An improved Monte-Carlo model of the Varian EPID separating support arm and rear-housing backscatter

NASA Astrophysics Data System (ADS)

Monville, M. E.; Kuncic, Z.; Greer, P. B.

2014-03-01

Previous investigators of EPID dosimetric properties have ascribed the backscatter, that contaminates dosimetric EPID images, to its supporting arm. Accordingly, Monte-Carlo (MC) EPID models have approximated the backscatter signal from the layers under the detector and the robotic support arm using either uniform or non-uniform solid water slabs, or through convolutions with back-scatter kernels. The aim of this work is to improve the existent MC models by measuring and modelling the separate backscatter contributions of the robotic arm and the rear plastic housing of the EPID. The EPID plastic housing is non-uniform with a 11.9 cm wide indented section that runs across the cross-plane direction in the superior half of the EPID which is 1.75 cm closer to the EPID sensitive layer than the rest of the housing. The thickness of the plastic housing is 0.5 cm. Experiments were performed with and without the housing present by removing all components of the EPID from the housing. The robotic support arm was not present for these measurements. A MC model of the linear accelerator and the EPID was modified to include the rear-housing indentation and results compared to the measurement. The rear housing was found to contribute a maximum of 3% additional signal. The rear housing contribution to the image is non-uniform in the in-plane direction with 2% asymmetry across the central 20 cm of an image irradiating the entire detector. The MC model was able to reproduce this non-uniform contribution. The EPID rear housing contributes a non-uniform backscatter component to the EPID image, which has not been previously characterized. This has been incorporated into an improved MC model of the EPID.

Development of an accurate EPID-based output measurement and dosimetric verification tool for electron beam therapy.

PubMed

Ding, Aiping; Xing, Lei; Han, Bin

2015-07-01

To develop an efficient and robust tool for output measurement and absolute dose verification of electron beam therapy by using a high spatial-resolution and high frame-rate amorphous silicon flat panel electronic portal imaging device (EPID). The dosimetric characteristics of the EPID, including saturation, linearity, and ghosting effect, were first investigated on a Varian Clinac 21EX accelerator. The response kernels of the individual pixels of the EPID to all available electron energies (6, 9, 12, 16, and 20 MeV) were calculated by using Monte Carlo (MC) simulations, which formed the basis to deconvolve an EPID raw images to the incident electron fluence map. The two-dimensional (2D) dose distribution at reference depths in water was obtained by using the constructed fluence map with a MC simulated pencil beam kernel with consideration of the geometric and structural information of the EPID. Output factor measurements were carried out with the EPID at a nominal source-surface distance of 100 cm for 2 × 2, 3 × 3, 6 × 6, 10 × 10, and 15 × 15 cm(2) fields for all available electron energies, and the results were compared with that measured in a solid water phantom using film and a Farmer-type ion chamber. The dose distributions at a reference depth specific to each energy and the flatness and symmetry of the 10 × 10 cm(2) electron beam were also measured using EPID, and the results were compared with ion chamber array and water scan measurements. Finally, three patient cases with various field sizes and irregular cutout shapes were also investigated. EPID-measured dose changed linearly with the monitor units and showed little ghosting effect for dose rate up to 600 MU/min. The flatness and symmetry measured with the EPID were found to be consistent with ion chamber array and water scan measurements. The EPID-measured output factors for standard square fields of 2 × 2, 3 × 3, 6 × 6, 10 × 10, 15 × 15 cm(2) agreed with film and ion chamber measurements. The average discrepancy between EPID and ion chamber/film measurements was 0.81% ± 0.60% (SD) and 1.34% ± 0.75%, respectively. For the three clinical cases, the difference in output between the EPID- and ion chamber array measured values was found to be 1.13% ± 0.11%, 0.54% ± 0.10%, and 0.74% ± 0.11%, respectively. Furthermore, the γ-index analysis showed an excellent agreement between the EPID- and ion chamber array measured dose distributions: 100% of the pixels passed the criteria of 3%/3 mm. When the γ-index was set to be 2%/2 mm, the pass rate was found to be 99.0% ± 0.07%, 98.2% ± 0.14%, and 100% for the three cases. The EPID dosimetry system developed in this work provides an accurate and reliable tool for routine output measurement and dosimetric verification of electron beam therapy. Coupled with its portability and ease of use, the proposed system promises to replace the current film-based approach for fast and reliable assessment of small and irregular electron field dosimetry.

Experimental investigation of the response of an amorphous silicon EPID to intensity modulated radiotherapy beams.

PubMed

Greer, Peter B; Vial, Philip; Oliver, Lyn; Baldock, Clive

2007-11-01

The aim of this work was to experimentally determine the difference in response of an amorphous silicon (a-Si) electronic portal imaging device (EPID) to the open and multileaf collimator (MLC) transmitted beam components of intensity modulated radiation therapy (IMRT) beams. EPID dose response curves were measured for open and MLC transmitted (MLCtr) 10 x 10 cm2 beams at central axis and with off axis distance using a shifting field technique. The EPID signal was obtained by replacing the flood-field correction with a pixel sensitivity variation matrix correction. This signal, which includes energy-dependent response, was then compared to ion-chamber measurements. An EPID calibration method to remove the effect of beam energy variations on EPID response was developed for IMRT beams. This method uses the component of open and MLCtr fluence to an EPID pixel calculated from the MLC delivery file and applies separate radially dependent calibration factors for each component. The calibration procedure does not correct for scatter differences between ion chamber in water measurements and EPID response; these must be accounted for separately with a kernel-based approach or similar method. The EPID response at central axis for the open beam was found to be 1.28 +/- 0.03 of the response for the MLCtr beam, with the ratio increasing to 1.39 at 12.5 cm off axis. The EPID response to MLCtr radiation did not change with off-axis distance. Filtering the beam with copper plates to reduce the beam energy difference between open and MLCtr beams was investigated; however, these were not effective at reducing EPID response differences. The change in EPID response for uniform sliding window IMRT beams with MLCtr dose components from 0.3% to 69% was predicted to within 2.3% using the separate EPID response calibration factors for each dose component. A clinical IMRT image calibrated with this method differed by nearly 30% in high MLCtr regions from an image calibrated with an open beam calibration factor only. Accounting for the difference in EPID response to open and MLCtr radiation should improve IMRT dosimetry with a-Si EPIDs.

Image movement of the Elekta EPID during gantry rotation: Effects on the verification of dose distributions.

PubMed

Köhn, J; Licher, J; Mielke, M; Loutfi-Krauss, B; Blümer, N; Heine, B; Rödel, C; Scherf, C; Ramm, U

2017-02-01

The use of Electronic Portal Imaging Devices (EPIDs) to acquire dosimetric information, especially for 3D-back-projection, has been increasingly extended. For a precise back-projection, the accurate knowledge of the movement characteristics of the EPID during gantry rotation is an essential requirement. Measurements were conducted with different alignments of steel balls, which were mounted on the treatment table to avoid secondary effects such as the mechanical sag of gantry or jaws. The image movement of the EPID was determined by comparing the predicted projections of the phantoms with the EPID acquired image. Effects on dosimetric verifications were evaluated by γ-evaluation. The measurement results showed that the shift of the EPID image is larger in Y direction than in X direction. A maximum rotation of 0.3° and nodding of 2.4° of the detector was calculated. Changes in SDD were found up to 10mm. The angles of nodding are overall higher at discrete gantry angles in comparison to images detected for continuous rotation. Using these results we were able to correct the EPID images used for verification measurements. γ-evaluation revealed a significantly improved agreement between planned and measured EPID signal values. The measurement methods and algorithms introduced in this study are simple and comprehensive. Using these methods and algorithms we were able to quantify the major effects on geometrical and dosimetric characteristics. This allows the correction of EPID signal measurements for these effects related to the gantry angle, leading to an improved γ-evaluation for treatment plans. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

A Monte Carlo calculation model of electronic portal imaging device for transit dosimetry through heterogeneous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Jihyung; Jung, Jae Won, E-mail: jungj@ecu.edu; Kim, Jong Oh

2016-05-15

Purpose: To develop and evaluate a fast Monte Carlo (MC) dose calculation model of electronic portal imaging device (EPID) based on its effective atomic number modeling in the XVMC code. Methods: A previously developed EPID model, based on the XVMC code by density scaling of EPID structures, was modified by additionally considering effective atomic number (Z{sub eff}) of each structure and adopting a phase space file from the EGSnrc code. The model was tested under various homogeneous and heterogeneous phantoms and field sizes by comparing the calculations in the model with measurements in EPID. In order to better evaluate themore » model, the performance of the XVMC code was separately tested by comparing calculated dose to water with ion chamber (IC) array measurement in the plane of EPID. Results: In the EPID plane, calculated dose to water by the code showed agreement with IC measurements within 1.8%. The difference was averaged across the in-field regions of the acquired profiles for all field sizes and phantoms. The maximum point difference was 2.8%, affected by proximity of the maximum points to penumbra and MC noise. The EPID model showed agreement with measured EPID images within 1.3%. The maximum point difference was 1.9%. The difference dropped from the higher value of the code by employing the calibration that is dependent on field sizes and thicknesses for the conversion of calculated images to measured images. Thanks to the Z{sub eff} correction, the EPID model showed a linear trend of the calibration factors unlike those of the density-only-scaled model. The phase space file from the EGSnrc code sharpened penumbra profiles significantly, improving agreement of calculated profiles with measured profiles. Conclusions: Demonstrating high accuracy, the EPID model with the associated calibration system may be used for in vivo dosimetry of radiation therapy. Through this study, a MC model of EPID has been developed, and their performance has been rigorously investigated for transit dosimetry.« less

SU-G-BRB-10: New Generation of High Frame-Rate and High Spatial-Resolution EPID QA System for Full-Body MLC-Based Robotic Radiosurgery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, B; Xing, L; Wang, L

Purpose: To systematically investigate an ultra-high spatial-resolution amorphous silicon flat-panel electronic portal imaging device (EPID) for MLC-based full-body robotic radiosurgery geometric and dosimetric quality assurance (QA). Methods: The high frame-rate and ultra-high spatial resolution EPID is an outstanding detector for measuring profiles, MLC-shaped radiosurgery field aperture verification, and small field dosimetry. A Monte Carlo based technique with a robotic linac specific response and calibration is developed to convert a raw EPID-measured image of a radiosurgery field into water-based dose distribution. The technique is applied to measure output factors and profiles for 6MV MLC-defined radiosurgery fields with various sizes ranging frommore » 7.6mm×7.7mm to 100mm×100.1mm and the results are compared with the radiosurgery diode scan measurements in water tank. The EPID measured field sizes and the penumbra regions are analyzed to evaluate the MLC positioning accuracy. Results: For all MLC fields, the EPID measured output factors of MLC-shaped fields are in good agreement with the diode measurements. The mean output difference between the EPID and diode measurement is 0.05±0.87%. The max difference is −1.33% for 7.6mm×7.7mm field. The MLC field size derived from the EPID measurements are in good agreement comparing to the diode scan result. For crossline field sizes, the mean difference is −0.17mm±0.14mm with a maximum of −0.35mm for the 30.8mm×30.8mm field. For inline field sizes, the mean difference is +0.08mm±0.18mm with a maximum of +0.45mm for the 100mm×100.1mm field. The high resolution EPID is able to measure the whole radiation field, without the need to align the detector center perfectly at field center as diode or ion chamber measurement. The setup time is greatly reduced so that the whole process is possible for machine and patient-specific QA. Conclusion: The high spatial-resolution EPID is proved to be an accurate and efficient tool for QA of MLC-equipped robotic radiosurgery system.« less

SU-F-T-567: Sensitivity and Reproducibility of the Portal Imaging Panel for Routine FFF QC and Patient Plan Dose Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willett, A; Gilmore, M; Rowbottom, C

2016-06-15

Purpose: The purpose of this work was to see if the EPID is a viable alternative to other QA devices for routine FFF QA and plan dose measurements. Methods: Sensitivity measurements were made to assess response to small changes in field size and beam steering. QA plans were created where field size was varied from baseline values (5–5.5cm, 20–20.5cm). Beam steering was adjusted by altering values in service mode (Symmetry 0–3%). Plans were measured using the Varian portal imager (aS1200 DMI panel), QA3 (Sun Nuclear), and Starcheck Maxi (PTW). FFF beam parameters as stated in Fogliata et al were calculated.more » Constancy measurements were taken using all 3 QC devices to measure a MLC defined 20×20cm field. Two clinical SABR patient plans were measured on a Varian Edge linac, using the Portal Dosimetry module in ARIA, and results compared with analysis made using Delta4 (ScandiDos). Results: The EPID and the Starcheck performed better at detecting clinically relevant changes in field size with the QA3 performing better when detecting similar changes in beam symmetry. Consistency measurements with the EPID and Starcheck were equivalent, with comparable standard deviations. Clinical plan measurements on the EPID compared well with Delta4 results at 3%/1mm. Conclusion: Our results show that for FFF QA measurements such as field size and symmetry, using the EPID is a viable alternative to other QA devices. The EPID could potentially be used for QC measurements with a focus on geometric accuracy, such as MLC positional QA, due to its high resolution compared to other QA devices (EPID 0.34mm, Starcheck 3mm, QA3 5mm). Good agreement between Delta4 and portal dosimetry also indicated the EPID may be a suitable alternative for measurement of clinical plans.« less

SU-E-T-88: Comprehensive Automated Daily QA for Hypo- Fractionated Treatments

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuinness, C; Morin, O

2014-06-01

Purpose: The trend towards more SBRT treatments with fewer high dose fractions places increased importance on daily QA. Patient plan specific QA with 3%/3mm gamma analysis and daily output constancy checks may not be enough to guarantee the level of accuracy required for SBRT treatments. But increasing the already extensive amount of QA procedures that are required is a daunting proposition. We performed a feasibility study for more comprehensive automated daily QA that could improve the diagnostic capabilities of QA without increasing workload. Methods: We performed the study on a Siemens Artiste linear accelerator using the integrated flat panel EPID.more » We included square fields, a picket fence, overlap and representative IMRT fields to measure output, flatness, symmetry, beam center, and percent difference from the standard. We also imposed a set of machine errors: MLC leaf position, machine output, and beam steering to compare with the standard. Results: Daily output was consistent within +/− 1%. Change in steering current by 1.4% and 2.4% resulted in a 3.2% and 6.3% change in flatness. 1 and 2mm MLC leaf offset errors were visibly obvious in difference plots, but passed a 3%/3mm gamma analysis. A simple test of transmission in a picket fence can catch a leaf offset error of a single leaf by 1mm. The entire morning QA sequence is performed in less than 30 minutes and images are automatically analyzed. Conclusion: Automated QA procedures could be used to provide more comprehensive information about the machine with less time and human involvement. We have also shown that other simple tests are better able to catch MLC leaf position errors than a 3%/3mm gamma analysis commonly used for IMRT and modulated arc treatments. Finally, this information could be used to watch trends of the machine and predict problems before they lead to costly machine downtime.« less

Clinical validation of an in-house EPID dosimetry system for IMRT QA at the Prince of Wales Hospital

NASA Astrophysics Data System (ADS)

Tyler, M.; Vial, P.; Metcalfe, P.; Downes, S.

2013-06-01

In this study a simple method using standard flood-field corrected Electronic Portal Imaging Device (EPID) images for routine Intensity Modulated Radiation Therapy (IMRT) Quality Assurance (QA) was investigated. The EPID QA system was designed and tested on a Siemens Oncor Impression linear accelerator with an OptiVue 1000ST EPID panel (Siemens Medical Solutions USA, Inc, USA) and an Elekta Axesse linear accelerator with an iViewGT EPID (Elekta AB, Sweden) for 6 and 10 MV IMRT fields with Step-and-Shoot and dynamic-MLC delivery. Two different planning systems were used for patient IMRT field generation for comparison with the measured EPID fluences. All measured IMRT plans had >95% agreement to the planning fluences (using 3 cGy / 3 mm Gamma Criteria) and were comparable to the pass-rates calculated using a 2-D diode array dosimeter.

WE-DE-BRA-06: Evaluation of the Imaging Performance of a Novel Water-Equivalent EPID

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blake, SJ; The Ingham Institute, Liverpool, NSW; Cheng, J

Purpose: To evaluate the megavoltage imaging performance of a novel, water-equivalent electronic portal imaging device (EPID) developed for simultaneous imaging and dosimetry applications in radiotherapy. Methods: A novel EPID prototype based on active matrix flat panel imager technology has been developed by our group and previously reported to exhibit a water-equivalent dose response. It was constructed by replacing all components above the photodiode detector in a standard clinical EPID (including the copper plate and phosphor screen) with a 15 × 15 cm{sup 2} array of plastic scintillator fibers. Individual fibers measured 0.5 × 0.5 × 30 mm{sup 3}. Spatial resolutionmore » was evaluated experimentally relative to that of a standard EPID with the thin slit technique to measure the modulation transfer function (MTF) for 6 MV x-ray beams. Monte Carlo (MC) EPID models were used to benchmark simulated MTFs against the measurements. The zero spatial frequency detective quantum efficiency (DQE(0)) was simulated for both EPID configurations and a preliminary optimization of the prototype was performed by evaluating DQE(0) as a function of fiber length up to 50 mm. Results: The MC-simulated DQE(0) for the prototype EPID configuration was ∼7 times greater than that of the standard EPID. The prototype’s DQE(0) also increased approximately linearly with fiber length, from ∼1% at 5 mm length to ∼11% at 50 mm length. The standard EPID MTF was greater than the prototype EPID’s for all spatial frequencies, reflecting the trade off between x-ray detection efficiency and spatial resolution with thick scintillators. Conclusion: This study offers promising evidence that a water-equivalent EPID previously demonstrated for radiotherapy dosimetry may also be used for radiotherapy imaging applications. Future studies on optimising the detector design will be performed to develop a next-generation prototype that offers improved megavoltage imaging performance, with the aim to at least match that of current clinical EPIDs. Funding for this project was provided by an Australian Research Council Linkage Project grant (2015) between The University of Sydney, South Western Sydney Local Health District and Perkin-Elmer Pty Ltd.« less

Transit dosimetry in IMRT with an a-Si EPID in direct detection configuration

NASA Astrophysics Data System (ADS)

Sabet, Mahsheed; Rowshanfarzad, Pejman; Vial, Philip; Menk, Frederick W.; Greer, Peter B.

2012-08-01

In this study an amorphous silicon electronic portal imaging device (a-Si EPID) converted to direct detection configuration was investigated as a transit dosimeter for intensity modulated radiation therapy (IMRT). After calibration to dose and correction for a background offset signal, the EPID-measured absolute IMRT transit doses for 29 fields were compared to a MatriXX two-dimensional array of ionization chambers (as reference) using Gamma evaluation (3%, 3 mm). The MatriXX was first evaluated as reference for transit dosimetry. The accuracy of EPID measurements was also investigated by comparison of point dose measurements by an ionization chamber on the central axis with slab and anthropomorphic phantoms in a range of simple to complex fields. The uncertainty in ionization chamber measurements in IMRT fields was also investigated by its displacement from the central axis and comparison with the central axis measurements. Comparison of the absolute doses measured by the EPID and MatriXX with slab phantoms in IMRT fields showed that on average 96.4% and 97.5% of points had a Gamma index<1 in head and neck and prostate fields, respectively. For absolute dose comparisons with anthropomorphic phantoms, the values changed to an average of 93.6%, 93.7% and 94.4% of points with Gamma index<1 in head and neck, brain and prostate fields, respectively. Point doses measured by the EPID and ionization chamber were within 3% difference for all conditions. The deviations introduced in the response of the ionization chamber in IMRT fields were<1%. The direct EPID performance for transit dosimetry showed that it has the potential to perform accurate, efficient and comprehensive in vivo dosimetry for IMRT.

Characterization of the a-Si EPID in the unity MR-linac for dosimetric applications.

PubMed

Torres-Xirau, I; Olaciregui-Ruiz, I; Baldvinsson, G; Mijnheer, B J; van der Heide, U A; Mans, A

2018-01-09

Electronic portal imaging devices (EPIDs) are frequently used in external beam radiation therapy for dose verification purposes. The aim of this study was to investigate the dose-response characteristics of the EPID in the Unity MR-linac (Elekta AB, Stockholm, Sweden) relevant for dosimetric applications under clinical conditions. EPID images and ionization chamber (IC) measurements were used to study the effects of the magnetic field, the scatter generated in the MR housing reaching the EPID, and inhomogeneous attenuation from the MR housing. Dose linearity and dose rate dependencies were also determined. The magnetic field strength at EPID level did not exceed 10 mT, and dose linearity and dose rate dependencies proved to be comparable to that on a conventional linac. Profiles of fields, delivered with and without the magnetic field, were indistinguishable. The EPID center had an offset of 5.6 cm in the longitudinal direction, compared to the beam central axis, meaning that large fields in this direction will partially fall outside the detector area and not be suitable for verification. Beam attenuation by the MRI scanner and the table is gantry angle dependent, presenting a minimum attenuation of 67% relative to the 90° measurement. Repeatability, observed over two months, was within 0.5% (1 SD). In order to use the EPID for dosimetric applications in the MR-linac, challenges related to the EPID position, scatter from the MR housing, and the inhomogeneous, gantry angle-dependent attenuation of the beam will need to be solved.

Characterization of the a-Si EPID in the unity MR-linac for dosimetric applications

NASA Astrophysics Data System (ADS)

Torres-Xirau, I.; Olaciregui-Ruiz, I.; Baldvinsson, G.; Mijnheer, B. J.; van der Heide, U. A.; Mans, A.

2018-01-01

Electronic portal imaging devices (EPIDs) are frequently used in external beam radiation therapy for dose verification purposes. The aim of this study was to investigate the dose-response characteristics of the EPID in the Unity MR-linac (Elekta AB, Stockholm, Sweden) relevant for dosimetric applications under clinical conditions. EPID images and ionization chamber (IC) measurements were used to study the effects of the magnetic field, the scatter generated in the MR housing reaching the EPID, and inhomogeneous attenuation from the MR housing. Dose linearity and dose rate dependencies were also determined. The magnetic field strength at EPID level did not exceed 10 mT, and dose linearity and dose rate dependencies proved to be comparable to that on a conventional linac. Profiles of fields, delivered with and without the magnetic field, were indistinguishable. The EPID center had an offset of 5.6 cm in the longitudinal direction, compared to the beam central axis, meaning that large fields in this direction will partially fall outside the detector area and not be suitable for verification. Beam attenuation by the MRI scanner and the table is gantry angle dependent, presenting a minimum attenuation of 67% relative to the 90° measurement. Repeatability, observed over two months, was within 0.5% (1 SD). In order to use the EPID for dosimetric applications in the MR-linac, challenges related to the EPID position, scatter from the MR housing, and the inhomogeneous, gantry angle-dependent attenuation of the beam will need to be solved.

Quantifying the performance of in vivo portal dosimetry in detecting four types of treatment parameter variations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bojechko, C.; Ford, E. C., E-mail: eford@uw.edu

Purpose: To quantify the ability of electronic portal imaging device (EPID) dosimetry used during treatment (in vivo) in detecting variations that can occur in the course of patient treatment. Methods: Images of transmitted radiation from in vivo EPID measurements were converted to a 2D planar dose at isocenter and compared to the treatment planning dose using a prototype software system. Using the treatment planning system (TPS), four different types of variability were modeled: overall dose scaling, shifting the positions of the multileaf collimator (MLC) leaves, shifting of the patient position, and changes in the patient body contour. The gamma passmore » rate was calculated for the modified and unmodified plans and used to construct a receiver operator characteristic (ROC) curve to assess the detectability of the different parameter variations. The detectability is given by the area under the ROC curve (AUC). The TPS was also used to calculate the impact of the variations on the target dose–volume histogram. Results: Nine intensity modulation radiation therapy plans were measured for four different anatomical sites consisting of 70 separate fields. Results show that in vivo EPID dosimetry was most sensitive to variations in the machine output, AUC = 0.70 − 0.94, changes in patient body habitus, AUC = 0.67 − 0.88, and systematic shifts in the MLC bank positions, AUC = 0.59 − 0.82. These deviations are expected to have a relatively small clinical impact [planning target volume (PTV) D{sub 99} change <7%]. Larger variations have even higher detectability. Displacements in the patient’s position and random variations in MLC leaf positions were not readily detectable, AUC < 0.64. The D{sub 99} of the PTV changed by up to 57% for the patient position shifts considered here. Conclusions: In vivo EPID dosimetry is able to detect relatively small variations in overall dose, systematic shifts of the MLC’s, and changes in the patient habitus. Shifts in the patient’s position which can introduce large changes in the target dose coverage were not readily detected.« less

Linear array measurements of enhanced dynamic wedge and treatment planning system (TPS) calculation for 15 MV photon beam and comparison with electronic portal imaging device (EPID) measurements.

PubMed

Petrovic, Borislava; Grzadziel, Aleksandra; Rutonjski, Laza; Slosarek, Krzysztof

2010-09-01

Enhanced dynamic wedges (EDW) are known to increase drastically the radiation therapy treatment efficiency. This paper has the aim to compare linear array measurements of EDW with the calculations of treatment planning system (TPS) and the electronic portal imaging device (EPID) for 15 MV photon energy. The range of different field sizes and wedge angles (for 15 MV photon beam) were measured by the linear chamber array CA 24 in Blue water phantom. The measurement conditions were applied to the calculations of the commercial treatment planning system XIO CMS v.4.2.0 using convolution algorithm. EPID measurements were done on EPID-focus distance of 100 cm, and beam parameters being the same as for CA24 measurements. Both depth doses and profiles were measured. EDW linear array measurements of profiles to XIO CMS TPS calculation differ around 0.5%. Profiles in non-wedged direction and open field profiles practically do not differ. Percentage depth doses (PDDs) for all EDW measurements show the difference of not more than 0.2%, while the open field PDD is almost the same as EDW PDD. Wedge factors for 60 deg wedge angle were also examined, and the difference is up to 4%. EPID to linear array differs up to 5%. The implementation of EDW in radiation therapy treatments provides clinicians with an effective tool for the conformal radiotherapy treatment planning. If modelling of EDW beam in TPS is done correctly, a very good agreement between measurements and calculation is obtained, but EPID cannot be used for reference measurements.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Passarge, M; Fix, M K; Manser, P

Purpose: To create and test an accurate EPID-frame-based VMAT QA metric to detect gross dose errors in real-time and to provide information about the source of error. Methods: A Swiss cheese model was created for an EPID-based real-time QA process. The system compares a treatmentplan- based reference set of EPID images with images acquired over each 2° gantry angle interval. The metric utilizes a sequence of independent consecutively executed error detection Methods: a masking technique that verifies infield radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment to quantify rotation, scaling andmore » translation; standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each test were determined. For algorithm testing, twelve different types of errors were selected to modify the original plan. Corresponding predictions for each test case were generated, which included measurement-based noise. Each test case was run multiple times (with different noise per run) to assess the ability to detect introduced errors. Results: Averaged over five test runs, 99.1% of all plan variations that resulted in patient dose errors were detected within 2° and 100% within 4° (∼1% of patient dose delivery). Including cases that led to slightly modified but clinically equivalent plans, 91.5% were detected by the system within 2°. Based on the type of method that detected the error, determination of error sources was achieved. Conclusion: An EPID-based during-treatment error detection system for VMAT deliveries was successfully designed and tested. The system utilizes a sequence of methods to identify and prevent gross treatment delivery errors. The system was inspected for robustness with realistic noise variations, demonstrating that it has the potential to detect a large majority of errors in real-time and indicate the error source. J. V. Siebers receives funding support from Varian Medical Systems.« less

SU-F-T-229: A Novel Method for EPID-Based In-Vivo Exit Dose Verification for Intensity Modulated Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Z; Wang, J; Peng, J

Purpose: Electronic portal imaging device (EPID) can be used to acquire a two-dimensional exit dose distribution during treatment delivery, thus allowing the in-vivo verification of the dose delivery through a comparison of measured portal images to predicted portal dose images (PDI). The aim of this study was to present a novel method to easily and accurately predict PDI, and to establish an EPID-based in-vivo dose verification method during IMRT treatments. Methods: We developed a model to determine the predicted portal dose at the same plane of the EPID detector location. The Varian EPID (aS1000) positions at 150cm source-to-detector-distance (SDD), andmore » can be used to acquire in-vivo exit dose using Portal Dosimetry (PD) function. Our model was generated to make an equivalent water thickness represent the buildup plate of EPID. The exit dose at extend SDD plane with patient CT data in the beam can be calculated as the predicted PDI in the treatment planning system (TPS). After that, the PDI was converted to the fluence at SDD of 150cm using the inverse square law coded in MATLAB. Five head-and-neck and prostate IMRT patient plans contain 32 fields were investigated to evaluate the feasibility of this new method. The measured EPID image was compared with PDI using the gamma analysis. Results: The average results for cumulative dose comparison were 81.9% and 91.6% for 3%, 3mm and 4%, 4mm gamma criteria, respectively. Results indicate that the patient transit dosimetry predicted algorithm compares well with EPID measured PD doses for test situations. Conclusion: Our new method can be used as an easy and feasible tool for online EPID-based in-vivo dose delivery verification for IMRT treatments. It can be implemented for fast detecting those obvious treatment delivery errors for individual field and patient quality assurance.« less

SU-F-T-476: Performance of the AS1200 EPID for Periodic Photon Quality Assurance

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeMarco, J; Fraass, B; Yang, W

2016-06-15

Purpose: To assess the dosimetric performance of a new amorphous silicon flat-panel electronic portal imaging device (EPID) suitable for high-intensity, flattening-filter-free delivery mode. Methods: An EPID-based QA suite was created with automation to periodically monitor photon central-axis output and two-dimensional beam profile constancy as a function of gantry angle and dose-rate. A Varian TrueBeamTM linear accelerator installed with Developer Mode was used to customize and deliver XML script routines for the QA suite using the dosimetry mode image acquisition for an aS1200 EPID. Automatic post-processing software was developed to analyze the resulting DICOM images. Results: The EPID was used tomore » monitor photon beam output constancy (central-axis), flatness, and symmetry over a period of 10 months for four photon beam energies (6x, 15x, 6xFFF, and 10xFFF). EPID results were consistent to those measured with a standard daily QA check device. At the four cardinal gantry angles, the standard deviation of the EPID central-axis output was <0.5%. Likewise, EPID measurements were independent for the wide range of dose rates (including up to 2400 mu/min for 10xFFF) studied with a standard deviation of <0.8% relative to the nominal dose rate for each energy. Also, profile constancy and field size measurements showed good agreement with the reference acquisition of 0° gantry angle and nominal dose rate. XML script files were also tested for MU linearity and picket-fence delivery. Using Developer Mode, the test suite was delivered in <60 minutes for all 4 photon energies with 4 dose rates per energy and 5 picket-fence acquisitions. Conclusion: Dosimetry image acquisition using a new EPID was found to be accurate for standard and high-intensity photon beams over a broad range of dose rates over 10 months. Developer Mode provided an efficient platform to customize the EPID acquisitions by using custom script files which significantly reduced the time. This work was funded in part by Varian Medical Systems.« less

New developments in EPID-based 3D dosimetry in The Netherlands Cancer Institute

NASA Astrophysics Data System (ADS)

Mijnheer, B.; Rozendaal, R.; Olaciregui-Ruiz, I.; González, P.; van Oers, R.; Mans, A.

2017-05-01

EPID-based offline 3D in vivo dosimetry is performed routinely in The Netherlands Cancer Institute for almost all RT treatments. The 3D dose distribution is reconstructed using the EPID primary dose in combination with a back-projection algorithm and compared with the planned dose distribution. Recently the method was adapted for real-time dose verification, performing 3D dose verification in less than 300 ms, which is faster than the current portal frame acquisition rate. In this way a possibility is created for halting the linac in case of large delivery errors. Furthermore, a new method for pre-treatment QA was developed in which the EPID primary dose behind a phantom or patient is predicted using the CT data of that phantom or patient in combination with in-air EPID measurements. This virtual EPID primary transit dose is then used to reconstruct the 3D dose distribution within the phantom or patient geometry using the same dose engine as applied offline. In order to assess the relevance of our clinically applied alert criteria, we investigated the sensitivity of our EPID-based 3D dose verification system to detect delivery errors in VMAT treatments. This was done through simulation by modifying patient treatment plans, as well as experimentally by performing EPID measurements during the irradiation of an Alderson phantom, both after deliberately introducing errors during VMAT delivery. In this presentation these new developments will be elucidated.

Pixel response-based EPID dosimetry for patient specific QA.

PubMed

Han, Bin; Ding, Aiping; Lu, Minghui; Xing, Lei

2017-01-01

Increasing use of high dose rate, flattening filter free (FFF), and/or small-sized field beams presents a significant challenge to the medical physics community. In this work, we develop a strategy of using a high spatial resolution and high frame rate amorphous silicon flat panel electronic portal imaging device (EPID) for dosimetric measurements of these challenging cases, as well as for conventional external beam therapy. To convert a series of raw EPID-measured radiation field images into water-based dose distribution, a pixel-to-pixel dose-response function of the EPID specific to the linac is essential. The response function was obtained by using a Monte Carlo simulation of the photon transport in the EPID with a comprehensive calibration. After the raw image was converted into the primary incident photon fluence, the fluence was further convolved into a water-based dose distribution of the dynamic field by using a pregenerated pencil-beam kernel. The EPID-based dosimetric measurement technique was validated using beams with and without flattening filter of all energies available in Varian TrueBeam STx™. Both regularly and irregularly shaped fields measured using a PTW 729 ion chamber array in plastic water phantom. The technique was also applied to measure the distribution for a total of 23 treatment plans of different energies to evaluate the accuracy of the proposed approach. The EPID measurements of square fields of 4 × 4 cm 2 to 20 × 20 cm 2 , circular fields of 2-15 cm diameters, rectangular fields of various sizes, and irregular MLC fields were in accordance with measurements using a Farmer chamber and/or ion chamber array. The 2D absolute dose maps generated from EPID raw images agreed with ion chamber measurements to within 1.5% for all fields. For the 23 patient cases examined in this work, the average γ-index passing rate were found to be 99.2 ± 0.6%, 97.4 ± 2.4%, and 72.6 ± 8.4%, respectively, for criterions of 3 mm/3%, 2 mm/2%, and 1 mm/1%. The high spatial resolution and high frame rate EPID provides an accurate and efficient dosimetric tool for QA of modern radiation therapy. Accurate absolute 2D dose maps can be generated from the system for an independent dosimetric verification of treatment delivery. © 2016 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

A dual two dimensional electronic portal imaging device transit dosimetry model based on an empirical quadratic formalism

PubMed Central

Metwaly, M; Glegg, M; Baggarley, S P; Elliott, A

2015-01-01

Objective: This study describes a two dimensional electronic portal imaging device (EPID) transit dosimetry model that can predict either: (1) in-phantom exit dose, or (2) EPID transit dose, for treatment verification. Methods: The model was based on a quadratic equation that relates the reduction in intensity to the equivalent path length (EPL) of the attenuator. In this study, two sets of quadratic equation coefficients were derived from calibration dose planes measured with EPID and ionization chamber in water under reference conditions. With two sets of coefficients, EPL can be calculated from either EPID or treatment planning system (TPS) dose planes. Consequently, either the in-phantom exit dose or the EPID transit dose can be predicted from the EPL. The model was tested with two open, five wedge and seven sliding window prostate and head and neck intensity-modulated radiation therapy (IMRT) fields on phantoms. Results were analysed using absolute gamma analysis (3%/3 mm). Results: The open fields gamma pass rates were >96.8% for all comparisons. For wedge and IMRT fields, comparisons between predicted and TPS-computed in-phantom exit dose resulted in mean gamma pass rate of 97.4% (range, 92.3–100%). As for the comparisons between predicted and measured EPID transit dose, the mean gamma pass rate was 97.5% (range, 92.6–100%). Conclusion: An EPID transit dosimetry model that can predict in-phantom exit dose and EPID transit dose was described and proven to be valid. Advances in knowledge: The described model is practical, generic and flexible to encourage widespread implementation of EPID dosimetry for the improvement of patients' safety in radiotherapy. PMID:25969867

Markerless EPID image guided dynamic multi-leaf collimator tracking for lung tumors

NASA Astrophysics Data System (ADS)

Rottmann, J.; Keall, P.; Berbeco, R.

2013-06-01

Compensation of target motion during the delivery of radiotherapy has the potential to improve treatment accuracy, dose conformity and sparing of healthy tissue. We implement an online image guided therapy system based on soft tissue localization (STiL) of the target from electronic portal images and treatment aperture adaptation with a dynamic multi-leaf collimator (DMLC). The treatment aperture is moved synchronously and in real time with the tumor during the entire breathing cycle. The system is implemented and tested on a Varian TX clinical linear accelerator featuring an AS-1000 electronic portal imaging device (EPID) acquiring images at a frame rate of 12.86 Hz throughout the treatment. A position update cycle for the treatment aperture consists of four steps: in the first step at time t = t0 a frame is grabbed, in the second step the frame is processed with the STiL algorithm to get the tumor position at t = t0, in a third step the tumor position at t = ti + δt is predicted to overcome system latencies and in the fourth step, the DMLC control software calculates the required leaf motions and applies them at time t = ti + δt. The prediction model is trained before the start of the treatment with data representing the tumor motion. We analyze the system latency with a dynamic chest phantom (4D motion phantom, Washington University). We estimate the average planar position deviation between target and treatment aperture in a clinical setting by driving the phantom with several lung tumor trajectories (recorded from fiducial tracking during radiotherapy delivery to the lung). DMLC tracking for lung stereotactic body radiation therapy without fiducial markers was successfully demonstrated. The inherent system latency is found to be δt = (230 ± 11) ms for a MV portal image acquisition frame rate of 12.86 Hz. The root mean square deviation between tumor and aperture position is smaller than 1 mm. We demonstrate the feasibility of real-time markerless DMLC tracking with a standard LINAC-mounted (EPID).

Detection and correction for EPID and gantry sag during arc delivery using cine EPID imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rowshanfarzad, Pejman; Sabet, Mahsheed; O'Connor, Daryl J.

2012-02-15

Purpose: Electronic portal imaging devices (EPIDs) have been studied and used for pretreatment and in-vivo dosimetry applications for many years. The application of EPIDs for dosimetry in arc treatments requires accurate characterization of the mechanical sag of the EPID and gantry during rotation. Several studies have investigated the effects of gravity on the sag of these systems but each have limitations. In this study, an easy experiment setup and accurate algorithm have been introduced to characterize and correct for the effect of EPID and gantry sag during arc delivery. Methods: Three metallic ball bearings were used as markers in themore » beam: two of them fixed to the gantry head and the third positioned at the isocenter. EPID images were acquired during a 360 deg. gantry rotation in cine imaging mode. The markers were tracked in EPID images and a robust in-house developed MATLAB code was used to analyse the images and find the EPID sag in three directions as well as the EPID + gantry sag by comparison to the reference gantry zero image. The algorithm results were then tested against independent methods. The method was applied to compare the effect in clockwise and counter clockwise gantry rotations and different source-to-detector distances (SDDs). The results were monitored for one linear accelerator over a course of 15 months and six other linear-accelerators from two treatment centers were also investigated using this method. The generalized shift patterns were derived from the data and used in an image registration algorithm to correct for the effect of the mechanical sag in the system. The Gamma evaluation (3%, 3 mm) technique was used to investigate the improvement in alignment of cine EPID images of a fixed field, by comparing both individual images and the sum of images in a series with the reference gantry zero image. Results: The mechanical sag during gantry rotation was dependent on the gantry angle and was larger in the in-plane direction, although the patterns were not identical for various linear-accelerators. The reproducibility of measurements was within 0.2 mm over a period of 15 months. The direction of gantry rotation and SDD did not affect the results by more than 0.3 mm. Results of independent tests agreed with the algorithm within the accuracy of the measurement tools. When comparing summed images, the percentage of points with Gamma index <1 increased from 85.4% to 94.1% after correcting for the EPID sag, and to 99.3% after correction for gantry + EPID sag. Conclusions: The measurement method and algorithms introduced in this study use cine-images, are highly accurate, simple, fast, and reproducible. It tests all gantry angles and provides a suitable automatic analysis and correction tool to improve EPID dosimetry and perform comprehensive linac QA for arc treatments.« less

Poster — Thur Eve — 17: In-phantom and Fluence-based Measurements for Quality Assurance of Volumetric-driven Adaptation of Arc Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaly, B; Hoover, D; Mitchell, S

2014-08-15

During volumetric modulated arc therapy (VMAT) of head and neck cancer, some patients lose weight which may result in anatomical deviations from the initial plan. If these deviations are substantial a new treatment plan can be designed for the remainder of treatment (i.e., adaptive planning). Since the adaptive treatment process is resource intensive, one possible approach to streamlining the quality assurance (QA) process is to use the electronic portal imaging device (EPID) to measure the integrated fluence for the adapted plans instead of the currently-used ArcCHECK device (Sun Nuclear). Although ArcCHECK is recognized as the clinical standard for patient-specific VMATmore » plan QA, it has limited length (20 cm) for most head and neck field apertures and has coarser detector spacing than the EPID (10 mm vs. 0.39 mm). In this work we compared measurement of the integrated fluence using the EPID with corresponding measurements from the ArcCHECK device. In the past year nine patients required an adapted plan. Each of the plans (the original and adapted) is composed of two arcs. Routine clinical QA was performed using the ArcCHECK device, and the same plans were delivered to the EPID (individual arcs) in integrated mode. The dose difference between the initial plan and adapted plan was compared for ArcCHECK and EPID. In most cases, it was found that the EPID is more sensitive in detecting plan differences. Therefore, we conclude that EPID provides a viable alternative for QA of the adapted head and neck plans and should be further explored.« less

Dose-to-water conversion for the backscatter-shielded EPID: A frame-based method to correct for EPID energy response to MLC transmitted radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zwan, Benjamin J., E-mail: benjamin.zwan@uon.edu.au; O’Connor, Daryl J.; King, Brian W.

2014-08-15

Purpose: To develop a frame-by-frame correction for the energy response of amorphous silicon electronic portal imaging devices (a-Si EPIDs) to radiation that has transmitted through the multileaf collimator (MLC) and to integrate this correction into the backscatter shielded EPID (BSS-EPID) dose-to-water conversion model. Methods: Individual EPID frames were acquired using a Varian frame grabber and iTools acquisition software then processed using in-house software developed inMATLAB. For each EPID image frame, the region below the MLC leaves was identified and all pixels in this region were multiplied by a factor of 1.3 to correct for the under-response of the imager tomore » MLC transmitted radiation. The corrected frames were then summed to form a corrected integrated EPID image. This correction was implemented as an initial step in the BSS-EPID dose-to-water conversion model which was then used to compute dose planes in a water phantom for 35 IMRT fields. The calculated dose planes, with and without the proposed MLC transmission correction, were compared to measurements in solid water using a two-dimensional diode array. Results: It was observed that the integration of the MLC transmission correction into the BSS-EPID dose model improved agreement between modeled and measured dose planes. In particular, the MLC correction produced higher pass rates for almost all Head and Neck fields tested, yielding an average pass rate of 99.8% for 2%/2 mm criteria. A two-sample independentt-test and fisher F-test were used to show that the MLC transmission correction resulted in a statistically significant reduction in the mean and the standard deviation of the gamma values, respectively, to give a more accurate and consistent dose-to-water conversion. Conclusions: The frame-by-frame MLC transmission response correction was shown to improve the accuracy and reduce the variability of the BSS-EPID dose-to-water conversion model. The correction may be applied as a preprocessing step in any pretreatment portal dosimetry calculation and has been shown to be beneficial for highly modulated IMRT fields.« less

TU-G-BRD-08: In-Vivo EPID Dosimetry: Quantifying the Detectability of Four Classes of Errors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ford, E; Phillips, M; Bojechko, C

Purpose: EPID dosimetry is an emerging method for treatment verification and QA. Given that the in-vivo EPID technique is in clinical use at some centers, we investigate the sensitivity and specificity for detecting different classes of errors. We assess the impact of these errors using dose volume histogram endpoints. Though data exist for EPID dosimetry performed pre-treatment, this is the first study quantifying its effectiveness when used during patient treatment (in-vivo). Methods: We analyzed 17 patients; EPID images of the exit dose were acquired and used to reconstruct the planar dose at isocenter. This dose was compared to the TPSmore » dose using a 3%/3mm gamma criteria. To simulate errors, modifications were made to treatment plans using four possible classes of error: 1) patient misalignment, 2) changes in patient body habitus, 3) machine output changes and 4) MLC misalignments. Each error was applied with varying magnitudes. To assess the detectability of the error, the area under a ROC curve (AUC) was analyzed. The AUC was compared to changes in D99 of the PTV introduced by the simulated error. Results: For systematic changes in the MLC leaves, changes in the machine output and patient habitus, the AUC varied from 0.78–0.97 scaling with the magnitude of the error. The optimal gamma threshold as determined by the ROC curve varied between 84–92%. There was little diagnostic power in detecting random MLC leaf errors and patient shifts (AUC 0.52–0.74). Some errors with weak detectability had large changes in D99. Conclusion: These data demonstrate the ability of EPID-based in-vivo dosimetry in detecting variations in patient habitus and errors related to machine parameters such as systematic MLC misalignments and machine output changes. There was no correlation found between the detectability of the error using the gamma pass rate, ROC analysis and the impact on the dose volume histogram. Funded by grant R18HS022244 from AHRQ.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jassal, K; Sarkar, B; Mohanti, B

Objective: The study presents the application of a simple concept of statistical process control (SPC) for pre-treatment quality assurance procedure analysis for planar dose measurements performed using 2D-array and a-Si electronic portal imaging device (a-Si EPID). Method: A total of 195 patients of four different anatomical sites: brain (n1=45), head & neck (n2=45), thorax (n3=50) and pelvis (n4=55) were selected for the study. Pre-treatment quality assurance for the clinically acceptable IMRT/VMAT plans was measured with 2D array and a-Si EPID of the accelerator. After the γ-analysis, control charts and the quality index Cpm was evaluated for each cohort. Results: Meanmore » and σ of γ ( 3%/3 mm) were EPID γ %≤1= 99.9% ± 1.15% and array γ %<1 = 99.6% ± 1.06%. Among all plans γ max was consistently lower than for 2D array as compared to a-Si EPID. Fig.1 presents the X-bar control charts for every cohort. Cpm values for a-Si EPID were found to be higher than array, detailed results are presented in table 1. Conclusion: Present study demonstrates the significance of control charts used for quality management purposes in newer radiotherapy clinics. Also, provides a pictorial overview of the clinic performance for the advanced radiotherapy techniques.Higher Cpm values for EPID indicate its higher efficiency than array based measurements.« less

Source position verification and dosimetry in HDR brachytherapy using an EPID.

PubMed

Smith, R L; Taylor, M L; McDermott, L N; Haworth, A; Millar, J L; Franich, R D

2013-11-01

Accurate treatment delivery in high dose rate (HDR) brachytherapy requires correct source dwell positions and dwell times to be administered relative to each other and to the surrounding anatomy. Treatment delivery inaccuracies predominantly occur for two reasons: (i) anatomical movement or (ii) as a result of human errors that are usually related to incorrect implementation of the planned treatment. Electronic portal imaging devices (EPIDs) were originally developed for patient position verification in external beam radiotherapy and their application has been extended to provide dosimetric information. The authors have characterized the response of an EPID for use with an (192)Ir brachytherapy source to demonstrate its use as a verification device, providing both source position and dosimetric information. Characterization of the EPID response using an (192)Ir brachytherapy source included investigations of reproducibility, linearity with dose rate, photon energy dependence, and charge build-up effects associated with exposure time and image acquisition time. Source position resolution in three dimensions was determined. To illustrate treatment verification, a simple treatment plan was delivered to a phantom and the measured EPID dose distribution compared with the planned dose. The mean absolute source position error in the plane parallel to the EPID, for dwells measured at 50, 100, and 150 mm source to detector distances (SDD), was determined to be 0.26 mm. The resolution of the z coordinate (perpendicular distance from detector plane) is SDD dependent with 95% confidence intervals of ± 0.1, ± 0.5, and ± 2.0 mm at SDDs of 50, 100, and 150 mm, respectively. The response of the EPID is highly linear to dose rate. The EPID exhibits an over-response to low energy incident photons and this nonlinearity is incorporated into the dose calibration procedure. A distance (spectral) dependent dose rate calibration procedure has been developed. The difference between measured and planned dose is less than 2% for 98.0% of pixels in a two-dimensional plane at an SDD of 100 mm. Our application of EPID dosimetry to HDR brachytherapy provides a quality assurance measure of the geometrical distribution of the delivered dose as well as the source positions, which is not possible with any current HDR brachytherapy verification system.

Clinical implementation and rapid commissioning of an EPID based in-vivo dosimetry system.

PubMed

Hanson, Ian M; Hansen, Vibeke N; Olaciregui-Ruiz, Igor; van Herk, Marcel

2014-10-07

Using an Electronic Portal Imaging Device (EPID) to perform in-vivo dosimetry is one of the most effective and efficient methods of verifying the safe delivery of complex radiotherapy treatments. Previous work has detailed the development of an EPID based in-vivo dosimetry system that was subsequently used to replace pre-treatment dose verification of IMRT and VMAT plans. Here we show that this system can be readily implemented on a commercial megavoltage imaging platform without modification to EPID hardware and without impacting standard imaging procedures. The accuracy and practicality of the EPID in-vivo dosimetry system was confirmed through a comparison with traditional TLD in-vivo measurements performed on five prostate patients.The commissioning time required for the EPID in-vivo dosimetry system was initially prohibitive at approximately 10 h per linac. Here we present a method of calculating linac specific EPID dosimetry correction factors that allow a single energy specific commissioning model to be applied to EPID data from multiple linacs. Using this method reduced the required per linac commissioning time to approximately 30 min.The validity of this commissioning method has been tested by analysing in-vivo dosimetry results of 1220 patients acquired on seven linacs over a period of 5 years. The average deviation between EPID based isocentre dose and expected isocentre dose for these patients was (-0.7  ±  3.2)%.EPID based in-vivo dosimetry is now the primary in-vivo dosimetry tool used at our centre and has replaced nearly all pre-treatment dose verification of IMRT treatments.

Clinical implementation and rapid commissioning of an EPID based in-vivo dosimetry system

NASA Astrophysics Data System (ADS)

Hanson, Ian M.; Hansen, Vibeke N.; Olaciregui-Ruiz, Igor; van Herk, Marcel

2014-10-01

Using an Electronic Portal Imaging Device (EPID) to perform in-vivo dosimetry is one of the most effective and efficient methods of verifying the safe delivery of complex radiotherapy treatments. Previous work has detailed the development of an EPID based in-vivo dosimetry system that was subsequently used to replace pre-treatment dose verification of IMRT and VMAT plans. Here we show that this system can be readily implemented on a commercial megavoltage imaging platform without modification to EPID hardware and without impacting standard imaging procedures. The accuracy and practicality of the EPID in-vivo dosimetry system was confirmed through a comparison with traditional TLD in-vivo measurements performed on five prostate patients. The commissioning time required for the EPID in-vivo dosimetry system was initially prohibitive at approximately 10 h per linac. Here we present a method of calculating linac specific EPID dosimetry correction factors that allow a single energy specific commissioning model to be applied to EPID data from multiple linacs. Using this method reduced the required per linac commissioning time to approximately 30 min. The validity of this commissioning method has been tested by analysing in-vivo dosimetry results of 1220 patients acquired on seven linacs over a period of 5 years. The average deviation between EPID based isocentre dose and expected isocentre dose for these patients was (-0.7  ±  3.2)%. EPID based in-vivo dosimetry is now the primary in-vivo dosimetry tool used at our centre and has replaced nearly all pre-treatment dose verification of IMRT treatments.

SU-F-T-240: EPID-Based Quality Assurance for Dosimetric Credentialing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miri, N; Lehmann, J; Vial, P

Purpose: We propose a novel dosimetric audit method for clinical trials using EPID measurements at each center and a standardized EPID to dose conversion algorithm. The aim of this work is to investigate the applicability of the EPID method to different linear accelerator, EPID and treatment planning system (TPS) combinations. Methods: Combination of delivery and planning systems were three Varian linacs including one Pinnacle and two Eclipse TPS and, two ELEKTA linacs including one Pinnacle and one Monaco TPS. All Varian linacs had the same EPID structure and similarly for the ELEKTA linacs. Initially, dose response of the EPIDs wasmore » investigated by acquiring integrated pixel value (IPV) of the central area of 10 cm2 images versus MUs, 5-400 MU. Then, the EPID to dose conversion was investigated for different system combinations. Square field size images, 2, 3, 4, 6, 10, 15, 20, 25 cm2 acquired by all systems were converted to dose at isocenter of a virtual flat phantom then the dose was compared to the corresponding TPS dose. Results: All EPIDs showed a relatively linear behavior versus MU except at low MUs which showed irregularities probably due to initial inaccuracies of irradiation. Furthermore, for all the EPID models, the model predicted TPS dose with a mean dose difference percentage of 1.3. However the model showed a few inaccuracies for ELEKTA EPID images at field sizes larger than 20 cm2. Conclusion: The EPIDs demonstrated similar behavior versus MU and the model was relatively accurate for all the systems. Therefore, the model could be employed as a global dosimetric method to audit clinical trials. Funding has been provided from Department of Radiation Oncology, TROG Cancer Research and the University of Newcastle. Narges Miri is a recipient of a University of Newcastle postgraduate scholarship.« less

TH-AB-202-02: Real-Time Verification and Error Detection for MLC Tracking Deliveries Using An Electronic Portal Imaging Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Zwan, B; Central Coast Cancer Centre, Gosford, NSW; Colvill, E

2016-06-15

Purpose: The added complexity of the real-time adaptive multi-leaf collimator (MLC) tracking increases the likelihood of undetected MLC delivery errors. In this work we develop and test a system for real-time delivery verification and error detection for MLC tracking radiotherapy using an electronic portal imaging device (EPID). Methods: The delivery verification system relies on acquisition and real-time analysis of transit EPID image frames acquired at 8.41 fps. In-house software was developed to extract the MLC positions from each image frame. Three comparison metrics were used to verify the MLC positions in real-time: (1) field size, (2) field location and, (3)more » field shape. The delivery verification system was tested for 8 VMAT MLC tracking deliveries (4 prostate and 4 lung) where real patient target motion was reproduced using a Hexamotion motion stage and a Calypso system. Sensitivity and detection delay was quantified for various types of MLC and system errors. Results: For both the prostate and lung test deliveries the MLC-defined field size was measured with an accuracy of 1.25 cm{sup 2} (1 SD). The field location was measured with an accuracy of 0.6 mm and 0.8 mm (1 SD) for lung and prostate respectively. Field location errors (i.e. tracking in wrong direction) with a magnitude of 3 mm were detected within 0.4 s of occurrence in the X direction and 0.8 s in the Y direction. Systematic MLC gap errors were detected as small as 3 mm. The method was not found to be sensitive to random MLC errors and individual MLC calibration errors up to 5 mm. Conclusion: EPID imaging may be used for independent real-time verification of MLC trajectories during MLC tracking deliveries. Thresholds have been determined for error detection and the system has been shown to be sensitive to a range of delivery errors.« less

Time dependent pre-treatment EPID dosimetry for standard and FFF VMAT.

PubMed

Podesta, Mark; Nijsten, Sebastiaan M J J G; Persoon, Lucas C G G; Scheib, Stefan G; Baltes, Christof; Verhaegen, Frank

2014-08-21

Methods to calibrate Megavoltage electronic portal imaging devices (EPIDs) for dosimetry have been previously documented for dynamic treatments such as intensity modulated radiotherapy (IMRT) using flattened beams and typically using integrated fields. While these methods verify the accumulated field shape and dose, the dose rate and differential fields remain unverified. The aim of this work is to provide an accurate calibration model for time dependent pre-treatment dose verification using amorphous silicon (a-Si) EPIDs in volumetric modulated arc therapy (VMAT) for both flattened and flattening filter free (FFF) beams. A general calibration model was created using a Varian TrueBeam accelerator, equipped with an aS1000 EPID, for each photon spectrum 6 MV, 10 MV, 6 MV-FFF, 10 MV-FFF. As planned VMAT treatments use control points (CPs) for optimization, measured images are separated into corresponding time intervals for direct comparison with predictions. The accuracy of the calibration model was determined for a range of treatment conditions. Measured and predicted CP dose images were compared using a time dependent gamma evaluation using criteria (3%, 3 mm, 0.5 sec). Time dependent pre-treatment dose verification is possible without an additional measurement device or phantom, using the on-board EPID. Sufficient data is present in trajectory log files and EPID frame headers to reliably synchronize and resample portal images. For the VMAT plans tested, significantly more deviation is observed when analysed in a time dependent manner for FFF and non-FFF plans than when analysed using only the integrated field. We show EPID-based pre-treatment dose verification can be performed on a CP basis for VMAT plans. This model can measure pre-treatment doses for both flattened and unflattened beams in a time dependent manner which highlights deviations that are missed in integrated field verifications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saleh, Z; Tang, X; Song, Y

Purpose: To investigate the long term stability and viability of using EPID-based daily output QA via in-house and vendor driven protocol, to replace conventional QA tools and improve QA efficiency. Methods: Two Varian TrueBeam machines (TB1&TB2) equipped with electronic portal imaging devices (EPID) were employed in this study. Both machines were calibrated per TG-51 and used clinically since Oct 2014. Daily output measurement for 6/15 MV beams were obtained using SunNuclear DailyQA3 device as part of morning QA. In addition, in-house protocol was implemented for EPID output measurement (10×10 cm fields, 100 MU, 100cm SID, output defined over an ROImore » of 2×2 cm around central axis). Moreover, the Varian Machine Performance Check (MPC) was used on both machines to measure machine output. The EPID and DailyQA3 based measurements of the relative machine output were compared and cross-correlated with monthly machine output as measured by an A12 Exradin 0.65cc Ion Chamber (IC) serving as ground truth. The results were correlated using Pearson test. Results: The correlations among DailyQA3, in-house EPID and Varian MPC output measurements, with the IC for 6/15 MV were similar for TB1 (0.83–0.95) and TB2 (0.55–0.67). The machine output for the 6/15MV beams on both machines showed a similar trend, namely an increase over time as indicated by all measurements, requiring a machine recalibration after 6 months. This drift is due to a known issue with pressurized monitor chamber which tends to leak over time. MPC failed occasionally but passed when repeated. Conclusion: The results indicate that the use of EPID for daily output measurements has the potential to become a viable and efficient tool for daily routine LINAC QA, thus eliminating weather (T,P) and human setup variability and increasing efficiency of the QA process.« less

SU-E-T-781: Using An Electronic Portal Imaging Device (EPID) for Correlating Linac Photon Beam Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yaddanapudi, S; Cai, B; Sun, B

2015-06-15

Purpose: Electronic portal imaging devices (EPIDs) have proven to be useful for measuring several parameters of interest in linear accelerator (linac) quality assurance (QA). The purpose of this project was to evaluate the feasibility of using EPIDs for determining linac photon beam energies. Methods: Two non-clinical Varian TrueBeam linacs (Varian Medical Systems, Palo Alto, CA) with 6MV and 10MV photon beams were used to perform the measurements. The linacs were equipped with an amorphous silicon based EPIDs (aSi1000) that were used for the measurements. We compared the use of flatness versus percent depth dose (PDD) for predicting changes in linacmore » photon beam energy. PDD was measured in 1D water tank (Sun Nuclear Corporation, Melbourne FL) and the profiles were measured using 2D ion-chamber array (IC-Profiler, Sun Nuclear) and the EPID. Energy changes were accomplished by varying the bending magnet current (BMC). The evaluated energies conformed with the AAPM TG142 tolerance of ±1% change in PDD. Results: BMC changes correlating with a ±1% change in PDD corresponded with a change in flatness of ∼1% to 2% from baseline values on the EPID. IC Profiler flatness values had the same correlation. We observed a similar trend for the 10MV beam energy changes. Our measurements indicated a strong correlation between changes in linac photon beam energy and changes in flatness. For all machines and energies, beam energy changes produced change in the uniformity (AAPM TG-142), varying from ∼1% to 2.5%. Conclusions: EPID image analysis of beam profiles can be used to determine linac photon beam energy changes. Flatness-based metrics or uniformity as defined by AAPM TG-142 were found to be more sensitive to linac photon beam energy changes than PDD. Research funding provided by Varian Medical Systems. Dr. Sasa Mutic receives compensation for providing patient safety training services from Varian Medical Systems, the sponsor of this study.« less

SU-F-P-36: Automation of Linear Accelerator Star Shot Measurement with Advanced XML Scripting and Electronic Portal Imaging Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, N; Knutson, N; Schmidt, M

Purpose: To verify a method used to automatically acquire jaw, MLC, collimator and couch star shots for a Varian TrueBeam linear accelerator utilizing Developer Mode and an Electronic Portal Imaging Device (EPID). Methods: An XML script was written to automate motion of the jaws, MLC, collimator and couch in TrueBeam Developer Mode (TBDM) to acquire star shot measurements. The XML script also dictates MV imaging parameters to facilitate automatic acquisition and recording of integrated EPID images. Since couch star shot measurements cannot be acquired using a combination of EPID and jaw/MLC collimation alone due to a fixed imager geometry, amore » method utilizing a 5mm wide steel ruler placed on the table and centered within a 15×15cm2 open field to produce a surrogate of the narrow field aperture was investigated. Four individual star shot measurements (X jaw, Y jaw, MLC and couch) were obtained using our proposed as well as traditional film-based method. Integrated EPID images and scanned measurement films were analyzed and compared. Results: Star shot (X jaw, Y jaw, MLC and couch) measurements were obtained in a single 5 minute delivery using the TBDM XML script method compared to 60 minutes for equivalent traditional film measurements. Analysis of the images and films demonstrated comparable isocentricity results, agreeing within 0.3mm of each other. Conclusion: The presented automatic approach of acquiring star shot measurements using TBDM and EPID has proven to be more efficient than the traditional film approach with equivalent results.« less

Validation of a method for in vivo 3D dose reconstruction for IMRT and VMAT treatments using on-treatment EPID images and a model-based forward-calculation algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Uytven, Eric, E-mail: eric.vanuytven@cancercare.mb.ca; Van Beek, Timothy; McCowan, Peter M.

2015-12-15

Purpose: Radiation treatments are trending toward delivering higher doses per fraction under stereotactic radiosurgery and hypofractionated treatment regimens. There is a need for accurate 3D in vivo patient dose verification using electronic portal imaging device (EPID) measurements. This work presents a model-based technique to compute full three-dimensional patient dose reconstructed from on-treatment EPID portal images (i.e., transmission images). Methods: EPID dose is converted to incident fluence entering the patient using a series of steps which include converting measured EPID dose to fluence at the detector plane and then back-projecting the primary source component of the EPID fluence upstream of themore » patient. Incident fluence is then recombined with predicted extra-focal fluence and used to calculate 3D patient dose via a collapsed-cone convolution method. This method is implemented in an iterative manner, although in practice it provides accurate results in a single iteration. The robustness of the dose reconstruction technique is demonstrated with several simple slab phantom and nine anthropomorphic phantom cases. Prostate, head and neck, and lung treatments are all included as well as a range of delivery techniques including VMAT and dynamic intensity modulated radiation therapy (IMRT). Results: Results indicate that the patient dose reconstruction algorithm compares well with treatment planning system computed doses for controlled test situations. For simple phantom and square field tests, agreement was excellent with a 2%/2 mm 3D chi pass rate ≥98.9%. On anthropomorphic phantoms, the 2%/2 mm 3D chi pass rates ranged from 79.9% to 99.9% in the planning target volume (PTV) region and 96.5% to 100% in the low dose region (>20% of prescription, excluding PTV and skin build-up region). Conclusions: An algorithm to reconstruct delivered patient 3D doses from EPID exit dosimetry measurements was presented. The method was applied to phantom and patient data sets, as well as for dynamic IMRT and VMAT delivery techniques. Results indicate that the EPID dose reconstruction algorithm presented in this work is suitable for clinical implementation.« less

Development and implementation of EPID-based quality assurance tests for the small animal radiation research platform (SARRP).

PubMed

Anvari, Akbar; Poirier, Yannick; Sawant, Amit

2018-04-28

Although small animal image-guided radiotherapy (SA-IGRT) systems are used increasingly in preclinical research, tools for performing routine quality assurance (QA) have not been optimized and are not readily available. Robust, efficient, and reliable QA tools are needed to ensure the accuracy and reproducibility of SA-IGRT systems. Several investigators have reported custom-made phantoms and protocols for SA-IGRT systems QA. These are typically time and resource intensive and are therefore not well suited to the preclinical radiotherapy environment, in which physics support is limited and routine QA is performed by technical staff. We investigated the use of the inbuilt electronic portal imaging device (EPID) to develop and validate routine QA tests and procedures. In this work, we focus on the Xstrahl Small Animal Radiation Research Platform (SARRP) EPID. However, the methodology and tests developed here are applicable to any SA-IGRT system that incorporates an EPID. We performed a comprehensive characterization of the dosimetric properties of the camera-based EPID at kilovoltage energies over a 11-month period, including detector warm-up time, radiation dose history effect, stability and short- and long-term reproducibility, gantry angle dependency, output factor, and linearity of the EPID response. We developed a test to measure the constancy of beam quality in terms of half-value layer and tube peak potential using the EPID. We verified the SARRP daily output and beam profile constancy using the imager. We investigated the use of the imager to monitor beam-targeting accuracy at various gantry and couch angles. The EPID response was stable and reproducible, exhibiting maximum variations of ≤0.3% and ≤1.9% for short and long terms, respectively. The detector showed no dependence on response at different gantry angles, with a maximum variation ≤0.5%. We found close agreement in output factor measurement between the portal imager and reference dosimeters, with maximum differences ≤3% for ionization chamber and ≤1.7% for Gafchromic EBT3 dosimetry film, respectively. We have shown that the EPID response is linear with tube current (mA) for the entire range of tube kilovoltage peak. Notably, a close relationship was seen between the detector response vs mA slope, and the kilovoltage peak, allowing an independent verification of kilovoltage peak stability based solely on EPID response. In addition to dosimetry tests, according to the beam-targeting measurement using portal images, maximum displacement of the central axis of the x-ray beam (due to sag) was 0.76 ± 0.09 mm at gantry 135°/couch 0° and 0.89 ± 0.06 mm at gantry 0°/couch -135°. We performed the first comprehensive analysis on the dosimetric properties of an EPID operating at kilovoltage x-ray energies. We characterized the detector performance over a 11-month period. Our results indicate that the imager is a stable and convenient tool for SARRP routine QA tests. We then developed EPID-based tests to perform routine SA-IGRT systems QA tasks, such as verifying constancy of beam quality, energy, output, and profile measurements, relative output factors, and beam targeting. © 2018 American Association of Physicists in Medicine.

WE-G-213CD-03: A Dual Complementary Verification Method for Dynamic Tumor Tracking on Vero SBRT.

PubMed

Poels, K; Depuydt, T; Verellen, D; De Ridder, M

2012-06-01

to use complementary cine EPID and gimbals log file analysis for in-vivo tracking accuracy monitoring. A clinical prototype of dynamic tracking (DT) was installed on the Vero SBRT system. This prototype version allowed tumor tracking by gimballed linac rotations using an internal-external correspondence model. The DT prototype software allowed the detailed logging of all applied gimbals rotations during tracking. The integration of an EPID on the vero system allowed the acquisition of cine EPID images during DT. We quantified the tracking error on cine EPID (E-EPID) by subtracting the target center (fiducial marker detection) and the field centroid. Dynamic gimbals log file information was combined with orthogonal x-ray verification images to calculate the in-vivo tracking error (E-kVLog). The correlation between E-kVLog and E-EPID was calculated for validation of the gimbals log file. Further, we investigated the sensitivity of the log file tracking error by introducing predefined systematic tracking errors. As an application we calculate gimbals log file tracking error for dynamic hidden target tests to investigate gravity effects and decoupled gimbals rotation from gantry rotation. Finally, calculating complementary cine EPID and log file tracking errors evaluated the clinical accuracy of dynamic tracking. A strong correlation was found between log file and cine EPID tracking error distribution during concurrent measurements (R=0.98). We found sensitivity in the gimbals log files to detect a systematic tracking error up to 0.5 mm. Dynamic hidden target tests showed no gravity influence on tracking performance and high degree of decoupled gimbals and gantry rotation during dynamic arc dynamic tracking. A submillimetric agreement between clinical complementary tracking error measurements was found. Redundancy of the internal gimbals log file with x-ray verification images with complementary independent cine EPID images was implemented to monitor the accuracy of gimballed tumor tracking on Vero SBRT. Research was financially supported by the Flemish government (FWO), Hercules Foundation and BrainLAB AG. © 2012 American Association of Physicists in Medicine.

SU-E-T-171: Missing Dose in Integrated EPID Images.

PubMed

King, B; Seymour, E; Nitschke, K

2012-06-01

A dosimetric artifact has been observed with Varian EPIDs in the presence of beam interrupts. This work determines the root cause and significance of this artifact. Integrated mode EPID images were acquired both with and without a manual beam interrupt for rectangular, sliding gap IMRT fields. Simultaneously, the individual frames were captured on a separate computer using a frame-grabber system. Synchronization of the individual frames with the integrated images allowed the determination of precisely how the EPID behaved during regular operation as well as when a beam interrupt was triggered. The ability of the EPID to reliably monitor a treatment in the presence of beam interrupts was tested by comparing the difference between the interrupt and non-interrupt images. The interrupted images acquired in integrated acquisition mode displayed unanticipated behaviour in the region of the image where the leaves were located when the beam interrupt was triggered. Differences greater than 5% were observed as a result of the interrupt in some cases, with the discrepancies occurring in a non-uniform manner across the imager. The differences measured were not repeatable from one measurement to another. Examination of the individual frames showed that the EPID was consistently losing a small amount of dose at the termination of every exposure. Inclusion of one additional frame in every image rectified the unexpected behaviour, reducing the differences to 1% or less. Although integrated EPID images nominally capture the entire dose delivered during an exposure, a small amount of dose is consistently being lost at the end of every exposure. The amount of missing dose is random, depending on the exact beam termination time within a frame. Inclusion of an extra frame at the end of each exposure effectively rectifies the problem, making the EPID more suitable for clinical dosimetry applications. The authors received support from Varian Medical Systems in the form of software and equipment loans as well as technical support. © 2012 American Association of Physicists in Medicine.

MO-AB-BRA-03: Development of Novel Real Time in Vivo EPID Treatment Verification for Brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fonseca, G; Podesta, M; Reniers, B

2016-06-15

Purpose: High Dose Rate (HDR) brachytherapy treatments are employed worldwide to treat a wide variety of cancers. However, in vivo dose verification remains a challenge with no commercial dosimetry system available to verify the treatment dose delivered to the patient. We propose a novel dosimetry system that couples an independent Monte Carlo (MC) simulation platform and an amorphous silicon Electronic Portal Imaging Device (EPID) to provide real time treatment verification. Methods: MC calculations predict the EPID response to the photon fluence emitted by the HDR source by simulating the patient, the source dwell positions and times, and treatment complexities suchmore » as tissue compositions/densities and different applicators. Simulated results are then compared against EPID measurements acquired with ∼0.14s time resolution which allows dose measurements for each dwell position. The EPID has been calibrated using an Ir-192 HDR source and experiments were performed using different phantoms, including tissue equivalent materials (PMMA, lung and bone). A source positioning accuracy of 0.2 mm, without including the afterloader uncertainty, was ensured using a robotic arm moving the source. Results: An EPID can acquire 3D Cartesian source positions and its response varies significantly due to differences in the material composition/density of the irradiated object, allowing detection of changes in patient geometry. The panel time resolution allows dose rate and dwell time measurements. Moreover, predicted EPID images obtained from clinical treatment plans provide anatomical information that can be related to the patient anatomy, mostly bone and air cavities, localizing the source inside of the patient using its anatomy as reference. Conclusion: Results obtained show the feasibility of the proposed dose verification system that is capable to verify all the brachytherapy treatment steps in real time providing data about treatment delivery quality and also applicator/structure motion during or between treatments.« less

NOTE: A method for controlling image acquisition in electronic portal imaging devices

NASA Astrophysics Data System (ADS)

Glendinning, A. G.; Hunt, S. G.; Bonnett, D. E.

2001-02-01

Certain types of camera-based electronic portal imaging devices (EPIDs) which initiate image acquisition based on sensing a change in video level have been observed to trigger unreliably at the beginning of dynamic multileaf collimation sequences. A simple, novel means of controlling image acquisition with an Elekta linear accelerator (Elekta Oncology Systems, Crawley, UK) is proposed which is based on illumination of a photodetector (ORP-12, Silonex Inc., Plattsburgh, NY, USA) by the electron gun of the accelerator. By incorporating a simple trigger circuit it is possible to derive a beam on/off status signal which changes at least 100 ms before any dose is measured by the accelerator. The status signal does not return to the beam-off state until all dose has been delivered and is suitable for accelerator pulse repetition frequencies of 50-400 Hz. The status signal is thus a reliable means of indicating the initiation and termination of radiation exposure, and thus controlling image acquisition of such EPIDs for this application.

SU-F-T-562: Validation of EPID-Based Dosimetry for FSRS Commissioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Y; Saleh, Z; Obcemea, C

Purpose: The prevailing approach to frameless SRS (fSRS) small field dosimetry is Gafchromic film. Though providing continuous information, its intrinsic uncertainties in fabrication, response, scan, and calibration often make film dosimetry subject to different interpretations. In this study, we explored the feasibility of using EPID portal dosimetry as a viable alternative to film for small field dosimetry. Methods: Plans prescribed a dose of 21 Gy were created on a flat solid water phantom with Eclipse V11 and iPlan for small static square fields (1.0 to 3.0 cm). In addition, two clinical test plans were computed by employing iPlan on amore » CIRS Kesler head phantom for target dimensions of 1.2cm and 2.0cm. Corresponding portal dosimetry plans were computed using the Eclipse TPS and delivered on a Varian TrueBeam machine. EBT-XD film dosimetry was performed as a reference. The isocenter doses were measured using EPID, OSLD, stereotactic diode, and CC01 ion chamber. Results: EPID doses at the center of the square field were higher than Eclipse TPS predicted portal doses, with the mean difference being 2.42±0.65%. Doses measured by EBT-XD film, OSLD, stereotactic diode, and CC01 ion chamber revealed smaller differences (except OSLDs), with mean differences being 0.36±3.11%, 4.12±4.13%, 1.7±2.76%, 1.45±2.37% for Eclipse and −1.36±0.85%, 2.38±4.2%, −0.03±0.50%, −0.27±0.78% for iPlan. The profiles measured by EPID and EBT-XD film resembled TPS (Eclipse and iPlan) predicted ones within 3.0%. For the two clinical test plans, the EPID mean doses at the center of field were 2.66±0.68% and 2.33±0.32% higher than TPS predicted doses. Conclusion: We found that results obtained with EPID portal dosimetry were slightly higher (∼2%) than those obtained with EBT-XD film, diode, and CC01 ion chamber with the exception of OSLDs, but well within IROC tolerance (5.0%). Therefore, EPID has the potential to become a viable real-time alternative method to film dosimetry.« less

TH-E-BRE-05: Analysis of Dosimetric Characteristics in Two Leaf Motion Calculator Algorithms for Sliding Window IMRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, L; Huang, B; Rowedder, B

Purpose: The Smart leaf motion calculator (SLMC) in Eclipse treatment planning system is an advanced fluence delivery modeling algorithm as it takes into account fine MLC features including inter-leaf leakage, rounded leaf tips, non-uniform leaf thickness, and the spindle cavity etc. In this study, SLMC and traditional Varian LMC (VLMC) algorithms were investigated, for the first time, in dosimetric characteristics and delivery accuracy of sliding window (SW) IMRT. Methods: The SW IMRT plans of 51 cancer cases were included to evaluate dosimetric characteristics and dose delivery accuracy from leaf motion calculated by SLMC and VLMC, respectively. All plans were deliveredmore » using a Varian TrueBeam Linac. The DVH and MUs of the plans were analyzed. Three patient specific QA tools - independent dose calculation software IMSure, Delta4 phantom, and EPID portal dosimetry were also used to measure the delivered dose distribution. Results: Significant differences in the MUs were observed between the two LMCs (p≤0.001).Gamma analysis shows an excellent agreement between the planned dose distribution calculated by both LMC algorithms and delivered dose distribution measured by three QA tools in all plans at 3%/3 mm, leading to a mean pass rate exceeding 97%. The mean fraction of pixels with gamma < 1 of SLMC is slightly lower than that of VLMC in the IMSure and Delta4 results, but higher in portal dosimetry (the highest spatial resolution), especially in complex cases such as nasopharynx. Conclusion: The study suggests that the two LMCs generates the similar target coverage and sparing patterns of critical structures. However, SLMC is modestly more accurate than VLMC in modeling advanced MLC features, which may lead to a more accurate dose delivery in SW IMRT. Current clinical QA tools might not be specific enough to differentiate the dosimetric discrepancies at the millimeter level calculated by these two LMC algorithms. NIH/NIGMS grant U54 GM104944, Lincy Endowed Assistant Professorship.« less

SU-F-T-486: A Simple Approach to Performing Light Versus Radiation Field Coincidence Quality Assurance Using An Electronic Portal Imaging Device (EPID)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herchko, S; Ding, G

2016-06-15

Purpose: To develop an accurate, straightforward, and user-independent method for performing light versus radiation field coincidence quality assurance utilizing EPID images, a simple phantom made of readily-accessible materials, and a free software program. Methods: A simple phantom consisting of a blocking tray, graph paper, and high-density wire was constructed. The phantom was used to accurately set the size of a desired light field and imaged on the electronic portal imaging device (EPID). A macro written for use in ImageJ, a free image processing software, was then use to determine the radiation field size utilizing the high density wires on themore » phantom for a pixel to distance calibration. The macro also performs an analysis on the measured radiation field utilizing the tolerances recommended in the AAPM Task Group #142. To verify the accuracy of this method, radiochromic film was used to qualitatively demonstrate agreement between the film and EPID results, and an additional ImageJ macro was used to quantitatively compare the radiation field sizes measured both with the EPID and film images. Results: The results of this technique were benchmarked against film measurements, which have been the gold standard for testing light versus radiation field coincidence. The agreement between this method and film measurements were within 0.5 mm. Conclusion: Due to the operator dependency associated with tracing light fields and measuring radiation fields by hand when using film, this method allows for a more accurate comparison between the light and radiation fields with minimal operator dependency. Removing the need for radiographic or radiochromic film also eliminates a reoccurring cost and increases procedural efficiency.« less

Comparative performance evaluation of a new a-Si EPID that exceeds quad high-definition resolution.

PubMed

McConnell, Kristen A; Alexandrian, Ara; Papanikolaou, Niko; Stathakis, Sotiri

2018-01-01

Electronic portal imaging devices (EPIDs) are an integral part of the radiation oncology workflow for treatment setup verification. Several commercial EPID implementations are currently available, each with varying capabilities. To standardize performance evaluation, Task Group Report 58 (TG-58) and TG-142 outline specific image quality metrics to be measured. A LinaTech Image Viewing System (IVS), with the highest commercially available pixel matrix (2688x2688 pixels), was independently evaluated and compared to an Elekta iViewGT (1024x1024 pixels) and a Varian aSi-1000 (1024x768 pixels) using a PTW EPID QC Phantom. The IVS, iViewGT, and aSi-1000 were each used to acquire 20 images of the PTW QC Phantom. The QC phantom was placed on the couch and aligned at isocenter. The images were exported and analyzed using the epidSoft image quality assurance (QA) software. The reported metrics were signal linearity, isotropy of signal linearity, signal-tonoise ratio (SNR), low contrast resolution, and high-contrast resolution. These values were compared between the three EPID solutions. Computed metrics demonstrated comparable results between the EPID solutions with the IVS outperforming the aSi-1000 and iViewGT in the low and high-contrast resolution analysis. The performance of three commercial EPID solutions have been quantified, evaluated, and compared using results from the PTW QC Phantom. The IVS outperformed the other panels in low and high-contrast resolution, but to fully realize the benefits of the IVS, the selection of the monitor on which to view the high-resolution images is important to prevent down sampling and visual of resolution.

A new approach for the pixel map sensitivity (PMS) evaluation of an electronic portal imaging device (EPID)

PubMed Central

Lucio, Francesco; Calamia, Elisa; Russi, Elvio; Marchetto, Flavio

2013-01-01

When using an electronic portal imaging device (EPID) for dosimetric verifications, the calibration of the sensitive area is of paramount importance. Two calibration methods are generally adopted: one, empirical, based on an external reference dosimeter or on multiple narrow beam irradiations, and one based on the EPID response simulation. In this paper we present an alternative approach based on an intercalibration procedure, independent from external dosimeters and from simulations, and is quick and easy to perform. Each element of a detector matrix is characterized by a different gain; the aim of the calibration procedure is to relate the gain of each element to a reference one. The method that we used to compute the relative gains is based on recursive acquisitions with the EPID placed in different positions, assuming a constant fluence of the beam for subsequent deliveries. By applying an established procedure and analysis algorithm, the EPID calibration was repeated in several working conditions. Data show that both the photons energy and the presence of a medium between the source and the detector affect the calibration coefficients less than 1%. The calibration coefficients were then applied to the acquired images, comparing the EPID dose images with films. Measurements were performed with open field, placing the film at the level of the EPID. The standard deviation of the distribution of the point‐to‐point difference is 0.6%. An approach of this type for the EPID calibration has many advantages with respect to the standard methods — it does not need an external dosimeter, it is not related to the irradiation techniques, and it is easy to implement in the clinical practice. Moreover, it can be applied in case of transit or nontransit dosimetry, solving the problem of the EPID calibration independently from the dose reconstruction method. PACS number: 87.56.‐v PMID:24257285

MO-FG-CAMPUS-TeP1-05: Rapid and Efficient 3D Dosimetry for End-To-End Patient-Specific QA of Rotational SBRT Deliveries Using a High-Resolution EPID

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Y M; Han, B; Xing, L

2016-06-15

Purpose: EPID-based patient-specific quality assurance provides verification of the planning setup and delivery process that phantomless QA and log-file based virtual dosimetry methods cannot achieve. We present a method for EPID-based QA utilizing spatially-variant EPID response kernels that allows for direct calculation of the entrance fluence and 3D phantom dose. Methods: An EPID dosimetry system was utilized for 3D dose reconstruction in a cylindrical phantom for the purposes of end-to-end QA. Monte Carlo (MC) methods were used to generate pixel-specific point-spread functions (PSFs) characterizing the spatially non-uniform EPID portal response in the presence of phantom scatter. The spatially-variant PSFs weremore » decomposed into spatially-invariant basis PSFs with the symmetric central-axis kernel as the primary basis kernel and off-axis representing orthogonal perturbations in pixel-space. This compact and accurate characterization enables the use of a modified Richardson-Lucy deconvolution algorithm to directly reconstruct entrance fluence from EPID images without iterative scatter subtraction. High-resolution phantom dose kernels were cogenerated in MC with the PSFs enabling direct recalculation of the resulting phantom dose by rapid forward convolution once the entrance fluence was calculated. A Delta4 QA phantom was used to validate the dose reconstructed in this approach. Results: The spatially-invariant representation of the EPID response accurately reproduced the entrance fluence with >99.5% fidelity with a simultaneous reduction of >60% in computational overhead. 3D dose for 10{sub 6} voxels was reconstructed for the entire phantom geometry. A 3D global gamma analysis demonstrated a >95% pass rate at 3%/3mm. Conclusion: Our approach demonstrates the capabilities of an EPID-based end-to-end QA methodology that is more efficient than traditional EPID dosimetry methods. Displacing the point of measurement external to the QA phantom reduces the necessary complexity of the phantom itself while offering a method that is highly scalable and inherently generalizable to rotational and trajectory based deliveries. This research was partially supported by Varian.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rottmann, J; Berbeco, R; Keall, P

Purpose: To maximize normal tissue sparing for treatments requiring motion encompassing margins. Motion mitigation techniques including DMLC or couch tracking can freeze tumor motion within the treatment aperture potentially allowing for smaller treatment margins and thus better sparing of normal tissue. To enable for a safe application of this concept in the clinic we propose adapting margins dynamically in real-time during radiotherapy delivery based on personalized tumor localization confidence. To demonstrate technical feasibility we present a phantom study. Methods: We utilize a realistic anthropomorphic dynamic thorax phantom with a lung tumor model embedded close to the spine. The tumor, amore » 3D-printout of a patient's GTV, is moved 15mm peak-to-peak by diaphragm compression and monitored by continuous EPID imaging in real-time. Two treatment apertures are created for each beam, one representing ITV -based and the other GTV-based margin expansion. A soft tissue localization (STiL) algorithm utilizing the continuous EPID images is employed to freeze tumor motion within the treatment aperture by means of DMLC tracking. Depending on a tracking confidence measure (TCM), the treatment aperture is adjusted between the ITV and the GTV leaf. Results: We successfully demonstrate real-time personalized margin adjustment in a phantom study. We measured a system latency of about 250 ms which we compensated by utilizing a respiratory motion prediction algorithm (ridge regression). With prediction in place we observe tracking accuracies better than 1mm. For TCM=0 (as during startup) an ITV-based treatment aperture is chosen, for TCM=1 a GTV-based aperture and for 0« less

Dosimetric verification of radiation therapy including intensity modulated treatments, using an amorphous-silicon electronic portal imaging device

NASA Astrophysics Data System (ADS)

Chytyk-Praznik, Krista Joy

Radiation therapy is continuously increasing in complexity due to technological innovation in delivery techniques, necessitating thorough dosimetric verification. Comparing accurately predicted portal dose images to measured images obtained during patient treatment can determine if a particular treatment was delivered correctly. The goal of this thesis was to create a method to predict portal dose images that was versatile and accurate enough to use in a clinical setting. All measured images in this work were obtained with an amorphous silicon electronic portal imaging device (a-Si EPID), but the technique is applicable to any planar imager. A detailed, physics-motivated fluence model was developed to characterize fluence exiting the linear accelerator head. The model was further refined using results from Monte Carlo simulations and schematics of the linear accelerator. The fluence incident on the EPID was converted to a portal dose image through a superposition of Monte Carlo-generated, monoenergetic dose kernels specific to the a-Si EPID. Predictions of clinical IMRT fields with no patient present agreed with measured portal dose images within 3% and 3 mm. The dose kernels were applied ignoring the geometrically divergent nature of incident fluence on the EPID. A computational investigation into this parallel dose kernel assumption determined its validity under clinically relevant situations. Introducing a patient or phantom into the beam required the portal image prediction algorithm to account for patient scatter and attenuation. Primary fluence was calculated by attenuating raylines cast through the patient CT dataset, while scatter fluence was determined through the superposition of pre-calculated scatter fluence kernels. Total dose in the EPID was calculated by convolving the total predicted incident fluence with the EPID-specific dose kernels. The algorithm was tested on water slabs with square fields, agreeing with measurement within 3% and 3 mm. The method was then applied to five prostate and six head-and-neck IMRT treatment courses (˜1900 clinical images). Deviations between the predicted and measured images were quantified. The portal dose image prediction model developed in this thesis work has been shown to be accurate, and it was demonstrated to be able to verify patients' delivered radiation treatments.

SU-E-T-646: Quality Assurance of Truebeam Multi-Leaf Collimator Using a MLC QA Phantom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, J; Lu, J; Hong, D

2015-06-15

Purpose: To perform a routine quality assurance procedure for Truebeam multi-leaf collimator (MLC) using MLC QA phantom, verify the stability and reliability of MLC during the treatment. Methods: MLC QA phantom is a specialized phantom for MLC quality assurance (QA), and contains five radio-opaque spheres that are embedded in an “L” shape. The phantom was placed isocentrically on the Truebeam treatment couch for the tests. A quality assurance plan was setted up in the Eclipse v10.0, the fields that need to be delivered in order to acquire the necessary images, the MLC shapes can then be obtained by the images.more » The images acquired by the electronic portal imaging device (EPID), and imported into the PIPSpro software for the analysis. The tests were delivered twelve weeks (once a week) to verify consistency of the delivery, and the images are acquired in the same manner each time. Results: For the Leaf position test, the average position error was 0.23mm±0.02mm (range: 0.18mm∼0.25mm). The Leaf width was measured at the isocenter, the average error was 0.06mm±0.02mm (range: 0.02mm∼0.08mm) for the Leaf width test. Multi-Port test showed the dynamic leaf shift error, the average error was 0.28mm±0.03mm (range: 0.2mm∼0.35mm). For the leaf transmission test, the average inter-leaf leakage value was 1.0%±0.17% (range: 0.8%∼1.3%) and the average inter-bank leakage value was 32.6%±2.1% (range: 30.2%∼36.1%). Conclusion: By the test of 12 weeks, the MLC system of the Truebeam is running in a good condition and the MLC system can be steadily and reliably carried out during the treatment. The MLC QA phantom is a useful test tool for the MLC QA.« less

Cine EPID evaluation of two non-commercial techniques for DIBH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jensen, Christopher; Urribarri, Jaime; Cail, Daniel

2014-02-15

Purpose: To evaluate the efficacy of two noncommercial techniques for deep inspiration breathhold (DIBH) treatment of left-sided breast cancer (LSBC) usingcine electronic portal imaging device (EPID) images. Methods: 23 875 EPID images of 65 patients treated for LSBC at two different cancer treatment centers were retrieved. At the Milford Regional Cancer Center, DIBH stability was maintained by visual alignment of inroom lasers and patient skin tattoos (TAT). At the South Shore Hospital, a distance-measuring laser device (RTSSD) was implemented. For both centers,cine EPID images were acquired at least once per week during beam-on. Chest wall position relative to image boundary wasmore » measured and tracked over the course of treatment for every patient and treatment fraction for which data were acquired. Results: Median intrabeam chest motion was 0.31 mm for the TAT method and 0.37 mm for the RTSSD method. The maximum excursions exceeded our treatment protocol threshold of 3 mm in 0.3% of cases (TAT) and 1.2% of cases (RTSSD). The authors did not observe a clinically significant difference between the two datasets. Conclusions: Both noncommercial techniques for monitoring the DIBH location provided DIBH stability within the predetermined treatment protocol parameters (<3 mm). The intreatment imaging offered by the EPID operating incine mode facilitates retrospective analysis and validation of both techniques.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fuangrod, T; Simpson, J; Greer, P

Purpose: A real-time patient treatment delivery verification system using EPID (Watchdog) has been developed as an advanced patient safety tool. In a pilot study data was acquired for 119 prostate and head and neck (HN) IMRT patient deliveries to generate body-site specific action limits using statistical process control. The purpose of this study is to determine the sensitivity of Watchdog to detect clinically significant errors during treatment delivery. Methods: Watchdog utilizes a physics-based model to generate a series of predicted transit cine EPID images as a reference data set, and compares these in real-time to measured transit cine-EPID images acquiredmore » during treatment using chi comparison (4%, 4mm criteria) after the initial 2s of treatment to allow for dose ramp-up. Four study cases were used; dosimetric (monitor unit) errors in prostate (7 fields) and HN (9 fields) IMRT treatments of (5%, 7%, 10%) and positioning (systematic displacement) errors in the same treatments of (5mm, 7mm, 10mm). These errors were introduced by modifying the patient CT scan and re-calculating the predicted EPID data set. The error embedded predicted EPID data sets were compared to the measured EPID data acquired during patient treatment. The treatment delivery percentage (measured from 2s) where Watchdog detected the error was determined. Results: Watchdog detected all simulated errors for all fields during delivery. The dosimetric errors were detected at average treatment delivery percentage of (4%, 0%, 0%) and (7%, 0%, 0%) for prostate and HN respectively. For patient positional errors, the average treatment delivery percentage was (52%, 43%, 25%) and (39%, 16%, 6%). Conclusion: These results suggest that Watchdog can detect significant dosimetric and positioning errors in prostate and HN IMRT treatments in real-time allowing for treatment interruption. Displacements of the patient require longer to detect however incorrect body site or very large geographic misses will be detected rapidly.« less

Verification of quality parameters for portal images in radiotherapy.

PubMed

Pesznyák, Csilla; Polgár, István; Weisz, Csaba; Király, Réka; Zaránd, Pál

2011-03-01

The purpose of the study was to verify different values of quality parameters of portal images in radiotherapy. We investigated image qualities of different field verification systems. Four EPIDs (Siemens OptiVue500aSi(®), Siemens BeamView Plus(®), Elekta iView(®) and Varian PortalVision™) were investigated with the PTW EPID QC PHANTOM(®) and compared with two portal film systems (Kodak X-OMAT(®) cassette with Kodak X-OMAT V(®) film and Kodak EC-L Lightweight(®) cassette with Kodak Portal Localisation ReadyPack(®) film). A comparison of the f50 and f25 values of the modulation transfer functions (MTFs) belonging to each of the systems revealed that the amorphous silicon EPIDs provided a slightly better high contrast resolution than the Kodak Portal Localisation ReadyPack(®) film with the EC-L Lightweight(®) cassette. The Kodak X-OMAT V(®) film gave a poor low contrast resolution: from the existing 27 holes only 9 were detectable. On the base of physical characteristics, measured in this work, the authors suggest the use of amorphous-silicon EPIDs producing the best image quality. Parameters of the EPIDs with scanning liquid ionisation chamber (SLIC) were very stable. The disadvantage of older versions of EPIDs like SLIC and VEPID is a poor DICOM implementation, and the modulation transfer function (MTF) values (f50 and f25) are less than that of aSi detectors.

An assessment of a 3D EPID-based dosimetry system using conventional two- and three-dimensional detectors for VMAT.

PubMed

Stevens, S; Dvorak, P; Spevacek, V; Pilarova, K; Bray-Parry, M; Gesner, J; Richmond, A

2018-01-01

To provide a 3D dosimetric evaluation of a commercial portal dosimetry system using 2D/3D detectors under ideal conditions using VMAT. A 2D ion chamber array, radiochromic film and gel dosimeter were utilised to provide a dosimetric evaluation of transit phantom and pre-treatment 'fluence' EPID back-projected dose distributions for a standard VMAT plan. In-house 2D and 3D gamma methods compared pass statistics relative to each dosimeter and TPS dose distributions. Fluence mode and transit EPID dose distributions back-projected onto phantom geometry produced 2D gamma pass rates in excess of 97% relative to other tested detectors and exported TPS dose planes when a 3%, 3 mm global gamma criterion was applied. Use of a gel dosimeter within a glass vial allowed comparison of measured 3D dose distributions versus EPID 3D dose and TPS calculated distributions. 3D gamma comparisons between modalities at 3%, 3 mm gave pass rates in excess of 92%. Use of fluence mode was indicative of transit results under ideal conditions with slightly reduced dose definition. 3D EPID back projected dose distributions were validated against detectors in both 2D and 3D. Cross validation of transit dose delivered to a patient is limited due to reasons of practicality and the tests presented are recommended as a guideline for 3D EPID dosimetry commissioning; allowing direct comparison between detector, TPS, fluence and transit modes. The results indicate achievable gamma scores for a complex VMAT plan in a homogenous phantom geometry and contributes to growing experience of 3D EPID dosimetry. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Characterization of a commercial multileaf collimator used for intensity modulated radiation therapy.

PubMed

Low, D A; Sohn, J W; Klein, E E; Markman, J; Mutic, S; Dempsey, J F

2001-05-01

The characteristics of a commercial multileaf collimator (MLC) to deliver static and dynamic multileaf collimation (SMLC and DMLC, respectively) were investigated to determine their influence on intensity modulated radiation therapy (IMRT) treatment planning and quality assurance. The influence of MLC leaf positioning accuracy on sequentially abutted SMLC fields was measured by creating abutting fields with selected gaps and overlaps. These data were also used to measure static leaf positioning precision. The characteristics of high leaf-velocity DMLC delivery were measured with constant velocity leaf sequences starting with an open field and closing a single leaf bank. A range of 1-72 monitor units (MU) was used providing a range of leaf velocities. The field abutment measurements yielded dose errors (as a percentage of the open field max dose) of 16.7+/-0.7% mm(-1) and 12.8+/-0.7% mm(-1) for 6 MV and 18 MV photon beams, respectively. The MLC leaf positioning precision was 0.080+/-0.018 mm (single standard deviation) highlighting the excellent delivery hardware tolerances for the tested beam delivery geometry. The high leaf-velocity DMLC measurements showed delivery artifacts when the leaf sequence and selected monitor units caused the linear accelerator to move the leaves at their maximum velocity while modulating the accelerator dose rate to deliver the desired leaf and MU sequence (termed leaf-velocity limited delivery). According to the vendor, a unique feature to their linear accelerator and MLC is that the dose rate is reduced to provide the correct cm MU(-1) leaf velocity when the delivery is leaf-velocity limited. However, it was found that the system delivered roughly 1 MU per pulse when the delivery was leaf-velocity limited causing dose profiles to exhibit discrete steps rather than a smooth dose gradient. The root mean square difference between the steps and desired linear gradient was less than 3% when more than 4 MU were used. The average dose per MU was greater and less than desired for closing and opening leaf patterns, respectively, when the delivery was leaf-velocity limited. The results indicated that the dose delivery artifacts should be minor for most clinical cases, but limit the assumption of dose linearity when significantly reducing the delivered dose for dosimeter characterization studies or QA measurements.

Suitability of markerless EPID tracking for tumor position verification in gated radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serpa, Marco; University Clinic for Radiotherapy and Radio-Oncology, Landeskrankenhaus Salzburg, Paracelsus Medical University Clinics, 5020 Salzburg; Department of Physics and Astronomy, University of Canterbury, Christchurch 8140

2014-03-15

Purpose: To maximize the benefits of respiratory gated radiotherapy (RGRT) of lung tumors real-time verification of the tumor position is required. This work investigates the feasibility of markerless tracking of lung tumors during beam-on time in electronic portal imaging device (EPID) images of the MV therapeutic beam. Methods: EPID movies were acquired at ∼2 fps for seven lung cancer patients with tumor peak-to-peak motion ranges between 7.8 and 17.9 mm (mean: 13.7 mm) undergoing stereotactic body radiotherapy. The external breathing motion of the abdomen was synchronously measured. Both datasets were retrospectively analyzed inPortalTrack, an in-house developed tracking software. The authorsmore » define a three-step procedure to run the simulations: (1) gating window definition, (2) gated-beam delivery simulation, and (3) tumor tracking. First, an amplitude threshold level was set on the external signal, defining the onset of beam-on/-off signals. This information was then mapped onto a sequence of EPID images to generate stamps of beam-on/-hold periods throughout the EPID movies in PortalTrack, by obscuring the frames corresponding to beam-off times. Last, tumor motion in the superior-inferior direction was determined on portal images by the tracking algorithm during beam-on time. The residual motion inside the gating window as well as target coverage (TC) and the marginal target displacement (MTD) were used as measures to quantify tumor position variability. Results: Tumor position monitoring and estimation from beam's-eye-view images during RGRT was possible in 67% of the analyzed beams. For a reference gating window of 5 mm, deviations ranging from 2% to 86% (35% on average) were recorded between the reference and measured residual motion. TC (range: 62%–93%; mean: 77%) losses were correlated with false positives incidence rates resulting mostly from intra-/inter-beam baseline drifts, as well as sudden cycle-to-cycle fluctuations in exhale positions. Both phenomena can lead to considerable deviations (with MTD values up to a maximum of 7.8 mm) from the intended tumor position, and in turn may result in a marginal miss. The difference between tumor traces determined within the gating window against ground truth trajectory maps was 1.1 ± 0.7 mm on average (range: 0.4–2.3 mm). Conclusions: In this retrospective analysis of motion data, it is demonstrated that the system is capable of determining tumor positions in the plane perpendicular to the beam direction without the aid of fiducial markers, and may hence be suitable as an online verification tool in RGRT. It may be possible to use the tracking information to enable on-the-fly corrections to intra-/inter-beam variations by adapting the gating window by means of a robotic couch.« less

Epid cine acquisition mode for in vivo dosimetry in dynamic arc radiation therapy

NASA Astrophysics Data System (ADS)

Fidanzio, Andrea; Mameli, Alessandra; Placidi, Elisa; Greco, Francesca; Stimato, Gerardina; Gaudino, Diego; Ramella, Sara; D'Angelillo, Rolando; Cellini, Francesco; Trodella, Lucio; Cilla, Savino; Grimaldi, Luca; D'Onofrio, Guido; Azario, Luigi; Piermattei, Angelo

2008-02-01

In this paper the cine acquisition mode of an electronic portal imaging device (EPID) has been calibrated and tested to determine the in vivo dose for dynamic conformal arc radiation therapy (DCAT). The EPID cine acquisition mode, that allows a frame acquisition rate of one image every 1.66 s, was studied with a monitor unit rate equal to 100 UM/min. In these conditions good signal stability, ±1% (2SD) evaluated during three months, signal reproducibility within ±0.8% (2SD) and linearity with dose and dose rate within ±1% (2SD) were obtained. The transit signal, St, (due to the transmitted beam below the phantom) measured by the EPID cine acquisition mode was used to determine, (i) a set of correlation functions, F(w,L), defined as the ratio between St and the dose at half thickness, Dm, measured in solid water phantoms of different thicknesses, w and with square fields of side L, (ii) a set of factors, f(d,L), that take into account the different X-ray scatter contribution from the phantom to the St signal as a function of the variation, d, of the air gap between the phantom and the EPID. The reconstruction of the isocenter dose, Diso, for DCAT was obtained convolving the transit signal values, obtained at different gantry angles, with the respective reconstruction factors determined by a house-made software. The method was tested with cylindrical and anthropomorphic phantoms and the results show that the reconstructed Diso values can be obtained with an accuracy within ±2.5% in cylindrical phantom and within ±3.4% for anthropomorphic phantom. In conclusion, the transit dosimetry by EPID was assessed to be adequate to perform DCAT in vivo dosimetry, that is not realizable with the other traditional techniques. Moreover, the method proposed here could be implemented to supply in vivo dose values in real time.

Current status of 3D EPID-based in vivo dosimetry in The Netherlands Cancer Institute

NASA Astrophysics Data System (ADS)

Mijnheer, B.; Olaciregui-Ruiz, I.; Rozendaal, R.; Spreeuw, H.; van Herk, M.; Mans, A.

2015-01-01

3D in vivo dose verification using a-Si EPIDs is performed routinely in our institution for almost all RT treatments. The EPID-based 3D dose distribution is reconstructed using a back-projection algorithm and compared with the planned dose distribution using 3D gamma evaluation. Dose-reconstruction and gamma-evaluation software runs automatically, and deviations outside the alert criteria are immediately available and investigated, in combination with inspection of cone-beam CT scans. The implementation of our 3D EPID- based in vivo dosimetry approach was able to replace pre-treatment verification for more than 90% of the patient treatments. Clinically relevant deviations could be detected for approximately 1 out of 300 patient treatments (IMRT and VMAT). Most of these errors were patient related anatomical changes or deviations from the routine clinical procedure, and would not have been detected by pre-treatment verification. Moreover, 3D EPID-based in vivo dose verification is a fast and accurate tool to assure the safe delivery of RT treatments. It provides clinically more useful information and is less time consuming than pre-treatment verification measurements. Automated 3D in vivo dosimetry is therefore a prerequisite for large-scale implementation of patient-specific quality assurance of RT treatments.

Automated Leaf Tracking using Multi-view Image Sequences of Maize Plants for Leaf-growth Monitoring

NASA Astrophysics Data System (ADS)

Das Choudhury, S.; Awada, T.; Samal, A.; Stoerger, V.; Bashyam, S.

2017-12-01

Extraction of phenotypes with botanical importance by analyzing plant image sequences has the desirable advantages of non-destructive temporal phenotypic measurements of a large number of plants with little or no manual intervention in a relatively short period of time. The health of a plant is best interpreted by the emergence timing and temporal growth of individual leaves. For automated leaf growth monitoring, it is essential to track each leaf throughout the life cycle of the plant. Plants are constantly changing organisms with increasing complexity in architecture due to variations in self-occlusions and phyllotaxy, i.e., arrangements of leaves around the stem. The leaf cross-overs pose challenges to accurately track each leaf using single view image sequence. Thus, we introduce a novel automated leaf tracking algorithm using a graph theoretic approach by multi-view image sequence analysis based on the determination of leaf-tips and leaf-junctions in the 3D space. The basis of the leaf tracking algorithm is: the leaves emerge using bottom-up approach in the case of a maize plant, and the direction of leaf emergence strictly alternates in terms of direction. The algorithm involves labeling of the individual parts of a plant, i.e., leaves and stem, following graphical representation of the plant skeleton, i.e., one-pixel wide connected line obtained from the binary image. The length of the leaf is measured by the number of pixels in the leaf skeleton. To evaluate the performance of the algorithm, a benchmark dataset is indispensable. Thus, we publicly release University of Nebraska-Lincoln Component Plant Phenotyping dataset-2 (UNL-CPPD-2) consisting of images of the 20 maize plants captured by visible light camera of the Lemnatec Scanalyzer 3D high throughout plant phenotyping facility once daily for 60 days from 10 different views. The dataset is aimed to facilitate the development and evaluation of leaf tracking algorithms and their uniform comparisons.

SU-C-201-05: Silicon Array Dosimeter in Situ with Electronic Portal Image Device for Simultaneous Transit Dose and Image Verification in Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshpande, S; Alhujaili, S; Vial, P

Purpose: To investigate an Electronic Portal Imaging Device (EPID) coupled to a 2D array dosimeter to provide simultaneous imaging and dose verification. Methods: The novel dual detector configuration comprised of a 2D diode array dosimeter, referred to as a Magic Plate (MP) placed directly on a standard EPID. Dose response of the MP was evaluated by measuring the detector’s response with respect to off-axis position and field size with 30 cm of solid water (SW) acting as a transit object in the beam. Measurements were performed with 3, 5, 10 and 15 mm SW build-up and compared to 2D ionisationmore » chamber array (ICA) measurements and the PinnacleTM treatment planning system (TPS) at a source to detector distance of 150 cm with a 6 MV beam. Clinical dosimetric performance was evaluated by measuring a number of intensity-modulated radiation therapy (IMRT) beams in transit geometry. Imaging performance of the EPID was quantified by measuring the contrast-to-noise ratio (CNR) and spatial resolution. Images of a Rando phantom were used for qualitative assessment. Results: Measured MP off-axis and field size response agreed within 2% of TPS and ICA responses when measured using 15 mm SW build-up. Clinical IMRT beams had gamma pass rates of ≥95% at 3%/3mm criteria. Measured CNR and spatial resolution (f50) were 264.96, 210.6, and 0.41, 0.40 with build-up of 5 and 15 mm respectively for the dual detector configuration. CNR and spatial resolution of 643.9 and 0.41 were measured for standard EPID. CNR was quantitatively worse in the dual detector configuration. Differences in imaging performance were not visible in a qualitative assessment using a Rando phantom. Conclusion: Combining a prototype MP 2D dosimeter with a conventional EPID did not significantly detract from the performance of either device and has the potential for simultaneous on-line patient transit dosimetry and image assessment in radiation therapy. Cancer Institute NSW Australia(Research Equipment Grant 10/REG/1-20) and Cancer Council NSW (Grant ID RG 1-06)« less

Feasibility study on inverse four-dimensional dose reconstruction using the continuous dose-image of EPID

PubMed Central

Yeo, Inhwan Jason; Jung, Jae Won; Yi, Byong Yong; Kim, Jong Oh

2013-01-01

Purpose: When an intensity-modulated radiation beam is delivered to a moving target, the interplay effect between dynamic beam delivery and the target motion due to miss-synchronization can cause unpredictable dose delivery. The portal dose image in electronic portal imaging device (EPID) represents radiation attenuated and scattered through target media. Thus, it may possess information about delivered radiation to the target. Using a continuous scan (cine) mode of EPID, which provides temporal dose images related to target and beam movements, the authors’ goal is to perform four-dimensional (4D) dose reconstruction. Methods: To evaluate this hypothesis, first, the authors have derived and subsequently validated a fast method of dose reconstruction based on virtual beamlet calculations of dose responses using a test intensity-modulated beam. This method was necessary for processing a large number of EPID images pertinent for four-dimensional reconstruction. Second, cine mode acquisition after summation over all images was validated through comparison with integration mode acquisition on EPID (IAS3 and aS1000) for the test beam. This was to confirm the agreement of the cine mode with the integrated mode, specifically for the test beam, which is an accepted mode of image acquisition for dosimetry with EPID. Third, in-phantom film and exit EPID dosimetry was performed on a moving platform using the same beam. Heterogeneous as well as homogeneous phantoms were used. The cine images were temporally sorted at 10% interval. The authors have performed dose reconstruction to the in-phantom plane from the sorted cine images using the above validated method of dose reconstruction. The reconstructed dose from each cine image was summed to compose a total reconstructed dose from the test beam delivery, and was compared with film measurements. Results: The new method of dose reconstruction was validated showing greater than 95.3% pass rates of the gamma test with the criteria of dose difference of 3% and distance to agreement of 3 mm. The dose comparison of the reconstructed dose with the measured dose for the two phantoms showed pass rates higher than 96.4% given the same criteria. Conclusions: Feasibility of 4D dose reconstruction was successfully demonstrated in this study. The 4D dose reconstruction demonstrated in this study can be a promising dose validation method for radiation delivery on moving organs. PMID:23635250

A Swiss cheese error detection method for real-time EPID-based quality assurance and error prevention.

PubMed

Passarge, Michelle; Fix, Michael K; Manser, Peter; Stampanoni, Marco F M; Siebers, Jeffrey V

2017-04-01

To develop a robust and efficient process that detects relevant dose errors (dose errors of ≥5%) in external beam radiation therapy and directly indicates the origin of the error. The process is illustrated in the context of electronic portal imaging device (EPID)-based angle-resolved volumetric-modulated arc therapy (VMAT) quality assurance (QA), particularly as would be implemented in a real-time monitoring program. A Swiss cheese error detection (SCED) method was created as a paradigm for a cine EPID-based during-treatment QA. For VMAT, the method compares a treatment plan-based reference set of EPID images with images acquired over each 2° gantry angle interval. The process utilizes a sequence of independent consecutively executed error detection tests: an aperture check that verifies in-field radiation delivery and ensures no out-of-field radiation; output normalization checks at two different stages; global image alignment check to examine if rotation, scaling, and translation are within tolerances; pixel intensity check containing the standard gamma evaluation (3%, 3 mm) and pixel intensity deviation checks including and excluding high dose gradient regions. Tolerances for each check were determined. To test the SCED method, 12 different types of errors were selected to modify the original plan. A series of angle-resolved predicted EPID images were artificially generated for each test case, resulting in a sequence of precalculated frames for each modified treatment plan. The SCED method was applied multiple times for each test case to assess the ability to detect introduced plan variations. To compare the performance of the SCED process with that of a standard gamma analysis, both error detection methods were applied to the generated test cases with realistic noise variations. Averaged over ten test runs, 95.1% of all plan variations that resulted in relevant patient dose errors were detected within 2° and 100% within 14° (<4% of patient dose delivery). Including cases that led to slightly modified but clinically equivalent plans, 89.1% were detected by the SCED method within 2°. Based on the type of check that detected the error, determination of error sources was achieved. With noise ranging from no random noise to four times the established noise value, the averaged relevant dose error detection rate of the SCED method was between 94.0% and 95.8% and that of gamma between 82.8% and 89.8%. An EPID-frame-based error detection process for VMAT deliveries was successfully designed and tested via simulations. The SCED method was inspected for robustness with realistic noise variations, demonstrating that it has the potential to detect a large majority of relevant dose errors. Compared to a typical (3%, 3 mm) gamma analysis, the SCED method produced a higher detection rate for all introduced dose errors, identified errors in an earlier stage, displayed a higher robustness to noise variations, and indicated the error source. © 2017 American Association of Physicists in Medicine.

Dose-response characteristics of an amorphous silicon EPID.

PubMed

Winkler, Peter; Hefner, Alfred; Georg, Dietmar

2005-10-01

Electronic portal imaging devices (EPIDs) were originally developed for the purpose of patient setup verification. Nowadays, they are increasingly used as dosimeters (e.g., for IMRT verification and linac-specific QA). A prerequisite for any clinical dosimetric application is a detailed understanding of the detector's dose-response behavior. The aim of this study is to investigate the dosimetric properties of an amorphous silicon EPID (Elekta IVIEWGT) with respect to three photon beam qualities: 6, 10, and 25 MV. The EPID showed an excellent temporal stability on short term as well as on long term scales. The stability throughout the day was strongly influenced by warming up, which took several hours and affected EPID response by 2.5%. Ghosting effects increased the sensitivity of the EPID. They became more pronounced with decreasing time intervals between two exposures as well as with increasing dose. Due to ghosting, changes in pixel sensitivity amounted up to 16% (locally) for the 25 MV photon beam. It was observed that the response characteristics of our EPID depended on dose as well as on dose rate. Doubling the dose rate increased the EPID sensitivity by 1.5%. This behavior was successfully attributed to a dose per frame effect, i.e., a nonlinear relationship between the EPID signal and the dose which was delivered to the panel between two successive readouts. The sensitivity was found to vary up to 10% in the range of 1 to 1000 monitor units. This variation was governed by two independent effects. For low doses, the EPID signal was reduced due to the linac's changing dose rate during startup. Furthermore, the detector reading was influenced by intrabeam variations of EPID sensitivity, namely, an increase of detector response during uniform exposure. For the beam qualities which were used, the response characteristics of the EPID did not depend on energy. Differences in relative dose-response curves resulted from energy dependent temporal output characteristics of the accelerator. If ghosting is prevented from affecting the results and all dose-response effects are properly corrected for, the EPID signal becomes independent of dose rate, dose, and exposure time.

SU-F-T-313: Clinical Results of a New Customer Acceptance Test for Elekta VMAT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rusk, B; Fontenot, J

Purpose: To report the results of a customer acceptance test (CAT) for VMAT treatments for two matched Elekta linear accelerators. Methods: The CAT tests were performed on two clinically matched Elekta linear accelerators equipped with a 160-leaf MLC. Functional tests included performance checks of the control system during dynamic movements of the diaphragms, MLC, and gantry. Dosimetric tests included MLC picket fence tests at static and variable dose rates and a diaphragm alignment test, all performed using the on-board EPID. Additionally, beam symmetry during arc delivery was measured at the four cardinal angles for high and low dose rate modesmore » using a 2D detector array. Results of the dosimetric tests were analyzed using the VMAT CAT analysis tool. Results: Linear accelerator 1 (LN1) met all stated CAT tolerances. Linear accelerator 2 (LN2) passed the geometric, beam symmetry, and MLC position error tests but failed the relative dose average test for the diaphragm abutment and all three picket fence fields. Though peak doses in the abutment regions were consistent, the average dose was below the stated tolerance corresponding to a leaf junction that was too narrow. Despite this, no significant differences in patient specific VMAT quality assurance measured were observed between the accelerators and both passed monthly MLC quality assurance performed with the Hancock test. Conclusion: Results from the CAT showed LN2 with relative dose averages in the abutment regions of the diaphragm and MLC tests outside the tolerances resulting from differences in leaf gap distances. Tolerances of the dose average tests from the CAT may be small enough to detect MLC errors which do not significantly affect patient QA or the routine MLC tests.« less

The sensitivity of patient specific IMRT QC to systematic MLC leaf bank offset errors.

PubMed

Rangel, Alejandra; Palte, Gesa; Dunscombe, Peter

2010-07-01

Patient specific IMRT QC is performed routinely in many clinics as a safeguard against errors and inaccuracies which may be introduced during the complex planning, data transfer, and delivery phases of this type of treatment. The purpose of this work is to evaluate the feasibility of detecting systematic errors in MLC leaf bank position with patient specific checks. 9 head and neck (H&N) and 14 prostate IMRT beams were delivered using MLC files containing systematic offsets (+/- 1 mm in two banks, +/- 0.5 mm in two banks, and 1 mm in one bank of leaves). The beams were measured using both MAPCHECK (Sun Nuclear Corp., Melbourne, FL) and the aS1000 electronic portal imaging device (Varian Medical Systems, Palo Alto, CA). Comparisons with calculated fields, without offsets, were made using commonly adopted criteria including absolute dose (AD) difference, relative dose difference, distance to agreement (DTA), and the gamma index. The criteria most sensitive to systematic leaf bank offsets were the 3% AD, 3 mm DTA for MAPCHECK and the gamma index with 2% AD and 2 mm DTA for the EPID. The criterion based on the relative dose measurements was the least sensitive to MLC offsets. More highly modulated fields, i.e., H&N, showed greater changes in the percentage of passing points due to systematic MLC inaccuracy than prostate fields. None of the techniques or criteria tested is sufficiently sensitive, with the population of IMRT fields, to detect a systematic MLC offset at a clinically significant level on an individual field. Patient specific QC cannot, therefore, substitute for routine QC of the MLC itself.

A novel EPID design for enhanced contrast and detective quantum efficiency

NASA Astrophysics Data System (ADS)

Rottmann, Joerg; Morf, Daniel; Fueglistaller, Rony; Zentai, George; Star-Lack, Josh; Berbeco, Ross

2016-09-01

Beams-eye-view imaging applications such as real-time soft-tissue motion estimation are hindered by the inherently low image contrast of electronic portal imaging devices (EPID) currently available for clinical use. We introduce and characterize a novel EPID design that provides substantially increased detective quantum efficiency (DQE), contrast-to-noise ratio (CNR) and sensitivity without degradation in spatial resolution. The prototype design features a stack of four conventional EPID layers combined with low noise integrated readout electronics. Each layer consists of a copper plate, a scintillator (\\text{G}{{\\text{d}}2}{{\\text{O}}2}{{\\text{S}}{}}\\text{:Tb} ) and a photodiode/TFT-switch (aSi:H). We characterize the prototype’s signal response to a 6 MV photon beam in terms of modulation transfer function (MTF), DQE and CNR. The presampled MTF is estimated using a slanted slit technique, the DQE is calculated from measured normalized noise power spectra (nNPS) and the MTF and CNR is estimated using a Las Vegas contrast phantom. The prototype has been designed and built to be interchangeable with the current clinical EPID on the Varian TrueBeam platform (AS-1200) in terms of size and data output specifications. Performance evaluation is conducted in absolute values as well as in relative terms using the Varian AS-1200 EPID as a reference detector. A fivefold increase of DQE(0) to about 6.7% was observed by using the four-layered design versus the AS-1200 reference detector. No substantial differences are observed between each layer’s individual MTF and the one for all four layers operating combined indicating that defocusing due to beam divergence is negligible. Also, using four layers instead of one increases the signal to noise ratio by a factor of 1.7.

Detection of IMRT delivery errors based on a simple constancy check of transit dose by using an EPID

NASA Astrophysics Data System (ADS)

Baek, Tae Seong; Chung, Eun Ji; Son, Jaeman; Yoon, Myonggeun

2015-11-01

Beam delivery errors during intensity modulated radiotherapy (IMRT) were detected based on a simple constancy check of the transit dose by using an electronic portal imaging device (EPID). Twenty-one IMRT plans were selected from various treatment sites, and the transit doses during treatment were measured by using an EPID. Transit doses were measured 11 times for each course of treatment, and the constancy check was based on gamma index (3%/3 mm) comparisons between a reference dose map (the first measured transit dose) and test dose maps (the following ten measured dose maps). In a simulation using an anthropomorphic phantom, the average passing rate of the tested transit dose was 100% for three representative treatment sites (head & neck, chest, and pelvis), indicating that IMRT was highly constant for normal beam delivery. The average passing rate of the transit dose for 1224 IMRT fields from 21 actual patients was 97.6% ± 2.5%, with the lower rate possibly being due to inaccuracies of patient positioning or anatomic changes. An EPIDbased simple constancy check may provide information about IMRT beam delivery errors during treatment.

[Statistical process control applied to intensity modulated radiotherapy pretreatment controls with portal dosimetry].

PubMed

Villani, N; Gérard, K; Marchesi, V; Huger, S; François, P; Noël, A

2010-06-01

The first purpose of this study was to illustrate the contribution of statistical process control for a better security in intensity modulated radiotherapy (IMRT) treatments. This improvement is possible by controlling the dose delivery process, characterized by pretreatment quality control results. So, it is necessary to put under control portal dosimetry measurements (currently, the ionisation chamber measurements were already monitored by statistical process control thanks to statistical process control tools). The second objective was to state whether it is possible to substitute ionisation chamber with portal dosimetry in order to optimize time devoted to pretreatment quality control. At Alexis-Vautrin center, pretreatment quality controls in IMRT for prostate and head and neck treatments were performed for each beam of each patient. These controls were made with an ionisation chamber, which is the reference detector for the absolute dose measurement, and with portal dosimetry for the verification of dose distribution. Statistical process control is a statistical analysis method, coming from industry, used to control and improve the studied process quality. It uses graphic tools as control maps to follow-up process, warning the operator in case of failure, and quantitative tools to evaluate the process toward its ability to respect guidelines: this is the capability study. The study was performed on 450 head and neck beams and on 100 prostate beams. Control charts, showing drifts, both slow and weak, and also both strong and fast, of mean and standard deviation have been established and have shown special cause introduced (manual shift of the leaf gap of the multileaf collimator). Correlation between dose measured at one point, given with the EPID and the ionisation chamber has been evaluated at more than 97% and disagreement cases between the two measurements were identified. The study allowed to demonstrate the feasibility to reduce the time devoted to pretreatment controls, by substituting the ionisation chamber's measurements with those performed with EPID, and also that a statistical process control monitoring of data brought security guarantee. 2010 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

MO-FG-CAMPUS-TeP1-01: An Efficient Method of 3D Patient Dose Reconstruction Based On EPID Measurements for Pre-Treatment Patient Specific QA

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, R; Lee, C; Calvary Mater Newcastle, Newcastle

Purpose: To demonstrate an efficient and clinically relevant patient specific QA method by reconstructing 3D patient dose from 2D EPID images for IMRT plans. Also to determine the usefulness of 2D QA metrics when assessing 3D patient dose deviations. Methods: Using the method developed by King et al (Med Phys 39(5),2839–2847), EPID images of IMRT fields were acquired in air and converted to dose at 10 cm depth (SAD setup) in a flat virtual water phantom. Each EPID measured dose map was then divided by the corresponding treatment planning system (TPS) dose map calculated with an identical setup, to derivemore » a 2D “error matrix”. For each field, the error matrix was used to adjust the doses along the respective ray lines in the original patient 3D dose. All field doses were combined to derive a reconstructed 3D patient dose for quantitative analysis. A software tool was developed to efficiently implement the entire process and was tested with a variety of IMRT plans for 2D (virtual flat phantom) and 3D (in-patient) QA analysis. Results: The method was tested on 60 IMRT plans. The mean (± standard deviation) 2D gamma (2%,2mm) pass rate (2D-GPR) was 97.4±3.0% and the mean 2D gamma index (2D-GI) was 0.35±0.06. The 3D PTV mean dose deviation was 1.8±0.8%. The analysis showed very weak correlations between both the 2D-GPR and 2D-GI when compared with PTV mean dose deviations (R2=0.3561 and 0.3632 respectively). Conclusion: Our method efficiently calculates 3D patient dose from 2D EPID images, utilising all of the advantages of an EPID-based dosimetry system. In this study, the 2D QA metrics did not predict the 3D patient dose deviation. This tool allows reporting of the 3D volumetric dose parameters thus providing more clinically relevant patient specific QA.« less

SU-F-T-260: Using Portal Image Device for Pre-Treatment QA in Volumetric Modulated Arc Plans with Flattening Filter Free (FFF) Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qu, H; Qi, P; Yu, N

Purpose: To implement and validate a method of using electronic portal image device (EPID) for pre-treatment quality assurance (QA) of volumetric modulated arc therapy (VMAT) plans using flattering filter free (FFF) beams for stereotactic body radiotherapy (SBRT). Methods: On Varian Edge with 6MV FFF beam, open field (from 2×2 cm to 20×20 cm) EPID images were acquired with 200 monitor unit (MU) at the image device to radiation source distance of 150cm. With 10×10 open field and calibration unit (CU) provided by vendor to EPID image pixel, a dose conversion factor was determined by dividing the center dose calculated frommore » the treatment planning system (TPS) to the corresponding CU readout on the image. Water phantom measured beam profile and the output factors for various field sizes were further correlated to those of EPID images. The dose conversion factor and correction factors were then used for converting the portal images to the planner dose distributions of clinical fields. A total of 28 VMAT fields of 14 SBRT plans (8 lung, 2 prostate, 2 liver and 2 spine) were measured. With 10% low threshold cutoff, the delivered dose distributions were compared to the reference doses calculated in water phantom from the TPS. A gamma index analysis was performed for the comparison in percentage dose difference/distance-to-agreement specifications. Results: The EPID device has a linear response to the open fields with increasing MU. For the clinical fields, the gamma indices between the converted EPID dose distributions and the TPS calculated 2D dose distributions were 98.7%±1.1%, 94.0%±3.4% and 70.3%±7.7% for the criteria of 3%/3mm, 2%/2mm and 1%/1mm, respectively. Conclusion: Using a portal image device, a high resolution and high accuracy portal dosimerty was achieved for pre-treatment QA verification for SBRT VMAT plans with FFF beams.« less

Daily QA of linear accelerators using only EPID and OBI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Baozhou, E-mail: bsun@radonc.wustl.edu; Goddu, S. Murty; Yaddanapudi, Sridhar

2015-10-15

Purpose: As treatment delivery becomes more complex, there is a pressing need for robust quality assurance (QA) tools to improve efficiency and comprehensiveness while simultaneously maintaining high accuracy and sensitivity. This work aims to present the hardware and software tools developed for comprehensive QA of linear accelerator (LINAC) using only electronic portal imaging devices (EPIDs) and kV flat panel detectors. Methods: A daily QA phantom, which includes two orthogonally positioned phantoms for QA of MV-beams and kV onboard imaging (OBI) is suspended from the gantry accessory holder to test both geometric and dosimetric components of a LINAC and an OBI.more » The MV component consists of a 0.5 cm water-equivalent plastic sheet incorporating 11 circular steel plugs for transmission measurements through multiple thicknesses and one resolution plug for MV-image quality testing. The kV-phantom consists of a Leeds phantom (TOR-18 FG phantom supplied by Varian) for testing low and high contrast resolutions. In the developed process, the existing LINAC tools were used to automate daily acquisition of MV and kV images and software tools were developed for simultaneous analysis of these images. A method was developed to derive and evaluate traditional QA parameters from these images [output, flatness, symmetry, uniformity, TPR{sub 20/10}, and positional accuracy of the jaws and multileaf collimators (MLCs)]. The EPID-based daily QA tools were validated by performing measurements on a detuned 6 MV beam to test its effectiveness in detecting errors in output, symmetry, energy, and MLC positions. The developed QA process was clinically commissioned, implemented, and evaluated on a Varian TrueBeam LINAC (Varian Medical System, Palo Alto, CA) over a period of three months. Results: Machine output constancy measured with an EPID (as compared against a calibrated ion-chamber) is shown to be within ±0.5%. Beam symmetry and flatness deviations measured using an EPID and a 2D ion-chamber array agree within ±0.5% and ±1.2% for crossline and inline profiles, respectively. MLC position errors of 0.5 mm can be detected using a picket fence test. The field size and phantom positioning accuracy can be determined within 0.5 mm. The entire daily QA process takes ∼15 min to perform tests for 5 photon beams, MLC tests, and imaging checks. Conclusions: The exclusive use of EPID-based QA tools, including a QA phantom and simultaneous analysis software tools, has been demonstrated as a viable, efficient, and comprehensive process for daily evaluation of LINAC performance.« less

Automated x-ray/light field congruence using the LINAC EPID panel.

PubMed

Polak, Wojciech; O'Doherty, Jim; Jones, Matt

2013-03-01

X-ray/light field alignment is a test described in many guidelines for the routine quality control of clinical linear accelerators (LINAC). Currently, the gold standard method for measuring alignment is through utilization of radiographic film. However, many modern LINACs are equipped with an electronic portal imaging device (EPID) that may be used to perform this test and thus subsequently reducing overall cost, processing, and analysis time, removing operator dependency and the requirement to sustain the departmental film processor. This work describes a novel method of utilizing the EPID together with a custom inhouse designed jig and automatic image processing software allowing measurement of the light field size, x-ray field size, and congruence between them. The authors present results of testing the method for aS1000 and aS500 Varian EPID detectors for six LINACs at a range of energies (6, 10, and 15 MV) in comparison with the results obtained from the use of radiographic film. Reproducibility of the software in fully automatic operation under a range of operating conditions for a single image showed a congruence of 0.01 cm with a coefficient of variation of 0. Slight variation in congruence repeatability was noted through semiautomatic processing by four independent operators due to manual marking of positions on the jig. Testing of the methodology using the automatic method shows a high precision of 0.02 mm compared to a maximum of 0.06 mm determined by film processing. Intraindividual examination of operator measurements of congruence was shown to vary as much as 0.75 mm. Similar congruence measurements of 0.02 mm were also determined for a lower resolution EPID (aS500 model), after rescaling of the image to the aS1000 image size. The designed methodology was proven to be time efficient, cost effective, and at least as accurate as using the gold standard radiographic film. Additionally, congruence testing can be easily performed for all four cardinal gantry angles which can be difficult when using radiographic film. Therefore, the authors propose it can be used as an alternative to the radiographic film method allowing decommissioning of the film processor.

Poster — Thur Eve — 25: Sensitivity to inhomogeneities for an in-vivo EPID dosimetry method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peca, Stefano; Brown, Derek; Department of Physics and Astronomy, University of Calgary, Calgary, AB

2014-08-15

Introduction: The electronic portal imaging device (EPID) has the potential to be used for in vivo dosimetry during radiotherapy as an additional dose delivery check. We recently proposed a simple method of using the EPID for 2D-IVD based on correlation ratios. In this work we have investigated the sensitivity of our EPID-IVD to inhomogeneities. Methods: We used slab phantoms that simulate water, bone, and lung, arranged in various geometries. To simulate body contours non-orthogonal to the field, we used a water wedge. CT data of these phantoms was imported into MATLAB, in conjunction with EPID images acquired during irradiation, tomore » calculate dose inside the phantom in isocenter plane. Each phantom was irradiated using a linear accelerator while images were acquired with the EPID (cine mode). Comparisons between EPID-calculated and TPS dose maps were: pixel-by-pixel dose difference, and 3%,3mm gamma evaluation. Results: In the homogeneous case, CAX dose difference was <1%, and 3%,3mm gamma analysis yielded 99% of points with gamma<1. For the inhomogeneous phantoms, agreement decreased with increasing inhomogeneity reaching up to 10% CAX dose difference with 10cm of lung. Results from the water wedge phantom suggest that the EPID-calculated dose can account for surface irregularities of approximately ±3cm. Conclusions: The EPID-based IVD investigated has limitations in the presence of large inhomogeneities. Nonetheless, CAX doses never differed by >15% from the TPS. This suggests that this EPID-IVD is capable of detecting gross dose delivery errors even in the presence of inhomogeneities, supporting its utility as an additional patient safety device.« less

Dosimetry in radiotherapy using a-Si EPIDs: Systems, methods, and applications focusing on 3D patient dose estimation

NASA Astrophysics Data System (ADS)

McCurdy, B. M. C.

2013-06-01

An overview is provided of the use of amorphous silicon electronic portal imaging devices (EPIDs) for dosimetric purposes in radiation therapy, focusing on 3D patient dose estimation. EPIDs were originally developed to provide on-treatment radiological imaging to assist with patient setup, but there has also been a natural interest in using them as dosimeters since they use the megavoltage therapy beam to form images. The current generation of clinically available EPID technology, amorphous-silicon (a-Si) flat panel imagers, possess many characteristics that make them much better suited to dosimetric applications than earlier EPID technologies. Features such as linearity with dose/dose rate, high spatial resolution, realtime capability, minimal optical glare, and digital operation combine with the convenience of a compact, retractable detector system directly mounted on the linear accelerator to provide a system that is well-suited to dosimetric applications. This review will discuss clinically available a-Si EPID systems, highlighting dosimetric characteristics and remaining limitations. Methods for using EPIDs in dosimetry applications will be discussed. Dosimetric applications using a-Si EPIDs to estimate three-dimensional dose in the patient during treatment will be overviewed. Clinics throughout the world are implementing increasingly complex treatments such as dynamic intensity modulated radiation therapy and volumetric modulated arc therapy, as well as specialized treatment techniques using large doses per fraction and short treatment courses (ie. hypofractionation and stereotactic radiosurgery). These factors drive the continued strong interest in using EPIDs as dosimeters for patient treatment verification.

Clinical Implementation of a Model-Based In Vivo Dose Verification System for Stereotactic Body Radiation Therapy-Volumetric Modulated Arc Therapy Treatments Using the Electronic Portal Imaging Device.

PubMed

McCowan, Peter M; Asuni, Ganiyu; Van Uytven, Eric; VanBeek, Timothy; McCurdy, Boyd M C; Loewen, Shaun K; Ahmed, Naseer; Bashir, Bashir; Butler, James B; Chowdhury, Amitava; Dubey, Arbind; Leylek, Ahmet; Nashed, Maged

2017-04-01

To report findings from an in vivo dosimetry program implemented for all stereotactic body radiation therapy patients over a 31-month period and discuss the value and challenges of utilizing in vivo electronic portal imaging device (EPID) dosimetry clinically. From December 2013 to July 2016, 117 stereotactic body radiation therapy-volumetric modulated arc therapy patients (100 lung, 15 spine, and 2 liver) underwent 602 EPID-based in vivo dose verification events. A developed model-based dose reconstruction algorithm calculates the 3-dimensional dose distribution to the patient by back-projecting the primary fluence measured by the EPID during treatment. The EPID frame-averaging was optimized in June 2015. For each treatment, a 3%/3-mm γ comparison between our EPID-derived dose and the Eclipse AcurosXB-predicted dose to the planning target volume (PTV) and the ≥20% isodose volume were performed. Alert levels were defined as γ pass rates <85% (lung and liver) and <80% (spine). Investigations were carried out for all fractions exceeding the alert level and were classified as follows: EPID-related, algorithmic, patient setup, anatomic change, or unknown/unidentified errors. The percentages of fractions exceeding the alert levels were 22.6% for lung before frame-average optimization and 8.0% for lung, 20.0% for spine, and 10.0% for liver after frame-average optimization. Overall, mean (± standard deviation) planning target volume γ pass rates were 90.7% ± 9.2%, 87.0% ± 9.3%, and 91.2% ± 3.4% for the lung, spine, and liver patients, respectively. Results from the clinical implementation of our model-based in vivo dose verification method using on-treatment EPID images is reported. The method is demonstrated to be valuable for routine clinical use for verifying delivered dose as well as for detecting errors. Copyright © 2017 Elsevier Inc. All rights reserved.

Clinical Implementation of a Model-Based In Vivo Dose Verification System for Stereotactic Body Radiation Therapy–Volumetric Modulated Arc Therapy Treatments Using the Electronic Portal Imaging Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCowan, Peter M., E-mail: pmccowan@cancercare.mb.ca; Asuni, Ganiyu; Van Uytven, Eric

Purpose: To report findings from an in vivo dosimetry program implemented for all stereotactic body radiation therapy patients over a 31-month period and discuss the value and challenges of utilizing in vivo electronic portal imaging device (EPID) dosimetry clinically. Methods and Materials: From December 2013 to July 2016, 117 stereotactic body radiation therapy–volumetric modulated arc therapy patients (100 lung, 15 spine, and 2 liver) underwent 602 EPID-based in vivo dose verification events. A developed model-based dose reconstruction algorithm calculates the 3-dimensional dose distribution to the patient by back-projecting the primary fluence measured by the EPID during treatment. The EPID frame-averaging was optimized in Junemore » 2015. For each treatment, a 3%/3-mm γ comparison between our EPID-derived dose and the Eclipse AcurosXB–predicted dose to the planning target volume (PTV) and the ≥20% isodose volume were performed. Alert levels were defined as γ pass rates <85% (lung and liver) and <80% (spine). Investigations were carried out for all fractions exceeding the alert level and were classified as follows: EPID-related, algorithmic, patient setup, anatomic change, or unknown/unidentified errors. Results: The percentages of fractions exceeding the alert levels were 22.6% for lung before frame-average optimization and 8.0% for lung, 20.0% for spine, and 10.0% for liver after frame-average optimization. Overall, mean (± standard deviation) planning target volume γ pass rates were 90.7% ± 9.2%, 87.0% ± 9.3%, and 91.2% ± 3.4% for the lung, spine, and liver patients, respectively. Conclusions: Results from the clinical implementation of our model-based in vivo dose verification method using on-treatment EPID images is reported. The method is demonstrated to be valuable for routine clinical use for verifying delivered dose as well as for detecting errors.« less

SU-F-T-295: MLCs Performance and Patient-Specific IMRT QA Using Log File Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osman, A; American University of Biuret Medical Center, Biuret; Maalej, N

2016-06-15

Purpose: To analyze the performance of the multi-leaf collimators (MLCs) from the log files recorded during the intensity modulated radiotherapy (IMRT) treatment and to construct the relative fluence maps and do the gamma analysis to compare the planned and executed MLCs movement. Methods: We developed a program to extract and analyze the data from dynamic log files (dynalog files) generated from sliding window IMRT delivery treatments. The program extracts the planned and executed (actual or delivered) MLCs movement, calculates and compares the relative planned and executed fluences. The fluence maps were used to perform the gamma analysis (with 3% dosemore » difference and 3 mm distance to agreement) for 3 IMR patients. We compared our gamma analysis results with those obtained from portal dose image prediction (PDIP) algorithm performed using the EPID. Results: For 3 different IMRT patient treatments, the maximum difference between the planned and the executed MCLs positions was 1.2 mm. The gamma analysis results of the planned and delivered fluences were in good agreement with the gamma analysis from portal dosimetry. The maximum difference for number of pixels passing the gamma criteria (3%/3mm) was 0.19% with respect to portal dosimetry results. Conclusion: MLC log files can be used to verify the performance of the MLCs. Patientspecific IMRT QA based on MLC movement log files gives similar results to EPID dosimetry results. This promising method for patient-specific IMRT QA is fast, does not require dose measurements in a phantom, can be done before the treatment and for every fraction, and significantly reduces the IMRT workload. The author would like to thank King Fahd University of petroleum and Minerals for the support.« less

3D Dose reconstruction: Banding artefacts in cine mode EPID images during VMAT delivery

NASA Astrophysics Data System (ADS)

Woodruff, H. C.; Greer, P. B.

2013-06-01

Cine (continuous) mode images obtained during VMAT delivery are heavily degraded by banding artefacts. We have developed a method to reconstruct the pulse sequence (and hence dose deposited) from open field images. For clinical VMAT fields we have devised a frame averaging strategy that greatly improves image quality and dosimetric information for three-dimensional dose reconstruction.

Poster — Thur Eve — 10: Partial kV CBCT, complete kV CBCT and EPID in breast treatment: a dose comparison study for skin, breasts, heart and lungs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roussin, E; Archambault, L K; Wierzbicki, W

The advantages of kilovoltage cone beam CT (kV CBCT) imaging over electronic portal imaging device (EPID) such as accurate 3D anatomy, soft tissue visualization, fast rigid registration and enhanced precision on patient positioning has lead to its increasing use in clinics. The benefits of this imaging technique are at the cost of increasing the dose to healthy surrounding organs. Our center has moved toward the use of daily partial rotation kV CBCT to restrict the dose to healthy tissues. This study aims to better quantify radiation doses from different image-guidance techniques such as tangential EPID, complete and partial kV CBCTmore » for breast treatments. Cross-calibrated ionization chambers and kV calibrated Gafchromic films were used to measure the dose to the heart, lungs, breasts and skin. It was found that performing partial kV CBCT decreases the heart dose by about 36%, the lungs dose by 31%, the contralateral breast dose by 41% and the ipsilateral breast dose by 43% when compared to a full rotation CBCT. The skin dose measured for a full rotation CBCT was about 0.8 cGy for the contralateral breast and about 0.3 cGy for the ipsilateral breast. The study is still ongoing and results on skin doses for partial rotation kV CBCT as well as for tangential EPID images are upcoming.« less

A study on dosimetric properties of electronic portal imaging device and its use as a quality assurance tool in Volumetric Modulated Arc Therapy

PubMed Central

Sukumar, Prabakar; Padmanaban, Sriram; Jeevanandam, Prakash; Syam Kumar, S.A.; Nagarajan, Vivekanandan

2011-01-01

Aim In this study, the dosimetric properties of the electronic portal imaging device were examined and the quality assurance testing of Volumetric Modulated Arc Therapy was performed. Background RapidArc involves the variable dose rate, leaf speed and the gantry rotation. The imager was studied for the effects like dose, dose rate, field size, leaf speed and sag during gantry rotation. Materials and methods A Varian RapidArc machine equipped with 120 multileaf collimator and amorphous silicon detector was used for the study. The characteristics that are variable in RapidArc treatment were studied for the portal imager. The accuracy of a dynamic multileaf collimator position at different gantry angles and during gantry rotation was examined using the picket fence test. The control of the dose rate and gantry speed was verified using a test field irradiating seven strips of the same dose with different dose rate and gantry speeds. The control over leaf speed during arc was verified by irradiating four strips of different leaf speeds with the same dose in each strip. To verify the results, the RapidArc test procedure was compared with the X-Omat film and verified for a period of 6 weeks using EPID. Results The effect of gantry rotation on leaf accuracy was minimal. The dose in segments showed good agreement with mean deviation of 0.8% for dose rate control and 1.09% for leaf speed control over different gantry speeds. Conclusion The results provided a precise control of gantry speed, dose rate and leaf speeds during RapidArc delivery and were consistent over 6 weeks. PMID:24376989

A method for removing arm backscatter from EPID images

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, Brian W.; Greer, Peter B.; School of Mathematical and Physical Sciences, University of Newcastle, Newcastle, New South Wales 2308

2013-07-15

Purpose: To develop a method for removing the support arm backscatter from images acquired using current Varian electronic portal imaging devices (EPIDs).Methods: The effect of arm backscatter on EPID images was modeled using a kernel convolution method. The parameters of the model were optimized by comparing on-arm images to off-arm images. The model was used to develop a method to remove the effect of backscatter from measured EPID images. The performance of the backscatter removal method was tested by comparing backscatter corrected on-arm images to measured off-arm images for 17 rectangular fields of different sizes and locations on the imager.more » The method was also tested using on- and off-arm images from 42 intensity modulated radiotherapy (IMRT) fields.Results: Images generated by the backscatter removal method gave consistently better agreement with off-arm images than images without backscatter correction. For the 17 rectangular fields studied, the root mean square difference of in-plane profiles compared to off-arm profiles was reduced from 1.19% (standard deviation 0.59%) on average without backscatter removal to 0.38% (standard deviation 0.18%) when using the backscatter removal method. When comparing to the off-arm images from the 42 IMRT fields, the mean {gamma} and percentage of pixels with {gamma} < 1 were improved by the backscatter removal method in all but one of the images studied. The mean {gamma} value (1%, 1 mm) for the IMRT fields studied was reduced from 0.80 to 0.57 by using the backscatter removal method, while the mean {gamma} pass rate was increased from 72.2% to 84.6%.Conclusions: A backscatter removal method has been developed to estimate the image acquired by the EPID without any arm backscatter from an image acquired in the presence of arm backscatter. The method has been shown to produce consistently reliable results for a wide range of field sizes and jaw configurations.« less

TU-C-BRE-11: 3D EPID-Based in Vivo Dosimetry: A Major Step Forward Towards Optimal Quality and Safety in Radiation Oncology Practice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mijnheer, B; Mans, A; Olaciregui-Ruiz, I

Purpose: To develop a 3D in vivo dosimetry method that is able to substitute pre-treatment verification in an efficient way, and to terminate treatment delivery if the online measured 3D dose distribution deviates too much from the predicted dose distribution. Methods: A back-projection algorithm has been further developed and implemented to enable automatic 3D in vivo dose verification of IMRT/VMAT treatments using a-Si EPIDs. New software tools were clinically introduced to allow automated image acquisition, to periodically inspect the record-and-verify database, and to automatically run the EPID dosimetry software. The comparison of the EPID-reconstructed and planned dose distribution is donemore » offline to raise automatically alerts and to schedule actions when deviations are detected. Furthermore, a software package for online dose reconstruction was also developed. The RMS of the difference between the cumulative planned and reconstructed 3D dose distributions was used for triggering a halt of a linac. Results: The implementation of fully automated 3D EPID-based in vivo dosimetry was able to replace pre-treatment verification for more than 90% of the patient treatments. The process has been fully automated and integrated in our clinical workflow where over 3,500 IMRT/VMAT treatments are verified each year. By optimizing the dose reconstruction algorithm and the I/O performance, the delivered 3D dose distribution is verified in less than 200 ms per portal image, which includes the comparison between the reconstructed and planned dose distribution. In this way it was possible to generate a trigger that can stop the irradiation at less than 20 cGy after introducing large delivery errors. Conclusion: The automatic offline solution facilitated the large scale clinical implementation of 3D EPID-based in vivo dose verification of IMRT/VMAT treatments; the online approach has been successfully tested for various severe delivery errors.« less

SU-E-J-70: Evaluation of Multiple Isocentric Intensity Modulated and Volumetric Modulated Arc Therapy Techniques Using Portal Dosimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muralidhar, K Raja; Pangam, S; Kolla, J

2015-06-15

Purpose: To develop a method for verification of dose distribution in a patient during treatment using multiple isocentric Intensity modulated and volumetric modulated arc therapy techniques with portal dosimetry. Methods: Varian True Beam accelerator, equipped with an aS1000 megavoltage electronic portal imaging device (EPID) has an integrated image mode for portal dosimetry (PD). The source-to-imager distance was taken at 150 cm to avoid collision to the table. Fourteen fractions were analyzed for this study. During shift in a single plan from one isocenter to another isocenter, EPID also shifted longitudinally for each field by taking the extent of divergence ofmore » beam into the consideration for EPID distance of 150cm. Patients were given treatment everyday with EPID placed in proper position for each field. Several parameters were obtained by comparing the dose distribution between fractions to fraction. The impact of the intra-fraction and inter-fraction of the patient in combination with isocenter shift of the beams were observed. Results: During treatment, measurements were performed by EPID and were evaluated by the gamma method. Analysis was done between fractions for multiple isocenter treatments. The pass rates of the gamma analysis with a criterion of 3% and 3 mm for the 14 fractions were over 97.8% with good consistency. Whereas maximum gamma exceeded the criteria in few fractions (in<1 cc vol). Average gamma was observed in the criteria of 0.5%. Maximum dose difference and average dose differences were less than 0.22 CU and 0.01 CU for maximum tolerance of 1.0 CU and 0.2 CU respectively. Conclusion: EPID with extended distance is ideal method to verify the multiple isocentric dose distribution in patient during treatment, especially cold and hot spots in junction dose. Verification of shifts as well as the dose differences between each fraction due to inter-fraction and intra-fraction of the patient can be derived.« less

A system for EPID-based real-time treatment delivery verification during dynamic IMRT treatment.

PubMed

Fuangrod, Todsaporn; Woodruff, Henry C; van Uytven, Eric; McCurdy, Boyd M C; Kuncic, Zdenka; O'Connor, Daryl J; Greer, Peter B

2013-09-01

To design and develop a real-time electronic portal imaging device (EPID)-based delivery verification system for dynamic intensity modulated radiation therapy (IMRT) which enables detection of gross treatment delivery errors before delivery of substantial radiation to the patient. The system utilizes a comprehensive physics-based model to generate a series of predicted transit EPID image frames as a reference dataset and compares these to measured EPID frames acquired during treatment. The two datasets are using MLC aperture comparison and cumulative signal checking techniques. The system operation in real-time was simulated offline using previously acquired images for 19 IMRT patient deliveries with both frame-by-frame comparison and cumulative frame comparison. Simulated error case studies were used to demonstrate the system sensitivity and performance. The accuracy of the synchronization method was shown to agree within two control points which corresponds to approximately ∼1% of the total MU to be delivered for dynamic IMRT. The system achieved mean real-time gamma results for frame-by-frame analysis of 86.6% and 89.0% for 3%, 3 mm and 4%, 4 mm criteria, respectively, and 97.9% and 98.6% for cumulative gamma analysis. The system can detect a 10% MU error using 3%, 3 mm criteria within approximately 10 s. The EPID-based real-time delivery verification system successfully detected simulated gross errors introduced into patient plan deliveries in near real-time (within 0.1 s). A real-time radiation delivery verification system for dynamic IMRT has been demonstrated that is designed to prevent major mistreatments in modern radiation therapy.

Third party EPID with IGRT capability retrofitted onto an existing medical linear accelerator

PubMed Central

Odero, DO; Shimm, DS

2009-01-01

Radiation therapy requires precision to avoid unintended irradiation of normal organs. Electronic Portal Imaging Devices (EPIDs), can help with precise patient positioning for accurate treatment. EPIDs are now bundled with new linear accelerators, or they can be purchased from the Linac manufacturer for retrofit. Retrofitting a third party EPID to a linear accelerator can pose challenges. The authors describe a relatively inexpensive third party CCD camera-based EPID manufactured by TheraView (Cablon Medical B.V.), installed onto a Siemens Primus linear accelerator, and integrated with a Lantis record and verify system, an Oldelft simulator with Digital Therapy Imaging (DTI) unit, and a Philips ADAC Pinnacle treatment planning system (TPS). This system integrates well with existing equipment and its software can process DICOM images from other sources. The system provides a complete imaging system that eliminates the need for separate software for portal image viewing, interpretation, analysis, archiving, image guided radiation therapy and other image management applications. It can also be accessed remotely via safe VPN tunnels. TheraView EPID retrofit therefore presents an example of a less expensive alternative to linear accelerator manufacturers’ proprietary EPIDs suitable for implementation in third world countries radiation therapy departments which are often faced with limited financial resources. PMID:21611056

Third party EPID with IGRT capability retrofitted onto an existing medical linear accelerator.

PubMed

Odero, D O; Shimm, D S

2009-07-01

Radiation therapy requires precision to avoid unintended irradiation of normal organs. Electronic Portal Imaging Devices (EPIDs), can help with precise patient positioning for accurate treatment. EPIDs are now bundled with new linear accelerators, or they can be purchased from the Linac manufacturer for retrofit. Retrofitting a third party EPID to a linear accelerator can pose challenges. The authors describe a relatively inexpensive third party CCD camera-based EPID manufactured by TheraView (Cablon Medical B.V.), installed onto a Siemens Primus linear accelerator, and integrated with a Lantis record and verify system, an Oldelft simulator with Digital Therapy Imaging (DTI) unit, and a Philips ADAC Pinnacle treatment planning system (TPS). This system integrates well with existing equipment and its software can process DICOM images from other sources. The system provides a complete imaging system that eliminates the need for separate software for portal image viewing, interpretation, analysis, archiving, image guided radiation therapy and other image management applications. It can also be accessed remotely via safe VPN tunnels. TheraView EPID retrofit therefore presents an example of a less expensive alternative to linear accelerator manufacturers' proprietary EPIDs suitable for implementation in third world countries radiation therapy departments which are often faced with limited financial resources.

MO-FG-202-01: A Fast Yet Sensitive EPID-Based Real-Time Treatment Verification System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmad, M; Nourzadeh, H; Neal, B

2016-06-15

Purpose: To create a real-time EPID-based treatment verification system which robustly detects treatment delivery and patient attenuation variations. Methods: Treatment plan DICOM files sent to the record-and-verify system are captured and utilized to predict EPID images for each planned control point using a modified GPU-based digitally reconstructed radiograph algorithm which accounts for the patient attenuation, source energy fluence, source size effects, and MLC attenuation. The DICOM and predicted images are utilized by our C++ treatment verification software which compares EPID acquired 1024×768 resolution frames acquired at ∼8.5hz from Varian Truebeam™ system. To maximize detection sensitivity, image comparisons determine (1) ifmore » radiation exists outside of the desired treatment field; (2) if radiation is lacking inside the treatment field; (3) if translations, rotations, and magnifications of the image are within tolerance. Acquisition was tested with known test fields and prior patient fields. Error detection was tested in real-time and utilizing images acquired during treatment with another system. Results: The computational time of the prediction algorithms, for a patient plan with 350 control points and 60×60×42cm^3 CT volume, is 2–3minutes on CPU and <27 seconds on GPU for 1024×768 images. The verification software requires a maximum of ∼9ms and ∼19ms for 512×384 and 1024×768 resolution images, respectively, to perform image analysis and dosimetric validations. Typical variations in geometric parameters between reference and the measured images are 0.32°for gantry rotation, 1.006 for scaling factor, and 0.67mm for translation. For excess out-of-field/missing in-field fluence, with masks extending 1mm (at isocenter) from the detected aperture edge, the average total in-field area missing EPID fluence was 1.5mm2 the out-of-field excess EPID fluence was 8mm^2, both below error tolerances. Conclusion: A real-time verification software, with EPID images prediction algorithm, was developed. The system is capable of performing verifications between frames acquisitions and identifying source(s) of any out-of-tolerance variations. This work was supported in part by Varian Medical Systems.« less

WE-D-BRA-04: Online 3D EPID-Based Dose Verification for Optimum Patient Safety

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spreeuw, H; Rozendaal, R; Olaciregui-Ruiz, I

2015-06-15

Purpose: To develop an online 3D dose verification tool based on EPID transit dosimetry to ensure optimum patient safety in radiotherapy treatments. Methods: A new software package was developed which processes EPID portal images online using a back-projection algorithm for the 3D dose reconstruction. The package processes portal images faster than the acquisition rate of the portal imager (∼ 2.5 fps). After a portal image is acquired, the software seeks for “hot spots” in the reconstructed 3D dose distribution. A hot spot is in this study defined as a 4 cm{sup 3} cube where the average cumulative reconstructed dose exceedsmore » the average total planned dose by at least 20% and 50 cGy. If a hot spot is detected, an alert is generated resulting in a linac halt. The software has been tested by irradiating an Alderson phantom after introducing various types of serious delivery errors. Results: In our first experiment the Alderson phantom was irradiated with two arcs from a 6 MV VMAT H&N treatment having a large leaf position error or a large monitor unit error. For both arcs and both errors the linac was halted before dose delivery was completed. When no error was introduced, the linac was not halted. The complete processing of a single portal frame, including hot spot detection, takes about 220 ms on a dual hexacore Intel Xeon 25 X5650 CPU at 2.66 GHz. Conclusion: A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for various kinds of gross delivery errors. The detection of hot spots was proven to be effective for the timely detection of these errors. Current work is focused on hot spot detection criteria for various treatment sites and the introduction of a clinical pilot program with online verification of hypo-fractionated (lung) treatments.« less

A back-projection algorithm in the presence of an extra attenuating medium: towards EPID dosimetry for the MR-Linac

NASA Astrophysics Data System (ADS)

Torres-Xirau, I.; Olaciregui-Ruiz, I.; Rozendaal, R. A.; González, P.; Mijnheer, B. J.; Sonke, J.-J.; van der Heide, U. A.; Mans, A.

2017-08-01

In external beam radiotherapy, electronic portal imaging devices (EPIDs) are frequently used for pre-treatment and for in vivo dose verification. Currently, various MR-guided radiotherapy systems are being developed and clinically implemented. Independent dosimetric verification is highly desirable. For this purpose we adapted our EPID-based dose verification system for use with the MR-Linac combination developed by Elekta in cooperation with UMC Utrecht and Philips. In this study we extended our back-projection method to cope with the presence of an extra attenuating medium between the patient and the EPID. Experiments were performed at a conventional linac, using an aluminum mock-up of the MRI scanner housing between the phantom and the EPID. For a 10 cm square field, the attenuation by the mock-up was 72%, while 16% of the remaining EPID signal resulted from scattered radiation. 58 IMRT fields were delivered to a 20 cm slab phantom with and without the mock-up. EPID reconstructed dose distributions were compared to planned dose distributions using the γ -evaluation method (global, 3%, 3 mm). In our adapted back-projection algorithm the averaged {γmean} was 0.27+/- 0.06 , while in the conventional it was 0.28+/- 0.06 . Dose profiles of several square fields reconstructed with our adapted algorithm showed excellent agreement when compared to TPS.

A quantification of the effectiveness of EPID dosimetry and software-based plan verification systems in detecting incidents in radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bojechko, Casey; Phillps, Mark; Kalet, Alan

Purpose: Complex treatments in radiation therapy require robust verification in order to prevent errors that can adversely affect the patient. For this purpose, the authors estimate the effectiveness of detecting errors with a “defense in depth” system composed of electronic portal imaging device (EPID) based dosimetry and a software-based system composed of rules-based and Bayesian network verifications. Methods: The authors analyzed incidents with a high potential severity score, scored as a 3 or 4 on a 4 point scale, recorded in an in-house voluntary incident reporting system, collected from February 2012 to August 2014. The incidents were categorized into differentmore » failure modes. The detectability, defined as the number of incidents that are detectable divided total number of incidents, was calculated for each failure mode. Results: In total, 343 incidents were used in this study. Of the incidents 67% were related to photon external beam therapy (EBRT). The majority of the EBRT incidents were related to patient positioning and only a small number of these could be detected by EPID dosimetry when performed prior to treatment (6%). A large fraction could be detected by in vivo dosimetry performed during the first fraction (74%). Rules-based and Bayesian network verifications were found to be complimentary to EPID dosimetry, able to detect errors related to patient prescriptions and documentation, and errors unrelated to photon EBRT. Combining all of the verification steps together, 91% of all EBRT incidents could be detected. Conclusions: This study shows that the defense in depth system is potentially able to detect a large majority of incidents. The most effective EPID-based dosimetry verification is in vivo measurements during the first fraction and is complemented by rules-based and Bayesian network plan checking.« less

SU-F-T-261: Reconstruction of Initial Photon Fluence Based On EPID Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seliger, T; Engenhart-Cabillic, R; Czarnecki, D

2016-06-15

Purpose: Verifying an algorithm to reconstruct relative initial photon fluence for clinical use. Clinical EPID and CT images were acquired to reconstruct an external photon radiation treatment field. The reconstructed initial photon fluence could be used to verify the treatment or calculate the applied dose to the patient. Methods: The acquired EPID images were corrected for scatter caused by the patient and the EPID with an iterative reconstruction algorithm. The transmitted photon fluence behind the patient was calculated subsequently. Based on the transmitted fluence the initial photon fluence was calculated using a back-projection algorithm which takes the patient geometry andmore » its energy dependent linear attenuation into account. This attenuation was gained from the acquired cone-beam CT or the planning CT by calculating a water-equivalent radiological thickness for each irradiation direction. To verify the algorithm an inhomogeneous phantom consisting of three inhomogeneities was irradiated by a static 6 MV photon field and compared to a reference flood field image. Results: The mean deviation between the reconstructed relative photon fluence for the inhomogeneous phantom and the flood field EPID image was 3% rising up to 7% for off-axis fluence. This was probably caused by the used clinical EPID calibration, which flattens the inhomogeneous fluence profile of the beam. Conclusion: In this clinical experiment the algorithm achieved good results in the center of the field while it showed high deviation of the lateral fluence. This could be reduced by optimizing the EPID calibration, considering the off-axis differential energy response. In further progress this and other aspects of the EPID, eg. field size dependency, CT and dose calibration have to be studied to realize a clinical acceptable accuracy of 2%.« less

TH-AB-201-10: Portal Dosimetry with Elekta IViewDose:Performance of the Simplified Commissioning Approach Versus Full Commissioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kydonieos, M; Folgueras, A; Florescu, L

2016-06-15

Purpose: Elekta recently developed a solution for in-vivo EPID dosimetry (iViewDose, Elekta AB, Stockholm, Sweden) in conjunction with the Netherlands Cancer Institute (NKI). This uses a simplified commissioning approach via Template Commissioning Models (TCMs), consisting of a subset of linac-independent pre-defined parameters. This work compares the performance of iViewDose using a TCM commissioning approach with that corresponding to full commissioning. Additionally, the dose reconstruction based on the simplified commissioning approach is validated via independent dose measurements. Methods: Measurements were performed at the NKI on a VersaHD™ (Elekta AB, Stockholm, Sweden). Treatment plans were generated with Pinnacle 9.8 (Philips Medical Systems,more » Eindhoven, The Netherlands). A farmer chamber dose measurement and two EPID images were used to create a linac-specific commissioning model based on a TCM. A complete set of commissioning measurements was collected and a full commissioning model was created.The performance of iViewDose based on the two commissioning approaches was compared via a series of set-to-work tests in a slab phantom. In these tests, iViewDose reconstructs and compares EPID to TPS dose for square fields, IMRT and VMAT plans via global gamma analysis and isocentre dose difference. A clinical VMAT plan was delivered to a homogeneous Octavius 4D phantom (PTW, Freiburg, Germany). Dose was measured with the Octavius 1500 array and VeriSoft software was used for 3D dose reconstruction. EPID images were acquired. TCM-based iViewDose and 3D Octavius dose distributions were compared against the TPS. Results: For both the TCM-based and the full commissioning approaches, the pass rate, mean γ and dose difference were >97%, <0.5 and <2.5%, respectively. Equivalent gamma analysis results were obtained for iViewDose (TCM approach) and Octavius for a VMAT plan. Conclusion: iViewDose produces similar results with the simplified and full commissioning approaches. Good agreement is obtained between iViewDose (simplified approach) and the independent measurement tool. This research is funded by Elekta Limited.« less

WE-D-BRA-03: Four-Dimensional Dose Reconstruction Through Retrospective Phase Determination Using Cine Images of Electronic Portal Imaging Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, J; Jung, J; Yi, B

2015-06-15

Purpose: To test a method to reconstruct a four-dimensional (4D) dose distribution using the correlation of pre-calculated 4D electronic portal imaging device (EPID) images and measured cine-EPID images. Methods: 1. A phantom designed to simulate a tumor in lung (a polystyrene block with 3.0 cm diameter embedded in cork) was placed on a sinusoidally moving platform with 2 cm amplitude and 4 sec/cycle. Ten-phase 4D CT images were acquired for treatment planning and dose reconstruction. A 6MV photon beam was irradiated on the phantom with static (field size=5×8.5 cm{sup 2}) and dynamic fields (sliding windows, 10×10 cm{sup 2}, X1 MLCmore » closing in parallel with the tumor movement). 2. 4D and 3D doses were calculated forwardly on PTV (1 cm margin). 3. Dose images on EPID under the fields were calculated for 10 phases. 4. Cine EPID images were acquired during irradiation. 5. Their acquisition times were correlated to the phases of the phantom at which irradiation occurred by inter-comparing calculated “reference” EPID images with measured images (2D gamma comparison). For the dynamic beam, the tumor was hidden under MLCs during a portion of irradiation time; the correlation performed when the tumor was visible was extrapolated. 6. Dose for each phase was reconstructed on the 4D CT images and summed over all phases. The summation was compared with forwardly calculated 4D and 3D dose distributions. Monte Carlo methods were used for all calculations. Results: For the open and dynamic beams, the 4D reconstructed doses showed the pass rates of 92.7 % and 100 %, respectively, at the isocenter plane given 3% / 3 mm criteria. The better agreement of the dynamic beam was from its dose gradient which blurred the otherwise sharp difference between forward and reconstructed doses. This also contributed slightly better agreement in DVH of PTV. Conclusion: The feasibility of 4D reconstruction was demonstrated.« less

Feasibility study on the verification of actual beam delivery in a treatment room using EPID transit dosimetry.

PubMed

Baek, Tae Seong; Chung, Eun Ji; Son, Jaeman; Yoon, Myonggeun

2014-12-04

The aim of this study is to evaluate the ability of transit dosimetry using commercial treatment planning system (TPS) and an electronic portal imaging device (EPID) with simple calibration method to verify the beam delivery based on detection of large errors in treatment room. Twenty four fields of intensity modulated radiotherapy (IMRT) plans were selected from four lung cancer patients and used in the irradiation of an anthropomorphic phantom. The proposed method was evaluated by comparing the calculated dose map from TPS and EPID measurement on the same plane using a gamma index method with a 3% dose and 3 mm distance-to-dose agreement tolerance limit. In a simulation using a homogeneous plastic water phantom, performed to verify the effectiveness of the proposed method, the average passing rate of the transit dose based on gamma index was high enough, averaging 94.2% when there was no error during beam delivery. The passing rate of the transit dose for 24 IMRT fields was lower with the anthropomorphic phantom, averaging 86.8% ± 3.8%, a reduction partially due to the inaccuracy of TPS calculations for inhomogeneity. Compared with the TPS, the absolute value of the transit dose at the beam center differed by -0.38% ± 2.1%. The simulation study indicated that the passing rate of the gamma index was significantly reduced, to less than 40%, when a wrong field was erroneously irradiated to patient in the treatment room. This feasibility study suggested that transit dosimetry based on the calculation with commercial TPS and EPID measurement with simple calibration can provide information about large errors for treatment beam delivery.

SU-E-T-364: 6X FFF and 10X FFF Portal Dosimetry Output Factor Verification: Application for SRS/SBRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulam, M; Bellon, M; Gopal, A

2014-06-01

Purpose: To enhance portal dosimetry of high dose rate SRS/SBRT plan verifications with extensive imager measurement of output factors (OF). Methods: Electronic portal image dosimetry (EPID), implemented on the Varian Edge allows for acquisition of its two energies: 6X FFF and 10 FFF (1400 and 2400 MU/min, respectively) at source to imager distance (SID) =100cm without imager saturation. Square and rectangular aSi OF following EPID calibration were obtained. Data taken was similar to that obtained during beam commissioning (of almost all field sizes from 1×1 to 15×15 and 20×20 cm{sup 2}, [Trilogy] and [Edge], respectively) to construct a table usingmore » the OF tool for use in the Portal Dosimetry Prediction Algorithm (PDIP v11). The Trilogy 6x SRS 1000 MU/min EPID data were taken at 140 SID. The large number of OF were obtained for comparison to that obtained with diode detectors and ion chambers (cc13 for >3×3 field size). As Edge PDIP verification is currently ongoing, EPID measurements of three SRS/SBRT plans for the Trilogy were taken and compared to results obtained prior to these measurements. Results: The relative difference output factors of field sizes 2×2 and higher compared to commissioning data were (mean+/-SD, [range]): Edge 6X (−1.9+/−2.9%, [−5.9%,3.1%]), Edge 10X (−0.7+/−1.2%, [− 3.3%,0.8%] and Trilogy (0.03+/−0.5%, [−1.4%,1.1%]) with EPID over predicting. The results for the 140 SID showed excellent agreement throughout except at the 1×1 to 1×15 and 15×1 field sizes where differences were: −10.6%, −6.0% and −5.8%. The differences were also most pronounced for the 1×1 at 100 SID. They were −7.4% and −11.5% for 6X and 10X, respectively. The Gamma (3%, 1mm) for three clinical plans improved by 8.7+/−1.8%. Conclusion: Results indicate that imager output factor measurements at any SID of high dose rate SRS/SBRT are quite reliable for portal dosimetry plan verification except for the smallest fields. This work was not funded by Varian Oncology Systems. Some authors have other work partly funded by Varian Oncology Systems.« less

TH-CD-207A-02: Implementation of Live EPID-Based Inspiration Level Assessment (LEILA) for Deepinspiration Breath-Hold (DIBH) Monitoring Using MV Fluoroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, J; The University of Sydney, Sydney; The University of Newcastle, Newcastle

Purpose: As prior work has shown that current DIBH monitoring approaches using surrogate measures (marker block on chest) do not always correspond with the clinical quantity of interest (lung depth, LD), a software tool and workflow are introduced to use MV fluoroscopy during treatment for real-time / Live EPID-based Inspiration Level Assessment (LEILA). Methods: A prototype software tool calculates and displays the LD during the treatment of left sided breast cancer. Calculations are based on MV cine images which are acquired with the treatment beam thereby not incurring any additional imaging dose. Image capture and processing are implemented using amore » dedicated frame grabber computer. The calculation engine automatically detects image orientation and includes provisions for large treatment fields that exceed the size of the EPID panel. LD is measured along a line profile in the middle of the field. LEILA’s interface displays the current MV image, a reference image (DRR), the current LD, as well as a trace of LD over treatment time. The display includes patient specific LD tolerances. Tolerances are specified for each field and loaded before the treatment. A visual warning is generated when the tolerance is exceeded. LEILA is initially run in parallel with current DIBH techniques. When later run by itself DIBH setup will be done using skin marks and room laser. Results: Offline tests of LEILA confirmed accurate automatic LD measurement for a variety of patient geometries. Deployment of the EPID during all left sided breast treatments was well tolerated by patients and staff during a multi-month pilot. The frame grabber provides 11 frames-per-second; the MATLAB based LEILA prototype software can analyze five frames-per-second standalone on standard desktop hardware. Conclusion: LEILA provides an automated approach to quantitatively monitor LD on MV images during DIBH treatment. Future improvements include a database and further speed optimization.« less

TU-FG-201-01: 18-Month Clinical Experience of a Linac Daily Quality Assurance (QA) Solution Using Only EPID and OBI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, B; Sun, B; Yaddanapudi, S

Purpose: To describe the clinical use of a Linear Accelerator (Linac) DailyQA system with only EPID and OBI. To assess the reliability over an 18-month period and improve the robustness of this system based on QA failure analysis. Methods: A DailyQA solution utilizing an in-house designed phantom, combined EPID and OBI image acquisitions, and a web-based data analysis and reporting system was commissioned and used in our clinic to measure geometric, dosimetry and imaging components of a Varian Truebeam Linac. During an 18-month period (335 working days), the Daily QA results, including the output constancy, beam flatness and symmetry, uniformity,more » TPR20/10, MV and KV imaging quality, were collected and analyzed. For output constancy measurement, an independent monthly QA system with an ionization chamber (IC) and annual/incidental TG51 measurements with ADCL IC were performed and cross-compared to Daily QA system. Thorough analyses were performed on the recorded QA failures to evaluate the machine performance, optimize the data analysis algorithm, adjust the tolerance setting and improve the training procedure to prevent future failures. Results: A clinical workflow including beam delivery, data analysis, QA report generation and physics approval was established and optimized to suit daily clinical operation. The output tests over the 335 working day period cross-correlated with the monthly QA system within 1.3% and TG51 results within 1%. QA passed with one attempt on 236 days out of 335 days. Based on the QA failures analysis, the Gamma criteria is revised from (1%, 1mm) to (2%, 1mm) considering both QA accuracy and efficiency. Data analysis algorithm is improved to handle multiple entries for a repeating test. Conclusion: We described our 18-month clinical experience on a novel DailyQA system using only EPID and OBI. The long term data presented demonstrated the system is suitable and reliable for Linac daily QA.« less

Comparison of forward- and back-projection in vivo EPID dosimetry for VMAT treatment of the prostate

NASA Astrophysics Data System (ADS)

Bedford, James L.; Hanson, Ian M.; Hansen, Vibeke N.

2018-01-01

In the forward-projection method of portal dosimetry for volumetric modulated arc therapy (VMAT), the integrated signal at the electronic portal imaging device (EPID) is predicted at the time of treatment planning, against which the measured integrated image is compared. In the back-projection method, the measured signal at each gantry angle is back-projected through the patient CT scan to give a measure of total dose to the patient. This study aims to investigate the practical agreement between the two types of EPID dosimetry for prostate radiotherapy. The AutoBeam treatment planning system produced VMAT plans together with corresponding predicted portal images, and a total of 46 sets of gantry-resolved portal images were acquired in 13 patients using an iViewGT portal imager. For the forward-projection method, each acquisition of gantry-resolved images was combined into a single integrated image and compared with the predicted image. For the back-projection method, iViewDose was used to calculate the dose distribution in the patient for comparison with the planned dose. A gamma index for 3% and 3 mm was used for both methods. The results were investigated by delivering the same plans to a phantom and repeating some of the deliveries with deliberately introduced errors. The strongest agreement between forward- and back-projection methods is seen in the isocentric intensity/dose difference, with moderate agreement in the mean gamma. The strongest correlation is observed within a given patient, with less correlation between patients, the latter representing the accuracy of prediction of the two methods. The error study shows that each of the two methods has its own distinct sensitivity to errors, but that overall the response is similar. The forward- and back-projection EPID dosimetry methods show moderate agreement in this series of prostate VMAT patients, indicating that both methods can contribute to the verification of dose delivered to the patient.

Software tool for portal dosimetry research.

PubMed

Vial, P; Hunt, P; Greer, P B; Oliver, L; Baldock, C

2008-09-01

This paper describes a software tool developed for research into the use of an electronic portal imaging device (EPID) to verify dose for intensity modulated radiation therapy (IMRT) beams. A portal dose image prediction (PDIP) model that predicts the EPID response to IMRT beams has been implemented into a commercially available treatment planning system (TPS). The software tool described in this work was developed to modify the TPS PDIP model by incorporating correction factors into the predicted EPID image to account for the difference in EPID response to open beam radiation and multileaf collimator (MLC) transmitted radiation. The processes performed by the software tool include; i) read the MLC file and the PDIP from the TPS, ii) calculate the fraction of beam-on time that each point in the IMRT beam is shielded by MLC leaves, iii) interpolate correction factors from look-up tables, iv) create a corrected PDIP image from the product of the original PDIP and the correction factors and write the corrected image to file, v) display, analyse, and export various image datasets. The software tool was developed using the Microsoft Visual Studio.NET framework with the C# compiler. The operation of the software tool was validated. This software provided useful tools for EPID dosimetry research, and it is being utilised and further developed in ongoing EPID dosimetry and IMRT dosimetry projects.

Automatic detection of MLC relative position errors for VMAT using the EPID-based picket fence test

NASA Astrophysics Data System (ADS)

Christophides, Damianos; Davies, Alex; Fleckney, Mark

2016-12-01

Multi-leaf collimators (MLCs) ensure the accurate delivery of treatments requiring complex beam fluences like intensity modulated radiotherapy and volumetric modulated arc therapy. The purpose of this work is to automate the detection of MLC relative position errors  ⩾0.5 mm using electronic portal imaging device-based picket fence tests and compare the results to the qualitative assessment currently in use. Picket fence tests with and without intentional MLC errors were measured weekly on three Varian linacs. The picket fence images analysed covered a time period ranging between 14-20 months depending on the linac. An algorithm was developed that calculated the MLC error for each leaf-pair present in the picket fence images. The baseline error distributions of each linac were characterised for an initial period of 6 months and compared with the intentional MLC errors using statistical metrics. The distributions of median and one-sample Kolmogorov-Smirnov test p-value exhibited no overlap between baseline and intentional errors and were used retrospectively to automatically detect MLC errors in routine clinical practice. Agreement was found between the MLC errors detected by the automatic method and the fault reports during clinical use, as well as interventions for MLC repair and calibration. In conclusion the method presented provides for full automation of MLC quality assurance, based on individual linac performance characteristics. The use of the automatic method has been shown to provide early warning for MLC errors that resulted in clinical downtime.

SU-G-BRA-06: Quantification of Tracking Performance of a Multi-Layer Electronic Portal Imaging Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Y; Rottmann, J; Myronakis, M

2016-06-15

Purpose: The purpose of this study was to quantify the improvement in tumor tracking, with and without fiducial markers, afforded by employing a multi-layer (MLI) electronic portal imaging device (EPID) over the current state-of-the-art, single-layer, digital megavolt imager (DMI) architecture. Methods: An ideal observer signal-to-noise ratio (d’) approach was used to quantify the ability of an MLI EPID and a current, state-of-the-art DMI EPID to track lung tumors from the treatment beam’s-eye-view. Using each detector modulation transfer function (MTF) and noise power spectrum (NPS) as inputs, a detection task was employed with object functions describing simple three-dimensional Cartesian shapes (spheresmore » and cylinders). Marker-less tumor tracking algorithms often use texture discrimination to differentiate benign and malignant tissue. The performance of such algorithms is simulated by employing a discrimination task for the ideal observer, which measures the ability of a system to differentiate two image quantities. These were defined as the measured textures for benign and malignant lung tissue. Results: The NNPS of the MLI ∼25% of that of the DMI at the expense of decreased MTF at intermediate frequencies (0.25≤« less

Synchronized moving aperture radiation therapy (SMART): superimposing tumor motion on IMRT MLC leaf sequences under realistic delivery conditions

NASA Astrophysics Data System (ADS)

Xu, Jun; Papanikolaou, Nikos; Shi, Chengyu; Jiang, Steve B.

2009-08-01

Synchronized moving aperture radiation therapy (SMART) has been proposed to account for tumor motions during radiotherapy in prior work. The basic idea of SMART is to synchronize the moving radiation beam aperture formed by a dynamic multileaf collimator (DMLC) with the tumor motion induced by respiration. In this paper, a two-dimensional (2D) superimposing leaf sequencing method is presented for SMART. A leaf sequence optimization strategy was generated to assure the SMART delivery under realistic delivery conditions. The study of delivery performance using the Varian LINAC and the Millennium DMLC showed that clinical factors such as collimator angle, dose rate, initial phase and machine tolerance affect the delivery accuracy and efficiency. An in-house leaf sequencing software was developed to implement the 2D superimposing leaf sequencing method and optimize the motion-corrected leaf sequence under realistic clinical conditions. The analysis of dynamic log (Dynalog) files showed that optimization of the leaf sequence for various clinical factors can avoid beam hold-offs which break the synchronization of SMART and fail the SMART dose delivery. Through comparison between the simulated delivered fluence map and the planed fluence map, it was shown that the motion-corrected leaf sequence can greatly reduce the dose error.

Synchronized moving aperture radiation therapy (SMART): superimposing tumor motion on IMRT MLC leaf sequences under realistic delivery conditions.

PubMed

Xu, Jun; Papanikolaou, Nikos; Shi, Chengyu; Jiang, Steve B

2009-08-21

Synchronized moving aperture radiation therapy (SMART) has been proposed to account for tumor motions during radiotherapy in prior work. The basic idea of SMART is to synchronize the moving radiation beam aperture formed by a dynamic multileaf collimator (DMLC) with the tumor motion induced by respiration. In this paper, a two-dimensional (2D) superimposing leaf sequencing method is presented for SMART. A leaf sequence optimization strategy was generated to assure the SMART delivery under realistic delivery conditions. The study of delivery performance using the Varian LINAC and the Millennium DMLC showed that clinical factors such as collimator angle, dose rate, initial phase and machine tolerance affect the delivery accuracy and efficiency. An in-house leaf sequencing software was developed to implement the 2D superimposing leaf sequencing method and optimize the motion-corrected leaf sequence under realistic clinical conditions. The analysis of dynamic log (Dynalog) files showed that optimization of the leaf sequence for various clinical factors can avoid beam hold-offs which break the synchronization of SMART and fail the SMART dose delivery. Through comparison between the simulated delivered fluence map and the planed fluence map, it was shown that the motion-corrected leaf sequence can greatly reduce the dose error.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berry, Sean L., E-mail: BerryS@MSKCC.org; Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York; Polvorosa, Cynthia

Purpose: To prospectively evaluate a 2-dimensional transit dosimetry algorithm's performance on a patient population and to analyze the issues that would arise in a widespread clinical adoption of transit electronic portal imaging device (EPID) dosimetry. Methods and Materials: Eleven patients were enrolled on the protocol; 9 completed and were analyzed. Pretreatment intensity modulated radiation therapy (IMRT) patient-specific quality assurance was performed using a stringent local 3%, 3-mm γ criterion to verify that the planned fluence had been appropriately transferred to and delivered by the linear accelerator. Transit dosimetric EPID images were then acquired during treatment and compared offline with predictedmore » transit images using a global 5%, 3-mm γ criterion. Results: There were 288 transit images analyzed. The overall γ pass rate was 89.1% ± 9.8% (average ± 1 SD). For the subset of images for which the linear accelerator couch did not interfere with the measurement, the γ pass rate was 95.7% ± 2.4%. A case study is presented in which the transit dosimetry algorithm was able to identify that a lung patient's bilateral pleural effusion had resolved in the time between the planning CT scan and the treatment. Conclusions: The EPID transit dosimetry algorithm under consideration, previously described and verified in a phantom study, is feasible for use in treatment delivery verification for real patients. Two-dimensional EPID transit dosimetry can play an important role in indicating when a treatment delivery is inconsistent with the original plan.« less

Use of electronic portal imaging devices for electron treatment verification.

PubMed

Kairn, T; Aland, T; Crowe, S B; Trapp, J V

2016-03-01

This study aims to help broaden the use of electronic portal imaging devices (EPIDs) for pre-treatment patient positioning verification, from photon-beam radiotherapy to photon- and electron-beam radiotherapy, by proposing and testing a method for acquiring clinically-useful EPID images of patient anatomy using electron beams, with a view to enabling and encouraging further research in this area. EPID images used in this study were acquired using all available beams from a linac configured to deliver electron beams with nominal energies of 6, 9, 12, 16 and 20 MeV, as well as photon beams with nominal energies of 6 and 10 MV. A widely-available heterogeneous, approximately-humanoid, thorax phantom was used, to provide an indication of the contrast and noise produced when imaging different types of tissue with comparatively realistic thicknesses. The acquired images were automatically calibrated, corrected for the effects of variations in the sensitivity of individual photodiodes, using a flood field image. For electron beam imaging, flood field EPID calibration images were acquired with and without the placement of blocks of water-equivalent plastic (with thicknesses approximately equal to the practical range of electrons in the plastic) placed upstream of the EPID, to filter out the primary electron beam, leaving only the bremsstrahlung photon signal. While the electron beam images acquired using a standard (unfiltered) flood field calibration were observed to be noisy and difficult to interpret, the electron beam images acquired using the filtered flood field calibration showed tissues and bony anatomy with levels of contrast and noise that were similar to the contrast and noise levels seen in the clinically acceptable photon beam EPID images. The best electron beam imaging results (highest contrast, signal-to-noise and contrast-to-noise ratios) were achieved when the images were acquired using the higher energy electron beams (16 and 20 MeV) when the EPID was calibrated using an intermediate (12 MeV) electron beam energy. These results demonstrate the feasibility of acquiring clinically-useful EPID images of patient anatomy using electron beams and suggest important avenues for future investigation, thus enabling and encouraging further research in this area. There is manifest potential for the EPID imaging method proposed in this work to lead to the clinical use of electron beam imaging for geometric verification of electron treatments in the future.

SU-D-201-06: Remote Dosmetric Auditing of VMAT Deliveries for Clinical Trials Using EPID

DOE Office of Scientific and Technical Information (OSTI.GOV)

Legge, K; Miri, N; Lehmann, J

2016-06-15

Purpose: To develop a method for remote dosimetric auditing the delivery of VMAT using EPID which allows for simple, inexpensive and time efficient dosimetric credentialing for clinical trials. Methods: Remote centers are provided with CT datasets and planning guidelines to produce VMAT plans for a head and neck and a post-prostatectomy treatment. Plans are transferred in the planning system to two virtual water equivalent phantoms, one flat and one cylindrical. Cine images are acquired during VMAT delivery to the EPID in air with gantry angle recorded in image headers. Centers also deliver provided calibration plans to enable EPID signal tomore » dose conversion, determination of the central axis, and correction of EPID sag prior to analysis. EPID images and planned doses are sent to the central site. EPID cine images are converted to dose in the virtual phantoms using an established backprojection method (King et al., Med.Phys. 2012) with EPID backscatter correction. Individual arcs (with gantry angles collapsed to zero) are evaluated at 10 cm depth in the flat phantom using 2D gamma, and total doses are evaluated in the cylindrical phantom using 3D gamma. Results are reported for criteria of 3%,3mm, 3%,2mm and 2%,2mm for all points greater than 10% of global maximum. Results: The pilot study for Varian centers has commenced, and three centers have been audited for head and neck plans and two for post-prostatectomy plans to date. The mean pass rate for arc-by-arc 2D analysis at 3%,3mm is 99.5% and for 3D analysis is 95.8%. A method for Elekta linacs using an inclinometer for gantry angle information is under development. Conclusion: Preliminary results for this new method are promising. The method takes advantage of EPID equipment available at most centers and clinically established software to provide a feasible, low cost solution to credentialing centers for clinical trials. Funding has been provided from Calvary Mater Newcastle Department of Radiation Oncology, TROG Cancer Research and the University of Newcastle. Kimberley Legge is the recipient of an Australian Postgraduate Award. Narges Miri is a recipient of a University of Newcastle postgraduate scholarship.« less

SU-E-T-490: Independent Three-Dimensional (3D) Dose Verification of VMAT/SBRT Using EPID and Cloud Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, A; Han, B; Bush, K

Purpose: Dosimetric verification of VMAT/SBRT is currently performed on one or two planes in a phantom with either film or array detectors. A robust and easy-to-use 3D dosimetric tool has been sought since the advent of conformal radiation therapy. Here we present such a strategy for independent 3D VMAT/SBRT plan verification system by a combined use of EPID and cloud-based Monte Carlo (MC) dose calculation. Methods: The 3D dosimetric verification proceeds in two steps. First, the plan was delivered with a high resolution portable EPID mounted on the gantry, and the EPID-captured gantry-angle-resolved VMAT/SBRT field images were converted into fluencemore » by using the EPID pixel response function derived from MC simulations. The fluence was resampled and used as the input for an in-house developed Amazon cloud-based MC software to reconstruct the 3D dose distribution. The accuracy of the developed 3D dosimetric tool was assessed using a Delta4 phantom with various field sizes (square, circular, rectangular, and irregular MLC fields) and different patient cases. The method was applied to validate VMAT/SBRT plans using WFF and FFF photon beams (Varian TrueBeam STX). Results: It was found that the proposed method yielded results consistent with the Delta4 measurements. For points on the two detector planes, a good agreement within 1.5% were found for all the testing fields. Patient VMAT/SBRT plan studies revealed similar level of accuracy: an average γ-index passing rate of 99.2± 0.6% (3mm/3%), 97.4± 2.4% (2mm/2%), and 72.6± 8.4 % ( 1mm/1%). Conclusion: A valuable 3D dosimetric verification strategy has been developed for VMAT/SBRT plan validation. The technique provides a viable solution for a number of intractable dosimetry problems, such as small fields and plans with high dose gradient.« less

SU-F-SPS-06: Implementation of a Back-Projection Algorithm for 2D in Vivo Dosimetry with An EPID System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez Reyes, B; Rodriguez Perez, E; Sosa Aquino, M

Purpose: To implement a back-projection algorithm for 2D dose reconstructions for in vivo dosimetry in radiation therapy using an Electronic Portal Imaging Device (EPID) based on amorphous silicon. Methods: An EPID system was used to calculate dose-response function, pixel sensitivity map, exponential scatter kernels and beam hardenig correction for the back-projection algorithm. All measurements were done with a 6 MV beam. A 2D dose reconstruction for an irradiated water phantom (30×30×30 cm{sup 3}) was done to verify the algorithm implementation. Gamma index evaluation between the 2D reconstructed dose and the calculated with a treatment planning system (TPS) was done. Results:more » A linear fit was found for the dose-response function. The pixel sensitivity map has a radial symmetry and was calculated with a profile of the pixel sensitivity variation. The parameters for the scatter kernels were determined only for a 6 MV beam. The primary dose was estimated applying the scatter kernel within EPID and scatter kernel within the patient. The beam hardening coefficient is σBH= 3.788×10{sup −4} cm{sup 2} and the effective linear attenuation coefficient is µAC= 0.06084 cm{sup −1}. The 95% of points evaluated had γ values not longer than the unity, with gamma criteria of ΔD = 3% and Δd = 3 mm, and within the 50% isodose surface. Conclusion: The use of EPID systems proved to be a fast tool for in vivo dosimetry, but the implementation is more complex that the elaborated for pre-treatment dose verification, therefore, a simplest method must be investigated. The accuracy of this method should be improved modifying the algorithm in order to compare lower isodose curves.« less

RNA-Sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction

USDA-ARS?s Scientific Manuscript database

Cercospora beticola causes Cercospora leaf spot of sugarbeet. Cercospora leaf spot management measures often include application of the sterol demethylation inhibitor (DMI) class of fungicides. The reliance on DMIs and the consequent selection pressures imposed by their widespread use has led to th...

Feasibility Study for Markerless Tracking of Lung Tumors in Stereotactic Body Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richter, Anne, E-mail: richter_a3@klinik.uni-wuerzburg.d; Wilbert, Juergen; Baier, Kurt

2010-10-01

Purpose: To evaluate the feasibility and accuracy of a method for markerless tracking of lung tumors in electronic portal imaging device (EPID) movies and to analyze intra- and interfractional variations in tumor motion. Methods and Materials: EPID movies were acquired during stereotactic body radiotherapy (SBRT) given to 40 patients with 49 pulmonary targets and retrospectively analyzed. Tumor visibility and tracking accuracy were determined by three observers. Tumor motion of 30 targets was analyzed in detail via four-dimensional computed tomography (4DCT) and EPID in the superior-inferior direction for intra- and interfractional variations. Results: Tumor visibility was sufficient for markerless tracking inmore » 47% of the EPID movies. Tumor size and visibility in the DRR were correlated with visibility in the EPID images. The difference between automatic and manual tracking was a maximum of 2 mm for 98.3% in the x direction and 89.4% in the y direction. Motion amplitudes in 4DCT images (range, 0.7-17.9 mm; median, 4.9 mm) were closely correlated with amplitudes in the EPID movies. Intrafractional and interfractional variability of tumor motion amplitude were of similar magnitude: 1 mm on average to a maximum of 4 mm. A change in moving average of more than {+-}1 mm, {+-}2 mm, and {+-}4 mm were observed in 47.1%, 17.1%, and 4.5% of treatment time for all trajectories, respectively. Mean tumor velocity was 3.4 mm/sec, to a maximum 61 mm/sec. Conclusions: Tracking of pulmonary tumors in EPID images without implanted markers was feasible in 47% of all treatment beams. 4DCT is representative of the evaluation of mean breathing motion on average, but larger deviations occurred in target motion between treatment planning and delivery effort a monitoring during delivery.« less

An in vivo dose verification method for SBRT-VMAT delivery using the EPID.

PubMed

McCowan, P M; Van Uytven, E; Van Beek, T; Asuni, G; McCurdy, B M C

2015-12-01

Radiation treatments have become increasingly more complex with the development of volumetric modulated arc therapy (VMAT) and the use of stereotactic body radiation therapy (SBRT). SBRT involves the delivery of substantially larger doses over fewer fractions than conventional therapy. SBRT-VMAT treatments will strongly benefit from in vivo patient dose verification, as any errors in delivery can be more detrimental to the radiobiology of the patient as compared to conventional therapy. Electronic portal imaging devices (EPIDs) are available on most commercial linear accelerators (Linacs) and their documented use for dosimetry makes them valuable tools for patient dose verification. In this work, the authors customize and validate a physics-based model which utilizes on-treatment EPID images to reconstruct the 3D dose delivered to the patient during SBRT-VMAT delivery. The SBRT Linac head, including jaws, multileaf collimators, and flattening filter, were modeled using Monte Carlo methods and verified with measured data. The simulation provides energy spectrum data that are used by their "forward" model to then accurately predict fluence generated by a SBRT beam at a plane above the patient. This fluence is then transported through the patient and then the dose to the phosphor layer in the EPID is calculated. Their "inverse" model back-projects the EPID measured focal fluence to a plane upstream of the patient and recombines it with the extra-focal fluence predicted by the forward model. This estimate of total delivered fluence is then forward projected onto the patient's density matrix and a collapsed cone convolution algorithm calculates the dose delivered to the patient. The model was tested by reconstructing the dose for two prostate, three lung, and two spine SBRT-VMAT treatment fractions delivered to an anthropomorphic phantom. It was further validated against actual patient data for a lung and spine SBRT-VMAT plan. The results were verified with the treatment planning system (TPS) (ECLIPSE AAA) dose calculation. The SBRT-VMAT reconstruction model performed very well when compared to the TPS. A stringent 2%/2 mm χ-comparison calculation gave pass rates better than 91% for the prostate plans, 88% for the lung plans, and 86% for the spine plans for voxels containing 80% or more of the prescribed dose. Patient data were 86% for the lung and 95% for the spine. A 3%/3 mm χ-comparison was also performed and gave pass rates better than 93% for all plan types. The authors have customized and validated a robust, physics-based model that calculates the delivered dose to a patient for SBRT-VMAT delivery using on-treatment EPID images. The accuracy of the results indicates that this approach is suitable for clinical implementation. Future work will incorporate this model into both offline and real-time clinical adaptive radiotherapy.

Qualitative Evaluation of Fiducial Markers for Radiotherapy Imaging

PubMed Central

Chan, Maria F.; Cohen, Gil’ad N.; Deasy, Joseph O.

2016-01-01

Purpose To evaluate visibility, artifacts, and distortions of various commercial markers in magnetic resonance imaging (MRI), computer tomography (CT), and ultrasound imaging used for radiotherapy planning and treatment guidance. Methods We compare 2 solid gold markers, 4 gold coils, and 1 polymer marker from 3 vendors. Imaging modalities used were 3-T and 1.5-T GE MRIs, Siemens Sequoia 512 Ultrasound, Phillips Big Bore CT, Varian Trilogy linear accelerator (cone-beam CT [CBCT], on-board imager kilovoltage [OBI-kV], electronic portal imaging device megavoltage [EPID-MV]), and Medtronic O-ARM CBCT. Markers were imaged in a 30 × 30 × 10 cm3 custom bolus phantom. In one experiment, Surgilube was used around the markers to reduce air gaps. Images were saved in Digital Imaging and Communications in Medicine (DICOM) format and analyzed using an in-house software. Profiles across the markers were used for objective comparison of the markers’ signals. The visibility and artifacts/distortions produced by each marker were assessed qualitatively and quantitatively. Results All markers are visible in CT, CBCT, OBI-kV, and ultrasound. Gold markers below 0.75 mm in diameter are not visible in EPID-MV images. The larger the markers, the more CT and CBCT image artifacts there are, yet the degree of the artifact depends on scan parameters and the scanner itself. Visibility of gold coils of 0.75 mm diameter or larger is comparable across all imaging modalities studied. The polymer marker causes minimal artifacts in CT and CBCT but has poor visibility in EPID-MV. Gold coils of 0.5 mm exhibit poor visibility in MRI and EPID-MV due to their small size. Gold markers are more visible in 3-T T1 gradient-recalled echo than in 1.5-T T1 fast spin-echo, depending on the scan sequence. In this study, all markers are clearly visible on ultrasound. Conclusion All gold markers are visible in CT, CBCT, kV, and ultrasound; however, only the large diameter markers are visible in MV. When MR and EPID-MV imagers are used, the selection of fiducial markers is not straightforward. For hybrid kV/MV image-guided radiotherapy imaging, larger diameter markers are suggested. If using kV imaging alone, smaller sized markers may be used in smaller sized patients in order to reduce artifacts. Only larger diameter gold markers are visible across all imaging modalities. PMID:25230715

SU-F-T-350: Continuous Leaf Optimization (CLO) for IMRT Leaf Sequencing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, T; Chen, M; Jiang, S

Purpose: To study a new step-and-shoot IMRT leaf sequencing model that avoids the two main pitfalls of conventional leaf sequencing: (1) target fluence being stratified into a fixed number of discrete levels and/or (2) aperture leaf positions being restricted to a discrete set of locations. These assumptions induce error into the sequence or reduce the feasible region of potential plans, respectively. Methods: We develop a one-dimensional (single leaf pair) methodology that does not make assumptions (1) or (2) that can be easily extended to a multi-row model. The proposed continuous leaf optimization (CLO) methodology takes in an existing set ofmore » apertures and associated intensities, or solution “seed,” and improves the plan without the restrictiveness of 1or (2). It then uses a first-order descent algorithm to converge onto a locally optimal solution. A seed solution can come from models that assume (1) and (2), thus allowing the CLO model to improve upon existing leaf sequencing methodologies. Results: The CLO model was applied to 208 generated target fluence maps in one dimension. In all cases for all tested sequencing strategies, the CLO model made improvements on the starting seed objective function. The CLO model also was able to keep MUs low. Conclusion: The CLO model can improve upon existing leaf sequencing methods by avoiding the restrictions of (1) and (2). By allowing for more flexible leaf positioning, error can be reduced when matching some target fluence. This study lays the foundation for future models and solution methodologies that can incorporate continuous leaf positions explicitly into the IMRT treatment planning model. Supported by Cancer Prevention & Research Institute of Texas (CPRIT) - ID RP150485.« less

An initial study on the estimation of time-varying volumetric treatment images and 3D tumor localization from single MV cine EPID images

PubMed Central

Mishra, Pankaj; Li, Ruijiang; Mak, Raymond H.; Rottmann, Joerg; Bryant, Jonathan H.; Williams, Christopher L.; Berbeco, Ross I.; Lewis, John H.

2014-01-01

Purpose: In this work the authors develop and investigate the feasibility of a method to estimate time-varying volumetric images from individual MV cine electronic portal image device (EPID) images. Methods: The authors adopt a two-step approach to time-varying volumetric image estimation from a single cine EPID image. In the first step, a patient-specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient-specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculated through deformable image registration (DIR) of a reference 4DCT phase image (typically peak-exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen-coefficients. To generate a new volumetric image, the eigen-coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen-coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image. Results: The algorithm was tested on (1) Eight digital eXtended CArdiac-Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root-mean-squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data. Conclusions: The authors introduced a novel method of estimating volumetric time-varying images from single cine EPID images and a PCA-based lung motion model. This is the first method to estimate volumetric time-varying images from single MV cine EPID images, and has the potential to provide volumetric information with no additional imaging dose to the patient. PMID:25086523

An initial study on the estimation of time-varying volumetric treatment images and 3D tumor localization from single MV cine EPID images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Pankaj, E-mail: pankaj.mishra@varian.com; Mak, Raymond H.; Rottmann, Joerg

2014-08-15

Purpose: In this work the authors develop and investigate the feasibility of a method to estimate time-varying volumetric images from individual MV cine electronic portal image device (EPID) images. Methods: The authors adopt a two-step approach to time-varying volumetric image estimation from a single cine EPID image. In the first step, a patient-specific motion model is constructed from 4DCT. In the second step, parameters in the motion model are tuned according to the information in the EPID image. The patient-specific motion model is based on a compact representation of lung motion represented in displacement vector fields (DVFs). DVFs are calculatedmore » through deformable image registration (DIR) of a reference 4DCT phase image (typically peak-exhale) to a set of 4DCT images corresponding to different phases of a breathing cycle. The salient characteristics in the DVFs are captured in a compact representation through principal component analysis (PCA). PCA decouples the spatial and temporal components of the DVFs. Spatial information is represented in eigenvectors and the temporal information is represented by eigen-coefficients. To generate a new volumetric image, the eigen-coefficients are updated via cost function optimization based on digitally reconstructed radiographs and projection images. The updated eigen-coefficients are then multiplied with the eigenvectors to obtain updated DVFs that, in turn, give the volumetric image corresponding to the cine EPID image. Results: The algorithm was tested on (1) Eight digital eXtended CArdiac-Torso phantom datasets based on different irregular patient breathing patterns and (2) patient cine EPID images acquired during SBRT treatments. The root-mean-squared tumor localization error is (0.73 ± 0.63 mm) for the XCAT data and (0.90 ± 0.65 mm) for the patient data. Conclusions: The authors introduced a novel method of estimating volumetric time-varying images from single cine EPID images and a PCA-based lung motion model. This is the first method to estimate volumetric time-varying images from single MV cine EPID images, and has the potential to provide volumetric information with no additional imaging dose to the patient.« less

SU-G-JeP1-08: Dual Modality Verification for Respiratory Gating Using New Real- Time Tumor Tracking Radiotherapy System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shiinoki, T; Hanazawa, H; Shibuya, K

Purpose: The respirato ry gating system combined the TrueBeam and a new real-time tumor-tracking radiotherapy system (RTRT) was installed. The RTRT system consists of two x-ray tubes and color image intensifiers. Using fluoroscopic images, the fiducial marker which was implanted near the tumor was tracked and was used as the internal surrogate for respiratory gating. The purposes of this study was to develop the verification technique of the respiratory gating with the new RTRT using cine electronic portal image device images (EPIDs) of TrueBeam and log files of the RTRT. Methods: A patient who underwent respiratory gated SBRT of themore » lung using the RTRT were enrolled in this study. For a patient, the log files of three-dimensional coordinate of fiducial marker used as an internal surrogate were acquired using the RTRT. Simultaneously, the cine EPIDs were acquired during respiratory gated radiotherapy. The data acquisition was performed for one field at five sessions during the course of SBRT. The residual motion errors were calculated using the log files (E{sub log}). The fiducial marker used as an internal surrogate into the cine EPIDs was automatically extracted by in-house software based on the template-matching algorithm. The differences between the the marker positions of cine EPIDs and digitally reconstructed radiograph were calculated (E{sub EPID}). Results: Marker detection on EPID using in-house software was influenced by low image contrast. For one field during the course of SBRT, the respiratory gating using the RTRT showed the mean ± S.D. of 95{sup th} percentile E{sub EPID} were 1.3 ± 0.3 mm,1.1 ± 0.5 mm,and those of E{sub log} were 1.5 ± 0.2 mm, 1.1 ± 0.2 mm in LR and SI directions, respectively. Conclusion: We have developed the verification method of respiratory gating combined TrueBeam and new real-time tumor-tracking radiotherapy system using EPIDs and log files.« less

Rapid portal imaging with a high-efficiency, large field-of-view detector.

PubMed

Mosleh-Shirazi, M A; Evans, P M; Swindell, W; Symonds-Tayler, J R; Webb, S; Partridge, M

1998-12-01

The design, construction, and performance evaluation of an electronic portal imaging device (EPID) are described. The EPID has the same imaging geometry as the current mirror-based systems except for the x-ray detection stage, where a two-dimensional (2D) array of 1 cm thick CsI(Tl) detector elements are utilized. The approximately 18% x-ray quantum efficiency of the scintillation detector and its 30 x 40 cm2 field-of-view at the isocenter are greater than other area-imaging EPIDs. The imaging issues addressed are theoretical and measured signal-to-noise ratio, linearity of the imaging chain, influence of frame-summing on image quality and image calibration. Portal images of test objects and a humanoid phantom are used to measure the performance of the system. An image quality similar to the current devices is achieved but with a lower dose. With approximately 1 cGy dose delivered by a 6 MV beam, a 2 mm diam structure of 1.3% contrast and an 18 mm diam object of 0.125% contrast can be resolved without using image-enhancement methods. A spatial resolution of about 2 mm at the isocenter is demonstrated. The capability of the system to perform fast sequential imaging, synchronized with the radiation pulses, makes it suitable for patient motion studies and verification of intensity-modulated beams as well as its application in cone-beam megavoltage computed tomography.

SU-C-BRD-07: Three-Dimensional Dose Reconstruction in the Presence of Inhomogeneities Using Fast EPID-Based Back-Projection Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Q; Cao, R; Pei, X

2015-06-15

Purpose: Three-dimensional dose verification can detect errors introduced by the treatment planning system (TPS) or differences between planned and delivered dose distribution during the treatment. The aim of the study is to extend a previous in-house developed three-dimensional dose reconstructed model in homogeneous phantom to situtions in which tissue inhomogeneities are present. Methods: The method was based on the portal grey images from an electronic portal imaging device (EPID) and the relationship between beamlets and grey-scoring voxels at the position of the EPID. The relationship was expressed in the form of grey response matrix that was quantified using thickness-dependence scattermore » kernels determined by series of experiments. From the portal grey-value distribution information measured by the EPID the two-dimensional incident fluence distribution was reconstructed based on the grey response matrix using a fast iterative algorithm. The accuracy of this approach was verified using a four-field intensity-modulated radiotherapy (IMRT) plan for the treatment of lung cancer in anthopomorphic phantom. Each field had between twenty and twenty-eight segments and was evaluated by comparing the reconstructed dose distribution with the measured dose. Results: The gamma-evaluation method was used with various evaluation criteria of dose difference and distance-to-agreement: 3%/3mm and 2%/2 mm. The dose comparison for all irradiated fields showed a pass rate of 100% with the criterion of 3%/3mm, and a pass rate of higher than 92% with the criterion of 2%/2mm. Conclusion: Our experimental results demonstrate that our method is capable of accurately reconstructing three-dimensional dose distribution in the presence of inhomogeneities. Using the method, the combined planning and treatment delivery process is verified, offing an easy-to-use tool for the verification of complex treatments.« less

SU-F-J-114: On-Treatment Imagereconstruction Using Transit Images of Treatment Beams Through Patient and Thosethrough Planning CT Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, H; Cho, S; Cheong, K

Purpose: To reconstruct patient images at the time of radiation delivery using measured transit images of treatment beams through patient and calculated transit images through planning CT images. Methods: We hypothesize that the ratio of the measured transit images to the calculated images may provide changed amounts of the patient image between times of planning CT and treatment. To test, we have devised lung phantoms with a tumor object (3-cm diameter) placed at iso-center (simulating planning CT) and off-center by 1 cm (simulating treatment). CT images of the two phantoms were acquired; the image of the off-centered phantom, unavailable clinically,more » represents the reference on-treatment image in the image quality of planning CT. Cine-transit images through the two phantoms were also acquired in EPID from a non-modulated 6 MV beam when the gantry was rotated 360 degrees; the image through the centered phantom simulates calculated image. While the current study is a feasibility study, in reality our computational EPID model can be applicable in providing accurate transit image from MC simulation. Changed MV HU values were reconstructed from the ratio between two EPID projection data, converted to KV HU values, and added to the planning CT, thereby reconstructing the on-treatment image of the patient limited to the irradiated region of the phantom. Results: The reconstructed image was compared with the reference image. Except for local HU differences>200 as a maximum, excellent agreement was found. The average difference across the entire image was 16.2 HU. Conclusion: We have demonstrated the feasibility of a method of reconstructing on-treatment images of a patient using EPID image and planning CT images. Further studies will include resolving the local HU differences and investigation on the dosimetry impact of the reconstructed image.« less

Clinical Experience and Evaluation of Patient Treatment Verification With a Transit Dosimeter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ricketts, Kate, E-mail: k.ricketts@ucl.ac.uk; Department of Radiotherapy Physics, Royal Berkshire NHS Foundation Trust, Reading; Navarro, Clara

2016-08-01

Purpose: To prospectively evaluate a protocol for transit dosimetry on a patient population undergoing intensity modulated radiation therapy (IMRT) and to assess the issues in clinical implementation of electronic portal imaging devices (EPIDs) for treatment verification. Methods and Materials: Fifty-eight patients were enrolled in the study. Amorphous silicon EPIDs were calibrated for dose and used to acquire images of delivered fields. Measured EPID dose maps were back-projected using the planning computed tomographic (CT) images to calculate dose at prespecified points within the patient and compared with treatment planning system dose offline using point dose difference and point γ analysis. Themore » deviation of the results was used to inform future action levels. Results: Two hundred twenty-five transit images were analyzed, composed of breast, prostate, and head and neck IMRT fields. Patient measurements demonstrated the potential of the dose verification protocol to model dose well under complex conditions: 83.8% of all delivered beams achieved the initial set tolerance level of Δ{sub D} of 0 ± 5 cGy or %Δ{sub D} of 0% ± 5%. Importantly, the protocol was also sensitive to anatomic changes and spotted that 3 patients from 20 measured prostate patients had undergone anatomic change in comparison with the planning CT. Patient data suggested an EPID-reconstructed versus treatment planning system dose difference action level of 0% ± 7% for breast fields. Asymmetric action levels were more appropriate for inversed IMRT fields, using absolute dose difference (−2 ± 5 cGy) or summed field percentage dose difference (−6% ± 7%). Conclusions: The in vivo dose verification method was easy to use and simple to implement, and it could detect patient anatomic changes that impacted dose delivery. The system required no extra dose to the patient or treatment time delay and so could be used throughout the course of treatment to identify and limit systematic and random errors in dose delivery for patient groups.« less

Clinical Experience and Evaluation of Patient Treatment Verification With a Transit Dosimeter.

PubMed

Ricketts, Kate; Navarro, Clara; Lane, Katherine; Blowfield, Claire; Cotten, Gary; Tomala, Dee; Lord, Christine; Jones, Joanne; Adeyemi, Abiodun

2016-08-01

To prospectively evaluate a protocol for transit dosimetry on a patient population undergoing intensity modulated radiation therapy (IMRT) and to assess the issues in clinical implementation of electronic portal imaging devices (EPIDs) for treatment verification. Fifty-eight patients were enrolled in the study. Amorphous silicon EPIDs were calibrated for dose and used to acquire images of delivered fields. Measured EPID dose maps were back-projected using the planning computed tomographic (CT) images to calculate dose at prespecified points within the patient and compared with treatment planning system dose offline using point dose difference and point γ analysis. The deviation of the results was used to inform future action levels. Two hundred twenty-five transit images were analyzed, composed of breast, prostate, and head and neck IMRT fields. Patient measurements demonstrated the potential of the dose verification protocol to model dose well under complex conditions: 83.8% of all delivered beams achieved the initial set tolerance level of ΔD of 0 ± 5 cGy or %ΔD of 0% ± 5%. Importantly, the protocol was also sensitive to anatomic changes and spotted that 3 patients from 20 measured prostate patients had undergone anatomic change in comparison with the planning CT. Patient data suggested an EPID-reconstructed versus treatment planning system dose difference action level of 0% ± 7% for breast fields. Asymmetric action levels were more appropriate for inversed IMRT fields, using absolute dose difference (-2 ± 5 cGy) or summed field percentage dose difference (-6% ± 7%). The in vivo dose verification method was easy to use and simple to implement, and it could detect patient anatomic changes that impacted dose delivery. The system required no extra dose to the patient or treatment time delay and so could be used throughout the course of treatment to identify and limit systematic and random errors in dose delivery for patient groups. Copyright © 2016 Elsevier Inc. All rights reserved.

Lifetime return on investment increases with leaf lifespan among 10 Australian woodland species.

PubMed

Falster, Daniel S; Reich, Peter B; Ellsworth, David S; Wright, Ian J; Westoby, Mark; Oleksyn, Jacek; Lee, Tali D

2012-01-01

• Co-occurring species often differ in their leaf lifespan (LL) and it remains unclear how such variation is maintained in a competitive context. Here we test the hypothesis that leaves of long-LL species yield a greater return in carbon (C) fixed per unit C or nutrient invested by the plant than those of short-LL species. • For 10 sympatric woodland species, we assessed three-dimensional shoot architecture, canopy openness, leaf photosynthetic light response, leaf dark respiration and leaf construction costs across leaf age sequences. We then used the YPLANT model to estimate light interception and C revenue along the measured leaf age sequences. This was done under a series of simulations that incorporated the potential covariates of LL in an additive fashion. • Lifetime return in C fixed per unit C, N or P invested increased with LL in all simulations. • In contrast to other recent studies, our results show that extended LL confers a fundamental economic advantage by increasing a plant's return on investment in leaves. This suggests that time-discounting effects, that is, the compounding of income that arises from quick reinvestment of C revenue, are key in allowing short-LL species to succeed in the face of this economic handicap. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Frame average optimization of cine-mode EPID images used for routine clinical in vivo patient dose verification of VMAT deliveries

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCowan, P. M., E-mail: pmccowan@cancercare.mb.ca; McCurdy, B. M. C.; Medical Physics Department, CancerCare Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba R3E 0V9

Purpose: The in vivo 3D dose delivered to a patient during volumetric modulated arc therapy (VMAT) delivery can be calculated using electronic portal imaging device (EPID) images. These images must be acquired in cine-mode (i.e., “movie” mode) in order to capture the time-dependent delivery information. The angle subtended by each cine-mode EPID image during an arc can be changed via the frame averaging number selected within the image acquisition software. A large frame average number will decrease the EPID’s angular resolution and will result in a decrease in the accuracy of the dose information contained within each image. Alternatively, lessmore » EPID images acquired per delivery will decrease the overall 3D patient dose calculation time, which is appealing for large-scale clinical implementation. Therefore, the purpose of this study was to determine the optimal frame average value per EPID image, defined as the highest frame averaging that can be used without an appreciable loss in 3D dose reconstruction accuracy for VMAT treatments. Methods: Six different VMAT plans and six different SBRT-VMAT plans were delivered to an anthropomorphic phantom. Delivery was carried out on a Varian 2300ix model linear accelerator (Linac) equipped with an aS1000 EPID running at a frame acquisition rate of 7.5 Hz. An additional PC was set up at the Linac console area, equipped with specialized frame-grabber hardware and software packages allowing continuous acquisition of all EPID frames during delivery. Frames were averaged into “frame-averaged” EPID images using MATLAB. Each frame-averaged data set was used to calculate the in vivo dose to the patient and then compared to the single EPID frame in vivo dose calculation (the single frame calculation represents the highest possible angular resolution per EPID image). A mean percentage dose difference of low dose (<20% prescription dose) and high dose regions (>80% prescription dose) was calculated for each frame averaged scenario for each plan. The authors defined their unacceptable loss of accuracy as no more than a ±1% mean dose difference in the high dose region. Optimal frame average numbers were then determined as a function of the Linac’s average gantry speed and the dose per fraction. Results: The authors found that 9 and 11 frame averages were suitable for all VMAT and SBRT-VMAT treatments, respectively. This resulted in no more than a 1% loss to any of the dose region’s mean percentage difference when compared to the single frame reconstruction. The optimized number was dependent on the treatment’s dose per fraction and was determined to be as high as 14 for 12 Gy/fraction (fx), 15 for 8 Gy/fx, 11 for 6 Gy/fx, and 9 for 2 Gy/fx. Conclusions: The authors have determined an optimal EPID frame averaging number for multiple VMAT-type treatments. These are given as a function of the dose per fraction and average gantry speed. These optimized values are now used in the authors’ clinical, 3D, in vivo patient dosimetry program. This provides a reduction in calculation time while maintaining the authors’ required level of accuracy in the dose reconstruction.« less

A novel method for patient exit and entrance dose prediction based on water equivalent path length measured with an amorphous silicon electronic portal imaging device.

PubMed

Kavuma, Awusi; Glegg, Martin; Metwaly, Mohamed; Currie, Garry; Elliott, Alex

2010-01-21

In vivo dosimetry is one of the quality assurance tools used in radiotherapy to monitor the dose delivered to the patient. Electronic portal imaging device (EPID) images for a set of solid water phantoms of varying thicknesses were acquired and the data fitted onto a quadratic equation, which relates the reduction in photon beam intensity to the attenuation coefficient and material thickness at a reference condition. The quadratic model is used to convert the measured grey scale value into water equivalent path length (EPL) at each pixel for any material imaged by the detector. For any other non-reference conditions, scatter, field size and MU variation effects on the image were corrected by relative measurements using an ionization chamber and an EPID. The 2D EPL is linked to the percentage exit dose table, for different thicknesses and field sizes, thereby converting the plane pixel values at each point into a 2D dose map. The off-axis ratio is corrected using envelope and boundary profiles generated from the treatment planning system (TPS). The method requires field size, monitor unit and source-to-surface distance (SSD) as clinical input parameters to predict the exit dose, which is then used to determine the entrance dose. The measured pixel dose maps were compared with calculated doses from TPS for both entrance and exit depth of phantom. The gamma index at 3% dose difference (DD) and 3 mm distance to agreement (DTA) resulted in an average of 97% passing for the square fields of 5, 10, 15 and 20 cm. The exit dose EPID dose distributions predicted by the algorithm were in better agreement with TPS-calculated doses than phantom entrance dose distributions.

A novel method for patient exit and entrance dose prediction based on water equivalent path length measured with an amorphous silicon electronic portal imaging device

NASA Astrophysics Data System (ADS)

Kavuma, Awusi; Glegg, Martin; Metwaly, Mohamed; Currie, Garry; Elliott, Alex

2010-01-01

In vivo dosimetry is one of the quality assurance tools used in radiotherapy to monitor the dose delivered to the patient. Electronic portal imaging device (EPID) images for a set of solid water phantoms of varying thicknesses were acquired and the data fitted onto a quadratic equation, which relates the reduction in photon beam intensity to the attenuation coefficient and material thickness at a reference condition. The quadratic model is used to convert the measured grey scale value into water equivalent path length (EPL) at each pixel for any material imaged by the detector. For any other non-reference conditions, scatter, field size and MU variation effects on the image were corrected by relative measurements using an ionization chamber and an EPID. The 2D EPL is linked to the percentage exit dose table, for different thicknesses and field sizes, thereby converting the plane pixel values at each point into a 2D dose map. The off-axis ratio is corrected using envelope and boundary profiles generated from the treatment planning system (TPS). The method requires field size, monitor unit and source-to-surface distance (SSD) as clinical input parameters to predict the exit dose, which is then used to determine the entrance dose. The measured pixel dose maps were compared with calculated doses from TPS for both entrance and exit depth of phantom. The gamma index at 3% dose difference (DD) and 3 mm distance to agreement (DTA) resulted in an average of 97% passing for the square fields of 5, 10, 15 and 20 cm. The exit dose EPID dose distributions predicted by the algorithm were in better agreement with TPS-calculated doses than phantom entrance dose distributions.

An in vivo dose verification method for SBRT–VMAT delivery using the EPID

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCowan, P. M., E-mail: peter.mccowan@cancercare.mb.ca; Medical Physics Department, CancerCare Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba R3E 0V9; Van Uytven, E.

2015-12-15

Purpose: Radiation treatments have become increasingly more complex with the development of volumetric modulated arc therapy (VMAT) and the use of stereotactic body radiation therapy (SBRT). SBRT involves the delivery of substantially larger doses over fewer fractions than conventional therapy. SBRT–VMAT treatments will strongly benefit from in vivo patient dose verification, as any errors in delivery can be more detrimental to the radiobiology of the patient as compared to conventional therapy. Electronic portal imaging devices (EPIDs) are available on most commercial linear accelerators (Linacs) and their documented use for dosimetry makes them valuable tools for patient dose verification. In thismore » work, the authors customize and validate a physics-based model which utilizes on-treatment EPID images to reconstruct the 3D dose delivered to the patient during SBRT–VMAT delivery. Methods: The SBRT Linac head, including jaws, multileaf collimators, and flattening filter, were modeled using Monte Carlo methods and verified with measured data. The simulation provides energy spectrum data that are used by their “forward” model to then accurately predict fluence generated by a SBRT beam at a plane above the patient. This fluence is then transported through the patient and then the dose to the phosphor layer in the EPID is calculated. Their “inverse” model back-projects the EPID measured focal fluence to a plane upstream of the patient and recombines it with the extra-focal fluence predicted by the forward model. This estimate of total delivered fluence is then forward projected onto the patient’s density matrix and a collapsed cone convolution algorithm calculates the dose delivered to the patient. The model was tested by reconstructing the dose for two prostate, three lung, and two spine SBRT–VMAT treatment fractions delivered to an anthropomorphic phantom. It was further validated against actual patient data for a lung and spine SBRT–VMAT plan. The results were verified with the treatment planning system (TPS) (ECLIPSE AAA) dose calculation. Results: The SBRT–VMAT reconstruction model performed very well when compared to the TPS. A stringent 2%/2 mm χ-comparison calculation gave pass rates better than 91% for the prostate plans, 88% for the lung plans, and 86% for the spine plans for voxels containing 80% or more of the prescribed dose. Patient data were 86% for the lung and 95% for the spine. A 3%/3 mm χ-comparison was also performed and gave pass rates better than 93% for all plan types. Conclusions: The authors have customized and validated a robust, physics-based model that calculates the delivered dose to a patient for SBRT–VMAT delivery using on-treatment EPID images. The accuracy of the results indicates that this approach is suitable for clinical implementation. Future work will incorporate this model into both offline and real-time clinical adaptive radiotherapy.« less

Heat tolerance in a wild Oryza species is attributed to maintenance of Rubisco activation by a thermally stable Rubisco activase ortholog.

PubMed

Scafaro, Andrew P; Gallé, Alexander; Van Rie, Jeroen; Carmo-Silva, Elizabete; Salvucci, Michael E; Atwell, Brian J

2016-08-01

The mechanistic basis of tolerance to heat stress was investigated in Oryza sativa and two wild rice species, Oryza meridionalis and Oryza australiensis. The wild relatives are endemic to the hot, arid Australian savannah. Leaf elongation rates and gas exchange were measured during short periods of supra-optimal heat, revealing species differences. The Rubisco activase (RCA) gene from each species was sequenced. Using expressed recombinant RCA and leaf-extracted RCA, the kinetic properties of the two isoforms were studied under high temperatures. Leaf elongation was undiminished at 45°C in O. australiensis. The net photosynthetic rate was almost 50% slower in O. sativa at 45°C than at 28°C, while in O. australiensis it was unaffected. Oryza meridionalis exhibited intermediate heat tolerance. Based on previous reports that RCA is heat-labile, the Rubisco activation state was measured. It correlated positively with leaf elongation rates across all three species and four periods of exposure to 45°C. Sequence analysis revealed numerous polymorphisms in the RCA amino acid sequence from O. australiensis. The O. australiensis RCA enzyme was thermally stable up to 42°C, contrasting with RCA from O. sativa, which was inhibited at 36°C. We attribute heat tolerance in the wild species to thermal stability of RCA, enabling Rubisco to remain active. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

A feasibility study of treatment verification using EPID cine images for hypofractionated lung radiotherapy

NASA Astrophysics Data System (ADS)

Tang, Xiaoli; Lin, Tong; Jiang, Steve

2009-09-01

We propose a novel approach for potential online treatment verification using cine EPID (electronic portal imaging device) images for hypofractionated lung radiotherapy based on a machine learning algorithm. Hypofractionated radiotherapy requires high precision. It is essential to effectively monitor the target to ensure that the tumor is within the beam aperture. We modeled the treatment verification problem as a two-class classification problem and applied an artificial neural network (ANN) to classify the cine EPID images acquired during the treatment into corresponding classes—with the tumor inside or outside of the beam aperture. Training samples were generated for the ANN using digitally reconstructed radiographs (DRRs) with artificially added shifts in the tumor location—to simulate cine EPID images with different tumor locations. Principal component analysis (PCA) was used to reduce the dimensionality of the training samples and cine EPID images acquired during the treatment. The proposed treatment verification algorithm was tested on five hypofractionated lung patients in a retrospective fashion. On average, our proposed algorithm achieved a 98.0% classification accuracy, a 97.6% recall rate and a 99.7% precision rate. This work was first presented at the Seventh International Conference on Machine Learning and Applications, San Diego, CA, USA, 11-13 December 2008.

Detectability and anatomical correlation of middle ear cholesteatoma using fused thin slice non-echo planar imaging diffusion-weighted image and magnetic resonance cisternography (FTS-nEPID).

PubMed

Kanoto, Masafumi; Sugai, Yukio; Hosoya, Takaaki; Toyoguchi, Yuuki; Konno, Yoshihiro; Watarai, Fumika; Ito, Tsukasa; Watanabe, Tomoo; Kakehata, Seiji

2015-12-01

Cholesteatomas show high intensity in diffusion-weighted imaging (DWI). We performed fused thin slice non-echo planar imaging (EPI) DWI and magnetic resonance cisternography (FTS-nEPID) for cholesteatoma patients to increase the detectability of FTS-nEPID for cholesteatoma. The subjects are 77 consecutive patients who underwent FTS-nEPID as a preoperative study (mean age: 53.3±21.8, 47 men and 30 women). Otorhinolaryngologists performed the operations. We anatomically classified the middle ear into four portions. A radiologist evaluated the images for cholesteatoma and assessed the anatomical invasive range in four portions using only FTS-nEPID. We classified large cholesteatomas that invaded more than three portions and small ones that invaded less than two portions based on the results obtained from surgery, and calculated the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). For all cholesteatomas with an existing diagnosis, the sensitivity, specificity, PPV, and NPV were 71%, 70%, 94%, and 27%, respectively. In anatomical evaluation, the sensitivity, specificity, PPV, and NPV were 49%, 85%, 77%, and 64%, respectively. For large cholesteatomas with an existing diagnosis, the sensitivity was 86%. In anatomical evaluation, the sensitivity, specificity, PPV, and NPV were 51%, 57%, 88%, and 18%, respectively. For small cholesteatomas with an existing diagnosis, the sensitivity, specificity, PPV, and NPV were 59%, 78%, 92%, and 30%, respectively. In anatomical evaluation, the sensitivity, specificity, PPV, and NPV were 40%, 85%, 60%, and 71%, respectively. FTS-nEPID may be useful for diagnosing cholesteatomas. Further research is needed for anatomical evaluation because there were many false-negative results. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification and molecular characterization of a new recombinant begomovirus and associated betasatellite DNA infecting Capsicum annuum in India.

PubMed

Bhatt, Bhavin S; Chahwala, Fenisha D; Rathod, Sangeeta; Singh, Achuit K

2016-05-01

Capsicum annuum (Chilli) is a perennial herbaceous plant that is cultivated as an annual crop throughout the world, including India. Chilli leaf curl disease (ChiLCD) is a major biotic constraint, causing major losses in chilli production. During 2014, leaf samples of chilli plants displaying leaf curl disease were collected from the Ahmedabad district of Gujarat, India. These samples were used to isolate, clone and sequence viral genomic DNA and an associated betasatellite DNA molecule. Sequence analysis showed 90.4 % nucleotide sequence identity to the previously reported chilli leaf curl virus-[India:Guntur:2009] (ChiLCV-[IN:Gun:09]. As per ICTV nomenclature rules, ChiLCV-Ahm represents a new species of begomovirus, and we therefore propose the name chilli leaf curl Ahmedabad virus-[India:Ahmedabad:2014] (ChiLCAV-[IN:Ahm:14]). The associated betasatellite DNA showed a maximum of 93.5 % nucleotide sequence identity to a previously reported tomato leaf curl Bangladesh betasatellite and may be named tomato leaf curl Bangladesh betasatellite-[India:Ahmedabad:Chilli:2014].

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.)

PubMed Central

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-01-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ variety, ‘Yonekura’. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the ‘spiny-leaf type’ as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding. PMID:26175625

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

PubMed

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-06-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

Use of local noise power spectrum and wavelet analysis in quantitative image quality assurance for EPIDs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Soyoung

Purpose: To investigate the use of local noise power spectrum (NPS) to characterize image noise and wavelet analysis to isolate defective pixels and inter-subpanel flat-fielding artifacts for quantitative quality assurance (QA) of electronic portal imaging devices (EPIDs). Methods: A total of 93 image sets including custom-made bar-pattern images and open exposure images were collected from four iViewGT a-Si EPID systems over three years. Global quantitative metrics such as modulation transform function (MTF), NPS, and detective quantum efficiency (DQE) were computed for each image set. Local NPS was also calculated for individual subpanels by sampling region of interests within each subpanelmore » of the EPID. The 1D NPS, obtained by radially averaging the 2D NPS, was fitted to a power-law function. The r-square value of the linear regression analysis was used as a singular metric to characterize the noise properties of individual subpanels of the EPID. The sensitivity of the local NPS was first compared with the global quantitative metrics using historical image sets. It was then compared with two commonly used commercial QA systems with images collected after applying two different EPID calibration methods (single-level gain and multilevel gain). To detect isolated defective pixels and inter-subpanel flat-fielding artifacts, Haar wavelet transform was applied on the images. Results: Global quantitative metrics including MTF, NPS, and DQE showed little change over the period of data collection. On the contrary, a strong correlation between the local NPS (r-square values) and the variation of the EPID noise condition was observed. The local NPS analysis indicated image quality improvement with the r-square values increased from 0.80 ± 0.03 (before calibration) to 0.85 ± 0.03 (after single-level gain calibration) and to 0.96 ± 0.03 (after multilevel gain calibration), while the commercial QA systems failed to distinguish the image quality improvement between the two calibration methods. With wavelet analysis, defective pixels and inter-subpanel flat-fielding artifacts were clearly identified as spikes after thresholding the inversely transformed images. Conclusions: The proposed local NPS (r-square values) showed superior sensitivity to the noise level variations of individual subpanels compared with global quantitative metrics such as MTF, NPS, and DQE. Wavelet analysis was effective in detecting isolated defective pixels and inter-subpanel flat-fielding artifacts. The proposed methods are promising for the early detection of imaging artifacts of EPIDs.« less

Complete nucleotide sequence of a monopartite Begomovirus and associated satellites infecting Carica papaya in Nepal.

PubMed

Shahid, M S; Yoshida, S; Khatri-Chhetri, G B; Briddon, R W; Natsuaki, K T

2013-06-01

Carica papaya (papaya) is a fruit crop that is cultivated mostly in kitchen gardens throughout Nepal. Leaf samples of C. papaya plants with leaf curling, vein darkening, vein thickening, and a reduction in leaf size were collected from a garden in Darai village, Rampur, Nepal in 2010. Full-length clones of a monopartite Begomovirus, a betasatellite and an alphasatellite were isolated. The complete nucleotide sequence of the Begomovirus showed the arrangement of genes typical of Old World begomoviruses with the highest nucleotide sequence identity (>99 %) to an isolate of Ageratum yellow vein virus (AYVV), confirming it as an isolate of AYVV. The complete nucleotide sequence of betasatellite showed greater than 89 % nucleotide sequence identity to an isolate of Tomato leaf curl Java betasatellite originating from Indonesian. The sequence of the alphasatellite displayed 92 % nucleotide sequence identity to Sida yellow vein China alphasatellite. This is the first identification of these components in Nepal and the first time they have been identified in papaya.

Automating linear accelerator quality assurance.

PubMed

Eckhause, Tobias; Al-Hallaq, Hania; Ritter, Timothy; DeMarco, John; Farrey, Karl; Pawlicki, Todd; Kim, Gwe-Ya; Popple, Richard; Sharma, Vijeshwar; Perez, Mario; Park, SungYong; Booth, Jeremy T; Thorwarth, Ryan; Moran, Jean M

2015-10-01

The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers. The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suite at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs. For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (<0.12 mm) for all Linacs. Considering both log files and EPID measurements, all parameters were well within published tolerance values. Variations in collimator angle, MLC position, and gantry sag were also evaluated for all Linacs. The performance of the TrueBeam Linac model was shown to be consistent based on automated analysis of trajectory log files and EPID images acquired during delivery of a standardized test suite. The results can be compared directly to tolerance thresholds. In addition, sharing of results from standard tests across institutions can facilitate the identification of QA process and Linac changes. These reference values are presented along with the standard deviation for common tests so that the test suite can be used by other centers to evaluate their Linac performance against those in this consortium.

SU-F-P-39: End-To-End Validation of a 6 MV High Dose Rate Photon Beam, Configured for Eclipse AAA Algorithm Using Golden Beam Data, for SBRT Treatments Using RapidArc

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferreyra, M; Salinas Aranda, F; Dodat, D

Purpose: To use end-to-end testing to validate a 6 MV high dose rate photon beam, configured for Eclipse AAA algorithm using Golden Beam Data (GBD), for SBRT treatments using RapidArc. Methods: Beam data was configured for Varian Eclipse AAA algorithm using the GBD provided by the vendor. Transverse and diagonals dose profiles, PDDs and output factors down to a field size of 2×2 cm2 were measured on a Varian Trilogy Linac and compared with GBD library using 2% 2mm 1D gamma analysis. The MLC transmission factor and dosimetric leaf gap were determined to characterize the MLC in Eclipse. Mechanical andmore » dosimetric tests were performed combining different gantry rotation speeds, dose rates and leaf speeds to evaluate the delivery system performance according to VMAT accuracy requirements. An end-to-end test was implemented planning several SBRT RapidArc treatments on a CIRS 002LFC IMRT Thorax Phantom. The CT scanner calibration curve was acquired and loaded in Eclipse. PTW 31013 ionization chamber was used with Keithley 35617EBS electrometer for absolute point dose measurements in water and lung equivalent inserts. TPS calculated planar dose distributions were compared to those measured using EPID and MapCheck, as an independent verification method. Results were evaluated with gamma criteria of 2% dose difference and 2mm DTA for 95% of points. Results: GBD set vs. measured data passed 2% 2mm 1D gamma analysis even for small fields. Machine performance tests show results are independent of machine delivery configuration, as expected. Absolute point dosimetry comparison resulted within 4% for the worst case scenario in lung. Over 97% of the points evaluated in dose distributions passed gamma index analysis. Conclusion: Eclipse AAA algorithm configuration of the 6 MV high dose rate photon beam using GBD proved efficient. End-to-end test dose calculation results indicate it can be used clinically for SBRT using RapidArc.« less

Virtual EPID standard phantom audit (VESPA) for remote IMRT and VMAT credentialing

NASA Astrophysics Data System (ADS)

Miri, Narges; Lehmann, Joerg; Legge, Kimberley; Vial, Philip; Greer, Peter B.

2017-06-01

A virtual EPID standard phantom audit (VESPA) has been implemented for remote auditing in support of facility credentialing for clinical trials using IMRT and VMAT. VESPA is based on published methods and a clinically established IMRT QA procedure, here extended to multi-vendor equipment. Facilities are provided with comprehensive instructions and CT datasets to create treatment plans. They deliver the treatment directly to their EPID without any phantom or couch in the beam. In addition, they deliver a set of simple calibration fields per instructions. Collected EPID images are uploaded electronically. In the analysis, the dose is projected back into a virtual cylindrical phantom. 3D gamma analysis is performed. 2D dose planes and linear dose profiles are provided and can be considered when needed for clarification. In addition, using a virtual flat-phantom, 2D field-by-field or arc-by-arc gamma analyses are performed. Pilot facilities covering a range of planning and delivery systems have performed data acquisition and upload successfully. Advantages of VESPA are (1) fast turnaround mainly driven by the facility’s capability of providing the requested EPID images, (2) the possibility for facilities performing the audit in parallel, as there is no need to wait for a phantom, (3) simple and efficient credentialing for international facilities, (4) a large set of data points, and (5) a reduced impact on resources and environment as there is no need to transport heavy phantoms or audit staff. Limitations of the current implementation of VESPA for trials credentialing are that it does not provide absolute dosimetry, therefore a Level I audit is still required, and that it relies on correctly delivered open calibration fields, which are used for system calibration. The implemented EPID based IMRT and VMAT audit system promises to dramatically improve credentialing efficiency for clinical trials and wider applications.

Virtual EPID standard phantom audit (VESPA) for remote IMRT and VMAT credentialing.

PubMed

Miri, Narges; Lehmann, Joerg; Legge, Kimberley; Vial, Philip; Greer, Peter B

2017-06-07

A virtual EPID standard phantom audit (VESPA) has been implemented for remote auditing in support of facility credentialing for clinical trials using IMRT and VMAT. VESPA is based on published methods and a clinically established IMRT QA procedure, here extended to multi-vendor equipment. Facilities are provided with comprehensive instructions and CT datasets to create treatment plans. They deliver the treatment directly to their EPID without any phantom or couch in the beam. In addition, they deliver a set of simple calibration fields per instructions. Collected EPID images are uploaded electronically. In the analysis, the dose is projected back into a virtual cylindrical phantom. 3D gamma analysis is performed. 2D dose planes and linear dose profiles are provided and can be considered when needed for clarification. In addition, using a virtual flat-phantom, 2D field-by-field or arc-by-arc gamma analyses are performed. Pilot facilities covering a range of planning and delivery systems have performed data acquisition and upload successfully. Advantages of VESPA are (1) fast turnaround mainly driven by the facility's capability of providing the requested EPID images, (2) the possibility for facilities performing the audit in parallel, as there is no need to wait for a phantom, (3) simple and efficient credentialing for international facilities, (4) a large set of data points, and (5) a reduced impact on resources and environment as there is no need to transport heavy phantoms or audit staff. Limitations of the current implementation of VESPA for trials credentialing are that it does not provide absolute dosimetry, therefore a Level I audit is still required, and that it relies on correctly delivered open calibration fields, which are used for system calibration. The implemented EPID based IMRT and VMAT audit system promises to dramatically improve credentialing efficiency for clinical trials and wider applications.

MO-D-213-08: Remote Dosimetric Credentialing for Clinical Trials with the Virtual EPID Standard Phantom Audit (VESPA)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, J; University of Sydney, Sydney, NSW; Miri, N

Purpose: Report on implementation of a Virtual EPID Standard Phantom Audit (VESPA) for IMRT to support credentialing of facilities for clinical trials. Data is acquired by local facility staff and transferred electronically. Analysis is performed centrally. Methods: VESPA is based on published methods and a clinically established IMRT QA procedure, here extended to multi-vendor equipment. Facilities, provided with web-based comprehensive instructions and CT datasets, create IMRT treatment plans. They deliver the treatments directly to their EPID without phantom or couch in the beam. They also deliver a set of simple calibration fields. Collected EPID images are uploaded electronically. In themore » analysis, the dose is projected back into a virtual phantom and 3D gamma analysis is performed. 2D dose planes and linear dose profiles can be analysed when needed for clarification. Results: Pilot facilities covering a range of planning and delivery systems have performed data acquisition and upload successfully. Analysis showed agreement comparable to local experience with the method. Advantages of VESPA are (1) fast turnaround mainly driven by the facility’s capability to provide the requested EPID images, (2) the possibility for facilities performing the audit in parallel, as there is no need to wait for a phantom, (3) simple and efficient credentialing for international facilities, (4) a large set of data points, and (5) a reduced impact on resources and environment as there is no need to transport heavy phantoms or audit staff. Limitations of the current implementation of VESPA for trials credentialing are that it does not provide absolute dosimetry, therefore a Level 1 audit still required, and that it relies on correctly delivered open calibration fields, which are used for system calibration. Conclusion: The implemented EPID based IMRT audit system promises to dramatically improve credentialing efficiency for clinical trials and wider applications. VESPA for VMAT will follow soon.« less

SU-E-T-133: Assessing IMRT Treatment Delivery Accuracy and Consistency On a Varian TrueBeam Using the SunNuclear PerFraction EPID Dosimetry Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dieterich, S; Trestrail, E; Holt, R

2015-06-15

Purpose: To assess if the TrueBeam HD120 collimator is delivering small IMRT fields accurately and consistently throughout the course of treatment using the SunNuclear PerFraction software. Methods: 7-field IMRT plans for 8 canine patients who passed IMRT QA using SunNuclear Mapcheck DQA were selected for this study. The animals were setup using CBCT image guidance. The EPID fluence maps were captured for each treatment field and each treatment fraction, with the first fraction EPID data serving as the baseline for comparison. The Sun Nuclear PerFraction Software was used to compare the EPID data for subsequent fractions using a Gamma (3%/3mm)more » pass rate of 90%. To simulate requirements for SRS, the data was reanalyzed using a Gamma (3%/1mm) pass rate of 90%. Low-dose, low- and high gradient thresholds were used to focus the analysis on clinically relevant parts of the dose distribution. Results: Not all fractions could be analyzed, because during some of the treatment courses the DICOM tags in the EPID images intermittently change from CU to US (unspecified), which would indicate a temporary loss of EPID calibration. This technical issue is still being investigated. For the remaining fractions, the vast majority (7/8 of patients, 95% of fractions, and 96.6% of fields) are passing the less stringent Gamma criteria. The more stringent Gamma criteria caused a drop in pass rate (90 % of fractions, 84% of fields). For the patient with the lowest pass rate, wet towel bolus was used. Another patient with low pass rates experienced masseter muscle wasting. Conclusion: EPID dosimetry using the PerFraction software demonstrated that the majority of fields passed a Gamma (3%/3mm) for IMRT treatments delivered with a TrueBeam HD120 MLC. Pass rates dropped for a DTA of 1mm to model SRS tolerances. PerFraction pass rates can flag missing bolus or internal shields. Sanjeev Saini is an employee of Sun Nuclear Corporation. For this study, a pre-release version of PerFRACTION 1.1 software from Sun Nuclear Corporation was used.« less

SU-F-T-263: Dosimetric Characteristics of the Cine Acquisition Mode of An A-Si EPID

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bawazeer, O; Deb, P; Sarasanandarajah, S

2016-06-15

Purpose: To investigate the dosimetric characteristics of Varian a-Si-500 electronic portal imaging device (EPID) operated in cine mode particularly considering linearity with delivered dose, dose rate, field size, phantom thickness, MLC speed and common IMRT fields. Methods: The EPID that attached to a Varian Clinac 21iX linear accelerator, was irradiated with 6 and 18 MV using 600 MU/min. Image acquisition is controlled by the IAS3 software, Trigger delay was 6 ms, BeamOnDelay and FrameStartDelay were zero. Different frame rates were utilized. Cine mode response was calculated using MATLAB as summation of mean pixel values in a region of interest ofmore » the acquired images. The performance of cine mode was compared to integrated mode and dose measurements in water using CC13 ionization chamber. Results: Figure1 illustrates that cine mode has nonlinear response for small MU, when delivering 10 MU was about 0.5 and 0.64 for 6 and 18 MV respectively. This is because the missing acquired images that were calculated around four images missing in each delivery. With the increase MU the response became linear and comparable with integrated mode and ionization chamber within 2%. Figure 2 shows that cine mode has comparable response with integrated mode and ionization chamber within 2% with changing dose rate for 10 MU delivered. This indicates that the dose rate change has no effect on nonlinearity of cine mode response. Except nonlinearity, cine mode is well matched to integrated mode response within 2% for field size, phantom thickness, MLC speed dependences. Conclusion: Cine mode has similar dosimetric characteristics to integrated mode with open and IMRT fields, and the main limitation with cine mode is missing images. Therefore, the calibration of EPID images with this mode should be run with large MU, and when IMRT verification field has low MU, the correction for missing images are required.« less

Correction of scatter in megavoltage cone-beam CT

NASA Astrophysics Data System (ADS)

Spies, L.; Ebert, M.; Groh, B. A.; Hesse, B. M.; Bortfeld, T.

2001-03-01

The role of scatter in a cone-beam computed tomography system using the therapeutic beam of a medical linear accelerator and a commercial electronic portal imaging device (EPID) is investigated. A scatter correction method is presented which is based on a superposition of Monte Carlo generated scatter kernels. The kernels are adapted to both the spectral response of the EPID and the dimensions of the phantom being scanned. The method is part of a calibration procedure which converts the measured transmission data acquired for each projection angle into water-equivalent thicknesses. Tomographic reconstruction of the projections then yields an estimate of the electron density distribution of the phantom. It is found that scatter produces cupping artefacts in the reconstructed tomograms. Furthermore, reconstructed electron densities deviate greatly (by about 30%) from their expected values. The scatter correction method removes the cupping artefacts and decreases the deviations from 30% down to about 8%.

First Complete Squash leaf curl China virus Genomic Segment DNA-A Sequence from East Timor

PubMed Central

Maina, Solomon; Edwards, Owain R.; de Almeida, Luis; Ximenes, Abel

2017-01-01

ABSTRACT We present here the first complete Squash leaf curl China virus (SLCCV) genomic segment DNA-A sequence from East Timor. It was isolated from a pumpkin plant. When compared with 15 complete SLCCV DNA-A genome sequences from other world regions, it most resembled the Malaysian isolate MC1 sequence. PMID:28619789

Performance optimization of the Varian aS500 EPID system.

PubMed

Berger, Lucie; François, Pascal; Gaboriaud, Geneviève; Rosenwald, Jean-Claude

2006-01-01

Today, electronic portal imaging devices (EPIDs) are widely used as a replacement to portal films for patient position verification, but the image quality is not always optimal. The general aim of this study was to optimize the acquisition parameters of an amorphous silicon EPID commercially available for clinical use in radiation therapy with the view to avoid saturation of the system. Special attention was paid to selection of the parameter corresponding to the number of rows acquired between accelerator pulses (NRP) for various beam energies and dose rates. The image acquisition system (IAS2) has been studied, and portal image acquisition was found to be strongly dependent on the accelerator pulse frequency. This frequency is set for each "energy - dose rate" combination of the linear accelerator. For all combinations, the image acquisition parameters were systematically changed to determine their influence on the performances of the Varian aS500 EPID system. New parameters such as the maximum number of rows (MNR) and the number of pulses per frame (NPF) were introduced to explain portal image acquisition theory. Theoretical and experimental values of MNR and NPF were compared, and they were in good agreement. Other results showed that NRP had a major influence on detector saturation and dose per image. A rule of thumb was established to determine the optimum NRP value to be used. This practical application was illustrated by a clinical example in which the saturation of the aSi EPID was avoided by NRP optimization. Moreover, an additional study showed that image quality was relatively insensitive to this parameter.

Development and implementation of an EPID-based method for localizing isocenter.

PubMed

Hyer, Daniel E; Mart, Christopher J; Nixon, Earl

2012-11-08

The aim of this study was to develop a phantom and analysis software that could be used to quickly and accurately determine the location of radiation isocenter to an accuracy of less than 1 mm using the EPID (Electronic Portal Imaging Device). The proposed solution uses a collimator setting of 10 × 10 cm2 to acquire EPID images of a new phantom constructed from LEGO blocks. Images from a number of gantry and collimator angles are analyzed by automated analysis software to determine the position of the jaws and center of the phantom in each image. The distance between a chosen jaw and the phantom center is then compared to the same distance measured after a 180° collimator rotation to determine if the phantom is centered in the dimension being investigated. Repeated tests show that the system is reproducibly independent of the imaging session, and calculated offsets of the phantom from radiation isocenter are a function of phantom setup only. Accuracy of the algorithm's calculated offsets were verified by imaging the LEGO phantom before and after applying the calculated offset. These measurements show that the offsets are predicted with an accuracy of approximately 0.3 mm, which is on the order of the detector's pitch. Comparison with a star-shot analysis yielded agreement of isocenter location within 0.5 mm. Additionally, the phantom and software are completely independent of linac vendor, and this study presents results from two linac manufacturers. A Varian Optical Guidance Platform (OGP) calibration array was also integrated into the phantom to allow calibration of the OGP while the phantom is positioned at radiation isocenter to reduce setup uncertainty in the calibration. This solution offers a quick, objective method to perform isocenter localization as well as laser alignment and OGP calibration on a monthly basis.

Parameterization of Forest Canopies with the PROSAIL Model

NASA Astrophysics Data System (ADS)

Austerberry, M. J.; Grigsby, S.; Ustin, S.

2013-12-01

Particularly in forested environments, arboreal characteristics such as Leaf Area Index (LAI) and Leaf Inclination Angle have a large impact on the spectral characteristics of reflected radiation. The reflected spectrum can be measured directly with satellites or airborne instruments, including the MASTER and AVIRIS instruments. This particular project dealt with spectral analysis of reflected light as measured by AVIRIS compared to tree measurements taken from the ground. Chemical properties of leaves including pigment concentrations and moisture levels were also measured. The leaf data was combined with the chemical properties of three separate trees, and served as input data for a sequence of simulations with the PROSAIL Model, a combination of PROSPECT and Scattering by Arbitrarily Inclined Leaves (SAIL) simulations. The output was a computed reflectivity spectrum, which corresponded to the spectra that were directly measured by AVIRIS for the three trees' exact locations within a 34-meter pixel resolution. The input data that produced the best-correlating spectral output was then cross-referenced with LAI values that had been obtained through two entirely separate methods, NDVI extraction and use of the Beer-Lambert law with airborne LiDAR. Examination with regressive techniques between the measured and modeled spectra then enabled a determination of the trees' probable structure and leaf parameters. Highly-correlated spectral output corresponded well to specific values of LAI and Leaf Inclination Angle. Interestingly, it appears that varying Leaf Angle Distribution has little or no noticeable effect on the PROSAIL model. Not only is the effectiveness and accuracy of the PROSAIL model evaluated, but this project is a precursor to direct measurement of vegetative indices exclusively from airborne or satellite observation.

Exobasidium maculosum, a new species causing leaf and fruit spots on blueberry in the southeastern USA and its relationship with other Exobasidium spp. parasitic to blueberry and cranberry.

PubMed

Brewer, Marin Talbot; Turner, Ashley N; Brannen, Phillip M; Cline, William O; Richardson, Elizabeth A

2014-01-01

Exobasidium leaf and fruit spot of blueberry (Vaccinium section Cyanococcus) is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA. To determine whether this disease is caused by a new species of Exobasidium, we studied the morphology and phylogenetic relationship of the causal fungus compared with other members of the genus, including the type species E. vaccinii and other species that parasitize blueberry and cranberry (V. macrocarpon). Both scanning electron microscopy and light microscopy were used for morphological characterization. For phylogenetic analyses, we sequenced the large subunit of the rDNA (LSU) from 10 isolates collected from leaf or fruit spots of rabbiteye blueberry (V. virgatum), highbush blueberry (V. corymbosum) and southern highbush blueberry (Vaccinium interspecific hybrid) from Georgia and North Carolina and six isolates from leaf spots of lowbush blueberry (V. angustifolium) from Maine and Nova Scotia, Canada. LSU was sequenced from isolates causing red leaf disease of lowbush blueberry and red leaf spot (E. rostrupii) and red shoot (E. perenne) of cranberry. In addition, LSU sequences from GenBank, including sequences with high similarity to the emerging parasite and from Exobasidium spp. parasitizing other Vaccinium spp. and related hosts, were obtained. All sequences were aligned and subjected to phylogenetic analyses. Results indicated that the emerging parasite in the southeastern USA differs morphologically and phylogenetically from other described species and is described herein as Exobasidium maculosum. Within the southeastern USA, clustering based on host species, host tissue type (leaf or fruit) or geographic region was not detected; however, leaf spot isolates from lowbush blueberry were genetically different and likely represent a unique species. © 2014 by The Mycological Society of America.

A new betasatellite associated with cotton leaf curl Burewala virus infecting tomato in India: influence on symptoms and viral accumulation.

PubMed

Kumar, Jitendra; Gunapati, Samatha; Singh, Sudhir P; Kumar, Abhinav; Lalit, Adarsh; Sharma, Naresh C; Puranik, Rekha; Tuli, Rakesh

2013-06-01

A begomovirus and its associated alpha- and betasatellite were detected in tomato plants affected with leaf curl disease. Based on a nucleotide sequence identity of 99 %, this begomovirus was designated an isolate of cotton leaf curl Burewala virus (CLCuBuV). The alphasatellite exhibited 93 % sequence identity to cotton leaf curl Burewala alphasatellite (CLCuBuA) and is hence referred to here as a variant of CLCuBuA. The detected betasatellite was recombinant in nature and showed 70 % sequence identity to the known betasatellites. Inoculation of healthy tomato with CLCuBuV plus betasatellite, either in the presence or the absence of alphasatellite, led to typical leaf curling, while inoculation with CLCuBuV in the absence of betasatellite resulted in mild symptoms. This confirmed the role of the betasatellite in expression of disease symptoms. We propose to name the newly detected betasatellite tomato leaf curl Hajipur betasatellite (ToLCHJB).

Molecular characterization of a distinct monopartite begomovirus associated with betasatellites and alphasatellites infecting Pisum sativum in Nepal.

PubMed

Shahid, M S; Pudashini, B J; Khatri-Chhetri, G B; Briddon, R W; Natsuaki, K T

2017-04-01

Pea (Pisum sativum) plants exhibiting leaf distortion, yellowing, stunted growth and reduction in leaf size from Rampur, Nepal were shown to be infected by a begomovirus in association with betasatellites and alphasatellites. The begomovirus associated with the disease showed only low levels of nucleotide sequence identity (<91%) to previously characterized begomoviruses. This finding indicates that the pea samples were infected with an as yet undescribed begomovirus for which the name Pea leaf distortion virus (PLDV) is proposed. Two species of betasatellite were identified in association with PLDV. One group of sequences had high (>78%) nucleotide sequence identity to isolates of Ludwigia leaf distortion betasatellite (LuLDB), and the second group had less than 78% to all other betasatellite sequences. This showed PLDV to be associated with either LuLDB or a previously undescribed betasatellite for which the name Pea leaf distortion betasatellite is proposed. Two types of alphasatellites were identified in the PLDV-infected pea plants. The first type showed high levels of sequence identity to Ageratum yellow vein alphasatellite, and the second type showed high levels of identity to isolates of Sida yellow vein China alphasatellite. These are the first begomovirus, betasatellites and alphasatellites isolated from pea.

Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7

PubMed Central

Rangarajan, Erumbi S.; Li, Yunge; Iannuzzi, Pietro; Tocilj, Ante; Hung, Li-Wei; Matte, Allan; Cygler, Miroslaw

2004-01-01

The crystal structure of the flavoprotein Pad1 from Escherichia coli O157:H7 complexed with the cofactor FMN has been determined by the multiple anomalous diffraction method and refined at 2.0 Å resolution. This protein is a paralog of UbiX (3-octaprenyl-4-hydroxybenzoate carboxylyase, 51% sequence identity) that catalyzes the third step in ubiquinone biosynthesis and to Saccharomyces cerevisiae Pad1 (54% identity), an enzyme that confers resistance to the antimicrobial compounds phenylacrylic acids through decarbox-ylation of these compounds. Each Pad1 monomer consists of a typical Rossmann fold containing a non–covalently bound molecule of FMN. The fold of Pad1 is similar to MrsD, an enzyme associated with lantibiotic synthesis; EpiD, a peptidyl-cysteine decarboxylase; and AtHAL3a, the enzyme, which decarboxylates 4′-phosphopantothenoylcysteine to 4′-phosphopantetheine during coenzyme A biosynthesis, all with a similar location of the FMN binding site at the interface between two monomers, yet each having little sequence similarity to one another. All of these proteins associate into oligomers, with a trimer forming the common structural unit in each case. In MrsD and EpiD, which belong to the homo-dodecameric flavin-containing cysteine decarboxylase (HFCD) family, these trimers associate further into dodecamers. Pad1 also forms dodecamers, although the association of the trimers is completely different, resulting in exposure of a different side of the trimer unit to the solvent. This exposure affects the location of the substrate binding site and, specifically, its access to the FMN cofactor. Therefore, Pad1 forms a separate family, distinguishable from the HFCD family. PMID:15459342

Complete genome sequence of an isolate of papaya leaf distortion mosaic virus from commercialized PRSV-resistant transgenic papaya in China.

PubMed

Tuo, D; Shen, W; Yan, P; Li, Ch; Gao, L; Li, X; Li, H; Zhou, P

2013-01-01

Papaya leaf distortion mosaic virus is highly destructive to commercial papaya production. Here, the complete genome sequence was determined for an isolate of papaya leaf distortion mosaic virus, designated PLDMV-DF, infecting the commercialized papaya ringspot virus (PRSV)-resistant transgenic papaya from China. Excluding the 3'-poly (A) tail, the sequence shares high sequence identity to several PLDMV isolates from Taiwan and Japan and is phylogenetically most closely related to the isolate from Japan. Infection of PLDMV-DF in transgenic PRSV-resistant papaya may indicate emergence of this disease in genetically engineered plants. The reported sequence for this isolate may help generate bi-transgenic papaya resistant to PRSV and PLDMV.

A new virus in Luteoviridae is associated with raspberry leaf curl disease

USDA-ARS?s Scientific Manuscript database

To determine the etiology of Raspberry Leaf Curl Disease (RLCD), which causes leaf curling, leaf distortion, leaf chlorosis, shoot dwarfing, shoot proliferation in raspberries and can kill plants within three years, a next generation sequences approach was applied. Two red raspberry plants collected...

MO-F-CAMPUS-J-05: Using 2D Relative Gamma Analysis From EPID Image as a Predictor of Plan Deterioration Due to Anatomical Changes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piron, O; Varfalvy, N; Archambault, L

2015-06-15

Purpose: One of the side effects of radiotherapy for head and neck (H&N) cancer is the patient’s anatomical changes. The changes can strongly affect the planned dose distribution. In this work, our goal is to demonstrate that relative analysis of EPID images is a fast and simple method to detect anatomical changes that can have a strong dosimetric impact on the treatment plan for H&N patients. Methods: EPID images were recorded at every beam and all fractions for 50 H&N patients. Of these, five patients that showed important anatomical changes were selected to evaluate dosimetric impacts of these changes andmore » to correlate them with a 2D relative gamma analysis of EPID images. The planning CT and original contours were deformed onto CBCTs (one mid treatment and one at the end of treatment). By using deformable image registration, it was possible to map accurate CT numbers from the planning CT to the anatomy of the day obtained with CBCTs. Clinical treatment plan were then copied on the deformed dataset and dose was re-computed. In parallel, EPID images were analysed using the gamma index (3%3mm) relative to the first image. Results: It was possible to divide patients in two distinct, statistically different (p<0.001) categories using an average gamma index of 0.5 as a threshold. Below this threshold no significant dosimetric degradation of the plan are observed. Above this threshold two types of plan deterioration were seen: (1) target dose increases, but coverage remains adequate while dose to at least one OAR increases beyond tolerances; (2) the OAR doses remain low, but the target dose is reduced and coverage becomes inadequate. Conclusion: Relative analysis gamma of EPID images could indeed be a fast and simple method to detect anatomical changes that can potentially deteriorates treatment plan for H&N patients. This work was supported in part by Varian Medical System.« less

SU-C-304-05: Use of Local Noise Power Spectrum and Wavelets in Comprehensive EPID Quality Assurance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, S; Gopal, A; Yan, G

2015-06-15

Purpose: As EPIDs are increasingly used for IMRT QA and real-time treatment verification, comprehensive quality assurance (QA) of EPIDs becomes critical. Current QA with phantoms such as the Las Vegas and PIPSpro™ can fail in the early detection of EPID artifacts. Beyond image quality assessment, we propose a quantitative methodology using local noise power spectrum (NPS) to characterize image noise and wavelet transform to identify bad pixels and inter-subpanel flat-fielding artifacts. Methods: A total of 93 image sets including bar-pattern images and open exposure images were collected from four iViewGT a-Si EPID systems over three years. Quantitative metrics such asmore » modulation transform function (MTF), NPS and detective quantum efficiency (DQE) were computed for each image set. Local 2D NPS was calculated for each subpanel. A 1D NPS was obtained by radial averaging the 2D NPS and fitted to a power-law function. R-square and slope of the linear regression analysis were used for panel performance assessment. Haar wavelet transformation was employed to identify pixel defects and non-uniform gain correction across subpanels. Results: Overall image quality was assessed with DQE based on empirically derived area under curve (AUC) thresholds. Using linear regression analysis of 1D NPS, panels with acceptable flat fielding were indicated by r-square between 0.8 and 1, and slopes of −0.4 to −0.7. However, for panels requiring flat fielding recalibration, r-square values less than 0.8 and slopes from +0.2 to −0.4 were observed. The wavelet transform successfully identified pixel defects and inter-subpanel flat fielding artifacts. Standard QA with the Las Vegas and PIPSpro phantoms failed to detect these artifacts. Conclusion: The proposed QA methodology is promising for the early detection of imaging and dosimetric artifacts of EPIDs. Local NPS can accurately characterize the noise level within each subpanel, while the wavelet transforms can detect bad pixels and inter-subpanel flat fielding artifacts.« less

Verification of respiratory-gated radiotherapy with new real-time tumour-tracking radiotherapy system using cine EPID images and a log file

NASA Astrophysics Data System (ADS)

Shiinoki, Takehiro; Hanazawa, Hideki; Yuasa, Yuki; Fujimoto, Koya; Uehara, Takuya; Shibuya, Keiko

2017-02-01

A combined system comprising the TrueBeam linear accelerator and a new real-time tumour-tracking radiotherapy system, SyncTraX, was installed at our institution. The objectives of this study are to develop a method for the verification of respiratory-gated radiotherapy with SyncTraX using cine electronic portal image device (EPID) images and a log file and to verify this treatment in clinical cases. Respiratory-gated radiotherapy was performed using TrueBeam and the SyncTraX system. Cine EPID images and a log file were acquired for a phantom and three patients during the course of the treatment. Digitally reconstructed radiographs (DRRs) were created for each treatment beam using a planning CT set. The cine EPID images, log file, and DRRs were analysed using a developed software. For the phantom case, the accuracy of the proposed method was evaluated to verify the respiratory-gated radiotherapy. For the clinical cases, the intra- and inter-fractional variations of the fiducial marker used as an internal surrogate were calculated to evaluate the gating accuracy and set-up uncertainty in the superior-inferior (SI), anterior-posterior (AP), and left-right (LR) directions. The proposed method achieved high accuracy for the phantom verification. For the clinical cases, the intra- and inter-fractional variations of the fiducial marker were  ⩽3 mm and  ±3 mm in the SI, AP, and LR directions. We proposed a method for the verification of respiratory-gated radiotherapy with SyncTraX using cine EPID images and a log file and showed that this treatment is performed with high accuracy in clinical cases. This work was partly presented at the 58th Annual meeting of American Association of Physicists in Medicine.

Verification of respiratory-gated radiotherapy with new real-time tumour-tracking radiotherapy system using cine EPID images and a log file.

PubMed

Shiinoki, Takehiro; Hanazawa, Hideki; Yuasa, Yuki; Fujimoto, Koya; Uehara, Takuya; Shibuya, Keiko

2017-02-21

A combined system comprising the TrueBeam linear accelerator and a new real-time tumour-tracking radiotherapy system, SyncTraX, was installed at our institution. The objectives of this study are to develop a method for the verification of respiratory-gated radiotherapy with SyncTraX using cine electronic portal image device (EPID) images and a log file and to verify this treatment in clinical cases. Respiratory-gated radiotherapy was performed using TrueBeam and the SyncTraX system. Cine EPID images and a log file were acquired for a phantom and three patients during the course of the treatment. Digitally reconstructed radiographs (DRRs) were created for each treatment beam using a planning CT set. The cine EPID images, log file, and DRRs were analysed using a developed software. For the phantom case, the accuracy of the proposed method was evaluated to verify the respiratory-gated radiotherapy. For the clinical cases, the intra- and inter-fractional variations of the fiducial marker used as an internal surrogate were calculated to evaluate the gating accuracy and set-up uncertainty in the superior-inferior (SI), anterior-posterior (AP), and left-right (LR) directions. The proposed method achieved high accuracy for the phantom verification. For the clinical cases, the intra- and inter-fractional variations of the fiducial marker were  ⩽3 mm and  ±3 mm in the SI, AP, and LR directions. We proposed a method for the verification of respiratory-gated radiotherapy with SyncTraX using cine EPID images and a log file and showed that this treatment is performed with high accuracy in clinical cases.

Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala).

PubMed

Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H

2013-04-02

Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.

SU-F-T-527: A Novel Dynamic Multileaf Collimator Leaf-Sequencing Algorithm in Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jing, J; Lin, H; Chow, J

Purpose: A novel leaf-sequencing algorithm is developed for generating arbitrary beam intensity profiles in discrete levels using dynamic multileaf collimator (MLC). The efficiency of this dynamic MLC leaf-sequencing method was evaluated using external beam treatment plans delivered by intensity modulated radiation therapy technique. Methods: To qualify and validate this algorithm, integral test for the beam segment of MLC generated by the CORVUS treatment planning system was performed with clinical intensity map experiments. The treatment plans were optimized and the fluence maps for all photon beams were determined. This algorithm started with the algebraic expression for the area under the beammore » profile. The coefficients in the expression can be transformed into the specifications for the leaf-setting sequence. The leaf optimization procedure was then applied and analyzed for clinical relevant intensity profiles in cancer treatment. Results: The macrophysical effect of this method can be described by volumetric plan evaluation tools such as dose-volume histograms (DVHs). The DVH results are in good agreement compared to those from the CORVUS treatment planning system. Conclusion: We developed a dynamic MLC method to examine the stability of leaf speed including effects of acceleration and deceleration of leaf motion in order to make sure the stability of leaf speed did not affect the intensity profile generated. It was found that the mechanical requirements were better satisfied using this method. The Project is sponsored by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry.« less

Variable Number of Tandem Repeat Markers in the Genome Sequence of Mycosphaerella Fijiensis, the Causal Agent of Black Leaf Streak Disease of Banana (Musa spp.)

USDA-ARS?s Scientific Manuscript database

Mycosphaerella fijiensis, the causal agent of banana leaf streak disease (commonly known as black Sigatoka), is the most devastating pathogen attacking bananas (Musa spp). Recently the whole genome sequence of M. fijiensis became available. This sequence was screened for the presence of Variable Num...

Mapping and genomic targeting of the major leaf shape gene (L) in Upland cotton (Gossypium hirsutum L.).

PubMed

Andres, Ryan J; Bowman, Daryl T; Kaur, Baljinder; Kuraparthy, Vasu

2014-01-01

A major leaf shape locus (L) was mapped with molecular markers and genomically targeted to a small region in the D-genome of cotton. By using expression analysis and candidate gene mapping, two LMI1 -like genes are identified as possible candidates for leaf shape trait in cotton. Leaf shape in cotton is an important trait that influences yield, flowering rates, disease resistance, lint trash, and the efficacy of foliar chemical application. The leaves of okra leaf cotton display a significantly enhanced lobing pattern, as well as ectopic outgrowths along the lobe margins when compared with normal leaf cotton. These phenotypes are the hallmark characteristics of mutations in various known modifiers of leaf shape that culminate in the mis/over-expression of Class I KNOX genes. To better understand the molecular and genetic processes underlying leaf shape in cotton, a normal leaf accession (PI607650) was crossed to an okra leaf breeding line (NC05AZ21). An F2 population of 236 individuals confirmed the incompletely dominant single gene nature of the okra leaf shape trait in Gossypium hirsutum L. Molecular mapping with simple sequence repeat markers localized the leaf shape gene to 5.4 cM interval in the distal region of the short arm of chromosome 15. Orthologous mapping of the closely linked markers with the sequenced diploid D-genome (Gossypium raimondii) tentatively resolved the leaf shape locus to a small genomic region. RT-PCR-based expression analysis and candidate gene mapping indicated that the okra leaf shape gene (L (o) ) in cotton might be an upstream regulator of Class I KNOX genes. The linked molecular markers and delineated genomic region in the sequenced diploid D-genome will assist in the future high-resolution mapping and map-based cloning of the leaf shape gene in cotton.

Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

PubMed

Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

2015-01-01

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

Sequence of Changes in Maize Responding to Soil Water Deficit and Related Critical Thresholds

PubMed Central

Ma, Xueyan; He, Qijin; Zhou, Guangsheng

2018-01-01

The sequence of changes in crop responding to soil water deficit and related critical thresholds are essential for better drought damage classification and drought monitoring indicators. This study was aimed to investigate the critical thresholds of maize growth and physiological characteristics responding to changing soil water and to reveal the sequence of changes in maize responding to soil water deficit both in seedling and jointing stages based on 2-year’s maize field experiment responding to six initial soil water statuses conducted in 2013 and 2014. Normal distribution tolerance limits were newly adopted to identify critical thresholds of maize growth and physiological characteristics to a wide range of soil water status. The results showed that in both stages maize growth characteristics related to plant water status [stem moisture content (SMC) and leaf moisture content (LMC)], leaf gas exchange [net photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs)], and leaf area were sensitive to soil water deficit, while biomass-related characteristics were less sensitive. Under the concurrent weather conditions and agronomic managements, the critical soil water thresholds in terms of relative soil moisture of 0–30 cm depth (RSM) of maize SMC, LMC, net Pn, Tr, Gs, and leaf area were 72, 65, 62, 60, 58, and 46%, respectively, in seedling stage, and 64, 64, 51, 53, 48, and 46%, respectively, in jointing stage. It indicated that there is a sequence of changes in maize responding to soil water deficit, i.e., their response sequences as soil water deficit intensified: SMC ≥ LMC > leaf gas exchange > leaf area in both stages. This sequence of changes in maize responding to soil water deficit and related critical thresholds may be better indicators of damage classification and drought monitoring. PMID:29765381

A novel algorithm for the reconstruction of an entrance beam fluence from treatment exit patient portal dosimetry images

NASA Astrophysics Data System (ADS)

Sperling, Nicholas Niven

The problem of determining the in vivo dosimetry for patients undergoing radiation treatment has been an area of interest since the development of the field. Most methods which have found clinical acceptance work by use of a proxy dosimeter, e.g.: glass rods, using radiophotoluminescence; thermoluminescent dosimeters (TLD), typically CaF or LiF; Metal Oxide Silicon Field Effect Transistor (MOSFET) dosimeters, using threshold voltage shift; Optically Stimulated Luminescent Dosimeters (OSLD), composed of Carbon doped Aluminum Dioxide crystals; RadioChromic film, using leuko-dye polymers; Silicon Diode dosimeters, typically p-type; and ion chambers. More recent methods employ Electronic Portal Image Devices (EPID), or dosimeter arrays, for entrance or exit beam fluence determination. The difficulty with the proxy in vivo dosimetery methods is the requirement that they be placed at the particular location where the dose is to be determined. This precludes measurements across the entire patient volume. These methods are best suited where the dose at a particular location is required. The more recent methods of in vivo dosimetry make use of detector arrays and reconstruction techniques to determine dose throughout the patient volume. One method uses an array of ion chambers located upstream of the patient. This requires a special hardware device and places an additional attenuator in the beam path, which may not be desirable. A final approach is to use the existing EPID, which is part of most modern linear accelerators, to image the patient using the treatment beam. Methods exist to deconvolve the detector function of the EPID using a series of weighted exponentials. Additionally, this method has been extended to determine in vivo dosimetry. The method developed here employs the use of EPID images and an iterative deconvolution algorithm to reconstruct the impinging primary beam fluence on the patient. This primary fluence may then be employed to determine dose through the entire patient volume. The method requires patient specific information, including a CT for deconvolution/dose reconstruction. With the large-scale adoption of Cone Beam CT (CBCT) systems on modern linear accelerators, a treatment time CT is readily available for use in this deconvolution and in dose representation.

The impact of cine EPID image acquisition frame rate on markerless soft-tissue tracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yip, Stephen, E-mail: syip@lroc.harvard.edu; Rottmann, Joerg; Berbeco, Ross

2014-06-15

Purpose: Although reduction of the cine electronic portal imaging device (EPID) acquisition frame rate through multiple frame averaging may reduce hardware memory burden and decrease image noise, it can hinder the continuity of soft-tissue motion leading to poor autotracking results. The impact of motion blurring and image noise on the tracking performance was investigated. Methods: Phantom and patient images were acquired at a frame rate of 12.87 Hz with an amorphous silicon portal imager (AS1000, Varian Medical Systems, Palo Alto, CA). The maximum frame rate of 12.87 Hz is imposed by the EPID. Low frame rate images were obtained bymore » continuous frame averaging. A previously validated tracking algorithm was employed for autotracking. The difference between the programmed and autotracked positions of a Las Vegas phantom moving in the superior-inferior direction defined the tracking error (δ). Motion blurring was assessed by measuring the area change of the circle with the greatest depth. Additionally, lung tumors on 1747 frames acquired at 11 field angles from four radiotherapy patients are manually and automatically tracked with varying frame averaging. δ was defined by the position difference of the two tracking methods. Image noise was defined as the standard deviation of the background intensity. Motion blurring and image noise are correlated with δ using Pearson correlation coefficient (R). Results: For both phantom and patient studies, the autotracking errors increased at frame rates lower than 4.29 Hz. Above 4.29 Hz, changes in errors were negligible withδ < 1.60 mm. Motion blurring and image noise were observed to increase and decrease with frame averaging, respectively. Motion blurring and tracking errors were significantly correlated for the phantom (R = 0.94) and patient studies (R = 0.72). Moderate to poor correlation was found between image noise and tracking error with R −0.58 and −0.19 for both studies, respectively. Conclusions: Cine EPID image acquisition at the frame rate of at least 4.29 Hz is recommended. Motion blurring in the images with frame rates below 4.29 Hz can significantly reduce the accuracy of autotracking.« less

Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance.

PubMed

Ganeshan, Seedhabadee; Sharma, Pallavi; Young, Lester; Kumar, Ashwani; Fowler, D Brian; Chibbar, Ravindra N

2011-03-01

Low-temperature (LT) tolerance in winter wheat (Triticum aestivum L.) is an economically important but complex trait. Four selected wheat genotypes, a winter hardy cultivar, Norstar, a tender spring cultivar, Manitou and two near-isogenic lines with Vrn-A1 (spring Norstar) and vrn-A1 (winter Manitou) alleles of Manitou and Norstar were cold-acclimated at 6°C and crown and leaf tissues were collected at 0, 2, 14, 21, 35, 42, 56 and 70 days of cold acclimation. cDNA-AFLP profiling was used to determine temporal expression profiles of transcripts during cold-acclimation in crown and leaf tissues, separately to determine if LT regulatory circuitries in crown and leaf tissues could be delineated using this approach. Screening 64 primer combinations identified 4,074 and 2,757 differentially expressed transcript-derived fragments (TDFs) out of which 38 and 16% were up-regulated as compared to 3 and 6% that were down-regulated in crown and leaf tissues, respectively. DNA sequencing of TDFs revealed sequences common to both tissues including genes coding for DEAD-box RNA helicase, choline-phosphate cytidylyltransferase and delta-1-pyrroline carboxylate synthetase. TDF specific to crown tissues included genes coding for phospahtidylinositol kinase, auxin response factor protein and brassinosteroid insensitive 1-associated receptor kinase. In leaf, genes such as methylene tetrahydrofolate reductase, NADH-cytochrome b5 reductase and malate dehydrogenase were identified. However, 30 and 14% of the DNA sequences from the crown and leaf tissues, respectively, were hypothetical or unknown proteins. Cluster analysis of up-, down-regulated and unique TDFs, DNA sequence and real-time PCR validation, infer that mechanisms operating in crown and leaf tissue in response to LT are differently regulated and warrant further studies.

Draft genome sequence of rice orange leaf phytoplasma from Guangdong, China

USDA-ARS?s Scientific Manuscript database

The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, P. R. China, was sequenced. The draft LD1genome is 599,264 bp with GC content of 28.2%, 647 predicted open reading frames and 33 RNA genes....

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

PubMed Central

Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

2017-01-01

To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat. PMID:28932215

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease.

PubMed

Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

2017-01-01

To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae . Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae . Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

Optimisation of the imaging and dosimetric characteristics of an electronic portal imaging device employing plastic scintillating fibres using Monte Carlo simulations.

PubMed

Blake, S J; McNamara, A L; Vial, P; Holloway, L; Kuncic, Z

2014-11-21

A Monte Carlo model of a novel electronic portal imaging device (EPID) has been developed using Geant4 and its performance for imaging and dosimetry applications in radiotherapy has been characterised. The EPID geometry is based on a physical prototype under ongoing investigation and comprises an array of plastic scintillating fibres in place of the metal plate/phosphor screen in standard EPIDs. Geometrical and optical transport parameters were varied to investigate their impact on imaging and dosimetry performance. Detection efficiency was most sensitive to variations in fibre length, achieving a peak value of 36% at 50 mm using 400 keV x-rays for the lengths considered. Increases in efficiency for longer fibres were partially offset by reductions in sensitivity. Removing the extra-mural absorber surrounding individual fibres severely decreased the modulation transfer function (MTF), highlighting its importance in maximising spatial resolution. Field size response and relative dose profile simulations demonstrated a water-equivalent dose response and thus the prototype's suitability for dosimetry applications. Element-to-element mismatch between scintillating fibres and underlying photodiode pixels resulted in a reduced MTF for high spatial frequencies and quasi-periodic variations in dose profile response. This effect is eliminated when fibres are precisely matched to underlying pixels. Simulations strongly suggest that with further optimisation, this prototype EPID may be capable of simultaneous imaging and dosimetry in radiotherapy.

SU-F-T-262: Commissioning Varian Portal Dosimetry for EPID-Based Patient Specific QA in a Non-Aria Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmidt, M; Knutson, N; University of Rhode Island, Kingston, RI

2016-06-15

Purpose: Development of an in-house program facilitates a workflow that allows Electronic Portal Imaging Device (EPID) patient specific quality assurance (QA) measurements to be acquired and analyzed in the Portal Dosimetry Application (Varian Medical Systems, Palo Alto, CA) using a non-Aria Record and Verify (R&V) system (MOSAIQ, Elekta, Crawley, UK) to deliver beams in standard clinical treatment mode. Methods: Initial calibration of an in-house software tool includes characterization of EPID dosimetry parameters by importing DICOM images of varying delivered MUs to determine linear mapping factors in order to convert image pixel values to Varian-defined Calibrated Units (CU). Using this information,more » the Portal Dose Image Prediction (PDIP) algorithm was commissioned by converting images of various field sizes to output factors using the Eclipse Scripting Application Programming Interface (ESAPI) and converting a delivered configuration fluence to absolute dose units. To verify the algorithm configuration, an integrated image was acquired, exported directly from the R&V client, automatically converted to a compatible, calibrated dosimetric image, and compared to a PDIP calculated image using Varian’s Portal Dosimetry Application. Results: For two C-Series and one TrueBeam Varian linear accelerators, gamma comparisons (global 3% / 3mm) of PDIP algorithm predicted dosimetric images and images converted via the inhouse system demonstrated agreement for ≥99% of all pixels, exceeding vendor-recommended commissioning guidelines. Conclusion: Combinations of a programmatic image conversion tool and ESAPI allow for an efficient and accurate method of patient IMRT QA incorporating a 3rd party R&V system.« less

Generation and Analysis of a Large-Scale Expressed Sequence Tag Database from a Full-Length Enriched cDNA Library of Developing Leaves of Gossypium hirsutum L

PubMed Central

Pang, Chaoyou; Fan, Shuli; Song, Meizhen; Yu, Shuxun

2013-01-01

Background Cotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. Methodology/Principal Findings In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. Conclusions/Significance These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in G. hirsutum and comparative genomics among Gossypium species. PMID:24146870

Litter Breakdown and Microbial Succession on Two Submerged Leaf Species in a Small Forested Stream

PubMed Central

Newman, Molli M.; Liles, Mark R.; Feminella, Jack W.

2015-01-01

Microbial succession during leaf breakdown was investigated in a small forested stream in west-central Georgia, USA, using multiple culture-independent techniques. Red maple (Acer rubrum) and water oak (Quercus nigra) leaf litter were incubated in situ for 128 days, and litter breakdown was quantified by ash-free dry mass (AFDM) method and microbial assemblage composition using phospholipid fatty acid analysis (PLFA), ribosomal intergenic spacer analysis (RISA), denaturing gradient gel electrophoresis (DGGE), and bar-coded next-generation sequencing of 16S rRNA gene amplicons. Leaf breakdown was faster for red maple than water oak. PLFA revealed a significant time effect on microbial lipid profiles for both leaf species. Microbial assemblages on maple contained a higher relative abundance of bacterial lipids than oak, and oak microbial assemblages contained higher relative abundance of fungal lipids than maple. RISA showed that incubation time was more important in structuring bacterial assemblages than leaf physicochemistry. DGGE profiles revealed high variability in bacterial assemblages over time, and sequencing of DGGE-resolved amplicons indicated several taxa present on degrading litter. Next-generation sequencing revealed temporal shifts in dominant taxa within the phylum Proteobacteria, whereas γ-Proteobacteria dominated pre-immersion and α- and β-Proteobacteria dominated after 1 month of instream incubation; the latter groups contain taxa that are predicted to be capable of using organic material to fuel further breakdown. Our results suggest that incubation time is more important than leaf species physicochemistry in influencing leaf litter microbial assemblage composition, and indicate the need for investigation into seasonal and temporal dynamics of leaf litter microbial assemblage succession. PMID:26098687

Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.

PubMed

Chauhan, Sushma; Rahman, Hifzur; Mastan, Shaik G; Pamidimarri, D V N Sudheer; Reddy, Muppala P

2018-07-20

Begomoviruses belong to the family Geminiviridae are associated with several disease symptoms, such as mosaic and leaf curling in Jatropha curcas. The molecular characterization of these viral strains will help in developing management strategies to control the disease. In this study, J. curcas that was infected with begomovirus and showed acute leaf curling symptoms were identified. DNA-A segment from pathogenic viral strain was isolated and sequenced. The sequenced genome was assembled and characterized in detail. The full-length DNA-A sequence was covered by primer walking. The genome sequence showed the general organization of DNA-A from begomovirus by the distribution of ORFs in both viral and anti-viral strands. The genome size ranged from 2844 bp-2852 bp. Three strains with minor nucleotide variations were identified, and a phylogenetic analysis was performed by comparing the DNA-A segments from other reported begomovirus isolates. The maximum sequence similarity was observed with Euphorbia yellow mosaic virus (FN435995). In the phylogenetic tree, no clustering was observed with previously reported begomovirus strains isolated from J. curcas host. The strains isolated in this study belong to new begomoviral strain that elicits symptoms of leaf curling in J. curcas. The results indicate that the probable origin of the strains is from Jatropha mosaic virus infecting J. gassypifolia. The strains isolated in this study are referred as Jatropha curcas leaf curl India virus (JCLCIV) based on the major symptoms exhibited by host J. curcas. Copyright © 2018 Elsevier B.V. All rights reserved.

Identification of a disease complex involving a novel monopartite begomovirus with beta- and alphasatellites associated with okra leaf curl disease in Oman.

PubMed

Akhtar, Sohail; Khan, Akhtar J; Singh, Achuit S; Briddon, Rob W

2014-05-01

Okra leaf curl disease (OLCD) is an important viral disease of okra in tropical and subtropical areas. The disease is caused by begomovirus-satellite complexes. A begomovirus and associated betasatellite and alphasatellite were identified in symptomatic okra plants from Barka, in the Al-Batinah region of Oman. Analysis of the begomovirus sequences showed them to represent a new begomovirus most closely related to cotton leaf curl Gezira virus (CLCuGeV), a begomovirus of African origin. The sequences showed less than 85 % nucleotide sequence identity to CLCuGeV isolates. The name okra leaf curl Oman virus (OLCOMV) is proposed for the new virus. Further analysis revealed that the OLCOMV is a recombinant begomovirus that evolved by the recombination of CLCuGeV isolates with tomato yellow leaf curl virus-Oman (TYLCV-OM). An alpha- and a betasatellite were also identified from the same plant sample, which were also unique when compared to sequences available in the databases. However, although the betasatellite appeared to be of African origin, the alphasatellite was most closely related to alphasatellites originating from South Asia. This is the first report of a begomovirus-satellite complex infecting okra in Oman.

SU-E-T-458: Determining Threshold-Of-Failure for Dead Pixel Rows in EPID-Based Dosimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gersh, J; Wiant, D

Purpose: A pixel correction map is applied to all EPID-based applications on the TrueBeam (Varian Medical Systems, Palo Alto, CA). When dead pixels are detected, an interpolative smoothing algorithm is applied using neighboring-pixel information to supplement missing-pixel information. The vendor suggests that when the number of dead pixels exceeds 70,000, the panel should be replaced. It is common for entire detector rows to be dead, as well as their neighboring rows. Approximately 70 rows can be dead before the panel reaches this threshold. This study determines the number of neighboring dead-pixel rows that would create a large enough deviation inmore » measured fluence to cause failures in portal dosimetry (PD). Methods: Four clinical two-arc VMAT plans were generated using Eclipse's AXB algorithm and PD plans were created using the PDIP algorithm. These plans were chosen to represent those commonly encountered in the clinic: prostate, lung, abdomen, and neck treatments. During each iteration of this study, an increasing number of dead-pixel rows are artificially applied to the correction map and a fluence QA is performed using the EPID (corrected with this map). To provide a worst-case-scenario, the dead-pixel rows are chosen so that they present artifacts in the highfluence region of the field. Results: For all eight arc-fields deemed acceptable via a 3%/3mm gamma analysis (pass rate greater than 99%), VMAT QA yielded identical results with a 5 pixel-width dead zone. When 10 dead lines were present, half of the fields had pass rates below the 99% pass rate. With increasing dead rows, the pass rates were reduced substantially. Conclusion: While the vendor still suggests to request service at the point where 70,000 dead rows are measured (as recommended by the vendor), the authors suggest that service should be requested when there are greater than 5 consecutive dead rows.« less

The stability of liquid-filled matrix ionization chamber electronic portal imaging devices for dosimetry purposes.

PubMed

Louwe, R J W; Tielenburg, R; van Ingen, K M; Mijnheer, B J; van Herk, M B

2004-04-01

This study was performed to determine the stability of liquid-filled matrix ionization chamber (LiFi-type) electronic portal imaging devices (EPID) for dosimetric purposes. The short- and long-term stability of the response was investigated, as well as the importance of factors influencing the response (e.g., temperature fluctuations, radiation damage, and the performance of the electronic hardware). It was shown that testing the performance of the electronic hardware as well as the short-term stability of the imagers may reveal the cause of a poor long-term stability of the imager response. In addition, the short-term stability was measured to verify the validity of the fitted dose-response curve immediately after beam startup. The long-term stability of these imagers could be considerably improved by correcting for room temperature fluctuations and gradual changes in response due to radiation damage. As a result, the reproducibility was better than 1% (1 SD) over a period of two years. The results of this study were used to formulate recommendations for a quality control program for portal dosimetry. The effect of such a program was assessed by comparing the results of portal dosimetry and in vivo dosimetry using diodes during the treatment of 31 prostate patients. The improvement of the results for portal dosimetry was consistent with the deviations observed with the reproducibility tests in that particular period. After a correction for the variation in response of the imager, the average difference between the measured and prescribed dose during the treatment of prostate patients was -0.7%+/-1.5% (1 SD), and -0.6%+/-1.1% (1 SD) for EPID and diode in vivo dosimetry, respectively. It can be concluded that a high stability of the response can be achieved for this type of EPID by applying a rigorous quality control program.

Development of Novel Treatment Plan Verification Techniques for Prostate Intensity Modulation Arc Therapy

DTIC Science & Technology

2010-03-01

is to develop a novel clinical useful delivered-dose verification protocol for modern prostate VMAT using Electronic Portal Imaging Device (EPID...technique. A number of important milestones have been accomplished, which include (i) calibrated CBCT HU vs. electron density curve; (ii...prostate  VMAT  using  Electronic   Portal  Imaging  Device  (EPID)  and  onboard Cone beam Computed Tomography (CBCT).  The specific aims of this project

The CC-NB-LRR-Type Rdg2a Resistance Gene Confers Immunity to the Seed-Borne Barley Leaf Stripe Pathogen in the Absence of Hypersensitive Cell Death

PubMed Central

Collins, Nicholas C.; Consonni, Gabriella; Stanca, Antonio M.; Schulze-Lefert, Paul; Valè, Giampiero

2010-01-01

Background Leaf stripe disease on barley (Hordeum vulgare) is caused by the seed-transmitted hemi-biotrophic fungus Pyrenophora graminea. Race-specific resistance to leaf stripe is controlled by two known Rdg (Resistance to Drechslera graminea) genes: the H. spontaneum-derived Rdg1a and Rdg2a, identified in H. vulgare. The aim of the present work was to isolate the Rdg2a leaf stripe resistance gene, to characterize the Rdg2a locus organization and evolution and to elucidate the histological bases of Rdg2a-based leaf stripe resistance. Principal Findings We describe here the positional cloning and functional characterization of the leaf stripe resistance gene Rdg2a. At the Rdg2a locus, three sequence-related coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NB-LRR) encoding genes were identified. Sequence comparisons suggested that paralogs of this resistance locus evolved through recent gene duplication, and were subjected to frequent sequence exchange. Transformation of the leaf stripe susceptible cv. Golden Promise with two Rdg2a-candidates under the control of their native 5′ regulatory sequences identified a member of the CC-NB-LRR gene family that conferred resistance against the Dg2 leaf stripe isolate, against which the Rdg2a-gene is effective. Histological analysis demonstrated that Rdg2a-mediated leaf stripe resistance involves autofluorescing cells and prevents pathogen colonization in the embryos without any detectable hypersensitive cell death response, supporting a cell wall reinforcement-based resistance mechanism. Conclusions This work reports about the cloning of a resistance gene effective against a seed borne disease. We observed that Rdg2a was subjected to diversifying selection which is consistent with a model in which the R gene co-evolves with a pathogen effector(s) gene. We propose that inducible responses giving rise to physical and chemical barriers to infection in the cell walls and intercellular spaces of the barley embryo tissues represent mechanisms by which the CC-NB-LRR-encoding Rdg2a gene mediates resistance to leaf stripe in the absence of hypersensitive cell death. PMID:20844752

IMRT sequencing for a six-bank multi-leaf system.

PubMed

Topolnjak, R; van der Heide, U A; Lagendijk, J J W

2005-05-07

In this study, we present a sequencer for delivering step-and-shoot IMRT using a six-bank multi-leaf system. Such a system was proposed earlier and combines a high-resolution field-shaping ability with a large field size. It consists of three layers of two opposing leaf banks with 1 cm leaves. The layers are rotated relative to each other at 60 degrees . A low-resolution mode of sequencing is achieved by using one layer of leaves as primary MLC, while the other two are used to improve back-up collimation. For high-resolution sequencing, an algorithm is presented that creates segments shaped by all six banks. Compared to a hypothetical mini-MLC with 0.4 cm leaves, a similar performance can be achieved, but a trade-off has to be made between accuracy and the number of segments.

Dynamic tumor tracking using the Elekta Agility MLC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fast, Martin F., E-mail: martin.fast@icr.ac.uk; Nill, Simeon, E-mail: simeon.nill@icr.ac.uk; Bedford, James L.

2014-11-01

Purpose: To evaluate the performance of the Elekta Agility multileaf collimator (MLC) for dynamic real-time tumor tracking. Methods: The authors have developed a new control software which interfaces to the Agility MLC to dynamically program the movement of individual leaves, the dynamic leaf guides (DLGs), and the Y collimators (“jaws”) based on the actual target trajectory. A motion platform was used to perform dynamic tracking experiments with sinusoidal trajectories. The actual target positions reported by the motion platform at 20, 30, or 40 Hz were used as shift vectors for the MLC in beams-eye-view. The system latency of the MLCmore » (i.e., the average latency comprising target device reporting latencies and MLC adjustment latency) and the geometric tracking accuracy were extracted from a sequence of MV portal images acquired during irradiation for the following treatment scenarios: leaf-only motion, jaw + leaf motion, and DLG + leaf motion. Results: The portal imager measurements indicated a clear dependence of the system latency on the target position reporting frequency. Deducting the effect of the target frequency, the leaf adjustment latency was measured to be 38 ± 3 ms for a maximum target speed v of 13 mm/s. The jaw + leaf adjustment latency was 53 ± 3 at a similar speed. The system latency at a target position frequency of 30 Hz was in the range of 56–61 ms for the leaves (v ≤ 31 mm/s), 71–78 ms for the jaw + leaf motion (v ≤ 25 mm/s), and 58–72 ms for the DLG + leaf motion (v ≤ 59 mm/s). The tracking accuracy showed a similar dependency on the target position frequency and the maximum target speed. For the leaves, the root-mean-squared error (RMSE) was between 0.6–1.5 mm depending on the maximum target speed. For the jaw + leaf (DLG + leaf) motion, the RMSE was between 0.7–1.5 mm (1.9–3.4 mm). Conclusions: The authors have measured the latency and geometric accuracy of the Agility MLC, facilitating its future use for clinical tracking applications.« less

[Association of phytoplasma with Bermuda grass white-leaf disease].

PubMed

Tan, Weijun; Chen, Yong; Zhang, Wu; Han, Chengchou; Tan, Zhiyuan; Zhang, Juming

2008-10-01

Bermuda grass white leaf is an important disease on Bermuda grass all over the world. The aim of this research is to identify the pathogen which leads to Bermuda grass white leaf occurring on the Chinese mainland. PCR amplification technique, sequence analysis and Southern hybridization were used. A 1.3 kb fragment was amplified by PCR phytoplasma universal primers and total DNA sample extracted from ill Bermuda grass as the amplified template. Sequence analysis of the amplified fragment indicated it clustered into Candidatus Phytoplasm Cynodontis. Southern hybridization analysis showed differential cingulums. The pathogen of Bermuda grass white leaf on the Chinese mainland contains phytoplasma, which provides a scientific basis for further identification, prevention and control of the disease.

SU-G-BRB-06: Commissioning and Evaluation of EPID-Based in Vivo Dosimetry Software Using a Tissue-Maximum Ratio Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Held, M; Cheung, J; Morin, O

Purpose: To commission and evaluate an in vivo EPID-based transit dosimetry software (EPIgray, DOSIsoft, Cachan, France) using simple fields and TG119-based IMRT treatment plans. Methods: EPIgray was commissioned on a Truebeam based on finite tissue-maximum ratio (fTMR) measurements with solid water blocks of thicknesses between 0 and 37 cm. Field sizes varied from 2×2 to 20×20 cm{sup 2}. Subsequently, treatment plans of single and opposed beams with field sizes between 4×4 and 15×15 cm{sup 2} as well as IMRT plans were measured to evaluate the dose reconstruction accuracy. Single field dose predictions were made for anterior-posterior and lateral beams. IMRTmore » plans were created based on TG119 recommendations. The reconstructed dose was compared to the planned dose for selected points at isocenter and away from isocenter. Results: For single square fields, the dose in EPIgray was reconstructed within 3% accuracy at isocenter relative to the planned dose. Similarly, the relative deviation of the total dose was accurately reconstructed within 3% for all IMRT plans with points placed inside a high dose region near the isocenter. Predictions became less accurate than 5% when the evaluation point was outside the majority of IMRT beam segments. Additionally, points 5 cm or more away from the isocenter or within an avoidance structure were predicted less reliably. Conclusion: EPIgray formalism accuracy is adequate for an efficient error detection system. It provides immediate intra-fractional feedback on the delivery of treatment plans without affecting the treatment beam. Besides the EPID, no additional hardware is required, which makes it accessible to all clinics. The software evaluates point dose measurements to verify treatment plan delivery and patient positioning within 5% accuracy, depending on the placement of evaluation points. EPIgray is not intended to replace patient-specific quality assurance but should be utilized as an additional layer of safety for continuous patient treatment verification. This research is supported by DOSIsoft.« less

Continuous intensity map optimization (CIMO): A novel approach to leaf sequencing in step and shoot IMRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao Daliang; Earl, Matthew A.; Luan, Shuang

2006-04-15

A new leaf-sequencing approach has been developed that is designed to reduce the number of required beam segments for step-and-shoot intensity modulated radiation therapy (IMRT). This approach to leaf sequencing is called continuous-intensity-map-optimization (CIMO). Using a simulated annealing algorithm, CIMO seeks to minimize differences between the optimized and sequenced intensity maps. Two distinguishing features of the CIMO algorithm are (1) CIMO does not require that each optimized intensity map be clustered into discrete levels and (2) CIMO is not rule-based but rather simultaneously optimizes both the aperture shapes and weights. To test the CIMO algorithm, ten IMRT patient cases weremore » selected (four head-and-neck, two pancreas, two prostate, one brain, and one pelvis). For each case, the optimized intensity maps were extracted from the Pinnacle{sup 3} treatment planning system. The CIMO algorithm was applied, and the optimized aperture shapes and weights were loaded back into Pinnacle. A final dose calculation was performed using Pinnacle's convolution/superposition based dose calculation. On average, the CIMO algorithm provided a 54% reduction in the number of beam segments as compared with Pinnacle's leaf sequencer. The plans sequenced using the CIMO algorithm also provided improved target dose uniformity and a reduced discrepancy between the optimized and sequenced intensity maps. For ten clinical intensity maps, comparisons were performed between the CIMO algorithm and the power-of-two reduction algorithm of Xia and Verhey [Med. Phys. 25(8), 1424-1434 (1998)]. When the constraints of a Varian Millennium multileaf collimator were applied, the CIMO algorithm resulted in a 26% reduction in the number of segments. For an Elekta multileaf collimator, the CIMO algorithm resulted in a 67% reduction in the number of segments. An average leaf sequencing time of less than one minute per beam was observed.« less

The role of corchorus in spreading of tomato yellow leaf curl virus on tomato in Jeddah, Saudi Arabia.

PubMed

Sohrab, Sayed Sartaj

2016-03-01

Corchorus (Corchorus capsularis L. and Corchorus olitorius L.) is one of the most important fiber crops grown in tropical and subtropical regions throughout the world. Field survey was conducted and naturally infected leaf samples were collected from corchorus and tomato plants in Jeddah, Saudi Arabia. The causal virus was transmitted by whiteflies to tomato plants and begomovirus infection was confirmed by Polymerase chain reaction. The complete viral genome and associated betasatellites were amplified, cloned and sequenced from both corchorus and tomato samples. The genetic variability and phylogenetic relationships were determined for both isolates (corchorus and tomato). The complete genome sequences showed highest (99.5 % nt) similarity with tomato yellow leaf curl virus (TYLCV) and formed closest cluster with TYLCV-Tomato reported from Jizan and Al-Qasim, Saudi Arabia and betasatellites sequences showed highest similarity (99.8 % nt) with Tomato yellow leaf curl betasatellites-Jeddah followed by Tomato yellow leaf curl Oman betasatellites and formed closed cluster with TYLCV-Tomato. On the basis of results obtained from whiteflies transmission, sequence similarity and phylogenetic relationships; it is concluded that the identified virus could be a variant of TYLCV circulating in the Kingdom. The significance of this study demonstrated that the corchorus is serving as reservoir and alternative host and playing an important role in spreading the begomovirus associated disease in the Kingdom of Saudi Arabia.

Complete nucleotide sequences of okra isolates of Cotton leaf curl Gezira virus and their associated DNA-beta from Niger.

PubMed

Shih, S L; Kumar, S; Tsai, W S; Lee, L M; Green, S K

2009-01-01

Okra (Abelmoschus esculentus) is a major crop in Niger. In the fall of 2007, okra leaf curl disease was observed in Niger and the begomovirus and DNA-beta satellite were found associated with the disease. The complete nucleotide sequences of DNA-A (FJ469626 and FJ469627) and associated DNA-beta satellites (FJ469628 and FJ469629) were determined from two samples. This is the first report of molecular characterization of okra-infecting begomovirus and their associated DNA-beta from Niger. The begomovirus and DNA-beta have been identified as Cotton leaf curl Gezira virus and Cotton leaf curl Gezira betasatellite, respectively, which are reported to also infect okra in Egypt, Mali and Sudan.

Portal imaging based definition of the planning target volume during pelvic irradiation for gynecological malignancies.

PubMed

Mock, U; Dieckmann, K; Wolff, U; Knocke, T H; Pötter, R

1999-08-01

Geometrical accuracy in patient positioning can vary substantially during external radiotherapy. This study estimated the set-up accuracy during pelvic irradiation for gynecological malignancies for determination of safety margins (planning target volume, PTV). Based on electronic portal imaging devices (EPID), 25 patients undergoing 4-field pelvic irradiation for gynecological malignancies were analyzed with regard to set-up accuracy during the treatment course. Regularly performed EPID images were used in order to systematically assess the systematic and random component of set-up displacements. Anatomical matching of verification and simulation images was followed by measuring corresponding distances between the central axis and anatomical features. Data analysis of set-up errors referred to the x-, y-,and z-axes. Additionally, cumulative frequencies were evaluated. A total of 50 simulation films and 313 verification images were analyzed. For the anterior-posterior (AP) beam direction mean deviations along the x- and z-axes were 1.5 mm and -1.9 mm, respectively. Moreover, random errors of 4.8 mm (x-axis) and 3.0 mm (z-axis) were determined. Concerning the latero-lateral treatment fields, the systematic errors along the two axes were calculated to 2.9 mm (y-axis) and -2.0 mm (z-axis) and random errors of 3.8 mm and 3.5 mm were found, respectively. The cumulative frequency of misalignments < or =5 mm showed values of 75% (AP fields) and 72% (latero-lateral fields). With regard to cumulative frequencies < or =10 mm quantification revealed values of 97% for both beam directions. During external pelvic irradiation therapy for gynecological malignancies, EPID images on a regular basis revealed acceptable set-up inaccuracies. Safety margins (PTV) of 1 cm appear to be sufficient, accounting for more than 95% of all deviations.

Respiratory gating during stereotactic body radiotherapy for lung cancer reduces tumor position variability.

PubMed

Saito, Tetsuo; Matsuyama, Tomohiko; Toya, Ryo; Fukugawa, Yoshiyuki; Toyofuku, Takamasa; Semba, Akiko; Oya, Natsuo

2014-01-01

We evaluated the effects of respiratory gating on treatment accuracy in lung cancer patients undergoing lung stereotactic body radiotherapy by using electronic portal imaging device (EPID) images. Our study population consisted of 30 lung cancer patients treated with stereotactic body radiotherapy (48 Gy/4 fractions/4 to 9 days). Of these, 14 were treated with- (group A) and 16 without gating (group B); typically the patients whose tumors showed three-dimensional respiratory motion ≧5 mm were selected for gating. Tumor respiratory motion was estimated using four-dimensional computed tomography images acquired during treatment simulation. Tumor position variability during all treatment sessions was assessed by measuring the standard deviation (SD) and range of tumor displacement on EPID images. The two groups were compared for tumor respiratory motion and position variability using the Mann-Whitney U test. The median three-dimensional tumor motion during simulation was greater in group A than group B (9 mm, range 3-30 mm vs. 2 mm, range 0-4 mm; p<0.001). In groups A and B the median SD of the tumor position was 1.1 mm and 0.9 mm in the craniocaudal- (p = 0.24) and 0.7 mm and 0.6 mm in the mediolateral direction (p = 0.89), respectively. The median range of the tumor position was 4.0 mm and 3.0 mm in the craniocaudal- (p = 0.21) and 2.0 mm and 1.5 mm in the mediolateral direction (p = 0.20), respectively. Although patients treated with respiratory gating exhibited greater respiratory tumor motion during treatment simulation, tumor position variability in the EPID images was low and comparable to patients treated without gating. This demonstrates the benefit of respiratory gating.

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties.

PubMed

Rama Reddy, Nagaraja Reddy; Mehta, Rucha Harishbhai; Soni, Palak Harendrabhai; Makasana, Jayanti; Gajbhiye, Narendra Athamaram; Ponnuchamy, Manivel; Kumar, Jitendra

2015-01-01

Senna (Cassia angustifolia Vahl.) is a world's natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of Cassia angustifolia using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with 'green plant database (txid 33090)', Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties

PubMed Central

Rama Reddy, Nagaraja Reddy; Mehta, Rucha Harishbhai; Soni, Palak Harendrabhai; Makasana, Jayanti; Gajbhiye, Narendra Athamaram; Ponnuchamy, Manivel; Kumar, Jitendra

2015-01-01

Senna (Cassia angustifolia Vahl.) is a world’s natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of Cassia angustifolia using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with ‘green plant database (txid 33090)’, Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna. PMID:26098898

Recent evolution of a novel begomovirus causing tomato leaf curl disease in the Al-Batinah region of Oman.

PubMed

Khan, Akhtar J; Akhtar, Sohail; Singh, Achuit K; Al-Shehi, Adel A; Al-Matrushi, Abdulrahman M; Ammara, Ume; Briddon, Rob W

2014-03-01

For last two decades, begomoviruses (family Geminiviridae) have been a major constraint for tomato production in Oman, particularly in the Al-Batinah region, the major agricultural area of Oman. Farms in the Al-Batinah region were surveyed during January-March and November-December in 2012 and January-February in 2013. Leaf samples of tomato plants showing typical leaf curl disease symptoms were collected and analyzed for begomoviruses. Out of fifteen begomovirus clones sequenced, seven were shown to be tomato yellow leaf curl virus strain Oman (TYLCV-OM); three, chili leaf curl virus strain Oman (ChLCV-OM); and one, tomato leaf curl Oman virus (ToLCOMV) - viruses that have previously been shown to occur in Oman. Four sequences were shown to have relatively low percent identity values to known begomoviruses, with the highest (86 %) to isolates of pepper leaf curl Lahore virus, indicating that these should be included in a new species, for which the name "Tomato leaf curl Al Batinah virus" (ToLCABV) is proposed. Although the betasatellite tomato leaf curl betasatellite (ToLCB; 7 full-length sequences isolated) was identified with some isolates of ChLCV-OM, TYLCV-OM and ToLCOMV, it was not identified in association with any of the ToLCABV isolates. Analysis of the sequences of the TYLCV-OM and ToLCOMV isolates characterized here did not show them to differ significantly from previously characterized isolates of these viruses. The three isolates of ChLCV-OM characterized were shown to have a recombination pattern distinct from earlier characterized isolates. ToLCABV was shown to have resulted from recombination between ChLCV-OM and ToLCOMV. A clone of ToLCABV was infectious by Agrobacterium-mediated inoculation to Nicotiana benthamiana and tomato, inducing symptoms typical of those seen in tomato in the field. Additionally, ToLCABV was shown to be able to interact in planta with ToLCB, resulting in a change in symptom phenotype, although the betasatellite did not appear to affect viral DNA levels.

Late Quaternary climate and environmental reconstruction based on leaf wax analyses in the loess sequence of Möhlin, Switzerland

NASA Astrophysics Data System (ADS)

Wüthrich, Lorenz; Bliedtner, Marcel; Kathrin Schäfer, Imke; Zech, Jana; Shajari, Fatemeh; Gaar, Dorian; Preusser, Frank; Salazar, Gary; Szidat, Sönke; Zech, Roland

2017-12-01

We present the results of leaf wax analyses (long-chain n-alkanes) from the 6.8 m deep loess sequence of Möhlin, Switzerland, spanning the last ˜ 70 kyr. Leaf waxes are well preserved and occur in sufficient amounts only down to 0.4 m and below 1.8 m depth, so no paleoenvironmental reconstructions can be done for marine isotope stage (MIS) 2. Compound-specific δ2Hwax analyses yielded similar values for late MIS 3 compared to the uppermost samples, indicating that various effects (e.g., more negative values due to lower temperatures, more positive values due to an enriched moisture source) cancel each other out. A pronounced ˜ 30 ‰ shift towards more negative values probably reflects more humid conditions before ˜ 32 ka. Radiocarbon dating of the n-alkanes corroborates the stratigraphic integrity of leaf waxes and their potential for dating loess-paleosol sequences (LPS) back to ˜ 30 ka.

High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

USDA-ARS?s Scientific Manuscript database

High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early leaf spot (ELS), late leaf spot (LLS), and Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use ...

Draft genome sequence of Xylella fastidiosa pear leaf scorch strain in Taiwan

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain (PLS229) isolated from pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan is reported. The bacterium has a genome size of 2,733,013 bp with a G+C content of 53.1%. The PLS229 strain genome was annotated to have 3,259 open readin...

Molecular Characterization of the Meyer Lemon Isolate of Citrus Tatter Leaf Virus: Complete Genome Sequence and Development of Biologically Active In Vitro Transcripts

USDA-ARS?s Scientific Manuscript database

Citrus tatter leaf virus isolated from Meyer lemon trees (CTLV-ML) from California and Florida induces bud union incompatibility of citrus trees grafted on the widely used trifoliate and trifoliate hybrid rootstocks. The complete genome sequence of CTLV-ML was determined to be 6,495 nucleotides (nts...

Draft Genome Sequence of Cercospora arachidicola, Cause of Early Leaf Spot in Peanut

USDA-ARS?s Scientific Manuscript database

Cercospora arachidicola and Cercosporidium personatum, causal agents of early and late leaf spot, respectively, are important fungal pathogens of peanut. Leaf spot disease is a major contributor to the economic losses experienced by peanut farmers and the industry. Though peanut germplasms with so...

Arabidopsis ASYMMETRIC LEAVES2 protein required for leaf morphogenesis consistently forms speckles during mitosis of tobacco BY-2 cells via signals in its specific sequence.

PubMed

Luo, Lilan; Ando, Sayuri; Sasabe, Michiko; Machida, Chiyoko; Kurihara, Daisuke; Higashiyama, Tetsuya; Machida, Yasunori

2012-09-01

Leaf primordia with high division and developmental competencies are generated around the periphery of stem cells at the shoot apex. Arabidopsis ASYMMETRIC-LEAVES2 (AS2) protein plays a key role in the regulation of many genes responsible for flat symmetric leaf formation. The AS2 gene, expressed in leaf primordia, encodes a plant-specific nuclear protein containing an AS2/LOB domain with cysteine repeats (C-motif). AS2 proteins are present in speckles in and around the nucleoli, and in the nucleoplasm of some leaf epidermal cells. We used the tobacco cultured cell line BY-2 expressing the AS2-fused yellow fluorescent protein to examine subnuclear localization of AS2 in dividing cells. AS2 mainly localized to speckles (designated AS2 bodies) in cells undergoing mitosis and distributed in a pairwise manner during the separation of sets of daughter chromosomes. Few interphase cells contained AS2 bodies. Deletion analyses showed that a short stretch of the AS2 amino-terminal sequence and the C-motif play negative and positive roles, respectively, in localizing AS2 to the bodies. These results suggest that AS2 bodies function to properly distribute AS2 to daughter cells during cell division in leaf primordia; and this process is controlled at least partially by signals encoded by the AS2 sequence itself.

SU-E-T-164: Clinical Implementation of ASi EPID Panels for QA of IMRT/VMAT Plans.

PubMed

Hosier, K; Wu, C; Beck, K; Radevic, M; Asche, D; Bareng, J; Kroner, A; Lehmann, J; Logsdon, M; Dutton, S; Rosenthal, S

2012-06-01

To investigate various issues for clinical implementation of aSi EPID panels for IMRT/VMAT QA. Six linacs are used in our clinic for EPID-based plan QA; two Varian Truebeams, two Varian 2100 series, two Elekta Infiniti series. Multiple corrections must be accounted for in the calibration of each panel for dosimetric use. Varian aSi panels are calibrated with standard dark field, flood field, and 40×40 diagonal profile for beam profile correction. Additional corrections to account for off-axis and support arm backscatter are needed for larger field sizes. Since Elekta iViewGT system does not export gantry angle with images, a third-party inclinometer must be physically mounted to back of linac gantry and synchronized with data acquisition via iViewGT PC clock. A T/2 offset correctly correlates image and gantry angle for arc plans due to iView image time stamp at the end of data acquisition for each image. For both Varian and Elekta panels, a 5 MU 10×10 calibration field is used to account for the nonlinear MU to dose response at higher energies. Acquired EPID images are deconvolved via a high pass filter in Fourier space and resultant fluence maps are used to reconstruct a 3D dose 'delivered' to patient using DosimetryCheck. Results are compared to patient 3D dose computed by TPS using a 3D-gamma analysis. 120 IMRT and 100 VMAT cases are reported. Two 3D gamma quantities (Gamma(V10) and Gamma(PTV)) are proposed for evaluating QA results. The Gamma(PTV) is sensitive to MLC offsets while Gamma(V10) is sensitive to gantry rotations. When a 3mm/3% criteria and 90% or higher 3D gamma pass rate is used, all IMRT and 90% of VMAT QA pass QA. After appropriate calibration of aSi panels and setup of image acquisition systems, EPID based 3D dose reconstruction method is found clinically feasible. © 2012 American Association of Physicists in Medicine.

SU-F-T-540: Comprehensive Fluence Delivery Optimization with Multileaf Collimation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weppler, S; Villarreal-Barajas, J; Department of Medical Physics, Tom Baker Cancer Center, Calgary, Alberta

2016-06-15

Purpose: Multileaf collimator (MLC) leaf sequencing is performed via commercial black-box implementations, on which a user has limited to no access. We have developed an explicit, generic MLC sequencing model to serve as a tool for future investigations of fluence map optimization, fluence delivery optimization, and rotational collimator delivery methods. Methods: We have developed a novel, comprehensive model to effectively account for a variety of transmission and penumbra effects previously treated on an ad hoc basis in the literature. As the model is capable of quantifying a variety of effects, we utilize the asymmetric leakage intensity across each leaf tomore » deliver fluence maps with pixel size smaller than the narrowest leaf width. Developed using linear programming and mixed integer programming formulations, the model is implemented using state of the art open-source solvers. To demonstrate the versatility of the algorithm, a graphical user interface (GUI) was developed in MATLAB capable of accepting custom leaf specifications and transmission parameters. As a preliminary proof-ofconcept, we have sequenced the leaves of a Varian 120 Leaf Millennium MLC for five prostate cancer patient fields and one head and neck field. Predetermined fluence maps have been processed by data smoothing methods to obtain pixel sizes of 2.5 cm{sup 2}. The quality of output was analyzed using computer simulations. Results: For the prostate fields, an average root mean squared error (RMSE) of 0.82 and gamma (0.5mm/0.5%) of 91.4% were observed compared to RMSE and gamma (0.5mm/0.5%) values of 7.04 and 34.0% when the leakage considerations were omitted. Similar results were observed for the head and neck case. Conclusion: A model to sequence MLC leaves to optimality has been proposed. Future work will involve extensive testing and evaluation of the method on clinical MLCs and comparison with black-box leaf sequencing algorithms currently used by commercial treatment planning systems.« less

Noseleaf dynamics during pulse emission in horseshoe bats.

PubMed

Feng, Lin; Gao, Li; Lu, Hongwang; Müller, Rolf

2012-01-01

Horseshoe bats emit their biosonar pulses nasally and diffract the outgoing ultrasonic waves by conspicuous structures that surrounded the nostrils. Here, we report quantitative experimental data on the motion of a prominent component of these structures, the anterior leaf, using synchronized laser Doppler vibrometry and acoustic recordings in the greater horseshoe bat (Rhinolophus ferrumequinum). The vibrometry data has demonstrated non-random motion patterns in the anterior leaf. In these patterns, the outer rim of the walls of the anterior leaf twitches forward and inwards to decrease the aperture of the noseleaf and increase the curvature of its surfaces. Noseleaf displacements were correlated with the emitted ultrasonic pulses. After their onset, the inward displacements increased monotonically towards their maximum value which was always reached within the duration of the biosonar pulse, typically towards its end. In other words, the anterior leaf's surfaces were moving inwards during most of the pulse. Non-random motions were not present in all recorded pulse trains, but could apparently be switched on or off. Such switches happened between sequences of consecutive pulses but were never observed between individual pulses within a sequence. The amplitudes of the emitted biosonar pulse and accompanying noseleaf movement were not correlated in the analyzed data set. The measured velocities of the noseleaf surface were too small to induce Doppler shifts of a magnitude with a likely significance. However, the displacement amplitudes were significant in comparison with the overall size of the anterior leaf and the sound wavelengths. These results indicate the possibility that horseshoe bats use dynamic sensing principles on the emission side of their biosonar system. Given the already available evidence that such mechanisms exist for biosonar reception, it may be hypothesized that time-variant mechanisms play a pervasive role in the biosonar sensing of horseshoe bats.

Controls on declining carbon balance with leaf age among 10 woody species in Australian woodland: do leaves have zero daily net carbon balances when they die?

PubMed

Reich, Peter B; Falster, Daniel S; Ellsworth, David S; Wright, Ian J; Westoby, Mark; Oleksyn, Jacek; Lee, Tali D

2009-01-01

* Here, we evaluated how increased shading and declining net photosynthetic capacity regulate the decline in net carbon balance with increasing leaf age for 10 Australian woodland species. We also asked whether leaves at the age of their mean life-span have carbon balances that are positive, zero or negative. * The net carbon balances of 2307 leaves on 53 branches of the 10 species were estimated. We assessed three-dimensional architecture, canopy openness, photosynthetic light response functions and dark respiration rate across leaf age sequences on all branches. We used YPLANT to estimate light interception and to model carbon balance along the leaf age sequences. * As leaf age increased to the mean life-span, increasing shading and declining photosynthetic capacity each separately reduced daytime carbon gain by approximately 39% on average across species. Together, they reduced daytime carbon gain by 64% on average across species. * At the age of their mean life-span, almost all leaves had positive daytime carbon balances. These per leaf carbon surpluses were of a similar magnitude to the estimated whole-plant respiratory costs per leaf. Thus, the results suggest that a whole-plant economic framework, including respiratory costs, may be useful in assessing controls on leaf longevity.

Four-dimensional dose reconstruction through in vivo phase matching of cine images of electronic portal imaging device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Jihyung; Jung, Jae Won, E-mail: jungj@ecu.ed

Purpose: A method is proposed to reconstruct a four-dimensional (4D) dose distribution using phase matching of measured cine images to precalculated images of electronic portal imaging device (EPID). Methods: (1) A phantom, designed to simulate a tumor in lung (a polystyrene block with a 3 cm diameter embedded in cork), was placed on a sinusoidally moving platform with an amplitude of 1 cm and a period of 4 s. Ten-phase 4D computed tomography (CT) images of the phantom were acquired. A planning target volume (PTV) was created by adding a margin of 1 cm around the internal target volume ofmore » the tumor. (2) Three beams were designed, which included a static beam, a theoretical dynamic beam, and a planning-optimized dynamic beam (PODB). While the theoretical beam was made by manually programming a simplistic sliding leaf motion, the planning-optimized beam was obtained from treatment planning. From the three beams, three-dimensional (3D) doses on the phantom were calculated; 4D dose was calculated by means of the ten phase images (integrated over phases afterward); serving as “reference” images, phase-specific EPID dose images under the lung phantom were also calculated for each of the ten phases. (3) Cine EPID images were acquired while the beams were irradiated to the moving phantom. (4) Each cine image was phase-matched to a phase-specific CT image at which common irradiation occurred by intercomparing the cine image with the reference images. (5) Each cine image was used to reconstruct dose in the phase-matched CT image, and the reconstructed doses were summed over all phases. (6) The summation was compared with forwardly calculated 4D and 3D dose distributions. Accounting for realistic situations, intratreatment breathing irregularity was simulated by assuming an amplitude of 0.5 cm for the phantom during a portion of breathing trace in which the phase matching could not be performed. Intertreatment breathing irregularity between the time of treatment and the time of planning CT was considered by utilizing the same reduced amplitude when the phantom was irradiated. To examine the phase matching in a humanoid environment, the matching was also performed in a digital phantom (4D XCAT phantom). Results: For the static, the theoretical, and the planning-optimized dynamic beams, the 4D reconstructed doses showed agreement with the forwardly calculated 4D doses within the gamma pass rates of 92.7%, 100%, and 98.1%, respectively, at the isocenter plane given by 3%/3 mm criteria. Excellent agreement in dose volume histogram of PTV and lung-PTV was also found between the two 4D doses, while substantial differences were found between the 3D and the 4D doses. The significant breathing irregularities modeled in this study were found not to be noticeably affecting the reconstructed dose. The phase matching was performed equally well in a digital phantom. Conclusions: The method of retrospective phase determination of a moving object under irradiation provided successful 4D dose reconstruction. This method will provide accurate quality assurance and facilitate adaptive therapy when distinguishable objects such as well-defined tumors, diaphragm, and organs with markers (pancreas and liver) are covered by treatment beam apertures.« less

Four-dimensional dose reconstruction through in vivo phase matching of cine images of electronic portal imaging device.

PubMed

Yoon, Jihyung; Jung, Jae Won; Kim, Jong Oh; Yi, Byong Yong; Yeo, Inhwan

2016-07-01

A method is proposed to reconstruct a four-dimensional (4D) dose distribution using phase matching of measured cine images to precalculated images of electronic portal imaging device (EPID). (1) A phantom, designed to simulate a tumor in lung (a polystyrene block with a 3 cm diameter embedded in cork), was placed on a sinusoidally moving platform with an amplitude of 1 cm and a period of 4 s. Ten-phase 4D computed tomography (CT) images of the phantom were acquired. A planning target volume (PTV) was created by adding a margin of 1 cm around the internal target volume of the tumor. (2) Three beams were designed, which included a static beam, a theoretical dynamic beam, and a planning-optimized dynamic beam (PODB). While the theoretical beam was made by manually programming a simplistic sliding leaf motion, the planning-optimized beam was obtained from treatment planning. From the three beams, three-dimensional (3D) doses on the phantom were calculated; 4D dose was calculated by means of the ten phase images (integrated over phases afterward); serving as "reference" images, phase-specific EPID dose images under the lung phantom were also calculated for each of the ten phases. (3) Cine EPID images were acquired while the beams were irradiated to the moving phantom. (4) Each cine image was phase-matched to a phase-specific CT image at which common irradiation occurred by intercomparing the cine image with the reference images. (5) Each cine image was used to reconstruct dose in the phase-matched CT image, and the reconstructed doses were summed over all phases. (6) The summation was compared with forwardly calculated 4D and 3D dose distributions. Accounting for realistic situations, intratreatment breathing irregularity was simulated by assuming an amplitude of 0.5 cm for the phantom during a portion of breathing trace in which the phase matching could not be performed. Intertreatment breathing irregularity between the time of treatment and the time of planning CT was considered by utilizing the same reduced amplitude when the phantom was irradiated. To examine the phase matching in a humanoid environment, the matching was also performed in a digital phantom (4D XCAT phantom). For the static, the theoretical, and the planning-optimized dynamic beams, the 4D reconstructed doses showed agreement with the forwardly calculated 4D doses within the gamma pass rates of 92.7%, 100%, and 98.1%, respectively, at the isocenter plane given by 3%/3 mm criteria. Excellent agreement in dose volume histogram of PTV and lung-PTV was also found between the two 4D doses, while substantial differences were found between the 3D and the 4D doses. The significant breathing irregularities modeled in this study were found not to be noticeably affecting the reconstructed dose. The phase matching was performed equally well in a digital phantom. The method of retrospective phase determination of a moving object under irradiation provided successful 4D dose reconstruction. This method will provide accurate quality assurance and facilitate adaptive therapy when distinguishable objects such as well-defined tumors, diaphragm, and organs with markers (pancreas and liver) are covered by treatment beam apertures.

Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

PubMed

Ahrenfeldt, Johanne; Skaarup, Carina; Hasman, Henrik; Pedersen, Anders Gorm; Aarestrup, Frank Møller; Lund, Ole

2017-01-05

Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods. Our aim was to create a benchmark data set that mimics sequencing data of the sort that might be collected during an outbreak of an infectious disease. This was achieved by letting an E. coli hypermutator strain grow in the lab for 8 consecutive days, each day splitting the culture in two while also collecting samples for sequencing. The result is a data set consisting of 101 whole genome sequences with known phylogenetic relationship. Among the sequenced samples 51 correspond to internal nodes in the phylogeny because they are ancestral, while the remaining 50 correspond to leaves. We also used the newly created data set to compare three different online available methods that infer phylogenies from whole-genome sequencing reads: NDtree, CSI Phylogeny and REALPHY. One complication when comparing the output of these methods with the known phylogeny is that phylogenetic methods typically build trees where all observed sequences are placed as leafs, even though some of them are in fact ancestral. We therefore devised a method for post processing the inferred trees by collapsing short branches (thus relocating some leafs to internal nodes), and also present two new measures of tree similarity that takes into account the identity of both internal and leaf nodes. Based on this analysis we find that, among the investigated methods, CSI Phylogeny had the best performance, correctly identifying 73% of all branches in the tree and 71% of all clades. We have made all data from this experiment (raw sequencing reads, consensus whole-genome sequences, as well as descriptions of the known phylogeny in a variety of formats) publicly available, with the hope that other groups may find this data useful for benchmarking and exploring the performance of epidemiological methods. All data is freely available at: https://cge.cbs.dtu.dk/services/evolution_data.php .

IMRT and RapidArc commissioning of a TrueBeam linear accelerator using TG-119 protocol cases.

PubMed

Wen, Ning; Zhao, Bo; Kim, Jinkoo; Chin-Snyder, Karen; Bellon, Maria; Glide-Hurst, Carri; Barton, Kenneth; Chen, Daiquan; Chetty, Indrin J

2014-09-08

The purpose of this study is to evaluate the overall accuracy of intensity-modulated radiation therapy (IMRT) and RapidArc delivery using both flattening filter (FF) and flattening filter-free (FFF) modalities based on test cases developed by AAPM Task Group 119. Institutional confidence limits (CLs) were established as the baseline for patient specific treatment plan quality assurance (QA). The effects of gantry range, gantry speed, leaf speed, dose rate, as well as the capability to capture intentional errors, were evaluated by measuring a series of Picket Fence (PF) tests using the electronic portal imaging device (EPID) and EBT3 films. Both IMRT and RapidArc plans were created in a Solid Water phantom (30 × 30 × 15 cm3) for the TG-119 test cases representative of normal clinical treatment sites for all five photon energies (6X, 10X, 15X, 6X-FFF, 10X-FFF) and the Exact IGRT couch was included in the dose calculation. One high-dose point in the PTV and one low-dose point in the avoidance structure were measured with an ion chamber in each case for each energy. Similarly, two GAFCHROMIC EBT3 films were placed in the coronal planes to measure planar dose distributions in both high- and low-dose regions. The confidence limit was set to have 95% of the measured data fall within the tolerance. The mean of the absolute dose deviation for variable dose rate and gantry speed during RapidArc delivery was within 0.5% for all energies. The corresponding results for leaf speed tests were all within 0.4%. The combinations of dynamic leaf gap (DLG) and MLC transmission factor were optimized based on the ion chamber measurement results of RapidArc delivery for each energy. The average 95% CLs for the high-dose point in the PTV were 0.030 ± 0.007 (range, 0.022-0.038) for the IMRT plans and 0.029 ± 0.011 (range, 0.016-0.043) for the RapidArc plans. For low-point dose in the avoidance structures, the CLs were 0.029 ± 0.006 (range, 0.024-0.039) for the IMRT plans and 0.027 ± 0.013 (range, 0.017-0.047) for the RapidArc plans. The average 95% CLs using 3%/3 mm gamma criteria in the high-dose region were 5.9 ± 2.7 (range, 1.4-8.6) and 3.9 ± 2.9 (range, 1.5-8.8) for IMRT and RapidArc plans, respectively. The average 95% CLs in the low-dose region were 5.3 ± 2.6 (range, 1.2-7.4) and 3.7 ± 2.8 (range, 1.8-8.3) for IMRT and RapidArc plans, respectively. Based on ion chamber, as well as film measurements, we have established CLs values to ensure the high precision of IMRT and RapidArc delivery for both FF and FFF modalities.

Lettuce necrotic leaf curl virus, a new plant virus infecting lettuce and a proposed member of the genus Torradovirus.

PubMed

Verbeek, Martin; Dullemans, Annette M; van Raaij, Henry M G; Verhoeven, Jacobus Th J; van der Vlugt, René A A

2014-04-01

A new virus was isolated from a lettuce plant grown in an open field in the Netherlands in 2011. This plant was showing conspicuous symptoms that consisted of necrosis and moderate leaf curling. The virus was mechanically transferred to indicator plants, and a total RNA extract of one of these indicator plants was used for next-generation sequencing. Analysis of the sequences that were obtained and further biological studies showed that the virus was related to, but clearly distinct from, viruses belonging to the genus Torradovirus. The name "lettuce necrotic leaf curl virus" (LNLCV) is proposed for this new torradovirus.

SU-F-T-236: Comparison of Two IMRT/VMAT QA Systems Using Gamma Index Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dogan, N; Denissova, S

2016-06-15

Purpose: The goal of this study is to assess differences in the Gamma index pass rates when using two commercial QA systems and provide optimum Gamma index parameters for pre-treatment patient specific QA. Methods: Twenty-two VMAT cases that consisted of prostate, lung, head and neck, spine, brain and pancreas, were included in this study. The verification plans have been calculated using AcurosXB(V11) algorithm for different dose grids (1.5mm, 2.5mm, 3mm). The measurements were performed on TrueBeam(Varian) accelerator using both EPID(S1000) portal imager and ArcCheck(SunNuclearCorp) devices. Gamma index criteria variation of 3%/3mm, 2%/3mm, 2%/2mm and threshold (TH) doses of 5% tomore » 50% were used in analysis. Results: The differences in Gamma pass rates between two devices are not statistically significant for 3%/3mm, yielding pass rate higher than 95%. Increase of lower dose TH showed reduced pass rates for both devices. ArcCheck’s more pronounced effect can be attributed to higher contribution of lower dose region spread. As expected, tightening criteria to 2%/2mm (TH: 10%) decreased Gamma pass rates below 95%. Higher EPID (92%) pass rates compared to ArcCheck (86%) probably due to better spatial resolution. Portal Dosimetry results showed lower Gamma pass rates for composite plans compared to individual field pass rates. This may be due to the expansion in the analyzed region which includes pixels not included in the separate field analysis. Decreasing dose grid size from 2.5mm to 1.5mm did not show statistically significant (p<0.05) differences in Gamma pass rates for both QA devices. Conclusion: Overall, both system measurements agree well with calculated dose when using gamma index criteria of 3%/3mm for a variety of VMAT cases. Variability between two systems increases using different dose GRID, TH and tighter gamma criteria and must be carefully assessed prior to clinical use.« less

SU-F-J-41: Experimental Validation of a Cascaded Linear System Model for MVCBCT with a Multi-Layer EPID

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Y; Rottmann, J; Myronakis, M

2016-06-15

Purpose: The purpose of this study was to validate the use of a cascaded linear system model for MV cone-beam CT (CBCT) using a multi-layer (MLI) electronic portal imaging device (EPID) and provide experimental insight into image formation. A validated 3D model provides insight into salient factors affecting reconstructed image quality, allowing potential for optimizing detector design for CBCT applications. Methods: A cascaded linear system model was developed to investigate the potential improvement in reconstructed image quality for MV CBCT using an MLI EPID. Inputs to the three-dimensional (3D) model include projection space MTF and NPS. Experimental validation was performedmore » on a prototype MLI detector installed on the portal imaging arm of a Varian TrueBeam radiotherapy system. CBCT scans of up to 898 projections over 360 degrees were acquired at exposures of 16 and 64 MU. Image volumes were reconstructed using a Feldkamp-type (FDK) filtered backprojection (FBP) algorithm. Flat field images and scans of a Catphan model 604 phantom were acquired. The effect of 2×2 and 4×4 detector binning was also examined. Results: Using projection flat fields as an input, examination of the modeled and measured NPS in the axial plane exhibits good agreement. Binning projection images was shown to improve axial slice SDNR by a factor of approximately 1.4. This improvement is largely driven by a decrease in image noise of roughly 20%. However, this effect is accompanied by a subsequent loss in image resolution. Conclusion: The measured axial NPS shows good agreement with the theoretical calculation using a linear system model. Binning of projection images improves SNR of large objects on the Catphan phantom by decreasing noise. Specific imaging tasks will dictate the implementation image binning to two-dimensional projection images. The project was partially supported by a grant from Varian Medical Systems, Inc. and grant No. R01CA188446-01 from the National Cancer Institute.« less

High quantum efficiency megavoltage imaging with thick scintillator detectors for image guided radiation therapy

NASA Astrophysics Data System (ADS)

Gopal, Arun

In image guided radiation therapy (IGRT), imaging devices serve as guidance systems to aid patient set-up and tumor volume localization. Traditionally, 2-D megavoltage x-ray imagers, referred to as electronic portal imaging devices (EPIDs), have been used for planar target localization, and have recently been extended to perform 3-D volumetric reconstruction via cone-beam computed tomography (CBCT). However, current EPIDs utilize thin and inefficient phosphor screen detectors and are subsequently limited by poor soft tissue visualization, which limits their use for CBCT. Therefore, the use of thick scintillation media as megavoltage x-ray detectors for greater x-ray sensitivity and enhanced image quality has recently been of significant interest. In this research, two candidates for thick scintillators: CsI(Tl) and terbium doped scintillation glass were investigated in separate imaging configurations. In the first configuration, a thick scintillation crystal (TSC) consisting of a thick, monolithic slab of CsI(Tl) was coupled to a mirror-lens-camera system. The second configuration is based on a fiber-optic scintillation glass array (FOSGA), wherein the scintillation glass is drawn into long fiber-optic conduits, inserted into a grid-type housing constructed out of polymer-tungsten alloy, and coupled to an array of photodiodes for digital read-out. The imaging prototypes were characterized using theoretical studies and imaging measurements to obtain fundamental metrics of imaging performance. Spatial resolution was measured based on a modulation transfer function (MTF), noise was evaluated in terms of a noise power spectrum (NPS), and overall contrast was characterized in the form of detective quantum efficiency (DQE). The imaging studies were used to optimize the TSC and FOSGA imagers and propose prototype configurations for order-of-magnitude improvements in overall image quality. In addition, a fast and simple technique was developed to measure the MTF, NPS, and DQE metrics for clinical EPID and CBCT systems based on a novel adaptation of a traditional line-pair resolution bar-pattern. This research provides two significant benefits to radiotherapy: the characterization of a new generation of thick scintillator based megavoltage x-ray imagers for CBCT based IGRT, and the novel adaptation of fundamental imaging metrics from imaging research to routine clinical performance monitoring.

Implementation of IMRT and VMAT using Delta4 phantom and portal dosimetry as dosimetry verification tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daci, Lulzime, E-mail: lulzime.daci@nodlandssykehuset.no; Malkaj, Partizan, E-mail: malkaj-p@hotmail.com

2016-03-25

In this study we analyzed and compared the dose distribution of different IMRT and VMAT plans with the intent to provide pre-treatment quality assurance using two different tools. Materials/Methods: We have used the electronic portal imaging device EPID after calibration to dose and correction for the background offset signal and also the Delta4 phantom after en evaluation of angular sensitivity. The Delta4 phantom has a two-dimensional array with ionization chambers. We analyzed three plans for each anatomical site calculated by Eclipse treatment planning system. The measurements were analyzed using γ-evaluation method with passing criteria 3% absolute dose and 3 mm distancemore » to agreement (DTA). For all the plans the range of score has been from 97% to 99% for gantry fixed at 0° while for rotational planes there was a slightly decreased pass rates and above 95%. Point measurement with a ionization chamber were done in additional to see the accuracy of portal dosimetry and to evaluate the Delta4 device to various dose rates. Conclusions: Both Delt4 and Portal dosimetry shows good results between the measured and calculated doses. While Delta4 is more accurate in measurements EPID is more time efficient. We have decided to use both methods in the first steps of IMRT and VMAT implementation and later on to decide which of the tools to use depending on the complexity of plans, how much accurate we want to be and the time we have on the machine.« less

WE-A-BRE-01: Debate: To Measure or Not to Measure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moran, J; Miften, M; Mihailidis, D

2014-06-15

Recent studies have highlighted some of the limitations of patient-specific pre-treatment IMRT QA measurements with respect to assessing plan deliverability. Pre-treatment QA measurements are frequently performed with detectors in phantoms that do not involve any patient heterogeneities or with an EPID without a phantom. Other techniques have been developed where measurement results are used to recalculate the patient-specific dose volume histograms. Measurements continue to play a fundamental role in understanding the initial and continued performance of treatment planning and delivery systems. Less attention has been focused on the role of computational techniques in a QA program such as calculation withmore » independent dose calculation algorithms or recalculation of the delivery with machine log files or EPID measurements. This session will explore the role of pre-treatment measurements compared to other methods such as computational and transit dosimetry techniques. Efficiency and practicality of the two approaches will also be presented and debated. The speakers will present a history of IMRT quality assurance and debate each other regarding which types of techniques are needed today and for future quality assurance. Examples will be shared of situations where overall quality needed to be assessed with calculation techniques in addition to measurements. Elements where measurements continue to be crucial such as for a thorough end-to-end test involving measurement will be discussed. Operational details that can reduce the gamma tool effectiveness and accuracy for patient-specific pre-treatment IMRT/VMAT QA will be described. Finally, a vision for the future of IMRT and VMAT plan QA will be discussed from a safety perspective. Learning Objectives: Understand the advantages and limitations of measurement and calculation approaches for pre-treatment measurements for IMRT and VMAT planning Learn about the elements of a balanced quality assurance program involving modulated techniques Learn how to use tools and techniques such as an end-to-end test to enhance your IMRT and VMAT QA program.« less

Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key Stage in Rice Leaf Photosynthetic Development1[OPEN

PubMed Central

Yaapar, Muhammad N.; Wanchana, Samart; Thakur, Vivek; Quick, W. Paul

2016-01-01

Leaves are derived from heterotrophic meristem tissue that, at some point, must make the transition to autotrophy via the initiation of photosynthesis. However, the timing and spatial coordination of the molecular and cellular processes underpinning this switch are poorly characterized. Here, we report on the identification of a specific stage in rice (Oryza sativa) leaf development (P3/P4 transition) when photosynthetic competence is first established. Using a combined physiological and molecular approach, we show that elements of stomatal and vascular differentiation are coordinated with the onset of measurable light absorption for photosynthesis. Moreover, by exploring the response of the system to environmental perturbation, we show that the earliest stages of rice leaf development have significant plasticity with respect to elements of cellular differentiation of relevance for mature leaf photosynthetic performance. Finally, by performing an RNA sequencing analysis targeted at the early stages of rice leaf development, we uncover a palette of genes whose expression likely underpins the acquisition of photosynthetic capability. Our results identify the P3/P4 transition as a highly dynamic stage in rice leaf development when several processes for the initiation of photosynthetic competence are coordinated. As well as identifying gene targets for future manipulation of rice leaf structure/function, our data highlight a developmental window during which such manipulations are likely to be most effective. PMID:26813793

Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key Stage in Rice Leaf Photosynthetic Development.

PubMed

van Campen, Julia C; Yaapar, Muhammad N; Narawatthana, Supatthra; Lehmeier, Christoph; Wanchana, Samart; Thakur, Vivek; Chater, Caspar; Kelly, Steve; Rolfe, Stephen A; Quick, W Paul; Fleming, Andrew J

2016-03-01

Leaves are derived from heterotrophic meristem tissue that, at some point, must make the transition to autotrophy via the initiation of photosynthesis. However, the timing and spatial coordination of the molecular and cellular processes underpinning this switch are poorly characterized. Here, we report on the identification of a specific stage in rice (Oryza sativa) leaf development (P3/P4 transition) when photosynthetic competence is first established. Using a combined physiological and molecular approach, we show that elements of stomatal and vascular differentiation are coordinated with the onset of measurable light absorption for photosynthesis. Moreover, by exploring the response of the system to environmental perturbation, we show that the earliest stages of rice leaf development have significant plasticity with respect to elements of cellular differentiation of relevance for mature leaf photosynthetic performance. Finally, by performing an RNA sequencing analysis targeted at the early stages of rice leaf development, we uncover a palette of genes whose expression likely underpins the acquisition of photosynthetic capability. Our results identify the P3/P4 transition as a highly dynamic stage in rice leaf development when several processes for the initiation of photosynthetic competence are coordinated. As well as identifying gene targets for future manipulation of rice leaf structure/function, our data highlight a developmental window during which such manipulations are likely to be most effective. © 2016 American Society of Plant Biologists. All Rights Reserved.

Neofusicoccum ribis Associated with Leaf Blight on Rubber (Hevea brasiliensis) in Peninsular Malaysia

PubMed Central

Nyaka Ngobisa, A. I. C.; Zainal Abidin, M. A.; Wong, M. Y.; Wan Noordin, M. W. D.

2013-01-01

Hevea brasiliensis is a natural source of rubber and an important plantation tree species in Malaysia. Leaf blight disease caused by Fusicoccum substantially reduces the growth and performance of H. brasiliensis. The aim of this study was to use a combination of both morphological characteristics and molecular data to clarify the taxonomic position of the fungus associated with leaf blight disease. Fusicoccum species were isolated from infected leaves collected from plantations at 3 widely separated locations – Selangor, Perak, and Johor states – in Peninsular Malaysia in 2010. All the isolates were identified according to their conidial patterns and DNA sequences generated from internal transcribed spacers (ITS1 and ITS2), the 5.8S rRNA, and an unknown locus (BotF15) containing microsatellite repeats. Based on taxonomic and sequence data, Neofusicoccum ribis was identified as the main cause of leaf blight disease in H. brasiliensis in commercial plantations in Malaysia. A pathogenicity trial on detached leaves further confirmed that N. ribis causes leaf blight disease. N. ribis is an important leaf pathogen, and its detection in Malaysia has important implications for future planting of H. brasiliensis. PMID:25288924

Neofusicoccum ribis Associated with Leaf Blight on Rubber (Hevea brasiliensis) in Peninsular Malaysia.

PubMed

Nyaka Ngobisa, A I C; Zainal Abidin, M A; Wong, M Y; Wan Noordin, M W D

2013-03-01

Hevea brasiliensis is a natural source of rubber and an important plantation tree species in Malaysia. Leaf blight disease caused by Fusicoccum substantially reduces the growth and performance of H. brasiliensis. The aim of this study was to use a combination of both morphological characteristics and molecular data to clarify the taxonomic position of the fungus associated with leaf blight disease. Fusicoccum species were isolated from infected leaves collected from plantations at 3 widely separated locations - Selangor, Perak, and Johor states - in Peninsular Malaysia in 2010. All the isolates were identified according to their conidial patterns and DNA sequences generated from internal transcribed spacers (ITS1 and ITS2), the 5.8S rRNA, and an unknown locus (BotF15) containing microsatellite repeats. Based on taxonomic and sequence data, Neofusicoccum ribis was identified as the main cause of leaf blight disease in H. brasiliensis in commercial plantations in Malaysia. A pathogenicity trial on detached leaves further confirmed that N. ribis causes leaf blight disease. N. ribis is an important leaf pathogen, and its detection in Malaysia has important implications for future planting of H. brasiliensis.

Diversity of formyltetrahydrofolate synthetase genes in the rumens of roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed different diets.

PubMed

Li, Zhipeng; Henderson, Gemma; Yang, Yahan; Li, Guangyu

2017-01-01

Reductive acetogenesis by homoacetogens represents an alternative pathway to methanogenesis to remove metabolic hydrogen during rumen fermentation. In this study, we investigated the occurrence of homoacetogen in the rumens of pasture-fed roe deer (Capreolus pygargus) and sika deer (Cervus nippon) fed either oak-leaf-based (tannin-rich, 100 mg/kg dried matter), corn-stover-based, or corn-silage-based diets, by using formyltetrahydrofolate synthetase (FTHFS) gene sequences as a marker. The diversity and richness of FTHFS sequences was lowest in animals fed oak leaf, indicating that tannin-containing plants may affect rumen homoacetogen diversity. FTHFS amino acid sequences in the rumen of roe deer significantly differed from those of sika deer. The phylogenetic analyses showed that 44.8% of sequences in pasture-fed roe deer, and 72.1%, 81.1%, and 37.5% of sequences in sika deer fed oak-leaf-, corn-stover-, and corn-silage-based diets, respectively, may represent novel bacteria that have not yet been cultured. These results demonstrate that the rumens of roe deer and sika deer harbor potentially novel homoacetogens and that diet may influence homoacetogen community structure.

Poster — Thur Eve — 58: Dosimetric validation of electronic compensation for radiotherapy treatment planning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gräfe, James; Khan, Rao; Meyer, Tyler

2014-08-15

In this study we investigate the deliverability of dosimetric plans generated by the irregular surface compensator (ISCOMP) algorithm for 6 MV photon beams in Eclipse (Varian Medical System, CA). In contrast to physical tissue compensation, the electronic ISCOMP uses MLCs to dynamically modulate the fluence of a photon beam in order to deliver a uniform dose at a user defined plane in tissue. This method can be used to shield critical organs that are located within the treatment portal or improve dose uniformity by tissue compensation in inhomogeneous regions. Three site specific plans and a set of test fields weremore » evaluated using the γ-metric of 3%/ 3 mm on Varian EPID, MapCHECK, and Gafchromic EBT3 film with a clinical tolerance of >95% passing rates. Point dose measurements with an NRCC calibrated ionization chamber were also performed to verify the absolute dose delivered. In all cases the MapCHECK measured plans met the gamma criteria. The mean passing rate for the six EBT3 film field measurements was 96.2%, with only two fields at 93.4 and 94.0% passing rates. The EPID plans passed for fields encompassing the central ∼10 × 10 cm{sup 2} region of the detector; however for larger fields and greater off-axis distances discrepancies were observed and attributed to the profile corrections and modeling of backscatter in the portal dose calculation. The magnitude of the average percentage difference for 21 ion chamber point dose measurements and 17 different fields was 1.4 ± 0.9%, and the maximum percentage difference was −3.3%. These measurements qualify the algorithm for routine clinical use subject to the same pre-treatment patient specific QA as IMRT.« less

Real-time tracking of tumor motions and deformations along the leaf travel direction with the aid of a synchronized dynamic MLC leaf sequencer.

PubMed

Tacke, Martin; Nill, Simeon; Oelfke, Uwe

2007-11-21

Advanced radiotherapeutical techniques like intensity-modulated radiation therapy (IMRT) are based on an accurate knowledge of the location of the radiation target. An accurate dose delivery, therefore, requires a method to account for the inter- and intrafractional target motion and the target deformation occurring during the course of treatment. A method to compensate in real time for changes in the position and shape of the target is the use of a dynamic multileaf collimator (MLC) technique which can be devised to automatically arrange the treatment field according to real-time image information. So far, various approaches proposed for leaf sequencers have had to rely on a priori known target motion data and have aimed to optimize the overall treatment time. Since for a real-time dose delivery the target motion is not known a priori, the velocity range of the leading leaves is restricted by a safety margin to c x v(max) while the following leaves can travel with an additional maximum speed to compensate for the respective target movements. Another aspect to be considered is the tongue and groove effect. A uniform radiation field can only be achieved if the leaf movements are synchronized. The method presented in this note is the first to combine a synchronizing sequencer and real-time tracking with a dynamic MLC. The newly developed algorithm is capable of online optimizing the leaf velocities by minimizing the overall treatment time while at the same time it synchronizes the leaf trajectories in order to avoid the tongue and groove effect. The simultaneous synchronization is performed with the help of an online-calculated mid-time leaf trajectory which is common for all leaf pairs and which takes into account the real-time target motion and deformation information.

A simple quality assurance test tool for the visual verification of light and radiation field congruent using electronic portal images device and computed radiography

PubMed Central

2012-01-01

Background The radiation field on most megavoltage radiation therapy units are shown by a light field projected through the collimator by a light source mounted inside the collimator. The light field is traditionally used for patient alignment. Hence it is imperative that the light field is congruent with the radiation field. Method A simple quality assurance tool has been designed for rapid and simple test of the light field and radiation field using electronic portal images device (EPID) or computed radiography (CR). We tested this QA tool using Varian PortalVision and Elekta iViewGT EPID systems and Kodak CR system. Results Both the single and double exposure techniques were evaluated, with double exposure technique providing a better visualization of the light-radiation field markers. The light and radiation congruency could be detected within 1 mm. This will satisfy the American Association of Physicists in Medicine task group report number 142 recommendation of 2 mm tolerance. Conclusion The QA tool can be used with either an EPID or CR to provide a simple and rapid method to verify light and radiation field congruence. PMID:22452821

Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques

PubMed Central

Xu, Wenjing; Shi, Lingling; Chan, Onchim; Li, Jiao; Casper, Peter; Zou, Xiaoming

2013-01-01

Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well. PMID:24367682

Identification of three genotypes of sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization.

PubMed

Viswanathan, R; Balamuralikrishnan, M; Karuppaiah, R

2008-12-01

Sugarcane yellow leaf virus (SCYLV) that causes yellow leaf disease (YLD) in sugarcane (recently reported in India) belongs to Polerovirus. Detailed studies were conducted to characterize the virus based on partial open reading frames (ORFs) 1 and 2 and complete ORFs 3 and 4 sequences in their genome. Reverse-transcriptase polymerase chain reaction (RT-PCR) was performed on 48 sugarcane leaf samples to detect the virus using a specific set of primers. Of the 48 samples, 36 samples (field samples with and without foliar symptoms) including 10 meristem culture derived plants were found to be positive to SCYLV infection. Additionally, an aphid colony collected from symptomatic sugarcane in the field was also found to be SCYLV positive. The amplicons from 22 samples were cloned, sequenced and acronymed as SCYLV-CB isolates. The nucleotide (nt) and amino acid (aa) sequence comparison showed a significant variation between SCYLV-CB and the database sequences at nt (3.7-5.1%) and aa (3.2-5.3%) sequence level in the CP coding region. However, the database sequences comprising isolates of three reported genotypes, viz., BRA, PER and REU, were observed with least nt and aa sequence dissimilarities (0.0-1.6%). The phylogenetic analyses of the overlapping ORFs (ORF 3 and ORF 4) of SCYLV encoding CP and MP determined in this study and additional sequences of 26 other isolates including an Indian isolate (SCYLV-IND) available from GenBank were distributed in four phylogenetic clusters. The SCYLV-CB isolates from this study lineated in two clusters (C1 and C2) and all the other isolates from the worldwide locations into another two clusters (C3 and C4). The sequence variation of the isolates in this study with the database isolates, even in the least variable region of the SCYLV genome, showed that the population existing in India is significantly different from rest of the world. Further, comparison of partial sequences encoding for ORFs 1 and 2 revealed that YLD in sugarcane in India is caused by at least three genotypes, viz., CUB, IND and BRA-PER, of which a majority of the samples were found infected with Cuban genotype (CUB) and lesser by IND and BRA-PER genotypes. The genotype IND was identified as a new genotype from this study, and this was found to have significant variation with the reported genotypes.

Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis.

PubMed

Kumar, Dhananjay; Dutta, Summi; Singh, Dharmendra; Prabhu, Kumble Vinod; Kumar, Manish; Mukhopadhyay, Kunal

2017-01-01

Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression. High-throughput sequencing was used for transcriptome-wide identification of miRNAs and their expression profiling in retort to leaf rust using mock and pathogen-inoculated resistant and susceptible near-isogenic wheat plants. A total of 1056 mature miRNAs were identified, of which 497 miRNAs were conserved and 559 miRNAs were novel. The pathogen-inoculated resistant plants manifested more miRNAs compared with the pathogen infected susceptible plants. The miRNA counts increased in susceptible isoline due to leaf rust, conversely, the counts decreased in the resistant isoline in response to pathogenesis illustrating precise spatial tuning of miRNAs during compatible and incompatible interaction. Stem-loop quantitative real-time PCR was used to profile 10 highly differentially expressed miRNAs obtained from high-throughput sequencing data. The spatio-temporal profiling validated the differential expression of miRNAs between the isolines as well as in retort to pathogen infection. Degradome analysis provided 701 predicted target genes associated with defense response, signal transduction, development, metabolism, and transcriptional regulation. The obtained results indicate that wheat isolines employ diverse arrays of miRNAs that modulate their target genes during compatible and incompatible interaction. Our findings contribute to increase knowledge on roles of microRNA in wheat-leaf rust interactions and could help in rust resistance breeding programs.

Two self-referencing methods for the measurement of beam spot position.

PubMed

Nyiri, Balazs J; Smale, Jason R; Gerig, Lee H

2012-12-01

Two quantitative methods of measuring electron beam spot position with respect to the collimator axis of rotation (CAOR) are described. Method 1 uses a cylindrical ion chamber (IC) mounted on a jig corotational with the collimator making the relationship among the chamber, jaws, and CAOR fixed and independent of collimator angle. A jaw parallel to the IC axis is set to zero and the IC position adjusted so that the IC signal is approximately 50% of the open field value, providing a large dose gradient in the region of the IC. The cGy∕MU value is measured as a function of collimator rotation, e.g., every 30°. If the beam spot does not lie on the CAOR, the signal from the ion chamber will vary with collimator rotation. Based on a measured spatial sensitivity, the distance of the beam spot from the CAOR can be calculated from the IC signal variation with rotation. The 2nd method is image based. Two stainless steel rods, 3 mm in diameter, are mounted to a jig attached to the Linac collimator. The rods, offset from the CAOR, lay in different planes normal to the CAOR, one at 158 cm SSD and the other at 70 cm SSD. As the collimator rotates the rods move tangent along an envelope circle, the centers of which are on the CAOR in their respective planes. Three images, each at a different collimator rotation, containing the shadows of both rods, are acquired on the Linac EPID. At each angle the shadow of the rods on the EPID defines lines tangent to the projection of the envelope circles. From these the authors determine the projected centers of the two circles at different heights. From the distance of these two points using the two heights and the source to EPID distance, the authors calculate the distance of the beam spot from the CAOR. Measurements with all two techniques were performed on an Elekta Linac. Measurements were performed with the beam spot in nominal clinical position and in a deliberately offset position. Measurements were also performed using the Flexmap image registration∕ball-bearing test. Within their uncertainties, both methods report the same beam spot displacement. In clinical use, a total of 203 monthly beam spot measurements on 14 different beams showed an average displacement of 0.11 mm (σ = 0.07 mm) in-plane and 0.10 mm (σ = 0.07 mm) cross-plane with maximum displacement of 0.37 mm in-plane and 0.34 mm cross-plane. The methods described provide a quantitative measure of beam spot position, are easy to use, and provide another tool for Linac setup and quality assurance. Fundamental to the techniques is that they are self-referencing-i.e., they do not require the user to independently define the CAOR.

Two self-referencing methods for the measurement of beam spot position

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nyiri, Balazs J.; Smale, Jason R.; Gerig, Lee H.

2012-12-15

Purpose: Two quantitative methods of measuring electron beam spot position with respect to the collimator axis of rotation (CAOR) are described. Methods: Method 1 uses a cylindrical ion chamber (IC) mounted on a jig corotational with the collimator making the relationship among the chamber, jaws, and CAOR fixed and independent of collimator angle. A jaw parallel to the IC axis is set to zero and the IC position adjusted so that the IC signal is approximately 50% of the open field value, providing a large dose gradient in the region of the IC. The cGy/MU value is measured as amore » function of collimator rotation, e.g., every 30 Degree-Sign . If the beam spot does not lie on the CAOR, the signal from the ion chamber will vary with collimator rotation. Based on a measured spatial sensitivity, the distance of the beam spot from the CAOR can be calculated from the IC signal variation with rotation. The 2nd method is image based. Two stainless steel rods, 3 mm in diameter, are mounted to a jig attached to the Linac collimator. The rods, offset from the CAOR, lay in different planes normal to the CAOR, one at 158 cm SSD and the other at 70 cm SSD. As the collimator rotates the rods move tangent along an envelope circle, the centers of which are on the CAOR in their respective planes. Three images, each at a different collimator rotation, containing the shadows of both rods, are acquired on the Linac EPID. At each angle the shadow of the rods on the EPID defines lines tangent to the projection of the envelope circles. From these the authors determine the projected centers of the two circles at different heights. From the distance of these two points using the two heights and the source to EPID distance, the authors calculate the distance of the beam spot from the CAOR. Measurements with all two techniques were performed on an Elekta Linac. Measurements were performed with the beam spot in nominal clinical position and in a deliberately offset position. Measurements were also performed using the Flexmap image registration/ball-bearing test. Results: Within their uncertainties, both methods report the same beam spot displacement. In clinical use, a total of 203 monthly beam spot measurements on 14 different beams showed an average displacement of 0.11 mm ({sigma}= 0.07 mm) in-plane and 0.10 mm ({sigma}= 0.07 mm) cross-plane with maximum displacement of 0.37 mm in-plane and 0.34 mm cross-plane. Conclusions: The methods described provide a quantitative measure of beam spot position, are easy to use, and provide another tool for Linac setup and quality assurance. Fundamental to the techniques is that they are self-referencing-i.e., they do not require the user to independently define the CAOR.« less

Characterization of apple stem grooving virus and apple chlorotic leaf spot virus identified in a crab apple tree.

PubMed

Li, Yongqiang; Deng, Congliang; Bian, Yong; Zhao, Xiaoli; Zhou, Qi

2017-04-01

Apple stem grooving virus (ASGV), apple chlorotic leaf spot virus (ACLSV), and prunus necrotic ringspot virus (PNRSV) were identified in a crab apple tree by small RNA deep sequencing. The complete genome sequence of ACLSV isolate BJ (ACLSV-BJ) was 7554 nucleotides and shared 67.0%-83.0% nucleotide sequence identity with other ACLSV isolates. A phylogenetic tree based on the complete genome sequence of all available ACLSV isolates showed that ACLSV-BJ clustered with the isolates SY01 from hawthorn, MO5 from apple, and JB, KMS and YH from pear. The complete nucleotide sequence of ASGV-BJ was 6509 nucleotides (nt) long and shared 78.2%-80.7% nucleotide sequence identity with other isolates. ASGV-BJ and the isolate ASGV_kfp clustered together in the phylogenetic tree as an independent clade. Recombination analysis showed that isolate ASGV-BJ was a naturally occurring recombinant.

Feasibility of Epidemiologic Research on Nonauditory Health Effects of Residential Aircraft Noise Exposure. Volume 3. Summary of Literature on Cardiovascular Effects on Noise Exposure

DTIC Science & Technology

1989-12-01

analyser epinephrine, dopamine, Cigala, F.; shop and sorting, and General Rodo cortisol measured Ricco, M.; matched for age, exposed personal dosimeters ...old sured by calibrated person- BP with semi-automatic de Vries, F. F.; duction depart- 31% 25-34 yrs.; al dosimeters with a short Waterpik...with without noise strain, history of hyper- tension excluded. 84 Table 3-23: continued. Suammuy of Epid oSl c Sades - contnud Bias and Potential

Genetic diversity and distribution of a distinct strain of Chili leaf curl virus and associated betasatellite infecting tomato and pepper in Oman.

PubMed

Khan, Akhtar J; Akhtar, Sohail; Al-Zaidi, Amal M; Singh, Achuit K; Briddon, Rob W

2013-10-01

Tomato and pepper are widely grown in Oman for local consumption. A countrywide survey was conducted during 2010-2011 to collect samples and assess the diversity of begomoviruses associated with leaf curl disease of tomato and pepper. A virus previously only identified on the Indian subcontinent, chili leaf curl virus (ChLCV), was found associated with tomato and pepper diseases in all vegetable grown areas of Oman. Some of the infected plant samples were also found to contain a betasatellite. A total of 19 potentially full-length begomovirus and eight betasatellite clones were sequenced. The begomovirus clones showed >96% nucleotide sequence identity, showing them to represent a single species. Comparisons to sequences available in the databases showed the highest levels of nucleotide sequence identity (88.0-91.1%) to isolates of the "Pakistan" strain of ChLCV (ChLCV-PK), indicating the virus from Oman to be a distinct strain, for which the name Oman strain (ChLCV-OM) is proposed. An analysis for recombination showed ChLCV-OM likely to have originated by recombination between ChLCV-PK (the major parent), pepper leaf curl Lahore virus and a third strain of ChLCV. The betasatellite sequences obtained were shown to have high levels of identity to isolates of tomato leaf curl betasatellite (ToLCB) previous shown to be present in Oman. For the disease in tomato Koch's postulates were satisfied by Agrobacterium-mediated inoculation of virus and betasatellites clones. This showed the symptoms induced by the virus in the presence of the betasatellite to be enhanced, although viral DNA levels were not affected. ChLCV-OM is the fourth begomovirus identified in tomato in Oman and the first in Capsicum. The significance of these findings is discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular characterization of a new begomovirus associated with leaf yellow mosaic disease of Jatropha curcas in India.

PubMed

Srivastava, Ashish; Kumar, S; Jaidi, Meraj; Raj, S K

2015-05-01

During a survey in June 2011, severe leaf yellow mosaic disease was observed on about 45 % plants of Jatropha curcas growing in the Katerniaghat wildlife sanctuary in India. An association of a begomovirus with disease was detected in 15 out of 20 samples by PCR using begomovirus genus-specific primers and total DNA isolated from symptomatic leaf samples. For identification of the begomovirus, the complete genome was amplified using a Phi-29 DNA-polymerase-based rolling-circle amplification kit and total DNA from five representative samples and then digested with BamHI. The linearized RCA products were cloned and sequenced. Their GenBank accession numbers are JN698954 (SKRK1) and JN135236 (SKRK2). The sequences of the two begomovirus isolates were 97 % identical to each other and no more than 86 % to those of jatropha mosaic India virus (JMIV, HM230683) and other begomoviruses reported worldwide. In phylogenetic analysis, SKRK1 and SKRK2 clustered together and showed distant relationships to jatropha mosaic India virus, Jatropha curcas mosaic virus, Indian cassava mosaic virus, Sri Lankan cassava mosaic virus and other begomoviruses. Based on 86 % sequence identities and distant phylogenetic relationships to JMIV and other begomoviruses and the begomovirus species demarcation criteria of the ICTV (<89 % sequence identity of complete DNA-A genome), the begomovirus isolates associated with leaf yellow mosaic disease of J. curcas were identified as members of a new begomovirus species and provisionally designated as jatropha leaf yellow mosaic Katerniaghat virus (JLYMKV). Agroinfectious clones of the DNA molecule of the begomovirus isolate were also generated, and the fulfillment of Koch's postulates was demonstrated in J. curcas plants.

SU-F-T-271: Comparing IMRT QA Pass Rates Before and After MLC Calibration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazza, A; Perrin, D; Fontenot, J

Purpose: To compare IMRT QA pass rates before and after an in-house MLC leaf calibration procedure. Methods: The MLC leaves and backup jaws on four Elekta linear accelerators with MLCi2 heads were calibrated using the EPID-based RIT Hancock Test as the means for evaluation. The MLCs were considered to be successfully calibrated when they could pass the Hancock Test with criteria of 1 mm jaw position tolerance, and 1 mm leaf position tolerance. IMRT QA results were collected pre- and postcalibration and analyzed using gamma analysis with 3%/3mm DTA criteria. AAPM TG-119 test plans were also compared pre- and post-calibration,more » at both 2%/2mm DTA and 3%/3mm DTA. Results: A weighted average was performed on the results for all four linear accelerators. The pre-calibration IMRT QA pass rate was 98.3 ± 0.1%, compared with the post-calibration pass rate of 98.5 ± 0.1%. The TG-119 test plan results showed more of an improvement, particularly at the 2%/2mm criteria. The averaged results were 89.1% pre and 96.1% post for the C-shape plan, 94.8% pre and 97.1% post for the multi-target plan, 98.6% pre and 99.7% post for the prostate plan, 94.7% pre and 94.8% post for the head/neck plan. Conclusion: The patient QA results did not show statistically significant improvement at the 3%/3mm DTA criteria after the MLC calibration procedure. However, the TG-119 test cases did show significant improvement at the 2%/2mm level.« less

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

PubMed

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

PubMed Central

Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

2016-01-01

Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

Characterization of Apricot pseudo-chlorotic leaf spot virus, A Novel Trichovirus Isolated from Stone Fruit Trees.

PubMed

Liberti, D; Marais, A; Svanella-Dumas, L; Dulucq, M J; Alioto, D; Ragozzino, A; Rodoni, B; Candresse, T

2005-04-01

ABSTRACT A trichovirus closely related to Apple chlorotic leaf spot virus (ACLSV) was detected in symptomatic apricot and Japanese plum from Italy. The Sus2 isolate of this agent cross-reacted with anti-ACLSV polyclonal reagents but was not detected by broad-specificity anti- ACLSV monoclonal antibodies. It had particles with typical trichovirus morphology but, contrary to ACLSV, was unable to infect Chenopodium quinoa and C. amaranticolor. The sequence of its genome (7,494 nucleotides [nt], missing only approximately 30 to 40 nt of the 5' terminal sequence) and the partial sequence of another isolate were determined. The new virus has a genomic organization similar to that of ACLSV, with three open reading frames coding for a replication-associated protein (RNA-dependent RNA polymerase), a movement protein, and a capsid protein, respectively. However, it had only approximately 65 to 67% nucleotide identity with sequenced isolates of ACLSV. The differences in serology, host range, genome sequence, and phylogenetic reconstructions for all viral proteins support the idea that this agent should be considered a new virus, for which the name Apricot pseudo-chlorotic leaf spot virus (APCLSV) is proposed. APCLSV shows substantial sequence variability and has been recovered from various Prunus sources coming from seven countries, an indication that it is likely to have a wide geographical distribution.

Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements

PubMed Central

Gowda, Malali

2016-01-01

Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice Magnaporthe isolates to understand the extent of genetic variation. We have sequenced the whole genome of the Magnaporthe isolates, infecting rice (leaf and neck), finger millet (leaf and neck), foxtail millet (leaf) and buffel grass (leaf). Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by Pot2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of Magnaporthe indicating an independent genome evolution orchestrated by multiple genomic factors. PMID:27658241

A proteomic analysis of leaf sheaths from rice.

PubMed

Shen, Shihua; Matsubae, Masami; Takao, Toshifumi; Tanaka, Naoki; Komatsu, Setsuko

2002-10-01

The proteins extracted from the leaf sheaths of rice seedlings were separated by 2-D PAGE, and analyzed by Edman sequencing and mass spectrometry, followed by database searching. Image analysis revealed 352 protein spots on 2-D PAGE after staining with Coomassie Brilliant Blue. The amino acid sequences of 44 of 84 proteins were determined; for 31 of these proteins, a clear function could be assigned, whereas for 12 proteins, no function could be assigned. Forty proteins did not yield amino acid sequence information, because they were N-terminally blocked, or the obtained sequences were too short and/or did not give unambiguous results. Fifty-nine proteins were analyzed by mass spectrometry; all of these proteins were identified by matching to the protein database. The amino acid sequences of 19 of 27 proteins analyzed by mass spectrometry were similar to the results of Edman sequencing. These results suggest that 2-D PAGE combined with Edman sequencing and mass spectrometry analysis can be effectively used to identify plant proteins.

Genetic structure and evolution of natural populations of viruses causing the tomato yellow leaf curl disease in Spain.

PubMed

Font, María Isabel; Rubio, Luis; Martínez-Culebras, Pedro Vicente; Jordá, Concepción

2007-09-01

The population structure and genetic variation of two begomoviruses: tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl virus (TYLCV) in tomato crops of Spain were studied from 1997 until 2001. Restriction digestion of a genomic region comprised of the CP coat protein gene (CPR) of 358 TYLC virus isolates enabled us to classify them into 14 haplotypes. Nucleotide sequences of two genomic regions: CPR, and the surrounding intergenic region (SIR) were determined for at least two isolates per haplotype. SIR was more variable than CPR and showed multiple recombination events whereas no recombination was detected within CPR. In all geographic regions except Murcia, the population was, or evolved to be composed of one predominant haplotype with a low genetic diversity (<0.0180). In Murcia, two successive changes of the predominant haplotype were observed in the best studied population. Phylogenetic analysis showed that the TYLCSV sequences determined clustered with sequences obtained from the GenBank of other TYLCSV Spanish isolates which were clearly separated from TYLCSV Italian isolates. Most of our TYLCV sequences were similar to those of isolates from Japan and Portugal, and the sequences obtained from TYLCV isolates from the Canary island of Lanzarote were similar to those of Caribbean TYLCV isolates.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Ziyu; Hooker, Brian S.; Anderson, Daniel B.

Optimization of Acidothermus cellulolyticus endoglucanase (E1) gene expression in transgenic potato (Solanum tuberosum L.) was examined in this study, where the E1 coding sequence was transcribed under control of a leaf specific promoter (tomato RbcS-3C) or the Mac promoter (a hybrid promoter of mannopine synthase promoter and cauliflower mosaic virus 35S promoter enhancer region). Average E1 activity in leaf extracts of potato transformants, in which E1 protein was targeted by a chloroplast signal peptide and an apoplast signal peptide were much higher than those by an E1 native signal peptide and a vacuole signal peptide. E1 protein accumulated up tomore » 2.6% of total leaf soluble protein, where E1 gene was under control of the RbcS-3C promoter, alfalfa mosaic virus 5-untranslated leader, and RbcS-2A signal peptide. E1 protein production, based on average E1 activity and E1 protein accumulation in leaf extracts, is higher in potato than those measured previously in transgenic tobacco bearing the same transgene constructs. Comparisons of E1 activity, protein accumulation, and relative mRNA levels showed that E1 expression under control of tomato RbcS-3C promoter was specifically localized in leaf tissues, while E1 gene was expressed in both leaf and tuber tissues under control of Mac promoter. This suggests dual-crop applications in which potato vines serve as enzyme production `bioreactors' while tubers are preserved for culinary applications.« less

Noseleaf Dynamics during Pulse Emission in Horseshoe Bats

PubMed Central

Feng, Lin; Gao, Li; Lu, Hongwang; Müller, Rolf

2012-01-01

Horseshoe bats emit their biosonar pulses nasally and diffract the outgoing ultrasonic waves by conspicuous structures that surrounded the nostrils. Here, we report quantitative experimental data on the motion of a prominent component of these structures, the anterior leaf, using synchronized laser Doppler vibrometry and acoustic recordings in the greater horseshoe bat (Rhinolophus ferrumequinum). The vibrometry data has demonstrated non-random motion patterns in the anterior leaf. In these patterns, the outer rim of the walls of the anterior leaf twitches forward and inwards to decrease the aperture of the noseleaf and increase the curvature of its surfaces. Noseleaf displacements were correlated with the emitted ultrasonic pulses. After their onset, the inward displacements increased monotonically towards their maximum value which was always reached within the duration of the biosonar pulse, typically towards its end. In other words, the anterior leaf’s surfaces were moving inwards during most of the pulse. Non-random motions were not present in all recorded pulse trains, but could apparently be switched on or off. Such switches happened between sequences of consecutive pulses but were never observed between individual pulses within a sequence. The amplitudes of the emitted biosonar pulse and accompanying noseleaf movement were not correlated in the analyzed data set. The measured velocities of the noseleaf surface were too small to induce Doppler shifts of a magnitude with a likely significance. However, the displacement amplitudes were significant in comparison with the overall size of the anterior leaf and the sound wavelengths. These results indicate the possibility that horseshoe bats use dynamic sensing principles on the emission side of their biosonar system. Given the already available evidence that such mechanisms exist for biosonar reception, it may be hypothesized that time-variant mechanisms play a pervasive role in the biosonar sensing of horseshoe bats. PMID:22574110

Study of the detective quantum efficiency for the kinestatic charge detector as a megavoltage imaging device

NASA Astrophysics Data System (ADS)

Samant, Sanjiv S.; Gopal, Arun; DiBianca, Frank A.

2003-06-01

Megavoltage x-ray imaging suffers from relatively poor contrast and spatial resolution compared to diagnostic kilovoltage x-ray imaging due to the dominant Compton scattering in the former. Recently available amorphous silicon/selenium based flat-panel imagers overcome many of the limitations of poor contrast and spatial resolution that affect conventional video based electronic portal imaging devices (EPIDs). An alternative technology is presented here: kinestatic charge detection (KCD). The KCD uses a slot photon beam, high-pressure gas (xenon, 100 atm) and a multi-ion rectangular chamber in scanning mode. An electric field is used to regulate the cation drift velocity. By matching the scanning speed with that of the cation drift, the cations remain static in the object frame of reference, allowing temporal integration of the signal. KCD imaging is characterized by reduced scatter and a high signal-to-noise ratio. Measurements and Monte Carlo simulations of modulation transfer function (MTF), noise power spectrum (NPS) and the detective quantum efficiency (DQE) of a prototype small field of view KCD detector (384 channels, 0.5 mm spacing) were carried out. Measurements yield DQE[0]=0.19 and DQE[0.5cy/mm]=0.01. KCD imaging is compared to film and commercial EPID systems using phantoms, with the KCD requiring an extremely low dose (0.1 cGy) per image. A proposed cylindrical chamber design with a higher ion-collection depth is expected to further improve image quality (DQE[0]>0.25).

Map-based cloning and characterization of the novel yellow-green leaf gene ys83 in rice (Oryza sativa).

PubMed

Ma, Xiaozhi; Sun, Xiaoqiu; Li, Chunmei; Huan, Rui; Sun, Changhui; Wang, Yang; Xiao, Fuliang; Wang, Qian; Chen, Purui; Ma, Furong; Zhang, Kuan; Wang, Pingrong; Deng, Xiaojian

2017-02-01

Leaf-color mutants have been extensively studied in rice, and many corresponding genes have been identified up to now. However, leaf-color mutation mechanisms are diverse and still need further research through identification of novel genes. In the present paper, we isolated a leaf-color mutant, ys83, in rice (Oryza sativa). The mutant displayed a yellow-green leaf phenotype at seedling stage, and then slowly turned into light-green leaf from late tillering stage. In its yellow leaves, photosynthetic pigment contents significantly decreased and the chloroplast development was retarded. The mutant phenotype was controlled by a recessive mutation in a nuclear gene on the short arm of rice chromosome 2. Map-based cloning and sequencing analysis suggested that the candidate gene was YS83 (LOC_Os02g05890) encoding a protein containing 165 amino acid residues. Gene YS83 was expressed in a wide range of tissues, and its encoded protein was targeted to the chloroplast. In the mutant, a T-to-A substitution occurred in coding sequence of gene YS83, which caused a premature translation of its encoded product. By introduction of the wild-type gene, the ys83 mutant recovered to normal green-leaf phenotype. Taken together, we successfully identified a novel yellow-green leaf gene YS83. In addition, number of productive panicles per plant and number of spikelets per panicle only reduced by 6.7% and 7.6%, respectively, meanwhile its seed setting rate and 1000-grain weight (seed size) were not significantly affected in the mutant, so leaf-color mutant gene ys83 could be used as a trait marker gene in commercial hybrid rice production. Copyright © 2016. Published by Elsevier Masson SAS.

SU-E-T-282: Dose Measurements with An End-To-End Audit Phantom for Stereotactic Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, R; Artschan, R; Thwaites, D

Purpose: Report on dose measurements as part of an end-to-end test for stereotactic radiotherapy, using a new audit tool, which allows audits to be performed efficiently either by an onsite team or as a postal audit. Methods: Film measurements have been performed with a new Stereotactic Cube Phantom. The phantom has been designed to perform Winston Lutz type position verification measurements and dose measurements in one setup. It comprises a plastic cube with a high density ball in its centre (used for MV imaging with film or EPID) and low density markers in the periphery (used for Cone Beam Computedmore » Tomography, CBCT imaging). It also features strategically placed gold markers near the posterior and right surfaces, which can be used to calculate phantom rotations on MV images. Slit-like openings allow insertion of film or other detectors.The phantom was scanned and small field treatment plans were created. The fields do not traverse any inhomogeneities of the phantom on their paths to the measurement location. The phantom was setup at the delivery system using CBCT imaging. The calculated treatment fields were delivered, each with a piece of radiochromic film (EBT3) placed in the anterior film holder of the phantom. MU had been selected in planning to achieve similar exposures on all films. Calibration films were exposed in solid water for dose levels around the expected doses. Films were scanned and analysed following established procedures. Results: Setup of the cube showed excellent suitability for CBCT 3D alignment. MV imaging with EPID allowed for clear identification of all markers. Film based dose measurements showed good agreement for MLC created fields down to 0.5 mm × 0.5 mm. Conclusion: An end-to-end audit phantom for stereotactic radiotherapy has been developed and tested.« less

Molecular analysis of new isolates of Tomato leaf curl Philippines virus and an associated betasatellite occurring in the Philippines.

PubMed

Sharma, Pradeep; Matsuda, N; Bajet, N B; Ikegami, M

2011-02-01

Three new begomovirus isolates and one betasatellite were obtained from a tomato plant exhibiting leaf curl symptom in Laguna, the Philippines. Typical begomovirus DNA components representing the three isolates (PH01, PH02 and PH03) were cloned, and their full-length sequences were determined to be 2754 to 2746 nucleotides. The genome organizations of these isolates were similar to those of other Old World monopartite begomoviruses. The sequence data indicated that PH01 and PH02 were variants of strain B of the species Tomato leaf curl Philippines virus, while PH03 was a variant of strain A of the species Tomato leaf curl Philippines virus. These isolates were designated ToLCPV-B[PH:Lag1:06], ToLCPV-B[PH:Lag2:06], and ToLCPV-A[PH:Lag3:06], respectively. Phylogenetic analysis revealed that the present isolates form a separate monophyletic cluster with indigenous begomoviruses reported earlier in the Philippines. A betasatellite isolated from same sample belongs to the betasatellite species Tomato leaf curl Philippines betasatellite and designated Tomato leaf curl Philippines betasatellite-[Philippines:Laguna1:2006], ToLCPHB-[PH:Lag1:06]. When co-inoculated with this betasatellite, tomato leaf curl Philippines virus induced severe symptoms in N. benthamiana and Solanum lycopersicum plants. Using a PVX-mediated transient assay, we found that the C4 and C2 proteins of tomato leaf curl Philippines virus and the βC1 protein of ToLCPHB-[PH:Lag1:06] function as a suppressor of RNA silencing.

Leaf-IT: An Android application for measuring leaf area.

PubMed

Schrader, Julian; Pillar, Giso; Kreft, Holger

2017-11-01

The use of plant functional traits has become increasingly popular in ecological studies because plant functional traits help to understand key ecological processes in plant species and communities. This also includes changes in diversity, inter- and intraspecific interactions, and relationships of species at different spatiotemporal scales. Leaf traits are among the most important traits as they describe key dimensions of a plant's life history strategy. Further, leaf area is a key parameter with relevance for other traits such as specific leaf area, which in turn correlates with leaf chemical composition, photosynthetic rate, leaf longevity, and carbon investment. Measuring leaf area usually involves the use of scanners and commercial software and can be difficult under field conditions. We present Leaf-IT, a new smartphone application for measuring leaf area and other trait-related areas. Leaf-IT is free, designed for scientific purposes, and runs on Android 4 or higher. We tested the precision and accuracy using objects with standardized area and compared the area measurements of real leaves with the well-established, commercial software WinFOLIA using the Altman-Bland method. Area measurements of standardized objects show that Leaf-IT measures area with high accuracy and precision. Area measurements with Leaf-IT of real leaves are comparable to those of WinFOLIA. Leaf-IT is an easy-to-use application running on a wide range of smartphones. That increases the portability and use of Leaf-IT and makes it possible to measure leaf area under field conditions typical for remote locations. Its high accuracy and precision are similar to WinFOLIA. Currently, its main limitation is margin detection of damaged leaves or complex leaf morphologies.

Beam’s-eye-view imaging during non-coplanar lung SBRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yip, Stephen S. F., E-mail: syip@lroc.harvard.edu; Rottmann, Joerg; Berbeco, Ross I.

Purpose: Beam’s-eye-view (BEV) imaging with an electronic portal imaging device (EPID) can be performed during lung stereotactic body radiation therapy (SBRT) to monitor the tumor location in real-time. Image quality for each patient and treatment field depends on several factors including the patient anatomy and the gantry and couch angles. The authors investigated the angular dependence of automatic tumor localization during non-coplanar lung SBRT delivery. Methods: All images were acquired at a frame rate of 12 Hz with an amorphous silicon EPID. A previously validated markerless lung tumor localization algorithm was employed with manual localization as the reference. From tenmore » SBRT patients, 12 987 image frames of 123 image sequences acquired at 48 different gantry–couch rotations were analyzed. δ was defined by the position difference of the automatic and manual localization. Results: Regardless of the couch angle, the best tracking performance was found in image sequences with a gantry angle within 20° of 250° (δ = 1.40 mm). Image sequences acquired with gantry angles of 150°, 210°, and 350° also led to good tracking performances with δ = 1.77–2.00 mm. Overall, the couch angle was not correlated with the tracking results. Among all the gantry–couch combinations, image sequences acquired at (θ = 30°, ϕ = 330°), (θ = 210°, ϕ = 10°), and (θ = 250°, ϕ = 30°) led to the best tracking results with δ = 1.19–1.82 mm. The worst performing combinations were (θ = 90° and 230°, ϕ = 10°) and (θ = 270°, ϕ = 30°) with δ > 3.5 mm. However, 35% (17/48) of the gantry–couch rotations demonstrated substantial variability in tracking performances between patients. For example, the field angle (θ = 70°, ϕ = 10°) was acquired for five patients. While the tracking errors were ≤1.98 mm for three patients, poor performance was found for the other two patients with δ ≥ 2.18 mm, leading to average tracking error of 2.70 mm. Only one image sequence was acquired for all other gantry–couch rotations (δ = 1.18–10.29 mm). Conclusions: Non-coplanar beams with gantry–couch rotation of (θ = 30°, ϕ = 330°), (θ = 210°, ϕ = 10°), and (θ = 250°, ϕ = 30°) have the highest accuracy for BEV lung tumor localization. Additionally, gantry angles of 150°, 210°, 250°, and 350° also offer good tracking performance. The beam geometries (θ = 90° and 230°, ϕ = 10°) and (θ = 270°, ϕ = 30°) are associated with substantial automatic localization errors. Overall, lung tumor visibility and tracking performance were patient dependent for a substantial number of the gantry–couch angle combinations studied.« less

Molecular characterization and phylogenetic relationships of Desmodium leaf distortion virus (DeLDV): a new begomovirus infecting Desmodium glabrum in Yucatan, Mexico.

PubMed

Hernández-Zepeda, Cecilia; Argüello-Astorga, Gerardo; Idris, Ali M; Carnevali, Germán; Brown, Judith K; Moreno-Valenzuela, Oscar A

2009-12-01

The complete DNA-A component sequence of Desmodium leaf distortion virus (DeLDV, Begomovirus) isolated in Yucatan was determined to be 2569 nucleotides (nt) in length, and it was most closely related to Cotton leaf crumple virus-California (CLCrV-[Cal]), at 76%. The complete DNA-B component sequence was 2514 nt in length, and shared its highest nucleotide identity (60%) with Potato yellow mosaic Trinidad virus (PYMTV). Phylogenetic analyses group the DeLDV DNA-A component in the SLCV clade, whereas, the DeLDV DNA-B was grouped with the Abutilon mosaic virus clade, which also contains PYMV, suggesting that the DeLDV components have distinct evolutionary histories, possibly as the result of recombination and reassortment.

On flattening filter‐free portal dosimetry

PubMed Central

Novais, Juan Castro; Molina López, María Yolanda; Maqueda, Sheila Ruiz

2016-01-01

Varian introduced (in 2010) the option of removing the flattening filter (FF) in their C‐Arm linacs for intensity‐modulated treatments. This mode, called flattening filter‐free (FFF), offers the advantage of a greater dose rate. Varian's “Portal Dosimetry” is an electronic portal imager device (EPID)‐based tool for IMRT verification. This tool lacks the capability of verifying flattening filter‐free (FFF) modes due to saturation and lack of an image prediction algorithm. (Note: the latest versions of this software and EPID correct these issues.) The objective of the present study is to research the feasibility of said verifications (with the older versions of the software and EPID). By placing the EPID at a greater distance, the images can be acquired without saturation, yielding a linearity similar to the flattened mode. For the image prediction, a method was optimized based on the clinically used algorithm (analytical anisotropic algorithm (AAA)) over a homogeneous phantom. The depth inside the phantom and its electronic density were tailored. An application was developed to allow the conversion of a dose plane (in DICOM format) to Varian's custom format for Portal Dosimetry. The proposed method was used for the verification of test and clinical fields for the three qualities used in our institution for IMRT: 6X, 6FFF and 10FFF. The method developed yielded a positive verification (more than 95% of the points pass a 2%/2 mm gamma) for both the clinical and test fields. This method was also capable of “predicting” static and wedged fields. A workflow for the verification of FFF fields was developed. This method relies on the clinical algorithm used for dose calculation and is able to verify the FFF modes, as well as being useful for machine quality assurance. The procedure described does not require new hardware. This method could be used as a verification of Varian's Portal Dose Image Prediction. PACS number(s): 87.53.Kn, 87.55.T‐, 87.56.bd, 87.59.‐e PMID:27455487

SU-E-T-62: A Preliminary Experience of Using EPID Transit Dosimetry for Monitoring Daily Dose Variations in Radiation Treatment Delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, R; Chisela, W

2015-06-15

Purpose: To investigate the use of EPID transit dosimetry for monitoring daily dose variations in radiation treatment delivery. Methods: A patient with head and neck cancer treated using nine field IMRT beams was used in this study. The prescription was 45 Gy in 25 fractions. A KV CBCT was acquired before each treatment on a Varian NTX linear accelerator. Integrated images using MV EPID were acquired for each treatment beam. Planning CT images, treatment plan, and daily integrated images were imported into a commercial QA software Dosimetry Check (v4r4 Math Resolutions, LLC, Columbia, MD) to calculate 3D dose of themore » day assuming 25 fractions treatment. Planning CT images were deformed and registered to each daily CBCT using Varian SmartAdapt (v11.MR2). ROIs were then propagated from planning CT to daily CBCT. The correlation between maximum, average dose of ROIs and ROI volume, center of mass shift, Dice Similarity Coefficient (DSC) were investigated. Results: Not all parameters investigated showed strong correlations. For PTV and CTV, the average dose has inverse correlation with their volume change (correlation coefficient −0.52, −0.50, respectively) and DSC (−0.59, −0.59, respectively). The average dose of right parotid has correlation with its volume change (0.56). The maximum dose of spinal cord has correlation with the center of mass superior-inferior shift (0.52) and inverse correlation with the center of mass anterior-posterior shift (−0.73). Conclusion: Transit dosimetry using EPID images collected during treatment delivery offers great potential to monitor daily dose variations due to patient anatomy change, motion, and setup errors in radiation treatment delivery. It can provide a patient-specific QA tool valuable for adaptive radiation therapy. Further work is needed to validate the technique.« less

A novel technique for VMAT QA with EPID in cine mode on a Varian TrueBeam linac

NASA Astrophysics Data System (ADS)

Liu, Bo; Adamson, Justus; Rodrigues, Anna; Zhou, Fugen; Yin, Fang-fang; Wu, Qiuwen

2013-10-01

Volumetric modulated arc therapy (VMAT) is a relatively new treatment modality for dynamic photon radiation therapy. Pre-treatment quality assurance (QA) is necessary and many efforts have been made to apply electronic portal imaging device (EPID)-based IMRT QA methods to VMAT. It is important to verify the gantry rotation speed during delivery as this is a new variable that is also modulated in VMAT. In this paper, we present a new technique to perform VMAT QA using an EPID. The method utilizes EPID cine mode and was tested on Varian TrueBeam in research mode. The cine images were acquired during delivery and converted to dose matrices after profile correction and dose calibration. A sub-arc corresponding to each cine image was extracted from the original plan and its portal image prediction was calculated. Several analyses were performed including 3D γ analysis (2D images + gantry angle axis), 2D γ analysis, and other statistical analyses. The method was applied to 21 VMAT photon plans of 3 photon energies. The accuracy of the cine image information was investigated. Furthermore, this method's sensitivity to machine delivery errors was studied. The pass rate (92.8 ± 1.4%) for 3D γ analysis was comparable to those from Delta4 system (99.9 ± 0.1%) under similar criteria (3%, 3 mm, 5% threshold and 2° angle to agreement) at 6 MV. The recorded gantry angle and start/stop MUs were found to have sufficient accuracy for clinical QA. Machine delivery errors can be detected through combined analyses of 3D γ, gantry angle, and percentage dose difference. In summary, we have developed and validated a QA technique that can simultaneously verify the gantry angle and delivered MLC fluence for VMAT treatment.This technique is efficient and its accuracy is comparable to other QA methods.

Craniocaudal Safety Margin Calculation Based on Interfractional Changes in Tumor Motion in Lung SBRT Assessed With an EPID in Cine Mode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ueda, Yoshihiro, E-mail: ueda-yo@mc.pref.osaka.jp; Miyazaki, Masayoshi; Nishiyama, Kinji

2012-07-01

Purpose: To evaluate setup error and interfractional changes in tumor motion magnitude using an electric portal imaging device in cine mode (EPID cine) during the course of stereotactic body radiation therapy (SBRT) for non-small-cell lung cancer (NSCLC) and to calculate margins to compensate for these variations. Materials and Methods: Subjects were 28 patients with Stage I NSCLC who underwent SBRT. Respiratory-correlated four-dimensional computed tomography (4D-CT) at simulation was binned into 10 respiratory phases, which provided average intensity projection CT data sets (AIP). On 4D-CT, peak-to-peak motion of the tumor (M-4DCT) in the craniocaudal direction was assessed and the tumor centermore » (mean tumor position [MTP]) of the AIP (MTP-4DCT) was determined. At treatment, the tumor on cone beam CT was registered to that on AIP for patient setup. During three sessions of irradiation, peak-to-peak motion of the tumor (M-cine) and the mean tumor position (MTP-cine) were obtained using EPID cine and in-house software. Based on changes in tumor motion magnitude ( Increment M) and patient setup error ( Increment MTP), defined as differences between M-4DCT and M-cine and between MTP-4DCT and MTP-cine, a margin to compensate for these variations was calculated with Stroom's formula. Results: The means ({+-}standard deviation: SD) of M-4DCT and M-cine were 3.1 ({+-}3.4) and 4.0 ({+-}3.6) mm, respectively. The means ({+-}SD) of Increment M and Increment MTP were 0.9 ({+-}1.3) and 0.2 ({+-}2.4) mm, respectively. Internal target volume-planning target volume (ITV-PTV) margins to compensate for Increment M, Increment MTP, and both combined were 3.7, 5.2, and 6.4 mm, respectively. Conclusion: EPID cine is a useful modality for assessing interfractional variations of tumor motion. The ITV-PTV margins to compensate for these variations can be calculated.« less

New calibration technique for KCD-based megavoltage imaging

NASA Astrophysics Data System (ADS)

Samant, Sanjiv S.; Zheng, Wei; DiBianca, Frank A.; Zeman, Herbert D.; Laughter, Joseph S.

1999-05-01

In megavoltage imaging, current commercial electronic portal imaging devices (EPIDs), despite having the advantage of immediate digital imaging over film, suffer from poor image contrast and spatial resolution. The feasibility of using a kinestatic charge detector (KCD) as an EPID to provide superior image contrast and spatial resolution for portal imaging has already been demonstrated in a previous paper. The KCD system had the additional advantage of requiring an extremely low dose per acquired image, allowing for superior imaging to be reconstructed form a single linac pulse per image pixel. The KCD based images utilized a dose of two orders of magnitude less that for EPIDs and film. Compared with the current commercial EPIDs and film, the prototype KCD system exhibited promising image qualities, despite being handicapped by the use of a relatively simple image calibration technique, and the performance limits of medical linacs on the maximum linac pulse frequency and energy flux per pulse delivered. This image calibration technique fixed relative image pixel values based on a linear interpolation of extrema provided by an air-water calibration, and accounted only for channel-to-channel variations. The counterpart of this for area detectors is the standard flat fielding method. A comprehensive calibration protocol has been developed. The new technique additionally corrects for geometric distortions due to variations in the scan velocity, and timing artifacts caused by mis-synchronization between the linear accelerator and the data acquisition system (DAS). The role of variations in energy flux (2 - 3%) on imaging is demonstrated to be not significant for the images considered. The methodology is presented, and the results are discussed for simulated images. It also allows for significant improvements in the signal-to- noise ratio (SNR) by increasing the dose using multiple images without having to increase the linac pulse frequency or energy flux per pulse. The application of this protocol to a KCD system under construction is expected shortly.

SU-E-T-269: Differential Hazard Analysis For Conventional And New Linac Acceptance Testing Procedures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harry, T; Yaddanapudi, S; Mutic, S

Purpose: New techniques and materials have recently been developed to expedite the conventional Linac Acceptance Testing Procedure (ATP). The new ATP method uses the Electronic Portal Imaging Device (EPID) for data collection and is presented separately. This new procedure is meant to be more efficient then conventional methods. While not clinically implemented yet, a prospective risk assessment is warranted for any new techniques. The purpose of this work is to investigate the risks and establish the pros and cons between the conventional approach and the new ATP method. Methods: ATP tests that were modified and performed with the EPID weremore » analyzed. Five domain experts (Medical Physicists) comprised the core analysis team. Ranking scales were adopted from previous publications related to TG 100. The number of failure pathways for each ATP test procedure were compared as well as the number of risk priority numbers (RPN’s) greater than 100 were compared. Results: There were fewer failure pathways with the new ATP compared to the conventional, 262 and 556, respectively. There were fewer RPN’s > 100 in the new ATP compared to the conventional, 41 and 115. Failure pathways and RPN’s > 100 for individual ATP tests on average were 2 and 3.5 times higher in the conventional ATP compared to the new, respectively. The pixel sensitivity map of the EPID was identified as a key hazard to the new ATP procedure with an RPN of 288 for verifying beam parameters. Conclusion: The significant decrease in failure pathways and RPN’s >100 for the new ATP mitigates the possibilities of a catastrophic error occurring. The Pixel Sensitivity Map determining the response and inherent characteristics of the EPID is crucial as all data and hence results are dependent on that process. Grant from Varian Medical Systems Inc.« less

Plant chlorophyll fluorescence: active and passive measurements at canopy and leaf scales with different nitrogen treatments

PubMed Central

Cendrero-Mateo, M. Pilar; Moran, M. Susan; Papuga, Shirley A.; Thorp, K.R.; Alonso, L.; Moreno, J.; Ponce-Campos, G.; Rascher, U.; Wang, G.

2016-01-01

Most studies assessing chlorophyll fluorescence (ChlF) have examined leaf responses to environmental stress conditions using active techniques. Alternatively, passive techniques are able to measure ChlF at both leaf and canopy scales. However, the measurement principles of both techniques are different, and only a few datasets concerning the relationships between them are reported in the literature. In this study, we investigated the potential for interchanging ChlF measurements using active techniques with passive measurements at different temporal and spatial scales. The ultimate objective was to determine the limits within which active and passive techniques are comparable. The results presented in this study showed that active and passive measurements were highly correlated over the growing season across nitrogen treatments at both canopy and leaf-average scale. At the single-leaf scale, the seasonal relation between techniques was weaker, but still significant. The variability within single-leaf measurements was largely related to leaf heterogeneity associated with variations in CO2 assimilation and stomatal conductance, and less so to variations in leaf chlorophyll content, leaf size or measurement inputs (e.g. light reflected and emitted by the leaf and illumination conditions and leaf spectrum). This uncertainty was exacerbated when single-leaf analysis was limited to a particular day rather than the entire season. We concluded that daily measurements of active and passive ChlF at the single-leaf scale are not comparable. However, canopy and leaf-average active measurements can be used to better understand the daily and seasonal behaviour of passive ChlF measurements. In turn, this can be used to better estimate plant photosynthetic capacity and therefore to provide improved information for crop management. PMID:26482242

Monte Carlo simulation of a novel water-equivalent electronic portal imaging device using plastic scintillating fibers.

PubMed

Teymurazyan, A; Pang, G

2012-03-01

Most electronic portal imaging devices (EPIDs) developed so far use a thin Cu plate/phosphor screen to convert x-ray energies into light photons, while maintaining a high spatial resolution. This results in a low x-ray absorption and thus a low quantum efficiency (QE) of approximately 2-4% for megavoltage (MV) x-rays. A significant increase of QE is desirable for applications such as MV cone-beam computed tomography (MV-CBCT). Furthermore, the Cu plate/phosphor screen contains high atomic number (high-Z) materials, resulting in an undesirable over-response to low energy x-rays (due to photoelectric effect) as well as high energy x-rays (due to pair production) when used for dosimetric verification. Our goal is to develop a new MV x-ray detector that has a high QE and uses low-Z materials to overcome the obstacles faced by current MV x-ray imaging technologies. A new high QE and low-Z EPID is proposed. It consists of a matrix of plastic scintillating fibers embedded in a water-equivalent medium and coupled to an optically sensitive 2D active matrix flat panel imager (AMFPI) for image readout. It differs from the previous approach that uses segmented crystalline scintillators made of higher density and higher atomic number materials to detect MV x-rays. The plastic scintillating fibers are focused toward the x-ray source to avoid image blurring due to oblique incidence of off-axis x-rays. When MV x-rays interact with the scintillating fibers in the detector, scintillation light will be produced. The light photons produced in a fiber core and emitted within the acceptance angle of the fiber will be guided toward the AMFPI by total internal reflection. A Monte Carlo simulation has been used to investigate imaging and dosimetric characteristics of the proposed detector under irradiation of MV x-rays. Properties, such as detection efficiency, modulation transfer function, detective quantum efficiency (DQE), energy dependence of detector response, and water-equivalence of dose response have been investigated. It has been found that the zero frequency DQE of the proposed detector can be up to 37% at 6 MV. The detector, also, is water-equivalent with a relatively uniform response to different energy x-rays as compared to current EPIDs. The results of our simulations show that, using plastic scintillating fibers, it is possible to construct a water-equivalent EPID that has a better energy response and a higher detection efficiency than current flat panel based EPIDs.

A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

PubMed Central

Li, Feng; Kitashiba, Hiroyasu; Inaba, Kiyofumi; Nishio, Takeshi

2009-01-01

For identification of genes responsible for varietal differences in flowering time and leaf morphological traits, we constructed a linkage map of Brassica rapa DNA markers including 170 EST-based markers, 12 SSR markers, and 59 BAC sequence-based markers, of which 151 are single nucleotide polymorphism (SNP) markers. By BLASTN, 223 markers were shown to have homologous regions in Arabidopsis thaliana, and these homologous loci covered nearly the whole genome of A. thaliana. Synteny analysis between B. rapa and A. thaliana revealed 33 large syntenic regions. Three quantitative trait loci (QTLs) for flowering time were detected. BrFLC1 and BrFLC2 were linked to the QTLs for bolting time, budding time, and flowering time. Three SNPs in the promoter, which may be the cause of low expression of BrFLC2 in the early-flowering parental line, were identified. For leaf lobe depth and leaf hairiness, one major QTL corresponding to a syntenic region containing GIBBERELLIN 20 OXIDASE 3 and one major QTL containing BrGL1, respectively, were detected. Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits. PMID:19884167

Study of a prototype high quantum efficiency thick scintillation crystal video-electronic portal imaging device.

PubMed

Samant, Sanjiv S; Gopal, Arun

2006-08-01

Image quality in portal imaging suffers significantly from the loss in contrast and spatial resolution that results from the excessive Compton scatter associated with megavoltage x rays. In addition, portal image quality is further reduced due to the poor quantum efficiency (QE) of current electronic portal imaging devices (EPIDs). Commercial video-camera-based EPIDs or VEPIDs that utilize a thin phosphor screen in conjunction with a metal buildup plate to convert the incident x rays to light suffer from reduced light production due to low QE (<2% for Eastman Kodak Lanex Fast-B). Flat-panel EPIDs that utilize the same luminescent screen along with an a-Si:H photodiode array provide improved image quality compared to VEPIDs, but they are expensive and can be susceptible to radiation damage to the peripheral electronics. In this article, we present a prototype VEPID system for high quality portal imaging at sub-monitor-unit (subMU) exposures based on a thick scintillation crystal (TSC) that acts as a high QE luminescent screen. The prototype TSC system utilizes a 12 mm thick transparent CsI(Tl) (thallium-activated cesium iodide) scintillator for QE=0.24, resulting in significantly higher light production compared to commercial phosphor screens. The 25 X 25 cm2 CsI(Tl) screen is coupled to a high spatial and contrast resolution Video-Optics plumbicon-tube camera system (1240 X 1024 pixels, 250 microm pixel width at isocenter, 12-bit ADC). As a proof-of-principle prototype, the TSC system with user-controlled camera target integration was adapted for use in an existing clinical gantry (Siemens BEAMVIEW(PLUS)) with the capability for online intratreatment fluoroscopy. Measurements of modulation transfer function (MTF) were conducted to characterize the TSC spatial resolution. The measured MTF along with measurements of the TSC noise power spectrum (NPS) were used to determine the system detective quantum efficiency (DQE). A theoretical expression of DQE(0) was developed to be used as a predictive model to propose improvements in the optics associated with the light detection. The prototype TSC provides DQE(0)=0.02 with its current imaging geometry, which is an order of magnitude greater than that for commercial VEPID systems and comparable to flat-panel imaging systems. Following optimization in the imaging geometry and the use of a high-end, cooled charge-coupled-device (CCD) camera system, the performance of the TSC is expected to improve even further. Based on our theoretical model, the expected DQE(0)=0.12 for the TSC system with the proposed improvements, which exceeds the performance of current flat-panel EPIDs. The prototype TSC provides high quality imaging even at subMU exposures (typical imaging dose is 0.2 MU per image), which offers the potential for daily patient localization imaging without increasing the weekly dose to the patient. Currently, the TSC is capable of limited frame-rate fluoroscopy for intratreatment visualization of patient motion at approximately 3 frames/second, since the achievable frame rate is significantly reduced by the limitations of the camera-control processor. With optimized processor control, the TSC is expected to be capable of intratreatment imaging exceeding 10 frames/second to monitor patient motion.

Sesbania bispinosa, a new host of a begomovirus-betasatellite complex in Pakistan

USDA-ARS?s Scientific Manuscript database

Severe leaf curling, yellowing and vein thickening symptoms, typical of begomoviruses infection, were observed on Sesbania bispinosa grown in cotton leaf curl disease affected cotton field in Pakistan. A begomovirus and its associated betasatellite were amplified and sequenced from these plants. Com...

Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma.

PubMed Central

Liefting, L W; Andersen, M T; Beever, R E; Gardner, R C; Forster, R L

1996-01-01

Phormium yellow leaf (PYL) phytoplasma causes a lethal disease of the monocotyledon, New Zealand flax (Phormium tenax). The 16S rRNA genes of PYL phytoplasma were amplified from infected flax by PCR and cloned, and the nucleotide sequences were determined. DNA sequencing and Southern hybridization analysis of genomic DNA indicated the presence of two copies of the 16S rRNA gene. The two 16S rRNA genes exhibited sequence heterogeneity in 4 nucleotide positions and could be distinguished by the restriction enzymes BpmI and BsrI. This is the first record in which sequence heterogeneity in the 16S rRNA genes of a phytoplasma has been determined by sequence analysis. A phylogenetic tree based on 16S rRNA gene sequences showed that PYL phytoplasma is most closely related to the stolbur and German grapevine yellows phytoplasmas, which form the stolbur subgroup of the aster yellows group. This phylogenetic position of PYL phytoplasma was supported by 16S/23S spacer region sequence data. PMID:8795200

Senna leaf curl virus: a novel begomovirus identified in Senna occidentalis.

PubMed

Kumar, Jitesh; Alok, Anshu; Kumar, Jitendra; Tuli, Rakesh

2016-09-01

Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that infect a variety of cultivated (crop) and non-cultivated (weed) plants. The present study identified a novel begomovirus and satellites (alpha- and betasatellite) in Senna occidentalis (syn. Cassia occidentalis) showing leaf curl symptoms. The begomovirus shared a maximum sequence identity of 88.6 % with french bean leaf curl virus (JQ866297), whereas the alphasatellite and the betasatellite shared identities of 98 % and 90 % with ageratum yellow vein India alphasatellite (LK054802) and papaya leaf curl betasatellite (HM143906), respectively. No other begomovirus or satellites were detected in the suspected plants. We propose to name the virus "senna leaf curl virus" (SenLCuV).

Scaling leaf measurements to estimate cotton canopy gas exchange

USDA-ARS?s Scientific Manuscript database

Diurnal leaf and canopy gas exchange of well watered field grown cotton were measured. Leaf measurements were made with a portable photosynthesis system and canopy measurements with open Canopy Evapo-Transpiration and Assimilation (CETA) systems. Leaf level measurements were arithmetically scaled to...

Genetical genomics of Populus leaf shape variation

DOE PAGES

Drost, Derek R.; Puranik, Swati; Novaes, Evandro; ...

2015-06-30

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree tomore » identify genetic factors controlling leaf shape. Here, the approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.« less

Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China.

PubMed

Gao, San-Ji; Lin, Yi-Hua; Pan, Yong-Bao; Damaj, Mona B; Wang, Qin-Nan; Mirkov, T Erik; Chen, Ru-Kai

2012-10-01

Sugarcane yellow leaf virus (SCYLV) (genus Polerovirus, family Luteoviridae), the causal agent of sugarcane yellow leaf disease (YLD), was first detected in China in 2006. To assess the distribution of SCYLV in the major sugarcane-growing Chinese provinces, leaf samples from 22 sugarcane clones (Saccharum spp. hybrid) showing YLD symptoms were collected and analyzed for infection by the virus using reverse transcription PCR (RT-PCR), quantitative RT-PCR, and immunological assays. A complete genomic sequence (5,879 nt) of the Chinese SCYLV isolate CHN-FJ1 and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned, and sequenced. The genomic sequence of the CHN-FJ1 isolate was found to share a high identity (98.4-99.1 %) with those of the Brazilian (BRA) genotype isolates and a low identity (86.5-86.9 %) with those of the CHN1 and Cuban (CUB) genotype isolates. The genetic diversity of these 14 Chinese SCYLV isolates was assessed along with that of 29 SCYLV isolates of worldwide origin reported in the GenBank database, based on the full or partial genomic sequence. Phylogenetic analysis demonstrated that all the 14 Chinese SCYLV isolates clustered into one large group with the BRA genotype and 12 other reported SCYLV isolates. In addition, five reported Chinese SCYLV isolates were grouped with the Peruvian (PER), CHN1 and CUB genotypes. We therefore speculated that at least four SCYLV genotypes, BRA, PER, CHN1, and CUB, are associated with YLD in China. Interestingly, a 39-nt deletion was detected in the sequence of the CHN-GD3 isolate, in the middle of the ORF1 region adjacent to the overlap between ORF1 and ORF2. This location is known to be one of the recombination breakpoints in the Luteoviridae family.

Beta vulgaris crop types: Genomic signatures of selection (GSS) using next generation sequencing of pooled samples

USDA-ARS?s Scientific Manuscript database

Beta vulgaris crop types represent highly diverged populations with distinct phenotypes resulting from long-term selection. Differential end use in the crop types includes: leaf quality (chard/leaf beet), root enlargement and biomass, (table beet, fodder beet, sugar beet), and secondary metabolite a...

Development of an oligonucleotide probe for Aureobasidium pullulans based on the small-subunit rRNA gene.

PubMed Central

Li, S; Cullen, D; Hjort, M; Spear, R; Andrews, J H

1996-01-01

Aureobasidium pullulans, a cosmopolitan yeast-like fungus, colonizes leaf surfaces and has potential as a biocontrol agent of pathogens. To assess the feasibility of rRNA as a target for A. pullulans-specific oligonucleotide probes, we compared the nucleotide sequences of the small-subunit rRNA (18S) genes of 12 geographically diverse A. pullulans strains. Extreme sequence conservation was observed. The consensus A. pullulans sequence was compared with other fungal sequences to identify potential probes. A 21-mer probe which hybridized to the 12 A. pullulans strains but not to 98 other fungi, including 82 isolates from the phylloplane, was identified. A 17-mer highly specific for Cladosporium herbarum was also identified. These probes have potential in monitoring and quantifying fungi in leaf surface and other microbial communities. PMID:8633850

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

PubMed Central

Suen, Garret; Holt, Carson; Abouheif, Ehab; Bornberg-Bauer, Erich; Bouffard, Pascal; Caldera, Eric J.; Cash, Elizabeth; Cavanaugh, Amy; Denas, Olgert; Elhaik, Eran; Favé, Marie-Julie; Gadau, Jürgen; Gibson, Joshua D.; Graur, Dan; Grubbs, Kirk J.; Hagen, Darren E.; Harkins, Timothy T.; Helmkampf, Martin; Hu, Hao; Johnson, Brian R.; Kim, Jay; Marsh, Sarah E.; Moeller, Joseph A.; Muñoz-Torres, Mónica C.; Murphy, Marguerite C.; Naughton, Meredith C.; Nigam, Surabhi; Overson, Rick; Rajakumar, Rajendhran; Reese, Justin T.; Scott, Jarrod J.; Smith, Chris R.; Tao, Shu; Tsutsui, Neil D.; Viljakainen, Lumi; Wissler, Lothar; Yandell, Mark D.; Zimmer, Fabian; Taylor, James; Slater, Steven C.; Clifton, Sandra W.; Warren, Wesley C.; Elsik, Christine G.; Smith, Christopher D.; Weinstock, George M.; Gerardo, Nicole M.; Currie, Cameron R.

2011-01-01

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host–microbe symbioses. PMID:21347285

Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)

PubMed Central

Wei, Chunhua; Chen, Xiner; Wang, Zhongyuan; Liu, Qiyan; Li, Hao; Zhang, Yong; Ma, Jianxiang; Yang, Jianqiang

2017-01-01

The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies. PMID:28704497

Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.).

PubMed

Wei, Chunhua; Chen, Xiner; Wang, Zhongyuan; Liu, Qiyan; Li, Hao; Zhang, Yong; Ma, Jianxiang; Yang, Jianqiang; Zhang, Xian

2017-01-01

The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.

Comparative Transcriptomics Unravel Biochemical Specialization of Leaf Tissues of Stevia for Diterpenoid Production1

PubMed Central

Kim, Mi Jung; Jin, Jingjing; Zheng, Junshi

2015-01-01

Stevia (Stevia rebaudiana) produces not only a group of diterpenoid glycosides known as steviol glycosides (SGs), but also other labdane-type diterpenoids that may be spatially separated from SGs. However, their biosynthetic routes and spatial distribution in leaf tissues have not yet been elucidated. Here, we integrate metabolome and transcriptome analyses of Stevia to explore the biosynthetic capacity of leaf tissues for diterpenoid metabolism. Tissue-specific chemical analyses confirmed that SGs were accumulated in leaf cells but not in trichomes. On the other hand, Stevia leaf trichomes stored other labdane-type diterpenoids such as oxomanoyl oxide and agatholic acid. RNA sequencing analyses from two different tissues of Stevia provided a comprehensive overview of dynamic metabolic activities in trichomes and leaf without trichomes. These metabolite-guided transcriptomics and phylogenetic and gene expression analyses clearly identified specific gene members encoding enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate pathway and the biosynthesis of steviol or other labdane-type diterpenoids. Additionally, our RNA sequencing analysis uncovered copalyl diphosphate synthase (SrCPS) and kaurene synthase1 (SrKS1) homologs, SrCPS2 and KS-like (SrKSL), which were specifically expressed in trichomes. In vitro and in planta assays showed that unlike SrCPS and SrKS1, SrCPS2 synthesized labda-13-en-8-ol diphosphate and successively catalyzed the formation of manoyl oxide and epi-manoyl oxide in combination with SrKSL. Our findings suggest that Stevia may have evolved to use distinct metabolic pathways to avoid metabolic interferences in leaf tissues for efficient production of diverse secondary metabolites. PMID:26438788

Role of "the frame cycle time" in portal dose imaging using an aS500-II EPID.

PubMed

Al Kattar Elbalaa, Zeina; Foulquier, Jean Noel; Orthuon, Alexandre; Elbalaa, Hanna; Touboul, Emmanuel

2009-09-01

This paper evaluates the role of an acquisition parameter, the frame cycle time "FCT", in the performance of an aS500-II EPID. The work presented rests on the study of the Varian EPID aS500-II and the image acquisition system 3 (IAS3). We are interested in integrated acquisition using asynchronous mode. For better understanding the image acquisition operation, we investigated the influence of the "frame cycle time" on the speed of acquisition, the pixel value of the averaged gray-scale frame and the noise, using 6 and 15MV X-ray beams and dose rates of 1-6Gy/min on 2100 C/D Linacs. In the integrated mode not synchronized to beam pulses, only one parameter the frame cycle time "FCT" influences the pixel value. The pixel value of the averaged gray-scale frame is proportional to this parameter. When the FCT <55ms (speed of acquisition V(f/s)>18 frames/s), the speed of acquisition becomes unstable and leads to a fluctuation of the portal dose response. A timing instability and saturation are detected when the dose per frame exceeds 1.53MU/frame. Rules were deduced to avoid saturation and to optimize this dosimetric mode. The choice of the acquisition parameter is essential for the accurate portal dose imaging.

Oxidative stress: A link between drought and aflatoxin contamination in maize

USDA-ARS?s Scientific Manuscript database

Host resistance to diseases, such as early leaf spot (ELS), late leaf spot (LLS) and Tomato spotted wilt virus (TSWV), is critical for increasing the yield and reducing the cost for peanut farmers. With the completion of the genome sequences of two diploid ancestors of cultivated peanut, we could ge...

Characterization of Xylella fastidiosa pear leaf scorch strain in Taiwan through whole genome sequence analyses

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa is a Gram-negative bacterium causing diseases in many economically important crops mostly in the Americas but also in Asia and Europe. A strain of X. fastidiosa was found to cause pear leaf scorch (PLS) disease in Taiwan in 1992. Because of nutritional fastidiousness, characteriza...

Evaluation of assembling methods on determination of whole genome sequence of Xylella fastidiosa blueberry bacterial leaf scorch strain

USDA-ARS?s Scientific Manuscript database

Blueberry bacterial leaf scorch (BBLS) disease, a threat to blueberry production in the Southern USA and potentially elsewhere, is caused by Xylella fastidiosa. Efficient control of BBLS requires knowledge of the pathogen. However, this is challenging because Xylella fastidiosa is difficult to cultu...

Two whole genome sequences of Xylella fastidiosa (strains M12 and M23) causing almond leaf scorch disease in California

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa is a Gram negative, nutritionally fastidious plant pathogenic bacterium that causes many economically important diseases including almond leaf scorch disease (ALSD) and Pierce’s disease of grape in California, as well as citrus variegated chlorosis in South America. Genome inform...

De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens

PubMed Central

Zhang, Xiaodong; Allan, Andrew C.; Li, Caixia; Wang, Yuanzhong; Yao, Qiuyang

2015-01-01

Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant’s roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian are limited. Next-generation sequencing (NGS) technologies can aid in supplying global gene expression profiles. In this study we present sequence and transcript abundance data for the root and leaf transcriptome of G. rigescens, obtained using the Illumina Hiseq2000. Over fifty million clean reads were obtained from leaf and root libraries. This yields 76,717 unigenes with an average length of 753 bp. Among these, 33,855 unigenes were identified as putative homologs of annotated sequences in public protein and nucleotide databases. Digital abundance analysis identified 3306 unigenes differentially enriched between leaf and root. Unigenes found in both tissues were categorized according to their putative functional categories. Of the differentially expressed genes, over 130 were annotated as related to terpenoid biosynthesis. This work is the first study of global transcriptome analyses in gentian. These sequences and putative functional data comprise a resource for future investigation of terpenoid biosynthesis in Gentianaceae species and annotation of the gentiopicroside biosynthetic pathway and its regulatory mechanisms. PMID:26006235

Molecular characterization and infectivity of Papaya leaf curl China virus infecting tomato in China.

PubMed

Zhang, Hui; Ma, Xin-ying; Qian, Ya-juan; Zhou, Xue-ping

2010-02-01

Papaya leaf curl China virus (PaLCuCNV) was previously reported as a distinct begomovirus infecting papaya in southern China. Based on molecular diagnostic survey, 13 PaLCuCNV isolates were obtained from tomato plants showing leaf curl symptoms in Henan and Guangxi Provinces of China. Complete nucleotide sequences of 5 representative isolates (AJ558116, AJ558117, AJ704604, FN256260, and FN297834) were determined to be 2738-2751 nucleotides, which share 91.7%-97.9% sequence identities with PaLCuCNV isolate G2 (AJ558123). DNA-beta was not found to be associated with PaLCuCNV isolates. To investigate the infectivity of PaLCuCNV, an infectious clone of PaLCuCNV-[CN:HeNZM1] was constructed and agro-inoculated into Nicotiana benthamiana, N. tabacum Samsun, N. glutinosa, Solanum lycopersicum and Petunia hybrida plants, which induced severe leaf curling and crinkling symptoms in these plants. Southern blot analysis and polymerase chain reaction (PCR) indicated a systemic infection of test plants by the agro-infectious clone.

Technical Note: Experimental results from a prototype high-field inline MRI-linac

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liney, G. P., E-mail: gary.liney@sswahs.nsw.gov.au

Purpose: The pursuit of real-time image guided radiotherapy using optimal tissue contrast has seen the development of several hybrid magnetic resonance imaging (MRI)-treatment systems, high field and low field, and inline and perpendicular configurations. As part of a new MRI-linac program, an MRI scanner was integrated with a linear accelerator to enable investigations of a coupled inline MRI-linac system. This work describes results from a prototype experimental system to demonstrate the feasibility of a high field inline MR-linac. Methods: The magnet is a 1.5 T MRI system (Sonata, Siemens Healthcare) was located in a purpose built radiofrequency (RF) cage enablingmore » shielding from and close proximity to a linear accelerator with inline (and future perpendicular) orientation. A portable linear accelerator (Linatron, Varian) was installed together with a multileaf collimator (Millennium, Varian) to provide dynamic field collimation and the whole assembly built onto a stainless-steel rail system. A series of MRI-linac experiments was performed to investigate (1) image quality with beam on measured using a macropodine (kangaroo) ex vivo phantom; (2) the noise as a function of beam state measured using a 6-channel surface coil array; and (3) electron contamination effects measured using Gafchromic film and an electronic portal imaging device (EPID). Results: (1) Image quality was unaffected by the radiation beam with the macropodine phantom image with the beam on being almost identical to the image with the beam off. (2) Noise measured with a surface RF coil produced a 25% elevation of background intensity when the radiation beam was on. (3) Film and EPID measurements demonstrated electron focusing occurring along the centerline of the magnet axis. Conclusions: A proof-of-concept high-field MRI-linac has been built and experimentally characterized. This system has allowed us to establish the efficacy of a high field inline MRI-linac and study a number of the technical challenges and solutions.« less

Association of tomato leaf curl Gujarat virus and tomato leaf curl Bangladesh betasatellite on papaya showing typical leaf curl symptoms in North India.

PubMed

Varun, Priyanka; Saxena, Sangeeta

2018-05-01

Papaya leaf curl is an economically important disease occurring in papaya growing tropical and subtropical areas. Papaya leaf curl virus, a begomovirus, is the main causative agent for the disease, but many other begomoviruses as well as betasatellites have also been reported on papaya leaf curl disease. Rapidly evolving host range of begomoviruses is a major issue for developing successful resistance strategies against begomoviral infection considering their expanding host range and mixed infection. In our study, we have identified the presence of begomovirus and associated satellite molecule on papaya showing severe leaf curl symptoms in Lucknow, India. Analysis of complete DNA-A component of this isolate (MG757245) revealed the highest similarity (91%) with tomato leaf curl Gujarat virus (ToLCuGuV), while sequence data of betasatellite (MG478451) showed maximum (89%) identity with tomato leaf curl Bangladesh betasatellite (ToLCuBB). This is the first report on identification of ToLCuGuV and ToLCuBB coinfecting papaya plants in Lucknow, Uttar Pradesh (India).

Isolation and expression profiling of GhNAC transcription factor genes in cotton (Gossypium hirsutum L.) during leaf senescence and in response to stresses.

PubMed

Shah, Syed Tariq; Pang, Chaoyou; Fan, Shuli; Song, Meizhen; Arain, Saima; Yu, Shuxun

2013-12-01

NAC (NAM, ATAF, and CUC) is a plant-specific transcription factor family with diverse roles in plant development and stress regulation. In this report, stress-responsive NAC genes (GhNAC8-GhNAC17) isolated from cotton (Gossypium hirsutum L.) were characterised in the context of leaf senescence and stress tolerance. The characterisation of NAC genes during leaf senescence has not yet been reported for cotton. Based on the sequence characterisation, these GhNACs could be classified into three groups belonging to three known NAC sub-families. Their predicted amino acid sequences exhibited similarities to NAC genes from other plant species. Senescent leaves were the sites of maximum expression for all GhNAC genes except GhNAC10 and GhNAC13, which showed maximum expression in fibres, collected from 25 days post anthesis (DPA) plants. The ten GhNAC genes displayed differential expression patterns and levels during natural and induced leaf senescence. Quantitative RT-PCR and promoter analyses suggest that these genes are induced by ABA, ethylene, drought, salinity, cold, heat, and other hormonal treatments. These results support a role for cotton GhNAC genes in transcriptional regulation of leaf senescence, stress tolerance and other developmental stages of cotton. © 2013.

Identification of a monopartite begomovirus associated with yellow vein mosaic of Mentha longifolia in Saudi Arabia.

PubMed

Sohrab, Sayed Sartaj; Daur, Ihsanullah

2018-02-01

Mentha is a very important crop grown and used extensively for many purposes in the Kingdom of Saudi Arabia. Begomoviruses are whitefly-transmitted viruses causing serious disease in many important plants exhibiting variable symptoms with significant economic loss globally. During farmers' field survey, yellow vein mosaic disease was observed in Mentha longifolia plants growing near tomato fields in Saudi Arabia. The causative agent was identified in 11 out of 19 samples using begomovirus-specific primers and the association of begomovirus with yellow vein mosaic disease in M. longifolia was confirmed. The full-length viral genome and betasatellite were amplified, cloned, and sequenced bidirectionally. The full DNA-A genome was found to have 2785 nucleotides with 1365 bp-associated betasatellite molecule. An attempt was made to amplify DNA-B, but none of the samples produced any positive amplicon of expected size which indicated the presence of monopartite begomovirus. The sequence identity matrix and phylogenetic analysis, based on full genome showed the highest identity (99.6%) with Tomato yellow leaf curl virus (TYLCV) and in phylogenetic analysis it formed a closed cluster with Tomato leaf curl virus infecting tomato and Corchorus crop in Saudi Arabia. The sequence analysis results of betasatellites showed the highest identity (98.9%) with Tomato yellow leaf curl betasatellites infecting tomato and phylogenetic analysis using betasatellites formed a close cluster with Tomato yellow leaf curl betasatellites infecting tomato and Corchorus crops, which has already been reported to cause yellow vein mosaic and leaf curl disease in many cultivated and weed crops growing in Saudi Arabia. The identified begomovirus associated with yellow vein mosaic disease in mentha could be a mutated strain of TYLCV and tentatively designated as TYLCV-Mentha isolate. Based on published data and latest information, this is the first report of identification of Tomato yellow leaf curl virus associated with yellow vein mosaic disease of M. longifolia from Saudi Arabia.

Optimization of image quality and dose for Varian aS500 electronic portal imaging devices (EPIDs).

PubMed

McGarry, C K; Grattan, M W D; Cosgrove, V P

2007-12-07

This study was carried out to investigate whether the electronic portal imaging (EPI) acquisition process could be optimized, and as a result tolerance and action levels be set for the PIPSPro QC-3V phantom image quality assessment. The aim of the optimization process was to reduce the dose delivered to the patient while maintaining a clinically acceptable image quality. This is of interest when images are acquired in addition to the planned patient treatment, rather than images being acquired using the treatment field during a patient's treatment. A series of phantoms were used to assess image quality for different acquisition settings relative to the baseline values obtained following acceptance testing. Eight Varian aS500 EPID systems on four matched Varian 600C/D linacs and four matched Varian 2100C/D linacs were compared for consistency of performance and images were acquired at the four main orthogonal gantry angles. Images were acquired using a 6 MV beam operating at 100 MU min(-1) and the low-dose acquisition mode. Doses used in the comparison were measured using a Farmer ionization chamber placed at d(max) in solid water. The results demonstrated that the number of reset frames did not have any influence on the image contrast, but the number of frame averages did. The expected increase in noise with corresponding decrease in contrast was also observed when reducing the number of frame averages. The optimal settings for the low-dose acquisition mode with respect to image quality and dose were found to be one reset frame and three frame averages. All patients at the Northern Ireland Cancer Centre are now imaged using one reset frame and three frame averages in the 6 MV 100 MU min(-1) low-dose acquisition mode. Routine EPID QC contrast tolerance (+/-10) and action (+/-20) levels using the PIPSPro phantom based around expected values of 190 (Varian 600C/D) and 225 (Varian 2100C/D) have been introduced. The dose at dmax from electronic portal imaging has been reduced by approximately 28%, and while the image quality has been reduced, the images produced are still clinically acceptable.

SU-E-J-112: The Impact of Cine EPID Image Acquisition Frame Rate On Markerless Soft-Tissue Tracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yip, S; Rottmann, J; Berbeco, R

2014-06-01

Purpose: Although reduction of the cine EPID acquisition frame rate through multiple frame averaging may reduce hardware memory burden and decrease image noise, it can hinder the continuity of soft-tissue motion leading to poor auto-tracking results. The impact of motion blurring and image noise on the tracking performance was investigated. Methods: Phantom and patient images were acquired at a frame rate of 12.87Hz on an AS1000 portal imager. Low frame rate images were obtained by continuous frame averaging. A previously validated tracking algorithm was employed for auto-tracking. The difference between the programmed and auto-tracked positions of a Las Vegas phantommore » moving in the superior-inferior direction defined the tracking error (δ). Motion blurring was assessed by measuring the area change of the circle with the greatest depth. Additionally, lung tumors on 1747 frames acquired at eleven field angles from four radiotherapy patients are manually and automatically tracked with varying frame averaging. δ was defined by the position difference of the two tracking methods. Image noise was defined as the standard deviation of the background intensity. Motion blurring and image noise were correlated with δ using Pearson correlation coefficient (R). Results: For both phantom and patient studies, the auto-tracking errors increased at frame rates lower than 4.29Hz. Above 4.29Hz, changes in errors were negligible with δ<1.60mm. Motion blurring and image noise were observed to increase and decrease with frame averaging, respectively. Motion blurring and tracking errors were significantly correlated for the phantom (R=0.94) and patient studies (R=0.72). Moderate to poor correlation was found between image noise and tracking error with R -0.58 and -0.19 for both studies, respectively. Conclusion: An image acquisition frame rate of at least 4.29Hz is recommended for cine EPID tracking. Motion blurring in images with frame rates below 4.39Hz can substantially reduce the accuracy of auto-tracking. This work is supported in part by the Varian Medical Systems, Inc.« less

High-Throughput Phenotyping of Maize Leaf Physiological and Biochemical Traits Using Hyperspectral Reflectance1[OPEN

PubMed Central

Yendrek, Craig R.; Tomaz, Tiago; Montes, Christopher M.; Cao, Youyuan; Morse, Alison M.; Brown, Patrick J.; McIntyre, Lauren M.; Leakey, Andrew D.B.

2017-01-01

High-throughput, noninvasive field phenotyping has revealed genetic variation in crop morphological, developmental, and agronomic traits, but rapid measurements of the underlying physiological and biochemical traits are needed to fully understand genetic variation in plant-environment interactions. This study tested the application of leaf hyperspectral reflectance (λ = 500–2,400 nm) as a high-throughput phenotyping approach for rapid and accurate assessment of leaf photosynthetic and biochemical traits in maize (Zea mays). Leaf traits were measured with standard wet-laboratory and gas-exchange approaches alongside measurements of leaf reflectance. Partial least-squares regression was used to develop a measure of leaf chlorophyll content, nitrogen content, sucrose content, specific leaf area, maximum rate of phosphoenolpyruvate carboxylation, [CO2]-saturated rate of photosynthesis, and leaf oxygen radical absorbance capacity from leaf reflectance spectra. Partial least-squares regression models accurately predicted five out of seven traits and were more accurate than previously used simple spectral indices for leaf chlorophyll, nitrogen content, and specific leaf area. Correlations among leaf traits and statistical inferences about differences among genotypes and treatments were similar for measured and modeled data. The hyperspectral reflectance approach to phenotyping was dramatically faster than traditional measurements, enabling over 1,000 rows to be phenotyped during midday hours over just 2 to 4 d, and offers a nondestructive method to accurately assess physiological and biochemical trait responses to environmental stress. PMID:28049858

De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L.) leaf transcriptome and identification of candidate genes related to fall dormancy.

PubMed

Zhang, Senhao; Shi, Yinghua; Cheng, Ningning; Du, Hongqi; Fan, Wenna; Wang, Chengzhang

2015-01-01

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa.

De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy

PubMed Central

Cheng, Ningning; Du, Hongqi; Fan, Wenna; Wang, Chengzhang

2015-01-01

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. The physiological, biochemical and molecular mechanisms causing fall dormancy and the related genes have not been well studied. In this study, we sequenced two standard varieties of alfalfa (dormant and non-dormant) at two time points and generated approximately 160 million high quality paired-end sequence reads using sequencing by synthesis (SBS) technology. The de novo transcriptome assembly generated a set of 192,875 transcripts with an average length of 856 bp representing about 165.1 Mb of the alfalfa leaf transcriptome. After assembly, 111,062 (57.6%) transcripts were annotated against the NCBI non-redundant database. A total of 30,165 (15.6%) transcripts were mapped to 323 Kyoto Encyclopedia of Genes and Genomes pathways. We also identified 41,973 simple sequence repeats, which can be used to generate markers for alfalfa, and 1,541 transcription factors were identified across 1,350 transcripts. Gene expression between dormant and non-dormant alfalfa at different time points were performed, and we identified several differentially expressed genes potentially related to fall dormancy. The Gene Ontology and pathways information were also identified. We sequenced and assembled the leaf transcriptome of alfalfa related to fall dormancy, and also identified some genes of interest involved in the fall dormancy mechanism. Thus, our research focused on studying fall dormancy in alfalfa through transcriptome sequencing. The sequencing and gene expression data generated in this study may be used further to elucidate the complete mechanisms governing fall dormancy in alfalfa. PMID:25799491

Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley.

PubMed

Bull, Carolee T; Clarke, Christopher R; Cai, Rongman; Vinatzer, Boris A; Jardini, Teresa M; Koike, Steven T

2011-07-01

Since 2002, severe leaf spotting on parsley (Petroselinum crispum) has occurred in Monterey County, CA. Either of two different pathovars of Pseudomonas syringae sensu lato were isolated from diseased leaves from eight distinct outbreaks and once from the same outbreak. Fragment analysis of DNA amplified between repetitive sequence polymerase chain reaction; 16S rDNA sequence analysis; and biochemical, physiological, and host range tests identified the pathogens as Pseudomonas syringae pv. apii and P. syringae pv. coriandricola. Koch's postulates were completed for the isolates from parsley, and host range tests with parsley isolates and pathotype strains demonstrated that P. syringae pv. apii and P. syringae pv. coriandricola cause leaf spot diseases on parsley, celery, and coriander or cilantro. In a multilocus sequence typing (MLST) approach, four housekeeping gene fragments were sequenced from 10 strains isolated from parsley and 56 pathotype strains of P. syringae. Allele sequences were uploaded to the Plant-Associated Microbes Database and a phylogenetic tree was built based on concatenated sequences. Tree topology directly corresponded to P. syringae genomospecies and P. syringae pv. apii was allocated appropriately to genomospecies 3. This is the first demonstration that MLST can accurately allocate new pathogens directly to P. syringae sensu lato genomospecies. According to MLST, P. syringae pv. coriandricola is a member of genomospecies 9, P. cannabina. In a blind test, both P. syringae pv. coriandricola and P. syringae pv. apii isolates from parsley were correctly identified to pathovar. In both cases, MLST described diversity within each pathovar that was previously unknown.

A rapid leaf-disc sampler for psychrometric water potential measurements.

PubMed

Wullschleger, S D; Oosterhuis, D M

1986-06-01

An instrument was designed which facilitates faster and more accurate sampling of leaf discs for psychrometric water potential measurements. The instrument consists of an aluminum housing, a spring-loaded plunger, and a modified brass-plated cork borer. The leaf-disc sampler was compared with the conventional method of sampling discs for measurement of leaf water potential with thermocouple psychrometers on a range of plant material including Gossypium hirsutum L., Zea mays L., and Begonia rex-cultorum L. The new sampler permitted a leaf disc to be excised and inserted into the psychrometer sample chamber in less than 7 seconds, which was more than twice as fast as the conventional method. This resulted in more accurate determinations of leaf water potential due to reduced evaporative water losses. The leaf-disc sampler also significantly reduced sample variability between individual measurements. This instrument can be used for many other laboratory and field measurements that necessitate leaf disc sampling.

Rice gene SDL/RNRS1, encoding the small subunit of ribonucleotide reductase, is required for chlorophyll synthesis and plant growth development.

PubMed

Qin, Ran; Zeng, Dongdong; Liang, Rong; Yang, Chengcong; Akhter, Delara; Alamin, Md; Jin, Xiaoli; Shi, Chunhai

2017-09-05

A new mutant named sdl (stripe and drooping leaf) was characterized from indica cultivar Zhenong 34 by ethylmethane sulfonate (EMS) mutagenesis. The mutant sdl exhibited development defects including stripe and drooping leaf, dwarfism and deformed floral organs. The gene SDL was found allelic to RNRS1 by map-based cloning, which was homologous to Arabidopsis TSO2 encoding the small subunit of ribonucleotide reductase. The gDNA sequencing results of sdl in mutant showed that there was a repetitive sequence insertion of 138-bp at the 475 th bp in the exon. The redundant sequence was conserved in SDL homologous proteins, which contained the active site (tyrosine), as well as two amino acids glutamate and histidine involved in the binding of iron. There were fewer chloroplasts and grana lamellas in sdl leaf compared with those of wild-type. Additionally, the stripe leaves of sdl seedlings were highly sensitive to temperature, since the chlorophyll content was increased with the temperature rising. The drooping leaf of sdl might be resulted from the disappearance of vascular bundles and mesophyll cells in both leaf midrib and lateral veins. Fittingly to the phenotypes of mutant sdl, the expression levels of genes associated with photosynthesis and chlorophyll synthesis were found to be down- or up-regulated at different temperatures in mutant sdl. Also, the transcriptional levels of genes related to plant height and floral organ formation showed obvious differences between wild-type and sdl. The "SDL/RNRS1" was, hence, required for the chlorophyll biosynthesis and also played pleiotropic roles in the regulation of plant development. Copyright © 2017. Published by Elsevier B.V.

Easy Leaf Area: Automated digital image analysis for rapid and accurate measurement of leaf area.

PubMed

Easlon, Hsien Ming; Bloom, Arnold J

2014-07-01

Measurement of leaf areas from digital photographs has traditionally required significant user input unless backgrounds are carefully masked. Easy Leaf Area was developed to batch process hundreds of Arabidopsis rosette images in minutes, removing background artifacts and saving results to a spreadsheet-ready CSV file. • Easy Leaf Area uses the color ratios of each pixel to distinguish leaves and calibration areas from their background and compares leaf pixel counts to a red calibration area to eliminate the need for camera distance calculations or manual ruler scale measurement that other software methods typically require. Leaf areas estimated by this software from images taken with a camera phone were more accurate than ImageJ estimates from flatbed scanner images. • Easy Leaf Area provides an easy-to-use method for rapid measurement of leaf area and nondestructive estimation of canopy area from digital images.

Automation of a Linear Accelerator Dosimetric Quality Assurance Program

NASA Astrophysics Data System (ADS)

Lebron Gonzalez, Sharon H.

According to the American Society of Radiation Oncology, two-thirds of all cancer patients will receive radiation therapy during their illness with the majority of the treatments been delivered by a linear accelerator (linac). Therefore, quality assurance (QA) procedures must be enforced in order to deliver treatments with a machine in proper conditions. The overall goal of this project is to automate the linac's dosimetric QA procedures by analyzing and accomplishing various tasks. First, the photon beam dosimetry (i.e. total scatter correction factor, infinite percentage depth dose (PDD) and profiles) were parameterized. Parameterization consists of defining the parameters necessary for the specification of a dosimetric quantity model creating a data set that is portable and easy to implement for different applications including: beam modeling data input into a treatment planning system (TPS), comparing measured and TPS modelled data, the QA of a linac's beam characteristics, and the establishment of a standard data set for comparison with other data, etcetera. Second, this parameterization model was used to develop a universal method to determine the radiation field size of flattened (FF), flattening-filter-free (FFF) and wedge beams which we termed the parameterized gradient method (PGM). Third, the parameterized model was also used to develop a profile-based method for assessing the beam quality of photon FF and FFF beams using an ionization chamber array. The PDD and PDD change was also predicted from the measured profile. Lastly, methods were created to automate the multileaf collimator (MLC) calibration and QA procedures as well as the acquisition of the parameters included in monthly and annual photon dosimetric QA. A two field technique was used for the calculation of the MLC leaf relative offsets using an electronic portal imaging device (EPID). A step-and-shoot technique was used to accurately acquire the radiation field size, flatness, symmetry, output and beam quality specifiers in a single delivery to an ionization chamber array for FF and FFF beams.

Alteration of Microbial Communities Colonizing Leaf Litter in a Temperate Woodland Stream by Growth of Trees under Conditions of Elevated Atmospheric CO2 ▿

PubMed Central

Kelly, John J.; Bansal, Amit; Winkelman, Jonathan; Janus, Lori R.; Hell, Shannon; Wencel, Marie; Belt, Patricia; Kuehn, Kevin A.; Rier, Steven T.; Tuchman, Nancy C.

2010-01-01

Elevated atmospheric CO2 can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO2 would result in changes in the size and composition of microbial communities colonizing leaves in a woodland stream. Three tree species, Populus tremuloides, Salix alba, and Acer saccharum, were grown under ambient (360 ppm) or elevated (720 ppm) CO2, and their leaves were incubated in a woodland stream. Elevated-CO2 treatment resulted in significant increases in the phenolic and tannin contents and C/N ratios of leaves. Microbial effects, which occurred only for P. tremuloides leaves, included decreased fungal biomass and decreased bacterial counts. Analysis of fungal and bacterial communities on P. tremuloides leaves via terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing revealed that fungal community composition was mostly unchanged by the elevated-CO2 treatment, whereas bacterial communities showed a significant shift in composition and a significant increase in diversity. Specific changes in bacterial communities included increased numbers of alphaproteobacterial and cytophaga-flavobacter-bacteroides (CFB) group sequences and decreased numbers of betaproteobacterial and firmicutes sequences, as well as a pronounced decrease in overall Gram-positive bacterial sequences. PMID:20543045

Alteration of microbial communities colonizing leaf litter in a temperate woodland stream by growth of trees under conditions of elevated atmospheric CO2.

PubMed

Kelly, John J; Bansal, Amit; Winkelman, Jonathan; Janus, Lori R; Hell, Shannon; Wencel, Marie; Belt, Patricia; Kuehn, Kevin A; Rier, Steven T; Tuchman, Nancy C

2010-08-01

Elevated atmospheric CO(2) can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO(2) would result in changes in the size and composition of microbial communities colonizing leaves in a woodland stream. Three tree species, Populus tremuloides, Salix alba, and Acer saccharum, were grown under ambient (360 ppm) or elevated (720 ppm) CO(2), and their leaves were incubated in a woodland stream. Elevated-CO(2) treatment resulted in significant increases in the phenolic and tannin contents and C/N ratios of leaves. Microbial effects, which occurred only for P. tremuloides leaves, included decreased fungal biomass and decreased bacterial counts. Analysis of fungal and bacterial communities on P. tremuloides leaves via terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing revealed that fungal community composition was mostly unchanged by the elevated-CO(2) treatment, whereas bacterial communities showed a significant shift in composition and a significant increase in diversity. Specific changes in bacterial communities included increased numbers of alphaproteobacterial and cytophaga-flavobacter-bacteroides (CFB) group sequences and decreased numbers of betaproteobacterial and firmicutes sequences, as well as a pronounced decrease in overall gram-positive bacterial sequences.

Characterization of expressed resistance gene analogs (RGAs) from peanut expressed sequence tags (ESTs)

USDA-ARS?s Scientific Manuscript database

Cultivated peanut (Arachis hypogaea L.) is one of the most important food legume crops grown worldwide, and is a major source for edible oil and protein. However, due to low genetic variation, peanut is very vulnerable to a variety of pathogens, such as early leaf spot, late leaf spot, rust and Toma...

Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci

USDA-ARS?s Scientific Manuscript database

Wheat is grown around the world and has been plagued by three rust fungi for centuries. Leaf rust, stripe rust, and stem rust each cause significant damage and can adapt quickly to overcome resistance that is present in wheat cultivars. Using advanced DNA sequencing technology, the genomes of leaf ...

Association analysis of bacterial leaf spot resistance and SNP markers derived from expressed sequence tags (ESTs) in lettuce (Lactuca sativa L.)

USDA-ARS?s Scientific Manuscript database

Bacterial leaf spot of lettuce, caused by Xanthomonas campestris pv. vitians, is a devastating disease of lettuce worldwide. Since there are no chemicals available for effective control of the disease, host-plant resistance is highly desirable to protect lettuce production. A total of 179 lettuce ge...

Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series.

PubMed

Blair, Matthew W; Hurtado, Natalia; Chavarro, Carolina M; Muñoz-Torres, Monica C; Giraldo, Martha C; Pedraza, Fabio; Tomkins, Jeff; Wing, Rod

2011-03-22

Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants. A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers. The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva Granada and Mesoamerica subgroup 1 (black beans) both with regards to gene expression and as sources of markers. However, we found few differences between SSR type and frequency between the G19833 leaf and DOR364 root tissue-derived ESTs. Overall, our work adds to the analysis of microsatellite frequency evaluation for common bean and provides a new set of 120 BMc markers which combined with the 248 previously developed BMc markers brings the total in this series to 368 markers. Once we include BMd markers, which are derived from GenBank sequences, the current total of gene-based markers from our laboratory surpasses 500 markers. These markers are basic for studies of the transcriptome of common bean and can form anchor points for genetic mapping studies in the future.

Verification of the linac isocenter for stereotactic radiosurgery using cine-EPID imaging and arc delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rowshanfarzad, Pejman; Sabet, Mahsheed; O' Connor, Daryl J.

2011-07-15

Purpose:Verification of the mechanical isocenter position is required as part of comprehensive quality assurance programs for stereotactic radiosurgery/radiotherapy (SRS/SRT) treatments. Several techniques have been proposed for this purpose but each of them has certain drawbacks. In this paper, a new efficient and more comprehensive method using cine-EPID images has been introduced for automatic verification of the isocenter with sufficient accuracy for stereotactic applications. Methods: Using a circular collimator fixed to the gantry head to define the field, EPID images of a Winston-Lutz phantom were acquired in cine-imaging mode during 360 deg. gantry rotations. A robust matlab code was developed tomore » analyze the data by finding the center of the field and the center of the ball bearing shadow in each image with sub-pixel accuracy. The distance between these two centers was determined for every image. The method was evaluated by comparison to results of a mechanical pointer and also by detection of a manual shift applied to the phantom position. The repeatability and reproducibility of the method were tested and it was also applied to detect couch and collimator wobble during rotation. Results:The accuracy of the algorithm was 0.03 {+-} 0.02 mm. The repeatability was less than 3 {mu}m and the reproducibility was less than 86 {mu}m. The time elapsed for the analysis of more than 100 cine images of Varian aS1000 and aS500 EPIDs were {approx}65 and 20 s, respectively. Processing of images taken in integrated mode took 0.1 s. The output of the analysis software is printable and shows the isocenter shifts as a function of angle in both in-plane and cross-plane directions. It gives warning messages where the shifts exceed the criteria for SRS/SRT and provides useful data for the necessary adjustments in the system including bearing system and/or room lasers. Conclusions: The comprehensive method introduced in this study uses cine-images, is highly accurate, fast, and independent of the observer. It tests all gantry angles and is suitable for pretreatment QA of the isocenter for stereotactic treatments.« less

A method for evaluating treatment quality using in vivo EPID dosimetry and statistical process control in radiation therapy.

PubMed

Fuangrod, Todsaporn; Greer, Peter B; Simpson, John; Zwan, Benjamin J; Middleton, Richard H

2017-03-13

Purpose Due to increasing complexity, modern radiotherapy techniques require comprehensive quality assurance (QA) programmes, that to date generally focus on the pre-treatment stage. The purpose of this paper is to provide a method for an individual patient treatment QA evaluation and identification of a "quality gap" for continuous quality improvement. Design/methodology/approach A statistical process control (SPC) was applied to evaluate treatment delivery using in vivo electronic portal imaging device (EPID) dosimetry. A moving range control chart was constructed to monitor the individual patient treatment performance based on a control limit generated from initial data of 90 intensity-modulated radiotherapy (IMRT) and ten volumetric-modulated arc therapy (VMAT) patient deliveries. A process capability index was used to evaluate the continuing treatment quality based on three quality classes: treatment type-specific, treatment linac-specific, and body site-specific. Findings The determined control limits were 62.5 and 70.0 per cent of the χ pass-rate for IMRT and VMAT deliveries, respectively. In total, 14 patients were selected for a pilot study the results of which showed that about 1 per cent of all treatments contained errors relating to unexpected anatomical changes between treatment fractions. Both rectum and pelvis cancer treatments demonstrated process capability indices were less than 1, indicating the potential for quality improvement and hence may benefit from further assessment. Research limitations/implications The study relied on the application of in vivo EPID dosimetry for patients treated at the specific centre. Sampling patients for generating the control limits were limited to 100 patients. Whilst the quantitative results are specific to the clinical techniques and equipment used, the described method is generally applicable to IMRT and VMAT treatment QA. Whilst more work is required to determine the level of clinical significance, the authors have demonstrated the capability of the method for both treatment specific QA and continuing quality improvement. Practical implications The proposed method is a valuable tool for assessing the accuracy of treatment delivery whilst also improving treatment quality and patient safety. Originality/value Assessing in vivo EPID dosimetry with SPC can be used to improve the quality of radiation treatment for cancer patients.

SU-E-T-379: Evaluation of An EPID-Based System for Daily Dosimetry Check by Comparison with a Widely-Used Ionization Chamber-Based Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDonald, D; Koch, N; Peng, J

2015-06-15

Purpose: To examine the feasibility of using Varian’s EPID-based Machine Performance Check (MPC) system to track daily machine output through comparison with Sun Nuclear’s DailyQA3 (DQA) device. Methods: Daily machine outputs for two photon energies (6 and 16MV) and five electron energies (6, 9, 12, 16, 20MeV) were measured for one month using both MPC and DQA. Baselines measurements for MPC were taken at the start of the measurement series, while DQA baselines were set at an earlier date. In order to make absolute comparisons with MPC, all DQA readings were referenced to the average of the first three DQAmore » readings in that series, minimizing systematic differences between the measurement techniques due to baseline differences. In addition to daily output measurements, weekly averages were also calculated and compared. Finally, the electron energy dependence of each measurement technique was examined by comparing energy-specific measurements to the average electron output of all energies each day. Results: For 6 and 16MV photons, the largest absolute percent differences between MPC and DQA were 0.60% and 0.73%, respectively. Weekly averages were within 0.17% and 0.23%, respectively. For all five electron energies, the greatest absolute percent differences between MPC and DQA for each energy ranged from 0.49%–0.83%. Weekly averages ranged from 0.07%–0.28%. DQA energy-specific electron readings matched the average electron output within 0.29% for all days and all energies. MPC energy-specific readings matched the average within 0.21% for 9–20MeV. However, 6MeV showed a larger distribution about the average with four days showing a difference greater than 0.30% and a maximum difference of 0.51%. Conclusion: MPC output measurements correlated well with the widely-used DQA3 for most beam energies, making it a reliable back up technique for daily output monitoring. However, MPC may display an energy dependence for lower electrons energies, requiring additional investigation.« less

Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics.

PubMed

Schilmiller, Anthony L; Miner, Dennis P; Larson, Matthew; McDowell, Eric; Gang, David R; Wilkerson, Curtis; Last, Robert L

2010-07-01

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.

Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics1[W][OA

PubMed Central

Schilmiller, Anthony L.; Miner, Dennis P.; Larson, Matthew; McDowell, Eric; Gang, David R.; Wilkerson, Curtis; Last, Robert L.

2010-01-01

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces β-caryophyllene and α-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells. PMID:20431087

Does leaf chemistry differentially affect breakdown in tropical vs temperate streams? Importance of standardized analytical techniques to measure leaf chemistry

Treesearch

Marcelo Ard& #243; n; Catherine M. Pringle; Susan L. Eggert

2009-01-01

Comparisons of the effects of leaf litter chemistry on leaf breakdown rates in tropical vs temperate streams are hindered by incompatibility among studies and across sites of analytical methods used to measure leaf chemistry. We used standardized analytical techniques to measure chemistry and breakdown rate of leaves from common riparian tree species at 2 sites, 1...

Comparative Transcriptomics Unravel Biochemical Specialization of Leaf Tissues of Stevia for Diterpenoid Production.

PubMed

Kim, Mi Jung; Jin, Jingjing; Zheng, Junshi; Wong, Limsoon; Chua, Nam-Hai; Jang, In-Cheol

2015-12-01

Stevia (Stevia rebaudiana) produces not only a group of diterpenoid glycosides known as steviol glycosides (SGs), but also other labdane-type diterpenoids that may be spatially separated from SGs. However, their biosynthetic routes and spatial distribution in leaf tissues have not yet been elucidated. Here, we integrate metabolome and transcriptome analyses of Stevia to explore the biosynthetic capacity of leaf tissues for diterpenoid metabolism. Tissue-specific chemical analyses confirmed that SGs were accumulated in leaf cells but not in trichomes. On the other hand, Stevia leaf trichomes stored other labdane-type diterpenoids such as oxomanoyl oxide and agatholic acid. RNA sequencing analyses from two different tissues of Stevia provided a comprehensive overview of dynamic metabolic activities in trichomes and leaf without trichomes. These metabolite-guided transcriptomics and phylogenetic and gene expression analyses clearly identified specific gene members encoding enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate pathway and the biosynthesis of steviol or other labdane-type diterpenoids. Additionally, our RNA sequencing analysis uncovered copalyl diphosphate synthase (SrCPS) and kaurene synthase1 (SrKS1) homologs, SrCPS2 and KS-like (SrKSL), which were specifically expressed in trichomes. In vitro and in planta assays showed that unlike SrCPS and SrKS1, SrCPS2 synthesized labda-13-en-8-ol diphosphate and successively catalyzed the formation of manoyl oxide and epi-manoyl oxide in combination with SrKSL. Our findings suggest that Stevia may have evolved to use distinct metabolic pathways to avoid metabolic interferences in leaf tissues for efficient production of diverse secondary metabolites. © 2015 American Society of Plant Biologists. All Rights Reserved.

Evaluation of the TrueBeam machine performance check (MPC) beam constancy checks for flattened and flattening filter-free (FFF) photon beams.

PubMed

Barnes, Michael P; Greer, Peter B

2017-01-01

Machine Performance Check (MPC) is an automated and integrated image-based tool for verification of beam and geometric performance of the TrueBeam linac. The aims of the study were to evaluate the MPC beam performance tests against current daily quality assurance (QA) methods, to compare MPC performance against more accurate monthly QA tests and to test the sensitivity of MPC to changes in beam performance. The MPC beam constancy checks test the beam output, uniformity, and beam center against the user defined baseline. MPC was run daily over a period of 5 months (n = 115) in parallel with the Daily QA3 device. Additionally, IC Profiler, in-house EPID tests, and ion chamber measurements were performed biweekly and results presented in a form directly comparable to MPC. The sensitivity of MPC was investigated using controlled adjustments of output, beam angle, and beam position steering. Over the period, MPC output agreed with ion chamber to within 0.6%. For an output adjustment of 1.2%, MPC was found to agree with ion chamber to within 0.17%. MPC beam center was found to agree with the in-house EPID method within 0.1 mm. A focal spot position adjustment of 0.4 mm (at isocenter) was measured with MPC beam center to within 0.01 mm. An average systematic offset of 0.5% was measured in the MPC uniformity and agreement of MPC uniformity with symmetry measurements was found to be within 0.9% for all beams. MPC uniformity detected a change in beam symmetry of 1.5% to within 0.3% and 0.9% of IC Profiler for flattened and FFF beams, respectively. © 2016 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

SU-E-T-24: Development and Implementation of an Automated Algorithm to Determine Radiation Isocenter, Radiation vs. Light Field Coincidence, and Analyze Strip Tests.

PubMed

Hyer, D; Mart, C

2012-06-01

The aim of this study was to develop a phantom and analysis software that could be used to quickly and accurately determine the location of radiation isocenter using the Electronic Portal Imaging Device (EPID). The phantom could then be used as a static reference point for performing other tests including: radiation vs. light field coincidence, MLC and Jaw strip tests, and Varian Optical Guidance Platform (OGP) calibration. The solution proposed uses a collimator setting of 10×10 cm to acquire EPID images of the new phantom constructed from LEGO® blocks. Images from a number of gantry and collimator angles are analyzed by the software to determine the position of the jaws and center of the phantom in each image. The distance between a chosen jaw and the phantom center is then compared to the same distance measured after a 180 degree collimator rotation to determine if the phantom is centered in the dimension being investigated. The accuracy of the algorithm's measurements were verified by independent measurement to be approximately equal to the detector's pitch. Light versus radiation field as well as MLC and Jaw strip tests are performed using measurements based on the phantom center once located at the radiation isocenter. Reproducibility tests show that the algorithm's results were objectively repeatable. Additionally, the phantom and software are completely independent of linac vendor and this study presents results from two major linac manufacturers. An OGP calibration array was also integrated into the phantom to allow calibration of the OGP while the phantom is positioned at radiation isocenter to reduce setup uncertainty contained in the calibration. This solution offers a quick, objective method to perform isocenter localization as well as laser alignment, OGP calibration, and other tests on a monthly basis. © 2012 American Association of Physicists in Medicine.

A Rapid Leaf-Disc Sampler for Psychrometric Water Potential Measurements 1

PubMed Central

Wullschleger, Stan D.; Oosterhuis, Derrick M.

1986-01-01

An instrument was designed which facilitates faster and more accurate sampling of leaf discs for psychrometric water potential measurements. The instrument consists of an aluminum housing, a spring-loaded plunger, and a modified brass-plated cork borer. The leaf-disc sampler was compared with the conventional method of sampling discs for measurement of leaf water potential with thermocouple psychrometers on a range of plant material including Gossypium hirsutum L., Zea mays L., and Begonia rex-cultorum L. The new sampler permitted a leaf disc to be excised and inserted into the psychrometer sample chamber in less than 7 seconds, which was more than twice as fast as the conventional method. This resulted in more accurate determinations of leaf water potential due to reduced evaporative water losses. The leaf-disc sampler also significantly reduced sample variability between individual measurements. This instrument can be used for many other laboratory and field measurements that necessitate leaf disc sampling. PMID:16664879

Development and application of triple antibody sandwich enzyme-linked immunosorbent assays for begomovirus detection using monoclonal antibodies against Tomato yellow leaf curl Thailand virus.

PubMed

Seepiban, Channarong; Charoenvilaisiri, Saengsoon; Warin, Nuchnard; Bhunchoth, Anjana; Phironrit, Namthip; Phuangrat, Bencharong; Chatchawankanphanich, Orawan; Attathom, Supat; Gajanandana, Oraprapai

2017-05-30

Tomato yellow leaf curl Thailand virus, TYLCTHV, is a begomovirus that causes severe losses of tomato crops in Thailand as well as several countries in Southeast and East Asia. The development of monoclonal antibodies (MAbs) and serological methods for detecting TYLCTHV is essential for epidemiological studies and screening for virus-resistant cultivars. The recombinant coat protein (CP) of TYLCTHV was expressed in Escherichia coli and used to generate MAbs against TYLCTHV through hybridoma technology. The MAbs were characterized and optimized to develop triple antibody sandwich enzyme-linked immunosorbent assays (TAS-ELISAs) for begomovirus detection. The efficiency of TAS-ELISAs for begomovirus detection was evaluated with tomato, pepper, eggplant, okra and cucurbit plants collected from several provinces in Thailand. Molecular identification of begomoviruses in these samples was also performed through PCR and DNA sequence analysis of the CP gene. Two MAbs (M1 and D2) were generated and used to develop TAS-ELISAs for begomovirus detection. The results of begomovirus detection in 147 field samples indicated that MAb M1 reacted with 2 begomovirus species, TYLCTHV and Tobacco leaf curl Yunnan virus (TbLCYnV), whereas MAb D2 reacted with 4 begomovirus species, TYLCTHV, TbLCYnV, Tomato leaf curl New Delhi virus (ToLCNDV) and Squash leaf curl China virus (SLCCNV). Phylogenetic analyses of CP amino acid sequences from these begomoviruses revealed that the CP sequences of begomoviruses recognized by the narrow-spectrum MAb M1 were highly conserved, sharing 93% identity with each other but only 72-81% identity with MAb M1-negative begomoviruses. The CP sequences of begomoviruses recognized by the broad-spectrum MAb D2 demonstrated a wider range of amino acid sequence identity, sharing 78-96% identity with each other and 72-91% identity with those that were not detected by MAb D2. TAS-ELISAs using the narrow-specificity MAb M1 proved highly efficient for the detection of TYLCTHV and TbLCYnV, whereas TAS-ELISAs using the broad-specificity MAb D2 were highly efficient for the detection of TYLCTHV, TbLCYnV, ToLCNDV and SLCCNV. Both newly developed assays allow for sensitive, inexpensive, high-throughput detection of begomoviruses in field plant samples, as well as screening for virus-resistant cultivars.

Comparison of dose accuracy between 2D array detectors and Epid for IMRT of nasopharynx cancer

NASA Astrophysics Data System (ADS)

Altiparmak, Duygu; Coban, Yasin; Merih, Adil; Avci, Gulhan Guler; Yigitoglu, Ibrahim

2017-02-01

The aim of this study is to perform the dosimetric controls of nasopharynx cancer patient's intensity modulated radiation therapy (IMRT) treatment plans that generated by treatment planing system (TPS) with using two different equipments and also to make comparison in terms of their reliability and practicability. This study has been performed at Radiation Oncology Department, Medicine Faculty in Gaziosmanpasa University by using the VARIAN CLINAC DHX linear accelerator which is operated in the range of 6 MV. Selected 10 nasopharynx patients planned in TPS (Eclipce V13.0) and approved for treatment by medical physicists and radiation oncologists. These plans recalculated on EPID and mapcheck which are 2D dosimetric equipments to obtain dose maps. To compare these two dosimetric equipments gamma analysis method has been preferred. Achieved data is presented and discussed.

Leaf oxygen and Carbon Isotopic Signatures Reflect Drought Resistance and Water Use Efficiency in the C4 Grass, Setaria viridis

NASA Astrophysics Data System (ADS)

Ellsworth, P.; Cousins, A. B.

2014-12-01

Low water availability is a major constraint in crop production, especially as agriculture is pushed to marginal lands. Therefore, improving drought resistance such as increasing water use efficiency (WUE) through plant breeding is needed to expand the range of soil water availability adequate for food production. With the goal of finding the genomic basis for WUE in C4 grasses, Setaria viridis makes an ideal model species because of its small size, short lifespan, and sequenced genome. Also it is part of the panicoid grass clade, which is one of the most important clades for food and biofuel production. In plant breeding programs, large numbers of genotypes must be quickly screened for drought resistance traits, but there is no well-defined method of screening for WUE in C4 grasses. However, bulk leaf oxygen (Δ18OBL) and carbon (δ13C) isotopic signatures have shown potential as recorders of transpiration rate (E) and stomatal conductance (gs), and combined with biomass production potentially serve as a measure of WUE. Values of Δ18OBL record differences in transpiration rate because leaf water becomes more enriched as transpiration rate decreases, and leaf tissue records the isotopic composition of leaf water in which it is synthesized. Additionally, in C4 plants δ13C values decrease as gs decreases but the change in δ13C in response to gs may not be adequate to tease apart differences in WUE. In this study, we grew S. viridis plants under well-watered and water-limited conditions to determine if Δ18OBL and δ13C could be used as proxies for E and gs, and be used to screen S. viridis for differences in WUE in breeding programs. The Δ18OBL and δ13C were significantly different between well-watered and water-limited plants and correlated with each other and with E, gs, and instantaneous water use efficiency (Anet/gs). Therefore, Δ18OBL and δ13C can be useful proxies to screen genotypes for drought resistance by recording differences in E, gs, and WUE. Measuring Δ18OBL and δ13C are relatively simple and quick, requiring the collection of a single leaf sample from each genotype instead of making laborious gas exchange measurements of E and gs.

Genotyping-by-sequencing to re-map QTL for type II Fusarium head blight and leaf rust resistance in a wheat-tall wheatgrass introgression recombinant inbred population

USDA-ARS?s Scientific Manuscript database

Fusarium graminaerum (Fusarium head blight; FHB) and Puccinia recondita Roberge ex Desmaz. f. sp. tritici Eriks. & E. Henn (leaf rust; LR) are two major fungal pathogens threatening the wheat crop; consequently identifying resistance genes from various sources is always of importance to wheat breede...

Using RNA-sequencing and in silico subtraction to identify resistance gene analog markers for Lr16 in wheat

USDA-ARS?s Scientific Manuscript database

Leaf rust, caused by Puccinia triticina Eriks., is one of the most widespread diseases of wheat worldwide and breeding for resistance is one of the most effective methods of control. Lr16 is a wheat leaf rust resistance gene that provides resistance at both the seedling and adult stages. Simple s...

De novo transcriptome sequencing and customized abscission zone-specific microarray as a new molecular tool for analysis of tomato organ abscission

USDA-ARS?s Scientific Manuscript database

Abscission, which is the process of organ separation, is a highly regulated process occurring as a final stage of organ development. In the tomato (Solanum lycopersicum) system, flower and leaf abscission was induced by flower removal or leaf deblading, leading to auxin depletion which results in in...

Using the conservative nature of fresh leaf surface density to measure foliar area

NASA Astrophysics Data System (ADS)

Castillo, Omar S.; Zaragoza, Esther M.; Alvarado, Carlos J.; Barrera, Maria G.; Dasgupta-Schubert, Nabanita

2014-10-01

For a herbaceous species, the inverse of the fresh leaf surface density, the Hughes constant, is nearly conserved. We apply the Hughes constant to develop an absolute method of leafarea measurement that requires no regression fits, prior calibrations or oven-drying. The Hughes constant was determined in situ using a known geometry and weights of a sub-set obtained from the fresh leaves whose areas are desired. Subsequently, the leaf-areas (at any desired stratification level), were derived by utilizing the Hughes constant and the masses of the fresh leaves. The proof of concept was established for leaf-discs of the plants Mandevilla splendens and Spathiphyllum wallisii. The conservativeness of the Hughes constant over individual leaf-zones and different leaftypes from the leaves of each species was quantitatively validated. Using the globally averaged Hughes constant for each species, the leaf-area of these and additional co-species plants, were obtained. The leaf-area-measurement-by-mass was cross-checked with standard digital image analysis. There were no statistically significant differences between the leaf-area-measurement-by-mass and the digital image analysis measured leaf-areas and the linear correlation between the two methods was very good. Leaf-areameasurement- by-mass was found to be rapid and simple with accuracies comparable to the digital image analysis method. The greatly reduced cost of leaf-area-measurement-by-mass could be beneficial for small agri-businesses in developing countries.

Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: A case study.

PubMed

Brown, Judith K; Ur-Rehman, Muhammad Zia; Avelar, Sofia; Chingandu, N; Hameed, Usman; Haider, Saleem; Ilyas, Muhammad

2017-09-15

At least five begomoviral species that cause leaf curl disease of cotton have emerged recently in Asia and Africa, reducing fiber quality and yield. The potential for the spread of these viruses to other cotton-vegetable growing regions throughout the world is extensive, owing to routine, global transport of alternative hosts of the leaf curl viruses, especially ornamentals. The research reported here describes the design and validation of polymerase chain reaction (PCR) primers undertaken to facilitate molecular detection of the two most-prevalent leaf curl-associated begomovirus-betasatellite complexes in the Indian Subcontinent and Africa, the Cotton leaf curl Kokhran virus-Burewala strain and Cotton leaf curl Gezira virus, endemic to Asia and Africa, respectively. Ongoing genomic diversification of these begomoviral-satellite complexes was evident based on nucleotide sequence alignments, and analysis of single nucleotide polymorphisms, both factors that created new challenges for primer design. The additional requirement for species and strain-specific, and betasatellite-specific primer design, imposes further constraints on primer design and validation due to the large number of related species and strains extant in 'core leaf curl virus complex', now with expanded distribution in south Asia, the Pacific region, and Africa-Arabian Peninsula that have relatively highly conserved coding and non-coding regions, which precludes much of the genome-betasatellite sequence when selecting primer 'targets'. Here, PCR primers were successfully designed and validated for detection of cloned viral genomes and betasatellites for representative 'core leaf curl' strains and species, distant relatives, and total DNA isolated from selected plant species. The application of molecular diagnostics to screen plant imports prior to export or release from ports of entry is expected to greatly reduce the likelihood of exotic leaf curl virus introductions that could dramatically affect the production of cotton as well as vegetable and ornamental crop hosts. Copyright © 2017 Elsevier B.V. All rights reserved.

Chronological Sequence of Leaf Phenology, Xylem and Phloem Formation and Sap Flow of Quercus pubescens from Abandoned Karst Grasslands

PubMed Central

Lavrič, Martina; Eler, Klemen; Ferlan, Mitja; Vodnik, Dominik; Gričar, Jožica

2017-01-01

Intra-annual variations in leaf development, radial growth, including the phloem part, and sap flow have rarely been studied in deciduous trees from drought-prone environments. In order to understand better the chronological order and temporal course of these processes, we monitored leaf phenology, xylem and phloem formation and sap flow in Quercus pubescens from abandoned karst grasslands in Slovenia during the growing season of 2014. We found that the initial earlywood vessel formation started before bud opening at the beginning of April. Buds started to open in the second half of April and full leaf unfolding occurred by the end of May. LAI values increased correspondingly with leaf development. About 28% of xylem and 22% of phloem annual increment were formed by the time of bud break. Initial earlywood vessels were fully lignified and ready for water transport, indicating that they are essential to provide hydraulic conductivity for axial water flow during leaf development. Sap flow became active and increasing contemporarily with leaf development and LAI values. Similar early spring patterns of xylem sap flow and LAI denoted that water transport in oaks broadly followed canopy leaf area development. In the initial 3 weeks of radial growth, phloem growth preceded that of xylem, indicating its priority over xylem at the beginning of the growing season. This may be related to the fact that after bud break, the developing foliage is a very large sink for carbohydrates but, at the same time, represents a small transpirational area. Whether the interdependence of the chronological sequence of the studied processes is fixed in Q. pubescens needs to be confirmed with more data and several years of analyses, although the ‘correct sequence’ of processes is essential for synchronized plant performance and response to environmental stress. PMID:28321232

QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.).

PubMed

Liu, Kaiye; Xu, Hao; Liu, Gang; Guan, Panfeng; Zhou, Xueyao; Peng, Huiru; Yao, Yingyin; Ni, Zhongfu; Sun, Qixin; Du, Jinkun

2018-04-01

QTL controlling flag leaf length, flag leaf width, flag leaf area and flag leaf angle were mapped in wheat. This study aimed to advance our understanding of the genetic mechanisms underlying morphological traits of the flag leaves of wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population derived from ND3331 and the Tibetan semi-wild wheat Zang1817 was used to identify quantitative trait loci (QTLs) controlling flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and flag leaf angle (FLANG). Using an available simple sequence repeat genetic linkage map, 23 putative QTLs for FLL, FLW, FLA, and FLANG were detected on chromosomes 1B, 2B, 3A, 3D, 4B, 5A, 6B, 7B, and 7D. Individual QTL explained 4.3-68.52% of the phenotypic variance in different environments. Four QTLs for FLL, two for FLW, four for FLA, and five for FLANG were detected in at least two environments. Positive alleles of 17 QTLs for flag leaf-related traits originated from ND3331 and 6 originated from Zang1817. QTLs with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1B, 4B, and 5A; these are potential target regions for fine-mapping and marker-assisted selection in wheat breeding programs.

Ratio of Cut Surface Area to Leaf Sample Volume for Water Potential Measurements by Thermocouple Psychrometers

PubMed Central

Walker, Sue; Oosterhuis, Derrick M.; Wiebe, Herman H.

1984-01-01

Evaporative losses from the cut edge of leaf samples are of considerable importance in measurements of leaf water potential using thermocouple psychrometers. The ratio of cut surface area to leaf sample volume (area to volume ratio) has been used to give an estimate of possible effects of evaporative loss in relation to sample size. A wide range of sample sizes with different area to volume ratios has been used. Our results using Glycine max L. Merr. cv Bragg indicate that leaf samples with area to volume values less than 0.2 square millimeter per cubic millimeter give psychrometric leaf water potential measurements that compare favorably with pressure chamber measurements. PMID:16663578

Usual and unusual development of the dicot leaf: involvement of transcription factors and hormones.

PubMed

Fambrini, Marco; Pugliesi, Claudio

2013-06-01

Morphological diversity exhibited by higher plants is essentially related to the tremendous variation of leaf shape. With few exceptions, leaf primordia are initiated postembryonically at the flanks of a group of undifferentiated and proliferative cells within the shoot apical meristem (SAM) in characteristic position for the species and in a regular phyllotactic sequence. Auxin is critical for this process, because genes involved in auxin biosynthesis, transport, and signaling are required for leaf initiation. Down-regulation of transcription factors (TFs) and cytokinins are also involved in the light-dependent leaf initiation pathway. Furthermore, mechanical stresses in SAM determine the direction of cell division and profoundly influence leaf initiation suggesting a link between physical forces, gene regulatory networks and biochemical gradients. After the leaf is initiated, its further growth depends on cell division and cell expansion. Temporal and spatial regulation of these processes determines the size and the shape of the leaf, as well as the internal structure. A complex array of intrinsic signals, including phytohormones and TFs control the appropriate cell proliferation and differentiation to elaborate the final shape and complexity of the leaf. Here, we highlight the main determinants involved in leaf initiation, epidermal patterning, and elaboration of lamina shape to generate small marginal serrations, more deep lobes or a dissected compound leaf. We also outline recent advances in our knowledge of regulatory networks involved with the unusual pattern of leaf development in epiphyllous plants as well as leaf morphology aberrations, such as galls after pathogenic attacks of pests.

Monitoring phenology of photosynthesis in temperate evergreen and mixed deciduous forests using the normalized difference vegetation index (NDVI) and the photochemical reflectance index (PRI) at leaf and canopy scales

NASA Astrophysics Data System (ADS)

Wong, C. Y.; Arain, M. A.; Ensminger, I.

2016-12-01

Evergreen conifers in boreal and temperate regions undergo strong seasonal changes in photoperiod and temperatures, which determines their phenology of high photosynthetic activity in the growing season and downregulation during the winter. Monitoring the timing of the transition between summer activity and winter downregulation in evergreens is difficult since this is a largely invisible process, unlike in deciduous trees that have a visible budding and a sequence of leaf unfolding in the spring and leaf abscission in the fall. The light-use efficiency (LUE) model estimates gross primary productivity (GPP) and may be parameterized using remotely sensed vegetation indices. Using spectral reflectance data, we derived the normalized difference vegetation index (NDVI), a measure of leaf "greenness", and the photochemical reflectance index (PRI), a proxy for chlorophyll:carotenoid ratios which is related to photosynthetic activity. To better understand the relationship between these vegetation indices and photosynthetic activity and to contrast this relationship between plant functional types, the phenology of NDVI, PRI and photosynthesis was monitored in an evergreen forest and a mixed deciduous forest at the leaf and canopy scale. Our data indicates that the LUE model can be parameterized by NDVI and PRI to track forest phenology. Differences in the sensitivity of PRI and NDVI will be discussed. These findings have implications to address the phenology of evergreen conifers by using PRI to complement NDVI in the LUE model, potentially improving model productivity estimates in northern hemisphere forests, that are dominated by conifers.

Leaf water potentials measured with a pressure chamber.

PubMed

Boyer, J S

1967-01-01

Leaf water potentials were estimated from the sum of the balancing pressure measured with a pressure chamber and the osmotic potential of the xylem sap in leafy shoots or leaves. When leaf water potentials in yew, rhododendron, and sunflower were compared with those measured with a thermocouple psychrometer known to indicate accurate values of leaf water potential, determinations were within +/- 2 bars of the psychrometer measurements with sunflower and yew. In rhododendron. water potentials measured with the pressure chamber plus xylem sap were 2.5 bars less negative to 4 bars more negative than psychrometer measurements.The discrepancies in the rhododendron measurements could be attributed, at least in part, to the filling of tissues other than xylem with xylem sap during measurements with the pressure chamber. It was concluded that, although stem characteristics may affect the measurements, pressure chamber determinations were sufficiently close to psychrometer measurements that the pressure chamber may be used for relative measurements of leaf water potentials, especially in sunflower and yew. For accurate determinations of leaf water potential, however, pressure chamber measurements must be calibrated with a thermocouple psychrometer.

Leaf Water Potentials Measured with a Pressure Chamber

PubMed Central

Boyer, J. S.

1967-01-01

Leaf water potentials were estimated from the sum of the balancing pressure measured with a pressure chamber and the osmotic potential of the xylem sap in leafy shoots or leaves. When leaf water potentials in yew, rhododendron, and sunflower were compared with those measured with a thermocouple psychrometer known to indicate accurate values of leaf water potential, determinations were within ± 2 bars of the psychrometer measurements with sunflower and yew. In rhododendron. water potentials measured with the pressure chamber plus xylem sap were 2.5 bars less negative to 4 bars more negative than psychrometer measurements. The discrepancies in the rhododendron measurements could be attributed, at least in part, to the filling of tissues other than xylem with xylem sap during measurements with the pressure chamber. It was concluded that, although stem characteristics may affect the measurements, pressure chamber determinations were sufficiently close to psychrometer measurements that the pressure chamber may be used for relative measurements of leaf water potentials, especially in sunflower and yew. For accurate determinations of leaf water potential, however, pressure chamber measurements must be calibrated with a thermocouple psychrometer. PMID:16656476

On-line estimations of delivered radiation doses in three-dimensional conformal radiotherapy treatments of carcinoma uterine cervix patients in linear accelerator

PubMed Central

Putha, Suman Kumar; Saxena, P. U.; Banerjee, S.; Srinivas, Challapalli; Vadhiraja, B. M.; Ravichandran, Ramamoorthy; Joan, Mary; Pai, K. Dinesh

2016-01-01

Transmission of radiation fluence through patient's body has a correlation to the planned target dose. A method to estimate the delivered dose to target volumes was standardized using a beam level 0.6 cc ionization chamber (IC) positioned at electronic portal imaging device (EPID) plane from the measured transit signal (St) in patients with cancer of uterine cervix treated with three-dimensional conformal radiotherapy (3DCRT). The IC with buildup cap was mounted on linear accelerator EPID frame with fixed source to chamber distance of 146.3 cm, using a locally fabricated mount. Sts were obtained for different water phantom thicknesses and radiation field sizes which were then used to generate a calibration table against calculated midplane doses at isocenter (Diso,TPS), derived from the treatment planning system. A code was developed using MATLAB software which was used to estimate the in vivo dose at isocenter (Diso,Transit) from the measured Sts. A locally fabricated pelvic phantom validated the estimations of Diso,Transit before implementing this method on actual patients. On-line dose estimations were made (3 times during treatment for each patient) in 24 patients. The Diso,Transit agreement with Diso,TPS in phantom was within 1.7% and the mean percentage deviation with standard deviation is −1.37% ±2.03% (n = 72) observed in patients. Estimated in vivo dose at isocenter with this method provides a good agreement with planned ones which can be implemented as part of quality assurance in pelvic sites treated with simple techniques, for example, 3DCRT where there is a need for documentation of planned dose delivery. PMID:28144114

On-line estimations of delivered radiation doses in three-dimensional conformal radiotherapy treatments of carcinoma uterine cervix patients in linear accelerator.

PubMed

Putha, Suman Kumar; Saxena, P U; Banerjee, S; Srinivas, Challapalli; Vadhiraja, B M; Ravichandran, Ramamoorthy; Joan, Mary; Pai, K Dinesh

2016-01-01

Transmission of radiation fluence through patient's body has a correlation to the planned target dose. A method to estimate the delivered dose to target volumes was standardized using a beam level 0.6 cc ionization chamber (IC) positioned at electronic portal imaging device (EPID) plane from the measured transit signal (S t ) in patients with cancer of uterine cervix treated with three-dimensional conformal radiotherapy (3DCRT). The IC with buildup cap was mounted on linear accelerator EPID frame with fixed source to chamber distance of 146.3 cm, using a locally fabricated mount. S t s were obtained for different water phantom thicknesses and radiation field sizes which were then used to generate a calibration table against calculated midplane doses at isocenter (D iso,TPS ), derived from the treatment planning system. A code was developed using MATLAB software which was used to estimate the in vivo dose at isocenter (D iso,Transit ) from the measured S t s. A locally fabricated pelvic phantom validated the estimations of D iso,Transit before implementing this method on actual patients. On-line dose estimations were made (3 times during treatment for each patient) in 24 patients. The D iso,Transit agreement with D iso,TPS in phantom was within 1.7% and the mean percentage deviation with standard deviation is -1.37% ±2.03% ( n = 72) observed in patients. Estimated in vivo dose at isocenter with this method provides a good agreement with planned ones which can be implemented as part of quality assurance in pelvic sites treated with simple techniques, for example, 3DCRT where there is a need for documentation of planned dose delivery.

The evolution, morphology, and development of fern leaves

PubMed Central

Vasco, Alejandra; Moran, Robbin C.; Ambrose, Barbara A.

2013-01-01

Leaves are lateral determinate structures formed in a predictable sequence (phyllotaxy) on the flanks of an indeterminate shoot apical meristem. The origin and evolution of leaves in vascular plants has been widely debated. Being the main conspicuous organ of nearly all vascular plants and often easy to recognize as such, it seems surprising that leaves have had multiple origins. For decades, morphologists, anatomists, paleobotanists, and systematists have contributed data to this debate. More recently, molecular genetic studies have provided insight into leaf evolution and development mainly within angiosperms and, to a lesser extent, lycophytes. There has been recent interest in extending leaf evolutionary developmental studies to other species and lineages, particularly in lycophytes and ferns. Therefore, a review of fern leaf morphology, evolution and development is timely. Here we discuss the theories of leaf evolution in ferns, morphology, and diversity of fern leaves, and experimental results of fern leaf development. We summarize what is known about the molecular genetics of fern leaf development and what future studies might tell us about the evolution of fern leaf development. PMID:24027574

SU-F-T-283: A Novel Device to Enable Portal Dosimetry for Flattening Filter Free Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faught, A; Wu, Q; Adamson, J

Purpose: Varian’s electronic portal imaging device (EPID) based portal dosimetry tool is a popular and effective means of performing IMRT QA. EPIDs for older models of the TrueBeam accelerator utilize a 40cmx30cm Image Detection Unit (IDU) that saturates at the center for standard source to imager distances with high dose rate flattening filter free (FFF) beams. This makes portal dosimetry not possible and an alternative means of IMRT QA necessary. We developed a filter that would attenuate the beam to a dose rate measureable by the IDU for portal dosimetry IMRT QA. Methods: Multipurpose 304 stainless steel plates were placedmore » on an accessory tray to attenuate the beam. Profiles of an open field measured on the IDU were acquired with varying number of plates to assess the thickness needed to reduce the maximum dose rates of 6XFFF and 10XFFF beams to measurable levels. A new portal dose image prediction (PDIP) model was commissioned based on open field measurements with plates in position, and a modified beam profile was input to portal dosimetry calibration at the console to empirically correct for attenuation and scatter. The portal dosimetry tool was used to assess agreement between predicted and measured doses for open 25×25cm{sup 2} fields and intensity modulated fields using 6XFFF and 10XFFF beams. Results: Thicknesses of 2.5cm and 3.8cm of steel were required to reduce the highest dose rates to a measureable level for 6XFFF and 10XFFF, respectively. Gamma analysis using a 3%/3mm relative criterion with the filter in place and using the new PDIP model resulted in 98.2% and 93.6% of pixels passing while intensity modulated fields showed passing rates of 98.2% and 99.0%. Conclusion: Use of the filter allows for portal dosimetry to be used for IMRT QA of FFF plans in place of purchasing a second option for IMRT QA.« less

Antagonism of Trichoderma isolates against Leucoagaricus gongylophorus (Singer) Möller.

PubMed

do Nascimento, Mariela Otoni; de Almeida Sarmento, Renato; Dos Santos, Gil Rodrigues; de Oliveira, Cléia Almeida; de Souza, Danival José

2017-08-01

Filamentous fungi from the genus Trichoderma are commonly found in soil. They are considered facultative mycoparasites, and are antagonists of other fungi such as the cultivar of leaf-cutting ants (Leucoagaricus gongylophorus). The aim of the present study was to bioprospect Trichoderma spp. from different soils collected from Gurupi, Tocantins, Brazil, for antagonistic effects against the mutualistic fungus of leaf-cutting ants. To isolate filamentous fungi, samples were collected from six locations. Preliminarily, isolates were identified by morphological analysis as belonging to Trichoderma. Trichoderma spp. had their internal transcribed spacer region (ITS) of ribosomal RNA genes (rRNA) sequenced to confirm species-level taxonomy. L. gongylophorus was isolated from a laboratory ant colony. Antagonistic properties of seven isolates of Trichoderma against L. gongylophorus were measured using paired disks in Petri dishes with potato dextrose agar medium (PDA). All Trichoderma isolates inhibited the growth of L. gongylophorus in Petri dishes. Isolate 2 of Trichoderma spirale group exhibited slow mycelial growth in the Petri dish, and a high rate of inhibition against L. gongylophorus. This isolate is a promising fungus for field tests of biological control methods for leaf-cutting ants. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome organization of Tobacco leaf curl Zimbabwe virus, a new, distinct monopartite begomovirus associated with subgenomic defective DNA molecules.

PubMed

Paximadis, M; Rey, M E

2001-12-01

The complete DNA A of the begomovirus Tobacco leaf curl Zimbabwe virus (TbLCZWV) was sequenced: it comprises 2767 nucleotides with six major open reading frames encoding proteins with molecular masses greater than 9 kDa. Full-length TbLCZWV DNA A tandem dimers, cloned in binary vectors (pBin19 and pBI121) and transformed into Agrobacterium tumefaciens, were systemically infectious upon agroinoculation of tobacco and tomato. Efforts to identify a DNA B component were unsuccessful. These findings suggest that TbLCZWV is a new member of the monopartite group of begomoviruses. Phylogenetic analysis identified TbLCZWV as a distinct begomovirus with its closest relative being Chayote mosaic virus. Abutting primer PCR amplified ca. 1300 bp molecules, and cloning and sequencing of two of these molecules revealed them to be subgenomic defective DNA molecules originating from TbLCZWV DNA A. Variable symptom severity associated with tobacco leaf curl disease and TbLCZWV is discussed.

Determination and analysis of the genome sequence of Spodoptera littoralis multiple nucleopolyhedrovirus

USDA-ARS?s Scientific Manuscript database

The Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV), a pathogen of the Egyptian cotton leaf worm Spodoptera littoralis, was subjected to sequencing of its entire DNA genome and bioassay analysis comparing its virulence to that of other baculoviruses. The annotated SpliMNPV genome of...

Comparison of the dye method with the thermocouple psychrometer for measuring leaf water potentials.

PubMed

Knipling, E B; Kramer, P J

1967-10-01

The dye method for measuring water potential was examined and compared with the thermocouple psychrometer method in order to evaluate its usefulness for measuring leaf water potentials of forest trees and common laboratory plants. Psychrometer measurements are assumed to represent the true leaf water potentials. Because of the contamination of test solutions by cell sap and leaf surface residues, dye method values of most species varied about 1 to 5 bars from psychrometer values over the leaf water potential range of 0 to -30 bars. The dye method is useful for measuring changes and relative values in leaf potential. Because of species differences in the relationships of dye method values to true leaf water potentials, dye method values should be interpreted with caution when comparing different species or the same species growing in widely different environments. Despite its limitations the dye method has a usefulness to many workers because it is simple, requires no elaborate equipment, and can be used in both the laboratory and field.

Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

PubMed

Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

2013-12-19

To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

Effect of Piper betle L. and its extracts on the growth and aflatoxin production by Aspergillus parasiticus.

PubMed

Chou, C C; Yu, R C

1984-01-01

Ground powder of the leaf and fruit of Piper betle L., a tropical spice plant grown in Southeast Asia, was prepared and extracted by chloroform, ethanol and water with one solvent only or with 3 solvents in sequence. The betel powder and various extracts were added to YES broth to determine their effects on the growth and aflatoxin production by Aspergillus parasiticus. Results showed that betel leaf powder exhibited higher antimycotic activity than fruit. One half percent of ground leaf powder completely inhibited the growth and aflatoxin production by A. parasiticus. Among the solvent extracts, chloroform and ethanol extracts of betel leaf prepared from a single solvent extraction showed more antimycotic activity. The ethanol extract of betel leaf at the level of 450 micrograms/ml would eliminate A. parasiticus growth and aflatoxin production. The antimycotic activity of this ethanol extract was most pronounced at pH 4.

Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes.

PubMed

Wyrwa, Katarzyna; Książkiewicz, Michał; Szczepaniak, Anna; Susek, Karolina; Podkowiński, Jan; Naganowska, Barbara

2016-09-01

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.

Temporal and Spatial Expression of a Polygalacturonase during Leaf and Flower Abscission in Oilseed Rape and Arabidopsis1

PubMed Central

González-Carranza, Zinnia Haydé; Whitelaw, Catherine Ann; Swarup, Ranjan; Roberts, Jeremy Alan

2002-01-01

During leaf abscission in oilseed rape (Brassica napus), cell wall degradation is brought about by the action of several hydrolytic enzymes. One of these is thought to be polygalacturonase (PG). Degenerate primers were used to isolate a PG cDNA fragment by reverse transcriptase-polymerase chain reaction from RNA extracted from ethylene-promoted leaf abscission zones (AZs), and in turn a full-length clone (CAW471) from an oilseed rape AZ cDNA library. The highest homology of this cDNA (82%) was to an Arabidopsis sequence that was predicted to encode a PG protein. Analysis of expression revealed that CAW471 mRNA accumulated in the AZ of leaves and reached a peak 24 h after ethylene treatment. Ethylene-promoted leaf abscission in oilseed rape was not apparent until 42 h after exposure to the gas, reaching 50% at 48 h and 100% by 56 h. In floral organ abscission, expression of CAW471 correlated with cell separation. Genomic libraries from oilseed rape and Arabidopsis were screened with CAW471 and the respective genomic clones PGAZBRAN and PGAZAT isolated. Characterization of these PG genes revealed that they had substantial homology within both the coding regions and in the 5′-upstream sequences. Fusion of a 1,476-bp 5′-upstream sequence of PGAZAT to β-glucuronidase or green fluorescent protein and transformation of Arabidopsis revealed that this fragment was sufficient to drive expression of these reporter genes in the AZs at the base of the anther filaments, petals, and sepals. PMID:11842157

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

PubMed Central

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

PubMed

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Psychrometric Field Measurement of Water Potential Changes following Leaf Excision.

PubMed

Savage, M J; Cass, A

1984-01-01

In situ measurement of sudden leaf water potential changes has not been performed under field conditions. A laboratory investigation involving the measurement of leaf water potential prior to and 2 to 200 minutes after excision of citrus leaves (Citrus jambhiri) showed good linear correlation (r = 0.99) between in situ leaf psychrometer and Scholander pressure chamber measurements. Following this, a field investigation was conducted which involved psychrometric measurement prior to petiole excision and 1 minute after excision. Simultaneous pressure chamber measurements were performed on neighboring leaves prior to the time of excision and then on the psychrometer leaf about 2 minutes after excision. These data indicate that within the first 2 minutes after excision, psychrometer and pressure chamber measurements were linearly correlated (r = 0.97). Under high evaporative demand conditions, the rate of water potential decrease was between 250 and 700 kilopascals in the first minute after excision. These results show that the thermocouple psychrometer can be used as a dynamic and nondestructive field technique for monitoring leaf water potential.

Psychrometric Field Measurement of Water Potential Changes following Leaf Excision 1

PubMed Central

Savage, Michael J.; Cass, Alfred

1984-01-01

In situ measurement of sudden leaf water potential changes has not been performed under field conditions. A laboratory investigation involving the measurement of leaf water potential prior to and 2 to 200 minutes after excision of citrus leaves (Citrus jambhiri) showed good linear correlation (r = 0.99) between in situ leaf psychrometer and Scholander pressure chamber measurements. Following this, a field investigation was conducted which involved psychrometric measurement prior to petiole excision and 1 minute after excision. Simultaneous pressure chamber measurements were performed on neighboring leaves prior to the time of excision and then on the psychrometer leaf about 2 minutes after excision. These data indicate that within the first 2 minutes after excision, psychrometer and pressure chamber measurements were linearly correlated (r = 0.97). Under high evaporative demand conditions, the rate of water potential decrease was between 250 and 700 kilopascals in the first minute after excision. These results show that the thermocouple psychrometer can be used as a dynamic and nondestructive field technique for monitoring leaf water potential. PMID:16663394

Gap probability - Measurements and models of a pecan orchard

NASA Technical Reports Server (NTRS)

Strahler, Alan H.; Li, Xiaowen; Moody, Aaron; Liu, YI

1992-01-01

Measurements and models are compared for gap probability in a pecan orchard. Measurements are based on panoramic photographs of 50* by 135 view angle made under the canopy looking upwards at regular positions along transects between orchard trees. The gap probability model is driven by geometric parameters at two levels-crown and leaf. Crown level parameters include the shape of the crown envelope and spacing of crowns; leaf level parameters include leaf size and shape, leaf area index, and leaf angle, all as functions of canopy position.

Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer.

PubMed

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Wang, Ke; Jiang, Ni; Feng, Hui; Chen, Guoxing; Liu, Qian; Xiong, Lizhong

2015-09-01

Leaves are the plant's solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Mapping of stripe rust resistance gene in an Aegilops caudate introgression line in wheat and its genetic association with leaf rust resistance.

PubMed

Toor, Puneet Inder; Kaur, Satinder; Bansal, Mitaly; Yadav, Bharat; Chhuneja, Parveen

2016-12-01

A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat-Ae. caudata introgression line (IL) T291- 2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well. Genetic association with leaf rust resistance revealed that two genes are located at a recombination distance of 13%. IL T291-2 had earlier been reported to carry introgressions on wheat chromosomes 2D, 3D, 4D, 5D, 6D and 7D. Genetic mapping indicated the introgression of stripe rust resistance gene on wheat chromosome 5DS in the region carrying leaf rust resistance gene LrAc, but as an independent introgression. Simple sequence repeat (SSR) and sequence-tagged site (STS) markers designed from the survey sequence data of 5DS enriched the target region harbouring stripe and leaf rust resistance genes. Stripe rust resistance locus, temporarily designated as YrAc, mapped at the distal most end of 5DS linked with a group of four colocated SSRs and two resistance gene analogue (RGA)-STS markers at a distance of 5.3 cM. LrAc mapped at a distance of 9.0 cM from the YrAc and at 2.8 cM from RGA-STS marker Ta5DS_2737450, YrAc and LrAc appear to be the candidate genes for marker-assisted enrichment of the wheat gene pool for rust resistance.

Phytophthora siskiyouensis, a new species from soil and water in southwest Oregon

Treesearch

Paul Reeser; Everett Hansen; Wendy Sutton

2008-01-01

An unknown Phytophthora species was recovered from rhododendron and tanoak leaf baits used for monitoring streams and soils in Southwestern Oregon for the presence of Phytophthora ramorum. Isolates of this species yielded ITS-DNA sequences that differed substantially from other Phytophthora sequences in GenBank....

Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing

USDA-ARS?s Scientific Manuscript database

Genotyping-by-sequencing (GBS) was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and Swiss chard) in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS) symptoms. However, ...

Targeted manipulation of leaf form via local growth repression.

PubMed

Malinowski, Robert; Kasprzewska, Ania; Fleming, Andrew J

2011-06-01

A classical view is that leaf shape is the result of local promotion of growth linked to cell proliferation. However, an alternative hypothesis is that leaf form is the result of local repression of growth in an otherwise growing system. Here we show that leaf form can indeed be manipulated in a directed fashion by local repression of growth. We show that targeting expression of an inhibitor of a cyclin-dependent kinase (KRP1) to the sinus area of developing leaves of Arabidopsis leads to local growth repression and the formation of organs with extreme lobing, including generation of leaflet-like organs. Directing KRP1 expression to other regions of the leaf using an miRNA target sequence tagging approach also leads to predictable novel leaf forms, and repression of growth in the leaf margin blocks the outgrowth of lobes, leading to a smoother perimeter. In addition, we show that decreased growth around the perimeter and across the leaf abaxial surface leads to a change in 3D form, as predicted by mechanical models of leaf growth. Our analysis provides experimental evidence that local repression of growth influences leaf shape, suggesting that it could be part of the mechanism of morphogenesis in plants in the context of an otherwise growing system. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Simultaneous minimization of leaf travel distance and tongue-and-groove effect for segmental intensity-modulated radiation therapy.

PubMed

Dai, Jianrong; Que, William

2004-12-07

This paper introduces a method to simultaneously minimize the leaf travel distance and the tongue-and-groove effect for IMRT leaf sequences to be delivered in segmental mode. The basic idea is to add a large enough number of openings through cutting or splitting existing openings for those leaf pairs with openings fewer than the number of segments so that all leaf pairs have the same number of openings. The cutting positions are optimally determined with a simulated annealing technique called adaptive simulated annealing. The optimization goal is set to minimize the weighted summation of the leaf travel distance and tongue-and-groove effect. Its performance was evaluated with 19 beams from three clinical cases; one brain, one head-and-neck and one prostate case. The results show that it can reduce the leaf travel distance and (or) tongue-and-groove effect; the reduction of the leaf travel distance reaches its maximum of about 50% when minimized alone; the reduction of the tongue-and-groove reaches its maximum of about 70% when minimized alone. The maximum reduction in the leaf travel distance translates to a 1 to 2 min reduction in treatment delivery time per fraction, depending on leaf speed. If the method is implemented clinically, it could result in significant savings in treatment delivery time, and also result in significant reduction in the wear-and-tear of MLC mechanics.

Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume

PubMed Central

Ma, Kaifeng; Sun, Lidan; Cheng, Tangren; Pan, Huitang; Wang, Jia; Zhang, Qixiang

2018-01-01

Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I∗ = 0.575, h∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width. PMID:29441078

Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume.

PubMed

Ma, Kaifeng; Sun, Lidan; Cheng, Tangren; Pan, Huitang; Wang, Jia; Zhang, Qixiang

2018-01-01

Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume . We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P . mume . And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity ( I ∗ = 0.575, h ∗ = 0.393) was higher than the genetic diversity ( I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.

Analysis of the Citrullus colocynthis Transcriptome during Water Deficit Stress

PubMed Central

Wang, Zhuoyu; Hu, Hongtao; Goertzen, Leslie R.; McElroy, J. Scott; Dane, Fenny

2014-01-01

Citrullus colocynthis is a very drought tolerant species, closely related to watermelon (C. lanatus var. lanatus), an economically important cucurbit crop. Drought is a threat to plant growth and development, and the discovery of drought inducible genes with various functions is of great importance. We used high throughput mRNA Illumina sequencing technology and bioinformatic strategies to analyze the C. colocynthis leaf transcriptome under drought treatment. Leaf samples at four different time points (0, 24, 36, or 48 hours of withholding water) were used for RNA extraction and Illumina sequencing. qRT-PCR of several drought responsive genes was performed to confirm the accuracy of RNA sequencing. Leaf transcriptome analysis provided the first glimpse of the drought responsive transcriptome of this unique cucurbit species. A total of 5038 full-length cDNAs were detected, with 2545 genes showing significant changes during drought stress. Principle component analysis indicated that drought was the major contributing factor regulating transcriptome changes. Up regulation of many transcription factors, stress signaling factors, detoxification genes, and genes involved in phytohormone signaling and citrulline metabolism occurred under the water deficit conditions. The C. colocynthis transcriptome data highlight the activation of a large set of drought related genes in this species, thus providing a valuable resource for future functional analysis of candidate genes in defense of drought stress. PMID:25118696

PCR amplification and sequences of cDNA clones for the small and large subunits of ADP-glucose pyrophosphorylase from barley tissues.

PubMed

Villand, P; Aalen, R; Olsen, O A; Lüthi, E; Lönneborg, A; Kleczkowski, L A

1992-06-01

Several cDNAs encoding the small and large subunit of ADP-glucose pyrophosphorylase (AGP) were isolated from total RNA of the starchy endosperm, roots and leaves of barley by polymerase chain reaction (PCR). Sets of degenerate oligonucleotide primers, based on previously published conserved amino acid sequences of plant AGP, were used for synthesis and amplification of the cDNAs. For either the endosperm, roots and leaves, the restriction analysis of PCR products (ca. 550 nucleotides each) has revealed heterogeneity, suggesting presence of three transcripts for AGP in the endosperm and roots, and up to two AGP transcripts in the leaf tissue. Based on the derived amino acid sequences, two clones from the endosperm, beps and bepl, were identified as coding for the small and large subunit of AGP, respectively, while a leaf transcript (blpl) encoded the putative large subunit of AGP. There was about 50% identity between the endosperm clones, and both of them were about 60% identical to the leaf cDNA. Northern blot analysis has indicated that beps and bepl are expressed in both the endosperm and roots, while blpl is detectable only in leaves. Application of the PCR technique in studies on gene structure and gene expression of plant AGP is discussed.

Transcriptome Profiling of Buffalograss Challenged with the Leaf Spot Pathogen Curvularia inaequalis.

PubMed

Amaradasa, Bimal S; Amundsen, Keenan

2016-01-01

Buffalograss (Bouteloua dactyloides) is a low maintenance U. S. native turfgrass species with exceptional drought, heat, and cold tolerance. Leaf spot caused by Curvularia inaequalis negatively impacts buffalograss visual quality. Two leaf spot susceptible and two resistant buffalograss lines were challenged with C. inaequalis. Samples were collected from treated and untreated leaves when susceptible lines showed symptoms. Transcriptome sequencing was done and differentially expressed genes were identified. Approximately 27 million raw sequencing reads were produced per sample. More than 86% of the sequencing reads mapped to an existing buffalograss reference transcriptome. De novo assembly of unmapped reads was merged with the existing reference to produce a more complete transcriptome. There were 461 differentially expressed transcripts between the resistant and susceptible lines when challenged with the pathogen and 1552 in its absence. Previously characterized defense-related genes were identified among the differentially expressed transcripts. Twenty one resistant line transcripts were similar to genes regulating pattern triggered immunity and 20 transcripts were similar to genes regulating effector triggered immunity. There were also nine up-regulated transcripts in resistance lines which showed potential to initiate systemic acquired resistance (SAR) and three transcripts encoding pathogenesis-related proteins which are downstream products of SAR. This is the first study characterizing changes in the buffalograss transcriptome when challenged with C. inaequalis.

Effect of solution and leaf surface polarity on droplet spread area and contact angle.

PubMed

Nairn, Justin J; Forster, W Alison; van Leeuwen, Rebecca M

2016-03-01

How much an agrochemical spray droplet spreads on a leaf surface can significantly influence efficacy. This study investigates the effect solution polarity has on droplet spreading on leaf surfaces and whether the relative leaf surface polarity, as quantified using the wetting tension dielectric (WTD) technique, influences the final spread area. Contact angles and spread areas were measured using four probe solutions on 17 species. Probe solution polarity was found to affect the measured spread area and the contact angle of the droplets on non-hairy leaves. Leaf hairs skewed the spread area measurement, preventing investigation of the influence of surface polarity on hairy leaves. WTD-measured leaf surface polarity of non-hairy leaves was found to correlate strongly with the effect of solution polarity on spread area. For non-polar leaf surfaces the spread area decreases with increasing solution polarity, for neutral surfaces polarity has no effect on spread area and for polar leaf surfaces the spread area increases with increasing solution polarity. These results attest to the use of the WTD technique as a means to quantify leaf surface polarity. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Analyses of Impact of Needle Surface Properties on Estimation of Needle Absorption Spectrum: Case Study with Coniferous Needle and Shoot Samples

PubMed Central

Yang, Bin; Knyazikhin, Yuri; Lin, Yi; Yan, Kai; Chen, Chi; Park, Taejin; Choi, Sungho; Mõttus, Matti; Rautiainen, Miina; Myneni, Ranga B.; Yan, Lei

2017-01-01

Leaf scattering spectrum is the key optical variable that conveys information about leaf absorbing constituents from remote sensing. It cannot be directly measured from space because the radiation scattered from leaves is affected by the 3D canopy structure. In addition, some radiation is specularly reflected at the surface of leaves. This portion of reflected radiation is partly polarized, does not interact with pigments inside the leaf and therefore contains no information about its interior. Very little empirical data are available on the spectral and angular scattering properties of leaf surfaces. Whereas canopy-structure effects are well understood, the impact of the leaf surface reflectance on estimation of leaf absorption spectra remains uncertain. This paper presents empirical and theoretical analyses of angular, spectral, and polarimetric measurements of light reflected by needles and shoots of Pinus koraiensis and Picea koraiensis species. Our results suggest that ignoring the leaf surface reflected radiation can result in an inaccurate estimation of the leaf absorption spectrum. Polarization measurements may be useful to account for leaf surface effects because radiation reflected from the leaf surface is partly polarized, whereas that from the leaf interior is not. PMID:28868160

A novel approach to EPID-based 3D volumetric dosimetry for IMRT and VMAT QA

NASA Astrophysics Data System (ADS)

Alhazmi, Abdulaziz; Gianoli, Chiara; Neppl, Sebastian; Martins, Juliana; Veloza, Stella; Podesta, Mark; Verhaegen, Frank; Reiner, Michael; Belka, Claus; Parodi, Katia

2018-06-01

Intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) are relatively complex treatment delivery techniques and require quality assurance (QA) procedures. Pre-treatment dosimetric verification represents a fundamental QA procedure in daily clinical routine in radiation therapy. The purpose of this study is to develop an EPID-based approach to reconstruct a 3D dose distribution as imparted to a virtual cylindrical water phantom to be used for plan-specific pre-treatment dosimetric verification for IMRT and VMAT plans. For each depth, the planar 2D dose distributions acquired in air were back-projected and convolved by depth-specific scatter and attenuation kernels. The kernels were obtained by making use of scatter and attenuation models to iteratively estimate the parameters from a set of reference measurements. The derived parameters served as a look-up table for reconstruction of arbitrary measurements. The summation of the reconstructed 3D dose distributions resulted in the integrated 3D dose distribution of the treatment delivery. The accuracy of the proposed approach was validated in clinical IMRT and VMAT plans by means of gamma evaluation, comparing the reconstructed 3D dose distributions with Octavius measurement. The comparison was carried out using (3%, 3 mm) criteria scoring 99% and 96% passing rates for IMRT and VMAT, respectively. An accuracy comparable to the one of the commercial device for 3D volumetric dosimetry was demonstrated. In addition, five IMRT and five VMAT were validated against the 3D dose calculation performed by the TPS in a water phantom using the same passing rate criteria. The median passing rates within the ten treatment plans was 97.3%, whereas the lowest was 95%. Besides, the reconstructed 3D distribution is obtained without predictions relying on forward dose calculation and without external phantom or dosimetric devices. Thus, the approach provides a fully automated, fast and easy QA procedure for plan-specific pre-treatment dosimetric verification.

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships

PubMed Central

2014-01-01

Background Miscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships. Results For M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance. Conclusions The ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum. PMID:24884969

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships.

PubMed

Kim, Changsoo; Lee, Tae-Ho; Guo, Hui; Chung, Sung Jin; Paterson, Andrew H; Kim, Do-Soon; Lee, Geung-Joo

2014-05-18

Miscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships. For M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance. The ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum.

Cloning and characterization of a serotonin N-acetyltransferase from a gymnosperm, loblolly pine (Pinus taeda).

PubMed

Park, Sangkyu; Byeon, Yeong; Lee, Hyoung Yool; Kim, Young-Soon; Ahn, Taeho; Back, Kyoungwhan

2014-10-01

Serotonin N-acetyltransferase (SNAT) is the penultimate enzyme in melatonin biosynthesis in both animals and plants. SNAT catalyzes serotonin into N-acetylserotonin, an immediate precursor for melatonin biosynthesis by N-acetylserotonin methyltransferase (ASMT). We cloned the SNAT gene from a gymnosperm loblolly pine (Pinus teada). The loblolly pine SNAT (PtSNAT) gene encodes 255 amino acids harboring a transit sequence with 67 amino acids and shows 67% amino acid identity with rice SNAT when comparing the mature polypeptide regions. Purified recombinant PtSNAT showed peak activity at 55°C with the K(m) (428 μM) and Vmax (3.9 nmol/min/mg protein) values. As predicted, PtSNAT localized to chloroplasts. The SNAT mRNA was constitutively expressed in all tissues, including leaf, bud, flower, and pinecone, whereas the corresponding protein was detected only in leaf. In accordance with the exclusive SNAT protein expression in leaf, melatonin was detected only in leaf at 0.45 ng per gram fresh weight. Sequence and phylogenetic analysis indicated that the gymnosperm PtSNAT had high homology with SNATs from all plant phyla (even with cyanobacteria), and formed a clade separated from the angiosperm SNATs, suggestive of direct gene transfer from cyanobacteria via endosymbiosis. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Online 3D EPID-based dose verification: Proof of concept.

PubMed

Spreeuw, Hanno; Rozendaal, Roel; Olaciregui-Ruiz, Igor; González, Patrick; Mans, Anton; Mijnheer, Ben; van Herk, Marcel

2016-07-01

Delivery errors during radiotherapy may lead to medical harm and reduced life expectancy for patients. Such serious incidents can be avoided by performing dose verification online, i.e., while the patient is being irradiated, creating the possibility of halting the linac in case of a large overdosage or underdosage. The offline EPID-based 3D in vivo dosimetry system clinically employed at our institute is in principle suited for online treatment verification, provided the system is able to complete 3D dose reconstruction and verification within 420 ms, the present acquisition time of a single EPID frame. It is the aim of this study to show that our EPID-based dosimetry system can be made fast enough to achieve online 3D in vivo dose verification. The current dose verification system was sped up in two ways. First, a new software package was developed to perform all computations that are not dependent on portal image acquisition separately, thus removing the need for doing these calculations in real time. Second, the 3D dose reconstruction algorithm was sped up via a new, multithreaded implementation. Dose verification was implemented by comparing planned with reconstructed 3D dose distributions delivered to two regions in a patient: the target volume and the nontarget volume receiving at least 10 cGy. In both volumes, the mean dose is compared, while in the nontarget volume, the near-maximum dose (D2) is compared as well. The real-time dosimetry system was tested by irradiating an anthropomorphic phantom with three VMAT plans: a 6 MV head-and-neck treatment plan, a 10 MV rectum treatment plan, and a 10 MV prostate treatment plan. In all plans, two types of serious delivery errors were introduced. The functionality of automatically halting the linac was also implemented and tested. The precomputation time per treatment was ∼180 s/treatment arc, depending on gantry angle resolution. The complete processing of a single portal frame, including dose verification, took 266 ± 11 ms on a dual octocore Intel Xeon E5-2630 CPU running at 2.40 GHz. The introduced delivery errors were detected after 5-10 s irradiation time. A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for two different kinds of gross delivery errors. Thus, online 3D dose verification has been technologically achieved.

TU-FG-201-06: Remote Dosimetric Auditing for Clinical Trials Using EPID Dosimetry: A Pilot Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miri, N; Legge, K; Greer, P

2016-06-15

Purpose: To perform a pilot study for remote dosimetric credentialing of intensity modulated radiation therapy (IMRT) based clinical trials. The study introduces a novel, time efficient and inexpensive dosimetry audit method for multi-center credentialing. The method employs electronic portal imaging device (EPID) to reconstruct delivered dose inside a virtual flat/cylindrical water phantom. Methods: Five centers, including different accelerator types and treatment planning systems (TPS), were asked to download two CT data sets of a Head and Neck (H&N) and Postprostatectomy (P-P) patients to produce benchmark plans. These were then transferred to virtual flat and cylindrical phantom data sets that weremore » also provided. In-air EPID images of the plans were then acquired, and the data sent to the central site for analysis. At the central site, these were converted to DICOM format, all images were used to reconstruct 2D and 3D dose distributions inside respectively the flat and cylindrical phantoms using inhouse EPID to dose conversion software. 2D dose was calculated for individual fields and 3D dose for the combined fields. The results were compared to corresponding TPS doses. Three gamma criteria were used, 3%3mm-3%/2mm–2%/2mm with a 10% dose threshold, to compare the calculated and prescribed dose. Results: All centers had a high pass rate for the criteria of 3%/3 mm. For 2D dose, the average of centers mean pass rate was 99.6% (SD: 0.3%) and 99.8% (SD: 0.3%) for respectively H&N and PP patients. For 3D dose, 3D gamma was used to compare the model dose with TPS combined dose. The mean pass rate was 97.7% (SD: 2.8%) and 98.3% (SD: 1.6%). Conclusion: Successful performance of the method for the pilot centers establishes the method for dosimetric multi-center credentialing. The results are promising and show a high level of gamma agreement and, the procedure is efficient, consistent and inexpensive. Funding has been provided from Department of Radiation Oncology, TROG Cancer Research and the University of Newcastle. Narges Miri is a recipient of a University of Newcastle postgraduate scholarship.« less

Investigation of the optimal backscatter for an aSi electronic portal imaging device.

PubMed

Ko, Lung; Kim, Jong Oh; Siebers, Jeffrey V

2004-05-07

The effects of backscattered radiation on the dosimetric response of the Varian aS500 amorphous silicon electronic portal imaging device (EPID) are studied. Measurements demonstrate that radiation backscattered from the EPID mechanical support structure causes 5% asymmetries in the detected signal. To minimize the effect of backscattered radiation from the support structure, this work proposes adding material downstream of the EPID phosphor which provides uniform backscattering material to the phosphor and attenuates backscatter from the support structure before it reaches the phosphor. Two material locations were studied: downstream of the existing image cassette and within the cassette, immediately downstream of the flat-panel imager glass panel. Monte Carlo simulations were used to determine the thicknesses of water, Pb and Cu backscattering materials required to saturate the backscattered signal response for 6 MV and 18 MV beams for material thicknesses up to 50 mm. Water was unable to saturate the backscattered signal for thicknesses up to 50 mm for both energies. For Pb, to obtain a signal within 1% of saturation, 3 mm was required at 6 MV, and 6.8 mm was required at 18 MV. For Cu, thicknesses of 20.6 mm and 22.6 mm were required for the 6 MV and 18 MV beams, respectively. For saturation thicknesses, at 6 MV, the Cu backscatter enhanced the signal more than for Pb (Cu 1.25, Pb 1.11), but at 18 MV the reverse was found (Cu 1.19, Pb 1.23). This is due to the fact that at 6 MV, the backscattered radiation signal is dominated by low-energy scattered photons, which are readily attenuated by the Pb, while at 18 MV, electron backscatter contributes substantially to the signal. Image blurring caused by backscatter spread was less for Pb than Cu. Placing Pb immediately downstream of the glass panel further reduced the signal spread and increased the backscatter enhancement to 1.20 and 1.39 for the 6 MV and 18 MV beams, respectively. Overall, it is determined that adding approximately 5 mm of Pb between the detector and the mechanical support structure will substantially reduce the nonuniformity in the backscattered signals for 6 MV and 18 MV photon beams.

A Varian DynaLog file-based procedure for patient dose-volume histogram-based IMRT QA.

PubMed

Calvo-Ortega, Juan F; Teke, Tony; Moragues, Sandra; Pozo, Miquel; Casals-Farran, Joan

2014-03-06

In the present study, we describe a method based on the analysis of the dynamic MLC log files (DynaLog) generated by the controller of a Varian linear accelerator in order to perform patient-specific IMRT QA. The DynaLog files of a Varian Millennium MLC, recorded during an IMRT treatment, can be processed using a MATLAB-based code in order to generate the actual fluence for each beam and so recalculate the actual patient dose distribution using the Eclipse treatment planning system. The accuracy of the DynaLog-based dose reconstruction procedure was assessed by introducing ten intended errors to perturb the fluence of the beams of a reference plan such that ten subsequent erroneous plans were generated. In-phantom measurements with an ionization chamber (ion chamber) and planar dose measurements using an EPID system were performed to investigate the correlation between the measured dose changes and the expected ones detected by the reconstructed plans for the ten intended erroneous cases. Moreover, the method was applied to 20 cases of clinical plans for different locations (prostate, lung, breast, and head and neck). A dose-volume histogram (DVH) metric was used to evaluate the impact of the delivery errors in terms of dose to the patient. The ionometric measurements revealed a significant positive correlation (R² = 0.9993) between the variations of the dose induced in the erroneous plans with respect to the reference plan and the corresponding changes indicated by the DynaLog-based reconstructed plans. The EPID measurements showed that the accuracy of the DynaLog-based method to reconstruct the beam fluence was comparable with the dosimetric resolution of the portal dosimetry used in this work (3%/3 mm). The DynaLog-based reconstruction method described in this study is a suitable tool to perform a patient-specific IMRT QA. This method allows us to perform patient-specific IMRT QA by evaluating the result based on the DVH metric of the planning CT image (patient DVH-based IMRT QA).

Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development.

PubMed

Ding, Mingquan; Jiang, Yurong; Cao, Yuefen; Lin, Lifeng; He, Shae; Zhou, Wei; Rong, Junkang

2014-02-10

Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1. Copyright © 2013 Elsevier B.V. All rights reserved.

Transcriptome Characterization of Cymbidium sinense 'Dharma' Using 454 Pyrosequencing and Its Application in the Identification of Genes Associated with Leaf Color Variation.

PubMed

Zhu, Genfa; Yang, Fengxi; Shi, Shanshan; Li, Dongmei; Wang, Zhen; Liu, Hailin; Huang, Dan; Wang, Caiyun

2015-01-01

The highly variable leaf color of Cymbidium sinense significantly improves its horticultural and economic value, and makes it highly desirable in the flower markets in China and Southeast Asia. However, little is understood about the molecular mechanism underlying leaf-color variations. In this study, we found the content of photosynthetic pigments, especially chlorophyll degradation metabolite in the leaf-color mutants is distinguished significantly from that in the wild type of Cymbidium sinense 'Dharma'. To further determine the candidate genes controlling leaf-color variations, we first sequenced the global transcriptome using 454 pyrosequencing. More than 0.7 million expressed sequence tags (ESTs) with an average read length of 445.9 bp were generated and assembled into 103,295 isotigs representing 68,460 genes. Of these isotigs, 43,433 were significantly aligned to known proteins in the public database, of which 29,299 could be categorized into 42 functional groups in the gene ontology system, 10,079 classified into 23 functional classifications in the clusters of orthologous groups system, and 23,092 assigned to 139 clusters of specific metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes. Among these annotations, 95 isotigs were designated as involved in chlorophyll metabolism. On this basis, we identified 16 key enzyme-encoding genes in the chlorophyll metabolism pathway, the full length cDNAs and expressions of which were further confirmed. Expression pattern indicated that the key enzyme-encoding genes for chlorophyll degradation were more highly expressed in the leaf color mutants, as was consistent with their lower chlorophyll contents. This study is the first to supply an informative 454 EST dataset for Cymbidium sinense 'Dharma' and to identify original leaf color-associated genes, which provide important resources to facilitate gene discovery for molecular breeding, marketable trait discovery, and investigating various biological process in this species.

Transcriptome Characterization of Cymbidium sinense 'Dharma' Using 454 Pyrosequencing and Its Application in the Identification of Genes Associated with Leaf Color Variation

PubMed Central

Shi, Shanshan; Li, Dongmei; Wang, Zhen; Liu, Hailin; Huang, Dan; Wang, Caiyun

2015-01-01

The highly variable leaf color of Cymbidium sinense significantly improves its horticultural and economic value, and makes it highly desirable in the flower markets in China and Southeast Asia. However, little is understood about the molecular mechanism underlying leaf-color variations. In this study, we found the content of photosynthetic pigments, especially chlorophyll degradation metabolite in the leaf-color mutants is distinguished significantly from that in the wild type of Cymbidium sinense 'Dharma'. To further determine the candidate genes controlling leaf-color variations, we first sequenced the global transcriptome using 454 pyrosequencing. More than 0.7 million expressed sequence tags (ESTs) with an average read length of 445.9 bp were generated and assembled into 103,295 isotigs representing 68,460 genes. Of these isotigs, 43,433 were significantly aligned to known proteins in the public database, of which 29,299 could be categorized into 42 functional groups in the gene ontology system, 10,079 classified into 23 functional classifications in the clusters of orthologous groups system, and 23,092 assigned to 139 clusters of specific metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes. Among these annotations, 95 isotigs were designated as involved in chlorophyll metabolism. On this basis, we identified 16 key enzyme-encoding genes in the chlorophyll metabolism pathway, the full length cDNAs and expressions of which were further confirmed. Expression pattern indicated that the key enzyme-encoding genes for chlorophyll degradation were more highly expressed in the leaf color mutants, as was consistent with their lower chlorophyll contents. This study is the first to supply an informative 454 EST dataset for Cymbidium sinense 'Dharma' and to identify original leaf color-associated genes, which provide important resources to facilitate gene discovery for molecular breeding, marketable trait discovery, and investigating various biological process in this species. PMID:26042676

Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection.

PubMed

Chandra, Saket; Kazmi, Andaleeb Z; Ahmed, Zainab; Roychowdhury, Gargi; Kumari, Veena; Kumar, Manish; Mukhopadhyay, Kunal

2017-07-01

NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.

Comparison of the Dye Method with the Thermocouple Psychrometer for Measuring Leaf Water Potentials 1

PubMed Central

Knipling, Edward B.; Kramer, Paul J.

1967-01-01

The dye method for measuring water potential was examined and compared with the thermocouple psychrometer method in order to evaluate its usefulness for measuring leaf water potentials of forest trees and common laboratory plants. Psychrometer measurements are assumed to represent the true leaf water potentials. Because of the contamination of test solutions by cell sap and leaf surface residues, dye method values of most species varied about 1 to 5 bars from psychrometer values over the leaf water potential range of 0 to −30 bars. The dye method is useful for measuring changes and relative values in leaf potential. Because of species differences in the relationships of dye method values to true leaf water potentials, dye method values should be interpreted with caution when comparing different species or the same species growing in widely different environments. Despite its limitations the dye method has a usefulness to many workers because it is simple, requires no elaborate equipment, and can be used in both the laboratory and field. PMID:16656657

Relative Water Content, Bidirectional Reflectance and Bidirectional Transmittance of the Interior of Detached Leaves During Dry Down.

NASA Technical Reports Server (NTRS)

Vanderbilt, Vern; Daughtry, Craig; Dahlgren, Robert

2015-01-01

Remotely sensing the water status of plants and the water content of canopies remain long-term goals of remote sensing research [1]. Estimates of canopy water content commonly involve measurements in the 900nm to 2000nm portion of the optical spectrum [1]. We have used optical polarization techniques to remove leaf surface reflection and to demonstrate that the visible light reflected by the interior of green healthy corn leaves measured in situ inversely depends upon the leaf relative water content (RWC) [2]. In the research reported here, we again used optical polarization techniques in order to remove the leaf surface reflection from our measurements. This allowed us to monitor the interiors of detached corn leaf samples during leaf dry down measuring for each sample the RWC, bidirectional spectral reflectance and bidirectional spectral transmittance over the wavelength range 450nm to 2,500nm. Our new results like our earlier results show light scattered by the leaf interior measured in the visible wavelength region generally increased as leaf RWC decreased. However, the spectral character and the much improved signal noise of our new results shows the RWC-linked visible light scattering changes are due to leaf structural changes. Our new results show that scattering changes that occur with changing leaf RWC are not attributable to molecular configuration changes in cellular pigments.

Influence of vegetation structure on lidar-derived canopy height and fractional cover in forested riparian buffers during leaf-off and leaf-on conditions.

PubMed

Wasser, Leah; Day, Rick; Chasmer, Laura; Taylor, Alan

2013-01-01

Estimates of canopy height (H) and fractional canopy cover (FC) derived from lidar data collected during leaf-on and leaf-off conditions are compared with field measurements from 80 forested riparian buffer plots. The purpose is to determine if existing lidar data flown in leaf-off conditions for applications such as terrain mapping can effectively estimate forested riparian buffer H and FC within a range of riparian vegetation types. Results illustrate that: 1) leaf-off and leaf-on lidar percentile estimates are similar to measured heights in all plots except those dominated by deciduous compound-leaved trees where lidar underestimates H during leaf off periods; 2) canopy height models (CHMs) underestimate H by a larger margin compared to percentile methods and are influenced by vegetation type (conifer needle, deciduous simple leaf or deciduous compound leaf) and canopy height variability, 3) lidar estimates of FC are within 10% of plot measurements during leaf-on periods, but are underestimated during leaf-off periods except in mixed and conifer plots; and 4) depth of laser pulse penetration lower in the canopy is more variable compared to top of the canopy penetration which may influence within canopy vegetation structure estimates. This study demonstrates that leaf-off lidar data can be used to estimate forested riparian buffer canopy height within diverse vegetation conditions and fractional canopy cover within mixed and conifer forests when leaf-on lidar data are not available.

Influence of Vegetation Structure on Lidar-derived Canopy Height and Fractional Cover in Forested Riparian Buffers During Leaf-Off and Leaf-On Conditions

PubMed Central

Wasser, Leah; Day, Rick; Chasmer, Laura; Taylor, Alan

2013-01-01

Estimates of canopy height (H) and fractional canopy cover (FC) derived from lidar data collected during leaf-on and leaf-off conditions are compared with field measurements from 80 forested riparian buffer plots. The purpose is to determine if existing lidar data flown in leaf-off conditions for applications such as terrain mapping can effectively estimate forested riparian buffer H and FC within a range of riparian vegetation types. Results illustrate that: 1) leaf-off and leaf-on lidar percentile estimates are similar to measured heights in all plots except those dominated by deciduous compound-leaved trees where lidar underestimates H during leaf off periods; 2) canopy height models (CHMs) underestimate H by a larger margin compared to percentile methods and are influenced by vegetation type (conifer needle, deciduous simple leaf or deciduous compound leaf) and canopy height variability, 3) lidar estimates of FC are within 10% of plot measurements during leaf-on periods, but are underestimated during leaf-off periods except in mixed and conifer plots; and 4) depth of laser pulse penetration lower in the canopy is more variable compared to top of the canopy penetration which may influence within canopy vegetation structure estimates. This study demonstrates that leaf-off lidar data can be used to estimate forested riparian buffer canopy height within diverse vegetation conditions and fractional canopy cover within mixed and conifer forests when leaf-on lidar data are not available. PMID:23382966

Leaf Assemblages across the Cretaceous-Tertiary Boundary in the Raton Basin, New Mexico and Colorado

NASA Astrophysics Data System (ADS)

Wolfe, Jack A.; Upchurch, Garland R., Jr.

1987-08-01

Analyses of leaf megafossil and dispersed leaf cuticle assemblages indicate that major ecologic disruption and high rates of extinction occurred in plant communities at the Cretaceous-Tertiary boundary in the Raton Basin. In diversity increase, the early Paleocene vegetational sequence mimics normal short-term ecologic succession, but on a far longer time scale. No difference can be detected between latest Cretaceous and early Paleocene temperatures, but precipitation markedly increased at the boundary. Higher survival rate of deciduous versus evergreen taxa supports occurrence of a brief cold interval (<1 year), as predicted in models of an “impact winter.”

Genetic analysis and mapping of adult plant resistance loci to leaf rust in durum wheat cultivar Bairds.

PubMed

Lan, Caixia; Basnet, Bhoja R; Singh, Ravi P; Huerta-Espino, Julio; Herrera-Foessel, Sybil A; Ren, Yong; Randhawa, Mandeep S

2017-03-01

New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds. CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5-60.8%, 9.0-14.3%, 2.8-13.9%, and 11.6-29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.

Plant Chlorophyll fluorescence: active and passive measurements at canopy and leaf scales with different nitrogen treatments

USDA-ARS?s Scientific Manuscript database

Most studies assessing chlorophyll fluorescence (ChlF) have examined leaf responses to environmental stress conditions using active techniques. Alternatively, passive techniques are able to measure ChlF at both leaf and canopy scales. However, although the measurement principles of both techniques a...

Molecular Characterization of Watermelon Chlorotic Stunt Virus (WmCSV) from Palestine

PubMed Central

Ali-Shtayeh, Mohammed S.; Jamous, Rana M.; Mallah, Omar B.; Abu-Zeitoun, Salam Y.

2014-01-01

The incidence of watermelon chlorotic stunt disease and molecular characterization of the Palestinian isolate of Watermelon chlorotic stunt virus (WmCSV-[PAL]) are described in this study. Symptomatic leaf samples obtained from watermelon Citrullus lanatus (Thunb.), and cucumber (Cucumis sativus L.) plants were tested for WmCSV-[PAL] infection by polymerase chain reaction (PCR) and Rolling Circle Amplification (RCA). Disease incidence ranged between 25%–98% in watermelon fields in the studied area, 77% of leaf samples collected from Jenin were found to be mixed infected with WmCSV-[PAL] and SLCV. The full-length DNA-A and DNA-B genomes of WmCSV-[PAL] were amplified and sequenced, and the sequences were deposited in the GenBank. Sequence analysis of virus genomes showed that DNA-A and DNA-B had 97.6%–99.42% and 93.16%–98.26% nucleotide identity with other virus isolates in the region, respectively. Sequence analysis also revealed that the Palestinian isolate of WmCSV shared the highest nucleotide identity with an isolate from Israel suggesting that the virus was introduced to Palestine from Israel. PMID:24956181

Molecular identification of a new begomovirus infecting yellow passion fruit (Passiflora edulis) in Colombia.

PubMed

Vaca-Vaca, Juan Carlos; Carrasco-Lozano, Emerson Clovis; López-López, Karina

2017-02-01

The complete genome sequence of a bipartite begomovirus (genus Begomovirus, family Geminiviridae) infecting yellow passion fruit (Passiflora edulis) in the state of Valle del Cauca (Colombia) has been determined. The complete DNA-A and DNA-B components were determined to be 2600 and 2572 nt in length, respectively. The DNA-A showed the highest nucleotide sequence identity (87.2 %) to bean dwarf mosaic virus (M88179), a begomovirus found in common bean crops in Colombia, and only 77.4 % identity to passion fruit severe leaf distortion virus (FJ972767), a begomovirus identified infecting passion fruit in Brazil. Based on its sequence identity to all other begomoviruses known to date and in accordance with the ICTV species demarcation criterion for the genus Begomovirus (≥91 % sequence identity for the complete DNA-A), the name passion fruit leaf distortion virus is proposed for this new begomovirus. To our knowledge, this is the first report of a bipartite begomovirus affecting passion fruit in Colombia and the second report of a geminivirus affecting this crop worldwide.

SU-C-201-04: Noise and Temporal Resolution in a Near Real-Time 3D Dosimeter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rilling, M; Centre de recherche sur le cancer, Universite Laval, Quebec City, QC; Radiation oncology department, CHU de Quebec, Quebec City, QC

Purpose: To characterize the performance of a real-time three-dimensional scintillation dosimeter in terms of signal-to-noise ratio (SNR) and temporal resolution of 3D dose measurements. This study quantifies its efficiency in measuring low dose levels characteristic of EBRT dynamic treatments, and in reproducing field profiles for varying multileaf collimator (MLC) speeds. Methods: The dosimeter prototype uses a plenoptic camera to acquire continuous images of the light field emitted by a 10×10×10 cm{sup 3} plastic scintillator. Using EPID acquisitions, ray tracing-based iterative tomographic algorithms allow millimeter-sized reconstruction of relative 3D dose distributions. Measurements were taken at 6MV, 400 MU/min with the scintillatormore » centered at the isocenter, first receiving doses from 1.4 to 30.6 cGy. Dynamic measurements were then performed by closing half of the MLCs at speeds of 0.67 to 2.5 cm/s, at 0° and 90° collimator angles. A reference static half-field was obtained for measured profile comparison. Results: The SNR steadily increases as a function of dose and reaches a clinically adequate plateau of 80 at 10 cGy. Below this, the decrease in light collected and increase in pixel noise diminishes the SNR; nonetheless, the EPID acquisitions and the voxel correlation employed in the reconstruction algorithms result in suitable SNR values (>75) even at low doses. For dynamic measurements at varying MLC speeds, central relative dose profiles are characterized by gradients at %D{sub 50} of 8.48 to 22.7 %/mm. These values converge towards the 32.8 %/mm-gradient measured for the static reference field profile, but are limited by the dosimeter’s current acquisition rate of 1Hz. Conclusion: This study emphasizes the efficiency of the 3D dose distribution reconstructions, while identifying limits of the current prototype’s temporal resolution in terms of dynamic EBRT parameters. This work paves the way for providing an optimized, second-generational real-time 3D scintillation dosimeter capable of highly efficient and precise dose measurements. The presenting author is financially supported by an Alexander-Graham Bell doctoral scholarship from the Natural Sciences and Engineering Research Council of Canada (NSERC).« less

The Genomes of Two Bat Species with Long Constant Frequency Echolocation Calls.

PubMed

Dong, Dong; Lei, Ming; Hua, Panyu; Pan, Yi-Hsuan; Mu, Shuo; Zheng, Guantao; Pang, Erli; Lin, Kui; Zhang, Shuyi

2017-01-01

Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats-the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Nondestructive and Real-time Measurement of Moisture in Plant

NASA Astrophysics Data System (ADS)

Ogawa, Yuichi; Kawase, Kodo; Mizuno, Maya; Yamashita, Masatsugu; Otani, Chiko

We constructed a THz transillumination system for water content monitoring, and we succeeded in measuring the moisture level in plants. Our measurement system uses a widely tunable coherent THz parametric oscillator source. As target we chose for this experiment a leaf of Japanese basil. The time variation of the water content in the leaf was monitored in two situations: a leaf freshly cut which is left to dry out, and the leaf of a water stressed plant. We found by real-time measurements that the water content of a cut leaf does not decrease uniformly in time. Also, the response to water stress is delayed by about 5-10 minutes. Furthermore, we demonstrated a moisture measurement using a transillumination THz imaging system. As target we chose for this experiment a leaf of Hedera helix held between two thin plastic sheets. The change of the moisture distribution is clearly visible. These results show that the method described here can be applied to nondestructive and real-time monitoring of water content in plants.

Pulvinus activity, leaf movement and leaf water-use efficiency of bush bean (Phaseplus vulgaris L.) in a hot environment.

PubMed

Raeini-Sarjaz, Mahmoud; Chalavi, Vida

2008-11-01

Pulvinus activity of Phaseolus species in response to environmental stimuli plays an essential role in heliotropic leaf movement. The aims of this study were to monitor the continuous daily pulvinus movement and pulvinus temperature, and to evaluate the effects of leaf movements, on a hot day, on instantaneous leaf water-use efficiency (WUEi), leaf gas exchange, and leaf temperature. Potted plants of Phaseolus vulgaris L. var. Provider were grown in Chicot sandy loam soil under well-watered conditions in a greenhouse. When the second trifoliate leaf was completely extended, one plant was selected to measure pulvinus movement using a beta-ray gauging (BRG) meter with a point source of thallium-204 (204Tl). Leaf gas exchange measurements took place on similar leaflets of three plants at an air temperature interval of 33-42 degrees C by a steady-state LI-6200 photosynthesis system. A copper-constantan thermocouple was used to monitor pulvinus temperature. Pulvinus bending followed the daily diurnal rhythm. Significant correlations were found between the leaf-incident angle and the stomatal conductance (R2 = 0.54; P < 0.01), and photosynthesis rate (R2 = 0.84; P < 0.01). With a reduction in leaf-incidence angle and increase in air temperature, WUEi was reduced. During the measurements, leaf temperature remained below air temperature and was a significant function of air temperature (r = 0.92; P < 0.01). In conclusion, pulvinus bending followed both light intensity and air temperature and influenced leaf gas exchange.

Rapid measurement of the three-dimensional distribution of leaf orientation and the leaf angle probability density function using terrestrial LiDAR scanning

USDA-ARS?s Scientific Manuscript database

Leaf orientation plays a fundamental role in many transport processes in plant canopies. At the plant or stand level, leaf orientation is often highly anisotropic and heterogeneous, yet most analyses neglect such complexity. In many cases, this is due to the difficulty in measuring the spatial varia...

Wheat productivity estimates using LANDSAT data

NASA Technical Reports Server (NTRS)

Nalepka, R. F.; Colwell, J. (Principal Investigator)

1975-01-01

The author has identified the following significant results. The electro-optical leaf area meter was the most accurate of the approaches tested on harvested wheat samples, but it is very time consuming. It was decided to infer leaf area from dry weight biomass after establishing a relationship between dry weight biomass and area as measured by the leaf area meter. There is a good correlation between leaf area as measured by the meter and dry leaf biomass. There is a less consistent relationship between stem area and stem biomass.

Silver-Foil Psychrometer for Measuring Leaf Water Potential in situ.

PubMed

Hoffman, G J; Rawlins, S L

1972-09-01

The water potential of leaves in situ can be measured without temperature control with a miniature, single-junction psychrometer constructed from silver foil and attached to the leaf with a silver-impregnated, conductive coating. The temperature of the psychrometer has been found to stay within 0.025 degrees C of the temperature of a simulated leaf when the latter temperature was changing at a rate of 1 degrees C per minute. Leaf water potentials can be measured with a precision of +/- 1 bar, or better.

Unveiling Members of Colletotrichum acutatum Species Complex Causing Colletotrichum Leaf Disease of Hevea brasiliensis in Sri Lanka.

PubMed

Hunupolagama, D M; Chandrasekharan, N V; Wijesundera, W S S; Kathriarachchi, H S; Fernando, T H P S; Wijesundera, R L C

2017-06-01

Colletotrichum is an important fungal genus with great diversity, which causes anthracnose of a variety of crop plants including rubber trees. Colletotrichum acutatum and Colletotrichum gloeosporioides have been identified as the major causative agents of Colletotrichum leaf disease of rubber trees in Sri Lanka based on morphology, pathogenicity, and the analysis of internally transcribed spacer sequences of the nuclear ribosomal DNA. This study has been conducted to investigate the members of the C. acutatum species complex causing rubber leaf disease using a morphological and multi gene approach. For the first time in Sri Lanka, Colletotrichum simmondsii, Colletotrichum laticiphilum, Colletotrichum nymphaeae, and Colletotrichum citri have been identified as causative agents of Colletotrichum leaf disease in addition to C. acutatum s. str. Among them, C. simmondsii has been recognized as the major causative agent.

Blue Light–Dependent Interaction between Cryptochrome2 and CIB1 Regulates Transcription and Leaf Senescence in Soybean[W

PubMed Central

Meng, Yingying; Li, Hongyu; Wang, Qin; Liu, Bin; Lin, Chentao

2013-01-01

Cryptochromes are blue light receptors that regulate light responses in plants, including various crops. The molecular mechanism of plant cryptochromes has been extensively investigated in Arabidopsis thaliana, but it has not been reported in any crop species. Here, we report a study of the mechanism of soybean (Glycine max) cryptochrome2 (CRY2a). We found that CRY2a regulates leaf senescence, which is a life history trait regulated by light and photoperiods via previously unknown mechanisms. We show that CRY2a undergoes blue light–dependent interaction with the soybean basic helix-loop-helix transcription activator CIB1 (for cryptochrome-interacting bHLH1) that specifically interacts with the E-box (CANNTG) DNA sequences. Analyses of transgenic soybean plants expressing an elevated or reduced level of the CRY2a or CIB1 demonstrate that CIB1 promotes leaf senescence, whereas CRY2a suppresses leaf senescence. Results of the gene expression and molecular interaction analyses support the hypothesis that CIB1 activates transcription of senescence-associated genes, such as WRKY DNA BINDING PROTEIN53b (WRKY53b), and leaf senescence. CIB1 interacts with the E-box–containing promoter sequences of the WRKY53b chromatin, whereas photoexcited CRY2a interacts with CIB1 to inhibit its DNA binding activity. These findings argue that CIB-dependent transcriptional regulation is an evolutionarily conserved CRY-signaling mechanism in plants, and this mechanism is opted in evolution to mediate light regulation of different aspects of plant development in different plant species. PMID:24272488

A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens.

PubMed

Yang, Qin; He, Yijian; Kabahuma, Mercy; Chaya, Timothy; Kelly, Amy; Borrego, Eli; Bian, Yang; El Kasmi, Farid; Yang, Li; Teixeira, Paulo; Kolkman, Judith; Nelson, Rebecca; Kolomiets, Michael; L Dangl, Jeffery; Wisser, Randall; Caplan, Jeffrey; Li, Xu; Lauter, Nick; Balint-Kurti, Peter

2017-09-01

Alleles that confer multiple disease resistance (MDR) are valuable in crop improvement, although the molecular mechanisms underlying their functions remain largely unknown. A quantitative trait locus, qMdr 9.02 , associated with resistance to three important foliar maize diseases-southern leaf blight, gray leaf spot and northern leaf blight-has been identified on maize chromosome 9. Through fine-mapping, association analysis, expression analysis, insertional mutagenesis and transgenic validation, we demonstrate that ZmCCoAOMT2, which encodes a caffeoyl-CoA O-methyltransferase associated with the phenylpropanoid pathway and lignin production, is the gene within qMdr 9.02 conferring quantitative resistance to both southern leaf blight and gray leaf spot. We suggest that resistance might be caused by allelic variation at the level of both gene expression and amino acid sequence, thus resulting in differences in levels of lignin and other metabolites of the phenylpropanoid pathway and regulation of programmed cell death.

De Novo Assembly, Functional Annotation and Comparative Analysis of Withania somnifera Leaf and Root Transcriptomes to Identify Putative Genes Involved in the Withanolides Biosynthesis

PubMed Central

Gupta, Parul; Goel, Ridhi; Pathak, Sumya; Srivastava, Apeksha; Singh, Surya Pratap; Sangwan, Rajender Singh; Asif, Mehar Hasan; Trivedi, Prabodh Kumar

2013-01-01

Withania somnifera is one of the most valuable medicinal plants used in Ayurvedic and other indigenous medicine systems due to bioactive molecules known as withanolides. As genomic information regarding this plant is very limited, little information is available about biosynthesis of withanolides. To facilitate the basic understanding about the withanolide biosynthesis pathways, we performed transcriptome sequencing for Withania leaf (101L) and root (101R) which specifically synthesize withaferin A and withanolide A, respectively. Pyrosequencing yielded 8,34,068 and 7,21,755 reads which got assembled into 89,548 and 1,14,814 unique sequences from 101L and 101R, respectively. A total of 47,885 (101L) and 54,123 (101R) could be annotated using TAIR10, NR, tomato and potato databases. Gene Ontology and KEGG analyses provided a detailed view of all the enzymes involved in withanolide backbone synthesis. Our analysis identified members of cytochrome P450, glycosyltransferase and methyltransferase gene families with unique presence or differential expression in leaf and root and might be involved in synthesis of tissue-specific withanolides. We also detected simple sequence repeats (SSRs) in transcriptome data for use in future genetic studies. Comprehensive sequence resource developed for Withania, in this study, will help to elucidate biosynthetic pathway for tissue-specific synthesis of secondary plant products in non-model plant organisms as well as will be helpful in developing strategies for enhanced biosynthesis of withanolides through biotechnological approaches. PMID:23667511

Dynamic energy-balance model predicting gestational weight gain

USDA-ARS?s Scientific Manuscript database

Gestational weight gains (GWGs) that exceed the 2009 Institute of Medicine recommended ranges increase risk of long-term postpartum weight retention; conversely, GWGs within the recommended ranges are more likely to result in positive maternal and fetal outcomes. Despite this evidence, recent epide...

The global distribution of leaf chlorophyll content and seasonal controls on carbon uptake

NASA Astrophysics Data System (ADS)

Croft, H.; Chen, J. M.; Luo, X.; Bartlett, P. A.; Staebler, R. M.; He, L.; Mo, G.; Luo, S.; Simic, A.; Arabian, J.; He, Y.; Zhang, Y.; Beringer, J.; Hutley, L. B.; Noland, T. L.; Arellano, P.; Stahl, C.; Homolová, L.; Bonal, D.; Malenovský, Z.; Yi, Q.; Amiri, R.

2017-12-01

Leaf chlorophyll (ChlLeaf) is crucial to biosphere-atmosphere exchanges of carbon and water, and the functioning of terrestrial ecosystems. Improving the accuracy of modelled photosynthetic carbon uptake is a central priority for understanding ecosystem response to a changing climate. A source of uncertainty within gross primary productivity (GPP) estimates is the failure to explicitly consider seasonal controls on leaf photosynthetic potential. Whilst the inclusion of ChlLeafinto carbon models has shown potential to provide a physiological constraint, progress has been hampered by the absence of a spatially-gridded, global chlorophyll product. Here, we present the first spatially-continuous, global view of terrestrial ChlLeaf, at weekly intervals. Satellite-derived ChlLeaf was modelled using a physically-based radiative transfer modelling approach, with a two stage model inversion method. 4-Scale and SAIL canopy models were first used to model leaf-level reflectance from ENIVSAT MERIS 300m satellite data. The PROSPECT leaf model was then used to derive ChlLeaf from the modelled leaf reflectance. This algorithm was validated using measured ChlLeaf data from 248 measurements within 26 field locations, covering six plant functional types (PFTs). Modelled results show very good relationships with measured data, particularly for deciduous broadleaf forests (R2 = 0.67; p<0.001) and croplands (R2 = 0.42; p<000.1). With all PFTs considered together, the overall validation against measured data was strong (R2 = 0.50; p<0.001). The incorporation of chlorophyll within a light-use efficiency GPP modelling approach and a Terrestrial Biosphere Model demonstrated that neglecting to account for seasonality in leaf physiology resulted in over-estimations in GPP at the start/end of a deciduous growing season, due to a divergence in canopy structure and leaf function. Across nine PFTs, Fluxnet eddy-covariance data was used to validate TBM GPP estimates using ChlLeaf-constrained Vcmax; reducing the seasonal bias and explaining 13%-49% of daily variations in GPP. This work demonstrates the importance of considering leaf pigment status in modelling photosynthetic carbon uptake. We anticipate that the global ChlLeaf product will make an important step towards improving the accuracy of global carbon budgets.

Validating LiDAR Derived Estimates of Canopy Height, Structure and Fractional Cover in Riparian Areas: A Comparison of Leaf-on and Leaf-off LiDAR Data

NASA Astrophysics Data System (ADS)

Wasser, L. A.; Chasmer, L. E.; Taylor, A.; Day, R.

2010-12-01

Characterization of riparian buffers is integral to understanding the landscape scale impacts of disturbance on wildlife and aquatic ecosystems. Riparian buffers may be characterized using in situ plot sampling or via high resolution remote sensing. Field measurements are time-consuming and may not cover a broad range of ecosystem types. Further, spectral remote sensing methods introduce a compromise between spatial resolution (grain) and area extent. Airborne LiDAR can be used to continuously map and characterize riparian vegetation structure and composition due to the three-dimensional reflectance of laser pulses within and below the canopy, understory and at the ground surface. The distance between reflections (or ‘returns’) allows for detection of narrow buffer corridors at the landscape scale. There is a need to compare leaf-off and leaf-on surveyed LiDAR data with in situ measurements to assess accuracy in landscape scale analysis. These comparisons are particularly important considering increased availability of leaf-off surveyed LiDAR datasets. And given this increased availability, differences between leaf-on and leaf-off derived LiDAR metrics are largely unknown for riparian vegetation of varying composition and structure. This study compares the effectiveness of leaf-on and leaf-off LiDAR in characterizing riparian buffers of varying structure and composition as compared to field measurements. Field measurements were used to validate LiDAR derived metrics. Vegetation height, canopy cover, density and overstory and understory species composition were recorded in 80 random plots of varying vegetation type, density and structure within a Pennsylvania watershed (-77.841, 40.818). Plot data were compared with LiDAR data collected during leaf on and leaf off conditions to determine 1) accuracy of LiDAR derived metrics compared to field measures and 2) differences between leaf-on and leaf-off LiDAR metrics. Results illustrate that differences exist between metrics derived from leaf on and leaf-off surveyed LiDAR. There is greater variability between the two datasets within taller deciduous and mixed (conifer and deciduous) vegetation compared to shorter deciduous and mixed vegetation. Differences decrease as stand density increases for both mixed and deciduous forests. LiDAR derived canopy height is more sensitive to understory vegetation as stand density decreases making measurement of understory vegetation in the field important in the validation process. Finally, while leaf-on LiDAR is often preferred for vegetation analysis, results suggest that leaf-off LiDAR may be sufficient to categorize vegetation into height classes to be used for landscape scale habitat models.

Comparison of direct and indirect methods for assessing leaf area index across a tropical rain forest landscape

Treesearch

Paulo C. Olivas; Steven F. Oberbauer; David B. Clark; Deborah A. Clark; Michael G. Ryan; Joseph J. O' Brien; Harlyn Ordonez

2013-01-01

Many functional properties of forests depend on the leaf area; however, measuring leaf area is not trivial in tall evergreen vegetation. As a result, leaf area is generally estimated indirectly by light absorption methods. These indirect methods are widely used, but have never been calibrated against direct measurements in tropical rain forests, either at point or...

In vivo dosimetry in UK external beam radiotherapy: current and future usage.

PubMed

MacDougall, Niall D; Graveling, Michael; Hansen, Vibeke N; Brownsword, Kevin; Morgan, Andrew

2017-04-01

Towards Safer Radiotherapy recommended that radiotherapy (RT) centres should have protocols in place for in vivo dosimetry (IVD) monitoring at the beginning of patient treatment courses (Donaldson S. Towards safer radiotherapy. R Coll Radiol 2008). This report determines IVD implementation in the UK in 2014, the methods used and makes recommendations on future use. Evidence from peer-reviewed journals was used in conjunction with the first survey of UK RT centre IVD practice since the publication of Towards Safer Radiotherapy. In March 2014, profession-specific questionnaires were sent to radiographer, clinical oncologist and physics staff groups in each of the 66 UK RT centres. Response rates from each group were 74%, 45% and 74%, respectively. 73% of RT centres indicated that they performed IVD. Diodes are the most popular IVD device. Thermoluminescent dosimeter (TLD) is still in use in a number of centres but not as a sole modality, being used in conjunction with diodes and/or electronic portal imaging device (EPID). The use of EPID dosimetry is increasing and is considered of most potential value for both geometric and dosimetric verification. Owing to technological advances, such as electronic data transfer, independent monitor unit checking and daily image-guided radiotherapy, the overall risk of adverse treatment events in RT has been substantially reduced. However, the use of IVD may prevent a serious radiation incident. Point dose IVD is not considered suited to the requirements of verifying advanced RT techniques, leaving EPID dosimetry as the current modality likely to be developed as a future standard. Advances in knowledge: An updated perspective on UK IVD use and provision of professional guidelines for future implementation.

In vivo dosimetry in UK external beam radiotherapy: current and future usage

PubMed Central

Graveling, Michael; Hansen, Vibeke N; Brownsword, Kevin; Morgan, Andrew

2017-01-01

Objective: Towards Safer Radiotherapy recommended that radiotherapy (RT) centres should have protocols in place for in vivo dosimetry (IVD) monitoring at the beginning of patient treatment courses (Donaldson S. Towards safer radiotherapy. R Coll Radiol 2008). This report determines IVD implementation in the UK in 2014, the methods used and makes recommendations on future use. Methods: Evidence from peer-reviewed journals was used in conjunction with the first survey of UK RT centre IVD practice since the publication of Towards Safer Radiotherapy. In March 2014, profession-specific questionnaires were sent to radiographer, clinical oncologist and physics staff groups in each of the 66 UK RT centres. Results: Response rates from each group were 74%, 45% and 74%, respectively. 73% of RT centres indicated that they performed IVD. Diodes are the most popular IVD device. Thermoluminescent dosimeter (TLD) is still in use in a number of centres but not as a sole modality, being used in conjunction with diodes and/or electronic portal imaging device (EPID). The use of EPID dosimetry is increasing and is considered of most potential value for both geometric and dosimetric verification. Conclusion: Owing to technological advances, such as electronic data transfer, independent monitor unit checking and daily image-guided radiotherapy, the overall risk of adverse treatment events in RT has been substantially reduced. However, the use of IVD may prevent a serious radiation incident. Point dose IVD is not considered suited to the requirements of verifying advanced RT techniques, leaving EPID dosimetry as the current modality likely to be developed as a future standard. Advances in knowledge: An updated perspective on UK IVD use and provision of professional guidelines for future implementation. PMID:28205452

Registration of clinical volumes to beams-eye-view images for real-time tracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bryant, Jonathan H.; Rottmann, Joerg; Lewis, John H.

2014-12-15

Purpose: The authors combine the registration of 2D beam’s eye view (BEV) images and 3D planning computed tomography (CT) images, with relative, markerless tumor tracking to provide automatic absolute tracking of physician defined volumes such as the gross tumor volume (GTV). Methods: During treatment of lung SBRT cases, BEV images were continuously acquired with an electronic portal imaging device (EPID) operating in cine mode. For absolute registration of physician-defined volumes, an intensity based 2D/3D registration to the planning CT was performed using the end-of-exhale (EoE) phase of the four dimensional computed tomography (4DCT). The volume was converted from Hounsfield unitsmore » into electron density by a calibration curve and digitally reconstructed radiographs (DRRs) were generated for each beam geometry. Using normalized cross correlation between the DRR and an EoE BEV image, the best in-plane rigid transformation was found. The transformation was applied to physician-defined contours in the planning CT, mapping them into the EPID image domain. A robust multiregion method of relative markerless lung tumor tracking quantified deviations from the EoE position. Results: The success of 2D/3D registration was demonstrated at the EoE breathing phase. By registering at this phase and then employing a separate technique for relative tracking, the authors are able to successfully track target volumes in the BEV images throughout the entire treatment delivery. Conclusions: Through the combination of EPID/4DCT registration and relative tracking, a necessary step toward the clinical implementation of BEV tracking has been completed. The knowledge of tumor volumes relative to the treatment field is important for future applications like real-time motion management, adaptive radiotherapy, and delivered dose calculations.« less

Comparison of low‐dose, half‐rotation, cone‐beam CT with electronic portal imaging device for registration of fiducial markers during prostate radiotherapy

PubMed Central

Wee, Leonard; Hackett, Sara Lyons; Jones, Andrew; Lim, Tee Sin; Harper, Christopher Stirling

2013-01-01

This study evaluated the agreement of fiducial marker localization between two modalities — an electronic portal imaging device (EPID) and cone‐beam computed tomography (CBCT) — using a low‐dose, half‐rotation scanning protocol. Twenty‐five prostate cancer patients with implanted fiducial markers were enrolled. Before each daily treatment, EPID and half‐rotation CBCT images were acquired. Translational shifts were computed for each modality and two marker‐matching algorithms, seed‐chamfer and grey‐value, were performed for each set of CBCT images. The localization offsets, and systematic and random errors from both modalities were computed. Localization performances for both modalities were compared using Bland‐Altman limits of agreement (LoA) analysis, Deming regression analysis, and Cohen's kappa inter‐rater analysis. The differences in the systematic and random errors between the modalities were within 0.2 mm in all directions. The LoA analysis revealed a 95% agreement limit of the modalities of 2 to 3.5 mm in any given translational direction. Deming regression analysis demonstrated that constant biases existed in the shifts computed by the modalities in the superior–inferior (SI) direction, but no significant proportional biases were identified in any direction. Cohen's kappa analysis showed good agreement between the modalities in prescribing translational corrections of the couch at 3 and 5 mm action levels. Images obtained from EPID and half‐rotation CBCT showed acceptable agreement for registration of fiducial markers. The seed‐chamfer algorithm for tracking of fiducial markers in CBCT datasets yielded better agreement than the grey‐value matching algorithm with EPID‐based registration. PACS numbers: 87.55.km, 87.55.Qr PMID:23835391

Assessing soybean leaf area and leaf biomass by spectral measurements

NASA Technical Reports Server (NTRS)

Holben, B. N.; Tucker, C. J.; Fan, C. J.

1979-01-01

Red and photographic infrared spectral radiances were correlated with soybean total leaf area index, green leaf area index, chlorotic leaf area index, green leaf biomass, chlorotic leaf biomass, and total biomass. The most significant correlations were found to exist between the IR/red radiance ratio data and green leaf area index and/or green leaf biomass (r squared equals 0.85 and 0.86, respectively). These findings demonstrate that remote sensing data can supply information basic to soybean canopy growth, development, and status by nondestructive determination of the green leaf area or green leaf biomass.

Comparison of Water Potentials Measured by In Situ Psychrometry and Pressure Chamber in Morphologically Different Species 1

PubMed Central

Turner, Neil C.; Spurway, R. A.; Schulze, E.-D.

1984-01-01

Leaf water potentials measured by in situ psychrometry were compared with leaf water potentials measured by the pressure chamber technique at various values of water potential in Helianthus annuus, Helianthus nuttallii, Vigna unguiculata, Nerium oleander, Pistacia vera, and Corylus avellana. In V. unguiculata, the leaf water potentials measured by the in situ psychrometer oscillated at the same periodicity as, and proportional to, the leaf conductance. In all species, potentials measured by in situ psychrometers operating in the psychrometric mode were linearly correlated with potentials measured with the pressure chamber. However, the in situ psychrometers underestimated the leaf water potential in the two Helianthus species at low water potentials and overestimated the water potential in P. vera, N. oleander, and C. avellana. The underestimation in the two Helianthus species at low water potentials resulted from differences in water potential across the leaf. The overestimation in P. vera, N. oleander, and C. avellana was considered to arise from low epidermal conductances in these species even after abrasion of the cuticle. Pressure-volume studies with Lycopersicon esculentum showed that less water was expressed from distal than proximal leaflets when the whole leaf was slowly pressurized. The implication of this for water relations characteristics obtained by pressure-volume techniques is discussed. We conclude that in situ psychrometers are suitable for following dynamic changes in leaf water potential, but should be used with caution on leaves with low epidermal conductances. PMID:16663415

Comparison of water potentials measured by in situ psychrometry and pressure chamber in morphologically different species.

PubMed

Turner, N C; Spurway, R A; Schulze, E D

1984-02-01

Leaf water potentials measured by in situ psychrometry were compared with leaf water potentials measured by the pressure chamber technique at various values of water potential in Helianthus annuus, Helianthus nuttallii, Vigna unguiculata, Nerium oleander, Pistacia vera, and Corylus avellana. In V. unguiculata, the leaf water potentials measured by the in situ psychrometer oscillated at the same periodicity as, and proportional to, the leaf conductance. In all species, potentials measured by in situ psychrometers operating in the psychrometric mode were linearly correlated with potentials measured with the pressure chamber. However, the in situ psychrometers underestimated the leaf water potential in the two Helianthus species at low water potentials and overestimated the water potential in P. vera, N. oleander, and C. avellana. The underestimation in the two Helianthus species at low water potentials resulted from differences in water potential across the leaf. The overestimation in P. vera, N. oleander, and C. avellana was considered to arise from low epidermal conductances in these species even after abrasion of the cuticle. Pressure-volume studies with Lycopersicon esculentum showed that less water was expressed from distal than proximal leaflets when the whole leaf was slowly pressurized. The implication of this for water relations characteristics obtained by pressure-volume techniques is discussed. We conclude that in situ psychrometers are suitable for following dynamic changes in leaf water potential, but should be used with caution on leaves with low epidermal conductances.

Spatial variation of dosimetric leaf gap and its impact on dose delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumaraswamy, Lalith K., E-mail: Lalith.Kumaraswamy@roswellpark.org; Schmitt, Jonathan D.; Bailey, Daniel W.

Purpose: During dose calculation, the Eclipse treatment planning system (TPS) retracts the multileaf collimator (MLC) leaf positions by half of the dosimetric leaf gap (DLG) value (measured at central axis) for all leaf positions in a dynamic MLC plan to accurately model the rounded leaf ends. The aim of this study is to map the variation of DLG along the travel path of each MLC leaf pair and quantify how this variation impacts delivered dose. Methods: 6 MV DLG values were measured for all MLC leaf pairs in increments of 1.0 cm (from the line intersecting the CAX and perpendicularmore » to MLC motion) to 13.0 cm off axis distance at dmax. The measurements were performed on two Varian linear accelerators, both employing the Millennium 120-leaf MLCs. The measurements were performed at several locations in the beam with both a Sun Nuclear MapCHECK device and a PTW pinpoint ion chamber. Results: The measured DLGs for the middle 40 MLC leaf pairs (each 0.5 cm width) at positions along a line through the CAX and perpendicular to MLC leaf travel direction were very similar, varying maximally by only 0.2 mm. The outer 20 MLC leaf pairs (each 1.0 cm width) have much lower DLG values, about 0.3–0.5 mm lower than the central MLC leaf pair, at their respective central line position. Overall, the mean and the maximum variation between the 0.5 cm width leaves and the 1.0 cm width leaf pairs are 0.32 and 0.65 mm, respectively. Conclusions: The spatial variation in DLG is caused by the variation of intraleaf transmission through MLC leaves. Fluences centered on the CAX would not be affected since DLG does not vary; but any fluences residing significantly off axis with narrow sweeping leaves may exhibit significant dose differences. This is due to the fact that there are differences in DLG between the true DLG exhibited by the 1.0 cm width outer leaves and the constant DLG value utilized by the TPS for dose calculation. Since there are large differences in DLG between the 0.5 cm width leaf pairs and 1.0 cm width leaf pairs, there is a need to correct the TPS plans, especially those with high modulation (narrow dynamic MLC gap), with 2D variation of DLG.« less

The Effect of Leaf Stacking on Leaf Reflectance and Vegetation Indices Measured by Contact Probe during the Season

PubMed Central

Neuwirthová, Eva; Lhotáková, Zuzana; Albrechtová, Jana

2017-01-01

The aims of the study were: (i) to compare leaf reflectance in visible (VIS) (400–700 nm), near-infrared (NIR) (740–1140 nm) and short-wave infrared (SWIR) (2000–2400 nm) spectral ranges measured monthly by a contact probe on a single leaf and a stack of five leaves (measurement setup (MS)) of two broadleaved tree species during the vegetative season; and (ii) to test if and how selected vegetation indices differ under these two MS. In VIS, the pigment-related spectral region, the effect of MS on reflectance was negligible. The major influence of MS on reflectance was detected in NIR (up to 25%), the structure-related spectral range; and weaker effect in SWIR, the water-related spectral range. Vegetation indices involving VIS wavelengths were independent of MS while indices combining wavelengths from both VIS and NIR were MS-affected throughout the season. The effect of leaf stacking contributed to weakening the correlation between the leaf chlorophyll content and selected vegetation indices due to a higher leaf mass per area of the leaf sample. The majority of MS-affected indices were better correlated with chlorophyll content in both species in comparison with MS-unaffected indices. Therefore, in terms of monitoring leaf chlorophyll content using the contact probe reflectance measurement, these MS-affected indices should be used with caution, as discussed in the paper. If the vegetation indices are used for assessment of plant physiological status in various times of the vegetative season, then it is essential to take into consideration their possible changes induced by the particular contact probe measurement setup regarding the leaf stacking. PMID:28538685

Generation of an infectious clone of a new Korean isolate of apple chlorotic leaf spot virus (ACLSV) driven by dual 35S and T7 promoters in a versatile binary vector

USDA-ARS?s Scientific Manuscript database

The full-length sequence of a new isolate of Apple chlorotic leaf spot virus (ACLSV) from Korea was divergent, but most closely related to the Japanese isolate A4, at 84% nucleotide identity. The full-length cDNA of the Korean isolate of ACLSV was cloned into a binary vector downstream of the bacter...

TOPICAL REVIEW: Electronic portal imaging devices: a review and historical perspective of contemporary technologies and research

NASA Astrophysics Data System (ADS)

Antonuk, Larry E.

2002-03-01

A review of electronic portal imaging devices (EPIDs) used in external beam, megavoltage radiation therapy is presented. The review consists of a brief introduction to the definition, role and clinical significance of portal imaging, along with a discussion of radiotherapy film systems and the motivations for EPIDs. This is followed by a summary of the challenges and constraints inherent to portal imaging along with a concise, historical review of the technologies that have been explored and developed. The paper then examines, in greater depth, the two first-generation technologies that have found widespread clinical use starting from the late 1980s. This is followed by a broad overview of the physics, operation, properties and advantages of active matrix, flat-panel, megavoltage imagers, presently being commercially introduced to clinical environments or expected to be introduced in the future. Finally, a survey of contemporary research efforts focused on improving portal imaging performance by addressing various weaknesses in existing commercial systems is presented.

In vivo dose verification of IMRT treated head and neck cancer patients.

PubMed

Engström, Per E; Haraldsson, Pia; Landberg, Torsten; Sand Hansen, Hanne; Aage Engelholm, Svend; Nyström, Håkan

2005-01-01

An independent in vivo dose verification procedure for IMRT treatments of head and neck cancers was developed. Results of 177 intracavitary TLD measurements from 10 patients are presented. The study includes data from 10 patients with cancer of the rhinopharynx or the thyroid treated with dynamic IMRT. Dose verification was performed by insertion of a flexible naso-oesophageal tube containing TLD rods and markers for EPID and simulator image detection. Part of the study focussed on investigating the accuracy of the TPS calculations in the presence of inhomogeneities. Phantom measurements and Monte Carlo simulations were performed for a number of geometries involving lateral electronic disequilibrium and steep density shifts. The in vivo TLD measurements correlated well with the predictions of the treatment planning system with a measured/calculated dose ratio of 1.002+/-0.051 (1 SD, N=177). The measurements were easily performed and well tolerated by the patients. We conclude that in vivo intracavitary dosimetry with TLD is suitable and accurate for dose determination in intensity-modulated beams.

Minimizing the average distance to a closest leaf in a phylogenetic tree.

PubMed

Matsen, Frederick A; Gallagher, Aaron; McCoy, Connor O

2013-11-01

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this article, we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Around Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, whereas PAM only gives a solution for the prespecified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, whereas the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.

Alteration in Auxin Homeostasis and Signaling by Overexpression Of PINOID Kinase Causes Leaf Growth Defects in Arabidopsis thaliana

PubMed Central

Saini, Kumud; Markakis, Marios N.; Zdanio, Malgorzata; Balcerowicz, Daria M.; Beeckman, Tom; De Veylder, Lieven; Prinsen, Els; Beemster, Gerrit T. S.; Vissenberg, Kris

2017-01-01

In plants many developmental processes are regulated by auxin and its directional transport. PINOID (PID) kinase helps to regulate this transport by influencing polar recruitment of PIN efflux proteins on the cellular membranes. We investigated how altered auxin levels affect leaf growth in Arabidopsis thaliana. Arabidopsis mutants and transgenic plants with altered PID expression levels were used to study the effect on auxin distribution and leaf development. Single knockouts showed small pleiotropic growth defects. Contrastingly, several leaf phenotypes related to changes in auxin concentrations and transcriptional activity were observed in PID overexpression (PIDOE) lines. Unlike in the knockout lines, the leaves of PIDOE lines showed an elevation in total indole-3-acetic acid (IAA). Accordingly, enhanced DR5-visualized auxin responses were detected, especially along the leaf margins. Kinematic analysis revealed that ectopic expression of PID negatively affects cell proliferation and expansion rates, yielding reduced cell numbers and small-sized cells in the PIDOE leaves. We used PIDOE lines as a tool to study auxin dose effects on leaf development and demonstrate that auxin, above a certain threshold, has a negative affect on leaf growth. RNA sequencing further showed how subtle PIDOE-related changes in auxin levels lead to transcriptional reprogramming of cellular processes. PMID:28659952

Characterization and pathogenicity of Fusarium species associated with leaf spot of mango (Mangifera indica L.).

PubMed

Omar, Nurul Husna; Mohd, Masratulhawa; Mohamed Nor, Nik Mohd Izham; Zakaria, Latiffah

2018-01-01

Leaf spot diseases are mainly caused by fungi including Fusarium. In the present study several species of Fusarium were isolated from the leaf spot lesion of mango (Mangifera indica L.) Based on morphological characteristics, TEF-1α sequences and phylogenetic analysis, five species were identified as F. proliferatum, F. semitectum, F. mangiferae, F. solani and F. chlamydosporum. Pathogenicity test indicated that representative isolates of F. proliferatum, F. semitectum and F. chlamydosporum were pathogenic on mango leaves causing leaf spot with low to moderate virulence. Nevertheless, abundance of spots on the leaf can disrupt photosynthesis which in turn reduced growth, and lead to susceptibility to infection by opportunistic pathogens due to weakening of the plant. Fusarium solani and F. mangiferae were non-pathogenic and it is possible that both species are saprophyte which associated with nutrient availability on the surface of the leaf through decaying leave tissues. The occurrence of Fusarium spp. on the leaf spot lesion and the effect from the disease needs to be considered when developing disease management method of mango cultivation as numerous spot on the leaves could effect the photosynthesis process and finally giving low yield and less quality of mango. Copyright © 2017. Published by Elsevier Ltd.

Leaf Responses to Mild Drought Stress in Natural Variants of Arabidopsis1[OPEN

PubMed Central

Clauw, Pieter; Coppens, Frederik; De Beuf, Kristof; Dhondt, Stijn; Van Daele, Twiggy; Maleux, Katrien; Storme, Veronique; Clement, Lieven; Gonzalez, Nathalie; Inzé, Dirk

2015-01-01

Although the response of plants exposed to severe drought stress has been studied extensively, little is known about how plants adapt their growth under mild drought stress conditions. Here, we analyzed the leaf and rosette growth response of six Arabidopsis (Arabidopsis thaliana) accessions originating from different geographic regions when exposed to mild drought stress. The automated phenotyping platform WIWAM was used to impose stress early during leaf development, when the third leaf emerges from the shoot apical meristem. Analysis of growth-related phenotypes showed differences in leaf development between the accessions. In all six accessions, mild drought stress reduced both leaf pavement cell area and number without affecting the stomatal index. Genome-wide transcriptome analysis (using RNA sequencing) of early developing leaf tissue identified 354 genes differentially expressed under mild drought stress in the six accessions. Our results indicate the existence of a robust response over different genetic backgrounds to mild drought stress in developing leaves. The processes involved in the overall mild drought stress response comprised abscisic acid signaling, proline metabolism, and cell wall adjustments. In addition to these known severe drought-related responses, 87 genes were found to be specific for the response of young developing leaves to mild drought stress. PMID:25604532

The relationship between leaf water status, gas exchange, and spectral reflectance in cotton leaves

NASA Technical Reports Server (NTRS)

Bowman, William D.

1989-01-01

Measurements of leaf spectral reflectance, the components of water potential, and leaf gas exchanges as a function of leaf water content were made to evaluate the use of NIR reflectance as an indicator of plant water status. Significant correlations were determined between spectral reflectance at 810 nm, 1665 nm, and 2210 nm and leaf relative water content, total water potential, and turgor pressure. However, the slopes of these relationships were relatively shallow and, when evaluated over the range of leaf water contents in which physiological activity occurs (e.g., photosynthesis), had lower r-squared values, and some relationships were not statistically significant. NIR reflectance varied primarily as a function of leaf water content, and not independently as a function of turgor pressure, which is a sensitive indicator of leaf water status. The limitations of this approach to measuring plant water stress are discussed.

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.).

PubMed

Andres, Ryan J; Coneva, Viktoriya; Frank, Margaret H; Tuttle, John R; Samayoa, Luis Fernando; Han, Sang-Won; Kaur, Baljinder; Zhu, Linglong; Fang, Hui; Bowman, Daryl T; Rojas-Pierce, Marcela; Haigler, Candace H; Jones, Don C; Holland, James B; Chitwood, Daniel H; Kuraparthy, Vasu

2017-01-03

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D 1 ), which is responsible for the major leaf shapes in cotton. The l-D 1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D 1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)

PubMed Central

Andres, Ryan J.; Coneva, Viktoriya; Frank, Margaret H.; Tuttle, John R.; Samayoa, Luis Fernando; Han, Sang-Won; Kaur, Baljinder; Zhu, Linglong; Fang, Hui; Bowman, Daryl T.; Rojas-Pierce, Marcela; Haigler, Candace H.; Jones, Don C.; Holland, James B.; Chitwood, Daniel H.; Kuraparthy, Vasu

2017-01-01

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype. PMID:27999177

Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants.

PubMed

Wilson-Sánchez, David; Rubio-Díaz, Silvia; Muñoz-Viana, Rafael; Pérez-Pérez, José Manuel; Jover-Gil, Sara; Ponce, María Rosa; Micol, José Luis

2014-09-01

The study and eventual manipulation of leaf development in plants requires a thorough understanding of the genetic basis of leaf organogenesis. Forward genetic screens have identified hundreds of Arabidopsis mutants with altered leaf development, but the genome has not yet been saturated. To identify genes required for leaf development we are screening the Arabidopsis Salk Unimutant collection. We have identified 608 lines that exhibit a leaf phenotype with full penetrance and almost constant expressivity and 98 additional lines with segregating mutant phenotypes. To allow indexing and integration with other mutants, the mutant phenotypes were described using a custom leaf phenotype ontology. We found that the indexed mutation is present in the annotated locus for 78% of the 553 mutants genotyped, and that in half of these the annotated T-DNA is responsible for the phenotype. To quickly map non-annotated T-DNA insertions, we developed a reliable, cost-effective and easy method based on whole-genome sequencing. To enable comprehensive access to our data, we implemented a public web application named PhenoLeaf (http://genetics.umh.es/phenoleaf) that allows researchers to query the results of our screen, including text and visual phenotype information. We demonstrated how this new resource can facilitate gene function discovery by identifying and characterizing At1g77600, which we found to be required for proximal-distal cell cycle-driven leaf growth, and At3g62870, which encodes a ribosomal protein needed for cell proliferation and chloroplast function. This collection provides a valuable tool for the study of leaf development, characterization of biomass feedstocks and examination of other traits in this fundamental photosynthetic organ. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, S; Kuo, L; Happersett, L

Purpose: To commission a custom 6MV-SRS-AAA Eclipse beam model for VMAT multiple lesions cranial SRS treatment on a Varian TrueBeam STx. Methods: Six clinical plans were created using a customized beam model with dosimetric-leaf-gap(DLG) optimized for clinical treatments. Each plan had 4–6 non-isocentric targets with size from 0.2 to 7.1cc. All fields were measured with EBT3 film in the coronal plane in a solid water phantom and with an AS1000 EPID using gantry rotation. In addition, an end-to-end test was performed with coronal and sagittal films in an anthropomorphic phantom verifying dosimetry and localization accuracy. Portal dose distributions were generatedmore » with a custom portal dosimetry algorithm(PDIP). Measured dose distributions were compared with calculations using average dose difference (DD), and gamma function, γ. Using a 1.25mm grid, the γ criteria, local DD ≤ 3% and 2mm distance-to-agreement, were applied in regions with dose 50% of maximum. Results: The respective DD and γ for all films were <±2% and >94.2%. The portal dose γ scores for all the plans were >94.9%. However, local regions with underdose >10%, were observed when targets were treated with the 5mm leaves. The same plans re-optimized with two isocenters such that all lesions were under the 2.5mm leaves did not show this effect. The DD and localization error of the end-to-end test were within 3.4% and 1.0mm respectively. Conclusion: The custom AAA beam model is capable of calculating acceptable dosimetry for targets using only the 2.5 mm leaves. This restricts lesions to within ±4cm of isocenter. The observed underdose beneath the 5mm leaves is attributed to a limitation in Eclipse that uses a single DLG representing the DLG’s of both 2.5mm and 5mm leaves. If lesions are >4cm from isocenter, a multiple isocenter technique should be considered to allow the use of only the 2.5mm leaves.« less

Resistance mechanisms and their difference between the root and leaf of Microsorum pteropus - A novel potential aquatic cadmium hyperaccumulator.

PubMed

Lan, Xin-Yu; Yang, Bin; Yan, Yun-Yun; Li, Xin-Yuan; Xu, Fu-Liu

2018-03-01

Microsorum pteropus (M. pteropus), an aquatic Polypodiaceae fern, was identified as a novel potential cadmium (Cd) hyperaccumulator in our previous study. This study reveals the Cd-resistance mechanisms and their difference between the root and leaf of M. pteropus based on analyses of photosynthesis, antioxidant systems and gene expression. A high level of Cd at 500μM was used to treat the samples to test the effects of this compound. Superoxide dismutase (SOD), peroxidase (POD), malondialdehyde (MDA) and flavonoids were used as indicators for antioxidant system changes. Five chlorophyll fluorescent parameters including the maximal photochemical efficiency of photosystem II (F v /F m ), effective quantum yield of photosystem II (Y(II)), photochemical quenching (qP), nonphotochemical quenching (qN) and electron transport rate (ETR) were measured to determine the photosynthetic changes. RNA-sequencing analysis was used to study the changes in gene expression. The results showed that after exposure to high levels of Cd, the concentrations of enzymatic oxidants (SOD and POD) were significantly increased, while the MDA levels were significantly decreased. There were no significant changes for the chlorophyll fluorescent parameters during Cd stress, which indicates that M. pteropus is highly effective at protecting itself. Certain functional genes, including photosystem genes and secondary metabolites, had significantly altered levels of expression. Different Cd-resistance mechanisms were found between the root and leaf tissues of M. pteropus. The root tissues of M. pteropus resist Cd damage using antioxidants, while its leaf tissues mainly protect themselves using photosystem self-protection. Copyright © 2017 Elsevier B.V. All rights reserved.

Phenoseasonal variability of subcanopy PAR and the effects of photointensity and photoperiod on the physiological ecology of Lindera benzoin

NASA Astrophysics Data System (ADS)

Hudson, J. E.; Levia, D. F., Jr.; Hudson, S.; Bais, H.; Legates, D. R.

2015-12-01

This work represents a novel approach to measuring photosynthetic photon flux density (PPFD), and spatiotemporal light dynamics, by utilizing an instrument capable of providing a 15-second spatially-integrated one meter linear average of the PPFD, obtaining measurements at multiple locations and elevations in the subcanopy over a full year for all cloud conditions. Nearly 4,600 individual observations of photosynthetically active radiation (PAR, 400-700 nm) were made over the seven phenoseasons of a deciduous forest in the Piedmont Region, Maryland. Additionally, to quantify of the effect of various photointensities on the physiological ecology of Lindera benzoin L. Blume (northern spicebush) grown in the lab, health was determined by monitoring physical growth and biomass, and by UV-vis spectrophotometry analysis of leaf extract. Results show understory PAR is typically less than 40% of open PAR. Leafless subcanopy PAR values were almost 10 times higher than leafed season PAR, and sunflecks often three orders of magnitude higher than mean subcanopy PAR during the leafed season. Phenoseason is responsible for nearly three-quarters of the variation between plant canopy levels. Spicebush growth occurred at study locations receiving higher incidence of PAR (> 64th percentile). UV-vis spectrophotometry analysis showed significant differences in root to shoot ratios, biomass, initial stomatal conductance, chlorophyll a and b, and carotenoids. Spicebush under lab conditions significantly alter their biomass and individual pigments and pigment ratios in response to high intensity light conditions. Results suggest temporal light sequences in the field may be a very important factor in the functional ecology of northern spicebush.

Online 3D EPID-based dose verification: Proof of concept

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spreeuw, Hanno; Rozendaal, Roel, E-mail: r.rozenda

Purpose: Delivery errors during radiotherapy may lead to medical harm and reduced life expectancy for patients. Such serious incidents can be avoided by performing dose verification online, i.e., while the patient is being irradiated, creating the possibility of halting the linac in case of a large overdosage or underdosage. The offline EPID-based 3D in vivo dosimetry system clinically employed at our institute is in principle suited for online treatment verification, provided the system is able to complete 3D dose reconstruction and verification within 420 ms, the present acquisition time of a single EPID frame. It is the aim of thismore » study to show that our EPID-based dosimetry system can be made fast enough to achieve online 3D in vivo dose verification. Methods: The current dose verification system was sped up in two ways. First, a new software package was developed to perform all computations that are not dependent on portal image acquisition separately, thus removing the need for doing these calculations in real time. Second, the 3D dose reconstruction algorithm was sped up via a new, multithreaded implementation. Dose verification was implemented by comparing planned with reconstructed 3D dose distributions delivered to two regions in a patient: the target volume and the nontarget volume receiving at least 10 cGy. In both volumes, the mean dose is compared, while in the nontarget volume, the near-maximum dose (D2) is compared as well. The real-time dosimetry system was tested by irradiating an anthropomorphic phantom with three VMAT plans: a 6 MV head-and-neck treatment plan, a 10 MV rectum treatment plan, and a 10 MV prostate treatment plan. In all plans, two types of serious delivery errors were introduced. The functionality of automatically halting the linac was also implemented and tested. Results: The precomputation time per treatment was ∼180 s/treatment arc, depending on gantry angle resolution. The complete processing of a single portal frame, including dose verification, took 266 ± 11 ms on a dual octocore Intel Xeon E5-2630 CPU running at 2.40 GHz. The introduced delivery errors were detected after 5–10 s irradiation time. Conclusions: A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for two different kinds of gross delivery errors. Thus, online 3D dose verification has been technologically achieved.« less

Predator-prey pursuit-evasion games in structurally complex environments.

PubMed

Morice, Sylvie; Pincebourde, Sylvain; Darboux, Frédéric; Kaiser, Wilfried; Casas, Jérôme

2013-11-01

Pursuit and evasion behaviors in many predator-prey encounters occur in a geometrically structured environment. The physical structures in the environment impose strong constraints on the perception and behavioral responses of both antagonists. Nevertheless, no experimental or theoretical study has tackled the issue of quantifying the role of the habitat's architecture on the joint trajectories during a predator-prey encounter. In this study, we report the influence of microtopography of forest leaf litter on the pursuit-evasion trajectories of wolf spiders Pardosa sp. attacking the wood cricket Nemobius sylvestris. Fourteen intact leaf litter samples of 1 m × 0.5 m were extracted from an oak-beech forest floor in summer and winter, with later samples having the most recently fallen leaves. Elevation was mapped at a spatial resolution of 0.5 mm using a laser scanner. Litter structuring patterns were identified by height transects and experimental semi-variograms. Detailed analysis of all visible leaf-fragments of one sample enabled us to relate the observed statistical patterns to the underlying geometry of individual elements. Video recording of pursuit-evasion sequences in arenas with flat paper or leaf litter enabled us to estimate attack and fleeing distances as a function of substrate. The compaction index, the length of contiguous flat surfaces, and the experimental variograms showed that the leaf litter was smoother in summer than in winter. Thus, weathering as well as biotic activities compacted and flattened the litter over time. We found good agreement between the size of the structuring unit of leaf litter and the distance over which attack and escape behaviors both were initiated (both ∼3 cm). There was a four-fold topographical effect on pursuit-escape sequences; compared with a flat surface, leaf litter (1) greatly reduced the likelihood of launching a pursuit, (2) reduced pursuit and escape distances by half, (3) put prey and predator on par in terms of pursuit and escape distances, and (4) reduced the likelihood of secondary pursuits, after initial escape of the prey, to nearly zero. Thus, geometry of the habitat strongly modulates the rules of pursuit-evasion in predator-prey interactions in the wild.

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables.

PubMed

Jackson, Colin R; Randolph, Kevin C; Osborn, Shelly L; Tyler, Heather L

2013-12-01

Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional culture-dependent methods. The use of pyrosequencing allowed for the identification of low abundance bacteria in leaf salad vegetables not detected by culture-dependent methods. The presence of a range of bacterial populations as endophytes presents an interesting phenomenon as these microorganisms cannot be removed by washing and are thus ingested during salad consumption.

Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

PubMed Central

2013-01-01

Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional culture-dependent methods. Conclusions The use of pyrosequencing allowed for the identification of low abundance bacteria in leaf salad vegetables not detected by culture-dependent methods. The presence of a range of bacterial populations as endophytes presents an interesting phenomenon as these microorganisms cannot be removed by washing and are thus ingested during salad consumption. PMID:24289725

SU-E-T-605: Performance Evaluation of MLC Leaf-Sequencing Algorithms in Head-And-Neck IMRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jing, J; Lin, H; Chow, J

2015-06-15

Purpose: To investigate the efficiency of three multileaf collimator (MLC) leaf-sequencing algorithms proposed by Galvin et al, Chen et al and Siochi et al using external beam treatment plans for head-and-neck intensity modulated radiation therapy (IMRT). Methods: IMRT plans for head-and-neck were created using the CORVUS treatment planning system. The plans were optimized and the fluence maps for all photon beams determined. Three different MLC leaf-sequencing algorithms based on Galvin et al, Chen et al and Siochi et al were used to calculate the final photon segmental fields and their monitor units in delivery. For comparison purpose, the maximum intensitymore » of fluence map was kept constant in different plans. The number of beam segments and total number of monitor units were calculated for the three algorithms. Results: From results of number of beam segments and total number of monitor units, we found that algorithm of Galvin et al had the largest number of monitor unit which was about 70% larger than the other two algorithms. Moreover, both algorithms of Galvin et al and Siochi et al have relatively lower number of beam segment compared to Chen et al. Although values of number of beam segment and total number of monitor unit calculated by different algorithms varied with the head-and-neck plans, it can be seen that algorithms of Galvin et al and Siochi et al performed well with a lower number of beam segment, though algorithm of Galvin et al had a larger total number of monitor units than Siochi et al. Conclusion: Although performance of the leaf-sequencing algorithm varied with different IMRT plans having different fluence maps, an evaluation is possible based on the calculated number of beam segment and monitor unit. In this study, algorithm by Siochi et al was found to be more efficient in the head-and-neck IMRT. The Project Sponsored by the Fundamental Research Funds for the Central Universities (J2014HGXJ0094) and the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry.« less

Leaf Size in Swietenia

Treesearch

Charles B. Briscoe; F. Bruce Lamb

1962-01-01

A study was made of the putative hybrid of bigleaf and small-leaf mahoganies. Initial measurements indicated that bigleaf mahogany can be distinguished from small-leaf mahogany by gross measurements of leaflets. Isolated mother trees yield typical progeny. Typical mother trees in mixed stands yield like progeny plus, usually, mediumleaf progeny. Mediumleaf mother trees...

The light response of mesophyll conductance is controlled by structure across leaf profiles.

PubMed

Théroux-Rancourt, Guillaume; Gilbert, Matthew E

2017-05-01

Mesophyll conductance to CO 2 (g m ) may respond to light either through regulated dynamic mechanisms or due to anatomical and structural factors. At low light, some layers of cells in the leaf cross-section approach photocompensation and contribute minimally to bulk leaf photosynthesis and little to whole leaf g m (g m,leaf ). Thus, the bulk g m,leaf will appear to respond to light despite being based upon cells having an anatomically fixed mesophyll conductance. Such behaviour was observed in species with contrasting leaf structure using the variable J or stable isotope method of measuring g m,leaf . A species with bifacial structure, Arbutus × 'Marina', and an isobilateral species, Triticum durum L., had contrasting responses of g m,leaf upon varying adaxial or abaxial illumination. Anatomical observations, when coupled with the proposed model of g m,leaf to photosynthetic photon flux density (PPFD) response, successfully represented the observed gas exchange data. The theoretical and observed evidence that g m,leaf apparently responds to light has large implications for how g m,leaf values are interpreted, particularly limitation analyses, and indicates the importance of measuring g m under full light saturation. Responses of g m,leaf to the environment should be treated as an emergent property of a distributed 3D structure, and not solely a leaf area-based phenomenon. © 2016 John Wiley & Sons Ltd.

A single-nucleotide polymorphism that accounts for allelic variation in the Lr34 gene and leaf rust reaction in hard winter wheat.

PubMed

Cao, Shuanghe; Carver, Brett F; Zhu, Xinkai; Fang, Tilin; Chen, Yihua; Hunger, Robert M; Yan, Liuling

2010-07-01

Leaf rust, caused by Puccinia triticina Eriks, is one of the most common and persistent wheat diseases in the US Great Plains. We report that the Lr34 gene was mapped in the center of a QTL for leaf rust reaction and explained 18-35% of the total phenotypic variation in disease severity of adult plants in a Jagger x 2174 population of recombinant inbred lines (RILs) field-tested for 3 years. The sequence of the complete Lr34 gene was determined for the susceptible Jagger allele and for the resistant 2174 allele. The two alleles had exactly the same sequence as the resistant allele reported previously in Chinese Spring at three polymorphic sites in intron 4, exon 11, and exon 12. A G/T polymorphism was found in exon 22, where a premature stop codon was found in the susceptible Jagger allele (Lr34E22s), confirming a previous report, due to a point mutation compared with the resistant 2174 allele (Lr34E22r). We have experimentally demonstrated a tight association between the point mutation at exon 22 of Lr34 and leaf rust susceptibility in a segregating biparental population. A PCR marker was developed to distinguish between the Lr34E22r and Lr34E22s alleles. A survey of 33 local hard winter wheat cultivars indicated that 7 cultivars carry the Lr34E22s allele and 26 cultivars carry the Lr34E22r allele. This study significantly improves our genetic understanding of allelic variation in the Lr34 gene and provides a functional molecular tool to improve leaf rust resistance in a major US wheat gene pool.

Isolation of nucleotide binding site-leucine rich repeat and kinase resistance gene analogues from sugarcane (Saccharum spp.).

PubMed

Glynn, Neil C; Comstock, Jack C; Sood, Sushma G; Dang, Phat M; Chaparro, Jose X

2008-01-01

Resistance gene analogues (RGAs) have been isolated from many crops and offer potential in breeding for disease resistance through marker-assisted selection, either as closely linked or as perfect markers. Many R-gene sequences contain kinase domains, and indeed kinase genes have been reported as being proximal to R-genes, making kinase analogues an additionally promising target. The first step towards utilizing RGAs as markers for disease resistance is isolation and characterization of the sequences. Sugarcane clone US01-1158 was identified as resistant to yellow leaf caused by the sugarcane yellow leaf virus (SCYLV) and moderately resistant to rust caused by Puccinia melanocephala Sydow & Sydow. Degenerate primers that had previously proved useful for isolating RGAs and kinase analogues in wheat and soybean were used to amplify DNA from sugarcane (Saccharum spp.) clone US-01-1158. Sequences generated from 1512 positive clones were assembled into 134 contigs of between two and 105 sequences. Comparison of the contig consensuses with the NCBI sequence database using BLASTx showed that 20 had sequence homology to nuclear binding site and leucine rich repeat (NBS-LRR) RGAs, and eight to kinase genes. Alignment of the deduced amino acid sequences with similar sequences from the NCBI database allowed the identification of several conserved domains. The alignment and resulting phenetic tree showed that many of the sequences had greater similarity to sequences from other species than to one another. The use of degenerate primers is a useful method for isolating novel sugarcane RGA and kinase gene analogues. Further studies are needed to evaluate the role of these genes in disease resistance.

Mitochondrial and Nuclear Ribosomal DNA Evidence Supports the Existence of a New Trichuris Species in the Endangered François’ Leaf-Monkey

PubMed Central

Liu, Guo-Hua; Gasser, Robin B.; Nejsum, Peter; Wang, Yan; Chen, Qiang; Song, Hui-Qun; Zhu, Xing-Quan

2013-01-01

The whipworm of humans, Trichuris trichiura, is responsible for a neglected tropical disease (NTD) of major importance in tropical and subtropical countries of the world. Whipworms also infect animal hosts, including pigs, dogs and non-human primates, cause clinical disease (trichuriasis) similar to that of humans. Although Trichuris species are usually considered to be host specific, it is not clear whether non-human primates are infected with T. trichiura or other species. In the present study, we sequenced the complete mitochondrial (mt) genome as well as the first and second internal transcribed spacers (ITS-1 and ITS-2) of Trichuris from the François’ leaf-monkey (langur), and compared them with homologous sequences from human- and pig-derived Trichuris. In addition, sequence comparison of a conserved mt ribosomal gene among multiple individual whipworms revealed substantial nucleotide differences among these three host species but limited sequence variation within each of them. The molecular data indicate that the monkey-derived whipworm is a separate species from that of humans. Future work should focus on detailed population genetic and morphological studies (by electron microscopy) of whipworms from various non-humans primates and humans. PMID:23840431

Mitochondrial and nuclear ribosomal DNA evidence supports the existence of a new Trichuris species in the endangered françois' leaf-monkey.

PubMed

Liu, Guo-Hua; Gasser, Robin B; Nejsum, Peter; Wang, Yan; Chen, Qiang; Song, Hui-Qun; Zhu, Xing-Quan

2013-01-01

The whipworm of humans, Trichuris trichiura, is responsible for a neglected tropical disease (NTD) of major importance in tropical and subtropical countries of the world. Whipworms also infect animal hosts, including pigs, dogs and non-human primates, cause clinical disease (trichuriasis) similar to that of humans. Although Trichuris species are usually considered to be host specific, it is not clear whether non-human primates are infected with T. trichiura or other species. In the present study, we sequenced the complete mitochondrial (mt) genome as well as the first and second internal transcribed spacers (ITS-1 and ITS-2) of Trichuris from the François' leaf-monkey (langur), and compared them with homologous sequences from human- and pig-derived Trichuris. In addition, sequence comparison of a conserved mt ribosomal gene among multiple individual whipworms revealed substantial nucleotide differences among these three host species but limited sequence variation within each of them. The molecular data indicate that the monkey-derived whipworm is a separate species from that of humans. Future work should focus on detailed population genetic and morphological studies (by electron microscopy) of whipworms from various non-humans primates and humans.

Leaf Phenology of Amazonian Canopy Trees as Revealed by Spectral and Physiochemical Measurements

NASA Astrophysics Data System (ADS)

Chavana-Bryant, C.; Gerard, F. F.; Malhi, Y.; Enquist, B. J.; Asner, G. P.

2013-12-01

The phenological dynamics of terrestrial ecosystems reflect the response of the Earth's biosphere to inter- and intra-annual dynamics of climatic and hydrological regimes. Some Dynamic Global Vegetation Models (GDVMs) have predicted that by 2050 the Amazon rainforest will begin to dieback (Cox et al. 2000, Nature) or that the ecosystem will become unsustainable (Salazar et al. 2007, GRL). One major component in DGVMs is the simulation of vegetation phenology, however, modelers are challenged with the estimation of tropical phenology which is highly complex. Current modeled phenology is based on observations of temperate vegetation and accurate representation of tropical phenology is long overdue. Remote sensing (RS) data are a key tool in monitoring vegetation dynamics at regional and global scales. Of the many RS techniques available, time-series analysis of vegetation indices (VIs) has become the most common approach in monitoring vegetation phenology (Samanta et al. 2010, GRL; Bradley et al. 2011, GCB). Our research focuses on investigating the influence that age related variation in the spectral reflectance and physiochemical properties of leaves may have on VIs of tropical canopies. In order to do this, we collected a unique leaf and canopy phenological dataset at two different Amazonian sites: Inselberg, French Guyana (FG) and Tambopata, Peru (PE). Hyperspectral reflectance measurements were collected from 4,102 individual leaves sampled to represent different leaf ages and vertical canopy positions (top, mid and low canopy) from 20 different canopy tree species (8 in FG and 12 in PE). These leaf spectra were complemented with 1) leaf physical measurements: fresh and dry weight, area and thickness, LMA and LWC and 2) leaf chemical measurements: %N, %C, %P, C:N and d13C. Canopy level observations included top-of-canopy reflectance measurements obtained using a multispectral 16-band radiometer, leaf demography (tot. number and age distribution) and branch structural measurements (space between leaves, min. and max. season's growth and diameter) of two 1m branches harvested from each canopy level. Both leaf and canopy-level observations where collected monthly when trees where not in flush and weekly during the period of leaf flushing. Here, we present our leaf spectral and physiochemical results. Results show 1) changes in leaf spectral and physiochemical properties related to leaf age, 2) the most significant changes in the leaves' spectrum during different stages in their life cycle, and 3) how leaf spectral changes are related to changes in the chemical and physical properties of the leaves as they progress through their life cycle. Future work will involve the incorporation of leaf and canopy observations into a light canopy interaction model to investigate the possibility that seasonal variation in VIs may be driven by leaf aging as well as by the shedding or appearance of new leaves.

LCE: leaf carbon exchange data set for tropical, temperate, and boreal species of North and Central America.

PubMed

Smith, Nicholas G; Dukes, Jeffrey S

2017-11-01

Leaf canopy carbon exchange processes, such as photosynthesis and respiration, are substantial components of the global carbon cycle. Climate models base their simulations of photosynthesis and respiration on an empirical understanding of the underlying biochemical processes, and the responses of those processes to environmental drivers. As such, data spanning large spatial scales are needed to evaluate and parameterize these models. Here, we present data on four important biochemical parameters defining leaf carbon exchange processes from 626 individuals of 98 species at 12 North and Central American sites spanning ~53° of latitude. The four parameters are the maximum rate of Rubisco carboxylation (V cmax ), the maximum rate of electron transport for the regeneration of Ribulose-1,5,-bisphosphate (J max ), the maximum rate of phosphoenolpyruvate carboxylase carboxylation (V pmax ), and leaf dark respiration (R d ). The raw net photosynthesis by intercellular CO 2 (A/C i ) data used to calculate V cmax , J max , and V pmax rates are also presented. Data were gathered on the same leaf of each individual (one leaf per individual), allowing for the examination of each parameter relative to others. Additionally, the data set contains a number of covariates for the plants measured. Covariate data include (1) leaf-level traits (leaf mass, leaf area, leaf nitrogen and carbon content, predawn leaf water potential), (2) plant-level traits (plant height for herbaceous individuals and diameter at breast height for trees), (3) soil moisture at the time of measurement, (4) air temperature from nearby weather stations for the day of measurement and each of the 90 d prior to measurement, and (5) climate data (growing season mean temperature, precipitation, photosynthetically active radiation, vapor pressure deficit, and aridity index). We hope that the data will be useful for obtaining greater understanding of the abiotic and biotic determinants of these important biochemical parameters and for evaluating and improving large-scale models of leaf carbon exchange. © 2017 by the Ecological Society of America.

Spectroscopic determination of leaf traits using infrared spectra

NASA Astrophysics Data System (ADS)

Buitrago, Maria F.; Groen, Thomas A.; Hecker, Christoph A.; Skidmore, Andrew K.

2018-07-01

Leaf traits characterise and differentiate single species but can also be used for monitoring vegetation structure and function. Conventional methods to measure leaf traits, especially at the molecular level (e.g. water, lignin and cellulose content), are expensive and time-consuming. Spectroscopic methods to estimate leaf traits can provide an alternative approach. In this study, we investigated high spectral resolution (6612 bands) emissivity measurements from the short to the long wave infrared (1.4-16.0 μm) of leaves from 19 different plant species ranging from herbaceous to woody, and from temperate to tropical types. At the same time, we measured 14 leaf traits to characterise a leaf, including chemical (e.g., leaf water content, nitrogen, cellulose) and physical features (e.g., leaf area and leaf thickness). We fitted partial least squares regression (PLSR) models across the SWIR, MWIR and LWIR for each leaf trait. Then, reduced models (PLSRred) were derived by iteratively reducing the number of bands in the model (using a modified Jackknife resampling method with a Martens and Martens uncertainty test) down to a few bands (4-10 bands) that contribute the most to the variation of the trait. Most leaf traits could be determined from infrared data with a moderate accuracy (65 < Rcv2 < 77% for observed versus predicted plots) based on PLSRred models, while the accuracy using the whole infrared range (6612 bands) presented higher accuracies, 74 < Rcv2 < 90%. Using the full SWIR range (1.4-2.5 μm) shows similarly high accuracies compared to the whole infrared. Leaf thickness, leaf water content, cellulose, lignin and stomata density are the traits that could be estimated most accurately from infrared data (with Rcv2 above 0.80 for the full range models). Leaf thickness, cellulose and lignin were predicted with reasonable accuracy from a combination of single infrared bands. Nevertheless, for all leaf traits, a combination of a few bands yields moderate to accurate estimations.

Leaf hydraulic conductance declines in coordination with photosynthesis, transpiration and leaf water status as soybean leaves age regardless of soil moisture

PubMed Central

Locke, Anna M.; Ort, Donald R.

2014-01-01

Photosynthesis requires sufficient water transport through leaves for stomata to remain open as water transpires from the leaf, allowing CO2 to diffuse into the leaf. The leaf water needs of soybean change over time because of large microenvironment changes over their lifespan, as leaves mature in full sun at the top of the canopy and then become progressively shaded by younger leaves developing above. Leaf hydraulic conductance (K leaf), a measure of the leaf’s water transport capacity, can often be linked to changes in microenvironment and transpiration demand. In this study, we tested the hypothesis that K leaf would decline in coordination with transpiration demand as soybean leaves matured and aged. Photosynthesis (A), stomatal conductance (g s) and leaf water potential (Ψleaf) were also measured at various leaf ages with both field- and chamber-grown soybeans to assess transpiration demand. K leaf was found to decrease as soybean leaves aged from maturity to shading to senescence, and this decrease was strongly correlated with midday A. Decreases in K leaf were further correlated with decreases in g s, although the relationship was not as strong as that with A. Separate experiments investigating the response of K leaf to drought demonstrated no acclimation of K leaf to drought conditions to protect against cavitation or loss of g s during drought and confirmed the effect of leaf age in K leaf observed in the field. These results suggest that the decline of leaf hydraulic conductance as leaves age keeps hydraulic supply in balance with demand without K leaf becoming limiting to transpiration water flux. PMID:25281701

Temporal relationships between spectral response and agronomic variables of a corn canopy

NASA Technical Reports Server (NTRS)

Kimes, D. S.; Markham, B. L.; Tucker, C. J.; Mcmurtrey, J. E., III

1981-01-01

Attention is given to an experiment in which spectral radiance data collected in three spectral regions are related to corn canopy variables. The study extends the work of Tucker et al. (1979) in that more detailed measurements of corn canopy variables were made using quantitative techniques. Wet and dry green leaf biomass is considered along with the green leaf area index, chlorotic leaf biomass, chlorotic leaf area, and leaf water content. In addition, spectral data were collected with a hand-held radiometer having Landsat-D Thematic Mapper (TM) bands TM3 (0.63-0.69 micrometers), TM4 (0.76-0.90 micrometers), and TM5 (1.55-1.75 micrometers). TM3, TM4, and TM5 seem to be well situated spectrally for making remotely sensed measurements related to chlorophyll concentration, leaf density, and leaf water content.

A novel method for quantification of beam's-eye-view tumor tracking performance.

PubMed

Hu, Yue-Houng; Myronakis, Marios; Rottmann, Joerg; Wang, Adam; Morf, Daniel; Shedlock, Daniel; Baturin, Paul; Star-Lack, Josh; Berbeco, Ross

2017-11-01

In-treatment imaging using an electronic portal imaging device (EPID) can be used to confirm patient and tumor positioning. Real-time tumor tracking performance using current digital megavolt (MV) imagers is hindered by poor image quality. Novel EPID designs may help to improve quantum noise response, while also preserving the high spatial resolution of the current clinical detector. Recently investigated EPID design improvements include but are not limited to multi-layer imager (MLI) architecture, thick crystalline and amorphous scintillators, and phosphor pixilation and focusing. The goal of the present study was to provide a method of quantitating improvement in tracking performance as well as to reveal the physical underpinnings of detector design that impact tracking quality. The study employs a generalizable ideal observer methodology for the quantification of tumor tracking performance. The analysis is applied to study both the effect of increasing scintillator thickness on a standard, single-layer imager (SLI) design as well as the effect of MLI architecture on tracking performance. The present study uses the ideal observer signal-to-noise ratio (d') as a surrogate for tracking performance. We employ functions which model clinically relevant tasks and generalized frequency-domain imaging metrics to connect image quality with tumor tracking. A detection task for relevant Cartesian shapes (i.e., spheres and cylinders) was used to quantitate trackability of cases employing fiducial markers. Automated lung tumor tracking algorithms often leverage the differences in benign and malignant lung tissue textures. These types of algorithms (e.g., soft-tissue localization - STiL) were simulated by designing a discrimination task, which quantifies the differentiation of tissue textures, measured experimentally and fit as a power-law in trend (with exponent β) using a cohort of MV images of patient lungs. The modeled MTF and NPS were used to investigate the effect of scintillator thickness and MLI architecture on tumor tracking performance. Quantification of MV images of lung tissue as an inverse power-law with respect to frequency yields exponent values of β = 3.11 and 3.29 for benign and malignant tissues, respectively. Tracking performance with and without fiducials was found to be generally limited by quantum noise, a factor dominated by quantum detective efficiency (QDE). For generic SLI construction, increasing the scintillator thickness (gadolinium oxysulfide - GOS) from a standard 290 μm to 1720 μm reduces noise to about 10%. However, 81% of this reduction is appreciated between 290 and 1000 μm. In comparing MLI and SLI detectors of equivalent individual GOS layer thickness, the improvement in noise is equal to the number of layers in the detector (i.e., 4) with almost no difference in MTF. Further, improvement in tracking performance was slightly less than the square-root of the reduction in noise, approximately 84-90%. In comparing an MLI detector with an SLI with a GOS scintillator of equivalent total thickness, improvement in object detectability is approximately 34-39%. We have presented a novel method for quantification of tumor tracking quality and have applied this model to evaluate the performance of SLI and MLI EPID designs. We showed that improved tracking quality is primarily limited by improvements in NPS. When compared to very thick scintillator SLI, employing MLI architecture exhibits the same gains in QDE, but by mitigating the effect of optical Swank noise, results in more dramatic improvements in tracking performance. © 2017 American Association of Physicists in Medicine.

In situ field measurement of leaf water potential using thermocouple psychrometers.

PubMed

Savage, M J; Wiebe, H H; Cass, A

1983-11-01

Thermocouple psychrometers are the only instruments which can measure the in situ water potential of intact leaves, and which can possibly be used to monitor leaf water potential. Unfortunately, their usefulness is limited by a number of difficulties, among them fluctuating temperatures and temperature gradients within the psychrometer, sealing of the psychrometer chamber to the leaf, shading of the leaf by the psychrometer, and resistance to water vapor diffusion by the cuticle when the stomates are closed. Using Citrus jambhiri, we have tested several psychrometer design and operational modifications and showed that in situ psychrometric measurements compared favorably with simultaneous Scholander pressure chamber measurements on neighboring leaves when the latter were corrected for the osmotic potential.

Development and implementation of an EPID‐based method for localizing isocenter

PubMed Central

Hyer, Daniel E.; Nixon, Earl

2012-01-01

The aim of this study was to develop a phantom and analysis software that could be used to quickly and accurately determine the location of radiation isocenter to an accuracy of less than 1 mm using the EPID (Electronic Portal Imaging Device). The proposed solution uses a collimator setting of 10×10cm2 to acquire EPID images of a new phantom constructed from LEGO blocks. Images from a number of gantry and collimator angles are analyzed by automated analysis software to determine the position of the jaws and center of the phantom in each image. The distance between a chosen jaw and the phantom center is then compared to the same distance measured after a 180° collimator rotation to determine if the phantom is centered in the dimension being investigated. Repeated tests show that the system is reproducibly independent of the imaging session, and calculated offsets of the phantom from radiation isocenter are a function of phantom setup only. Accuracy of the algorithm's calculated offsets were verified by imaging the LEGO phantom before and after applying the calculated offset. These measurements show that the offsets are predicted with an accuracy of approximately 0.3 mm, which is on the order of the detector's pitch. Comparison with a star‐shot analysis yielded agreement of isocenter location within 0.5 mm. Additionally, the phantom and software are completely independent of linac vendor, and this study presents results from two linac manufacturers. A Varian Optical Guidance Platform (OGP) calibration array was also integrated into the phantom to allow calibration of the OGP while the phantom is positioned at radiation isocenter to reduce setup uncertainty in the calibration. This solution offers a quick, objective method to perform isocenter localization as well as laser alignment and OGP calibration on a monthly basis. PACS number: 87.55.Qr PMID:23149787

Does leaf chemistry differentially affect breakdown in tropical versus temperate streams? Importance of standardized analytical techniques to measure leaf chemistry

Treesearch

Marcelo Ardon; Catherine M. Pringle; Susan L. Eggert

2009-01-01

Comparisons of the effects of leaf litter chemistry on leaf breakdown rates in tropical vs temperate streams are hindered by incompatibility among studies and across sites of analytical methods used to...

Phylogenetics and diversification of Cotyledon (Crassulaceae) inferred from nuclear and chloroplast DNA sequence data.

PubMed

Mort, Mark E; Levsen, Nicholas; Randle, Christopher P; Van Jaarsveld, Ernst; Palmer, Annie

2005-07-01

Crassulaceae includes approximately 35 genera and 1500 species of leaf and stem succulent flowering plants. The family is nearly cosmopolitan in distribution, but is particularly diverse in southern Africa, where five genera comprising approximately 325 species are found. One of these genera, Cotyledon, includes 10 species that are largely confined to South Africa, where they are commonly found on rocky hillsides, coastal flats, and cliff faces. Species of Cotyledon are characterized by five-parted, pendulous, sympetalous flowers, but the genus is highly diverse in growth form, flower color and size, and leaf morphology. One particularly variable species, C. orbiculata, has been divided into five varieties based on leaf morphology and biogeography; however, the monophyly of this species as well as the relationships among the varieties have not previously been investigated. Parsimony analyses of a combined data set of DNA sequences from chloroplast and nuclear genome provided the first estimate of phylogeny for Cotyledon, and resulted in two minimum-length trees and a fully resolved phylogeny for the genus. Results indicate that C. orbiculata is not monophyletic and suggest the need for additional studies and a revised classification within the genus.

De novo assembly and analysis of the Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis.

PubMed

Liu, Miaomiao; Zhu, Jinhang; Wu, Shengbing; Wang, Chenkai; Guo, Xingyi; Wu, Jiawen; Zhou, Meiqi

2018-04-11

Artemisia argyi Lev. et Vant. (A. argyi) is widely utilized for moxibustion in Chinese medicine, and the mechanism underlying terpenoid biosynthesis in its leaves is suggested to play an important role in its medicinal use. However, the A. argyi transcriptome has not been sequenced. Herein, we performed RNA sequencing for A. argyi leaf, root and stem tissues to identify as many as possible of the transcribed genes. In total, 99,807 unigenes were assembled by analysing the expression profiles generated from the three tissue types, and 67,446 of those unigenes were annotated in public databases. We further performed differential gene expression analysis to compare leaf tissue with the other two tissue types and identified numerous genes that were specifically expressed or up-regulated in leaf tissue. Specifically, we identified multiple genes encoding significant enzymes or transcription factors related to terpenoid synthesis. This study serves as a valuable resource for transcriptome information, as many transcribed genes related to terpenoid biosynthesis were identified in the A. argyi transcriptome, providing a functional genomic basis for additional studies on molecular mechanisms underlying the medicinal use of A. argyi.

Chloroplast Response to Low Leaf Water Potentials

PubMed Central

Boyer, J. S.; Potter, J. R.

1973-01-01

The effect of decreases in turgor on chloroplast activity was studied by measuring the photochemical activity of intact sunflower (Helianthus annuus L. cv. Russian Mammoth) leaves having low water potentials. Leaf turgor, calculated from leaf water potential and osmotic potential, was found to be affected by the dilution of cell contents by water in the cell walls, when osmotic potentials were measured with a thermocouple psychrometer. After the correction of measurements of leaf osmotic potential, both the thermocouple psychrometer and a pressure chamber indicated that turgor became zero in sunflower leaves at leaf water potentials of −10 bars. Since most of the loss in photochemical activity occurred at water potentials below −10 bars, it was concluded that turgor had little effect on the photochemical activity of the leaves. PMID:16658486

Chloroplast response to low leaf water potentials: I. Role of turgor.

PubMed

Boyer, J S; Potter, J R

1973-06-01

The effect of decreases in turgor on chloroplast activity was studied by measuring the photochemical activity of intact sunflower (Helianthus annuus L. cv. Russian Mammoth) leaves having low water potentials. Leaf turgor, calculated from leaf water potential and osmotic potential, was found to be affected by the dilution of cell contents by water in the cell walls, when osmotic potentials were measured with a thermocouple psychrometer. After the correction of measurements of leaf osmotic potential, both the thermocouple psychrometer and a pressure chamber indicated that turgor became zero in sunflower leaves at leaf water potentials of -10 bars. Since most of the loss in photochemical activity occurred at water potentials below -10 bars, it was concluded that turgor had little effect on the photochemical activity of the leaves.

Costs of measuring leaf area index of corn

NASA Technical Reports Server (NTRS)

Daughtry, C. S. T.; Hollinger, S. E.

1984-01-01

The magnitude of plant-to-plant variability of leaf area of corn plants selected from uniform plots was examined and four representative methods for measuring leaf area index (LAI) were evaluated. The number of plants required and the relative costs for each sampling method were calculated to detect 10, 20, and 50% differences in LAI using 0.05 and 0.01 tests of significance and a 90% probability of success (beta = 0.1). The natural variability of leaf area per corn plant was nearly 10%. Additional variability or experimental error may be introduced by the measurement technique employed and by nonuniformity within the plot. Direct measurement of leaf area with an electronic area meter had the lowest CV, required that the fewest plants be sampled, but required approximately the same amount of time as the leaf area/weight ratio method to detect comparable differences. Indirect methods based on measurements of length and width of leaves required more plants but less total time than the direct method. Unless the coefficients for converting length and width to area are verified frequently, the indirect methods may be biased. When true differences in LAI among treatments exceed 50% of mean, all four methods are equal. The method of choice depends on the resources available, the differences to be detected, and what additional information, such as leaf weight or stalk weight, is also desired.

Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea).

PubMed

Green, Jonathan P; Foster, Rosie; Wilkins, Lucas; Osorio, Daniel; Hartley, Susan E

2015-01-01

Leaf colour has been proposed to signal levels of host defence to insect herbivores, but we lack data on herbivory, leaf colour and levels of defence for wild host populations necessary to test this hypothesis. Such a test requires measurements of leaf spectra as they would be sensed by herbivore visual systems, as well as simultaneous measurements of chemical defences and herbivore responses to leaf colour in natural host-herbivore populations. In a large-scale field survey of wild cabbage (Brassica oleracea) populations, we show that variation in leaf colour and brightness, measured according to herbivore spectral sensitivities, predicts both levels of chemical defences (glucosinolates) and abundance of specialist lepidopteran (Pieris rapae) and hemipteran (Brevicoryne brassicae) herbivores. In subsequent experiments, P. rapae larvae achieved faster growth and greater pupal mass when feeding on plants with bluer leaves, which contained lower levels of aliphatic glucosinolates. Glucosinolate-mediated effects on larval performance may thus contribute to the association between P. rapae herbivory and leaf colour observed in the field. However, preference tests found no evidence that adult butterflies selected host plants based on leaf coloration. In the field, B. brassicae abundance varied with leaf brightness but greenhouse experiments were unable to identify any effects of brightness on aphid preference or performance. Our findings suggest that although leaf colour reflects both levels of host defences and herbivore abundance in the field, the ability of herbivores to respond to colour signals may be limited, even in species where performance is correlated with leaf colour.

Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea)

PubMed Central

Wilkins, Lucas; Osorio, Daniel; Hartley, Susan E.

2015-01-01

Leaf colour has been proposed to signal levels of host defence to insect herbivores, but we lack data on herbivory, leaf colour and levels of defence for wild host populations necessary to test this hypothesis. Such a test requires measurements of leaf spectra as they would be sensed by herbivore visual systems, as well as simultaneous measurements of chemical defences and herbivore responses to leaf colour in natural host-herbivore populations. In a large-scale field survey of wild cabbage (Brassica oleracea) populations, we show that variation in leaf colour and brightness, measured according to herbivore spectral sensitivities, predicts both levels of chemical defences (glucosinolates) and abundance of specialist lepidopteran (Pieris rapae) and hemipteran (Brevicoryne brassicae) herbivores. In subsequent experiments, P. rapae larvae achieved faster growth and greater pupal mass when feeding on plants with bluer leaves, which contained lower levels of aliphatic glucosinolates. Glucosinolate-mediated effects on larval performance may thus contribute to the association between P. rapae herbivory and leaf colour observed in the field. However, preference tests found no evidence that adult butterflies selected host plants based on leaf coloration. In the field, B. brassicae abundance varied with leaf brightness but greenhouse experiments were unable to identify any effects of brightness on aphid preference or performance. Our findings suggest that although leaf colour reflects both levels of host defences and herbivore abundance in the field, the ability of herbivores to respond to colour signals may be limited, even in species where performance is correlated with leaf colour. PMID:26353086

Leaf angle, tree species, and the functioning of broadleaf deciduous forest ecosystems

NASA Astrophysics Data System (ADS)

McNeil, B. E.; Brzostek, E. R.; Fahey, R. T.; King, C. J.; Flamenco, E. A.; Rescorl, S.; Erazo, D.; Heimerl, T.

2016-12-01

The effects of temperate forests on the global cycles of carbon, water, and energy depends strongly on how individual tree species adjust to the novel environmental conditions of the Anthropocene. Here, we seek to identify and understand ecological variability in one important component of tree canopies, the inclination angles of leaves. Leaf angle has important effects on forest albedo, photosynthesis, and evapotranspiration, but there is relatively little data to constrain the many models that include (or perhaps should include) this essential aspect of canopy architecture. We employ a relatively new technique for using an electronic protractor to measure leaf angles from leveled digital photographs. From a suite of observation platforms (e.g. UAVs, eddy flux towers, old fire towers) in Connecticut, Indiana, Maryland, Michigan, Pennsylvania, and West Virginia, USA, we have measured leaf angles periodically throughout the 2014, 2015, and 2016 growing seasons. Based on over 25,000 measurements taken from 15 tree species, we find highly significant differences in mean leaf angle by canopy position, tree species, location, and observation date. In addition to replicating findings where upper-canopy sun leaves are more vertical than lower-canopy shade leaves, our analysis on sun leaves also finds other ecologically meaningful differences. For instance, we find that the mesic, shade tolerant sugar maple had significantly more horizontal leaf angles than drought-resistant species such as white oak. Species also appear to have unique patterns of leaf angle phenology, with most species tending toward more vertical leaf angles during droughty conditions later in the year. We discuss these empirical results in light of an emerging theoretical framework that positions leaf angle as a functional trait. Like leaf traits such as %N or SLA, we suggest that leaf angle is an essential part of the adaptive resource strategy of each tree species. Finally, by linking our leaf angle data to new observations of spatial and temporal variations in near infrared reflectance measured from UAV, airborne, and satellite sensors, we highlight how species-specific patterns of leaf angle phenology could provide a new mechanism to better constrain model predictions of energy, water, and carbon fluxes from temperate forests.

Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts

PubMed Central

De Fine Licht, Henrik H.; Schiøtt, Morten; Rogowska-Wrzesinska, Adelina; Nygaard, Sanne; Roepstorff, Peter; Boomsma, Jacobus J.

2013-01-01

Leaf-cutting ants combine large-scale herbivory with fungus farming to sustain advanced societies. Their stratified colonies are major evolutionary achievements and serious agricultural pests, but the crucial adaptations that allowed this mutualism to become the prime herbivorous component of neotropical ecosystems has remained elusive. Here we show how coevolutionary adaptation of a specific enzyme in the fungal symbiont has helped leaf-cutting ants overcome plant defensive phenolic compounds. We identify nine putative laccase-coding genes in the fungal genome of Leucocoprinus gongylophorus cultivated by the leaf-cutting ant Acromyrmex echinatior. One of these laccases (LgLcc1) is highly expressed in the specialized hyphal tips (gongylidia) that the ants preferentially eat, and we confirm that these ingested laccase molecules pass through the ant guts and remain active when defecated on the leaf pulp that the ants add to their gardens. This accurate deposition ensures that laccase activity is highest where new leaf material enters the fungus garden, but where fungal mycelium is too sparse to produce extracellular enzymes in sufficient quantities to detoxify phenolic compounds. Phylogenetic analysis of LgLcc1 ortholog sequences from symbiotic and free-living fungi revealed significant positive selection in the ancestral lineage that gave rise to the gongylidia-producing symbionts of leaf-cutting ants and their non–leaf-cutting ant sister group. Our results are consistent with fungal preadaptation and subsequent modification of a particular laccase enzyme for the detoxification of secondary plant compounds during the transition to active herbivory in the ancestor of leaf-cutting ants between 8 and 12 Mya. PMID:23267060

Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts.

PubMed

De Fine Licht, Henrik H; Schiøtt, Morten; Rogowska-Wrzesinska, Adelina; Nygaard, Sanne; Roepstorff, Peter; Boomsma, Jacobus J

2013-01-08

Leaf-cutting ants combine large-scale herbivory with fungus farming to sustain advanced societies. Their stratified colonies are major evolutionary achievements and serious agricultural pests, but the crucial adaptations that allowed this mutualism to become the prime herbivorous component of neotropical ecosystems has remained elusive. Here we show how coevolutionary adaptation of a specific enzyme in the fungal symbiont has helped leaf-cutting ants overcome plant defensive phenolic compounds. We identify nine putative laccase-coding genes in the fungal genome of Leucocoprinus gongylophorus cultivated by the leaf-cutting ant Acromyrmex echinatior. One of these laccases (LgLcc1) is highly expressed in the specialized hyphal tips (gongylidia) that the ants preferentially eat, and we confirm that these ingested laccase molecules pass through the ant guts and remain active when defecated on the leaf pulp that the ants add to their gardens. This accurate deposition ensures that laccase activity is highest where new leaf material enters the fungus garden, but where fungal mycelium is too sparse to produce extracellular enzymes in sufficient quantities to detoxify phenolic compounds. Phylogenetic analysis of LgLcc1 ortholog sequences from symbiotic and free-living fungi revealed significant positive selection in the ancestral lineage that gave rise to the gongylidia-producing symbionts of leaf-cutting ants and their non-leaf-cutting ant sister group. Our results are consistent with fungal preadaptation and subsequent modification of a particular laccase enzyme for the detoxification of secondary plant compounds during the transition to active herbivory in the ancestor of leaf-cutting ants between 8 and 12 Mya.

Carrot yellow leaf virus is associated with carrot internal necrosis.

PubMed

Adams, Ian P; Skelton, Anna; Macarthur, Roy; Hodges, Tobias; Hinds, Howard; Flint, Laura; Nath, Palash Deb; Boonham, Neil; Fox, Adrian

2014-01-01

Internal necrosis of carrot has been observed in UK carrots for at least 10 years, and has been anecdotally linked to virus infection. In the 2009 growing season some growers had up to 10% of yield with these symptoms. Traditional diagnostic methods are targeted towards specific pathogens. By using a metagenomic approach with high throughput sequencing technology, other, as yet unidentified causes of root necrosis were investigated. Additionally a statistical analysis has shown which viruses are most closely associated with disease symptoms. Carrot samples were collected from a crop exhibiting root necrosis (102 Affected: 99 Unaffected) and tested for the presence of the established carrot viruses: Carrot red leaf virus (CtRLV), Carrot mottle virus (CMoV), Carrot red leaf associated viral RNA (CtRLVaRNA) and Parsnip yellow fleck virus (PYFV). The presence of these viruses was not associated with symptomatic carrot roots either as single viruses or in combinations. A sub-sample of carrots of mixed symptom status was subjected to MiSeq sequencing. The results from these tests suggested Carrot yellow leaf virus (CYLV) was associated with symptomatic roots. Additionally a novel Torradovirus, a novel Closterovirus and two novel Betaflexiviradae related plant viruses were detected. A specific diagnostic test was designed for CYLV. Of the 102 affected carrots, 98% were positive for CYLV compared to 22% of the unaffected carrots. From these data we conclude that although we have yet to practically demonstrate a causal link, CYLV appears to be strongly associated with the presence of necrosis of carrots.

Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules

PubMed Central

Marino, John A.; Perfecto, Ivette; Vandermeer, John

2015-01-01

The interaction of crop pests with their natural enemies is a fundament to their control. Natural enemies of fungal pathogens of crops are poorly known relative to those of insect pests, despite the diversity of fungal pathogens and their economic importance. Currently, many regions across Latin America are experiencing unprecedented epidemics of coffee rust (Hemileia vastatrix). Identification of natural enemies of coffee rust could aid in developing management strategies or in pinpointing species that could be used for biocontrol. In the present study, we characterized fungal communities associated with coffee rust lesions by single-molecule DNA sequencing of fungal rRNA gene bar codes from leaf discs (≈28 mm2) containing rust lesions and control discs with no rust lesions. The leaf disc communities were hyperdiverse in terms of fungi, with up to 69 operational taxonomic units (putative species) per control disc, and the diversity was only slightly reduced in rust-infected discs, with up to 63 putative species. However, geography had a greater influence on the fungal community than whether the disc was infected by coffee rust. Through comparisons between control and rust-infected leaf discs, as well as taxonomic criteria, we identified 15 putative mycoparasitic fungi. These fungi are concentrated in the fungal family Cordycipitaceae and the order Tremellales. These data emphasize the complexity of diverse fungi of unknown ecological function within a leaf that might influence plant disease epidemics or lead to the development of species for biocontrol of fungal disease. PMID:26567299

Galactinol synthase from kidney bean cotyledon and zucchini leaf. Purification and N-terminal sequences.

PubMed Central

Liu, J J; Odegard, W; de Lumen, B O

1995-01-01

Galactinol synthase (GS) was purified 1591-fold with a 3.9% recovery from the cotyledon of kidney bean (Phaseolus vulgaris) by a novel scheme consisting of ammonium sulfate fractionation followed by diethylaminoethyl, Affi-Gel Blue, and UDP-hexanolamine affinity chromatography. The purified enzyme had a specific activity of 8.75 mumol mg-1 min-1, a pH optimum of 7.0, and requirements for manganese ion and DTT. The enzyme exhibited a Km = 0.4 mM for UDP-galactose and a Km = 4.5 mM for myo-inositol. It was identified as a 38-kD peptide that co-purified with a 41- and a 43-kD peptide as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Purification to homogeneity was achieved by isolating the 38-kD peptide from the SDS-PAGE gel. To clarify conflicting reports in the literature about the relative molecular mass of purified GS from zucchini leaf (Cucurbita pepo), a similar scheme with modified eluting conditions was used to purify GS from this source. Zucchini leaf GS was purified to homogeneity and identified as a 36-kD peptide on SDS-PAGE. Partial N-terminal sequences of the 38-kD peptide from kidney bean cotyledon and the 36-kD peptide from zucchini leaf were obtained. To facilitate identification of GS during the purification, an assay utilizing thin-layer chromatography and an isotopic analytic imaging scanner was developed. PMID:7480343

New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

PubMed Central

Poulin, L.; Grygiel, P.; Magne, M.; Rodriguez-R, L. M.; Forero Serna, N.; Zhao, S.; El Rafii, M.; Dao, S.; Tekete, C.; Wonni, I.; Koita, O.; Pruvost, O.; Verdier, V.; Vernière, C.

2014-01-01

Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales. PMID:25398857

Analysis of the kinestatic charge detection system as a high detective quantum efficiency electronic portal imaging device.

PubMed

Samant, Sanjiv S; Gopal, Arun

2006-09-01

Megavoltage x-ray imaging suffers from reduced image quality due to low differential x-ray attenuation and large Compton scatter compared with kilovoltage imaging. Notwithstanding this, electronic portal imaging devices (EPIDs) are now widely used in portal verification in radiotherapy as they offer significant advantages over film, including immediate digital imaging and superior contrast range. However video-camera-based EPIDs (VEPIDs) are limited by problems of low light collection efficiency and significant light scatter, leading to reduced contrast and spatial resolution. Indirect and direct detection-based flat-panel EPIDs have been developed to overcome these limitations. While flat-panel image quality has been reported to exceed that achieved with portal film, these systems have detective quantum efficiency (DQE) limited by the thin detection medium and are sensitive to radiation damage to peripheral read-out electronics. An alternative technology for high-quality portal imaging is presented here: kinesatic charge detection (KCD). The KCD is a scanning tri-electrode ion-chamber containing high-pressure noble gas (xenon at 100 atm) used in conjunction with a strip-collimated photon beam. The chamber is scanned across the patient, and an external electric field is used to regulate the cation drift velocity. By matching the scanning velocity with that of the cation (i.e., ion) drift velocity, the cations remain static in the object frame of reference, allowing temporal integration of the signal. The KCD offers several advantages as a portal imaging system. It has a thick detector geometry with an active detection depth of 6.1 cm, compared to the sub-millimeter thickness of the phosphor layer in conventional phosphor screens, leading to an order of magnitude advantage in quantum efficiency (>0.3). The unique principle of and the use of the scanning strip-collimated x-ray beam provide further integration of charges in time, reduced scatter, and a significantly reduced imaging dose, enhancing the imaging signal-to-noise ratio (SNR) and leading to high DQE. While thick detectors usually suffer from reduced spatial resolution, the KCD provides good spatial resolution due to high gas pressure that limits the spread of scattered electrons, and a strip-collimated beam that significantly reduces the inclusion of scatter in the imaging signal. A 10 cm wide small-field-of-view (SFOV) prototype of the KCD is presented with a complete analysis of its imaging performance. Measurements of modulation transfer function (MTF), noise power spectrum (NPS), and DQE were in good agreement with Monte Carlo simulations. Imaging signal loss from recombination within the KCD chamber was measured at different gas pressures, ion drift velocities, and strip-collimation widths. Image quality for the prototype KCD was also observed with anthropomorphic phantom imaging in comparison with various commercial and research portal imaging systems, including VEPID, flat-panel imager, and conventional and high contrast film systems. KCD-based imaging provided very good contrast and good spatial resolution at very low imaging dose (0.1 cGy per image). For the prototype KCD, measurements yielded DQE(0)=0.19 and DQE(1 cy/mm)=0.004.

Diurnal leaf gas exchange survey, Feb2016-May2016, PA-SLZ, PA-PNM: Panama

DOE Data Explorer

Rogers, Alistair [Brookhaven National Lab; Serbin, Shawn [Brookhaven National Lab; Ely, Kim [Brookhaven National Lab; Wu, Jin [BNL; Wolfe, Brett [Smithsonian; Dickman, Turin [Los Alamos National Lab; Collins, Adam [Los Alamos National Lab; Detto, Matteo [Princeton; Grossiord, Charlotte [Los Alamos National Lab; McDowell, Nate [Los Alamos National Lab; Michaletz, Sean

2017-01-01

Diurnal leaf gas exchange survey measured on sunlit canopy trees on a monthly basis from Feb to May 2016 at SLZ and PNM. This data was collected as part of the 2016 ENSO campaign. See related datasets (existing and future) for further sample details, leaf water potential, LMA, leaf spectra, other gas exchange and leaf chemistry.

Leaf mass area, Feb2016-May2016, PA-SLZ, PA-PNM, PA-BCI: Panama

DOE Data Explorer

Ely, Kim [Brookhaven National Lab; Rogers, Alistair [Brookhaven National Lab; Serbin, Shawn [Brookhaven National Lab; Wu, Jin [BNL; Wolfe, Brett [Smithsonian; Dickman, Turin [Los Alamos National Lab; Collins, Adam [Los Alamos National Lab; Detto, Matteo [Princeton; Grossiord, Charlotte [Los Alamos National Lab; McDowell, Nate [Los Alamos National Lab; Michaletz, Sean

2017-01-01

Leaf mass per unit area measured on a monthly basis from Feb to April 2016 at SLZ and PNM. Data from BCI only available for March. This data was collected as part of the 2016 ENSO campaign. See related datasets (existing and future) for further sample details, leaf water potential, leaf spectra, gas exchange and leaf chemistry.

Diffuse and specular characteristics of leaf reflectance

NASA Technical Reports Server (NTRS)

Grant, Lois

1987-01-01

In this paper, the evolution of current understanding of the mechanisms of leaf reflectance is reviewed. The use of measurements of polarized reflectance to separate leaf reflectance into diffuse and specular components is discussed. A section on the factors influencing leaf reflectance - leaf structure and physiological disturbances - is included along with discussion on the manner in which these influences are manifested.

SU-E-T-01: 2-D Characterization of DLG Among All MLC Leaf Pairs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumaraswamy, L; Xu, Z; Podgorsak, M

Purpose: The aim of this study is to evaluate the variation of dosimetric leaf-gap (DLG) along the travel path of each MLC leaf pair. This study evaluates whether the spatial variations in DLG could cause dose differences between TPS-calculated and measured dose. Methods: The 6MV DLG values were measured for all leaf pairs in the direction of leaf motion using a 2-D diode array and 0.6cc ion chamber. These measurements were performed on two Varian Linacs, employing the Millennium 120-leaf MLC and a 2-D-DLG variation map was created via in-house software. Several test plans were created with sweeping MLC fieldsmore » using constant gaps from 2mm to 10mm and corrected for 2-D variation utilizing in-house software. Measurements were performed utilizing the MapCHECK at 5.0cm depth for plans with and without the 2-D DLG correction and compared to the TPS calculated dose via gamma analysis (3%/3mm). Results: The measured DLGs for the middle 40 MLC leaf pairs (0.5cm width) were very similar along the central superior-inferior axis, with maximum variation of 0.2mm. The outer 20 MLC leaf pairs (1.0cm width) have DLG values from 0.32mm (mean) to 0.65mm (maximum) lower than the central leaf-pair, depending on off-axis distance. Gamma pass rates for the 2mm, 4mm, and 6mm sweep plans increased by 23.2%, 28.7%, and 26.0% respectively using the 2-D-DLG correction. The most improved dose points occur in areas modulated by the 1.0cm leaf-pairs. The gamma pass rate for the 10mm sweep plan increased by only 7.7%, indicating that the 2D variation becomes less significant for dynamic plans with larger MLC gaps. Conclusion: Fluences residing significantly off-axis with narrow sweeping gaps may exhibit significant variations from planned dose due to large differences between the true DLG exhibited by the 1.0cm leaf-pairs versus the constant DLG value utilized by the TPS for dose calculation.« less

Expression patterns of TEL genes in Poaceae suggest a conserved association with cell differentiation.

PubMed

Paquet, Nicolas; Bernadet, Marie; Morin, Halima; Traas, Jan; Dron, Michel; Charon, Celine

2005-06-01

Poaceae species present a conserved distichous phyllotaxy (leaf position along the stem) and share common properties with respect to leaf initiation. The goal of this work was to determine if these common traits imply common genes. Therefore, homologues of the maize TERMINAL EAR1 gene in Poaceae were studied. This gene encodes an RNA-binding motif (RRM) protein, that is suggested to regulate leaf initiation. Using degenerate primers, one unique tel (terminal ear1-like) gene from seven Poaceae members, covering almost all the phylogenetic tree of the family, was identified by PCR. These genes present a very high degree of similarity, a much conserved exon-intron structure, and the three RRMs and TEL characteristic motifs. The evolution of tel sequences in Poaceae strongly correlates with the known phylogenetic tree of this family. RT-PCR gene expression analyses show conserved tel expression in the shoot apex in all species, suggesting functional orthology between these genes. In addition, in situ hybridization experiments with specific antisense probes show tel transcript accumulation in all differentiating cells of the leaf, from the recruitment of leaf founder cells to leaf margins cells. Tel expression is not restricted to initiating leaves as it is also found in pro-vascular tissues, root meristems, and immature inflorescences. Therefore, these results suggest that TEL is not only associated with leaf initiation but more generally with cell differentiation in Poaceae.

The Use of RNA Sequencing and Correlation Network Analysis to Study Potential Regulators of Crabapple Leaf Color Transformation.

PubMed

Yang, Tuo; Li, Keting; Hao, Suxiao; Zhang, Jie; Song, Tingting; Tian, Ji; Yao, Yuncong

2018-05-01

Anthocyanins are plant pigments that contribute to the color of leaves, flowers and fruits, and that are beneficial to human health in the form of dietary antioxidants. The study of a transformable crabapple cultivar, 'India magic', which has red buds and green mature leaves, using mRNA profiling of four leaf developmental stages, allowed us to characterize molecular mechanisms regulating red color formation in early leaf development and the subsequent rapid down-regulation of anthocyanin biosynthesis. This analysis of differential gene expression during leaf development revealed that ethylene signaling-responsive genes are up-regulated during leaf pigmentation. Genes in the ethylene response factor (ERF), SPL, NAC, WRKY and MADS-box transcription factor (TF) families were identified in two weighted gene co-expression network analysis (WGCNA) modules as having a close relationship to anthocyanin accumulation. Analyses of network hub genes indicated that SPL TFs are located in central positions within anthocyanin-related modules. Furthermore, cis-motif and yeast one-hybrid assays suggested that several anthocyanin biosynthetic or regulatory genes are potential targets of SPL8 and SPL13B. Transient silencing of these two genes confirmed that they play a role in co-ordinating anthocyanin biosynthesis and crabapple leaf development. We present a high-resolution method for identifying regulatory modules associated with leaf pigmentation, which provides a platform for functional genomic studies of anthocyanin biosynthesis.

[Physico-chemical characteristics of ambient particles settling upon leaf surface of six conifers in Beijing].

PubMed

Wang, Lei; Hasi, Eerdun; Liu, Lian-You; Gao, Shang-Yu

2007-03-01

The study on the density of ambient particles settling upon the leaf surface of six conifers in Beijing, the micro-configurations of the leaf surface, and the mineral and element compositions of the particles showed that at the same sites and for the same tree species, the density of the particles settling upon leaf surface increased with increasing ambient pollution, but for various tree species, it differed significantly, with the sequence of Sabina chinensis and Platycladus orientalis > Cedrus deodara and Pinus bungeana > P. tabulaeformis and Picea koraiensis. Due to the effects of road dust, low height leaf had a larger density of particles. The density of the particles was smaller in summer than in winter because of the rainfall and new leaf growth. The larger the roughness of leaf surface, the larger density of the particles was. In the particles, the overall content of SiO2, CaCO3, CaMg(CO3,), NaCl, 2CaSO4 . H2O, CaSO4 . 2H2O and Fe2O3 was about 10%-30%, and the main minerals were montmorillonite, illite, kaolinite and feldspar. The total content of 21 test elements in the particles reached 16%-37%, among which, Ca, Al, Fe, Mg, K, Na and S occupied 97% or more, while the others were very few and less affected by sampling sites and tree species.

A flexible Monte Carlo tool for patient or phantom specific calculations: comparison with preliminary validation measurements

NASA Astrophysics Data System (ADS)

Davidson, S.; Cui, J.; Followill, D.; Ibbott, G.; Deasy, J.

2008-02-01

The Dose Planning Method (DPM) is one of several 'fast' Monte Carlo (MC) computer codes designed to produce an accurate dose calculation for advanced clinical applications. We have developed a flexible machine modeling process and validation tests for open-field and IMRT calculations. To complement the DPM code, a practical and versatile source model has been developed, whose parameters are derived from a standard set of planning system commissioning measurements. The primary photon spectrum and the spectrum resulting from the flattening filter are modeled by a Fatigue function, cut-off by a multiplying Fermi function, which effectively regularizes the difficult energy spectrum determination process. Commonly-used functions are applied to represent the off-axis softening, increasing primary fluence with increasing angle ('the horn effect'), and electron contamination. The patient dependent aspect of the MC dose calculation utilizes the multi-leaf collimator (MLC) leaf sequence file exported from the treatment planning system DICOM output, coupled with the source model, to derive the particle transport. This model has been commissioned for Varian 2100C 6 MV and 18 MV photon beams using percent depth dose, dose profiles, and output factors. A 3-D conformal plan and an IMRT plan delivered to an anthropomorphic thorax phantom were used to benchmark the model. The calculated results were compared to Pinnacle v7.6c results and measurements made using radiochromic film and thermoluminescent detectors (TLD).

Genome sequencing and transposon mutagenesis of Burkholderia seminalis TC3.4.2R3 identify genes contributing to suppression of orchid necrosis caused by B. gladioli

USDA-ARS?s Scientific Manuscript database

Thirty six strains of Burkholderia spp. isolated from sugarcane were evaluated for biological control of leaf and pseudobulb necrosis of orchid caused by B. gladioli. Twenty nine of the sugarcane strains suppressed the disease in greenhouse assays. We generated a draft genomic sequence of one suppr...

De Novo whole genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 from blueberry in Georgia, USA

USDA-ARS?s Scientific Manuscript database

This study reports a de novo assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp with a G+C content of 51.8% and 2,943 open reading frames (ORFs) and 48 RNA genes....

Measurement of surface physical properties and radiation balance for KUREX-91 study

NASA Technical Reports Server (NTRS)

Walter-Shea, Elizabeth A.; Blad, Blaine L.; Mesarch, Mark A.; Hays, Cynthia J.

1992-01-01

Biophysical properties and radiation balance components were measured at the Streletskaya Steppe Reserve of the Russian Republic in July 1991. Steppe vegetation parameters characterized include leaf area index (LAI), leaf angle distribution, mean tilt angle, canopy height, leaf spectral properties, leaf water potential, fraction of absorbed photosynthetically active radiation (APAR), and incoming and outgoing shortwave and longwave radiation. Research results, biophysical parameters, radiation balance estimates, and sun-view geometry effects on estimating APAR are discussed. Incoming and outgoing radiation streams are estimated using bidirectional spectral reflectances and bidirectional thermal emittances. Good agreement between measured and modeled estimates of the radiation balance were obtained.

Diversity and Evolution of Salt Tolerance in the Genus Vigna

PubMed Central

Iseki, Kohtaro; Takahashi, Yu; Muto, Chiaki; Naito, Ken; Tomooka, Norihiko

2016-01-01

Breeding salt tolerant plants is difficult without utilizing a diversity of wild crop relatives. Since the genus Vigna (family Fabaceae) is comprised of many wild relatives adapted to various environmental conditions, we evaluated the salt tolerance of 69 accessions of this genus, including that of wild and domesticated accessions originating from Asia, Africa, Oceania, and South America. We grew plants under 50 mM and 200 mM NaCl for two weeks and then measured the biomass, relative quantum yield of photosystem II, leaf Na+ concentrations, and leaf K+ concentrations. The accessions were clustered into four groups: the most tolerant, tolerant, moderately susceptible, and susceptible. From the most tolerant group, we selected six accessions, all of which were wild accessions adapted to coastal environments, as promising sources of salt tolerance because of their consistently high relative shoot biomass and relative quantum yield. Interestingly, variations in leaf Na+ concentration were observed between the accessions in the most tolerant group, suggesting different mechanisms were responsible for their salt tolerance. Phylogenetic analysis with nuclear DNA sequences revealed that salt tolerance had evolved independently at least four times in the genus Vigna, within a relatively short period. The findings suggested that simple genetic changes in a few genes might have greatly affected salt tolerances. The elucidation of genetic mechanisms of salt tolerances in the selected accessions may contribute to improving the poor salt tolerance in legume crops. PMID:27736995

Low assimilation efficiency of photorespiratory ammonia in conifer leaves.

PubMed

Miyazawa, Shin-Ichi; Nishiguchi, Mitsuru; Futamura, Norihiro; Yukawa, Tomohisa; Miyao, Mitsue; Maruyama, Tsuyoshi Emilio; Kawahara, Takayuki

2018-06-09

Glutamine synthetase (GS) localized in the chloroplasts, GS2, is a key enzyme in the assimilation of ammonia (NH 3 ) produced from the photorespiration pathway in angiosperms, but it is absent from some coniferous species belonging to Pinaceae such as Pinus. We examined whether the absence of GS2 is common in conifers (Pinidae) and also addressed the question of whether assimilation efficiency of photorespiratory NH 3 differs between conifers that may potentially lack GS2 and angiosperms. Search of the expressed sequence tag database of Cryptomeria japonica, a conifer in Cupressaceae, and immunoblotting analyses of leaf GS proteins of 13 species from all family members in Pinidae revealed that all tested conifers exhibited only GS1 isoforms. We compared leaf NH 3 compensation point (γ NH3 ) and the increments in leaf ammonium content per unit photorespiratory activity (NH 3 leakiness), i.e. inverse measures of the assimilation efficiency, between conifers (C. japonica and Pinus densiflora) and angiosperms (Phaseolus vulgaris and two Populus species). Both γ NH3 and NH 3 leakiness were higher in the two conifers than in the three angiosperms tested. Thus, we concluded that the absence of GS2 is common in conifers, and assimilation efficiency of photorespiratory NH 3 is intrinsically lower in conifer leaves than in angiosperm leaves. These results imply that acquisition of GS2 in land plants is an adaptive mechanism for efficient NH 3 assimilation under photorespiratory environments.

Are leaf breakdown rates a useful measure of stream integrity along an agricultural landuse gradient?

Treesearch

E.M. Hagen; J.R. Webster; E.F. Benfield

2006-01-01

Biological indicators often are used to assess and manage water quality in anthropogenically altered stream systems. Leaf breakdown has the potential to be a good indicator of stream integrity because it integrates a varietyof biological, chemical, and physical conditions. Red maple (Acer rubrum L.) leaf breakdown rates were measured along a gradient...

In Situ Field Measurement of Leaf Water Potential Using Thermocouple Psychrometers 1

PubMed Central

Savage, Michael J.; Wiebe, Herman H.; Cass, Alfred

1983-01-01

Thermocouple psychrometers are the only instruments which can measure the in situ water potential of intact leaves, and which can possibly be used to monitor leaf water potential. Unfortunately, their usefulness is limited by a number of difficulties, among them fluctuating temperatures and temperature gradients within the psychrometer, sealing of the psychrometer chamber to the leaf, shading of the leaf by the psychrometer, and resistance to water vapor diffusion by the cuticle when the stomates are closed. Using Citrus jambhiri, we have tested several psychrometer design and operational modifications and showed that in situ psychrometric measurements compared favorably with simultaneous Scholander pressure chamber measurements on neighboring leaves when the latter were corrected for the osmotic potential. PMID:16663267

Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

PubMed Central

2011-01-01

Background Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. Results A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. Conclusions The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species. PMID:22014081

Direct leaf wetness measurements and its numerical analysis using a multi-layer atmosphere-soil-vegetation model at a grassland site in pre-alpine region in Germany

NASA Astrophysics Data System (ADS)

Katata, Genki; Held, Andreas; Mauder, Matthias

2014-05-01

The wetness of plant leaf surfaces (leaf wetness) is important in meteorological, agricultural, and environmental studies including plant disease management and the deposition process of atmospheric trace gases and particles. Although many models have been developed to predict leaf wetness, wetness data directly measured at the leaf surface for model validations are still limited. In the present study, the leaf wetness was monitored using seven electrical sensors directly clipped to living leaf surfaces of thin and broad-leaved grasses. The measurements were carried out at the pre-alpine grassland site in TERestrial ENvironmental Observatories (TERENO) networks in Germany from September 20 to November 8, 2013. Numerical simulations of a multi-layer atmosphere-SOiL-VEGetation model (SOLVEG) developed by the authors were carried out for analyzing the data. For numerical simulations, the additional routine meteorological data of wind speed, air temperature and humidity, radiation, rainfall, long-wave radiative surface temperature, surface fluxes, ceilometer backscatter, and canopy or snow depth were used. The model reproduced well the observed leaf wetness, net radiation, momentum and heat, water vapor, and CO2 fluxes, surface temperature, and soil temperature and moisture. In rain-free days, a typical diurnal cycle as a decrease and increase during the day- and night-time, respectively, was observed in leaf wetness data. The high wetness level was always monitored under rain, fog, and snowcover conditions. Leaf wetness was also often high in the early morning due to thawing of leaf surface water frozen during a cold night. In general, leaf wetness was well correlated with relative humidity (RH) in condensation process, while it rather depended on wind speed in evaporation process. The comparisons in RH-wetness relations between leaf characteristics showed that broad-leaved grasses tended to be wetter than thin grasses.

Scaling up stomatal conductance from leaf to canopy using a dual-leaf model for estimating crop evapotranspiration.

PubMed

Ding, Risheng; Kang, Shaozhong; Du, Taisheng; Hao, Xinmei; Zhang, Yanqun

2014-01-01

The dual-source Shuttleworth-Wallace model has been widely used to estimate and partition crop evapotranspiration (λET). Canopy stomatal conductance (Gsc), an essential parameter of the model, is often calculated by scaling up leaf stomatal conductance, considering the canopy as one single leaf in a so-called "big-leaf" model. However, Gsc can be overestimated or underestimated depending on leaf area index level in the big-leaf model, due to a non-linear stomatal response to light. A dual-leaf model, scaling up Gsc from leaf to canopy, was developed in this study. The non-linear stomata-light relationship was incorporated by dividing the canopy into sunlit and shaded fractions and calculating each fraction separately according to absorbed irradiances. The model includes: (1) the absorbed irradiance, determined by separately integrating the sunlit and shaded leaves with consideration of both beam and diffuse radiation; (2) leaf area for the sunlit and shaded fractions; and (3) a leaf conductance model that accounts for the response of stomata to PAR, vapor pressure deficit and available soil water. In contrast to the significant errors of Gsc in the big-leaf model, the predicted Gsc using the dual-leaf model had a high degree of data-model agreement; the slope of the linear regression between daytime predictions and measurements was 1.01 (R2 = 0.98), with RMSE of 0.6120 mm s-1 for four clear-sky days in different growth stages. The estimates of half-hourly λET using the dual-source dual-leaf model (DSDL) agreed well with measurements and the error was within 5% during two growing seasons of maize with differing hydrometeorological and management strategies. Moreover, the estimates of soil evaporation using the DSDL model closely matched actual measurements. Our results indicate that the DSDL model can produce more accurate estimation of Gsc and λET, compared to the big-leaf model, and thus is an effective alternative approach for estimating and partitioning λET.

Tadpoles of Early Breeding Amphibians are Negatively Affected by Leaf Litter From Invasive Chinese Tallow Trees

NASA Astrophysics Data System (ADS)

Leonard, N. E.

2005-05-01

As wetlands are invaded by Chinese tallow trees (Triadica sebifera), native trees are displaced and detrital inputs to amphibian breeding ponds are altered. I used a mesocosm experiment to examine the effect of Chinese tallow leaf litter on the survival to, size at, and time to metamorphosis of amphibian larvae. Fifty 1000-L cattle watering tanks were treated with 1500 g dry weight of one of five leaf litter treatments: Chinese tallow, laurel oak (Quercus laurifolia), water tupelo (Nyssa aquatica), slash pine (Pinus elliottii), or a 3:1:1:1 mixture. Each tank received 45 tadpoles of Pseudacris feriarum, Bufo terrestris, and Hyla cinerea in sequence according to their natural breeding phonologies. Every Pseudacris feriarum and Bufo terrestris tadpole exposed to Chinese tallow died prior to metamorphosis. Hyla cinerea survival in tanks with tallow-only was significantly lower than that observed for all other leaf treatments. Hyla cinerea tadpoles from tallow-only and mixed-leaf treatments were larger at metamorphosis and transformed faster than those in tanks with native leaves only. These results suggest that Chinese tallow leaf litter may negatively affect tadpoles of early breeding frogs and that Chinese tallow invasion may change the structure of amphibian communities in temporary ponds.

UV-B Inhibits Leaf Growth through Changes in Growth Regulating Factors and Gibberellin Levels1[OPEN

PubMed Central

Fina, Julieta; AbdElgawad, Hamada; Prinsen, Els

2017-01-01

Ultraviolet-B (UV-B) radiation affects leaf growth in a wide range of species. In this work, we demonstrate that UV-B levels present in solar radiation inhibit maize (Zea mays) leaf growth without causing any other visible stress symptoms, including the accumulation of DNA damage. We conducted kinematic analyses of cell division and expansion to understand the impact of UV-B radiation on these cellular processes. Our results demonstrate that the decrease in leaf growth in UV-B-irradiated leaves is a consequence of a reduction in cell production and a shortened growth zone (GZ). To determine the molecular pathways involved in UV-B inhibition of leaf growth, we performed RNA sequencing on isolated GZ tissues of control and UV-B-exposed plants. Our results show a link between the observed leaf growth inhibition and the expression of specific cell cycle and developmental genes, including growth-regulating factors (GRFs) and transcripts for proteins participating in different hormone pathways. Interestingly, the decrease in the GZ size correlates with a decrease in the concentration of GA19, the immediate precursor of the active gibberellin, GA1, by UV-B in this zone, which is regulated, at least in part, by the expression of GRF1 and possibly other transcription factors of the GRF family. PMID:28400494

Abamectin, pymetrozine and azadirachtin sequence as a unique solution to control the leafminer Liriomyza trifolii (Burgess) (Diptera: Agromyzidae) infesting garden beans (Phaseolus vulgaris L.) in Egypt.

PubMed

Saad, A S A; Massoud, M A; Abdel-Megeed, A A M; Hamid, N A; Mourad, A K K; Barakat, A S T

2007-01-01

Field trails were conducted to determine the performance of three different sequences as a unique solution for the control of the leaf miner Liriomyza trifolii (Burgess) (Diptera: Agromyzidae) infesting garden beans (Phaseolus vulgaris L.) during the two successive seasons of 2004 and 2005. Furthermore, during the evaluation period, the side effect against the ectoparasite Diglyphus isaea (Walker) (Hymenoptera: Eulophidae) was put into consideration. Meanwhile, the comparative evaluation of the pesticides alone showed that abamectin and azadirachtin were highly effective against Liriomyza trifolii, while carbosulfan, pymetrozine and thiamethoxam provided to be of a moderate effect. Moreover, carbosulfan showed harmful effect to the larvae of the ectoparasite Diglyphus isaea (Walker), while abamectin and azadirachtin gave a moderate effect. Thiamethoxam and the the detergent (Masrol 410) had slight effect in this respect. The highly effective sequence among the sequences was abamectin, pymetrozine and azadirachtin, against Liriomyza trifolii (Burgess), with slight harmful effect on Diglyphus isaea (Walker). However the sequence of azadirachtin, pymetrozine and abamectin had a moderate effect on Liriomyza trifolii (Burgess) and exhibited a slight toxic effect on Diglyphus isaea (Walker). In contrast, the sequence of carbosulfan, thiamethoxam and pymetrozine was the least effective and represented a slight effect on Diglyphus isaea (Walker). From this study, it was concluded that abamectin, pymetrozine and azadirachtin sequence has proved to be a unique solution for the control of the leaf miner Liriomyza trifolii (Burgess) infesting garden beans (Phaseolus vulgaris L.) in Egypt.

Leaf Litter Decomposition as a Functional Assessment of a Natural Stream Channel Design Project

NASA Astrophysics Data System (ADS)

Gentry, A.; Word, D.; Carreiro, M.; Jack, J.

2005-05-01

In October 2003, a 965m reach of Wilson Creek (Bernheim Research Forest, Kentucky, USA) was relocated, and meanders and riffle-pool sequences were restored, providing a unique opportunity to measure the re-establishment of post-restoration stream functions. Leaf litter bags were placed across riffles in the restored reach, in an upstream reference site and in two reference streams. Bags were collected for nine months, and mass loss, N dynamics and fungal ergosterol were measured. Daily mass loss rates in the restored and reference riffles in Wilson Creek were faster (k= -0.00759 and k= -0.00855, respectively) than those of the two reference streams (k= -0.00511 and k= -0.00308). This is equivalent to litter mean residence times of 132 days for the restored reach in Wilson, 117 days in the upstream reference site, and 196 and 325 days for the reference streams. It appears that the decay rate in the restored reach is similar to the upstream portion of Wilson Creek, indicating rapid mass loss recovery in the restored reach. We also determined that same-stream reference sites are important for evaluating the restoration of stream functions, because of high decay rate variation among nearby streams within the same watershed.

Convergent production and tolerance among 107 woody species and divergent production between shrubs and trees.

PubMed

He, Wei-Ming; Sun, Zhen-Kai

2016-02-08

Green leaves face two fundamental challenges (i.e., carbon fixation and stress tolerance) during their lifespan. However, the relationships between leaf production potential and leaf tolerance potential have not been explicitly tested with a broad range of plant species in the same environment. To do so, we conducted a field investigation based on 107 woody plants grown in a common garden and complementary laboratory measurements. The values, as measured by a chlorophyll meter, were significantly related to the direct measurements of chlorophyll content on a leaf area basis. Area-based chlorophyll content was positively correlated with root surface area, whole-plant biomass, leaf mass per area (LMA), and force to punch. Additionally, LMA had a positive correlation with force to punch. Shrubs had a higher leaf chlorophyll content than trees; however, shrubs and trees exhibited a similar leaf lifespan, force to punch, and LMA. These findings suggest that the production potential of leaves and their tolerance to stresses may be convergent in woody species and that the leaf production potential may differ between shrubs and trees. This study highlights the possibility that functional convergence and divergence might be linked to long-term selection pressures and genetic constraints.

Convergent production and tolerance among 107 woody species and divergent production between shrubs and trees

PubMed Central

He, Wei-Ming; Sun, Zhen-Kai

2016-01-01

Green leaves face two fundamental challenges (i.e., carbon fixation and stress tolerance) during their lifespan. However, the relationships between leaf production potential and leaf tolerance potential have not been explicitly tested with a broad range of plant species in the same environment. To do so, we conducted a field investigation based on 107 woody plants grown in a common garden and complementary laboratory measurements. The values, as measured by a chlorophyll meter, were significantly related to the direct measurements of chlorophyll content on a leaf area basis. Area-based chlorophyll content was positively correlated with root surface area, whole-plant biomass, leaf mass per area (LMA), and force to punch. Additionally, LMA had a positive correlation with force to punch. Shrubs had a higher leaf chlorophyll content than trees; however, shrubs and trees exhibited a similar leaf lifespan, force to punch, and LMA. These findings suggest that the production potential of leaves and their tolerance to stresses may be convergent in woody species and that the leaf production potential may differ between shrubs and trees. This study highlights the possibility that functional convergence and divergence might be linked to long-term selection pressures and genetic constraints. PMID:26854019

Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation.

PubMed

Pick, Thea R; Bräutigam, Andrea; Schlüter, Urte; Denton, Alisandra K; Colmsee, Christian; Scholz, Uwe; Fahnenstich, Holger; Pieruschka, Roland; Rascher, Uwe; Sonnewald, Uwe; Weber, Andreas P M

2011-12-01

We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from the point of emergence into the light to the tip in 10 continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, and photosynthetic rate measurements showed that the maize leaf undergoes a sink-to-source transition without an intermediate phase of C(3) photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination, showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C(4) photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C(4) photosynthesis. All data sets are included within the publication to serve as a resource for maize leaf systems biology.

Systems Analysis of a Maize Leaf Developmental Gradient Redefines the Current C4 Model and Provides Candidates for Regulation[W][OA

PubMed Central

Pick, Thea R.; Bräutigam, Andrea; Schlüter, Urte; Denton, Alisandra K.; Colmsee, Christian; Scholz, Uwe; Fahnenstich, Holger; Pieruschka, Roland; Rascher, Uwe; Sonnewald, Uwe; Weber, Andreas P.M.

2011-01-01

We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from the point of emergence into the light to the tip in 10 continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, and photosynthetic rate measurements showed that the maize leaf undergoes a sink-to-source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination, showed continuous gradients for all analyzed items. The absence of binary on–off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All data sets are included within the publication to serve as a resource for maize leaf systems biology. PMID:22186372

Use of Satellite data by the USDA to Forecast Global Vector-borne Human and Animal Diseases

USDA-ARS?s Scientific Manuscript database

In recent years satellite remote sensing has been used increasingly for public health applications. In this symposium, experts from four government departments and agencies with major roles in leading and promoting such applications will discuss the state of the art of using remote sensing for epide...

Titan Lifting Entry & Atmospheric Flight (T-LEAF) Science Mission

NASA Astrophysics Data System (ADS)

Lee, G.; Sen, B.; Ross, F.; Sokol, D.

2016-12-01

Northrop Grumman has been developing the Titan Lifting Entry & Atmospheric Flight (T-LEAF) sky rover to roam the lower atmosphere and observe at close quarters the lakes and plains of Saturn's ocean moon, Titan. T-LEAF also supports surface exploration and science by providing precision delivery of in-situ instruments to the surface of Titan. T-LEAF is a highly maneuverable sky rover and its aerodynamic shape (i.e., a flying wing) does not restrict it to following prevailing wind patterns on Titan, but allows mission operators to chart its course. This freedom of mobility allows T-LEAF to follow the shorelines of Titan's methane lakes, for example, or to target very specific surface locations. We will present a straw man concept of T-LEAF, including size, mass, power, on-board science payloads and measurement, and surface science dropsonde deployment CONOPS. We will discuss the various science instruments and their vehicle level impacts, such as meteorological and electric field sensors, acoustic sensors for measuring shallow depths, multi-spectral imagers, high definition cameras and surface science dropsondes. The stability of T-LEAF and its long residence time on Titan will provide for time to perform a large aerial survey of select prime surface targets deployment of dropsondes at selected locations surface measurements that are coordinated with on-board remote measurements communication relay capabilities to orbiter (or Earth). In this context, we will specifically focus upon key factors impacting the design and performance of T-LEAF science: science payload accommodation, constraints and opportunities characteristics of flight, payload deployment and measurement CONOPS in the Titan atmosphere. This presentation will show how these factors provide constraints as well as enable opportunities for novel long duration scientific studies of Titan's surface.

First Report of Leaf Spot Caused by Alternaria tenuissima on Black Chokeberry (Aronia melanocarpa) in Korea.

PubMed

Wee, Jung-In; Park, Jong-Han; Back, Chang-Gi; You, Young-Hyun; Chang, Taehyun

2016-09-01

In July 2015, diseased leaves of black chokeberry ( Aronia melanocarpa ) were observed in Danyang and Gochang, Korea. The symptoms appeared as circular or irregular brown leaf spots, from which Alternaria tenuissima was isolated. The isolates were cultured on potato dextrose agar, and their morphological characteristics were observed under a light microscope. The colonies were whitish to ash colored. The pathogenicity test on healthy black chokeberry leaves produced circular brown spots, in line with the original symptoms. Molecular analyses of the ITS, GPD, RPB2, and TEF genes were conducted to confirm the identity of the pathogen. The phylogeny of the multi-gene sequences indicated that the causal agent was A. tenuissima . This study is the first report of A. tenuissima leaf spot on black chokeberry ( A. melanocarpa ).

Short-read DNA sequencing yields microsatellite markers for Rheum

USDA-ARS?s Scientific Manuscript database

Identifying culinary rhubarb (Rheum ×hybridum Murray) cultivars using morphological characteristics is problematic due to variability within individual genotypes, variation caused by environmental factors, plant and leaf age, similarity between genetically diverse genotypes, multiple cultivar names ...

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

PubMed Central

2011-01-01

Background Abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses. Results A total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, short-term, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues. Conclusions The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods. PMID:21592389

A century of paraphyly: a molecular phylogeny of katydids (Orthoptera: Tettigoniidae) supports multiple origins of leaf-like wings.

PubMed

Mugleston, Joseph D; Song, Hojun; Whiting, Michael F

2013-12-01

The phylogenetic relationships of Tettigoniidae (katydids and bush-crickets) were inferred using molecular sequence data. Six genes (18S rDNA, 28S rDNA, Cytochrome Oxidase II, Histone 3, Tubulin Alpha I, and Wingless) were sequenced for 135 ingroup taxa representing 16 of the 19 extant katydid subfamilies. Five subfamilies (Tettigoniinae, Pseudophyllinae, Mecopodinae, Meconematinae, and Listroscelidinae) were found to be paraphyletic under various tree reconstruction methods (Maximum Likelihood, Bayesisan Inference and Maximum Parsimony). Seven subfamilies - Conocephalinae, Hetrodinae, Hexacentrinae, Saginae, Phaneropterinae, Phyllophorinae, and Lipotactinae - were each recovered as well-supported monophyletic groups. We mapped the small and exposed thoracic auditory spiracle (a defining character of the subfamily Pseudophyllinae) and found it to be homoplasious. We also found the leaf-like wings of katydids have been derived independently in at least six lineages. Copyright © 2013 Elsevier Inc. All rights reserved.

Morphological and molecular characterization of Magnaporthe oryzae (fungus) from infected rice leaf samples

NASA Astrophysics Data System (ADS)

Muni, Nurulhidayah Mat; Nadarajah, Kalaivani

2014-09-01

Magnaporthe oryzae is a plant-pathogenic fungus that causes a serious disease affecting rice called rice blast. Outbreaks of rice blast have been a threat to the global production of rice. This fungal disease is estimated to cause production losses of US55 million each year in South and Southeast Asia. It has been used as a primary model for elucidating various aspects of the host-pathogen interaction with its host. We have isolated five isolates of Magnaporthe oryzae from diseased leaf samples obtained from the field at Kompleks Latihan MADA, Kedah, Malaysia. We have identified the isolates using morphological and microscopic studies on the fungal spores and the lesions on the diseased leaves. Amplification of the internal transcribed spacer (ITS) was carried out with universal primers ITS1 and ITS4. The sequence of each isolates showed at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaporthe oryzae.

Detection and molecular characterization of tomato yellow leaf curl virus naturally infecting Lycopersicon esculentum in Egypt.

PubMed

Rabie, M; Ratti, C; Abdel Aleem, E; Fattouh, F

Tomato yellow leaf curl virus (TYLCV) infections of tomato crops in Egypt were widely spread in 2014. Infected symptomatic tomato plants from different governorates were sampled. TYLCV strains Israel and Mild (TYLCV-IL, TYLCV-Mild) were identified by multiplex and real-time PCR. In addition, nucleotide sequence analysis of the V1 and V2 protein genes, revealed ten TYLCV Egyptian isolates (TYLCV from TY1 to 10). Phylogenetic analysis showed their high degree of relatedness with TYLCV-IL Jordan isolate (98%). Here we have showed the complete nucleotide sequence of the TYLCV Egyptian isolate TY10, sampled from El Beheira. A high degree of similarity to other previously reported Egyptian isolates and isolates from Jordan and Japan reflect the importance of phylogenetic analysis in monitoring virus genetic diversity and possibilities for divergence of more virulent strains or genotypes.

Leaf habit and woodiness regulate different leaf economy traits at a given nutrient supply.

PubMed

Ordoñez, Jenny C; van Bodegom, Peter M; Witte, Jan-Philip M; Bartholomeus, Ruud P; van Dobben, Han F; Aerts, Rien

2010-11-01

The large variation in the relationships between environmental factors and plant traits observed in natural communities exemplifies the alternative solutions that plants have developed in response to the same environmental limitations. Qualitative attributes, such as growth form, woodiness, and leaf habit can be used to approximate these alternative solutions. Here, we quantified the extent to which these attributes affect leaf trait values at a given resource supply level, using measured plant traits from 105 different species (254 observations) distributed across 50 sites in mesic to wet plant communities in The Netherlands. For each site, soil total N, soil total P, and water supply estimates were obtained by field measurements and modeling. Effects of growth forms, woodiness, and leaf habit on relations between leaf traits (SLA, specific leaf area; LNC, leaf nitrogen concentration; and LPC, leaf phosphorus concentration) vs. nutrient and water supply were quantified using maximum-likelihood methods and Bonferroni post hoc tests. The qualitative attributes explained 8-23% of the variance within sites in leaf traits vs. soil fertility relationships, and therefore they can potentially be used to make better predictions of global patterns of leaf traits in relation to nutrient supply. However, at a given soil fertility, the strength of the effect of each qualitative attribute was not the same for all leaf traits. These differences may imply a differential regulation of the leaf economy traits at a given nutrient supply, in which SLA and LPC seem to be regulated in accordance to changes in plant size and architecture while LNC seems to be primarily regulated at the leaf level by factors related to leaf longevity.

Evaluation of water-use efficiency in foxtail millet (Setaria italica) using visible-near infrared and thermal spectral sensing techniques.

PubMed

Wang, Meng; Ellsworth, Patrick Z; Zhou, Jianfeng; Cousins, Asaph B; Sankaran, Sindhuja

2016-05-15

Water limitations decrease stomatal conductance (g(s)) and, in turn, photosynthetic rate (A(net)), resulting in decreased crop productivity. The current techniques for evaluating these physiological responses are limited to leaf-level measures acquired by measuring leaf-level gas exchange. In this regard, proximal sensing techniques can be a useful tool in studying plant biology as they can be used to acquire plant-level measures in a high-throughput manner. However, to confidently utilize the proximal sensing technique for high-throughput physiological monitoring, it is important to assess the relationship between plant physiological parameters and the sensor data. Therefore, in this study, the application of rapid sensing techniques based on thermal imaging and visual-near infrared spectroscopy for assessing water-use efficiency (WUE) in foxtail millet (Setaria italica (L.) P. Beauv) was evaluated. The visible-near infrared spectral reflectance (350-2500 nm) and thermal (7.5-14 µm) data were collected at regular intervals from well-watered and drought-stressed plants in combination with other leaf physiological parameters (transpiration rate-E, A(net), g(s), leaf carbon isotopic signature-δ(13)C(leaf), WUE). Partial least squares regression (PLSR) analysis was used to predict leaf physiological measures based on the spectral data. The PLSR modeling on the hyperspectral data yielded accurate and precise estimates of leaf E, gs, δ(13)C(leaf), and WUE with coefficient of determination in a range of 0.85-0.91. Additionally, significant differences in average leaf temperatures (~1°C) measured with a thermal camera were observed between well-watered plants and drought-stressed plants. In summary, the visible-near infrared reflectance data, and thermal images can be used as a potential rapid technique for evaluating plant physiological responses such as WUE. Copyright © 2016 Elsevier B.V. All rights reserved.

Biosorption of chromium (VI) from aqueous solutions and ANN modelling.

PubMed

Nag, Soma; Mondal, Abhijit; Bar, Nirjhar; Das, Sudip Kumar

2017-08-01

The use of sustainable, green and biodegradable natural wastes for Cr(VI) detoxification from the contaminated wastewater is considered as a challenging issue. The present research is aimed to assess the effectiveness of seven different natural biomaterials, such as jackfruit leaf, mango leaf, onion peel, garlic peel, bamboo leaf, acid treated rubber leaf and coconut shell powder, for Cr(VI) eradication from aqueous solution by biosorption process. Characterizations were conducted using SEM, BET and FTIR spectroscopy. The effects of operating parameters, viz., pH, initial Cr(VI) ion concentration, adsorbent dosages, contact time and temperature on metal removal efficiency, were studied. The biosorption mechanism was described by the pseudo-second-order model and Langmuir isotherm model. The biosorption process was exothermic, spontaneous and chemical (except garlic peel) in nature. The sequence of adsorption capacity was mango leaf > jackfruit leaf > acid treated rubber leaf > onion peel > bamboo leaf > garlic peel > coconut shell with maximum Langmuir adsorption capacity of 35.7 mg g -1 for mango leaf. The treated effluent can be reused. Desorption study suggested effective reuse of the adsorbents up to three cycles, and safe disposal method of the used adsorbents suggested biodegradability and sustainability of the process by reapplication of the spent adsorbent and ultimately leading towards zero wastages. The performances of the adsorbents were verified with wastewater from electroplating industry. The scale-up study reported for industrial applications. ANN modelling using multilayer perception with gradient descent (GD) and Levenberg-Marquart (LM) algorithm had been successfully used for prediction of Cr(VI) removal efficiency. The study explores the undiscovered potential of the natural waste materials for sustainable existence of small and medium sector industries, especially in the third world countries by protecting the environment by eco-innovation.

Characterization of petunia flower mottle virus (PetFMV), a new potyvirus infecting Petunia x hybrida.

PubMed

Feldhoff, A; Wetzel, T; Peters, D; Kellner, R; Krczal, G

1998-01-01

With the introduction of cutting-grown Petunia x hybrida plants on the European market, a new potyvirus which showed no serological reaction with antisera against any other potyviruses infecting petunias was discovered. Infected leaves contained flexuous rod-shaped virus particles of 750-800 nm in length and inclusion bodies (pinwheel structures) typical for potyviruses in ultrathin leaf sections. The purified coat protein with a Mr of approximately 36 kDa could be detected in Western immunoblots with a specific antibody to the coat protein of the petunia-infecting virus. The 3' end of the viral genome encompassing the 3' non-coding region, the coat protein gene, and part of the NIb gene was amplified from infected leaf material by IC/PCR using degenerate and specific primers. Sequences of PCR-generated cDNA clones were compared to other known sequences of potyviruses. Maximum homology of 56% was found in the 3' non-coding region between the petunia isolate and other potyviruses. A maximum homology of 69% was found between the amino acid sequence of the coat protein of the petunia isolate and corresponding sequences of other potyviruses. These data indicate that the petunia-infecting virus is a previously undescribed potyvirus and the name petunia flower mottle virus (PetFMV) is suggested.