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PubMed1981

Induction of tyrosine aminotransferase in H-35 hepatoma cells by cAMP captured in phospholipid vesicles.

The uptake, metabolism, and action of cAMP, captured within phospholipid vesicles, in H-35 hepatoma cells were studied. Sonication of lipids in buffer containing cAMP resulted in the formation of 300-A unilamellar lipid vesicles, capturing cAMP in the internal aqueous cavity. Incubation of H-35 hepatoma cells with vesicles containing cAMP (vesicle-cAMP) resulted in rapid incorporation of the vesicle content; apparent saturation of uptake was reached after approximately 30 min of incubation at 37 degrees C. Uptake of vesicle-cAMP was linear over a 10-fold vesicle concentration range. Pretreatment of cells with combined inhibitors of glycolysis and respiration inhibited vesicle uptake by 27%, suggesting vesicle fusion with the cell membrane as a predominant pathway of vesicle uptake. Studies on the metabolism of incorporated cAMP indicated that greater than 50% of the cell-associated radioactivity, derived from vesicle-[3H]cAMP, was preserved as cAMP at the end of a 20-min incubation at 37 degrees C. The incorporation of vesicle-cAMP by H-35 hepatoma cells resulted in increased tyrosine aminotransferase (TAT) activity. The concentration of vesicle-cAMP needed to produce a half-maximal increase in TAT activity was 10 microM, approximately two orders of magnitude lower than that of exogenously added dbcAMP. cAMP was ineffective when added extracellularly. The kinetic relationship of the cAMP-induced increase in TAT activity and the binding of cAMP to its receptor protein, in intact H-35 cells, was examined using vesicle-trapped 8-N3-cAMP, a photoaffinity labeling analogue of cAMP. Incubation of H-35 hepatoma cells with vesicle-8-N3-cAMP resulted in increased TAT activity, preceded by the binding of 8-N3-cAMP to the regulatory subunit of type II cAMP-dependent protein kinase. The use of lipid vesicles provides a means of modulating intracellular cAMP concentration without adding cyclic nucleotide in the millimolar concentration range to the extracellular medium. The increased efficiency of intracellular delivery of cyclic nucleotide with retention of biological activity, provides a useful technique in examining the relationship of occupancy of specific cAMP-receptor protein(s) and the occurrence of a cAMP-mediated biological response in intact cells.

Animals↗

PubMed1993

Determinant capture as a possible mechanism of protection afforded by major histocompatibility complex class II molecules in autoimmune disease.

How peptide-major histocompatibility complex (MHC) class II complexes are naturally generated is still unknown, but accumulating evidence suggests that unfolding proteins or long peptides can become bound to class II molecules at the dominant determinant before proteolytic cleavage. We have compared the immunogenicity of hen egg-white lysozyme (HEL) in nonobese diabetic (NOD), (NOD x BALB/c)F1, and E(d) alpha transgenic NOD mice. We find that a response to the subdominant ANOD-restricted determinant disappears upon introduction of an E(d) molecule, and is restored when scission of HEL separates this determinant from its adjoining, competitively dominant, E(d)-restricted determinant. This suggests that the E(d) molecule binds and protects its dominant determinant on a long peptide while captured neighboring determinants are lost during proteolysis. These results provide clear evidence for "determinant capture" as a mechanism of determinant selection during antigen processing and a possible explanation for MHC-protective effects in insulin-dependent diabetes mellitus.

Animals↗

PubMed2005

Innate NKT lymphocytes confer superior adaptive immunity via tumor-capturing dendritic cells.

If irradiated tumor cells could be rendered immunogenic, they would provide a safe, broad, and patient-specific array of antigens for immunotherapies. Prior approaches have emphasized genetic transduction of live tumor cells to express cytokines, costimulators, and surrogate foreign antigens. We asked if immunity could be achieved by delivering irradiated, major histocompatibility complex-negative plasmacytoma cells to maturing mouse dendritic cells (DCs) within lymphoid organs. Tumor cells injected intravenously (i.v.) were captured by splenic DCs, whereas subcutaneous (s.c.) injection led only to weak uptake in lymph node or spleen. The natural killer T (NKT) cells mobilizing glycolipid alpha-galactosyl ceramide, used to mature splenic DCs, served as an effective adjuvant to induce protective immunity. This adjuvant function was mimicked by a combination of poly IC and agonistic alphaCD40 antibody. The adjuvant glycolipid had to be coadministered with tumor cells i.v. rather than s.c. Specific resistance was generated both to a plasmacytoma and lymphoma. The resistance afforded by a single vaccination lasted >2 mo and required both CD4+ and CD8+ T cells. Mature tumor capturing DCs stimulated the differentiation of P1A tumor antigen-specific, CD8+ T cells and uniquely transferred tumor resistance to naive mice. Therefore, the access of dying tumor cells to DCs that are maturing to activated NKT cells efficiently induces long-lived adaptive resistance.

Adjuvants, Immunologic↗

PubMed2000

Neutron-Capture Element Abundances in the Globular Cluster M15.

High-resolution, high signal-to-noise ratio, blue-violet spectra of three red giant branch tip stars in M15 have been obtained with the Keck I High-Resolution Echelle Spectrograph. These spectra have been analyzed to determine the abundances of several neutron-capture elements, including the radioactive chronometer element thorium. There are two principal results of this study. First, the abundances of the heavier (Z>/=56) elements for each of the three stars is well matched by a scaled solar system r-process abundance distribution. Second, a weighted mean-observed Th/Eu ratio for the stars implies an age for the neutron-capture material in M15 stars of 14+/-3 Gyr, in reasonable agreement with other recent age estimates for Galactic globular clusters.

Journal Article↗

PubMed1992

A sensitive viral capture assay for detection of plasma viremia in HIV-infected individuals.

Human immunodeficiency virus was detected in the serum/plasma of individuals infected with human immunodeficiency virus (HIV) after capture of virions on microparticles coated with monoclonal antibodies to external and transmembrane proteins of HIV-1. We analyzed serial samples obtained from 6 individuals who seroconverted, 18 asymptomatic, and 12 AIDS patients. HIV-1 RNA was detected in all (29/29) seropositive samples and in 6 seronegative samples immediately preceding seroconversion. In contrast, HIV antigen was detected in 13/29 (45%) of seropositive samples. HIV-1 RNA was also detected in 3 antigen-negative samples from one individual 8-5 months prior to seroconversion and in one sample from another person 2 days before antigen positivity. The intensity of the polymerase chain reaction (PCR) signal paralleled the concentration of HIV antigen. Conversely, seropositive HIV antigen-negative samples gave a weaker PCR signal. HIV-1 RNA was detected in 10/18 (60%) samples from asymptomatic, HIV antigen-negative, individuals and in 11/12 (92%) specimens obtained from AIDS patients. The viral capture method may provide a sensitive, specific, and semiquantitative means of detecting circulating HIV at all stages of infection.

Acquired Immunodeficiency Syndrome↗

PubMed2006

Integrating haptic-tactile feedback into a video-capture-based virtual environment for rehabilitation.

Video-capture virtual reality (VR) systems are gaining popularity as intervention tools. To date, these platforms offer visual and audio feedback but do not provide haptic feedback. We contend that adding haptic feedback may enhance the quality of intervention for various theoretical and empirical reasons. This study aims to integrate haptic-tactile feedback into a video capture system (GX VR), which is currently applied for rehabilitation. The proposed multi-modal system can deliver audio-visual as well as vibrotactile feedback. The latter is provided via small vibratory discs attached to the patient's limbs. This paper describes the system, the guidelines of its design, and the ongoing usability study.

Computer Simulation↗

PubMed1981

Binding and capture of human interferon-alpha by reverse evaporation vesicles, multilamellar vesicles, and small unilamellar vesicles.

Liposomes of various physical and chemical compositions were prepared and their ability to externally bind and internally capture human interferon alpha (HuIFN-alpha) was determined. HuIFN-alpha was bound by preformed liposomes composed of either dipalmitoyl phosphatidyl choline alone or dipalmitoyl phosphatidic acid (calcium salt), and cholesterol, with or without a phosphatidyl choline component. HuIFN-alpha could also be internally captured within liposomes both of compositions that bound or did not bind interferon. The interferon could be associated with liposomes in at least three manners: bound to the outside surface of the liposome, associated partially within the liposomal membranes, or completely internalized either within the aqueous compartments of the liposome or completely buried within the liposomal bilayer membrane. HuIFN-alpha was stably-associated with reverse-evaporation vesicles, multilamellar vesicles, and small unilamellar vesicles for 30 days at 4 degrees C. Incubation of the multilamellar vesicles at 37 degrees C caused an initial decrease in the amount of externally bound interferon, and incubation with mouse serum caused a further dissociation of the externally-bound interferon. Depending on liposome composition, incubation at 37 degrees C either had little effect on stability of internalized interferon or caused leakage of internalized interferon.

Cholesterol↗

PubMed1997

Culture-specific strategies for capturing local dietary intake patterns.

To capture cultural reality and apply it to nutrition research, ethnographic research should be integrated with nutrition research and community-based nutrition research designs should be dictated by the local culture. Choosing the most appropriate dietary assessment for a study population requires attention to culture-specific technology for food acquisition, storage, exchange, processing, and preparation, as well as consideration of cultural rules pertaining to food distribution and consumption at the household level. Nutrition researchers should work with ethnographers to determine whether the assessment method used in a specific culture should capture the food intake of the household as a unit or of the individuals in each household.

Culture↗

PubMed2005

Prior information in behavioral capture-recapture methods: demographic influences on drug injectors' propensity to be listed in data sources and their drug-related mortality.

The authors present findings from a Bayesian analysis of Scotland's four primary capture-recapture data sources for 2000 that was carried out to estimate numbers of current injecting drug users by region (Greater Glasgow vs. elsewhere in Scotland), sex (male vs. female), and age group (15-34 years vs. > or =35 years). A secondary goal of the analysis was to obtain Bayesian estimates and credible intervals for the demographic influences on Scotland's drug-related death rate per 100 current injectors. Incorporation of informative priors altered the models with highest posterior probability. Expert opinion on how demography influenced Scottish drug injectors' propensity to be listed in different data sources was taken into account, along with external information about European injectors' drug-related death rates and male:female ratios. Higher drug-related mortality was confirmed in older drug injectors and those outside of Greater Glasgow. Female injectors' lower drug-related death rate was not sustained beyond 34 years of age. The authors recommend that demographic influences be accommodated in behavioral capture-recapture estimation, especially when it is a prelude to secondary analysis, such as the analysis of drug-related death rates presented here.

Adolescent↗

PubMed2006

Assessing the completeness of reporting of human immunodeficiency virus diagnoses in 2002-2003: capture-recapture methods.

To determine the completeness of reporting of human immunodeficiency virus (HIV) diagnoses to state surveillance systems, the authors used capture-recapture methods. The numbers of cases diagnosed in the areas were estimated using HIV diagnoses reported to nine surveillance programs by different sources (e.g., laboratories, health-care providers). To account for dependencies between reporting sources, the authors used log-linear models to estimate the number of cases that had been diagnosed but were not identified by any reporting sources. Completeness of reporting (observed cases/expected cases) was determined for two time frames: cases diagnosed within a 1-year period (from October 1, 2002, to September 30, 2003, for most US states) reported up to 6 months after that diagnosis period and cases diagnosed within a 6-month period reported up to 12 months after that diagnosis period. A total of 11,266 HIV diagnoses were reported for the 1-year period with 21,589 report documents. Completeness of reporting of HIV diagnoses was 76% (95% confidence interval: 66, 83) when allowing 6 months of reporting delay (range: 72-95%) and improved to 81% (95% confidence interval: 72, 88) with 12 months' follow-up. When reporting systems retain all relevant documents, capture-recapture is a feasible approach for assessing completeness of reporting of HIV diagnoses. Completeness should be measured by allowing 12-months' reporting delay.

Data Collection↗

PubMed2002

Influence of push element geometry on the capture efficiency of push-pull ventilation systems in surface treatment tanks.

A full-scale installation which simulates a surface treatment tank provided with a push-pull ventilation system has been designed. This study examines the influence of the geometry of the push element on the capture efficiency of the system. It is observed that: (i) capture efficiency increases with the number of holes because of the continuous curtain formed, the size of the holes having no significant effect within the range studied (5-20 mm diameter); (ii) the push element is best supported on the tank wall so that no air from outside penetrates below the emitting jets because in this way the impact of the curtain on the tank occurs earlier and losses are less; (iii) the best results are obtained when the holes are directed downwards towards the tank surface at an angle of between 22 and 45 degrees.

Air Pollutants, Occupational↗

PubMed2026

HiCPotts: An R/Bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of bias.

MOTIVATION: Chromosome Conformation Capture methods, including Hi-C, micro-C or Capture-C, are used to map chromatin interactions genome-wide. Most of the existing computational methods do not account for sources of bias (such as DNA accessibility, GC content or TE content) in the data. RESULTS: We previously developed ZipHiC, a Bayesian method based on the hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC), that uses zero-inflated Poisson distribution to model the noise, signal and false signal of the data and showed that this approach was able to detect bias from DNA accessibility, GC content and TE content in both Hi-C and micro-C data. Here, we present HiCPotts, another Bayesian method based on the HMRF model and the ABC that uses a zero-inflated Negative Binomial distribution instead to model the noise and signal of the data. We systematically show that HiCPotts reduces false positives and increases recovery of true interactions compared to ZipHiC, but also compared to other methods such as FastHiC, Juicer and HiCExplorer. Most importantly, we provide an R/Bioconductor package that allows modelling the noise, signal and false signal using various distributions such as the zero-inflated Negative Binomial (ZINB) and the zero-inflated Poisson distribution (ZIP). AVAILABILITY AND IMPLEMENTATION: https://bioconductor.org/packages/HiCPotts/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Approximate Bayesian Computation↗

PubMed2004

Capturing biological information with class-responsibility-collaboration cards.

UNLABELLED: Class-responsibility-collaboration (CRC) cards have been used extensively in the software industry for defining complex object-oriented software requirements. We have adapted this tool to capture information about biological components, collaborators and responsibilities within these collaborations, which is not captured by current annotation tools. CRC cards should provide a common ground that will facilitate communication between biologist and computer scientists. AVAILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4.

Computational Biology↗

PubMed2005

Capture by misleading information and its false acceptance in patients with traumatic brain injury.

Exposure to misleading information, presented after a critical episode, can alter or impair memory reports about that episode. Here, we examine vulnerability to misleading information in patients with traumatic brain injury (TBI). The ability to initiate an effective retrieval strategy and inhibit irrelevant or interfering information requires participation from the prefrontal cortices, which are susceptible to damage following brain injury. We report that TBI patients are more prone to interference effects produced by misleading information during a cued-recall task and are more likely to accept this information as the product of 'remembering' compared with healthy controls. The results are consistent with a model proposing that patients are captured by highly accessible responses eliminating their opportunity to engage in recollection. Correlations between the cued-recall interference task and other executive measures helped elucidate the processes underlying 'capture'. In TBI patients, reduced recollection produced by a misleading prime was associated with impaired prospective remembering when engaged in a background task. A common functional deficit that may underlie poor performance on both tasks is the failure to inhibit previously relevant but currently irrelevant information. Subjective reports pertaining to the subject's cued-recall response were indexed by electrodermal activity. In control subjects, larger skin conductance responses (SCRs) were associated with a greater frequency of guess reports, suggesting that SCRs provide a marker for uncertainty regarding the candidacy of a selected response. TBI patients did not show this relationship, suggesting that impairments of post-retrieval evaluation might also underlie greater false acceptance of misinformation. Discussion focuses on the role of the prefrontal cortex and cognitive processes that mediate the selection and evaluation of memories.

Adult↗

PubMed2004

Involvement of the ventral premotor cortex in controlling image motion of the hand during performance of a target-capturing task.

The ventral premotor cortex (PMv) has been implicated in the visual guidance of movement. To examine whether neuronal activity in the PMv is involved in controlling the direction of motion of a visual image of the hand or the actual movement of the hand, we trained a monkey to capture a target that was presented on a video display using the same side of its hand as was displayed on the video display. We found that PMv neurons predominantly exhibited premovement activity that reflected the image motion to be controlled, rather than the physical motion of the hand. We also found that the activity of half of such direction-selective PMv neurons depended on which side (left versus right) of the video image of the hand was used to capture the target. Furthermore, this selectivity for a portion of the hand was not affected by changing the starting position of the hand movement. These findings suggest that PMv neurons play a crucial role in determining which part of the body moves in which direction, at least under conditions in which a visual image of a limb is used to guide limb movements.

Animals↗

PubMed1997

A new set of Mu DNA transposition intermediates: alternate pathways of target capture preceding strand transfer.

Mu DNA transposition occurs within the context of higher order nucleoprotein structures or transpososomes. We describe a new set of transpososomes in which Mu B-bound target DNA interacts non-covalently with previously characterized intermediates prior to the actual strand transfer. This interaction can occur at several points along the reaction pathway: with the LER, the Type 0 or the Type 1 complexes. The formation of these target capture complexes, which rapidly undergo the strand transfer chemistry, is the rate-limiting step in the overall reaction. These complexes provide alternate pathways to strand transfer, thereby maximizing transposition potential. This versatility is in contrast to other characterized transposons, which normally capture target DNA only at a single point in their respective reaction pathways.

Bacteriophage mu↗

PubMed2003

Intrabodies based on intracellular capture frameworks that bind the RAS protein with high affinity and impair oncogenic transformation.

We have applied in vivo intracellular antibody capture (IAC) technology to isolate human intrabodies which bind to the oncogenic RAS protein. IAC facilitates the capture of antibody fragments, in this case single-chain Fvs (scFvs), which tolerate reducing environments, such as the cytoplasm of cancer cells. Three anti-RAS scFvs with different affinity, solubility and intracellular binding activity were characterized. The anti-RAS scFvs with highest affinity were expressed relatively poorly in mammalian cells, and greater soluble expression was achieved by mutating the antibody framework to canonical consensus scaffolds, previously derived from IAC, without losing antigen specificity. Mutagenesis experiments showed that the consensus scaffolds are functional as intrabody fragments without an intra-domain disulfide bond. Furthermore, we could convert an intrabody which does not bind RAS in mammalian cells into a high-affinity reagent capable of inhibiting RAS-mediated NIH 3T3 transformation by exchanging VH and VL complementarity-determining regions onto its consensus scaffold. These data show that the consensus scaffold is a robust framework by which to improve intrabody function.

3T3 Cells↗

PubMed2006

Ventricular capture by anodal pacemaker stimulation.

This report describes the case of an 86-year-old male with syncopal paroxysmal 2:1 atrioventricular block and a single chamber VVI pacemaker programmed to bipolar sensing and unipolar pacing. After recurrence of syncope, a complete loss of ventricular capture with regular ventricular sensing was observed on ECG; fluoroscopic examination suggested perforation of the right ventricle by the helix of the implanted screw-in lead. Reprogramming the pacemaker to bipolar pacing/sensing resulted in regular ventricular capture and sensing, suggesting effective anodal stimulation from the ring electrode permitting complete non-invasive palliation.

Aged, 80 and over↗