrate into DNA with different GC content than the surrounding chromosomal band. Our results suggest that chromosomal structure might influence integration of NUMTs.

Africa↗
PubMed1994

Identification of integrated Epstein-Barr virus in nasopharyngeal carcinoma using pulse field gel electrophoresis.

Integrated Epstein-Barr virus (EBV) was found in 4 of 17 pathologically diagnosed, EBV-positive nasopharyngeal carcinoma (NPC) biopsy samples using pulse field gel electrophoresis (PFGE). The analyses were carried out after digestion of biopsy DNA with rare restriction enzymes such as PacI, which does not cleave EBV due to the absence of the recognition sequence, and ClaI. Employing this technique, EBV integration in IB4, through EcoI, and Namalwa through the terminal repeats, was confirmed. We also established that integration of EBV in AW Ramos was through the terminal repeats. The Raji cell line was also found to harbour integrated virus in addition to episomal DNA. However, the site of integration could not be confirmed, since as the Raji DNA appeared to be heavily methylated and could not be cleaved with CPG rare cutters. As in the Raji cell line, the DNA of EBV in nasopharyngeal-carcinoma (NPC) biopsies also appeared to be methylated.

Animals↗
PubMed1995

The Agrobacterium tumefaciens virulence D2 protein is responsible for precise integration of T-DNA into the plant genome.

The VirD2 protein of Agrobacterium tumefaciens was shown to pilot T-DNA during its transfer to the plant cell nucleus. We analyze here its participation in the integration of T-DNA by using a virD2 mutant. This mutation reduces the efficiency of T-DNA transfer, but the efficiency of integration of T-DNA per se is unaffected. Southern and sequence analyses of integration events obtained with the mutated VirD2 protein revealed an aberrant pattern of integration. These results indicate that the wild-type VirD2 protein participates in ligation of the 5'-end of the T-strand to plant DNA and that this ligation step is not rate limiting for T-DNA integration.

Agrobacterium tumefaciens↗
PubMed2005

Poly(D,L-lactide) coating is capable of enhancing osseous integration of Schanz screws in the absence of infection.

Pin loosening is a major complication in external fixation. Biological and mechanical conditions play an important role in the maintenance and enhancement of the implant-bone interface in fracture fixation. It is thought that biodegradable coatings may be capable of preventing pin track infection and pin loosening. The goal of this study was therefore to analyze the influence of a biodegradeable coating on the osseous integration of Schanz' screws during fracture treatment. Standardized osteotomies (3-mm fracture gap) of the right tibiae were performed on 16 sheep and stabilized by an AO mono-lateral external fixator. Additional, mechanically less loaded Schanz' screws were also mounted. All screws were randomly coated with biodegradable poly(D,L-lactide). The sheep were sacrificed after 9 weeks. All screws were removed and rolled on blood agar plates for microbiological analysis. Histological sections of the pin tracks were histochemically and morphometrically analyzed. Clinically, no signs of severe infection were visible. Microbiological analysis revealed 14.8% colonization by Staphylococcus aureus in the coated and 29% in the uncoated screws. Histomorphometry of the bone surrounding the Schanz' screws revealed that significantly more osseous integration had occurred on poly(D,L-lactide)-coated screws in the absence of bacterial colonization. Significantly more bone remodeling and a higher osteoclastic activity was seen near the screw-bone interface in the uncoated screw group. Up to a threefold increase in new bone formation and more severe remodeling was observed around the screw entry compared to the pin exit in all groups. Loaded screws showed significantly more callus formation around the exit sites than their less loaded counterparts. In the present study, poly(D,L-lactide) coating of Schanz' screws was found to enhance osseous integration in the absence of bacterial colonization in sheep by causing less cortical remodeling and less osteoclastic activity in the cortices compared to uncoated screws. Additionally, the coating appeared to reduce the instances of pin track infections. Mechanical loading showed an adverse effect on bone formation and remodeling. It has been shown that both biological and mechanical factors play an important role in the maintenance of osseous integrity of the pin-bone interface. Poly(D,L-lactide) coating of Schanz' screws does not prevent osseous destruction and severe bacterial colonization along the pin tracts, but can improve osseous integration of Schanz' screws in the absence of infection.

Agar↗
PubMed2004

Modularity and integration in the hominoid scapula.

In this paper, several hypotheses of morphological integration within the hominoid (ape) scapula are tested. In particular, whether the scapula represents a set of developmental tissues sharing tight correlations between constituent parts (i.e., highly integrated) or is more modularly organized (i.e., covariation is greater within regions than between) is tested. Whether the patterns of integration in the scapula have changed over phylogenetic time or in response to selective forces is also examined. Results from two different analyses (matrix correlations and edge deviance) indicate traits comprising the blade and acromion, and to a weaker degree the glenoid, correlate highly with each other. The coracoid exhibits more independence from other parts of the scapula, perhaps reflecting its distinct evolutionary developmental history. Overall, similarity in species-specific patterns of correlation was high between all taxa. Correlation matrix similarity was significantly correlated with functional similarity and morphological distance, but not with phylogenetic distance. These results are congruent with other studies of integration that suggest correlation patterns remain stable over evolutionary time. There are changes associated with phylogeny, but the tight link between functional similarity and phylogenetic distance at this level of comparison presents possible challenges to interpretation. Overall similarities in the pattern of integration in all taxa might be better interpreted as relative strengthening or weakening of trait correlations rather than broadscale changes in the pattern of relationship between developmental regions. Larger sample sizes with greater taxonomic/functional breadth, and finer scale analyses of patterns of correlation are needed to test these hypotheses further.

Animals↗
PubMed1987

Presence of episomal and integrated human papillomavirus DNA sequences in cervical carcinoma.

Thirty surgical samples of squamous cell carcinoma of the cervix obtained from Chinese women were analysed for the presence of human papillomavirus (HPV) types 16 and 18 using Southern blot hybridization procedure. HPV16 was detected in 53% while HPV18 was found in only 6% of the samples analyzed. When compared with other reports, variation in the geographic distribution of these two HPV types in association with cervical carcinoma is noted. Thirty-seven and a half percent of the HPV16-positive samples contained this HPV type in episomal form and an equal number in cellular DNA-integrated form. The simultaneous presence of both episomal and integrated forms was found in the remaining 25% of the positive samples. The two HPV18-positive cases harbored only episomal viral genome and were not superinfected by HPV16. Analysis of the HPV16 integration samples showed that single integration events had probably occurred and some of the viral sequences had been lost on or subsequent to integration.

Carcinoma, Squamous Cell↗
PubMed2003

Sensorimotor integration in movement disorders.

Although current knowledge attributes movement disorders to a dysfunction of the basal ganglia-motor cortex circuits, abnormalities in the peripheral afferent inputs or in their central processing may interfere with motor program execution. We review the abnormalities of sensorimotor integration described in the various types of movement disorders. Several observations, including those of parkinsonian patients' excessive reliance on ongoing visual information during movement tasks, suggest that proprioception is defective in Parkinson's disease (PD). The disturbance of proprioceptive regulation, possibly related to the occurrence of abnormal muscle-stretch reflexes, might be important for generating hypometric or bradykinetic movements. Studies with somatosensory evoked potentials (SEPs), prepulse inhibition, and event-related potentials support the hypothesis of central abnormalities of sensorimotor integration in PD. In Huntington's disease (HD), changes in SEPs and long-latency stretch reflexes suggest that a defective gating of peripheral afferent input to the brain might impair sensorimotor integration in cortical motor areas, thus interfering with the processing of motor programs. Defective motor programming might contribute to some features of motor impairment in HD. Sensory symptoms are frequent in focal dystonia and sensory manipulation can modify the dystonic movements. In addition, specific sensory functions (kinaesthesia, spatial-temporal discrimination) can be impaired in patients with focal hand dystonia, thus leading to a "sensory overflow." Sensory input may be abnormal and trigger focal dystonia, or defective "gating" may cause an input-output mismatch in specific motor programs. Altogether, several observations strongly support the idea that sensorimotor integration is impaired in focal dystonia. Although elemental sensation is normal in patients with tics, tics can be associated with sensory phenomena. Some neurophysiological studies suggest that an altered "gating" mechanism also underlies the development of tics. This review underlines the importance of abnormal sensorimotor integration in the pathophysiology of movement disorders. Although the physiological mechanism remains unclear, the defect is of special clinical relevance in determining the development of focal dystonia.

Animals↗
PubMed1988

Evaluation of manual methods for integration of in vivo phosphorus NMR spectra.

Eight human subjects measured peak integrals from a set of simulated 31P NMR spectra by triangulation, by extrapolation of tangents from the baseline of computed integrals, and by cursor demarcation of computed integrals using standard commercial software. The test spectra were qualitatively similar to phosphorus spectra routinely acquired from mammalian skeletal muscle. All three of the above methods were found to underestimate the areas of relatively broad peaks (e.g., ATP peaks were underestimated by 20-40%), even when the peak signal/rms-noise ratio was better than 8/1. This bias resulted in major errors in calculated metabolite ratios. Of the three methods, triangulation was the least accurate, and showed the greatest variation between subjects. Cursor demarcation of computed integrals was the most accurate manual method. The same test spectra were also integrated by two fully-automated fitting algorithms. Although not free of bias, these methods were generally superior to the manual methods.

Adult↗
PubMed2004

Integrated first- and second-trimester Down syndrome screening test among unaffected IVF pregnancies.

OBJECTIVE: The aim of the current study was to assess the profile of markers that constitute the integrated test and to measure its false-positive rates (FPR) among a preselected group of unaffected IVF pregnancies. These results were compared with the reference laboratory values that reflect the general obstetric population, which underwent the same investigative protocol. METHODS: Ninety-nine unaffected singletons from IVF-pregnant women and 1781 controls, all evaluated by the same laboratory, underwent a nondisclosure integrated Down syndrome screening test. This test comprised first-trimester nuchal translucency (NT) and pregnancy-associated plasma protein-A (PAPP-A) assessment, followed by a midgestation quadruple test. Only upon completion of the integrated screening test, the parturient women were informed of its results. RESULTS: The mean maternal age of the study and the control group was 32.2 +/- 4 and 30.4 +/- 4 years respectively (t-test <0.005). The marker levels were expressed as multiples of the gestation-specific normal medians. The IVF group had lower PAPP-A (0.78 vs 1.03, t-test P < 0.05) and higher NT (1.14 vs 1.01, t-test P < 0.05) values, respectively. All the other markers were similar for both groups. On the basis of the integrated test, a higher rate of IVF pregnancies were defined as being screen-positive (6.1% vs 3.7%), although the values did not reach a level of statistical significance. CONCLUSIONS: Since NT alone yielded the same FPR as the integrated test, the option of various sonographic screening combinations in this group warrants further investigation.

Chorionic Gonadotropin↗
PubMed2001

Progesterone receptors as neuroendocrine integrators.

Intracellular progesterone receptors (PRs) are ligand-inducible transcription factors that mediate the majority of the effects of progesterone (P) on neuroendocrine functions. During the past decade, evidence has accumulated which suggest that PRs can also be activated independently of P, by signals propagated through membrane-bound receptors to the interior of cells. The activation of PRs by this type of "cross-talk" mechanism has been implicated in the physiological regulation of several important neuroendocrine processes, including estrous behavior and periovulatory hormone secretions. We review evidence that both ligand-dependent and ligand-independent activation of PRs occurs in central neurons and in anterior pituitary cells and that the convergence and summation of these signals at the PR serves to integrate neural and endocrine signals which direct several critically important neuroendocrine processes. An integrative function for PRs is reviewed in several physiological contexts, including the display of lordosis behavior in female rodents, the neurosecretion of gonadotropin-releasing hormone surges, secretion of preovulatory gonadotropin surges, and release of periovulatory follicle stimulating hormone surges. The weight of evidence indicates that cross talk at the intracellular PR is an essential component of the integrative mechanisms that direct each of these neuroendocrine events. The recurrence of PR's integrative actions in several different physiological contexts suggests that other intracellular steroid receptors similarly function as integrators of neural and endocrine signals in other neuroendocrine processes.

Animals↗
PubMed2001

Developing decision support systems for integrated coastal management in the tropics: is the ICM decision-making environment too complex for the development of a useable and useful DSS?

Integrated coastal management in the tropics requires the conservation of vulnerable and diverse ecosystems such as coral reefs and mangroves as well as the management of land and marine-based human activities. Decision-making for integrated coastal management involves multiple decision-makers and multiple stakeholders often with conflicting needs and interests. Decision support systems can be developed to improve our understanding of the inter-relationships between the natural and socio-economic variables and hence result in improved decision-making. The question is whether this decision making environment is actually too complex for the development of useful and useable decision support systems. This paper describes the components of the decision making environment and the components of a decision support system. It also explores the various techniques available to deal with different modelling needs, the constraints of inadequate data and the multi-objective decision making environment. In addition, different techniques of developing decision support systems can play important roles within integrated coastal management. Three coastal decision support systems are evaluated in terms of their design and role in integrated coastal management and are used to evaluate the potential to develop decision support systems for integrated coastal management.

Animals↗
PubMed2002

Event-related fMRI reveals cortical sites involved in contextual sentence integration.

We examined the effects of difficulty of sentential integration on blood oxygenation level-dependent contrast changes. Difficulty of integration was operationalized as the degree to which sentence-final nouns matched the expectations generated by preceding context. Nine young adults read short sentence fragments (e.g., "The pilot flies.") which were completed by highly expected nouns (e.g., "the plane"), unexpected yet semantically legal nouns (e.g., "the kite"), nouns that violated the verbs' selection restriction rules (e.g., "the book"), and pseudowords (e.g., "the foop") and made quick lexical decisions on the sentence-final item. Overall, word completions resulted in higher changes in activation than pseudoword completions. The largest of those changes were observed in left angular and posterior middle temporal gyri, suggesting that despite the lexical nature of the task, word stimuli embedded in sentence contexts triggered integrative-semantic processes beyond a lexical level. A region-of-interest analysis in left inferior frontal and left posterior middle temporal areas revealed activation for both unexpected and anomalous completions when compared to expected completions. Thus, while the underlying processing mechanisms may differ, sentential integration appears similarly effortful for these two types of completions. Our findings are consistent with previous reports of local increases in activation as a function of (syntactic) complexity, while extending the findings to processing demands of semantic integration. Because of its sensitivity to changes in semantic congruence and the implicit nature of the task involved, we argue that the present paradigm is well suited to study patients with potential semantic deficits after brain damage.

Adult↗
PubMed1997

Unmarked gene integration into the chromosome of Mycobacterium smegmatis via precise replacement of the pyrF gene.

After integration into the bacterial chromosome an exogenous gene may be stably expressed without continued selection for the recombinant locus. However, chromosomal integration events occur infrequently, requiring the concomitant integration of a drug resistance marker in order to identify colonies of recombinant cells. The generation of a drug-resistant recombinant strain can both reduce the in vivo applicability of the strain and preclude the use of recombinant vectors which use the same drug resistance marker. We have constructed a plasmid, pINT-delta, which allows recombination of exogenous genes onto the Mycobacterium smegmatis chromosome. The exogenous gene completely replaces the pyrF gene and the resultant strain lacks any exogenous drug resistance marker. The methodologies described herein are general and applicable even to those bacteria for which extrachromosomal plasmids are not available. Using pINT-delta we integrated the lacZ gene into the M. smegmatis chromosome via a precise exchange of lacZ and pyrF. The resultant strain was used to demonstrate that the expression of genes integrated at the pyrF locus is repressed twofold by inclusion of uracil in the growth medium. In addition, we used pINT-delta to construct an M. smegmatis strain with a precise deletion of its pyrF locus. This strain, TSm-627, grows normally in rich medium but does not grow in medium lacking uracil. TSm-627 cells allow the pyrF gene to be used as a selectable marker for growth on medium lacking uracil. In TSm-627 cells, the pyrF gene is also useful as a counterselectable marker on complete medium containing 5'-fluoroorotic acid and uracil. Two pyrF-containing plasmids, designed to exploit the new delta pyrF strain, have been constructed and their possible applications to problems in mycobacteriology are discussed.

Amino Acid Sequence↗
PubMed1998

Co-insertional replication is responsible for tandem multimer formation during plasmid integration into the Dictyostelium genome.

We investigated the establishment of integrating transformation vectors in the genome of Dictyostelium discoideum to gain insight into the formation of the plasmid insertions and to investigate the conditions that determine the number of plasmid copies present in such insertions. Transformation vectors conferring resistance to neomycin and/or blasticidin were introduced into the cell as a calcium phosphate coprecipitate or by electroporation. The integration of the plasmid DNA was based on either recombinational integration of plasmids or restriction enzyme-mediated integration. The genomic DNA of the resulting transformants was examined by Southern blot analysis of pulsed-field gels and by the recently published method of direct electroporation into Escherichia coli. The number of insertion sites was found to be dependent on the transformation method used, and the minimum number of plasmid copies per insertion site required for resistance depended on the type and the concentration of the selective drug. Cotransformation studies revealed a strictly homogeneous composition of vector multimers from any given insertion site. This suggests that multimers arise by co-insertional replication of a single plasmid monomer, rather than by subsequent additional insertion events involving homologous recombination. The multimerization of the integrated vector only occurred when the insertion was established by homologous recombination. Moreover, the number of plasmid copies appeared to be random, was established at the time of the transformation, and did not change with subsequent alterations to the selection regime.

Animals↗
PubMed1990

Integration of heterologous genes into the chromosome of Saccharomyces cerevisiae using a delta sequence of yeast retrotransposon Ty.

Distribution of a delta (delta) sequence of the Ty element on a chromosome of the yeast Saccharomyces cerevisiae was analysed by pulsed-field gel electrophoresis. More than 100 copies of the delta sequence were nonrandomly distributed on the chromosome. Using the delta sequence as a recombination site, mouse alpha-amylase and human beta-endorphin genes were introduced into the chromosomal DNA. The integration occurred on a particular chromosome in each case and the copy number was estimated as three to five. It was also found that single- or multi-copy integration occurred at a single or multiple sites on the particular chromosome. The integrants secreted alpha-amylase and beta-endorphin by three-to fivefold compared with single-copy integrants. This type of integration was mitotically stable over a period of 50 generations under non-selective conditions.

Chromosomes↗
PubMed1991

Integrative transformation of the ascomycete Podospora anserina: identification of the mating-type locus on chromosome VII of electrophoretically separated chromosomes.

Protoplasts of wild-type strain s and a long-lived extrachromosomal mutant (AL2) of the ascomycete Podospora anserina were transformed using a plasmid (pAN7-1) which contains the hygromycin B phosphotransferase gene (hph) of Escherichia coli under the control of Aspergillus nidulans regulatory sequences. After optimizing the transformation procedure, transformation efficiencies of 15-21 transformants/micrograms plasmid DNA were obtained. Using a second selectable vector (pBT3), which contains the beta-tubuline gene of a benomyl-resistant Neurospora crassa mutant, the co-transformation rate was determined. Southern blot hybridization experiments revealed that the transforming plasmid became integrated into the genome of the recipient either as a single copy or as multiple copies. In addition, the data from molecular as well as from classical genetic analyses indicated that in independent transformants vector integration occurred at different positions. The mitotic and meiotic stability of transformants proved to be dependent on the number of integrated plasmid copies. Genetic analyses revealed a transformant in which the integrated vector is closely linked to the mating-type locus. Fractionation of whole chromosomes by pulsed field gel electrophoresis and subsequent hybridization of the immobilized DNAs against radiolabelled vector sequences indicated the largest of seven chromosomes as the chromosome containing the integrated vector and thus the mating-type locus.

Ascomycota↗
PubMed1991

A learning network model of the neural integrator of the oculomotor system.

Certain premotor neurons of the oculomotor system fire at a rate proportional to desired eye velocity. Their output is integrated by a network of neurons to supply an eye position command to the motoneurons of the extraocular muscles. This network, known as the neural integrator, is calibrated during infancy and then maintained through development and trauma with remarkable precision. We have modeled this system with a self-organizing neural network that learns to integrate vestibular velocity commands to generate appropriate eye movements. It learns by using current eye movement on any given trial to calculate the amount of retinal image slip and this is used as the error signal. The synaptic weights are then changed using a straight-forward algorithm that is independent of the network configuration and does not necessitate backwards propagation of information. Minimization of the error in this fashion causes the network to develop multiple positive feedback loops that enable it to integrate a push-pull signal without integrating the background rate on which it rides. The network is also capable of recovering from various lesions and of generating more complicated signals to simulate induced post-saccadic drift and compensation for eye muscle mechanics.

Algorithms↗