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At least 343 records · Page 19Linked to original sources

PubMed2004

Plastic scintillation dosimetry for radiation therapy: minimizing capture of Cerenkov radiation noise.

Over the last decade, there has been an increased interest in scintillation dosimetry using small water-equivalent plastic scintillators, because of their favourable characteristics when compared with other more commonly used detector systems. Although plastic scintillators have been shown to have many desirable dosimetric properties, as yet there is no successful commercial detector system of this type available for routine clinical use in radiation oncology. The main factor preventing this new technology from realizing its full potential in commercial applications is the maximization of signal coupling efficiency and the minimization of noise capture. A principal constituent of noise is Cerenkov radiation. This study reports the calculated capture of Cerenkov radiation by an optical fibre in the special case where the radiation is generated by a relativistic particle on the fibre axis and the fibre axis is parallel to the Cerenkov cone. The fraction of radiation captured is calculated as a function of the fibre core refractive index and the refractive index difference between the core and the cladding of the fibre for relativistic particles. This is then used to deduce the relative intensity captured for a range of fibre core refractive indices and fibre core-cladding refractive index differences. It is shown that the core refractive index has little effect on the amount of radiation captured compared to the refractive index difference. The implications of this result for the design of radiation therapy plastic scintillation dosimeters are considered.

Anisotropy↗

PubMed1993

Detection of simian immunodeficiency virus and human immunodeficiency virus type 2 capsid antigens by a monoclonal antibody-based antigen capture assay.

We have tested the ability of a monoclonal antibody-based simian immunodeficiency virus (SIV) p27 capsid antigen assay to detect SIV antigen in supernatants from a variety of infected cell cultures. The antigen capture assay has a sensitivity of approximately 30 pg of SIV p27 capsid antigen/ml. The assay detected SIV p27 capsid antigen in cell culture supernatants from all six strains tested, detected the replication of SIV following the inoculation of the virus in peripheral blood mononuclear cell cultures earlier compared to reverse transcriptase assay, and was more sensitive in detection of the SIV antigen compared to human immunodeficiency virus type 1 (HIV-1) antigen capture assays. The SIV antigen capture assay was used to detect SIV antigen from serum samples and tissue cultures from eight of eight SIVB670-infected rhesus macaques (Macaca mulatta). Similar samples from four control rhesus macaques were negative when tested by the assay. The SIV antigen was detected in virus-infected monkeys during early time periods following inoculation (1 to 3 weeks) or during episodes of CD4+ lymphocytopenia and clinically evident disease. In addition, the SIV antigen capture assay positively identified each of three different HIV-2 strains in cell culture supernatants. The SIV antigen capture assay provides a sensitive and specific method to monitor SIV and HIV-2 capsid antigen in cell cultures and from infected animals. The assay will be an important tool in the utilization of SIV and HIV-2 primate models for HIV-induced acquired immunodeficiency disease syndrome.

Animals↗

PubMed2005

Development of a method for concentrating and purifying SARS coronavirus RNA by a magnetic bead capture system.

Severe acute respiratory syndrome (SARS) is a recently emerged infectious disease caused by a novel coronavirus, which has been designated the SARS coronavirus (SARS-CoV). To date, molecular assays for the detection of SARS-CoV has focused mainly on reverse transcriptase-PCR (RT-PCR) analysis of specimens. However, RT-PCR assays currently available have low sensitivity during the early stage of the disease in which the viral load in specimens is very low. A method for concentrating and purifying SARS-CoV RNA by a magnetic bead capture system was developed and followed by an RT-PCR assay in this study with the goal of improving the sensitivity of the RT-PCR method. This approach takes advantage of the cooperative interaction between adjacently hybridized oligonucleotides. A capture probe was covalently coupled to magnetic beads and a second probe, which anneals adjacent to the capture probe site, was prehybridized in solution to the target. It was shown that, when applied to SARS RNA samples, the sensitivity of nucleic acid capture RTPCR was about 10-fold greater than routine RT-PCR. This nucleic acid capture system was effective in improving the sensitivity of the RT-PCR, due to enriching and purifying SARS-CoV RNA. The method will be helpful for the early detection of the SARS-associated coronavirus.

DNA Primers↗

PubMed2003

Modelling cereal root systems for water and nitrogen capture: towards an economic optimum.

A quantitative model of wheat root systems is developed that links the size and distribution of the root system to the capture of water and nitrogen (which are assumed to be evenly distributed with depth) during grain filling, and allows estimates of the economic consequences of this capture to be assessed. A particular feature of the model is its use of summarizing concepts, and reliance on only the minimum number of parameters (each with a clear biological meaning). The model is then used to provide an economic sensitivity analysis of possible target characteristics for manipulating root systems. These characteristics were: root distribution with depth, proportional dry matter partitioning to roots, resource capture coefficients, shoot dry weight at anthesis, specific root weight and water use efficiency. From the current estimates of parameters it is concluded that a larger investment by the crop in fine roots at depth in the soil, and less proliferation of roots in surface layers, would improve yields by accessing extra resources. The economic return on investment in roots for water capture was twice that of the same amount invested for nitrogen capture.

Models, Theoretical↗

PubMed2026

RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.

MOTIVATION: Simulators that generate synthetic datasets help address the lack of ground truth for developing and benchmarking computational tools. Many read simulators assume uniform sampling across reference genomes; however, for newer capture-based sequencing technologies (e.g. TELSeq), this assumption is intentionally broken to oversample regions of interest. Along with systematic biases arising from probe multiplicity, sequence composition, and species abundances inherent to capture-based sequencing, this mismatch between modeling assumptions and the characteristics of real data necessitates the design of a new capture-based sequencing-specific simulator. RESULTS: We present RAmpSim, a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing models of platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. RAmpSim generally outperforms a uniform baseline with respect to position-based earth mover's distance when compared against the empirical coverage distribution. Classification analysis also shows high recall in recovering empirical high-coverage regions while outperforming a uniform baseline. AVAILABILITY: Code, example scripts, and data sources are available at https://github.com/az002/RAmpSim.git.

Metagenomics↗

PubMed1997

Factors responsible for target site selection in Tn10 transposition: a role for the DDE motif in target DNA capture.

Tn10, like several other transposons, exhibits a marked preference for integration into particular target sequences. Such sequences are referred to as integration hotspots and have been used to define a consensus target site in Tn10 transposition. We demonstrate that a Tn10 hotspot called HisG1, which was identified originally in vivo, also functions as an integration hotspot in vitro in a reaction where the HisG1 sequence is present on a short DNA oligomer. We use this in vitro system to define factors which are important for the capture of the HisG1 target site. We demonstrate that although divalent metal ions are not essential for HisG1 target capture, they greatly facilitate capture of a mutated HisG1 site. Analysis of catalytic transposase mutants further demonstrates that the DDE motif plays a critical role in 'divalent metal ion-dependent' target capture. Analysis of two other classes of transposase mutants, Exc+ Int- (which carry out transposon excision but not integration) and ATS (altered target specificity), demonstrates that while a particular ATS transposase binds HisG1 mutants better than wild-type transposase, Exc+ Int- mutants are defective in HisG1 capture, further defining the properties of these classes of mutants. Possible mechanisms for the above observations are considered.

Base Sequence↗

PubMed2001

Capture of DNA sequences at double-strand breaks in mammalian chromosomes.

To study double-strand break (DSB)-induced mutations in mammalian chromosomes, we transfected thymidine kinase (tk)-deficient mouse fibroblasts with a DNA substrate containing a recognition site for yeast endonuclease I-SceI embedded within a functional tk gene. To introduce a genomic DSB, cells were electroporated with a plasmid expressing endonuclease I-SceI, and clones that had lost tk function were selected. Among 253 clones analyzed, 78% displayed small deletions or insertions of several nucleotides at the DSB site. Surprisingly, approximately 8% of recovered mutations involved the capture of one or more DNA fragments. Among 21 clones that had captured DNA, 10 harbored a specific segment of the I-SceI expression plasmid mapping between two replication origins on the plasmid. Four clones had captured a long terminal repeat sequence from an intracisternal A particle (an endogenous retrovirus-like sequence) and one had captured what appears to be a cDNA copy of a moderately repetitive B2 sequence. Additional clones displayed segments of the tk gene and/or microsatellite sequences copied into the DSB. This first systematic study of DNA capture at DSBs in a mammalian genome suggests that DSB repair may play a considerable role in the evolution of eukaryotic genomes.

Animals↗

PubMed1998

Estimating deaths and injuries due to road traffic accidents in Karachi, Pakistan, through the capture-recapture method.

BACKGROUND: Road traffic accidents (RTA) are an important yet preventable cause of death and disability in developing countries like Pakistan. Yet accurate epidemiological data on injuries in developing country injuries is often difficult to obtain. We applied the capture-recapture method to estimate the death and injury rates due to RTA in Karachi. METHODS: We applied the two-sample capture-recapture method using traffic police records as one source of capture and the logs of a non-government ambulance service as the second capture source for the same 10 months and 20 days for which 1994 data were available. We generated a conservative adjusted estimate of injuries and deaths by considering entries in the two sources as matched if they reported the same date, time, and place, and at least one of the other matching variables, of name, vehicle registration number, vehicle types or patient outcome. We then compared the estimated rates with the police rates. RESULTS: In 1994 police reported 544 deaths and 793 injuries due to RTA while ambulance records noted 343 deaths and 2048 injuries. The capture-recapture analysis estimated at least 972 (95% CI: 912-1031) deaths and 18,936 (95% CI: 15,507-22,342) injuries attributable to RTA during the study period. Official sources counted only 56% of deaths and 4% of serious injuries. The estimated rates for the year 1994 were 185 injuries and 11.2 deaths per 100,000 population. CONCLUSION: Road traffic injuries and deaths in Karachi are a much more substantial health problem than is evident from official statistics.

Accidents↗

PubMed1999

Evaluating the reported prevalence of type 2 diabetes mellitus by the Oguni diabetes registry using a two-sample method of capture-recapture.

BACKGROUND: Capture-recapture methods have been widely employed in the study of wildlife populations and have recently been applied to count various human diseases and conditions. We have estimated the prevalence of type 2 diabetes mellitus by adjusting for the degree of undercount using a two-sample model of capture-recapture among men and women aged 50-69 in Oguni town, Japan. METHODS: Oguni town diabetes registry data were utilized as the first source. In the registry, only those who had experienced fasting plasma glucose of > or = 7.8 mmol/l (140 mg/dl) or 2 h plasma glucose after a 75 g oral glucose tolerance test (OGTT) of > or = 11.1 mmol/l (200 mg/dl) were counted as having diabetes. A second source was a sample study selecting 200 men and 200 women aged 50-69 randomly, which was conducted in August 1991. A 75 g OGTT was done in the morning. The 1985 World Health Organization criteria were used to classify the diabetes status of the participants. A two-sample model of capture-recapture methods was employed to estimate the total number of cases of diabetes and determine the ascertainment rates of the registry. RESULTS: The prevalence estimated by the diabetes registry was 7.1%. The prevalence from the sample study was 8.8% with a participation rate of 74%. Estimated prevalence employing the capture-recapture method was 13.1%. The ascertainment rate of the registry was 53.8%. CONCLUSIONS: Little is known about the prevalence of type 2 diabetes in local areas in Japan, the US and the world. Capture-recapture methods are likely to provide a means to accurately assess the prevalence of diabetes.

Aged↗

PubMed2004

Effects of height and adjacent surfaces on captures of Indianmeal moth (Lepidoptera: Pyralidae) in pheromone-baited traps.

Diamond-shaped pheromone-baited traps are used widely in food storage and food processing facilities for monitoring of Plodia interpunctella (Hübner), and here we evaluated to what extent trap captures were affected by 1) vertical placement of traps, 2) deployment of a horizontal landing platform to the diamond-shaped pheromone trap, and 3) placement of traps either freely exposed or along a sidewall. In the small sheds (height 1.8 m), traps were placed in three heights and significantly highest trap captures were obtained near the ceiling. When the same experiment was conducted in a larger room (height 6 m) with traps at seven heights, highest captures were obtained at both the lowest and highest traps. In a subsequent experiment, we deployed a horizontal platform to traps at seven heights and found that the importance of vertical placement became less important. Thus, it seemed that male moths preferred to orient to a pheromone source associated with a physical surface, such as the floor, ceiling, or landing platform. In a comparison of P. interpunctella male trap captures in a completely dark room (no visual cues), traps with a landing platform caught significantly more than traps without the platform. In a final experiment, we evaluated the effect of hanging traps either freely or adjacent to sidewalls, and significantly highest trap captures were obtained along side-walls. The results presented here suggest that deployment of a horizontal platform reduces the importance of the vertical placement of traps and seems to increase the trap efficiency, and we recommend placement of traps along sidewalls and/or near the ground.

Animals↗

PubMed1999

DNA hybridization on microparticles: determining capture-probe density and equilibrium dissociation constants.

Many DNA-probe assays utilize oligonucleotide-coated microparticles for capture of complementary nucleic acids from solution. During development of these assays, as well as in other particle-based nucleic acid applications, it is useful to know both the amount of duplex formation expected under various experimental conditions and the coating density of the capture oligonucleotide on the particle surface. We examined the simplest form of a DNA-probe microparticle assay: hybridization of a particle-bound capture oligonucleotide to its solution-phase complement. Fluorescein-labeled solution-phase oligonucleotide was hybridized to varying amounts of particles, and the amount of labeled oligonucleotide remaining in solution at equilibrium was measured. We present a simple two-state, all-or-none model for bimolecular hybridization of non-self-complementary sequences that can be used to calculate the equilibrium dissociation constant ( Kd ) from hybridization data. With experimental conditions where both the Kd value and the concentration of capture probe in the reaction are small relative to the concentration of labeled complementary oligonucleotide in the reaction, density of the capture probe on the particle's surface can also be determined. Kd values for particle-based hybridization were different from those obtained from solution-phase thermodynamic parameters. At higher temperatures, hybridization on particles was more efficient than hybridization in solution.

DNA↗

PubMed2001

An application of the two-source capture-recapture method to estimate the completeness of the Tuscany Cancer Registry, Italy.

The purpose of this study was to apply a two-way capture-recapture method to estimate the Tuscany Cancer Registry completeness, taking into account the presence of dependence between sources. Cases incident during 1995-1996 were flagged according to three sources of information: clinical notes, pathological reports and death certificates. For each group of cases notified by one source the dependence between the other two has been quantified and the completeness has been estimated by a two-way capture-recapture method. When only two (or substantially two) sources are dependent on each other it is possible to correct for it by pooling the two sources in a single group and comparing it with the remainder source by a two-way capture-recapture method. The capture-recapture method has been applied to the overall 12 387 incident cases and to 1569 female breast and 1443 lung cancer cases. After correction for the greatest dependence among the three couples of sources of information, the estimates of completeness were 97.4% for the whole case series, 88.7% for female breast and 99.6% for lung cancer. With the limit of multiple strong dependence between sources, the two-way capture-recapture method seems a simple and useful tool for estimating the completeness of cancer registration.

Female↗

PubMed2003

Participatory mapping of sex trade and enumeration of sex workers using capture-recapture methodology in Diego-Suarez, Madagascar.

BACKGROUND: Capture-recapture methodology has been employed to estimate the size of hidden or difficult-to-reach human populations such as sex workers, homeless persons, and intravenous drug users. This study took place in the context of efforts to improve the quality of curative and preventive services for sexually transmitted infections offered to sex workers in Diego-Suarez, Madagascar in partnership with sex workers. GOAL: The goal of this study was to better understand sex-trading practices, map out sex work sites, and estimate the size of a mobile sex-worker population in Diego-Suarez, Madagascar using methods that can be reproduced in other resource-poor settings. STUDY DESIGN: Forty sex workers were trained to function as field researchers. Key informants in designated neighborhoods were identified and interviewed. Basic maps of sex-trade sites were designed by hand. The number of sex workers in Diego-Suarez was estimated using capture-recapture methodology. An educational brochure was used to "capture" sex workers during a first phase, and "recapture" 2 weeks later. RESULTS: Most sex trade was street based and mobile. Capture-recapture methods estimated a total of 2684 sex workers (95% CI: 2588-2780) in Diego-Suarez, or approximately 12% of the 15- to 49-year-old female population in the city. CONCLUSION: Geographic mapping and capture-recapture proved to be low-cost and relatively easy to use techniques for counting a hard-to-reach population, such as female street-based sex workers. Sex workers can be capable fieldworkers, and their active participation in research concerning sex work should be considered whenever possible. A high proportion of women of reproductive age were found to engage in sex work, indicating that there is an urgent need to scale up sexually transmitted infection and HIV prevention activities targeting sex workers, their sexual partners, and the general population.

Adolescent↗

PubMed2001

Image charge effects on electron capture by dust grains in dusty plasmas.

Electron-capture processes by negatively charged dust grains from hydrogenic ions in dusty plasmas are investigated in accordance with the classical Bohr-Lindhard model. The attractive interaction between the electron in a hydrogenic ion and its own image charge inside the dust grain is included to obtain the total interaction energy between the electron and the dust grain. The electron-capture radius is determined by the total interaction energy and the kinetic energy of the released electron in the frame of the projectile dust grain. The classical straight-line trajectory approximation is applied to the motion of the ion in order to visualize the electron-capture cross section as a function of the impact parameter, kinetic energy of the projectile ion, and dust charge. It is found that the image charge inside the dust grain plays a significant role in the electron-capture process near the surface of the dust grain. The electron-capture cross section is found to be quite sensitive to the collision energy and dust charge.

Journal Article↗

PubMed2003

Electron capture rates on nuclei and implications for stellar core collapse.

Supernova simulations to date have assumed that during core collapse electron captures occur dominantly on free protons, while captures on heavy nuclei are Pauli blocked and are ignored. We have calculated rates for electron capture on nuclei with mass numbers A=65-112 for the temperatures and densities appropriate for core collapse. We find that these rates are large enough so that, in contrast to previous assumptions, electron capture on nuclei dominates over capture on free protons. This leads to significant changes in core collapse simulations.

Journal Article↗

PubMed2026

Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep-Sea Molluscs.

Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood. Here, we compared DNA recovery from four fresh and 12 ancient (eight radiocarbon-dated to 1671-1135 years old before present) deep-sea vesicomyid clam shells, including species Archivesica marissinica, A. nanshaensis and A. okutanii, using whole-genome sequencing (WGS) or target capture of ultraconserved elements (UCEs). WGS achieved 16.65% on-target read recovery of UCEs from fresh soft tissue, but < 1% from shell specimens. By contrast, UCE capture in the same specimen increased on-target reads by up to 155-fold, reaching 29.84% in fresh shells and up to 72-fold, reaching 19.89% in ancient shells. Target capture of UCEs recovered 142-1001 loci per sample compared to 0-230 with WGS alone. Ancient shells of A. marissinica and A. okutanii, based on reads mapped with bwa-mem2 and bbmap, exhibited characteristic post-mortem DNA damage signals, with average 5'-end C-to-T misincorporation rates of 3.46% and 15.97%, respectively, exceeding the levels observed in fresh A. marissinica shells (maximum 1.24%). UCE-based phylogenetic reconstructions incorporating shell ancient DNA recovered two major clades within Pliocardiinae, consistent with published phylogenomic trees. Together, these findings demonstrate that target-capture enrichment enables effective recovery of highly degraded DNA from ancient mollusc shells and supports robust phylogenetic inference at the intrageneric scale, expanding the utility of shells-one of the most abundant invertebrate remains-for evolutionary, biogeographic and conservation studies.

Animals↗

PubMed2003

Open capture-recapture models with heterogeneity: I. Cormack-Jolly-Seber model.

In open population capture-recapture studies, it is usually assumed that similar animals (e.g., of the same sex and age group) have similar survival rates and capture probabilities. These assumptions are generally perceived to be an oversimplification, and they can lead to incorrect model selection and biased parameter estimates. Allowing for individual variability in survival and capture probabilities among apparently similar animals is now becoming possible, due to advances in closed population models and improved computing power. This article presents a flexible framework of likelihood-based models which allow for individual heterogeneity in survival and capture rates. Heterogeneity is modeled using finite mixtures, which have enough flexibility of distribution shape to accommodate a wide variety of different patterns of individual variation. The models condition on the first capture of each animal, and include as a special case the Cormack-Jolly-Seber model. Model selection is done either using Akaike's information criterion or by likelihood ratio tests, making available checks of different influences on survival rates. Bias in parameter estimates is reduced by including individual heterogeneity. Model selection and bias reduction are important in population studies and for making informed management decisions.

Animals↗

PubMed2005

Modeling association among demographic parameters in analysis of open population capture-recapture data.

We present a hierarchical extension of the Cormack-Jolly-Seber (CJS) model for open population capture-recapture data. In addition to recaptures of marked animals, we model first captures of animals and losses on capture. The parameter set includes capture probabilities, survival rates, and birth rates. The survival rates and birth rates are treated as a random sample from a bivariate distribution, thus the model explicitly incorporates correlation in these demographic rates. A key feature of the model is that the likelihood function, which includes a CJS model factor, is expressed entirely in terms of identifiable parameters; losses on capture can be factored out of the model. Since the computational complexity of classical likelihood methods is prohibitive, we use Markov chain Monte Carlo in a Bayesian analysis. We describe an efficient candidate-generation scheme for Metropolis-Hastings sampling of CJS models and extensions. The procedure is illustrated using mark-recapture data for the moth Gonodontis bidentata.

Animals↗