bluuebunny/crossref_metadata_2025_split huggingface dataset:
Slow gantry rotation acquisition technique for on‐board four‐dimensional digital tomosynthesis
Authors: Maurer Jacqueline , Pan Tinsu , Yin Fang‐Fang 
Published: January 2010

Purpose:Four‐dimensional cone‐beam computed tomography (4D CBCT) has been investigated for motion imaging in the radiotherapy treatment room. The drawbacks of 4D CBCT are long scan times and high imaging doses. The aims of this study were to develop and investigate a slow gantry rotation acquisition protocol for four‐dimensional digital tomosynthesis (4D DTS) as a faster, lower dose alternative to 4D CBCT.Methods:This technique was implemented using an On‐Board Imager® kV imaging system (Varian Medical Systems, Palo Alto, CA) mounted on the gantry of a linear accelerator. The general procedure for 4D DTS imaging using slow gantry rotation acquisition consists of the following steps: (1) acquire projections over a limited gantry rotation angle in a single motion with constant frame rate and gantry rotation speed; (2) generate a respiratory signal and temporally match projection images with appropriate points from the respiratory signal; (3) use the respiratory signal to assign phases to each of the projection images; (4) sort projection images into phase bins; and (5) reconstruct phase images. Phantom studies were conducted to validate theoretically derived relationships between acquisition and respiratory parameters. Optimization of acquisition parameters was then conducted by simulating lung scans using patient data. Lung tumors with approximate volumes ranging from 0.12 to were studied.Results:A protocol for slow gantry rotation 4D DTS was presented. Equations were derived to express relationships between acquisition parameters (frame rate, phase window, and angular intervals between projections), respiratory cycle durations, and resulting acquisition times and numbers of projections. The phantom studies validated the relationships, and the patient studies resulted in determinations of appropriate acquisition parameters. The phase window must be set according to clinical goals. For 10% phase windows, we found that appropriate frame rates ranging from 2 to 5 frames/s, gantry rotation speeds ranging from 0.44 to 1.03°/s, and aiming for an approximate maximum angular interval of 3.4° between projections in phase bins were appropriate for dose, scan time, and tumor visibility optimization. Adequate tumor visibility was achieved for coronal 4D DTS images of all three lung tumors with acquisition times ranging from 0.45 to 2.12 min. vs 1.84 to 4.24 min for 4D CBCT. 4D DTS imaging doses ranged from 0.12 to 0.72 times the dose of a standard CBCT scan vs 0.48 to 1.44 times the dose of a standard CBCT scan for 4D CBCT.Conclusions:A slow gantry rotation acquisition technique for 4D DTS was developed and investigated. Study results indicated that 4D DTS is a feasible technique for imaging lung tumor motion in the treatment room and requires shorter acquisition times and less imaging dose than 4D CBCT for larger tumors that do not require large scan angles for sagittal views and for situations where only coronal views are needed to meet clinical needs.
Dosimetric accuracy of a deterministic radiation transport based brachytherapy treatment planning system. Part I: Single sources and bounded homogeneous geometries
Authors: Zourari K. , Pantelis E. , Moutsatsos A. , Petrokokkinos L. , Karaiskos P. , Sakelliou L. , Georgiou E. , Papagiannis P. 
Published: January 2010

Purpose:The aim of this work is to validate a deterministic radiation transport based treatment planning system (TPS) for single brachytherapy source dosimetry in homogeneous water geometries.Methods:TPS results were obtained using the deterministic radiation transport option of aBRACHYVISION v. 8.8 system for three characteristic source designs (VS2000, GMPlus HDR, and GMPlus PDR) with each source either centered in a 15 cm radius spherical water phantom, or positioned at varying distance away from the phantom center. Corresponding MC simulations were performed using the MCNPX code v.2.5.0 and source geometry models prepared using information provided by the manufacturers.Results:Comparison in terms of the AAPM TG‐43 dosimetric formalism quantities, as well as dose rate distributions per unit air kerma strength with a spatial resolution of 0.1 cm, yielded close agreement between TPS and MC results for the sources centered in the phantom. Besides some regions close to the source longitudinal axes where discrepancies could be characterized as systematic, overall agreement for all three sources studied is comparable to the statistical (type A) uncertainty of MC simulations (1% at the majority of points in the geometry increasing to 2%–3% at points lying both away from the source center and close to the source longitudinal axis). A corresponding good agreement was also found between TPS and MC results for the sources positioned away from the phantom center.Conclusions:Results of this work attest the capability of the TPS to accurately account for the scatter conditions regardless of the size or shape of a given geometry of dosimetric interest, and the position of a source within it. This is important since, as shown in the literature and summarized also in this work, these factors could introduce a significant dosimetric effect that is currently ignored in clinical treatment planning. It is concluded that the implementation of the deterministic radiation transport option of theBRACHYVISION v. 8.8 system for brachytherapy dosimetry in homogeneous water geometries yields results of comparable accuracy to the golden standard of Monte Carlo simulation, in clinically viable calculation times.
Influence of photon energy spectra from brachytherapy sources on Monte Carlo simulations of kerma and dose rates in water and air
Authors: Rivard Mark J. , Granero Domingo , Perez‐Calatayud Jose , Ballester Facundo 
Published: January 2010

Purpose:For a given radionuclide, there are several photon spectrum choices available to dosimetry investigators for simulating the radiation emissions from brachytherapy sources. This study examines the dosimetric influence of selecting the spectra for, , and on the final estimations of kerma and dose.Methods:For, , and , 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 , , and 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, , and , 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.
Scatter correction method for x‐ray CT using primary modulation: Phantom studies
Authors: Gao Hewei , Fahrig Rebecca , Bennett N. Robert , Sun Mingshan , Star‐Lack Josh , Zhu Lei 
Published: January 2010

Purpose:Scatter correction is a major challenge in x‐ray imaging using large area detectors. Recently, the authors proposed a promising scatter correction method for x‐ray computed tomography (CT) using primary modulation. Proof of concept was previously illustrated by Monte Carlo simulations and physical experiments on a small phantom with a simple geometry. In this work, the authors provide a quantitative evaluation of the primary modulation technique and demonstrate its performance in applications where scatter correction is more challenging.Methods:The authors first analyze the potential errors of the estimated scatter in the primary modulation method. On two tabletop CT systems, the method is investigated using three phantoms: A Catphan©600 phantom, an anthropomorphic chest phantom, and the Catphan©600 phantom with two annuli. Two different primary modulators are also designed to show the impact of the modulator parameters on the scatter correction efficiency. The first is an aluminum modulator with a weak modulation and a low modulation frequency, and the second is a copper modulator with a strong modulation and a high modulation frequency.Results:On the Catphan©600 phantom in the first study, the method reduces the error of the CT number in the selected regions of interest (ROIs) from 371.4 to 21.9 Hounsfield units (HU); the contrast to noise ratio also increases from 10.9 to 19.2. On the anthropomorphic chest phantom in the second study, which represents a more difficult case due to the high scatter signals and object heterogeneity, the method reduces the error of the CT number from 327 to 19 HU in the selected ROIs and from 31.4% to 5.7% on the overall average. The third study is to investigate the impact of object size on the efficiency of our method. The scatter‐to‐primary ratio estimation error on the Catphan©600 phantom without any annulus (20 cm in diameter) is at the level of 0.04, it rises to 0.07 and 0.1 on the phantom with an elliptical annulus (30 cm in the minor axis and 38 cm in the major axis) and with a circular annulus (38 cm in diameter).Conclusions:On the three phantom studies, good scatter correction performance of the proposed method has been demonstrated using both image comparisons and quantitative analysis. The theory and experiments demonstrate that a strong primary modulation that possesses a low transmission factor and a high modulation frequency is preferred for high scatter correction accuracy.
In SituImmunolocalization and Stage-Dependent Expression of a Secretory Serine Protease inLeishmania donovaniand Its Role as a Vaccine Candidate
Authors: Choudhury Rajdeep , Das Partha , Bhaumik Siddhartha Kumar , De Tripti , Chakraborti Tapati 
Published: January 2010

ABSTRACTProteases have been found to play essential roles in many biological processes, including the pathogenesis of leishmaniasis. Most parasites rely on their intracellular and extracellular protease repertoire to invade and multiply in mammalian host cells. However, few studies have addressed serine proteases inLeishmaniaand their role in host pathogenesis. Here we report the intracellular distribution of a novelL. donovanisecretory serine protease in the flagellar pocket, as determined by immunogold labeling. Flow cytometry and confocal immunofluorescence analysis revealed that the expression of the protease diminishes sequentially from virulent to attenuated strains of this species and is also highly associated with the metacyclic stage ofL. donovanipromastigotes. The level of internalization of parasites treated with the anti-115-kDa antibody into host macrophages was significantly reduced from that of non-antibody-treated parasites, suggesting that this serine protease probably plays a role in the infection process.In vivostudies confirmed that this serine protease is a potential vaccine candidate. Altogether, the 115-kDa serine protease might play vital roles inL. donovanipathogenesis and hence could be recognized as a potential candidate for drug design.
Phenotypic Definition of Effector and Memory T-Lymphocyte Subsets in Mice Chronically Infected withMycobacterium tuberculosis
Authors: Henao-Tamayo Marcela I. , Ordway Diane J. , Irwin Scott M. , Shang Shaobin , Shanley Crystal , Orme Ian M. 
Published: January 2010

ABSTRACTThe bacteriumMycobacterium tuberculosisremains one of the world's most successful pathogens, a situation that is aggravated by the fact that the existing vaccine,Mycobacterium bovisBCG, is not effective in adults. As with any vaccine, the purpose of giving BCG vaccination is to establish a long-lived state of memory immunity, but whether this is successfully completely established is still unclear. It is generally accepted that memory T cells can be divided into central and effector memory populations by function and by phenotype; however, the majority of data supporting this division have been generated using transgenic mouse models or mice that have recovered from acute viral infections. Tuberculosis, on the other hand, represents a persistent, chronic state of immunity in which the presence of memory T cells is far less well defined. We show here that mice vaccinated with BCG or chronically infected withM. tuberculosisestablish antigen-specific populations of cells within the lungs that predominantly express a cellular phenotype consistent with their being effector or effector memory cells. In contrast, cells with a central memory phenotype exist in much lower numbers in the lungs but can be found in significantly larger numbers in the spleen, where they may represent a potential reservoir. These data suggest that the effector-to-central-memory T-cell transition may well be minimal in these persisting mycobacterial infections, and they support a novel hypothesis that this may explain the fundamental basis of the failure of the BCG vaccine in humans.
Prime-Boost Immunization Using a DNA Vaccine Delivered by Attenuated
Salmonella enterica
Serovar Typhimurium and a Killed Vaccine Completely Protects Chickens from H5N1 Highly Pathogenic Avian Influenza Virus
Authors: Pan Zhiming , Zhang Xiaoming , Geng Shizhong , Fang Qiang , You Meng , Zhang Lei , Jiao Xinan , Liu Xiufan 
Published: January 2010

ABSTRACT

H5N1 highly pathogenic avian influenza virus (HPAIV) has posed a great threat not only for the poultry industry but also for human health. However, an effective vaccine to provide a full spectrum of protection is lacking in the poultry field. In the current study, a novel prime-boost vaccination strategy against H5N1 HPAIV was developed: chickens were first orally immunized with a hemagglutinin (HA) DNA vaccine delivered by attenuated
Salmonella enterica
serovar Typhimurium, and boosting with a killed vaccine followed. Chickens in the combined vaccination group but not in single vaccination and control groups were completely protected against disease following H5N1 HPAIV intranasal challenge, with no clinical signs and virus shedding. Chickens in the prime-boost group also generated significantly higher serum hemagglutination inhibition (HI) titers and intestinal mucosal IgA titers against avian influenza virus (AIV) and higher host immune cellular responses than those from other groups before challenge. These results demonstrated that the prime-boost vaccination strategy provides an effective way to prevent and control H5N1 highly pathogenic avian influenza virus.
Serum Bactericidal Antibody Response 1 Year after Meningococcal Polysaccharide Vaccination of Patients with Common Variable Immunodeficiency
Authors: Rezaei Nima , Siadat Seyed Davar , Aghamohammadi Asghar , Moin Mostafa , Pourpak Zahra , Norouzian Dariush , Mobarakeh Jalal Izadi , Aghasadeghi Mohammad Reza , Nejati Mehdi , Read Robert C. 
Published: January 2010

ABSTRACT

Some patients with common variable immunodeficiency (CVID) can generate an antibody response following vaccination with
Neisseria meningitidis
polysaccharide, but the duration of this protection is unknown. In this study, serum bactericidal antibody (SBA) responses to serogroup C
N. meningitidis
of 23 patients with CVID and 23 sex- and age-matched controls were measured 1 year after vaccination with the plain A/C meningococcal polysaccharide vaccine. The fold rise in serum bactericidal antibody geometric mean titers of the control group from prevaccination to 1 year postvaccination was significantly higher than that of the patient group (5.41- versus 2.96-fold,
P
= 0.009). Of 23 CVID patients, 8 had a poor response to vaccine (<4-fold rise) 3 weeks after vaccination, and low titers remained when measured 1 year later. Of the 15 CVID patients who had a normal response to vaccine (≥4-fold rise) 3 weeks after vaccination, 6 cases failed to maintain protective SBA titers, whereas the remaining 9 had protective titers 1 year after vaccination. Only one of the 23 controls, who developed protective SBA titers after 3 weeks, lost the protective titers after 1 year. Among the patients, the presence of bronchiectasis and/or splenomegaly at enrollment was associated with poor SBA response to vaccine at 3 weeks and/or failure to maintain protective levels at 1 year. The results of this study demonstrate that a number of CVID patients can produce protective antibody titers that can persist for 1 year after vaccination, which lends strong support to the inclusion of polysaccharide vaccine in the immunization program for CVID patients.
Characterization of
Slackia exigua
Isolated from Human Wound Infections, Including Abscesses of Intestinal Origin
Authors: Kim Keun-Sung , Rowlinson Marie-Claire , Bennion Robert , Liu Chengxu , Talan David , Summanen Paula , Finegold Sydney M. 
Published: January 2010

ABSTRACT

Eleven clinical strains isolated from infected wound specimens were subjected to polyphasic taxonomic analysis. Sequence analysis of the 16S rRNA gene showed that all 11 strains were phylogenetically related to
Slackia exigua
. Additionally, conventional and biochemical tests of 6 of the 11 strains were performed as supplementary methods to obtain phenotypic identification by comparison with the phenotypes of the relevant type strains.
S. exigua
has been considered an oral bacterial species in the family
Coriobacteriaceae
. This organism is fastidious and grows poorly, so it may easily be overlooked. The 16S rRNA gene sequences and the biochemical characteristics of four of the
S. exigua
strains isolated for this study from various infections indicative of an intestinal source were almost identical to those of the validated
S. exigua
type strain from an oral source and two of the
S. exigua
strains from oral sources evaluated in this study. Thus, we show for the first time that
S. exigua
species can be isolated from extraoral infections as well as from oral infections. The profiles of susceptibility to selected antimicrobials of this species were also investigated for the first time.
Analytical Performance Characteristics and Clinical Utility of a Novel Assay for Total Hepatitis C Virus Core Antigen Quantification
Authors: Ross R. S. , Viazov S. , Salloum S. , Hilgard P. , Gerken G. , Roggendorf M. 
Published: January 2010

ABSTRACT

The detection and quantification of hepatitis C virus (HCV) core antigen in serum or plasma by the use of different assay formats have previously been shown to represent useful markers of viral replication. In the present study, the intrinsic performance characteristics and the potential clinical utility of a novel assay for the quantification of total HCV core antigen were comprehensively assessed by using clinical serum samples and specimens contained in various evaluation panels. The Architect HCV Ag assay showed a specificity of 100%. The intra- and interassay coefficients of variation ranged from 3.6 to 8.0% and from 4.7 to 9.5%, respectively. Except for HCV genotype 2 isolates, the analytical sensitivity was always less than 10 fmol core antigen/liter, corresponding to approximately 500 to 3,000 IU of HCV RNA/ml. Linearity was guaranteed throughout the dynamic range (10 to 20,000 fmol/liter). When seroconversion panels were tested, the assay was not inferior to HCV RNA detection and reduced the preseroconversion period by 4 to 16 days. The results obtained by core antigen and HCV RNA quantification for 385 clinical specimens were correlated by regression analysis (
r
= 0.857), but the calculated conversion equation differed significantly from the line of identity. Monitoring of viral kinetics by use of either core antigen or RNA concentrations in 38 HCV-infected patients undergoing antiviral combination therapy resulted in very similarly shaped curves in all cases. Finally, the Architect HCV Ag assay was also shown to enable high-throughput screening of
in vitro
HCV RNA replication. With these results taken together, the Architect HCV Ag assay proved to be a specific, reproducible, highly sensitive, and clinically applicable test format which will find its future place in the context of virological HCV diagnostics.
Association of Serotypes of
Streptococcus pneumoniae
with Age in Invasive Pneumococcal Disease
Authors: Imöhl Matthias , Reinert Ralf René , Ocklenburg Christina , van der Linden Mark 
Published: January 2010

ABSTRACT
A total of 7,764 isolates from patients with invasive pneumococcal disease (IPD) were collected from 1992 to June 2006. Data on serotypes were available for 5,022 isolates (64.7% of all invasive isolates). Some 54.0% of the isolates originated from adults ≥16 years of age, and 46.0% were from children <16 years of age. The leading serotypes were 14, 23F, 1, 6B, 7F, 3, and 4. The serotypes significantly more common in children were 14, 6B, 19F, and 18C, while among adults, serotypes 3 and 4 were predominant. Serotype 7F was statistically more prevalent among children <4 months old than among the other age groups. Among children aged ≥4 months and <1 year, serotype 19F occurred statistically more frequently; and among children aged ≥1 year to <5 years, serotypes 14, 6B, and 18C were overrepresented. The serotypes predominantly affecting patients younger than the remaining collective of patients were 14, 6B, 19F, and 18C, while patients with IPD caused by serotypes 3, 4, and 9V were older than the collective, on average.
Aminoglycoside Resistance and Susceptibility Testing Errors in
Acinetobacter baumannii-calcoaceticus
Complex
Authors: Akers Kevin S. , Chaney Chris , Barsoumian Alice , Beckius Miriam , Zera Wendy , Yu Xin , Guymon Charles , Keen Edward F. , Robinson Brian J. , Mende Katrin , Murray Clinton K. 
Published: January 2010

ABSTRACT

Antimicrobial resistance is depleting the pharmacopeia of agents clinically useful against Gram-negative bacilli. As the number of active agents diminishes, accurate susceptibility testing becomes critical. We studied the susceptibilities of 107 isolates of the
Acinetobacter baumannii-calcoaceticus
complex to amikacin, gentamicin, and tobramycin using disk diffusion, Etest, as well as the Phoenix, Vitek 2, and MicroScan automated systems, and compared the results to those obtained by broth microdilution. Genes encoding aminoglycoside-modifying enzymes (AMEs) were detected by multiplex PCR, and clonal relationships were determined by pulsed-field gel electrophoresis. Tobramycin was the most active aminoglycoside (27.1% of isolates were susceptible). Disk diffusion and Etest tended to be more accurate than the Vitek 2, Phoenix, and MicroScan automated systems; but errors were noted with all methods. The Vitek 2 instrument incorrectly reported that more than one-third of the isolates were susceptible to amikacin (a very major error). Isolates were polyclonal, with 26 distinct strains, and carried multiple AME genes unrelated to the strain type. The presence of the
ant(2")-Ia
gene was statistically associated with resistance to each aminoglycoside. The AME genotype accounted for the resistance profile observed in a minority of isolates, suggesting the involvement of multiple resistance mechanisms. Hospital pharmacy records indicated the preferential use of amikacin over other aminoglycosides in the burn intensive care unit, where aminoglycoside resistance is prevalent. The resistance in that unit did not correlate with a predominant strain, AME genotype, or total annual aminoglycoside consumption. Susceptibility to tobramycin increased, even though susceptible isolates carried AME genotypes predicting the inactivation of tobramycin. Determination of the relative contribution of multiple concurrent resistance mechanisms may improve our understanding of aminoglycoside resistance in the
Acinetobacter baumannii-calcoaceticus
complex.