bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pleiotropic drug resistance transporter is involved in reduced sensitivity to multiple fungicide classes in Sclerotinia homoeocarpa (F.T. Bennett)
Authors: Sang Hyunkyu , Hulvey Jon , Popko James T. , Lopes John , Swaminathan Aishwarya , Chang Taehyun , Jung Geunhwa 
Published: July 2014

SummaryDollar spot, caused by Sclerotinia homoeocarpa, is a prevalent turfgrass disease, and the fungus exhibits widespread fungicide resistance in North America. In a previous study, an ABC‐G transporter, ShatrD, was associated with practical field resistance to demethylation inhibitor (DMI) fungicides. Mining of ABC‐G transporters, also known as pleiotropic drug resistance (PDR) transporters, from RNA‐Seq data gave an assortment of transcripts, several with high sequence similarity to functionally characterized transporters from Botrytis cinerea, and others with closest blastx hits from Aspergillus and Monilinia. In addition to ShatrD, another PDR transporter showed significant over‐expression in replicated RNA‐Seq data, and in a collection of field‐resistant isolates, as measured by quantitative polymerase chain reaction. These isolates also showed reduced sensitivity to unrelated fungicide classes. Using a yeast complementation system, we sought to test the hypothesis that this PDR transporter effluxes DMI as well as chemically unrelated fungicides. The transporter (ShPDR1) was cloned into the Gal1 expression vector and transformed into a yeast PDR transporter deletion mutant, AD12345678. Complementation assays indicated that ShPDR1 complemented the mutant in the presence of propiconazole (DMI), iprodione (dicarboximide) and boscalid (SDHI, succinate dehydrogenase inhibitor). Our results indicate that the over‐expression of ShPDR1 is correlated with practical field resistance to DMI fungicides and reduced sensitivity to dicarboximide and SDHI fungicides. These findings highlight the potential for the eventual development of a multidrug resistance phenotype in this pathogen. In addition, this study presents a pipeline for the discovery and validation of fungicide resistance genes using de novo next‐generation sequencing and molecular biology techniques in an unsequenced plant pathogenic fungus.
Genetic linkage map construction for white jute (Corchorus capsularis L.) using SRAP, ISSR and RAPD markers
Authors: Chen Yanping , Zhang Liwu , Qi Jianmin , Chen Hui , Tao Aifen , Xu Jiantang , Lin Lihui , Fan Pingping 
Published: July 2014

AbstractWhite jute (Corchorus capsularis) and dark jute (Corchorus olitorius) are two important cultivated crops that are used for natural fibre production. Some genetic maps have been developed for dark jute, but the genetic map information for white jute (C. capsularis) is limited. In this study, a linkage map comprising 44 sequence‐related amplified polymorphisms (SRAPs), 57 intersimple sequence repeats (ISSRs) and 18 randomly amplified polymorphic DNA (RAPD) covering 2185.7 cM with a mean density of 18.7 cM per locus was constructed in an F2 population consisting of 185 individuals derived from a cross between two diverse genotypes of ‘Xinxuan No. 1’ and ‘Qiongyueqing’ in white jute. These markers were evenly distributed in the linkage groups without any clustering. This genetic linkage map construction will facilitate the mapping of agronomic traits and marker‐assisted selection breeding in white jute.
Does Inequality Lead to a Financial Crisis? Revisited
Authors: Gu Xinhua , Huang Bihong 
Published: July 2014

AbstractFinancial crises have been attributed to rising income inequality via its induced high household leverage as observed in the USA and similar economies. Alternatively it has been suggested this is not a general relationship since it was found that inequality had no bearing on crises in 14 advanced countries over 1920–2008; instead, low interest rates and business cycle expansions are found to be the only two robust determinants of credit booms leading to crises. Using a similar dataset, this paper provides no support for the generality of the above findings by embracing country heterogeneity. The paper shows that real evidence still points back to the inequality‐leverage–crisis nexus for financialized economies. The implication is that finance can hardly be sustainable under rising inequality.
On Offshoring and Trade Deficit
Authors: Beladi Hamid , Oladi Reza 
Published: July 2014

AbstractThe paper constructs a general equilibrium model of North–South trade with nontraded goods, real exchange rate, and a continuum of components that North partly offshores to South. It is shown that a protectionary policy which restricts offshoring may have the unintended consequence of widening the trade deficit.
SU‐C‐18C‐02: Specifcation of X‐Ray Projection Angles Which Are Aligned with the Aortic Valve Plane From a Planar Image of a Valvuloplasty Balloon Inflated Across the Aortic Valve
Authors: Fetterly K , Mathew V 
Published: July 2014

Purpose:Transcatheter aortic valve replacement (TAVR) procedures provide a method to implant a prosthetic aortic valve via a minimallyinvasive, catheter‐based procedure. TAVR procedures require use of interventional fluoroscopy c‐arm projection angles which are aligned with the aortic valve plane to minimize prosthetic valve positioning error due to x‐ray imaging parallax. The purpose of this work is to calculate the continuous range of interventional fluoroscopy c‐arm projection angles which are aligned with the aortic valve plane from a single planar image of a valvuloplasty balloon inflated across the aortic valve.Methods:Computational methods to measure the 3D angular orientation of the aortic valve were developed. Required inputs include a planar x‐ray image of a known valvuloplasty balloon inflated across the aortic valve and specifications of x‐ray imaging geometry from the DICOM header of the image. A‐priori knowledge of the species‐specific typical range of aortic orientation is required to specify the sign of the angle of the long axis of the balloon with respect to the x‐ray beam. The methods were validated ex‐vivo and in a live pig.Results:Ex‐vivo experiments demonstrated that the angular orientation of a stationary inflated valvuloplasty balloon can be measured with precision less than 1 degree. In‐vivo pig experiments demonstrated that cardiac motion contributed to measurement variability, with precision less than 3 degrees. Error in specification of x‐ray geometry directly influences measurement accuracy.Conclusion:This work demonstrates that the 3D angular orientation of the aortic valve can be calculated precisely from a planar image of a valvuloplasty balloon inflated across the aortic valve and known x‐ray geometry. This method could be used to determine appropriate c‐arm angular projections during TAVR procedures to minimize x‐ray imaging parallax and thereby minimize prosthetic valve positioning errors.
SU‐C‐18C‐03: Dual‐Energy X‐Ray Fluoroscopy Imaging System
Authors: Virshup G , Fu D , Richmond M , Mostafavi H , Ganguly A 
Published: July 2014

Purpose:This work studies the clinical utility of dual energy (DE) subtraction fluoroscopy for fiducial‐free tumor tracking in lung radiation therapy (RT). Improvement in tumor visualization and quantification of tumor shift within a breathing cycle were analyzed.Methods:Twenty subjects who were undergoing RT for lung cancer were recruited following institutional review board approval. The subjects had a range of tumor sizes, locations in the lungs, and body sizes. An x‐ray imaging system was setup with the following components: (a) x‐ray tube (Varian G‐242, Varian Medical Systems (VMS), CA) (b) flat panel detector (4030CB, VMS, CA) and (c) x‐ray generator (EPS 50RF, EMD, Canada). Firmware and software modifications were made to the generator to allow 10 x‐ray pulse pairs with alternating low/high kV, 100 ms apart for ∼4s (one breathing cycle). Images were obtained at 4 angles: 0°, 45°, 90° and 135°. Weighted subtraction of a kV‐pair image set was used to create a “bone‐free” image of the lungs. The 2D tumor‐shift in each subtracted image and the 3D shift during a breathing cycle was calculated using all views.Results:The subjects enrolled had the following statistics: average age 62.3±7.1 years, 5 female/15 male, 11 had tumors on the right and 9 on the left and the average tumor size was ∼31.4±10.8 mm. X‐ray imaging conditions for the pulse pairs were: 70/120 kVp, 280/221 mA and 65/8 ms. For views where these parameters were insufficient 80/130 kVp, 280/221 mA and 60/12 ms was used. Tumor visibility improved for 0°, 45°, 90° and 135° in 100%, 55%, 75% and 80% of the cases respectively. Tumor shift during a breathing cycle was: 2.4±1.0 mm AP, 2.7±1.4 mm LR and 7.6±4.8 mm IS.Conclusion:DE subtraction fluoroscopy allowed improved visualization and quantification of movement of tumors in the lungs during a breathing cycle.This study was entirely funded by Varian Medical Systems
SU‐D‐18A‐04: Quantifying the Ability of Tumor Tracking to Spare Normal Tissue
Authors: Burger A , Buzurovic I , Hurwitz M , Mishra P , Williams C , Seco J , Lewis J 
Published: July 2014

Purpose:Tumor tracking allows for smaller tissue volumes to be treated, potentially reducing normal tissue damage. However, tumor tracking is a more complex treatment and has little benefit in some scenarios. Here we quantify the benefit of tumor tracking for a range of patients by estimating the dose of radiation to organs at risk and the normal tissue complication probability (NTCP) for both standard and tracking treatment plans. This comparison is performed using both patient 4DCT data and extended Cardiac‐Torso (XCAT) digital phantoms.Methods:We use 4DCT data for 10 patients. Additionally, we generate digital phantoms with motion derived from measured patient long tumor trajectories to compare standard and tracking treatment plans. The standard treatment is based on the average intensity projection (AIP) of 4DCT images taken over a breath cycle. The tracking treatment is based on doses calculated on images representing the anatomy at each time point. It is assumed that there are no errors in tracking the target. The NTCP values are calculated based on RTOG guidelines.Results:The mean reduction in the mean dose delivered was 5.5% to the lungs (from 7.3 Gy to 6.9 Gy) and 4.0% to the heart (from 12.5 Gy to 12.0 Gy). The mean reduction in the max dose delivered was 13% to the spinal cord (from 27.6 Gy to 24.0 Gy), 2.5% to the carina (from 31.7 Gy to 30.9 Gy), and 15% to the esophagus (from 69.6 Gy to 58.9 Gy). The mean reduction in the probability of 2nd degree radiation pneumonitis (RP) was 8.7% (3.1% to 2.8%) and the mean reduction in the effective volume was 6.8% (10.8% to 10.2%).Conclusions:Tumor tracking has the potential to reduce irradiation of organs at risk, and consequentially reduce the normal tissue complication probability. The benefits vary based on the clinical scenario.This study is supported by Varian Medical Systems, Inc.
SU‐D‐18A‐05: Assessing Elekta MLC Tracking Performance
Authors: Glitzner M , Crijns S , Lagendijk J , Raaymakers B 
Published: July 2014

Purpose:To investigate the technical feasibility of using Elekta MLCs in tracked radiotherapy, specifically to show the capability of an Agility MLC to follow model tumor trajectories using object tracking. The system performance of the MLC is to be assessed via dosimetric experiments and temporal response measures.Methods:The system observer in the tracking cascade consisted of a camera serving for this proof of concept; Images of a moving object were acquired continuously and decorrelated for the position information, which was fed forward to the RT computer controlling the MLC via an interface provided by Elekta. The 1D motion (in the direction of the leaves) was induced by a CIRS motion controller. Additionally, the aperture position was observed by means of the light field of the linac. Calculating the phase between aperture and object yielded the mean aperture lag for the current setup. The object was restricted to sinusoidal motion with a period of 10s. For dosimetry, GafChromic radiosensitive film was irradiated with a total dose of 1000MU using an aperture size of 40mm and a motion range of 30mm.Results:Object tracking can substantially reconstruct the geometric dose response of a static target. In the dynamic case, dose is smeared out into the legs of the static distribution, leading to a reduced plateau and increased FWHM of 5mm, compared to the static width of 38mm. The time‐lag between object and aperture was determined to be approximately 300ms for the current set‐up.Conclusion:We demonstrated a tracking experiment performed on a clinical Elekta linear accelator for the first time. Observed profile variations show the dosimetric impact of tracked delivery. The determined lag is a valuable descriptor for a future tracking cascade employing predictor filters. The performed experiments are generic and possible predecessors for future applications with MR‐Linac or ultrasound probes.Conflict of interest: this project is partly funded by Elekta.
SU‐D‐18A‐07: Towards 6‐Degree‐Of‐Freedom Real‐Time Motion Management in Cancer Radiotherapy
Authors: Huang C.Y. , Nasehi Tehrani J , Booth J , Keall P 
Published: July 2014

Purpose:Lung tumor motion has been identified as a major issue that deteriorates treatment efficacy for radiotherapy, especially for SBRT. As tighter PTV margins are applied due to translational compensation, tumor rotation will become the dominant factor limiting tumor targeting accuracy. This is the world‐first study quantifies lung tumor rotation by utilizing kV images with fiducial markers and a step towards 6‐degree‐of‐freedom real‐time cancer radiotherapy.Methods:Three or four gold coils were implanted as tumor surrogates in 3 lung cancer patients. 50 fractions of 8‐ minute, 10 Hz 4D CBCT projections were acquired for the patients immediately prior or after radiotherapy. The fiducial marker positions are segmented, reconstructed and used to determine tumour rotation by the iterative closest point algorithm. Different data acceptance and filtering methods were applied to accept data or smooth the marker trajectory.Results:The average rotation angles around the left/ right (LR), superior/inferior (SI), anterior/posterior (AP) rotations were found to be 0.8±4.2, ‐0.8±4.5 and 1.7±3.1 degrees respectively. For 28% of the treatment time, the lung tumors rotated more than 5° around the SI axis. Respiration‐induced rotational motion was detected in 2 of the 3 lung patients. This can be explained by the patient developed atelectasis during the treatment period. Interestingly, no heart beating component of rotation was observed in the power spectrum. Different rotational types were observed within the patient cohort with large variations in the magnitude of the rotation between patients.Conclusions:For the first time, continuous tumor rotation has been measured for lung patients with gold fiducial markers. Tumors were found to undergo rotations of more than 5° for almost a third of the total treatment time. The study also demonstrated the feasibility of using continuously kV images for real‐time lung tumour motion adaptive radiotherapy which can potentially reduce treatment margins and side effects.The authors acknowledge the financial support of an NHMRC Australia Fellowship.
SU‐D‐18C‐05: Variable Bolus Arterial Spin Labeling MRI for Accurate Cerebral Blood Flow and Arterial Transit Time Mapping
Authors: Johnston M , Jung Y 
Published: July 2014

Purpose:Arterial spin labeling (ASL) is an MRI perfusion imaging method from which quantitative cerebral blood flow (CBF) maps can be calculated. Acquisition with variable post‐labeling delays (PLD) and variable TRs allows for arterial transit time (ATT) mapping and leads to more accurate CBF quantification with a scan time saving of 48%. In addition, T1 and M0 maps can be obtained without a separate scan. In order to accurately estimate ATT and T1 of brain tissue from the ASL data, variable labeling durations were invented, entitled variable‐bolus ASL.Methods:All images were collected on a healthy subject with a 3T Siemens Skyra scanner. Variable‐bolus Psuedo‐continuous ASL (PCASL) images were collected with 7 TI times ranging 100‐4300ms in increments of 700ms with TR ranging 1000‐5200ms. All boluses were 1600ms when the TI allowed, otherwise the bolus duration was 100ms shorter than the TI. All TI times were interleaved to reduce sensitivity to motion. Voxel‐wise T1 and M0 maps were estimated using a linear least squares fitting routine from the average singal from each TI time. Then pairwise subtraction of each label/control pair and averaging for each TI time was performed. CBF and ATT maps were created using the standard model by Buxton et al. with a nonlinear fitting routine using the T1 tissue map.Results:CBF maps insensitive to ATT were produced along with ATT maps. Both maps show patterns and averages consistent with literature. The T1 map also shows typical T1 contrast.Conclusion:It has been demonstrated that variablebolus ASL produces CBF maps free from the errors due to ATT and tissue T1 variations and provides M0, T1, and ATT maps which have potential utility. This is accomplished with a single scan in a feasible scan time (under 6 minutes) with low sensivity to motion.
SU‐D‐9A‐01: Listmode‐Driven Optimal Gating (OG) Respiratory Motion Management: Potential Impact On Quantitative PET Imaging
Authors: Lee K , Hristov D 
Published: July 2014

Purpose:To evaluate the potential impact of listmode‐driven amplitude based optimal gating (OG) respiratory motion management technique on quantitative PET imaging.Methods:During the PET acquisitions, an optical camera tracked and recorded the motion of a tool placed on top of patients' torso. PET event data were utilized to detect and derive a motion signal that is directly coupled with a specific internal organ. A radioactivity‐trace was generated from listmode data by accumulating all prompt counts in temporal bins matching the sampling rate of the external tracking device. Decay correction for 18F was performed. The image reconstructions using OG respiratory motion management technique that uses 35% of total radioactivity counts within limited motion amplitudes were performed with external motion and radioactivity traces separately with ordered subset expectation maximization (OSEM) with 2 iterations and 21 subsets. Standard uptake values (SUVs) in a tumor region were calculated to measure the effect of using radioactivity trace for motion compensation. Motion‐blurred 3D static PET image was also reconstructed with all counts and the SUVs derived from OG images were compared with SUVs from 3D images.Results:A 5.7 % increase of the maximum SUV in the lesion was found for optimal gating image reconstruction with radioactivity trace when compared to a static 3D image. The mean and maximum SUVs on the image that was reconstructed with radioactivity trace were found comparable (0.4 % and 4.5 % increase, respectively) to the values derived from the image that was reconstructed with external trace.Conclusion:The image reconstructed using radioactivity trace showed that the blurring due to the motion was reduced with impact on derived SUVs. The resolution and contrast of the images reconstructed with radioactivity trace were comparable to the resolution and contrast of the images reconstructed with external respiratory traces.Research supported by Siemens
SU‐D‐9A‐02: Relative Effects of Threshold Choice and Spatial Resolution Modeling On SUV and Volume Quantification in F18‐FDG PET Imaging of Anal Cancer Patients
Authors: Zhao F , Bowsher J , Palta M , Czito B , Willett C , Yin F 
Published: July 2014

Purpose:PET imaging with F18‐FDG is utilized for treatment planning, treatment assessment, and prognosis. A region of interest (ROI) encompassing the tumor may be determined on the PET image, often by a threshold T on the PET standard uptake values (SUVs). Several studies have shown prognostic value for relevant ROI properties including maximum SUV value (SUVmax), metabolic tumor volume (MTV), and total glycolytic activity (TGA). The choice of threshold T may affect mean SUV value (SUVmean), MTV, and TGA. Recently spatial resolution modeling (SRM) has been introduced on many PET systems. SRM may also affect these ROI properties. The purpose of this work is to investigate the relative influence of SRM and threshold choice T on SUVmean, MTV, TGA, and SUVmax.Methods:For 9 anal cancer patients, 18F‐FDG PET scans were performed prior to treatment. PET images were reconstructed by 2 iterations of Ordered Subsets Expectation Maximization (OSEM), with and without SRM. ROI contours were generated by 5 different SUV threshold values T: 2.5, 3.0, 30%, 40%, and 50% of SUVmax. Paired‐samples t tests were used to compare SUVmean, MTV, and TGA (a) for SRM on versus off and (b) between each pair of threshold values T. SUVmax was also compared for SRM on versus off.Results:For almost all (57/60) comparisons of 2 different threshold values, SUVmean, MTV, and TGA showed statistically significant variation. For comparison of SRM on versus off, there were no statistically significant changes in SUVmax and TGA, but there were statistically significant changes in MTV for T=2.5 and T=3.0 and in SUVmean for all T.Conclusion:The near‐universal statistical significance of threshold choice T suggests that, regarding harmonization across sites, threshold choice may be a greater concern than choice of SRM. However, broader study is warranted, e.g. other iterations of OSEM should be considered.
SU‐D‐9A‐03: STAMP: Simulator for Texture Analysis in MRI/PET
Authors: Laberge S , Vallieres M , Levesque I R. , El Naqa I 
Published: July 2014

Purpose:To develop a convenient simulation platform to facilitate PET/MR image analysis with the prospect of gaining a better understanding of the influence of acquisition parameters on PET/MRI textural features. The simulation platform is demonstrated by showing textural variations of a representative case study using different image acquisition parameters.Methods:The simulation platform is composed of MRI simulators JEMRIS and SIMRI to achieve simulations of customized MRI sequences on sample tumor models. The PET simulator GATE is used to get 2D and 3D Monte Carlo acquisitions of voxelized PET sources using a phantom geometry and a customized scanner architecture. The platform incorporates a series of graphical user interfaces written in Matlab. Two GUIs are used to facilitate communication with the simulation executables installed on a computer cluster. A third GUI is used to collect and display the clinical and simulated images, as well as fused PET/MRI images, and perform computation of textural features. To illustrate the capabilities of this platform, one FDG‐PET and T1‐weighted (T1w) digitized tumor models were generated from clinical images of a soft‐tissue sarcoma patient. Numerically simulated MR images were produced using 3 different echo times (TE) and 5 different repetition times (TR). PET 2D images were simulated using an OSEM algorithm with 1 to 32 iterations and a post‐reconstruction Gaussian filter of 0, 2, 4 or 6 mm width.Results:STAMP was successfully used to produce numerically simulated FDG‐PET and MRI images, and to calculate their corresponding textures. Three typical textures (GLCM‐Contrast, GLSZM‐ZSV and NGTDM‐Coarseness) were found to vary by a range of 45% on average compared to reference scanning conditions in the case of FDG‐PET, and by a range of 40% in the case of T1w MRI.Conclusion:We have successfully developed a Matlab‐based simulation platform to facilitate PET/MRI texture image analysis for outcome prediction.