bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparisons of Anterior Plate Screw Pullout Strength Between Polyurethane Foams and Thoracolumbar Cadaveric Vertebrae
Authors: Nagaraja Srinidhi , Palepu Vivek
Published: August 2016

Synthetic polyurethane foams are frequently used in biomechanical testing of spinal medical devices. However, it is unclear what types of foam are most representative of human vertebral trabecular bone behavior, particularly for testing the bone–implant interface. Therefore, a study was conducted to compare polyurethane foam microstructure and screw pullout properties to human vertebrae. Cadaveric thoracolumbar vertebrae underwent microcomputed tomography to assess trabecular bone microstructure. Spine plate screws were implanted into the vertebral body and pullout testing was performed. The same procedure was followed for eight different densities (grades 5–30) of commercially available closed cell (CCF) and open cell foams (OCF). The results indicated that foam microstructural parameters such as volume fraction, strut thickness, strut spacing, and material density rarely matched that of trabecular bone. However, certain foams provided mechanical properties that were comparable to the cadavers tested. Pullout force and work to pullout for screws implanted into CCF grade 5 were similar to osteoporotic female cadavers. In addition, screw pullout forces and work to pullout in CCF grade 8, grade 10, and OCF grade 30 were similar to osteopenic male cadavers. All other OCF and CCF foams possessed pullout properties that were either significantly lower or higher than the cadavers tested. This study elucidated the types and densities of polyurethane foams that can represent screw pullout strength in human vertebral bone. Synthetic bone surrogates used for biomechanical testing should be selected based on bone quantity and quality of patients who may undergo device implantation.
Engineered Microvessels for the Study of Human Disease
Authors: Rayner Samuel G. , Zheng Ying
Published: August 2016

The microvasculature is an extensive, heterogeneous, and complex system that plays a critical role in human physiology and disease. It nourishes almost all living human cells and maintains a local microenvironment that is vital for tissue and organ function. Operating under a state of continuous flow, with an intricate architecture despite its small caliber, and subject to a multitude of biophysical and biochemical stimuli, the microvasculature can be a complex subject to study in the laboratory setting. Engineered microvessels provide an ideal platform that recapitulates essential elements of in vivo physiology and allows study of the microvasculature in a precise and reproducible way. Here, we review relevant structural and functional vascular biology, discuss different methods to engineer microvessels, and explore the applications of this exciting tool for the study of human disease.
An Ordinary Differential Equation Formulation for Multibody Dynamics: Nonholonomic Constraints
Authors: Haug Edward J.
Published: August 2016

A method is presented for formulating and numerically integrating ordinary differential equations of motion for nonholonomically constrained multibody systems. Tangent space coordinates are defined in configuration and velocity spaces as independent generalized coordinates that serve as state variables in the formulation, yielding ordinary differential equations of motion. Orthogonal-dependent coordinates and velocities are used to enforce constraints at position, velocity, and acceleration levels. Criteria that assure accuracy of constraint satisfaction and well conditioning of the reduced mass matrix in the equations of motion are used as the basis for updating local coordinates on configuration and velocity constraint manifolds, transparent to the user and at minimal computational cost. The formulation is developed for multibody systems with nonlinear holonomic constraints and nonholonomic constraints that are linear in velocity coordinates and nonlinear in configuration coordinates. A computational algorithm for implementing the approach is presented and used in the solution of three examples: one planar and two spatial. Numerical results using a fifth-order Runge–Kutta–Fehlberg explicit integrator verify that accurate results are obtained, satisfying all the three forms of kinematic constraint, to within error tolerances that are embedded in the formulation.
An Ontology for Reusable and Executable Decision Templates
Authors: Ming Zhenjun , Wang Guoxin , Yan Yan , Dal Santo Joseph , Allen Janet K. , Mistree Farrokh
Published: August 2016

Engineering design is increasingly recognized as a decision making process. Providing decision support is crucial to augment designers' decision-making capability in this process. In this paper, we present a template-based ontological method that integrates the decision-making mechanism with problem-specific information; thus, it can provide design decision support from both the “construct” and the “information” perspectives. The “construct,” namely, decision-making mechanism, is the utility-based Decision Support Problem (u-sDSP), which is a rigorous mathematical model that facilitates designers making multi-attribute selection decisions under uncertainty, while the information for decision making is archived as u-sDSP templates and represented using frame-based ontology to facilitate reuse, execution, and consistency-maintaining. This paper is an extension of our earlier work on the ontological modeling of the compromise decisions. The unique advantage of this ontology is that it captures both the declarative and procedural knowledge of selection decisions and represents them separately, thus facilitating designers reusing, executing previous documented decision knowledge to effect new decisions. The efficacy of ontology is demonstrated using a rapid prototyping (RP) resource selection example.
Open-Cell Metallic Porous Materials Obtained Through Space Holders—Part I: Production Methods. A Review
Authors: Stanev Lenko , Kolev Mihail , Drenchev Boris , Drenchev Ludmil
Published: August 2016

This article presents a review of current methods for production of metallic open-cell porous materials through space holders. The methods are divided into two major groups: on the basis of sintering and using liquid phase processing. Details about technologies are given, and their relations to structure parameters of obtained materials are discussed. Methods with 11 different space holders are described. The space holders could be metallic or nonmetallic (organic and inorganic) materials which could be leached or burned depending on removal technique. It is concluded that the flexible application of different space holders offers opportunities for obtaining large variety of metallic porous structures. A new line of development should be elaboration of complex techniques for production of porous structure with graded pore size and/or porosity which will meet various engineering requirements and will open new possibilities for applications as functional and structural elements. The next part of this work is devoted to the structure, the properties, and application of the open-cells porous materials obtained through space holders.
Identification of Friction Model Parameters Using the Inverse Harmonic Method
Authors: Hadji Abdallah , Mureithi Njuki
Published: August 2016

A hybrid friction model has been developed by Azizian and Mureithi (2013, “A Hybrid Friction Model for Dynamic Modeling of Stick–Slip Behavior,” ASME Paper No. PVP2013-97249) to simulate the general friction behavior between surfaces in contact. However, identification of the model parameters remains an unresolved problem. To identify the parameters of the friction model, the following quantities are required: contact forces (normal and tangential or friction forces), the slip velocity, and the displacement in the contact region. Simultaneous direct measurement of these quantities is difficult. In the present work, a beam clamped at one end and simply supported with the consideration of friction at the other is used as a mechanical amplifier of the friction effects at the microscopic level. Using this simplified approach, the contact forces, the sliding velocity, and the displacement can be indirectly obtained by measuring the beam vibration response. The inverse harmonic balance method is a new method based on nonlinear modal analysis which is developed in this work to calculate the contact forces. The method is based on the modal superposition principle and Fourier series expansion. Two formulations are possible: a harmonic form formulation and a subharmonic form formulation. The approach based on subharmonic forms coupled with spline fitting gave the best results for signal reconstruction. Signal reconstruction made it possible to accurately identify the parameters of the hybrid friction model with a multiple step approach.
Automatic Detection of Defects in a Swirl Burner Array Through an Exhaust Jet Pattern Analysis
Authors: Hartmann Ulrich , Hennecke Christoph , Dinkelacker Friedrich , Seume Joerg R.
Published: August 2016

A significant challenge in improving the regeneration process of jet engines is the reduction of engine down-time during inspection. As such, early defect detection without engine disassembly will speed up the regeneration process. Defects in the engines hot-gas path (HGP) influence the density distribution of the flow and lead to irregularities in the density distribution of the exhaust jet which can be detected with the optical background-oriented Schlieren (BOS) method in a tomographic setup. The present paper proposes a combination of tomographic BOS measurements and supervised learning algorithms to develop a methodology for an automatic defect detection system. In the first step, the methodology is tested by analyzing the exhaust jet of a swirl burner array with a nonuniform fuel-supply of single burners with tomographic BOS measurements. The measurements are used to implement a support vector machine (SVM) pattern recognition algorithm. It is shown that the reconstruction quality of tomographic BOS measurements is high enough to be combined with pattern recognition algorithms. The results strengthen the hypothesis that it is possible to automatically detect defects in jet engines with tomographic BOS measurements and pattern recognition algorithms.
How to Take Into Account Model Inaccuracy When Estimating the Uncertainty of the Result of Data Processing
Authors: Kreinovich Vladik , Kosheleva Olga , Pownuk Andrzej , Romero Rodrigo
Published: August 2016

In engineering design, it is important to guarantee that the values of certain quantities such as stress level, noise level, and vibration level, stay below a certain threshold in all possible situations, i.e., for all possible combinations of the corresponding internal and external parameters. Usually, the number of possible combinations is so large that it is not possible to physically test the system for all these combinations. Instead, we form a computer model of the system and test this model. In this testing, we need to take into account that the computer models are usually approximate. In this paper, we show that the existing techniques for taking model uncertainty into account overestimate the uncertainty of the results. We also show how we can get more accurate estimates.
Shape Optimization of the Pick-Up Tube in a Pitot-Tube Jet Pump
Authors: Meyer J. , Daróczy L. , Thévenin D.
Published: August 2016

At a very low specific speed (VLSS), pumps normally suffer from high disk friction losses. In order to solve this issue, it can be helpful to use a different centrifugal pump design, which is not often found in the pump industry: the Pitot-tube jet pump (PTJ pump). It shows superior performance at low specific speed due to a rather unconventional working principle, described in detail in this paper. The key design feature of the PTJ pump is the (fixed) pick-up tube. Its geometry has not varied over the last decades; it is referred to in this study as “initial” or “standard” design configuration. However, optimizing the pick-up tube might lead to a considerably higher performance. Therefore, a parameterized three-dimensional (3D) computer-aided design (CAD) model is used in this study to investigate the impact of shape deformation on pump performance with the help of computational fluid dynamics (CFD). Two CFD approaches are presented and compared for this purpose: a computationally efficient approach with limited accuracy (low-fidelity method) and a more detailed, but computationally more expensive, high-fidelity approach. Using both approaches, it is possible to obtain highly efficient PTJ pumps. As a consequence, first design rules can be derived. Finally, the optimized design has been tested for various operation points, showing that the performance is favorably impacted along the complete characteristic curve.
Sci‐Thur AM: YIS – 08: Automated Imaging Quality Assurance for Image‐Guided Small Animal Irradiators
Authors: Johnstone Chris , Bazalova‐Carter Magdalena
Published: August 2016

Purpose:

To develop quality assurance (QA) standards and tolerance levels for image quality of small animal irradiators.

Methods:

A fully automated in‐house QA software for image analysis of a commercial microCT phantom was created. Quantitative analyses of CT linearity, signal‐to‐noise ratio (SNR), uniformity and noise, geometric accuracy, modulation transfer function (MTF), and CT number evaluation was performed. Phantom microCT scans from seven institutions acquired with varying parameters (kVp, mA, time, voxel size, and frame rate) and five irradiator units (Xstrahl SARRP, PXI X‐RAD 225Cx, PXI X‐RAD SmART, GE explore CT/RT 140, and GE Explore CT 120) were analyzed. Multi‐institutional data sets were compared using our in‐house software to establish pass/fail criteria for each QA test.

Results:

CT linearity (R2>0.996) was excellent at all but Institution 2. Acceptable SNR (>35) and noise levels (<55HU) were obtained at four of the seven institutions, where failing scans were acquired with less than 120mAs. Acceptable MTF (>1.5 lp/mm for MTF=0.2) was obtained at all but Institution 6 due to the largest scan voxel size (0.35mm). The geometric accuracy passed (<1.5%) at five of the seven institutions.

Conclusion:

Our QA software can be used to rapidly perform quantitative imaging QA for small animal irradiators, accumulate results over time, and display possible changes in imaging functionality from its original performance and/or from the recommended tolerance levels. This tool will aid researchers in maintaining high image quality, enabling precise conformal dose delivery to small animals.
Sci‐Thur PM ‐ Colourful Interactions: Highlights 04: A Fast Quantitative MRI Acquisition and Processing Pipeline for Radiation Treatment Planning and Simulation
Authors: Jutras Jean‐David , De Zanche Nicola
Published: August 2016

MRI‐only Radiation Treatment Planning (RTP) is becoming increasingly popular because of a simplified work‐flow, and less inconvenience to the patient who avoids multiple scans. The advantages of MRI‐based RTP over traditional CT‐based RTP lie in its superior soft‐tissue contrast, and absence of ionizing radiation dose. The lack of electron‐density information in MRI can be addressed by automatic tissue classification. To distinguish bone from air, which both appear dark in MRI, an ultra‐short echo time (UTE) pulse sequence may be used. Quantitative MRI parametric maps can provide improved tissue segmentation/classification and better sensitivity in monitoring disease progression and treatment outcome than standard weighted images. Superior tumor contrast can be achieved on pure T1 images compared to conventional T1‐weighted images acquired in the same scan duration and voxel resolution.

In this study, we have developed a robust and fast quantitative MRI acquisition and post‐processing work‐flow that integrates these latest advances into the MRI‐based RTP of brain lesions. Using 3D multi‐echo FLASH images at two different optimized flip angles (both acquired in under 9 min, and 1mm isotropic resolution), parametric maps of T1, proton‐density (M0), and T2* are obtained with high contrast‐to‐noise ratio, and negligible geometrical distortions, water‐fat shifts and susceptibility effects. An additional 3D UTE MRI dataset is acquired (in under 4 min) and post‐processed to classify tissues for dose simulation. The pipeline was tested on four healthy volunteers and a clinical trial on brain cancer patients is underway.
Poster ‐ 10: QA of Ultrasound Images for Prostate Brachytherapy
Authors: Szpala Stanislaw , Kohli Kirpal S.
Published: August 2016

Purpose:

The current QA protocol of ultrasound systems used in prostate brachytherapy (TG128) addresses geometrical verifications, but the scope of evaluation of image quality is limited. We recognized importance of the latter in routine practice, and designed a protocol for QA of the images.

Methods:

Images of an ultrasound prostate phantom (CIRS053) were collected with BK Flex Focus 400. The images were saved as bmp after adjusting the gain to 50% for consistent results. Mean pixel values and signal to noise ratio were inspected in the representative sections of the phantom, including the mock prostate and the unechoic medium. Constancy of these numbers over a one year period was looked at.

Results:

The typical intensity in the mock prostate region in the transverse images ranged between 95 and 118 (out of 256), and the signal to noise was about 10. The intensity in the urethra region was about 170±40, and the unechoic medium was 2±2. The mean and the signal to noise ratio remained almost unchanged after a year, while the signal in the unechoic medium increased to about 7±4. Similar values were obtained in the sagittal images.

Conclusions:

The image analysis discussed above allows quick evaluation of constancy of the image quality. This may be also useful in troubleshooting image‐quality problems during routine exams, which might not be due to deterioration of the US system, but other reasons, e.g. variations in tissue properties or air being trapped between the probe and the anatomy.
Poster ‐ 14: Batch Effect Reduction in in‐vitro Raman Microscopic Radiosensitivity Study Using Ovarian Cancer Cells
Authors: Moradi Hamid , Murugkar Sangeeta , Ahmad Abrar , Shepherdson Dean , Nyiri Balazs , Vuong Nhung , Niedbala Gosia , Vanderhyden Barbara , Eapen Libni
Published: August 2016

Purpose:

To improve classification by reducing batch effect in samples from the ovarian carcinoma cell lines A2780s (parental wild type) and A2780cp (cisplatin cross‐radio‐resistant), before, right after, and 24 hours after irradiation to 10Gy.

Methods:

Spectra were acquired with a home built confocal Raman microscope in 3 distinct runs of six samples: unirradiated s&cp (control pair), then 0h and 24h after irradiation. The Raman spectra were noise reduced, then background subtracted with SMIRF algorithm. ∼35 cell spectra were collected from each sample in 1024 channels from 700cm‐1 to 1618cm‐1. The spectra were analyzed by regularized multiclass LDA.

For feature reduction the spectra were grouped into 3 overlapping group pairs: s‐cp, 0Gy–10Gy0h and 0Gy10–Gy24h. The three features, the three differences of the mean spectra were mapped to the analysis sub‐space by the inverse regularized covariance matrix. The batch effect noticeably confounded the dose and time effect.

Results:

To remove the batch effect, the 2+2=4D subspace extended by the covariance matrix of the means of the 0Gy control groups was subtracted from the spectra of each sample. Repeating the analysis on the spectra with the control group variability removed, the batch effect was dramatically reduced in the dose and time directions enabling sharp linear discrimination. The cell type classification also improved.

Conclusions:

We identified a efficient batch effect removal technique crucial to the applicability of Raman microscopy to radiosensitivity studies both on cell cultures and potential clinical diagnostic applications.
Poster ‐ 36: Effect of Planning Target Volume Coverage on the Dose Delivered in Lung Radiotherapy
Authors: Dekker Chris , Wierzbicki Marcin
Published: August 2016

Purpose:

In lung radiotherapy, breathing motion may be encompassed by contouring the internal target volume (ITV). Remaining uncertainties are included in a geometrical expansion to the planning target volume (PTV). In IMRT, the treatment is then optimized until a desired PTV fraction is covered by the appropriate dose. The resulting beams often carry high fluence in the PTV margin to overcome low lung density and to generate steep dose gradients. During treatment, the high density tumour can enter the PTV margin, potentially increasing target dose. Thus, planning lung IMRT with a reduced PTV dose may still achieve the desired ITV dose during treatment.

Methods:

A retrospective analysis was carried out with 25 IMRT plans prescribed to 63 Gy in 30 fractions. The plans were re‐normalized to cover various fractions of the PTV by different isodose lines. For each case, the isocentre was moved using 125 shifts derived from all 3D combinations of 0 mm, (PTV margin ‐ 1 mm), and PTV margin. After each shift, the dose was recomputed to approximate the delivered dose.

Results and Conclusion:

Our plans typically cover 95% of the PTV by 95% of the dose. Reducing the PTV covered to 94% did not significantly reduce the delivered ITV doses for (PTV margin ‐ 1 mm) shifts. Target doses were reduced significantly for all other shifts and planning goals studied. Thus, a reduced planning goal will likely deliver the desired target dose as long as the ITV rarely enters the last mm of the PTV margin.
Poster – 41: External marker block placement on the breast or chest wall for left‐sided deep inspiration breath‐hold radiotherapy
Authors: Conroy Leigh , Guebert Alexandra , Smith Wendy
Published: August 2016

Purpose:

We investigate DIBH breast radiotherapy using the Real‐time Position Management (RPM) system with the marker‐block placed on the target breast or chest wall.

Methods:

We measured surface dose for three different RPM marker‐blocks using EBT3 Gafchromic film at 0° and 30° incidence. A registration study was performed to determine the breast surface position that best correlates with overall internal chest wall position. Surface and chest wall contours from MV images of the medial tangent field were extracted for 15 patients. Surface contours were divided into three potential marker‐block positions on the breast: Superior, Middle, and Inferior. Translational registration was used to align the partial contours to the first‐fraction contour. Each resultant transformation matrix was applied to the chest wall contour, and the minimum distance between the reference chest wall contour and the transformed chest wall contour was evaluated for each pixel.

Results:

The measured surface dose for the 2‐dot, 6‐dot, and 4‐dot marker‐blocks at 0° incidence were 74%, 71%, and 77% of dose to dmax respectively. At 30° beam incidence this increased to 76%, 72%, and 81%. The best external surface position was patient and fraction dependent, with no consistent best choice.

Conclusions:

The increase in surface dose directly under the RPM block is approximately equivalent to 3 mm of bolus. No marker‐block position on the breast surface was found to be more representative of overall chest wall motion; therefore block positional stability and reproducibility can be used to determine optimal placement on the breast or chest wall.
Poster ‐ 43: Analysis of SBRT and SRS dose verification results using the Octavius 1000SRS detector
Authors: Cherpak Amanda
Published: August 2016

Purpose:

The Octavius 1000SRS detector was commissioned in December 2014 and is used routinely for verification of all SRS and SBRT plans. Results of verifications were analyzed to assess trends and limitations of the device and planning methods.

Methods:

Plans were delivered using a True Beam STx and results were evaluated using gamma analysis (95%, 3%/3mm) and absolute dose difference (5%). Verification results were analyzed based on several plan parameters including tumour volume, degree of modulation and prescribed dose.

Results:

During a 12 month period, a total of 124 patient plans were verified using the Octavius detector. Thirteen plans failed the gamma criteria, while 7 plans failed based on the absolute dose difference. When binned according to degree of modulation, a significant correlation was found between MU/cGy and both mean dose difference (r=0.78, p<0.05) and gamma (r=−0.60, p<0.05). When data was binned according to tumour volume, the standard deviation of average gamma dropped from 2.2% – 3.7% for the volumes less than 30 cm3 to below 1% for volumes greater than 30 cm3.

Conclusions:

The majority of plans and verification failures involved tumour volumes smaller than 30 cm3. This was expected due to the nature of disease treated with SBRT and SRS techniques and did not increase rate of failure. Correlations found with MU/cGy indicate that as modulation increased, results deteriorated but not beyond the previously set thresholds.
Poster ‐ 48: Clinical assessment of ExacTrac stereoscopic imaging of spine alignment for lung SBRT
Authors: Sattarivand Mike , Summers Clare , Robar James
Published: August 2016

Purpose:

To evaluate the validity of using spine as a surrogate for tumor positioning with ExacTrac stereoscopic imaging in lung stereotactic body radiation therapy (SBRT).

Methods:

Using the Novalis ExacTrac x‐ray system, 39 lung SBRT patients (182 treatments) were aligned before treatment with 6 degrees (6D) of freedom couch (3 translations, 3 rotations) based on spine matching on stereoscopic images. The couch was shifted to treatment isocenter and pre‐treatment CBCT was performed based on a soft tissue match around tumor volume. The CBCT data were used to measure residual errors following ExacTrac alignment. The thresholds for re‐aligning the patients based on CBCT were 3mm shift or 3° rotation (in any 6D). In order to evaluate the effect of tumor location on residual errors, correlations between tumor distance from spine and individual residual errors were calculated.

Results:

Residual errors were up to 0.5±2.4mm. Using 3mm/3° thresholds, 80/182 (44%) of the treatments required re‐alignment based on CBCT soft tissue matching following ExacTrac spine alignment. Most mismatches were in sup‐inf, ant‐post, and roll directions which had larger standard deviations. No correlation was found between tumor distance from spine and individual residual errors.

Conclusion:

ExacTrac stereoscopic imaging offers a quick pre‐treatment patient alignment. However, bone matching based on spine is not reliable for aligning lung SBRT patients who require soft tissue image registration from CBCT. Spine can be a poor surrogate for lung SBRT patient alignment even for proximal tumor volumes.
Poster ‐ 49: Assessment of Synchrony respiratory compensation error for CyberKnife liver treatment
Authors: Liu Ming , Cygler Joanna , Vandervoort Eric
Published: August 2016

The goal of this work is to quantify respiratory motion compensation errors for liver tumor patients treated by the CyberKnife system with Synchrony tracking, to identify patients with the smallest tracking errors and to eventually help coach patient's breathing patterns to minimize dose delivery errors. The accuracy of CyberKnife Synchrony respiratory motion compensation was assessed for 37 patients treated for liver lesions by analyzing data from system logfiles. A predictive model is used to modulate the direction of individual beams during dose delivery based on the positions of internally implanted fiducials determined using an orthogonal x‐ray imaging system and the current location of LED external markers. For each x‐ray pair acquired, system logfiles report the prediction error, the difference between the measured and predicted fiducial positions, and the delivery error, which is an estimate of the statistical error in the model overcoming the latency between x‐ray acquisition and robotic repositioning. The total error was calculated at the time of each x‐ray pair, for the number of treatment fractions and the number of patients, giving the average respiratory motion compensation error in three dimensions. The 99th percentile for the total radial error is 3.85 mm, with the highest contribution of 2.79 mm in superior/inferior (S/I) direction. The absolute mean compensation error is 1.78 mm radially with a 1.27 mm contribution in the S/I direction. Regions of high total error may provide insight into features predicting groups of patients with larger or smaller total errors.
Poster ‐ 53: Improving inter‐linac DMLC IMRT dose precision by fine tuning of MLC leaf calibration
Authors: Nakonechny Keith , Tran Muoi , Sasaki David , Beck James , Poirier Yannick , Malkoske Kyle
Published: August 2016

Purpose:

To develop a method to improve the inter‐linac precision of DMLC IMRT dosimetry.

Methods:

The distance between opposing MLC leaf banks (“gap size”) can be finely tuned on Varian linacs. The dosimetric effect due to small deviations from the nominal gap size (“gap error”) was studied by introducing known errors for several DMLC sliding gap sizes, and for clinical plans based on the TG119 test cases. The plans were delivered on a single Varian linac and the relationship between gap error and the corresponding change in dose was measured. The plans were also delivered on eight Varian 2100 series linacs (at two institutions) in order to quantify the inter‐linac variation in dose before and after fine tuning the MLC calibration.

Results:

The measured dose differences for each field agreed well with the predictions of LoSasso et al. Using the default MLC calibration, the variation in the physical MLC gap size was determined to be less than 0.4 mm between all linacs studied. The dose difference between the linacs with the largest and smallest physical gap was up to 5.4% (spinal cord region of the head and neck TG119 test case). This difference was reduced to 2.5% after fine tuning the MLC gap calibration.

Conclusions:

The inter‐linac dose precision for DMLC IMRT on Varian linacs can be improved using a simple modification of the MLC calibration procedure that involves fine adjustment of the nominal gap size.
Poster ‐ 55: Active Breathing Coordinator Based Treatment of Liver SBRT Patients
Authors: Karotki Aliaksandr , Erler Darby , Chu William , Chung Hans T.
Published: August 2016

Purpose:

Accuracy of treatment delivery for liver SBRT patients can be compromised by breathing induced motion. Recently we started using active breathing coordinator (ABC) to “freeze” the breathing motion. This work describes our initial experience with ABC based treatment of liver SBRT patients.

Methods:

Patients are treated in maximum exhale state with a minimum required breath hold time of 20 s. Fluoroscopy is used to assess diaphragm stability before both simulation and treatment. Depending on the proximity of organs at risk, 30–60 Gy are given in five fractions every other day and delivered via VMAT. CBCT is used for patient setup verification with robotic couch compensating for translations/rotations. An additional CBCT is acquired after every fraction to confirm patient's stability during treatment.

Results:

Six patients have successfully been treated using the ABC protocol so far with an approximate treatment time of 1 h. CBCT acquired after the treatment suggests that patients are stable and the liver position, when locked by ABC, is reproducible throughout the treatment (average deviation 1.9 mm). The major immediate benefit of using ABC is a drastic improvement in image quality of the CT simulation as well as CBCT images.

Conclusions:

ABC eliminates breathing motion and, as such, substantially improves the quality of the images acquired at CT simulation as well as CBCT images leading to more reliable dose delivery. The position of the liver remains stable for the duration of treatment when using the ABC system. The treatment is well tolerated by the patients.
Sci‐Fri PM: Radiation Therapy, Planning, Imaging, and Special Techniques ‐ 02: Feasibility of using multileaf collimation for stereotactic radiosurgery of arteriovenous malformation
Authors: Lee Young , Tsao May , Schwartz Michael , Ruschin Mark
Published: August 2016

SRS using linac and cones offers steep dose fall‐off but a tradeoff exists between conformality and treatment time, which depends on the number of isocentres. Purpose of this study is to quantify planning metrics between cones‐ and MLC‐based SRS for arteriovenous malformation(AVM).

Seven AVM cases treated with cones were re‐planned with MLC on Pinnacle treatment planning system. Planning target volume(PTV) was created with 1mm uniform margin to the AVM to account for MLC positional variation. Clinically‐planned prescription dose(15–25Gy) was used. Four plans were generated per case:non‐coplanar VMAT(ncV), single‐arc VMAT(saV), non‐coplanar IMRT(ncI), non‐coplanar conformal(ncC). Plans were compared for conformity(CI), heterogeneity(HI) and gradient(GI) indices and brain doses. Estimated treatment times and monitor units(MU) were compared.

Cone‐based plans required 2–6 isocentres. Though CI‐RTOG was similar for plans(median=0.98), CI‐Paddick was most favourable for ncV(median=0.86) and worst for cones(0.54). HI for MLC plans(median=1.19–1.27) were lower than cone‐based plans(1.43). GI was similar for all plans. For 2/7 ncC had brainstem maximum dose>16.7Gy and therefore were clinically unacceptable. Brain V12Gy,V10Gy,V2Gy were lowest in the cones plan. ncV brain V12Gy,V10Gy,V2Gy were lowest of all MLC‐based plans studied. Treatment MUs were similar for MLC‐based plans and up to 70% lower than clinically delivered plans.

ncV showed best conformality in this study. Of the MLC‐based plans, ncV also showed lowest normal tissue dose with reasonable treatment time.
Sci‐Fri PM: Radiation Therapy, Planning, Imaging, and Special Techniques ‐ 06: Patient‐specific QA Procedure for Gated VMAT SABR Treatments using 10x Beam in Flattening‐Filter Free Mode
Authors: Mestrovic Ante , Chitsazzadeh Shadi , Wells Derek M. , Gray Stephen
Published: August 2016

Purpose:

To develop a highly sensitive patient specific QA procedure for gated VMAT stereotactic ablative radiotherapy (SABR) treatments.

Methods:

A platform was constructed to attach the translational stage of a Quasar respiratory motion phantom to a pinpoint ion chamber insert and move the ion chamber inside the ArcCheck. The Quasar phantom controller uses a patient‐specific breathing pattern to translate the ion chamber in a superior‐inferior direction inside the ArcCheck. With this system the ion chamber is used to QA the correct phase of the gated delivery and the ArcCheck diodes are used to QA the overall dose distribution. This novel approach requires a single plan delivery for a complete QA of a gated plan. The sensitivity of the gating QA procedure was investigated with respect to the following parameters: PTV size, exhale duration, baseline drift, gating window size.

Results:

The difference between the measured dose to a point in the penumbra and the Eclipse calculated dose was under 2% for small residual motions. The QA procedure was independent of PTV size and duration of exhale. Baseline drift and gating window size, however, significantly affected the penumbral dose measurement, with differences of up to 30% compared to Eclipse.

Conclusion:

This study described a highly sensitive QA procedure for gated VMAT SABR treatments. The QA outcome was dependent on the gating window size and baseline drift. Analysis of additional patient breathing patterns is currently undergoing to determine a clinically relevant gating window size and an appropriate tolerance level for this procedure.
Balloon and Button Spectroscopy: A Hands-On Approach to Light and Matter
Authors: Ribaudo Joseph
Published: August 2016

Without question, one of the most useful tools an astronomer or physicist can employ to study the universe is spectroscopy. However, for students in introductory physics or astronomy classes, spectroscopy is a relatively abstract concept that combines new physics topics such as thermal radiation, atomic physics, and the wave and particle nature of light and matter. In response to this conceptual hurdle, we have developed an exercise where balloons represent stars, buttons represent photons, and students produce and interpret spectra by sorting colored buttons.
“Deflategate”: Time, Temperature, and Moisture Effects on Football Pressure
Authors: Blumenthal Jack , Beljak Lauren , Macatangay Dahlia-Marie , Helmuth-Malone Lilly , McWilliams Catharina , Raptis Sofia
Published: August 2016

In a recent paper in TPT, DiLisi and Rarick used the National Football League “Deflategate” controversy to introduce to physics students the physics of a bouncing ball. In this paper, we measure and analyze the environmental effects of time, ambient temperature, and moisture on the internal pressure of an NFL football. We focus on the rate of pressure recovery that occurs when a cold football (either wet or dry) is returned to the warm locker room environment where the pressure was initially measured. Both studies stem from the so-called NFL “Deflategate” controversy in which footballs that initially met a minimum internal pressure requirement were rechecked at halftime of the AFC Championship game, and in some cases were reported to have fallen below the minimum pressure requirement. The question is whether the pressure changes were due to environmental exposure or rather to some air being released from the balls, or both.
Smartphones and Time Zones
Authors: Baird William , Secrest Jeffery , Padgett Clifford , Johnson Wayne , Hagrelius Claire
Published: August 2016

Using the Sun to tell time is an ancient idea, but we can take advantage of modern technology to bring it into the 21st century for students in astronomy, physics, or physical science classes. We have employed smartphones, Google Earth, and 3D printing to find the moment of local noon at two widely separated locations. By reviewing GPS time-stamped photos from each place, we are able to illustrate that local noon is longitude-dependent and therefore explain the need for time zones.
And the Survey Says …
Authors: White Susan C.
Published: August 2016

Since 1987, the Statistical Research Center at the American Institute of Physics has regularly conducted a survey of high school physics teachers. This September we’re at it again. This fall, we will look for physics teachers at each of the 4,000+ schools with 12th grade in our nationally representative sample of public and private schools. We will use web searches, and we will contact the principal or science coordinator. In the spring of 2017, we will contact all the teachers who teach at least one physics class that we can identify. From prior rounds of the survey, we know that as many as 40% of the teachers who teach a physics class teach a majority of their classes in another subject.
A novel GABA-mediated corticotropin-releasing hormone secretory mechanism in the median eminence
Authors: Kakizawa Keisuke , Watanabe Miho , Mutoh Hiroki , Okawa Yuta , Yamashita Miho , Yanagawa Yuchio , Itoi Keiichi , Suda Takafumi , Oki Yutaka , Fukuda Atsuo
Published: August 2016

Excitatory GABAergic input from arcuate nucleus maintains steady-state CRH release from axon terminals with NKCC1-driven high [Cl
−
]
i
.
Rising sea levels will reduce extreme temperature variations in tide-dominated reef habitats
Authors: Lowe Ryan Joseph , Pivan Xavier , Falter James , Symonds Graham , Gruber Renee
Published: August 2016

Tidal and solar cycles interact to regulate temperature extremes in tide-dominated reefs and will be reduced with sea level rise.
Bones record demise of Andean state
Authors: Wade Lizzie
Published: August 2016

Violent death surged as drought and political turmoil doomed the Wari.
New polio cases in Nigeria spur massive response
Authors: Roberts Leslie
Published: August 2016

Country's hopes for polio-free status are dashed.
Mission possible: Rewriting the genetic code
Authors: Bohannon John
Published: August 2016

A research team is making steady progress at overhauling a bacterium's genome.
Quantum thermalization through entanglement in an isolated many-body system
Authors: Kaufman Adam M. , Tai M. Eric , Lukin Alexander , Rispoli Matthew , Schittko Robert , Preiss Philipp M. , Greiner Markus
Published: August 2016

To thermalize, or not to thermalize?

Intuition tells us that an isolated physical system subjected to a sudden change (i.e., quenching) will evolve in a way that maximizes its entropy. If the system is in a pure, zero-entropy quantum state, it is expected to remain so even after quenching. How do we then reconcile statistical mechanics with quantum laws? To address this question, Kaufman
et al.
used their quantum microscope to study strings of six rubidium atoms confined in the wells of an optical lattice (see the Perspective by Polkovnikov and Sels). When tunneling along the strings was suddenly switched on, the strings as a whole remained in a pure state, but smaller subsets of two or three atoms conformed to a thermal distribution. The force driving the thermalization was quantum entanglement.

Science
, this issue p.
794
; see also p.
752
Integration of omic networks in a developmental atlas of maize
Authors: Walley Justin W. , Sartor Ryan C. , Shen Zhouxin , Schmitz Robert J. , Wu Kevin J. , Urich Mark A. , Nery Joseph R. , Smith Laurie G. , Schnable James C. , Ecker Joseph. R. , Briggs Steven P.
Published: August 2016

Patterns of development regulation within tissues

Expression of a given gene at the RNA level does not always correlate with expression at the protein level for many organisms. Walley
et al.
have built an integrated atlas of gene expression and regulatory networks in developing maize, using the same tissue samples to measure the transcriptome, proteome, and phosphoproteome. Coexpression networks from the transcriptome and proteome showed little overlap with each other, even though they showed enrichment of similar pathways. Integration of mRNA, protein, and phosphoprotein data sets improved the predictive power of the gene regulatory networks.

Science
, this issue p.
814
Evaluation of Two Enzyme-Linked Immunosorbent Assay Kits for Chikungunya Virus IgM Using Samples from Deceased Organ and Tissue Donors
Authors: Prince Harry E. , Altrich Michelle L. , Nowicki Marek J.
Published: August 2016

The identification of nearly 3,500 cases of chikungunya virus (CHIKV) infection in U.S. residents returning in 2014 and 2015 from areas in which it is endemic has raised concerns within the transplant community that, should recently infected individuals become organ and/or tissue donors, CHIKV would be transmitted to transplant recipients. Thus, tests designed to detect recent CHIKV infection among U.S. organ and tissue donors may become necessary in the future. Accordingly, we evaluated 2 enzyme-linked immunosorbent assays (ELISAs) for CHIKV IgM readily available in the United States using 1,000 deidentified serum or plasma specimens collected from donors between November 2014 and March 2015. The Euroimmun indirect ELISA identified 38 reactive specimens; however, all 38 were negative for CHIKV IgG and IgM in immunofluorescence assays (IFAs) conducted at a reference laboratory and, thus, were falsely reactive in the Euroimmun CHIKV IgM assay. The InBios IgM-capture ELISA identified 26 reactive samples, and one was still reactive (index ≥ 1.00) when retested using the InBios kit with a background subtraction modification to identify false reactivity. This reactive specimen was CHIKV IgM negative but IgG positive by IFAs at two reference laboratories; plaque reduction neutralization testing (PRNT) demonstrated CHIKV-specific reactivity. The IgG and PRNT findings strongly suggest that the InBios CHIKV IgM-reactive result represents true reactivity, even though the IgM IFA result was negative. If testing organ/tissue donors for CHIKV IgM becomes necessary, the limitations of the currently available CHIKV IgM ELISAs and options for their optimization must be understood to avoid organ/tissue wastage due to falsely reactive results.
Differential Detection of Human Papillomavirus Genotypes and Cervical Intraepithelial Neoplasia by Four Commercial Assays
Authors: Rebolj Matejka , Bonde Jesper , Preisler Sarah , Ejegod Ditte , Rygaard Carsten , Lynge Elsebeth
Published: August 2016

Laboratories now can choose from >100 human papillomavirus (HPV) assays for cervical screening. Our previous analysis based on the data from the Danish Horizon study, however, showed that four widely used assays, Hybrid Capture 2 (HC2), cobas, CLART, and Aptima, frequently do not detect the same HPV infections. Here, we determined the characteristics of the concordant samples (all four assays returning a positive HPV test result) and discordant samples (all other HPV-positive samples) in primary cervical screening at 30 to 65 years of age (
n
= 2,859) and in a concurrent referral population from the same catchment area (
n
= 885). HPV testing followed the manufacturers' protocols. Women with abnormal cytology were managed according to the routine recommendations. Cytology-normal/HPV-positive women were invited for repeated testing in 18 months. Screening history and histologically confirmed cervical intraepithelial neoplasia (CIN) in 2.5 years after the baseline testing were determined from the national pathology register. HPV-positive women undergoing primary screening having concordant samples were more likely to harbor high-risk infections and less likely to harbor only low-risk infections than women with discordant samples. Additionally, assay signal strengths were substantially higher in concordant samples. More than 80% of ≥CIN2 results were found for women with concordant samples, and no ≥CIN2 results were found when the infection was detected by only one assay. These patterns were similar in the referral population despite the younger age and higher number of HPV infections. HPV test result discordance identified a cluster of low-risk HPV infections that were hardly ever associated with high-grade CIN and, almost exclusively, represented false-positive screening findings.
Force Sensitivity in Saccharomyces cerevisiae Flocculins
Authors: Chan Cho X. J. , El-Kirat-Chatel Sofiane , Joseph Ivor G. , Jackson Desmond N. , Ramsook Caleen B. , Dufrêne Yves F. , Lipke Peter N.
Published: August 2016

The
Saccharomyces cerevisiae
flocculins mediate the formation of cellular aggregates and biofilm-like mats, useful in clearing yeast from fermentations. An important property of fungal adhesion proteins, including flocculins, is the ability to form catch bonds, i.e., bonds that strengthen under tension. This strengthening is based, at least in part, on increased avidity of binding due to clustering of adhesins in cell surface nanodomains. This clustering depends on amyloid-like β-aggregation of short amino acid sequences in the adhesins. In
Candida albicans
adhesin Als5, shear stress from vortex mixing can unfold part of the protein to expose aggregation-prone sequences, and then adhesins aggregate into nanodomains. We therefore tested whether shear stress from mixing can increase flocculation activity by potentiating similar protein remodeling and aggregation in the flocculins. The results demonstrate the applicability of the Als adhesin model and provide a rational framework for the enhancement or inhibition of flocculation in industrial applications.