bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Monte Carlo collimator transport methods for photon treatment planning in radiotherapy
Authors: Schmidhalter D. , Manser P. , Frei D. , Volken W. , Fix M. K. 
Published: January 2010

Purpose:The aim of this work was a Monte Carlo (MC) based investigation of the impact of different radiation transport methods in collimators of a linear accelerator on photon beam characteristics, dose distributions, and efficiency. Thereby it is investigated if it is possible to use different simplifications in the radiation transport for some clinical situations in order to save calculation time.Methods:Within the Swiss Monte Carlo Plan, a GUI‐based framework for photon MC treatment planning, different MC methods are available for the radiation transport through the collimators [secondary jaws and multileaf collimator (MLC)]: EGSnrc (reference),, and Pin (an in‐house developed MC code). Additional nonfull transport methods were implemented in order to provide different complexity levels for the MC simulation: Considering collimator attenuation only, considering Compton scatter only or just the firstCompton process, and considering the collimators as totally absorbing. Furthermore, either a simple or an exact geometry of the collimators can be selected for the absorbing or attenuation method. Phasespaces directly above and dose distributions in a water phantom are analyzed for academic and clinical treatment fields using 6 and 15 MV beams, including intensity modulated radiation therapy with dynamic MLC.Results:For all MC transport methods, differences in the radial mean energy and radial energy fluence are within 1% inside the geometric field. Below the collimators, the energy fluence is underestimated for nonfull MC transport methods ranging from 5% for Compton to 100% for Absorbing. Gamma analysis using EGSnrc calculated doses as reference shows that the percentage of voxels fulfilling a 1% /1 mm criterion is at least 98% when using, Compton, or firstCompton transport methods. When using the methods Pin, Transmission, Flat‐Transmission, Flat‐Absorbing or Absorbing, the mean value of points fulfilling this criterion over all tested cases is 97%, 88%, 74%, 68%, or 65%, respectively. However, compared to EGSnrc calculations, the gain in efficiency is a factor of up to 10 for and up to 48 for the absorbing method.Conclusions:The results of this investigation suggest that it is an option to use a simple transport technique in the initial treatment planning process and use more accurate transport methods for the final dose calculation accepting longer calculation times.
A residual correction method for high‐resolution PET reconstruction with application to on‐the‐fly Monte Carlo based model of positron range
Authors: Fu Lin , Qi Jinyi 
Published: January 2010

Purpose:The quality of tomographic images is directly affected by the system model being used in image reconstruction. An accurate system matrix is desirable for high‐resolution image reconstruction, but it often leads to high computation cost. In this work the authors present a maximum a posteriori reconstruction algorithm with residual correction to alleviate the tradeoff between the model accuracy and the computation efficiency in image reconstruction.Methods:Unlike conventional iterative methods that assume that the system matrix is accurate, the proposed method reconstructs an image with a simplified system matrix and then removes the reconstruction artifacts through residual correction. Since the time‐consuming forward and back projection operations using the accurate system matrix are not required in every iteration, image reconstruction time can be greatly reduced.Results:The authors apply the new algorithm to high‐resolution positron emission tomography reconstruction with an on‐the‐fly Monte Carlo (MC) based positron range model. Computer simulations show that the new method is an order of magnitude faster than the traditional MC‐based method, whereas the visual quality and quantitative accuracy of the reconstructed images are much better than that obtained by using the simplified system matrix alone.Conclusions:The residual correction method can reconstruct high‐resolution images and is computationally efficient.
The effects of dose calculation resolution on dose accuracy for radiation therapy treatments of the lung. Part II. A comparison of dose distributions from an explicit lung model to dose distributions derived from a CT representation
Authors: Babcock Kerry , Sidhu Narinder 
Published: January 2010

Purpose:Due to limitations in computer memory and computation time, typical radiation therapy treatments are calculated with a voxel dimension on the order of several millimeters. The anatomy below this practical resolution is approximated as a homogeneous region uniform in atomic composition and density. The purpose of this article is to examine whether the exclusion of anatomic structure below the practical dose calculation resolution produces deviations in the resulting dose distributions.Methods:EGSnrc calculated dose distributions from the BRANCH lung model of Part I are compared and contrasted to dose distributions from a CT representation of the same BRANCH model for three different phases of the respiration cycle.Results:The exclusion of branching structures below a CT resolution of resulted in a deviation in dose. The deviation in dose was as high as 14% but was localized around the branching structures. There was no significant variation in the dose deviation as a function of either field size or lung density.Conclusions:The exclusion of explicit branching structures of the lung in a CT representation creates localized deviations in dose. To ensure accurate dose calculations, CT resolution must be increased.
Investigation of energy dependence of EBT and EBT‐2 Gafchromic film
Authors: Lindsay Patricia , Rink Alexandra , Ruschin Mark , Jaffray David 
Published: January 2010

Purpose:The purpose of this study was to quantify the extent of energy dependence of Gafchromic film to x‐ray energies ranging in quality from 105 kVp to 6 MV, and relate this dependency to the film's chemical composition and date of production.Methods:Lots of Gafchromic EBT film manufactured in 2004 and 2005 together with more recent batches produced in 2007 were evaluated for energy dependence. Multiple batches of EBT‐2 film were also evaluated. Energy dependence was quantified as—the ratio of net optical density (netOD) measured at a given energy relative to the netOD measured at 6 MV, as measured on a linear accelerator. was evaluated for beam qualities of 105 and 220 kVp on a clinical orthovoltage unit using two separate techniques—a flatbed scanner (Epson) and a real‐time fiber‐optic readout system. Neutron activation analysis for chlorine and bromine content was performed on all the films to determine whether the composition of the film had changed between batches of film exhibiting different energy dependence responses.Results:For batches of EBT manufactured in 2007, was 0.75 and was 0.85, indicating an under‐response at orthovoltage energies. These results were confirmed using both the Epson flatbed scanner as well as the real‐time readout system. For batches of EBT film manufactured before 2006, ranged from 0.9 to 1.0. The results from the neutron activation analysis confirmed a direct relationship between the concentration of chlorine and the magnitude of under‐response at orthovoltage energies. EBT‐2 film exhibited values ranging from 0.79 (under‐response) to 1.20 (over‐response) among batches containing varying concentrations of bromine, chlorine, and potassium.Conclusions:The results of this study indicated that differences in energy response of EBT and EBT‐2 films were due to differences in the chemical composition and therefore the effective atomic number of the film, which have changed over time. To achieve an energy independent dosimeter over a range of kilovoltage energies, the effective atomic number of the dosimeter must be closely matched to that of water. Small deviations in chemical composition can lead to large deviations in response as a function of energy.
Comparison of organ doses for patients undergoing balloon brachytherapy of the breast with HDR or electronic sources using Monte Carlo simulations in a heterogeneous human phantoma)
Authors: Mille Matthew M. , Xu X. George , Rivard Mark J. 
Published: January 2010

Purpose:Accelerated partial breast irradiation via interstitial balloon brachytherapy is a fast and effective treatment method for certain early stage breast cancers. The radiation can be delivered using a conventional high‐dose rate (HDR) gamma‐emitting source or a novel electronic brachytherapy (eBx) source which uses lower energy x rays that do not penetrate as far within the patient. A previous study [A. Dickler, M. C. Kirk, N. Seif, K. Griem, K. Dowlatshahi, D. Francescatti, and R. A. Abrams, “A dosimetric comparison of MammoSite high‐dose‐rate brachytherapy and Xoft Axxent electronic brachytherapy,” Brachytherapy 6, 164–168 (2007)] showed that the target dose is similar for HDR and eBx. This study compares these sources based on the dose received by healthy organs and tissues away from the treatment site.Methods:A virtual patient with left breast cancer was represented by a whole‐body, tissue‐heterogeneous female voxel phantom. Monte Carlo methods were used to calculate the dose to healthy organs in a virtual patient undergoing balloon brachytherapy of the left breast with HDR or eBx sources. The dose‐volume histograms for a few organs which received large doses were also calculated. Additional simulations were performed with all tissues in the phantom defined as water to study the effect of tissue inhomogeneities.Results:For both HDR and eBx, the largest mean organ doses were received by the ribs, thymus gland, left lung, heart, and sternum which were close to the brachytherapy source in the left breast. eBx yielded mean healthy organ doses that were more than a factor of smaller than for HDR for all organs considered, except for the three closest ribs. Excluding these ribs, the average and median dose‐reduction factors were and , respectively. The volume distribution of doses in nearby soft tissue organs that were outside the PTV were also improved with eBx. However, the maximum dose to the closest rib with the eBx source was 5.4 times greater than that of the HDR source. The ratio of tissue‐to‐water maximum rib dose for the eBx source was .Conclusions:The results of this study indicate that eBx may offer lower toxicity to most healthy tissues, except nearby bone. TG‐43 methods have a tendency to underestimate dose to bone, especially the ribs. Clinical studies evaluating the negative health effects caused by irradiating healthy organs are needed so that physicians can better understand when HDR or eBx might best benefit a patient.
Focal beam distortion and treatment planning for transrib focused ultrasound thermal therapy: A feasibility study using a two‐dimensional ultrasound phased array
Authors: Liu Hao‐Li , Hsu Chia‐Lung , Huang Sheng‐Min , Hsi Yi‐Wen 
Published: January 2010

Purpose:The purpose of this study is to numerically investigate the feasibility of employing a spherical‐section ultrasound phased array for transrib thermal ablation of liver tumors.Methods:Based on CT images, the authors performed a 3D reconstruction of the ribs and the surrounding soft tissues. A 3D pseudospectral time‐domain (PSTD) solver was used to assess wave propagation and the distribution of pressure, with the aim of determining the specific absorption rate (SAR) and the resulting thermal doses and dynamics. Phase aberrations caused by the interposed ribs were corrected to assess the efficacy of the device in improving the SAR gain between the ribs and the target positions.Results:Experimental results supported the usefulness of the PSTD solver for predicting the pressure distribution due to the interfering obstacle. In addition, the method allowed the correction of phase aberrations caused by the ribs, and a significant improvement (176%) in the SAR gain between the ribs and the target points was observed at specific frequencies.Conclusions:The method allowed successful tissue targeting without causing overheating of the ribs. One main advantage of this approach is the accurate estimation of phase aberration caused by heterogeneously porous ribs and other interposed tissues. This strategy might prove useful to assess the effectiveness and safety of focused ultrasound thermal ablation prior to transrib treatment.
Susceptibility gradient quantization by MRI signal response mapping (SIRMA) to dephaser
Authors: Franconi F. , Chapon C. , Le Jeune J. J. , Richomme P. , Lemaire L. 
Published: January 2010

Purpose:Susceptibility effects are a very efficient source of contrast in magnetic resonance imaging. However, detection is hampered by the fact the induced contrast is negative. In this work, the SIgnal Response MApping (SIRMA) to dephaser method is proposed to map susceptibility gradient to improve visualization.Methods:In conventional gradient echo acquisitions, the echo formation of susceptibility affected spins is shifted in‐space, the shift being proportional to the susceptibility gradient. Susceptibility gradients map can be produced by measuring this induced shifts. The SIRMA method measures these shifts from a series of dephased images collected with additional incremental dephasers. These additional dephasers correspond either to a slice refocusing gradient offset or to a reconstruction window off‐centering. The signal intensity profile as a function of the additional dephaser was determined on a pixel‐by‐pixel basis from the ensemble of dephased images. Susceptibility affected voxels presented a signal response profile maximum shifted compared to nonaffected voxels ones. Shift magnitude and sign were measured for each pixel to determine susceptibility gradients and produce a susceptibility gradient map.Results:In vitro experiments demonstrated the ability of the method to map gradient inhomogeneities induced by a cylinder. Quantization accuracy was evaluated comparing SIRMA images and simulations performed on the well‐characterized air filled cylinder model. Performances of the SIRMA method, evaluated in vitro on cylinders filled with various superparamagnetic iron oxide SPIO concentrations, showed limited influence of acquisition parameters. Robustness of the method was then assessed in vivo after an infusion of SPIO‐loaded nanocapsules into the rat brain using a convection‐enhanced drug delivery approach. The region of massive susceptibility gradient induced by the SPIO‐loaded nanocapsules was clearly delineated on SIRMA maps and images were compared to weighted images, Susceptibility Gradient Map (SGM), and histological Perl's staining slice. The potential for quantitative evaluation of SPIO distribution volume was demonstrated.Conclusions:The proposed method is a promising technique for a wide range of applications especially in molecular or cellular imaging with respect to its quantitative nature and its computational simplicity.
Optimization and Application of a Multiplex Bead-Based Assay To Quantify Serotype-Specific IgG againstStreptococcus pneumoniaePolysaccharides: Response to the Booster Vaccine after Immunization with the Pneumococcal 7-Valent Conjugate Vaccine
Authors: Elberse Karin E. M. , Tcherniaeva Irina , Berbers Guy A. M. , Schouls Leo M. 
Published: February 2010

ABSTRACTWe describe the optimization and application of a multiplex bead-based assay (Luminex) to quantify antibodies against polysaccharides of 13 pneumococcal serotypes. In the optimized multiplex immunoassay (MIA), intravenous immune globulin was introduced as an in-house reference serum, and nonspecific reacting antibodies were adsorbed with the commercial product pneumococcal C polysaccharides Multi. The antibody concentrations were assessed in 188 serum samples obtained pre- and post-booster vaccination at 11 months after administration of a primary series of the pneumococcal seven-valent conjugate vaccine (PCV-7) at 2, 3, and 4 months of age. The results of the MIA were compared with those of the ELISA for the serotypes included in the seven-valent conjugated polysaccharide vaccine and for a non-vaccine serotype, serotype 6A. The geometric mean concentrations of the antibodies determined by MIA were slightly higher than those determined by ELISA. The correlations between the assays were good, withR2values ranging from 0.84 to 0.91 for all serotypes except serotype 19F, for whichR2was 0.70. The concentrations of antibody against serotype 6A increased after the administration of PCV-7 due to cross-reactivity with serotype 6B. The differences between the results obtained by ELISA and MIA suggest that the internationally established protective threshold of 0.35 μg/ml should be reevaluated for use in the MIA and may need to be amended separately for each serotype.
Coincorporation of LpxL1 and PagL Mutant Lipopolysaccharides into Liposomes withNeisseria meningitidis Opacity Protein: Influence on Endotoxic and Adjuvant Activity
Authors: Arenas Jesús , van Dijken Harry , Kuipers Betsy , Hamstra Hendrik Jan , Tommassen Jan , van der Ley Peter 
Published: January 2010

ABSTRACTWild-type lipopolysaccharide (LPS) ofNeisseria meningitidisnormally contains six acyl chains. Penta-acylated LPS forms were generated through inactivation of thelpxL1gene or through the expression of theBordetella bronchiseptica pagLgene inN. meningitidis. The resulting LPS species, designated LpxL1 LPS and PagL LPS, respectively, display reduced endotoxic activity compared to wild-type LPS. Here, we determined the adjuvant potential of PagL LPS by comparison with the broadly used LpxL1 LPS. We also investigated the potential benefit for adjuvanticity of coincorporating these LPS species, together with the meningococcal opacity-associated protein OpaJ as a model antigen, in a liposomal delivery system. PagL LPS showed a higher endotoxic activity than LpxL1 LPS, and their incorporation into liposomes significantly reduced their endotoxic activity as determined by measuring the induction of interleukin-6 (IL-6) production in a murine macrophage cell line. To determine the adjuvant effect, BALB/c mice were immunized with OpaJ-containing liposomes and either free LPS or LPS coincorporated into the proteoliposomes. OpaJ-containing liposomes adjuvanted with AlPO4or not adjuvanted at all were included as control groups. In the appropriate dose, PagL LPS showed a superior adjuvant effect compared with LpxL1 LPS, and for both LPS types, free LPS showed a higher adjuvant effect than when coincorporated into the liposomes, as evidenced by higher titers of IgG2a and IgG2b antibodies against OpaJ+meningococci and higher bactericidal titers. In conclusion, PagL LPS is a better adjuvant than LpxL1 LPS, but coincorporation of either LPS into proteoliposomes did not improve their adjuvant activity.
IgA Antibody Response of Swine to Foot-and-Mouth Disease Virus Infection and Vaccination
Authors: Pacheco Juan M. , Butler John E. , Jew Jessica , Ferman Geoffrey S. , Zhu James , Golde William T. 
Published: January 2010

ABSTRACTFoot-and-mouth disease virus (FMDV) continues to be a significant economic problem worldwide. Control of the disease involves the use of killed-virus vaccines, a control measure developed decades ago. After natural infection, the primary site of replication of FMDV is the pharyngeal area, suggesting that a mucosal immune response is the most effective. Humoral immunity to killed-virus vaccination induces antibodies that can prevent the clinical disease but not local infection. Determining whether infection or vaccination stimulates IgA-mediated local immunity depends on the method of analysis. Different assays have been described to analyze the quality of antibody responses of cattle and swine to FMDV, including indirect double-antibody sandwich enzyme-linked immunosorbent assay (IDAS-ELISA) and antibody capture assay-ELISA (ACA-ELISA). We tested these assays on swine and show that vaccinated animals had FMDV-specific IgM and IgG but no IgA in either serum or saliva. After the infection, both assays detected FMDV-specific IgM, IgG, and IgA in serum. Notably, serum IgA was more readily detected using the ACA-ELISA, whereas IgA was not detected in saliva with this assay. FMDV-specific IgA antibodies were detected in saliva samples using the IDAS-ELISA. These data show that parenterally administered, killed-virus vaccine does not induce a mucosal antibody response to FMDV and illuminates limitations and appropriate applications of the two ELISAs used to measure FMDV-specific responses. Further, the presence of the IgA antivirus in serum correlates with the presence of such antibodies in saliva.
Diagnosing Human Anisakiasis: Recombinant Ani s 1 and Ani s 7 Allergens versus the UniCAP 100 Fluorescence Enzyme Immunoassay
Authors: Anadón A. M. , Rodríguez E. , Gárate M. T. , Cuéllar C. , Romarís F. , Chivato T. , Rodero M. , González-Díaz H. , Ubeira F. M. 
Published: January 2010

ABSTRACTCommercially available serological methods for serodiagnosis of human anisakiasis either are poorly specific or do not include some of the most relevantAnisakisallergens. The use of selected recombinant allergens may improve serodiagnosis. To compare the diagnostic and clinical values of enzyme-linked immunosorbent assay (ELISA) methods based on Ani s 1 and Ani s 7 recombinant allergens and of the UniCAP 100 fluorescence enzyme immunoassay (CAP FEIA) system, we tested sera from 495 allergic and 25 non-food-related allergic patients. The decay in specific IgE antibodies in serum was also investigated in 15 positive patients over a period of 6 to 38 months. Considering sera that tested positive by either Ani s 1 or Ani s 7 ELISA, the CAP FEIA classified 25% of sera as falsely positive, mainly in the group of patients with the lowest levels of anti-AnisakisIgE antibodies, and 1.28% of positive sera as falsely negative. Considering allergens individually, the overall sensitivities of Ani s 7 ELISA and Ani s 1 ELISA were 94% and 61%, respectively. The results also showed that anti-AnisakisIgE antibodies can be detected in serum for longer with Ani s 1 ELISA than with Ani s 7 ELISA and CAP FEIA (P< 0.01). Our findings suggest that ELISA methods with Ani s 7 and Ani s 1 allergens as targets of IgE antibodies are currently the best option for serodiagnosis of human anisakiasis, combining specificity and sensitivity. The different persistence of anti-Ani s 1 and anti-Ani s 7 antibodies in serum may help clinicians to distinguish between recent and oldAnisakisinfections.
Validation of a Medium-Throughput Method for Evaluation of Intracellular Growth of
Mycobacterium tuberculosis
Authors: Eklund Daniel , Welin Amanda , Schön Thomas , Stendahl Olle , Huygen Kris , Lerm Maria 
Published: January 2010

ABSTRACT

Intracellular pathogens such as
Mycobacterium tuberculosis
have adapted to a life inside host cells, in which they utilize host nutrients to replicate and spread. Ineffective methods for the evaluation of growth of intracellular pathogens in their true environment pose an obstacle for basic research and drug screening. Here we present the validation of a luminometry-based method for the analysis of intramacrophage growth of
M. tuberculosis
. The method, which is performed in a medium-throughput format, can easily be adapted for studies of other intracellular pathogens and cell types. The use of host cells in drug-screening assays dedicated to find antimicrobials effective against intracellular pathogens permits the discovery of not only novel antibiotics but also compounds with immunomodulatory and virulence-impairing activities, which may be future alternatives or complements to antibiotics.