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Author |
Peris, J.B.; Davis, P.; Cuevas, J.M.; Nebot, M.; Sanjuan, R. |
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Title |
Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1 |
Type |
Journal Article |
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Year |
2010 |
Publication |
Genetics |
Abbreviated Journal |
Genetics |
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Volume |
185 |
Issue |
2 |
Pages |
603-U308 |
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Abstract |
Empirical knowledge of the fitness effects of mutations is important for understanding many evolutionary processes, yet this knowledge is often hampered by several sources of measurement error and bias. Most of these problems can be solved using site-directed mutagenesis to engineer single mutations, an approach particularly suited for viruses due to their small genomes. Here, we used this technique to measure the fitness effect of 100 single-nucleotide substitutions in the bacteriophage f1, a filamentous single-strand DNA virus. We found that approximately one-fifth of all mutations are lethal. Viable ones reduced fitness by 11% on average and were accurately described by a log-normal distribution. More than 90% of synonymous substitutions were selectively neutral, while those affecting intergenic regions reduced fitness by 14% on average. Mutations leading to amino acid substitutions had an overall mean deleterious effect of 37%, which increased to 45% for those changing the amino acid polarity. Interestingly, mutations affecting early steps of the infection cycle tended to be more deleterious than those affecting late steps. Finally, we observed at least two beneficial mutations. Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria. |
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Address |
[Peris, Joan B.; Davis, Paulina; Cuevas, Jose M.; Sanjuan, Rafael] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolut, Valencia 46980, Spain, Email: rafael.sanjuan@uv.es |
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Genetics Soc Am |
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English |
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ISSN |
0016-6731 |
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Notes |
ISI:000281905200017 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
383 |
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Author |
Rodriguez, D. et al; Algora, A.; Rubio, B.; Tain, J.L. |
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Title |
MATS and LaSpec: High-precision experiments using ion traps and lasers at FAIR |
Type |
Journal Article |
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Year |
2010 |
Publication |
European Physical Journal-Special Topics |
Abbreviated Journal |
Eur. Phys. J.-Spec. Top. |
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Volume |
183 |
Issue |
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Pages |
1-123 |
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Abstract |
Nuclear ground state properties including mass, charge radii, spins and moments can be determined by applying atomic physics techniques such as Penning-trap based mass spectrometry and laser spectroscopy. The MATS and LaSpec setups at the low-energy beamline at FAIR will allow us to extend the knowledge of these properties further into the region far from stability. The mass and its inherent connection with the nuclear binding energy is a fundamental property of a nuclide, a unique “fingerprint”. Thus, precise mass values are important for a variety of applications, ranging from nuclear-structure studies like the investigation of shell closures and the onset of deformation, tests of nuclear mass models and mass formulas, to tests of the weak interaction and of the Standard Model. The required relative accuracy ranges from 10(-5) to below 10(-8) for radionuclides, which most often have half-lives well below 1 s. Substantial progress in Penning trap mass spectrometry has made this method a prime choice for precision measurements on rare isotopes. The technique has the potential to provide high accuracy and sensitivity even for very short-lived nuclides. Furthermore, ion traps can be used for precision decay studies and offer advantages over existing methods. With MATS (Precision Measurements of very short-lived nuclei using an Advanced Trapping System for highly-charged ions) at FAIR we aim to apply several techniques to very short-lived radionuclides: High-accuracy mass measurements, in-trap conversion electron and alpha spectroscopy, and trap-assisted spectroscopy. The experimental setup of MATS is a unique combination of an electron beam ion trap for charge breeding, ion traps for beam preparation, and a high-precision Penning trap system for mass measurements and decay studies. For the mass measurements, MATS offers both a high accuracy and a high sensitivity. A relative mass uncertainty of 10(-9) can be reached by employing highly-charged ions and a non-destructive Fourier-Transform Ion-Cyclotron-Resonance (FT-ICR) detection technique on single stored ions. This accuracy limit is important for fundamental interaction tests, but also allows for the study of the fine structure of the nuclear mass surface with unprecedented accuracy, whenever required. The use of the FT-ICR technique provides true single ion sensitivity. This is essential to access isotopes that are produced with minimum rates which are very often the most interesting ones. Instead of pushing for highest accuracy, the high charge state of the ions can also be used to reduce the storage time of the ions, hence making measurements on even shorter-lived isotopes possible. Decay studies in ion traps will become possible with MATS. Novel spectroscopic tools for in-trap high-resolution conversion-electron and charged-particle spectroscopy from carrier-free sources will be developed, aiming e. g. at the measurements of quadrupole moments and E0 strengths. With the possibility of both high-accuracy mass measurements of the shortest-lived isotopes and decay studies, the high sensitivity and accuracy potential of MATS is ideally suited for the study of very exotic nuclides that will only be produced at the FAIR facility. Laser spectroscopy of radioactive isotopes and isomers is an efficient and model-independent approach for the determination of nuclear ground and isomeric state properties. Hyperfine structures and isotope shifts in electronic transitions exhibit readily accessible information on the nuclear spin, magnetic dipole and electric quadrupole moments as well as root-mean-square charge radii. The dependencies of the hyperfine splitting and isotope shift on the nuclear moments and mean square nuclear charge radii are well known and the theoretical framework for the extraction of nuclear parameters is well established. These extracted parameters provide fundamental information on the structure of nuclei at the limits of stability. Vital information on both bulk and valence nuclear properties are derived and an exceptional sensitivity to changes in nuclear deformation is achieved. Laser spectroscopy provides the only mechanism for such studies in exotic systems and uniquely facilitates these studies in a model-independent manner. The accuracy of laser-spectroscopic-determined nuclear properties is very high. Requirements concerning production rates are moderate; collinear spectroscopy has been performed with production rates as few as 100 ions per second and laser-desorption resonance ionization mass spectroscopy (combined with beta-delayed neutron detection) has been achieved with rates of only a few atoms per second. This Technical Design Report describes a new Penning trap mass spectrometry setup as well as a number of complementary experimental devices for laser spectroscopy, which will provide a complete system with respect to the physics and isotopes that can be studied. Since MATS and LaSpec require high-quality low-energy beams, the two collaborations have a common beamline to stop the radioactive beam of in-flight produced isotopes and prepare them in a suitable way for transfer to the MATS and LaSpec setups, respectively. |
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Address |
[Rodriguez, D.; Lallena, A. M.] Univ Granada, Dept Fis Atom Mol & Nucl, E-18071 Granada, Spain, Email: danielrodriguez@ugr.es |
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Publisher |
Springer Heidelberg |
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English |
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Edition |
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ISSN |
1951-6355 |
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Notes |
ISI:000280061400001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ elepoucu @ |
Serial |
412 |
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Author |
Warnecke, S.; Sevryuk, M.B.; Ceperley, D.M.; Toennies, J.P.; Guardiola, R.; Navarro, J. |
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Title |
The structure of para-hydrogen clusters |
Type |
Journal Article |
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Year |
2010 |
Publication |
European Physical Journal D |
Abbreviated Journal |
Eur. Phys. J. D |
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Volume |
56 |
Issue |
3 |
Pages |
353-358 |
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Abstract |
The path integral Monte Carlo calculated radial distributions of para-hydrogen clusters (p-H-2) N consisting of N = 4-40 molecules interacting via a Lennard-Jones potential at T = 1.5 K show evidence for additional peaks compared to radial distributions calculated by diffusion Monte Carlo (T = 0 K) and path integral Monte Carlo at T <= 0.5 K. The difference in structures is attributed to quantum delocalization at the lowest temperature. The new structures at finite temperatures appear to be consistent with classical structures calculated for an effective Morse potential, which in order to account for the large zero point energy, is substantially softer than the Lennard-Jones potential. |
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Address |
[Warnecke, S.; Sevryuk, M. B.; Toennies, J. P.] Max Planck Inst Dynam & Self Org, D-37073 Gottingen, Germany, Email: navarro@ific.uv.es |
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Publisher |
Springer |
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English |
Summary Language |
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Original Title |
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Series Editor |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1434-6060 |
ISBN |
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Notes |
ISI:000274327600008 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ elepoucu @ |
Serial |
505 |
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Author |
CDF Collaboration (Aaltonen, T. et al); Cabrera, S.; Cuenca Almenar, C. |
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Title |
Study of multi-muon events produced in p (p)over-bar interactions at root s=1.96 TeV |
Type |
Journal Article |
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Year |
2010 |
Publication |
European Physical Journal C |
Abbreviated Journal |
Eur. Phys. J. C |
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Volume |
68 |
Issue |
1-2 |
Pages |
109-118 |
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Abstract |
We report the results of a study of multi-muon events produced at the Fermilab Tevatron collider and acquired with the CDF II detector using a dedicated dimuon trigger. The production cross section and kinematics of events in which both muon candidates are produced inside the beam pipe of radius 1.5 cm are successfully modeled by known processes which include heavy flavor production. In contrast, we are presently unable to fully account for the number and properties of the remaining events, in which at least one muon candidate is produced outside of the beam pipe, in terms of the same understanding of the CDF II detector, trigger, and event reconstruction. |
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Address |
[Chen, Y. C.; Hou, S.; Mitra, A.; Teng, P. K.; Tsai, S. -Y.; Wang, S. M.] Acad Sinica, Inst Phys, Taipei, Taiwan, Email: ptohos@fnal.gov |
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Springer |
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English |
Summary Language |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1434-6044 |
ISBN |
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Medium |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000279843400004 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
280 |
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Author |
Batist, L.; Gorska, M.; Grawe, H.; Janas, Z.; Kavatsyuk, M.; Karny, M.; Kirchner, R.; La Commara, M.; Mukha, I.; Plochocki, A.; Roeckl, E. |
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Title |
Systematics of Gamow-Teller beta decay “Southeast” of Sn-100 |
Type |
Journal Article |
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Year |
2010 |
Publication |
European Physical Journal A |
Abbreviated Journal |
Eur. Phys. J. A |
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Volume |
46 |
Issue |
1 |
Pages |
45-53 |
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Keywords |
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Abstract |
The energy centroids and integrated strengths of Gamow-Teller transitions in the beta(+) and electron-capture decay are analyzed for nuclei whose proton number Z and neutron number N are restricted to 44 <= Z <= 50 and 50 <= N <= 58. The analysis is based on data measured both with high-resolution gamma-ray spectrometry and total gamma-ray absorption techniques. The dependence of the considered quantities on the relative neutron excess are established after taking into account the effects due to the Coulomb interaction and mean-field level occupancies. An extrapolation of this dependence to the lightest known tin isotopes is used to estimate the decay characteristics of Sn-100 and Sn-101. The values extrapolated for the half-lives of Sn-100 and Sn-101 agree with experimental data. Using the extrapolated values together with shell model predictions, the Q values for the electron-capture decay of Sn-100 is evaluated. The quenching factor for beta(+) and the electron-capture decay of the nuclei under consideration here is established to be 0.56(2) with a possible weak dependence on N – Z. |
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Address |
[Batist, L.] St Petersburg Nucl Phys Inst, RU-188350 Gatchina, Russia, Email: batist@pnpi.spb.ru |
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Publisher |
Springer |
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Language |
English |
Summary Language |
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Original Title |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1434-6001 |
ISBN |
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Medium |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000282433500005 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ pastor @ |
Serial |
258 |
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Author |
Sanjuan, R.; Nebot, M.; Chirico, N.; Mansky, L.M.; Belshaw, R. |
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Title |
Viral Mutation Rates |
Type |
Journal Article |
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Year |
2010 |
Publication |
Journal of Virology |
Abbreviated Journal |
J. Virol. |
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Volume |
84 |
Issue |
19 |
Pages |
9733-9748 |
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Keywords |
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Abstract |
Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10(-8) to 10(-6) s/n/c for DNA viruses and from 10(-6) to 10(-4) s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut. |
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Address |
[Sanjuan, Rafael] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolutiva, Dept Genet, Valencia 46980, Spain, Email: rafael.sanjuan@uv.es |
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Publisher |
Amer Soc Microbiology |
Place of Publication |
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Language |
English |
Summary Language |
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Original Title |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0022-538x |
ISBN |
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Medium |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000282641800008 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ elepoucu @ |
Serial |
371 |
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Author |
Aguiar, P.; Rafecas, M.; Ortuño, J.E.; Kontaxakis, G.; Santos, A.; Pavia, J.; Rosetti, M. |
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Title |
Geometrical and Monte Carlo projectors in 3D PET reconstruction |
Type |
Journal Article |
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Year |
2010 |
Publication |
Medical Physics |
Abbreviated Journal |
Med. Phys. |
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Volume |
37 |
Issue |
11 |
Pages |
5691-5702 |
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Keywords |
3D PET; iterative reconstruction; list-mode reconstruction; ray-tracing techniques; Monte Carlo simulation; system response matrix |
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Abstract |
Purpose: In the present work, the authors compare geometrical and Monte Carlo projectors in detail. The geometrical projectors considered were the conventional geometrical Siddon ray-tracer (S-RT) and the orthogonal distance-based ray-tracer (OD-RT), based on computing the orthogonal distance from the center of image voxel to the line-of-response. A comparison of these geometrical projectors was performed using different point spread function (PSF) models. The Monte Carlo-based method under consideration involves an extensive model of the system response matrix based on Monte Carlo simulations and is computed off-line and stored on disk. Methods: Comparisons were performed using simulated and experimental data of the commercial small animal PET scanner rPET. Results: The results demonstrate that the orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions yield better images in terms of contrast and spatial resolution than those obtained after using the conventional method and the multiray-based S-RT. Furthermore, the Monte Carlo-based method yields slight improvements in terms of contrast and spatial resolution with respect to these geometrical projectors. Conclusions: The orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions represent satisfactory alternatives to factorizing the system matrix or to the conventional on-the-fly ray-tracing methods for list-mode reconstruction, where an extensive modeling based on Monte Carlo simulations is unfeasible. |
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Address |
[Aguiar, Pablo] Univ Santiago de Compostela, Dept Fis Particulas, Complexo Hosp Univ Santiago de Compostela, Fdn IDICHUS IDIS, Santiago De Compostela, Spain, Email: pablo.aguiar.fernandez@sergas.es |
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Amer Assoc Physicists Medicine Amer Inst Physics |
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Language |
English |
Summary Language |
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Series Editor |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0094-2405 |
ISBN |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000283747600015 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
338 |
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Author |
Ballester, F.; Granero, D.; Perez-Calatayud, J.; Venselaar, J.L.M.; Rivard, M.J. |
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Title |
Study of encapsulated Tm-170 sources for their potential use in brachytherapy |
Type |
Journal Article |
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Year |
2010 |
Publication |
Medical Physics |
Abbreviated Journal |
Med. Phys. |
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Volume |
37 |
Issue |
4 |
Pages |
1629-1637 |
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Keywords |
brachytherapy; cancer; dosimetry; prosthetics; radioisotopes; thulium |
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Abstract |
Methods: The authors have assumed a theoretical Tm-170 cylindrical source encapsulated with stainless steel and typical dimensions taken from the currently available HDR Ir-192 brachytherapy sources. The dose-rate distribution was calculated for this source using the GEANT4 Monte Carlo (MC) code considering both photon and electron Tm-170 spectra. The AAPM TG-43 U1 brachytherapy dosimetry parameters were derived. To study general properties of Tm-170 encapsulated sources, spherical sources encapsulated with stainless steel and platinum were also studied. Moreover, the influence of small variations in the active core and capsule dimensions on the dosimetric characteristics was assessed. Treatment times required for a Tm-170 source were compared to those for Ir-192 and Yb-169 for the same contained activity. Results: Due to the energetic beta spectrum and the large electron yield, the bremsstrahlung contribution to the dose was of the same order of magnitude as from the emitted gammas and characteristic x rays. Moreover, the electron spectrum contribution to the dose was significant up to 4 mm from the source center compared to the photon contribution. The dose-rate constant Lambda of the cylindrical source was 1.23 cGy h(-1) U-1. The behavior of the radial dose function showed promise for applications in brachytherapy. Due to the electron spectrum, the anisotropy was large for r < 6 mm. Variations in manufacturing tolerances did not significantly influence the final dosimetry data when expressed in cGy h(-1) U-1. For typical capsule dimensions, maximum reference dose rates of about 0.2, 10, and 2 Gy min(-1) would then be obtained for Tm-170, Ir-192, and Yb-169, respectively, resulting in treatment times greater than those for HDR Ir-192 brachytherapy. Conclusions: The dosimetric characteristics of source designs exploiting the low photon energy of Tm-170 were studied for potential application in HDR-brachytherapy. Dose-rate distributions were obtained for cylindrical and simplified spherical Tm-170 source designs (stainless steel and platinum capsule materials) using MC calculations. Despite the high activity of Tm-170, calculated treatment times were much longer than for Ir-192. |
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Address |
[Ballester, Facundo] Univ Valencia, Dept Atom Mol & Nucl Phys, E-46100 Burjassot, Spain, Email: fballest@uv.es |
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Publisher |
Amer Assoc Physicists Medicine Amer Inst Physics |
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English |
Summary Language |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0094-2405 |
ISBN |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000276211200027 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ elepoucu @ |
Serial |
478 |
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| Permanent link to this record |
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Author |
Rivard, M.J.; Granero, D.; Perez-Calatayud, J.; Ballester, F. |
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Title |
Influence of photon energy spectra from brachytherapy sources on Monte Carlo simulations of kerma and dose rates in water and air |
Type |
Journal Article |
| |
Year |
2010 |
Publication |
Medical Physics |
Abbreviated Journal |
Med. Phys. |
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Volume |
37 |
Issue |
2 |
Pages |
869-876 |
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Keywords |
biomedical materials; brachytherapy; dosimetry; iodine; iridium; Monte Carlo methods; palladium; radioisotopes |
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Abstract |
Methods: For Ir-192, I-125, and Pd-103, the authors considered from two to five published spectra. Spherical sources approximating common brachytherapy sources were assessed. Kerma and dose results from GEANT4, MCNP5, and PENELOPE-2008 were compared for water and air. The dosimetric influence of Ir-192, I-125, and Pd-103 spectral choice was determined. Results: For the spectra considered, there were no statistically significant differences between kerma or dose results based on Monte Carlo code choice when using the same spectrum. Water-kerma differences of about 2%, 2%, and 0.7% were observed due to spectrum choice for Ir-192, I-125, and Pd-103, respectively (independent of radial distance), when accounting for photon yield per Bq. Similar differences were observed for air-kerma rate. However, their ratio (as used in the dose-rate constant) did not significantly change when the various photon spectra were selected because the differences compensated each other when dividing dose rate by air-kerma strength. Conclusions: Given the standardization of radionuclide data available from the National Nuclear Data Center (NNDC) and the rigorous infrastructure for performing and maintaining the data set evaluations, NNDC spectra are suggested for brachytherapy simulations in medical physics applications. |
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Address |
[Rivard, Mark J.] Tufts Univ, Sch Med, Dept Radiat Oncol, Boston, MA 02111 USA, Email: mrivard@tuftsmedicalcenter.org |
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Publisher |
Amer Assoc Physicists Medicine Amer Inst Physics |
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English |
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0094-2405 |
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ISI:000274075600048 |
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yes |
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IFIC @ elepoucu @ |
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504 |
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Author |
Belver, D.; Cabanelas, P.; Castro, E.; Garzon, J.A.; Gil, A.; Gonzalez-Diaz, D.; Koenig, W.; Traxler, M. |
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Title |
Performance of the Low-Jitter High-Gain/Bandwidth Front-End Electronics of the HADES tRPC Wall |
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Journal Article |
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2010 |
Publication |
IEEE Transactions on Nuclear Science |
Abbreviated Journal |
IEEE Trans. Nucl. Sci. |
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57 |
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5 |
Pages |
2848-2856 |
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Keywords |
Charge to width algorithm; fast amplifying and digitizing electronics; front-end electronics; HADES; time of flight; timing RPC |
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Abstract |
A front-end electronics (FEE) chain for accurate time measurements has been developed for the new Resistive Plate Chamber (RPC)-based Time-of-Flight (TOF) wall of the High Acceptance Di-Electron Spectrometer (HADES). The wall covers an area of around 8 m(2) divided in 6 sectors. In total, 1122 4-gap timing RPC cells are read-out by 2244 time and charge sensitive channels. The FEE chain consists of 2 custom-made boards: a 4-channel Daughter BOard(DBO) and a 32-channel MotherBOard (MBO). The DBO uses a fast 2 GHz amplifier feeding a dual high-speed discriminator. The time and charge information are encoded, respectively, in the leading edge and the width of an LVDS signal. Each MBO houses up to 8 DBOs providing them regulated voltage supply, threshold values via DACs, test signals and, additionally, routing out a signal proportional to the channel multiplicity needed for a 1st level trigger decision. The MBO delivers LVDS signals to a multi-purpose Trigger Readout Board (TRB) for data acquisition. The FEE allows achieving a system resolution around 75 ps fulfilling comfortably the requirements of the HADES upgrade [1]. The commissioning of the whole RPC wall is finished and the 6 sectors are already mounted in their final position in the HADES spectrometer and ready to take data during the beam-times foreseen for 2010. |
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[Belver, Daniel; Cabanelas, P.; Castro, E.; Garzon, J. A.] Univ Santiago Compostela, LabCAF, Santiago De Compostela 15782, Spain, Email: daniel.belver@usc.es |
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Ieee-Inst Electrical Electronics Engineers Inc |
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English |
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0018-9499 |
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ISI:000283440400007 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ elepoucu @ |
Serial |
349 |
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