bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volume‐of‐interest (VOI) imaging in C‐arm flat‐detector CT for high image quality at reduced dose
Authors: Kolditz Daniel , Kyriakou Yiannis , Kalender Willi A. 
Published: June 2010

PurposeA novel method for flat‐detector computed tomography was developed to enable volume‐of‐interest (VOI) imaging at high resolution, low noise, and reduced dose. For this, a full low‐dose overview (OV) scan and a local high‐dose scan of a VOI are combined.MethodsThe first scan yields an overview of the whole object and enables the selection of an arbitrary VOI. The second scan of that VOI assures high image quality within the interesting volume. The combination of the two consecutive scans is based on a forward projection of the reconstructed OV volume that was registered to the VOI. The artificial projection data of the OV scan are combined with the measured VOI data in the raw data domain. Different projection values are matched by an appropriate transformation and weighting. The reconstruction is performed with a standard Feldkamp‐type algorithm. In simulations, the combination of OV scan and VOI scan was investigated on a mathematically described phantom. In measurements, spatial resolution and noise were evaluated with image quality phantoms. Modulation transfer functions and noise values were calculated. Measurements of an anthropomorphic head phantom were used to validate the proposed method for realistic applications, e.g., imaging stents. In Monte Carlo simulations, 3D dose distributions were calculated and dose values were assessed quantitatively.ResultsBy the proposed combination method, an image is generated which covers the whole object and provides the VOI at high image quality. In the OV image, a resolution of 0.7 lp/mm (line pairs per millimeter) and noise of 63.5 HU were determined. Inside the VOI, resolution was increased to 2.4 lp/mm and noise was decreased to 18.7 HU. For the performed measurements, the cumulative dose was significantly reduced in comparison to conventional scans by up to 93%. The dose of a high‐quality scan, for example, was reduced from 97 to less than 7 mGy, while keeping image quality constant within the VOI.ConclusionsThe proposed VOI application with two scans is an effective way to ensure high image quality within the VOI while simultaneously reducing the cumulative patient dose.
Dosimetric consequences of misalignment and realignment in prostate 3DCRT using intramodality ultrasound image guidance
Authors: Fraser Danielle J. , Chen Yong , Poon Emily , Cury Fabio L. , Falco Tony , Verhaegen Frank 
Published: June 2010

Purpose: It is common practice to correct for interfraction motion by shifting the patient from reference skin marks to better align the internal target at the linear accelerator's isocenter. Shifting the patient away from skin mark alignment causes the radiation beams to pass through a patient geometry different from that planned. Yet, dose calculations on the new geometry are not commonly performed. The intention of this work was to compare the dosimetric consequences of treating the patient with and without setup correction for the common clinical scenario of prostate interfraction motion.Methods: In order to account for prostate motion, 32 patients initially aligned to the room lasers via skin marks were realigned under the treatment beams by shifting the treatment couch based on ultrasound image guidance. An intramodality 3D ultrasound image guidance system was used to determine the setup correction, so that errors stemming from different tissue representations on different imaging modalities were eliminated. Two scenarios were compared to the reference static treatment plan: (1) Uncorrected patient alignment and (2) corrected patient alignment. Prostate displacement statistics and the dose to the clinical target volume (CTV), bladder, and rectum are reported. Monte Carlo dose calculation methods were employed.Results: Comparing the uncorrected and corrected scenarios using the static treatment plan as the reference, the average percent difference in for the CTV improved from −5.1% (range −40%, 1.3%) to 0.0% (−3.5%, 2.0%) and the average percent difference in for the bladder and rectum changed from −11% (−84%, 232%) to −8.3% (−61%, 5.2%) and from −47% (−100%, 108%) to 0.9% (−62%, 102%), respectively. There was no simple correlation between displacement and dose discrepancy before correction. After patient realignment, the prescribed dose to the CTV was achieved within 1% for 75% (24/32) of the patients. After patient realignment, 50% of the patients had doses that differed from the static treatment plan by 25% for the bladder and 8% for the rectum.Conclusions: The dose degradation due to prostate motion (before correction) is not accurately predicted from the average trends for all patients. Outliers included smaller displacements that lead to larger dosimetric differences in the corrected scenario, especially for the bladder and rectum, which exhibited doses substantially different from that planned.
Effect of multileaf collimator‐defined segment size on
Authors: Alaei Parham , Higgins Patrick 
Published: June 2010

PurposeTertiary multileaf collimators (MLCs) in certain linear accelerators have been found to influence the factor . This effect on is often ignored at the time of commissioning and beam data collection since the scatter/output factors are usually measured with the MLCs retracted. This may be a negligible effect for majority of conventional radiotherapy portals since the jaws are set to conform with MLCs as closely as possible. In the case of IMRT treatments, however, the jaw is often set at a fixed size, and the MLCs form the segments, or control points, of each beam, thus the difference between MLC and jaw settings may be significant.MethodsThe authors quantified the magnitude of this scatter difference for various field sizes defined by MLCs and jaws and characterized the variation in this scatter with MLC and jaw settings. They measured and factors for square fields (apertures) of different sizes for jaw settings from to .ResultsThe data indicate that the larger the difference between MLC‐defined aperture and jaw settings, the more significant the difference between the output factors. The authors fitted curves to the MLC output factors for any given jaw size in order to parametrize this aperture effect as a function of jaw and MLC setting.ConclusionsThe quantification of the change in the output factor due to MLCs may be important for better modeling of dose in IMRT deliveries and other applications such asin vivo dosimetry.
Fast simulation of yttrium‐90 bremsstrahlung photons with GATE
Authors: Rault Erwann , Staelens Steven , Van Holen Roel , De Beenhouwer Jan , Vandenberghe Stefaan 
Published: June 2010

PurposeMultiple investigators have recently reported the use of yttrium‐90 bremsstrahlung single photon emission computed tomography (SPECT) imaging for the dosimetry of targeted radionuclide therapies. Because Monte Carlo (MC) simulations are useful for studying SPECT imaging, this study investigates the MC simulation of bremsstrahlung photons in SPECT. To overcome the computationally expensive simulation of electrons, the authors propose a fast way to simulate the emission of bremsstrahlung photons based on prerecorded bremsstrahlung photon probability density functions (PDFs).MethodsThe accuracy of bremsstrahlung photon simulation is evaluated in two steps. First, the validity of the fast bremsstrahlung photon generator is checked. To that end, fast and analog simulations of photons emitted from a point source in a water phantom are compared. The same setup is then used to verify the accuracy of the bremsstrahlung photon simulations, comparing the results obtained with PDFs generated from both simulated and measured data to measurements. In both cases, the energy spectra and point spread functions of the photons detected in a scintillation camera are used.ResultsResults show that the fast simulation method is responsible for a 5% overestimation of the low‐energy fluence (below 75 keV) of the bremsstrahlung photons detected using a scintillation camera. The spatial distribution of the detected photons is, however, accurately reproduced with the fast method and a computational acceleration of ‐fold is achieved. When measured PDFs are used in the simulations, the simulated energy spectrum of photons emitted from a point source of in a water phantom and detected in a scintillation camera closely approximates the measured spectrum. The PSF of the photons imaged in the 50–300 keV energy window is also accurately estimated with a 12.4% underestimation of the full width at half maximum and 4.5% underestimation of the full width at tenth maximum.ConclusionsDespite its limited accuracy, the fast bremsstrahlung photon generator is well suited for the simulation of bremsstrahlung photons emitted in large homogeneous organs, such as the liver, and detected in a scintillation camera. The computational acceleration makes it very useful for future investigations of bremsstrahlung SPECT imaging.
The Italian affair: The employment of parallel‐plate ionization chambers for dose measurements in high dose‐per‐pulse IORT electron beams
Authors: Cella L. , Liuzzi R. , Salvatore M. 
Published: June 2010

PurposeAt the high dose‐per‐pulse rates used by some intraoperative radiotherapy (IORT) units, the employment of ionization chambers for dose measurements needs an appropriate correction for ion recombination. Through a revision of the existing literature, the authors compared different methods for the determination of the recombination correction factor and their impact on clinical dosimetry.MethodsA dosimetric characterization of IORT electron beams from a Linac Hitesys Novac7 (Aprilia‐Latina, Italy) was performed. Dose‐to‐water values were measured with dose‐per‐pulse independent chemical dosimeters (operated by the Italian Primary Standard Dosimetry Laboratory, ENEA) and compared to doses obtained by two different parallel‐plate ionization chamber models (Markus and Advanced Markus, PTW, Freiburg, Germany). For dose measurements using ionization chambers, the authors applied two different methods for the determination of the ion recombination correction factor , as suggested in previous articles. The first method is based on the experimental estimation of the free‐electron fraction values ; the second one is based on the “nonstandard” two‐voltage analysis including the free‐electron component.ResultsFor a Markus type chamber, there is a good agreement between the results on and those reported in the literature for both methods, while for the Advanced Markus chamber, no data are available for comparison.ConclusionsComparing values of obtained by dose‐per‐pulse independent dosimeters and by ionization chambers measurements corrected using the two different approaches, the authors can conclude that the factor determination is very critical and that only an experimental protocol using ionization chamber intercalibration can be considered reliable.
The influence of self‐absorption on PET and PET/CT shielding requirements
Authors: Elschot M. , de Wit T. C. , de Jong H. W. A. M. 
Published: June 2010

PurposeThe high energy (511 keV) annihilation photons used in positron emission tomography (PET) imaging generally require a substantial amount of lead to protect personnel and the general public from ionizing radiation. A cost‐effective design of the PET facility that ensures radiation does not exceed formal dose limits requires accurate estimation of the necessary PET shielding. The American Association of Physicists in Medicine (AAPM) Task Group 108 recently published broad beam transmission factors based on Monte Carlo calculations of 511 keV photons. In this work, an extension to the AAPM model is presented, based on Monte Carlo simulations including the effects of self‐absorption on the photon energy spectrum.MethodsMonte Carlo calculations were performed usingMCNPX. The photon energy spectrum after self‐absorption was computed by simulating a normal activity distribution in an anthropomorphic phantom. This spectrum was used to calculate the dose rate transmission factors for various wall thicknesses of lead, concrete, and iron. The method was validated by measurement and corresponding simulation of the transmission factors of an source in air and in PMMA. Furthermore, a method to generate 3D area dose rate maps of PET facilities incorporating the calculated transmission tables is presented and applied to several shielding situations.ResultsThe calculated self‐absorption correction factor and the broad beam transmission factors resulting from Monte Carlo simulations of a monoenergetic point source emitting 511 keV photons were in excellent agreement with the results of the AAPM publication (0.66 vs 0.64 and , respectively). However, when all radiation physics, i.e., also the effect of self‐absorption on the photon energy spectrum, is included in the Monte Carlo calculations, a substantial reduction in required shielding material was found. For example, including all radiation physics leads to 13.3 mm of lead required to obtain a typical transmission factor of 0.1, instead of 16.0 mm of lead when the AAPM data including only the self‐absorption correction factor are used. These findings were confirmed by the experimental measurements. The transmission factors produced in this work can be applied in the same manner as those estimated by AAPM to allow for a cost‐effective design of PET and PET/CT facilities without violating radiation safety regulations.ConclusionsTaking into account the effect of self‐absorption on the photon energy spectrum results in more accurate and cost‐effective shielding requirement estimations.
Outdoor air pollution is associated with rapid decline of lung function in α-1-antitrypsin deficiency
Authors: Wood Alice M , Harrison Roy M , Semple Sean , Ayres Jon G , Stockley Robert A 
Published: June 2010

IntroductionOutdoor air pollutants are associated with respiratory morbidity and mortality, but little longitudinal work has been undertaken in this area in chronic obstructive pulmonary disease (COPD). Patients with α-1-antitrypsin deficiency (AATD) typically exhibit faster decline of lung function than subjects with usual COPD and thus represent a group in whom studies of factors influencing decline may be more easily clarified.MethodsDecline of FEV1and KCO in subjects of the PiZZ genotype from the UK AATD registry were studied. Pollution levels (PM10, ozone, sulphur dioxide, nitrogen dioxide) during the exposure window were extracted from GIS maps, matching the measurement to each patient's home address. Clinical predictors of decline were sought using generalised estimating equations, and pollutants added to these subsequently. Single pollutant models were used due to multicollinearity.ResultsIn the FEV1decline analysis, higher baseline FEV1was associated with rapid decline of FEV1(p<0.001). High PM10exposure predicted more rapid decline of FEV1(p=0.024). In a similar analysis for KCO decline, higher baseline KCO predicted rapid decline (p<0.001) as did higher exposure to ozone (p=0.018). High PM10exposure also showed a trend towards this effect (p=0.056).ConclusionsExposure to ozone and PM10predicts decline of lung function in AATD.
Higher order properties and Bell inequality violation for the three-mode enhanced squeezed state
Authors: Zhang Shuang-Xi , Yuan Hong-Chun , Fan Hong-Yi 
Published: June 2010

By extending the usual two-mode squeezing operator S2 = exp[iλ(Q1P2 + Q2P1)] to the three-mode squeezing operator S3 = exp{iλ[Q1(P2 + P3) + Q2(P1 + P3) + Q3(P1 + P2)]}, we obtain the corresponding three-mode squeezed coherent state. The higher order properties of this state, such as higher order squeezing and higher order sub-Possonian photon statistics, are investigated. It is found that the new squeezed state not only can be squeezed to all even orders but also exhibits squeezing enhancement compared with the usual cases. In addition, we examine the violation of the Bell inequality for the three-mode squeezed states by using the formalism of Wigner representation.
Comparative analysis of predicted HLA binding of immunoglobulin idiotype sequences indicates T cell–mediated immunosurveillance in follicular lymphoma
Authors: Strothmeyer Anna-Maria , Papaioannou Dimitrios , Dühren-von Minden Marcus , Navarrete Marcelo , Zirlik Katja , Heining-Mikesch Kristina , Veelken Hendrik 
Published: June 2010

AbstractActive immunization with the idiotype of follicular lymphoma induces tumor-specific immunity. T cells induced in vivo by idiotype vaccination recognize human leukocyte antigen (HLA)–restricted hypervariable but not conserved idiotype peptides. We hypothesized that idiotype-directed T-cell immunity occurs naturally and performed a reverse immunology analysis of idiotype HLA binding in 39 follicular lymphoma patients. For every idiotype, the sum of HLA-A or -B binding scores of the 20 highest-scoring peptides was calculated for all 39 HLA types through the BIMAS algorithm. The idiotype sum score of every patient's lymphoma was compared on the respective patient's HLA type to the mean of the sum scores of the remaining 38 idiotypes. Autologous idiotypes had lower immunogenicity than allogeneic idiotypes. Dif ferential immunogenicity resided predominantly in all 3 complementarity-determining regions rather than in framework peptides. Idiotype immunogenicity was not changed by somatic hypermutation. These findings indicate T cell–mediated immunosurveillance of follicular lymphoma directed specifically against individual idiotype epitopes.
Cyclic nucleotides and mitogen-activated protein kinases: regulation of simvastatin in platelet activation
Authors: Lee Ye-Ming , Chen Wei-Fan , Chou Duen-Suey , Jayakumar Thanasekaran , Hou Ssu-Yu , Lee Jie-Jen , Hsiao George , Sheu Joen-Rong 
Published: June 2010

Abstract

Background
3-Hydroxy-3-methyl-glutaryl coenzyme A (HMG-CoA) reductase inhibitors (statins) have been widely used to reduce cardiovascular risk. These statins (i.e., simvastatin) may exert other effects besides from their cholesterol-lowering actions, including inhibition of platelet activation. Platelet activation is relevant to a variety of coronary heart diseases. Although the inhibitory effect of simvastatin in platelet activation has been studied; the detailed signal transductions by which simvastatin inhibit platelet activation has not yet been completely resolved.

Methods
The aim of this study was to systematically examine the detailed mechanisms of simvastatin in preventing platelet activation. Platelet aggregation, flow cytometric analysis, immunoblotting, and electron spin resonance studies were used to assess the antiplatelet activity of simvastatin.

Results
Simvastatin (20-50 μM) exhibited more-potent activity of inhibiting platelet aggregation stimulated by collagen than other agonists (i.e., thrombin). Simvastatin inhibited collagen-stimulated platelet activation accompanied by [Ca2+]i mobilization, thromboxane A2 (TxA2) formation, and phospholipase C (PLC)γ2, protein kinase C (PKC), and mitogen-activated protein kinases (i.e., p38 MAPK, JNKs) phosphorylation in washed platelets. Simvastatin obviously increased both cyclic AMP and cyclic GMP levels. Simvastatin markedly increased NO release, vasodilator-stimulated phosphoprotein (VASP) phosphorylation, and endothelial nitric oxide synthase (eNOS) expression. SQ22536, an inhibitor of adenylate cyclase, markedly reversed the simvastatin-mediated inhibitory effects on platelet aggregation, PLCγ2 and p38 MAPK phosphorylation, and simvastatin-mediated stimulatory effects on VASP and eNOS phosphorylation.

Conclusion
The most important findings of this study demonstrate for the first time that inhibitory effect of simvastatin in platelet activation may involve activation of the cyclic AMP-eNOS/NO-cyclic GMP pathway, resulting in inhibition of the PLCγ2-PKC-p38 MAPK-TxA2 cascade, and finally inhibition of platelet aggregation.
Scaffold filling, contig fusion and comparative gene order inference
Authors: Muñoz Adriana , Zheng Chunfang , Zhu Qian , Albert Victor A , Rounsley Steve , Sankoff David 
Published: June 2010

Abstract

Background
There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?

Results
Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.

Conclusions
The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.
Copy number variation and cytidine analogue cytotoxicity: A genome-wide association approach
Authors: Kalari Krishna R , Hebbring Scott J , Chai High Seng , Li Liang , Kocher Jean-Pierre A , Wang Liewei , Weinshilboum Richard M 
Published: June 2010

AbstractBackgroundThe human genome displays extensive copy-number variation (CNV). Recent discoveries have shown that large segments of DNA, ranging in size from hundreds to thousands of nucleotides, are either deleted or duplicated. This CNV may encompass genes, leading to a change in phenotype, including drug response phenotypes. Gemcitabine and 1-β-D-arabinofuranosylcytosine (AraC) are cytidine analogues used to treat a variety of cancers. Previous studies have shown that genetic variation may influence response to these drugs. In the present study, we set out to test the hypothesis that variation in copy number might contribute to variation in cytidine analogue response phenotypes.ResultsWe used a cell-based model system consisting of 197 ethnically-defined lymphoblastoid cell lines for which genome-wide SNP data were obtained using Illumina 550 and 650 K SNP arrays to study cytidine analogue cytotoxicity. 775 CNVs with allele frequencies > 1% were identified in 102 regions across the genome. 87/102 of these loci overlapped with previously identified regions of CNV. Association of CNVs with gemcitabine and AraC IC50values identified 11 regions with permutation p-values < 0.05. Multiplex ligation-dependent probe amplification assays were performed to verify the 11 CNV regions that were associated with this phenotype; with false positive and false negative rates for the in-silico findings of 1.3% and 0.04%, respectively. We also had basal mRNA expression array data for these same 197 cell lines, which allowed us to quantify mRNA expression for 41 probesets in or near the CNV regions identified. We found that 7 of those 41 genes were highly expressed in our lymphoblastoid cell lines, and one of the seven genes (SMYD3) that was significant in the CNV association study was selected for further functional experiments. Those studies showed that knockdown ofSMYD3, in pancreatic cancer cell lines increased gemcitabine and AraC resistance during cytotoxicity assay, consistent with the results of the association analysis.ConclusionsThese results suggest that CNVs may play a role in variation in cytidine analogue effect. Therefore, association studies of CNVs with drug response phenotypes in cell-based model systems, when paired with functional characterization, might help to identify CNV that contributes to variation in drug response.