bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and genetic diversity of pathogenic populations of Vibrio parahaemolyticus in coastal waters of Galicia, Spain
Authors: Rodriguez‐Castro Alba , Ansede‐Bermejo Juan , Blanco‐Abad Veronica , Varela‐Pet Jose , Garcia‐Martin Oscar , Martinez‐Urtaza Jaime 
Published: August 2009

SummaryThe natural reservoirs and biological characteristics of pathogenic populations of Vibrio parahaemolyticus in marine habitats remain unclear due to difficulties in obtaining pathogenic strains from the environment. The distribution and characteristics of pathogenic V. parahaemolyticus were investigated over 1 year in three coastal environments in Galicia (Spain), including areas of the major international ports in the region. Vibrio parahaemolyticus was present in 35.3% of the samples analysed, and 535 strains were isolated over the period of study. Virulence genes were detected in 94 strains with diverse genetic traits: 66 trh+/tdh−, 24 trh−/tdh+ and 4 trh+/tdh+. Different spatial and seasonal patterns were observed in relation to genetic traits. The trh+/tdh− strains were detected exclusively in northern areas and prevailed in the autumn, when seawater is warmer and less saline, whereas the trh−/tdh+ strains were found in all three areas throughout winter and spring. Characterization of potentially pathogenic strains from the environment revealed an unexpectedly diverse array of serotypes and pulsed‐field gel electrophoresis (PFGE) profiles (pulsotypes) that were unrelated to clinical strains of V. parahaemolyticus that are prevalent in Spain. The results of the current study provide a novel view of V. parahaemolyticus in Europe, in which diverse pathogenic groups are constitutive components of the environmental populations in coastal habitats.
Functional genomics to identify therapeutic prophylactic targets
Authors: Frank Christian G. , Bengoechea José A 
Published: August 2009

SummaryInfectious diseases are a leading cause of global human mortality. The use of antimicrobials remains the most common strategy for treatment. However, the isolation of pathogens resistant to virtually all antimicrobials makes it urgent to develop effective therapeutics based on new targets. Here we review a new drug discovery paradigm focusing on identifying and targeting host factors important for infection as well as pathogen determinants involved in disease progression. We summarize innovative strategies which by combining bioinformatics with transcriptomics and chemical genetics have already identified host factors essential for pathogen entry, survival and replication. We describe how the discovery of RNA interference which allows loss‐of‐function studies has facilitated functional genomic studies in human cells. It is expected that these studies will identify targets to be used as host‐directed drug therapy which, together with antimicrobials targeting microbial virulence factors, will efficiently eliminate the invading pathogen.
Bigger Is Bigger
Authors: Riendeau Diane 
Published: August 2009

When you really want to get a point across to your students, you set up explorations or experiments, and do demonstrations. Sometimes I find myself thinking, “If I only had….” This month's videos add “wow” factor to the experiences you provide for your students in the classroom!
Thanks to Jaime Stasiorowski (Deerfield High School), Tony Zito (Dutchess Community College), and Bob Beichner (NC State) and Chris Chiaverina for their contributions to this month's column.
Evaluation of the eclipse electron Monte Carlo dose calculation for small fields
Authors: Xu Zhigang , Walsh Sarah E. , Telivala Tejas P. , Meek Allen G. , Yang Guozhen 
Published: August 2009

Varian Medical Systems (Palo Alto, CA) has implemented the Monte Carlo electron dose calculation algorithm (eMC) in the Eclipse treatment planning system. Previous algorithms for electron treatment planning were limited in their calculation ability for small field depth doses and monitor units. An old rule of thumb to approximate the limiting cutout size for an electron field was determined by the lateral scatter equilibrium and approximated by E (MeV)/2.5 in centimeters of water. In this study, we compared eMC calculations and measurements of depth doses, isodose distributions, and monitor units for several different energy and small field cutout size combinations at different SSDs. Measurements were made using EBT film (International Specialty Products, Wayne, NJ) and a PinPoint ion chamber (PTW‐New York Corp., Hicksville, NY). Our results indicate that the eMC algorithm can accurately predict depth doses, isodose distributions, and monitor units (within 2.5%) for field sizes as small as 3.0 cm diameter for energies in the 6 to 20 MeV range at 100 cm SSD. Therefore, the previous energy dependent rule of thumb does not apply to the Eclipse electron Monte Carlo code. However, at extended SSDs (105–110 cm), the results show good agreement (within 4%) only for higher energies (12, 16, and 20 MeV) for a field size of 3 cm.PACS number: 87.53.Hv
Assessing prostate, bladder and rectal doses during image guided radiation therapy — need for plan adaptation?
Authors: Varadhan Raj , Hui Susanta K , Way Sarah , Nisi Kurt 
Published: August 2009

The primary application of Image‐Guided Radiotherapy (IGRT) in the treatment of localized prostate cancer has been to assist precise dose delivery to the tumor. With the ability to use in‐room Computed Tomography (CT) imaging modalities, the prostate, bladder and rectum can be imaged before each treatment and the actual doses delivered to these organs can be tracked using anatomy of the day. This study evaluates the dosimetric uncertainties caused by interfraction organ variation during IGRT for 10 patients using kilovoltage cone beam CT (kvCBCT) on the Elekta Synergy system and megavoltage CT (MVCT) on the TomoTherapy Hi·Art System. The actual delivered doses to the prostate, bladder and rectum were based on dose recomputation using CT anatomy of the day. The feasibility of dose calculation accuracy in kvCBCT images from the Elekta Synergy system was investigated using the ComTom phantom. Additionally, low contrast resolution, image uniformity, and spatial resolution between the three imaging modalities of kilovoltage CT (kvCT), kvCBCT and MVCT images, were quantitatively evaluated using the Catphan 600 phantom. The Planned Adaptive software was used on the TomoTherapy Hi·Art system to construct a cumulative Dose Volume Histogram (DVH), incorporating anatomical information provided by the daily MVCT scans. The cumulative DVH was examined to identify large deviation (10% or greater) between the planned and delivered mean doses. The study proposes a framework that applies the cumulative DVH to evaluate and adapt plans that are based on actual delivered doses. Due to the large deviation in CT number (›300 HU) between the kvCBCT images and the kvCT, a direct dose recomputation on the kvCBCT images from the Elekta Synergy system was found to be inaccurate. The maximum deviation to the prostate was only 2.7% in our kvCBCT study, when compared to the daily prescribed dose. However, there was a large daily variation in rectum and bladder doses based on the anatomy of the day. The maximum variation in rectum and bladder volumes receiving the percentage of prescribed dose was 12% and 40%, respectively. We have shown that by using Planned Adaptive software on the TomoTherapy Hi·Art system, plans can be adapted based on the image feedback from daily MVCT scans to allow the actual delivered doses to closely track the original planned doses.PACS number: 87.53.Tf
Time delays and margins in gated radiotherapy
Authors: Smith Wendy L. , Becker Nathan 
Published: August 2009

In gated radiotherapy, the accuracy of treatment delivery is determined by the accuracy with which both the imaging and treatment beams are gated. Time delays are of four types: (1) beam on imaging time delay is the time between the target entering the gated region and the first gated image acquisition; (2) beam off imaging time delay is the time between the target exiting a gated region and the last image acquisition; (3) beam on treatment time delay is the time between the target entering the gated region and the treatment beam on; and (4) beam off treatment time delay is the time between the target exiting the gated region and treatment beam off. Asynchronous time delays for the imaging and treatment systems may increase the required internal target volume (ITV) margin. We measured time delay on three fluoroscopy systems, and three linear accelerator treatment beams, varying gating type (amplitude vs. phase), beam energy, dose rate, and period. The average beam on imaging time delays were (amplitude, 1 SD), (phase); while the average beam off imaging time delays were (amplitude) and (phase). The average beam on treatment time delays were (amplitude, 1 SD), (phase); while the average beam off time delays for treatment beams were (amplitude) and (phase). The negative value indicates the images were acquired early, and the positive values show the treatment beam was triggered late. We present a technique for calculating the margin necessary to account for time delays. We found that the difference between these imaging and treatment time delays required a significant increase in the ITV margin in the direction of tumor motion at the gated level.PACS number: 87.53.Dq
Application of a 3D volumetric display for radiation therapy treatment planning I: quality assurance procedures
Authors: Gong Xing , Kirk Mike , Zusag Tom , Khelashvili Gocha , Chu James , Napoli Josh , Stutsman Sandy 
Published: August 2009

To design and implement a set of quality assurance tests for an innovative 3D volumetric display for radiation treatment planning applications. A genuine 3D display (Perspecta Spatial 3D, Actuality‐Systems Inc., Bedford, MA) has been integrated with the Pinnacle TPS (Philips Medical Systems, Madison WI), for treatment planning. The Perspecta 3D display renders a 25 cm diameter volume that is viewable from any side, floating within a translucent dome. In addition to displaying all 3D data exported from Pinnacle, the system provides a 3D mouse to define beam angles and apertures and to measure distance. The focus of this work is the design and implementation of a quality assurance program for 3D displays and specific 3D planning issues as guided by AAPM Task Group Report 53. A series of acceptance and quality assurance tests have been designed to evaluate the accuracy of CT images, contours, beams, and dose distributions as displayed on Perspecta. Three‐dimensional matrices, rulers and phantoms with known spatial dimensions were used to check Perspecta's absolute spatial accuracy. In addition, a system of tests was designed to confirm Perspecta's ability to import and display Pinnacle data consistently. CT scans of phantoms were used to confirm beam field size, divergence, and gantry and couch angular accuracy as displayed on Perspecta. Beam angles were verified through Cartesian coordinate system measurements and by CT scans of phantoms rotated at known angles. Beams designed on Perspecta were exported to Pinnacle and checked for accuracy. Dose at sampled points were checked for consistency with Pinnacle and agreed within 1% or 1 mm. All data exported from Pinnacle to Perspecta was displayed consistently. The 3D spatial display of images, contours, and dose distributions were consistent with Pinnacle display. When measured by the 3D ruler, the distances between any two points calculated using Perspecta agreed with Pinnacle within the measurement errorPACS number: 07.07.Hj, 87.55.Qr, 87.56.Da, 87.55.D‐; Radiation Treatment Planning
Expected clinical impact of the differences between planned and delivered dose distributions in helical tomotherapy for treating head and neck cancer using helical megavoltage CT images
Authors: Mavroidis Panayiotis , Stathakis Sotirios , Gutierrez Alonso , Esquivel Carlos , Shi Chenyu , Papanikolaou Nikos 
Published: August 2009

Helical Tomotherapy (HT) has become increasingly popular over the past few years. However, its clinical efficacy and effectiveness continues to be investigated. Pre‐treatment patient repositioning in highly conformal image‐guided radiation therapy modalities is a prerequisite for reducing setup uncertainties. A MVCT image set has to be acquired to account for daily changes in the patient's internal anatomy and setup position. Furthermore, a comparison should be performed to the kVCT study used for dosimetric planning, by a registration process that results in repositioning the patient according to specific transitional and rotational shifts. Different image registration techniques may lead to different repositioning of the patient and, as a result, to varying delivered doses. This study aims to investigate the expected effect of patient setup correction using the Hi·Art TomoTherapy system by employing radiobiological measures such as the biologically effective uniform dose and the complication‐free tumor control probability . In this study, a typical case of lung cancer with metastatic head and neck disease was investigated by developing a Helical Tomotherapy plan. For the TomoTherapy Hi·Art plan, the dedicated tomotherapy treatment planning station was used. Three dose distributions (planned and delivered with and without patient setup correction) were compared based on radiobiological measures by using the index and the concept as the common prescription point of the plans, and plotting the tissue response probabilities against the mean target dose for a range of prescription doses. The applied plan evaluation method shows that, in this cancer case, the planned and delivered dose distributions with and without patient setup correction give a of 81.6%, 80.9% and 72.2%, for a to the planning target volume (PTV) of 78.0Gy, 77.7Gy and 75.4Gy, respectively. The corresponding tumor control probabilities are 86.3%, 85.1% and 75.1%, whereas the total complication probabilities are 4.64%, 4.20% and 2.89%, respectively. HT can encompass the often large PTV required while minimizing the volume of the organs at risk receiving high dose. However, the effectiveness of an HT treatment plan can be considerably deteriorated if an accurate patient setup system is not available. Taking into account the dose‐response relations of the irradiated tumors and normal tissues, a radiobiological treatment plan evaluation can be performed, which may provide a closer association of the delivered treatment with the clinical outcome. In such situations, for effective evaluation and comparison of different treatment plans, traditional dose based evaluation tools can be complemented by the use of diagrams.PACS number: 87.55.Qr Quality assurance in radiotherapy
The effect of a limited number of projections and reconstruction algorithms on the image quality of megavoltage digital tomosynthesis
Authors: Sarkar Vikren , Shi Chengyu , Rassiah‐Szegedi Prema , Diaz Aidnag , Eng Tony , Papanikolaou Niko 
Published: August 2009

In order to investigate the effect of the number of projections on digital tomosynthesis image quality, images were acquired over a 40 degree arc and sampled into sets of 2 to 41 projections used as input to three different reconstruction algorithms: the shift‐and‐add, the Feldkamp‐Davis‐Kress filtered back projection algorithms, and the simultaneous algebraic reconstruction technique. The variation of several image characteristics, such as in‐plane resolution, contrast to noise ratio, artifact spread, volumetric accuracy, and dose, are investigated based on the reconstruction algorithms used and also the number of projections used as source data. The results suggest that only 11 projections are required since the various parameters checked do not improve much past that number. As a reconstruction algorithm, SART did best but took much longer to reconstruct images. Thus, if reconstruction time is a determining factor, filtered back‐projection looks like a better compromise.PACS number: 87.57.C‐, 87.57.nf, 87.57.Q‐, 87.59.‐e
Evaluation of new data processing algorithms for planar gated ventriculography (MUGA)
Authors: Fair Joanna R. , Heintz Philip H. , Telepak Robert J. 
Published: August 2009

Before implementing one of two new LVEF radionuclide gated ventriculogram (MUGA) systems, the results from 312 consecutive parallel patient studies were evaluated. Each gamma‐camera acquisition was simultaneously processed by semi‐automatic Medasys Pinnacle and by fully automatic and semiautomatic Philips nuclear medicine computer systems. The Philips systems yielded LVEF results within percentage points of the Medasys system in fewer than half of the studies. The remaining values were higher or lower than those from the long‐used Medasys system. These differences might have changed cancer patient chemotherapy clinical decisions. As a result, our institution elected not to implement either new system.PACS: 87.57.U‐ Nuclear medicine imaging
Determination of the photon beam attenuation by the BrainLAB imaging couch: angular and field size dependence
Authors: Njeh Christopher F , Raines Timothy W , Saunders Mark W 
Published: August 2009

Highly attenuating radiation treatment couches are no longer useful in the present era of IMRT‐ and IGRT‐utilizing radiotherapy. High tensile strength and low density carbon fiber couch tops present a useful alternative. The objective of this study is to quantify the attenuation of megavoltage photons through BrainLAB imaging couch top and headrest at various angles and field sizes. At normal incidence, the couch attenuated 6 MV photons by 4.9% and 3.4% for and field sizes, respectively. The headrest, alone, attenuated 6 MV photons by 2.5% and 1.6% for the same field sizes. There was no significant attenuation of the 18 MV beam by either the couch or the headrest. We further found attenuation to be gantry angle dependent, with the highest attenuation recorded at 120° – at which angle the couch attenuated the 6 MV photon beam by 10% for the and 8.3% for the field sizes. Similarly, an 18 MV photon beam was attenuated by 3.6% and 3.4% for the and field sizes, respectively. The highest attenuation for the headrest occurred at 110° gantry angle: for the 6 MV photon beam, the headrest attenuation was 6.3% and 5.6% (for the and field sizes, respectively); for the 18 MV, attenuation was 2.3% (for the field size) and 2.1% (for the field size). It would appear, therefore, that BrainLAB imaging couch and headrest in IMRT with posterior beams results in significant decreases in the dose delivered to the target.PACS number: 87.56.Da
New method for obtaining position and time structure of source in HDR remote afterloading brachytherapy unit utilizing light emission from scintillator
Authors: Kojima Haruna , Hanada Takashi , Katsuta Shoichi , Yorozu Atsunori , Maruyama Koichi 
Published: August 2009

When using a HDR remote afterloading brachytherapy unit, results of treatment can be greatly influenced by both source position and treatment time. The purpose of this study is to obtain information on the source of the HDR remote afterloading unit, such as its position and time structure, with the use of a simple system consisting of a plastic scintillator block and a charge‐coupled device (CCD) camera. The CCD camera was used for recording images of scintillation luminescence at a fixed rate of 30 frames per second in real time. The source position and time structure were obtained by analyzing the recorded images. For a preset source‐step‐interval of 5 mm, the measured value of the source position was , with a pixel resolution of 0.07 mm in the recorded images. For a preset transit time of 30 s, the measured value was s, when the time resolution of the CCD camera was 1/30 s. This system enabled us to obtain the source dwell time and movement time. Therefore, parameters such as source position, transit time, dwell time, and movement time at each dwell position can be determined quantitatively using this plastic scintillator‐CCD camera system.PACS number: 87.53.Jw
Statistical validation of a new helical tomotherapy patient transfer station
Authors: Zhuang Audrey H. , Liu An , Schultheiss Timothy E. , Wong Jeffrey Y.C. 
Published: August 2009

The purpose of this work is to evaluate statistically the accuracy of a patient transfer station (PTS), which automatically converts one planning‐station‐generated treatment plan to another one with a different beam model. In our department we have installed two Hi•Art tomotherapy systems (TomoTherapy Inc., Madison, WI), and patients often need to be transferred from one tomotherapy unit to the other. Thirty patients who underwent patient transfer between the two systems were evaluated. For each patient, dose differences between his/her original plan and PTS‐transferred plan were evaluated by comparing doses at 10 randomly selected positions in his/her CT images. The Pearson indexes were calculated to analyze the relationship of the deviations to other parameters, which include absolute dose levels, sites (targets or normal tissues), and the dose accuracy of original plans and that of transferred plans. The dose accuracy of a treatment plan was determined by comparing delivered doses at the center of a solid water phantom to planned doses at the same position. The calculated dose difference between original and transferred plans was, on average, ; the maximum deviation in absolute values was 1.9% in target volumes and 2.5% in normal organs. The errors generated during PTS‐based transferring process were random and did not show correlation with other parameters. The PTS took less than 10 minutes to generate a backup plan, much less than the approximately two hours needed to create a duplicate plan manually. The results show that a PTS‐transferred plan is an acceptable match to the original plan. With a physician's approval, a transferred plan is acceptable for treatment without the necessity of being revalidated in phantom. Thus far, all of our PTS plans have been approved by the treating physician without further optimization.PACS number: 87.55.km, 87.55.D‐