bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monte Carlo calculations of , the beam quality conversion factor
Authors: Muir B. R. , Rogers D. W. O. 
Published: November 2010

Purpose:To use EGSnrc Monte Carlo simulations to directly calculate beam quality conversion factors,, for 32 cylindrical ionization chambers over a range of beam qualities and to quantify the effect of systematic uncertainties on Monte Carlo calculations of . These factors are required to use the TG‐51 or TRS‐398 clinical dosimetry protocols for calibrating external radiotherapy beams.Methods:Ionization chambers are modeled either from blueprints or manufacturers' user's manuals. The dose‐to‐air in the chamber is calculated using the EGSnrc user‐code egs_chamber using 11 different tabulated clinical photon spectra for the incident beams. The dose to a small volume of water is also calculated in the absence of the chamber at the midpoint of the chamber on its central axis. Using a simple equation, is calculated from these quantities under the assumption that is constant with energy and compared to TG‐51 protocol and measured values.Results:Polynomial fits to the Monte Carlo calculated factors as a function of beam quality expressed as and are given for each ionization chamber. Differences are explained between Monte Carlo calculated values and values from the TG‐51 protocol or calculated using the computer program used for TG‐51 calculations. Systematic uncertainties in calculated values are analyzed and amount to a maximum of one standard deviation uncertainty of 0.99% if one assumes that photon cross‐section uncertainties are uncorrelated and 0.63% if they are assumed correlated. The largest components of the uncertainty are the constancy of and the uncertainty in the cross‐section for photons in water.Conclusions:It is now possible to calculate directly using Monte Carlo simulations. Monte Carlo calculations for most ionization chambers give results which are comparable to TG‐51 values. Discrepancies can be explained using individual Monte Carlo calculations of various correction factors which are more accurate than previously used values. For small ionization chambers with central electrodes composed of high‐Z materials, the effect of the central electrode is much larger than that for the aluminum electrodes in Farmer chambers.
Patient radiation dose in prospectively gated axial CT coronary angiography and retrospectively gated helical technique with a 320‐detector row CT scanner
Authors: Seguchi Shigenobu , Aoyama Takahiko , Koyama Shuji , Fujii Keisuke , Yamauchi‐Kawaura Chiyo 
Published: November 2010

Purpose:The aim of this study was to evaluate radiation dose to patients undergoing computed tomography coronary angiography (CTCA) for prospectively gated axial (PGA) technique and retrospectively gated helical (RGH) technique.Methods:Radiation doses were measured for a 320‐detector row CT scanner (Toshiba Aquilion ONE) using small sized silicon‐photodiode dosimeters, which were implanted at various tissue and organ positions within an anthropomorphic phantom for a standard Japanese adult male. Output signals from photodiode dosimeters were read out on a personal computer, from which organ and effective doses were computed according to guidelines published in the International Commission on Radiological Protection Publication 103.Results:Organs that received high doses were breast, followed by lung, esophagus, and liver. Breast doses obtained with PGA technique and a phase window width of 16% at a simulated heart rate of 60 beats per minute were 13 mGy compared to 53 mGy with RGH technique using electrocardiographically dependent dose modulation at the same phase window width as that in PGA technique. Effective doses obtained in this case were 4.7 and 20 mSv for the PGA and RGH techniques, respectively. Conversion factors of dose length product to the effective dose in PGA and RGH were 0.022 and with a scan length of 140 mm.Conclusions:CTCA performed with PGA technique provided a substantial effective dose reduction, i.e., 70%–76%, compared to RGH technique using the dose modulation at the same phase windows as those in PGA technique. Though radiation doses in CTCA with RGH technique were the same level as, or some higher than, those in conventional coronary angiography (CCA), the use of PGA technique reduced organ and effective doses to levels less than CCA except for breast dose.
Inverse planning for four‐dimensional (4D) volumetric modulated arc therapya)
Authors: Ma Yunzhi , Chang Daniel , Keall Paul , Xie Yiaoqin , Park Jae‐yoon , Suh Tae‐Suk , Xing Lei 
Published: November 2010

Purpose:To develop a 4D volumetric modulated arc therapy (VMAT) inverse planning framework.Methods:4D VMAT inverse planning aims to derive an aperture and weight modulated arc therapy treatment plan that optimizes the accumulated dose distribution from all gantry angles and breathing phases. Under an assumption that the gantry rotation and patient breathing are synchronized (i.e., there is a functional relationship between the phase of the patient breathing cycle and the beam angle), the authors compute the contribution from different respiration phases through the registration of the phased CT images. The accumulative dose distribution is optimized by iteratively adjusting the aperture shape and weight of each beam through the minimization of the planning objective function. For comparison, traditional 3D VMAT plans are also performed for the two cases and the performance of the proposed technique is demonstrated.Results:A framework for 4D VMAT inverse planning has been proposed. With the consideration of the extra dimension of time in VMAT, a tighter target margin can be achieved with a full duty cycle, which is otherwise not achievable simultaneously by either 3D VMAT optimization or gated VMAT.Conclusions:The 4D VMAT planning formulism proposed here provides useful insight on how the “time” dimension can be exploited in rotational arc therapy to maximally compensate for the intrafraction organ motion.
Maximum intensity projection (MIP) imaging using slice‐stacking MRIa)
Authors: Adamson Justus , Chang Zheng , Wang Zhiheng , Yin Fang‐Fang , Cai Jing 
Published: November 2010

Purpose:To evaluate the feasibility of acquiring maximum intensity projection (MIP) images using a novel slice‐stacking MRI (SS‐MRI) technique.Methods:The proposed technique employed a steady state acquisition sequence to image multiple axial slices. At each axial slice, the scan is repeated throughout one respiratory cycle. Four objects (small, medium, and large triangles, and a cylinder) moving with a patient breathing trajectory were imaged repeatedly for six times using the slice‐stacking MRI and 4D‐CT. and were reconstructed. The internal target volume (ITV) was segmented for each object on the six scans and compared between and . The medium triangle was also imaged with various motion patterns using slice‐stacking MRI, 4D‐CT, and sagittal cine‐MRI. The corresponding MIP images were reconstructed and volume/area measurements were performed and compared between different imaging methods. Three healthy volunteers underwent the slice‐stacking MRI and sagittal cine‐MRI scans. A region of interest (ROI) was selected and contoured for each subject in both and . The area of the selected ROI was computed and compared.Results:Volume comparison between and showed statistically insignificant ( in all cases) difference in the mean ITVs for all four objects. For the study of the medium triangle with multiple motion patterns, there was a good agreement in the measured ITVs between and (, correlation ), with a mean difference of . The area measurements between and also showed good agreement (, correlation ), with a mean difference of . For the healthy volunteer study, the average difference in the area of selected ROI was between and .Conclusions:These preliminary results showed good agreement in volume/area measurements between the slice‐stacking MRI technique and 4D‐CT/cine‐MRI, indicating that it is feasible to use this technique for MIP imaging.
Total variation superiorization schemes in proton computed tomography image reconstruction
Authors: Penfold S. N. , Schulte R. W. , Censor Y. , Rosenfeld A. B. 
Published: November 2010

Purpose: Iterative projection reconstruction algorithms are currently the preferred reconstruction method in proton computed tomography (pCT). However, due to inconsistencies in the measured data arising from proton energy straggling and multiple Coulomb scattering, the noise in the reconstructed image increases with successive iterations. In the current work, the authors investigated the use of total variation superiorization (TVS) schemes that can be applied as an algorithmic add‐on to perturbation‐resilient iterative projection algorithms for pCT image reconstruction.Methods: The block‐iterative diagonally relaxed orthogonal projections (DROP) algorithm was used for reconstructing GEANT4 Monte Carlo simulated pCT data sets. Two TVS schemes added on to DROP were investigated; the first carried out the superiorization steps once per cycle and the second once per block. Simplifications of these schemes, involving the elimination of the computationally expensive feasibility proximity checking step of the TVS framework, were also investigated. The modulation transfer function and contrast discrimination function were used to quantify spatial and density resolution, respectively.Results: With both TVS schemes, superior spatial and density resolution was achieved compared to the standard DROP algorithm. Eliminating the feasibility proximity check improved the image quality, in particular image noise, in the once‐per‐block superiorization, while also halving image reconstruction time. Overall, the greatest image quality was observed when carrying out the superiorization once per block and eliminating the feasibility proximity check.Conclusions: The low‐contrast imaging made possible with TVS holds a promise for its incorporation into future pCT studies.
Characterization of a multi‐axis ion chamber array
Authors: Simon Thomas A. , Kozelka Jakub , Simon William E. , Kahler Darren , Li Jonathan , Liu Chihray 
Published: November 2010

Purpose:The aim of this work was to characterize a multi‐axis ion chamber array (IC PROFILER™; Sun Nuclear Corporation, Melbourne, FL USA) that has the potential to simplify the acquisition of LINAC beam data.Methods:The IC PROFILER™ (orpanel) measurement response was characterized with respect to radiation beam properties, including dose, dose per pulse, pulse rate frequency (PRF), and energy. Panel properties were also studied, including detector‐calibration stability, power‐on time, backscatter dependence, and the panel's agreement with water tank measurements [profiles, fractional depth dose (FDD), and output factors].Results:The panel's relative deviation was typically within (±) 1% of an independent (or nominal) response for all properties that were tested. Notable results were (a) a detectable relative field shape change of with linear accelerator PRF changes; (b) a large range in backscatter thickness had a minimal effect on the measured dose distribution (typically less than 1%); (c) the error spread in profile comparison between the panel and scanning water tank (Blue Phantom™, CC13™; IBA Schwarzenbruck, DE) was approximately (±) 0.75%.Conclusions:The ability of the panel to accurately reproduce water tank profiles, FDDs, and output factors is an indication of its abilities as a dosimetry system. The benefits of using the panel versus a scanning water tank are less setup time and less error susceptibility. The same measurements (including device setup and breakdown) for both systems took 180 min with the water tank versus 30 min with the panel. The time‐savings increase as the measurement load is increased.
New Species Genetic Approach To Identify Strains of Mitis Group Streptococci That Are Donors of Rifampin Resistance to
Streptococcus pneumoniae
Authors: Ferrándiz María-José , Ardanuy Carmen , Liñares Josefina , Balsalobre Luz , García María Teresa , de la Campa Adela G. 
Published: November 2010

ABSTRACT

Eight rifampin-resistant streptococci of the mitis group were identified at the species level by using a concatenated 16S rRNA gene-
sodA-rpoB-hlpA
sequence. Characterization of their
rpoB
alleles showed single amino acid changes involved in rifampin resistance. Comparison of RpoB sequences from pneumococcal recombinant isolates, viridans isolates, and type strains revealed a species-specific amino acid signature, which allowed it to be ascertained that recombinant RpoBs were originated in genetic interchanges with
Streptococcus mitis
and
Streptococcus oralis
.
Evaluation of Ceftazidime and NXL104 in Two Murine Models of Infection Due to KPC-Producing
Klebsiella pneumoniae
Authors: Endimiani Andrea , Hujer Kristine M. , Hujer Andrea M. , Pulse Mark E. , Weiss William J. , Bonomo Robert A. 
Published: November 2010

ABSTRACT

We evaluated the efficacy of NXL104, a novel β-lactamase inhibitor, in combination with ceftazidime (CAZ) in two murine infection models (septicemia and thigh infection). We chose two KPC-producing
Klebsiella pneumoniae
strains (VA-361 and VA-406) showing MICs of CAZ of ≥256 μg/ml. Septicemia was induced by the intraperitoneal injection of KPC-producing
K. pneumoniae
followed 30 min later by a single subcutaneous treatment with CAZ alone or CAZ-NXL104 in ratios of 2:1, 4:1, 8:1, and 16:1. In this model, the median effective doses for 50% (ED
50
) of the animals for CAZ alone versus VA-361 and VA-406 were 1,578 and 709 mg/kg of body weight, respectively. When combined with NXL104 at 2:1, 4:1, 8:1, and 16:1 ratios, the CAZ ED
50
s for VA-361 and VA-406 were reduced to 8.1 and 3.5 mg/kg, 15.1 and 3.8 mg/kg, 16.9 and 7.2 mg/kg, and 29.5 and 12.1 mg/kg, respectively. For thigh infection, neutropenia was induced by the intraperitoneal injection of cyclophosphamide at days −4 and −1 preinfection. Infection was established by the intramuscular injection of KPC-producing
K. pneumoniae
into the right thigh. Mice were treated 1.5 h postinfection with either CAZ alone or CAZ-NXL104 at constant ratios of 4:1. When thighs were removed at 24 h postinfection, a >2-log CFU reduction was observed for mice treated with CAZ-NXL104 at doses of ≥128:32 mg/kg. In contrast, CAZ doses of ≥1,024 mg/kg were unable to reduce the numbers of CFU. Despite resistance to CAZ and possessing a complex β-lactamase background, NXL104 combined with CAZ proved to be very effective in murine models of infection due to contemporary highly resistant KPC-producing
K. pneumoniae
isolates.
Sawyeria marylandensis (Heterolobosea) Has a Hydrogenosome with Novel Metabolic Properties
Authors: Barberà Maria José , Ruiz-Trillo Iñaki , Tufts Julia Y. A. , Bery Amandine , Silberman Jeffrey D. , Roger Andrew J. 
Published: October 2010

ABSTRACT

Protists that live under low-oxygen conditions often lack conventional mitochondria and instead possess mitochondrion-related organelles (MROs) with distinct biochemical functions. Studies of mostly parasitic organisms have suggested that these organelles could be classified into two general types: hydrogenosomes and mitosomes. Hydrogenosomes, found in parabasalids, anaerobic chytrid fungi, and ciliates, metabolize pyruvate anaerobically to generate ATP, acetate, CO
2
, and hydrogen gas, employing enzymes not typically associated with mitochondria. Mitosomes that have been studied have no apparent role in energy metabolism. Recent investigations of free-living anaerobic protists have revealed a diversity of MROs with a wider array of metabolic properties that defy a simple functional classification. Here we describe an expressed sequence tag (EST) survey and ultrastructural investigation of the anaerobic heteroloboseid amoeba
Sawyeria marylandensis
aimed at understanding the properties of its MROs. This organism expresses typical anaerobic energy metabolic enzymes, such as pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenase, and associated hydrogenase maturases with apparent organelle-targeting peptides, indicating that its MRO likely functions as a hydrogenosome. We also identified 38 genes encoding canonical mitochondrial proteins in
S. marylandensis
, many of which possess putative targeting peptides and are phylogenetically related to putative mitochondrial proteins of its heteroloboseid relative
Naegleria gruberi
. Several of these proteins, such as a branched-chain alpha keto acid dehydrogenase, likely function in pathways that have not been previously associated with the well-studied hydrogenosomes of parabasalids. Finally, morphological reconstructions based on transmission electron microscopy indicate that the
S. marylandensis
MROs form novel cup-like structures within the cells. Overall, these data suggest that
Sawyeria marylandensis
possesses a hydrogenosome of mitochondrial origin with a novel combination of biochemical and structural properties.
Histidine Kinase Two-Component Response Regulator Proteins Regulate Reproductive Development, Virulence, and Stress Responses of the Fungal Cereal Pathogens Cochliobolus heterostrophus and Gibberella zeae
Authors: Oide Shinichi , Liu Jinyuan , Yun Sung-Hwan , Wu Dongliang , Michev Alex , Choi May Yee , Horwitz Benjamin A. , Turgeon B. Gillian 
Published: October 2010

ABSTRACT

Histidine kinase (HK) phosphorelay signaling is a major mechanism by which fungi sense their environment. The maize pathogen
Cochliobolus heterostrophus
has 21 HK genes, 4 candidate response regulator (RR) genes (
SSK1
,
SKN7
,
RIM15
,
REC1
), and 1 gene (
HPT1
) encoding a histidine phosphotransfer domain protein. Because most HKs are expected to signal through RRs, these were chosen for deletion. Except for pigment and slight growth alterations for
rim15
mutants, no measurable altered phenotypes were detected in
rim15
or
rec1
mutants. Ssk1p is required for virulence and affects fertility and proper timing of sexual development of heterothallic
C. heterostrophus
. Pseudothecia from crosses involving
ssk1
mutants ooze masses of single ascospores, and tetrads cannot be found. Wild-type pseudothecia do not ooze. Ssk1p represses asexual spore proliferation during the sexual phase, and lack of it dampens asexual spore proliferation during vegetative growth, compared to that of the wild type.
ssk1
mutants are heavily pigmented. Mutants lacking Skn7p do not display any of the above phenotypes; however, both
ssk1
and
skn7
mutants are hypersensitive to oxidative and osmotic stresses and
ssk1 skn7
mutants are more exaggerated in their spore-type balance phenotype and more sensitive to stress than single mutants.
ssk1
mutant phenotypes largely overlap
hog1
mutant phenotypes, and in both types of mutant, the Hog1 target gene,
MST1
, is not induced.
ssk1
and
hog1
mutants were examined in the homothallic cereal pathogen
Gibberella zeae
, and pathogenic and reproductive phases of development regulated by Ssk1 and Hog1 were found to mirror, but also vary from, those of
C. heterostrophus
.
The Yeast-Phase Virulence Requirement for α-Glucan Synthase Differs among Histoplasma capsulatum Chemotypes
Authors: Edwards Jessica A. , Alore Elizabeth A. , Rappleye Chad A. 
Published: October 2010

ABSTRACTHistoplasma capsulatumstrains can be classified into two chemotypes based on cell wall composition. The cell wall of chemotype II yeast contains a layer of α-(1,3)-glucan that masks immunostimulatory β-(1,3)-glucans from detection by the Dectin-1 receptor on host phagocytes. This α-(1,3)-glucan cell wall component is essential for chemotype IIHistoplasmavirulence. In contrast, chemotype I yeast cells lack α-(1,3)-glucanin vitro, yet they remain fully virulentin vivo. Analysis of the chemotype I α-glucan synthase (AGS1) locus revealed a 2.7-kb insertion in the promoter region that diminishesAGS1expression. Nonetheless,AGS1mRNA can be detected during respiratory infection with chemotype I yeast, suggesting that α-(1,3)-glucan could be produced duringin vivogrowth despite its absencein vitro. To directly test whetherAGS1contributes to chemotype I strain virulence, we preventedAGS1function by RNA interference and by insertional mutation. Loss ofAGS1function in chemotype I does not impair the cytotoxicity ofags1(−) mutant yeast to cultured macrophages, nor does it affect the intracellular growth of yeast. In a murine model of histoplasmosis, theags1(−) chemotype I mutant strains show no defect in lung infection or in extrapulmonary dissemination. Together, these studies demonstrate thatAGS1expression is dispensable for chemotype I yeast virulence, in contrast to the case for chemotype II yeast. Despite the absence of cell wall α-(1,3)-glucan, chemotype I yeast can avoid detection by Dectin-1 in a growth stage-dependent manner. This suggests the production of a uniqueHistoplasmachemotype I factor that, at least partially, circumvents the α-(1,3)-glucan requirement for yeast virulence.
Effect of Factor H-Binding Protein Sequence Variation on Factor H Binding and Survival ofNeisseria meningitidisin Human Blood
Authors: Dunphy Kathleen Y. , Beernink Peter T. , Brogioni Barbara , Granoff Dan M. 
Published: November 2010

ABSTRACTBinding of the complement inhibitor factor H (fH) to the surface ofNeisseria meningitidisis critical for evasion of innate host defenses. The meningococcal vaccine candidate factor H-binding protein (fHbp) serves as an fH ligand. We prepared 16 recombinant fHbp natural sequence variants. By enzyme-linked immunosorbent assay (ELISA), the variants from a New Zealand epidemic strain (fHbp ID 14) and from an endemic United Kingdom strain (ID 15) showed 10-fold lower fH binding than a reference fHbp from an epidemic Norwegian strain (ID 1). By surface plasmon resonance, association rate constants (ka) for fHbp ID 14 and 15 were similar to those for ID 1, but dissociation rate constants (kd) were 4- to 10-fold higher than those for ID 1. To determine the effect of fH affinity on fHbp fitness, we prepared isogenic mutants of strain H44/76 that expressed fHbp ID 1, 14, or 15. By flow cytometry, mutants expressing fHbp ID 14 or 15 had lower fH binding than ID 1. When incubated in plasma or blood of nonimmune donors, all three mutants showed similar increases in CFU/ml. In contrast, an isogenic fHbp knockout mutant, which grew well in broth, was rapidly killed in plasma or blood. Thus, although fHbp expression was required for survival of strain H44/76 in blood or plasma, expression of two natural fHbp sequence variants with lower fH affinity had minimal or no effect on nonimmune clearance. One reason may be the high fH concentrations in normal serum, which favor saturation of fH binding to fHbp, even when dissociation rates varied over 10-fold.
Cadherin Domains in the Polysaccharide-Degrading Marine Bacterium
Saccharophagus degradans
2-40 Are Carbohydrate-Binding Modules
Authors: Fraiberg Milana , Borovok Ilya , Bayer Edward A. , Weiner Ronald M. , Lamed Raphael 
Published: October 2010

ABSTRACT

The complex polysaccharide-degrading marine bacterium S
accharophagus degradans
strain 2-40 produces putative proteins that contain numerous cadherin and cadherin-like domains involved in intercellular contact interactions. The current study reveals that both domain types exhibit reversible calcium-dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium.
Draft Genome Sequence of the Anoxygenic Filamentous Phototrophic Bacterium
Oscillochloris trichoides
subsp. DG-6
Authors: Kuznetsov Boris B. , Ivanovsky Ruslan N. , Keppen Olga I. , Sukhacheva Marina V. , Bumazhkin Boris K. , Patutina Ekaterina O. , Beletsky Alexey V. , Mardanov Andrey V. , Baslerov Roman V. , Panteleeva Angela N. , Kolganova Tatjana V. , Ravin Nikolai V. , Skryabin Konstantin G. 
Published: October 2010

ABSTRACT

Oscillochloris trichoides
is a mesophilic, filamentous, photoautotrophic, nonsulfur, diazotrophic bacterium which is capable of carbon dioxide fixation via the reductive pentose phosphate cycle and possesses no assimilative sulfate reduction. Here, we present the draft genome sequence of
Oscillochloris trichoides
subsp. DG-6, the type strain of the species, which has permitted the prediction of genes for carbon and nitrogen metabolism and for the light-harvesting apparatus.