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The oculomotor neural integrator uses a behavior-related coordinate system.

Coordinate systems are a central issue in computational neuroscience: are they explicitly represented at some reductive level of brain function, and if so, are they only trivial products of associated anatomic geometries? This investigation examined these questions in the neural network that holds eye position, the so-called oculomotor integrator. Since neural activity in the integrator is behaviorally constrained by Listing's law to encode horizontal and vertical eye positions within Listing's plane and zero rotation about the orthogonal torsional axis, it was hypothesized that any integrator coordinate system would be developmentally predisposed to align with Listing's plane. A test for this hypothesis was developed with the use of a kinematically correct model of the three-dimensional saccade generator. Three mathematical integrators were used to represent the neuron populations that control torsional, vertical, and horizontal eye position. Simulated failure of the torsional and vertical integrators produced eye position drift that was parallel to the horizontal plane containing the intrinsic coordinate axes for these components. Furthermore, this drift settled toward a resting range parallel to the intrinsic vertical coordinate axis (for horizontal rotation). To experimentally identify these intrinsic population coordinates, three-dimensional eye positions were measured in four Macaca fascicularis after injection of muscimol into the mesencephalic interstitial nucleus of Cajal (INC), a technique that disrupts the torsional and vertical integrators (Crawford et al., 1991). INC inactivation produced exponential, position-dependent decay in vertical and torsional eye position. There was no position-dependent horizontal drift, but in the original coordinate system (defined arbitrarily by the measurement apparatus) there was a constant-direction horizontal drift. However, this extraneous horizontal drift was eliminated when the data were transformed into a coordinate system that aligned with Listing's plane. The direction of torsional drift correlated well (r = 0.85), across all experiments, with the normal to Listing's plane. On average, these two directions were only 0.06 degrees from perfect alignment. In contrast, drift direction did not correlate with stereotaxic coordinates (r = 0.10). Furthermore, the drift settled toward a range parallel to and correlated with Listing's plane (r = 0.94), whereas this range did not correlate well with stereotaxic coordinates (r = 0.02). On average, the resting range was aligned within 0.98 degrees of Listing's plane. Finally, this resting range was near orthogonal (average 91.9 degrees across all experiments) to the direction of torsional drift. These results show that integrator cell populations use an orthogonal, craniotopic coordinate system that aligns with Listing's plane.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Survey of management and housing in farrowing quarters among independent and integrated swine farms in Québec.

Forty-eight randomly selected owner-operated swine breeding farms (independent farms) and 38 belonging to 5 integrated organizations specializing in swine production chosen from the largest in the province of Québec (integrated farms) were separately described regarding their general characteristics, sow feeding, management practises, and housing features in farrowing quarters. The parallel description of these 2 groups of farms aids in understanding what is done in the field. It also provides insight into potential differences between independent and integrated farms. Generally speaking, production tended to be more specialized and concentrated in integrated organizations. Specifically, more new practises seemed to have been adopted on the integrated farms, and their stockpersons seemed to have a more proactive style of management in farrowing quarters. Increased size of operations, proximity of information sources, profits yielded by new practises, and ease of implementation are discussed as explanations for this higher rate of adoption of new techniques among the organizations. These differences between the independent farms and the integrated organizations appeared to be all related to basic differences in their respective sizes. Although some differences were observed within, as well as between, each organization, many similarities were found across the majority of farms within each organization, thus supporting the existence of policies specific to each organization. Although these findings have to be confirmed before being generalized, they tend to suggest that independent swine farms and integrated organizations should be considered differently.

Animal Husbandry↗

The pressure hold/drop integrity test; its correlation to diffusive flow.

The pressure-drop/hold procedure enables the diffusive flow integrity testing of filters to be performed without breaching the system downstream of the filter. It is not necessary to measure volumetrically the diffused gas on the downstream side of the filter. By means of pressure transducers the pressure loss is determined upstream; thus eliminating the threat of sepsis due to down-stream invasions. The pressure decay exercise can be used to characterize the various filter types. A constancy of filter manufacture is required for a given filter type. Unless the pressure drop exceeds the value established as the maximum allowable decay, the filter is judged to be integral. It qualifies as a sterilizing grade filter. Excessive pressure decays will also eventuate from leaks, as from improperly sealed housings. Performed prior to the filtration, the procedure serves to eliminate the wasteful use of an imperfect system, whether caused by faulty sealing, incorrect filter type or flawed filters. Where leaks are detected, the filter can be reexamined for its integrity. To enable the pressure-drop procedure to serve as an integrity test, the measured pressure decays require being correlated with organism retention data. This is made possible by the arithmetic conversion of the pressure decay curve into the conventional diffusive airflow curve established to have such a correlation. The transformation of the pressure-drop curve into the differential airflow plot is automatically performed by certain of the automated integrity test machines. These devices, utilizing pressure transducers, are capable of measuring small pressure drops with requisite sensitivity; gauges commonly are not. Moreover, as previously stated, the measurements are advantageously made on the upside of the filter. The use of automated test machines is, therefore, recommended for the performance of the pressure hold/drop integrity test in furtherance of the practice of filter integrity testing.

Diffusion↗

Pension integration and Social Security reform.

Many employer-provided pensions plans explicitly account for Social Security in their benefit formulas-a practice known as integration. Because integrated pensions are directly linked to Social Security, both the incidence and design of explicitly integrated plans are likely to be affected by changes in the current Social Security program. While integration has been mentioned as an important issue in discussions of Social Security reform, researchers have largely ignored the concept of pension integration. This article provides basic information about pension integration and addresses, in general terms, the relationship between Social Security reform and pension integration.

Female↗

Integrated medical care for patients with serious psychiatric illness: a randomized trial.

BACKGROUND: This randomized trial evaluated an integrated model of primary medical care for a cohort of patients with serious mental disorders. METHODS: A total of 120 individuals enrolled in a Veterans Affairs (VA) mental health clinic were randomized to receive primary medical care through an integrated care initiative located in the mental health clinic (n = 59) or through the VA general medicine clinic (n = 61). Veterans who obtained care in the integrated care clinic received on-site primary care and case management that emphasized preventive medical care, patient education, and close collaboration with mental health providers to improve access to and continuity of care. Analyses compared health process (use of medical services, quality of care, and satisfaction) and outcomes (health and mental health status and costs) between the groups in the year after randomization. RESULTS: Patients treated in the integrated care clinic were significantly more likely to have made a primary care visit and had a greater mean number of primary care visits than those in the usual care group. They were more likely to have received 15 of the 17 preventive measures outlined in clinical practice guidelines. Patients assigned to the integrated care clinic had a significantly greater improvement in health as measured by the physical component summary score of the 36-Item Short-Form Health Survey than patients assigned to the general medicine clinic (4.7 points vs -0.3 points, P<.001). There were no significant differences between the 2 groups in any of the measures of mental health symptoms or in total health care costs. CONCLUSION: On-site, integrated primary care was associated with improved quality and outcomes of medical care.

Adult↗

Most of the avian genome appears available for retroviral DNA integration.

Although retroviral integration requires specific viral DNA sequences, factors which govern the choice of a chromosomal target site within an infected cell are less clear. For example, certain chromosomal regions may be inaccessible to the viral integration machinery, while others may favor integration. A recent paper by Withers-Ward et al.(1) addresses this issue using a polymerase chain reaction-based assay capable of identifying single integration events within a large population of infected cells. Their results show that integration can occur into many different chromosomal regions, and that local DNA structure can influence the site of integration within a given region.

Animals↗

Non-random integration of Epstein-Barr virus in lymphoblastoid cell lines.

In order to examine the role of Epstein-Barr virus (EBV) in the immortalization of human B lymphocytes and in the pathogenesis of lymphoid malignancies, we investigated whether the EBV integration into the human genome is randomly distributed or whether the virus integrates preferentially at certain sites. Twelve in vitro immortalized human lymphoblastoid cell lines (LCLs), two in vivo infected LCLs, and one Burkitt's lymphoma cell line (EB2) were examined by non-radioactive in situ hybridization (ISH) with a biotinylated EBV probe. Recurrent hybridization sites were detected in all 15 cell lines. The chromosomes frequently carrying the EBV genome were chromosomes 1, 2, 4, and 5. In more than 70 chromosomal bands, a greater number of integration sites than expected was found (p < 0.05). Approximately half of these bands were involved in the majority of the cell lines (for example, 1p31, 1q43, 2p22, 3q28, 4q13, 5p14, 5q12, and 11p15) whereby band 5p14 was involved in all LCLs analyzed. Virtually no viral integrations were found on the sex chromosomes (X, Y). The majority of the EBV integrations was found in G-band-positive material (p < 0.0001). Thus, our findings clearly show that EBV integrates into the human genome in a non-random manner.

Adolescent↗

Quality of integrated care for patients with head and neck cancer: Development and measurement of clinical indicators.

BACKGROUND: To improve the quality of integrated care, we developed indicators for assessing current practice in a large reference center for head and neck oncology. METHODS: We defined a set of indicators based on integrated care literature, national evidence-based guidelines for patients with head and neck cancer, and the opinions of professionals and patients. We tested this set regarding assessment of current practice and clinimetric characteristics. RESULTS: The final set consisted of 8 integrated care indicators and 23 specific indicators for patients with head and neck cancer. Current practice assessment produced high scores for the integrated care indicators, but the specific indicators showed room for improvement. The practice test showed that 9 indicators had good applicability. CONCLUSIONS: The indicators, while based on evidence-based guidelines and the principles of integrated care, should incorporate patients' opinions and include a practice test. Our results show that the quality of integrated care for patients with head and neck cancer could be improved.

Comprehensive Health Care↗

Visualization of episomal and integrated Epstein-Barr virus DNA by fiber fluorescence in situ hybridization.

For many Epstein-Barr virus (EBV)-associated malignancies, it is still a matter of controversy whether infected cells harbor episomal or chromosomally integrated EBV genomes or both. It is well established that the expression of EBV genes per se carries oncogenic potential, but the discrimination between episomal and integrated forms is of great relevance because integration events can contribute to the oncogenic properties of EBV, whereas host cells that exclusively harbor viral episomes may not carry the risks mediated by chromosomal integration. This notion prompted us to establish a reliable technique that not only allows to unequivocally discriminate episomal from integrated EBV DNA, but also provides detailed insights into the genomic organization of the virus. Here, we show that dynamic molecular combing of host cell DNA combined with fluorescence in situ hybridization (FISH) using EBV-specific DNA probes facilitate unambiguous discrimination of episomal from integrated viral DNA. Furthermore, the detection of highly elongated internal repeat 1 (IR1) sequences provides evidence that this method permits detection of major genomic alterations within the EBV genome. Thus, fiber FISH may also provide valuable insights into the genomic organization of viral genomes other than EBV.

Burkitt Lymphoma↗

Analysis of proviral integration in human mammary epithelial cell lines immortalized by retroviral infection with a temperature-sensitive SV40 T-antigen construct.

A panel of eight conditionally immortal lines derived by infection of human breast epithelial cells with an amphotropic retrovirus transducing a ts mutant of SV40 large T-antigen was analyzed with respect to individual retroviral integration patterns. Each line contained multiple integration sites which were clonal and stable over extended passage. Similar integration patterns were observed between individual lines arising separately from the same stock of pre-immortal cells, suggesting a common progenitor. Retroviral integration analysis of pre-immortal cells at different stages of pre-crisis growth showed changes indicative of a progressive transition from polyclonality to clonality as the cells approached crisis. Each of the immortal lines contained a sub-set of the integration sites of their pre-immortal progenitors, with individual combinations and copy numbers of sites. Since all the cell lines appeared to originate from single foci in separate flasks, it is likely that each set arose from a common clone of pre-immortal cells as the result of separate genetic events. There was no evidence from this analysis to suggest that specific integration sites played any part either in the selection of pre-crisis clones or in the subsequent establishment of immortal lines.

Adult↗

DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes.

The choice of retroviral integration sites is strongly influenced by chromatin: integration in vitro occurs more efficiently into nucleosomal DNA than into naked DNA, and a characteristic pattern of preferred insertion sites with a 10 bp periodicity is observed at the outer face of the nucleosomal DNA. At least three features of nucleosomal DNA could be responsible for the creation of these favored sites: the presence of histones, attachment of the DNA to a protein surface, and DNA bending. To test each of these possibilities, we studied integration in vitro with human immunodeficiency virus and murine leukemia virus integrases into four model targets that mimic features of nucleosomal DNA: (i) catabolite activator protein-DNA complexes; (ii) lac repressor-operator complexes; (iii) lac repressor-induced loops; and (iv) intrinsically bent A-tract DNA. We found that bending of the target DNA can create favored integration sites at the outer face of the helix, irrespective of whether the bent DNA is attached to a protein surface. Our findings offer an explanation for the preferred usage of nucleosomes as integration targets. In addition, they suggest that bending of the target DNA might be an intrinsic feature of the integration reaction.

Base Sequence↗

Recurrence of WHV integration in the b3n locus in woodchuck hepatocellular carcinoma.

Frequent occurrence of woodchuck hepatitis virus DNA (WHV DNA) integration into or in proximity to myc oncogenes and in the win locus of cellular genome in woodchuck hepatocellular carcinomas (HCC) has been described by several authors. We report a further cellular locus as a recurrent target for WHV integration in woodchuck HCCs. A WHV DNA integration and its cellular flanking regions were cloned from a HCC developed in a chronically WHV-infected woodchuck. Sequence analysis showed integration of rearranged C, PreS1, and 5' truncated X regions of the WHV genome, located in a cellular locus previously described for WHV integration in another woodchuck HCC. The two integration sites are only about 0.5 kb apart. In addition to Alu-like repeats and a gag-like coding region, previously described, we found several features of MAR (matrix attachment region) chromosomal sequences in the normal cellular locus, leading us to predict that part of it might be a previously unrecognized MAR.

Animals↗

Analysis of the integration functions of phi304L: an integrase module among corynephages.

Plasmid p12929 was shown to integrate into the chromosome of Corynebacterium glutamicum RM3 and BL15. The minimal integrating fragment was subsequently defined. The arms flanking the integrated plasmid (attL and attR) were identified, allowing for the determination of the attP and the attB attachment sites. The attB site is located at the 3' end of an ORF presenting 62-78% identity with L19 ribosomal proteins. Integration in the attB site does not result in the inactivation of this gene because its end is also present on the attR arm of the integrated plasmid and is reconstituted. The minimal integrating fragment is 1663 bp long and contains two ORFs. The int ORF was identified as phi304L integrase on the basis of the amino acid homologies it shared with the tyrosine recombinases of the lambda integrase family. Moreover this integrase is highly homologous throughout its sequence with the integrase of phi16 corynephage, the percentage of identity reaching 89% at the NH2 end. The identity also extends upstream of the initiation codon, while both phages are elsewhere nonhomologous. An integrase module was proposed to explain this extensive homology.

Amino Acid Sequence↗

Race, integration and family planning in Trinidad and Tobago.

"The study considered the effect of the integration of the health services on family planning in Trinidad and Tobago. A drop-out study was based on a sample of six clinics, three representing integrated and three clinics that were non-integrated or vertical. Efforts were also made to solicit the views of a sample of drop outs, current acceptors and health-care providers. The study found that there were characteristics of the population from which acceptors were drawn that were more important in explaining utilization than the question of integration or non-integration of the clinics. Many of the problems were organizational and could, with adequate financing, be met by an even higher level of integration."

Americas↗

Chromosomal localization of HTLV-1 viral integration sites using in situ hybridization: detection of a novel IL2R fragment.

The presence of human T-cell leukemia virus (HTLV-1) in patients with adult T-cell leukemia (ATL) was investigated by Southern blotting and in situ hybridization. In all seven patients, HTLV-1 provirus was detected. A large and variable number of labeled restriction fragments were observed, indicating multiple integrations. Two of the patients analyzed by in situ hybridization had two, while the third patient had three, sites of viral integration on six different chromosomes, suggesting random integration. A single site of integration was shared by two patients, which was on chromosome 10 at bands p11-->p15. One of these sites was on an apparently normal chromosome 10 and the other was on a derivative chromosome 10,t(10;14)(p12;q32). The interleukin 2 receptor (IL2R) has previously been localized to this region (10p14-->p15). The alpha-chain of the IL2R is continuously expressed on affected T-cells in this disease. Southern blotting with pIL2R showed the presence of a novel 3.5 kb fragment in five out of the seven patients. This novel fragment has not been previously reported. No direct correlation was found between the novel 3.5 kb fragment, present in patients both cytogenetically normal and abnormal, and viral integration in the 10p11-->p15 region in two patients. Therefore, it is suggested that the presence of the 3.5 kb fragment and the numerous chromosomal breaks associated with this disease may not be direct results of viral integration.

Blotting, Southern↗

Stochastic events in the amplification of HTLV-I integration sites by linker-mediated PCR.

Human T-cell leukaemia virus type I (HTLV-I) proviral integration sites from an asymptomatic carrier and from the MT4 cell line were analysed by linker-mediated PCR (LMPCR) and inverse PCR (IPCR). LMPCR was more sensitive, allowing detection of a greater number of integrated proviruses. Reconstruction experiments using a cloned integrated HTLV-1 provirus indicated that > 100 copies were necessary to be detected frequently by LMPCR. To circumvent this problem, the LMPCR analysis was performed approximately 20 times per sample. Thus, for the MT4 cell line, the seven major integration sites were accompanied by approximately 20 clones of lesser frequency. For an asymptomatic HTLV-I carrier, nine integration sites were identified in a single amplfication, while a further 9 followed from 14 additional reactions. These findings show that there is a stochastic element to sampling HTLV-I integration sites by LMPCR, which tends to underestimate the actual number of HTLV-I bearing clones. Accordingly, those detected in at least two reactions represent the most abundant clones.

Base Sequence↗

Systems integration.

The paper presents a view of systems integration, from an ergonomics/human factors perspective, emphasising the process of systems integration as is carried out by humans. The first section discusses some of the fundamental issues in systems integration, such as the significance of systems boundaries, systems lifecycle and systems entropy, issues arising from complexity, the implications of systems immortality, and so on. The next section outlines various generic processes for executing systems integration, to act as guides for practitioners. These address both the design of the system to be integrated and the preparation of the wider system in which the integration will occur. Then the next section outlines some of the human-specific issues that would need to be addressed in such processes; for example, indeterminacy and incompleteness, the prediction of human reliability, workload issues, extended situation awareness, and knowledge lifecycle management. For all of these, suggestions and further readings are proposed. Finally, the conclusions section reiterates in condensed form the major issues arising from the above.

Algorithms↗

HIV-1 integration sites are flanked by potential MARs that alone can act as promoters.

Matrix attachment regions (MARs) are cis regulatory elements that modulate gene expression in a tissue and cell stage specific manner. Recent reports show that viral integration within the genome takes place at nonrandom active genes. We have checked for the presence of MARs in the vicinity of the reported 524 HIV-1 integration sites. Our studies show that in 92.5% cases, MARs flank the integration sites. Similarly, for adeno-associated virus, two potential MARs were present next to the integration site on the human chromosome. Earlier we have shown that short MAR sequences present upstream of HIV-1 LTR promote processive transcription at a distance. Here, using a well-studied IgH-MAR and another potential MAR from p53 promoter, we demonstrate that MARs alone can act as promoters. Thus, we propose that MAR elements near the HIV-1 integration sites can act as potential promoters, which may facilitate proviral integration and transcription.

Chromosome Mapping↗