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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 |
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English |
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ISSN |
0022-538x |
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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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English |
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ISSN |
0094-2405 |
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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 |
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ISSN |
0094-2405 |
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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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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 |
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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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Amer Assoc Physicists Medicine Amer Inst Physics |
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Language |
English |
Summary Language |
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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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Conference |
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Notes |
ISI:000274075600048 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
yes |
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Call Number |
IFIC @ elepoucu @ |
Serial |
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 |
Type |
Journal Article |
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Year |
2010 |
Publication |
IEEE Transactions on Nuclear Science |
Abbreviated Journal |
IEEE Trans. Nucl. Sci. |
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Volume |
57 |
Issue |
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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Address |
[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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Publisher |
Ieee-Inst Electrical Electronics Engineers Inc |
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Language |
English |
Summary Language |
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Series Issue |
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Edition |
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ISSN |
0018-9499 |
ISBN |
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Conference |
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Notes |
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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