Translational Position Research Articles

Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome

Ribonucleotides misincorporated by replicative DNA polymerases are by far the most common DNA lesion. The presence of ribonucleotides in DNA is associated with genome instability, causing replication stress, chromosome fragility, gross chromosomal rearrangements, and other mutagenic events. Furthermore, nucleosome and chromatin assembly as well as nucleosome positioning are affected by the presence of ribonucleotides. Notably, nucleosome formation is significantly reduced by a single ribonucleotide. Single ribonucleotides are primarily removed from DNA by the ribonucleotide excision repair (RER) pathway via the RNase H2 enzyme, which incises the DNA backbone on the 5′-side of the ribonucleotide. While the structural implications of a single ribonucleotide in free duplex DNA have been well studied, how a single ribonucleotide embedded in nucleosomal DNA impacts nucleosome structure and dynamics, and the possible consequent impact on RER, have not been explored. We have carried out 3.5 μs molecular dynamics simulations of a single ribonucleotide incorporated at various translational and rotational positions in a nucleosome core particle. We find that the presence of the 2′−OH group on the ribose impacts the local conformation and dynamics of both the ribonucleotide and nearby DNA nucleotides as well as their interactions with histones; the nature of these disturbances depends on the rotational and translational setting, including whether the ribose faces toward or away from the histones. The ribonucleotide’s preferred C3′-endo pucker is stabilized by interactions with the histones, and furthermore the ribonucleotide can cause dynamic local duplex disturbance involving an abnormal C3′-endo population of the adjacent deoxyribose pucker, minor groove opening, ruptured Watson-Crick pairing, and duplex unwinding that are governed by translation-dependent histone-nucleotide interactions. Possible effects of these disturbances on RER are considered.

Accurate and efficient data acquisition methods for high-resolution angle-resolved photoemission microscopy

Angle-resolved photoemission spectroscopy (ARPES) is a powerful experimental technique in materials science, as it can directly probe electronic states inside solids in energy (E) and momentum (k) space. As an advanced technique, spatially-resolved ARPES using a well-focused light source (high-resolution ARPES microscopy) has recently attracted growing interests because of its capability to obtain local electronic information at micro- or nano-metric length scales. However, there exist several technical challenges to guarantee high precision in determining translational and rotational positions in reasonable measurement time. Here we present two methods of obtaining k-space mapping and real-space imaging in high-resolution ARPES microscopy. One method is for k-space mapping measurements that enables us to keep a target position on a sample surface during sample rotation by compensating rotation-induced displacements (tracing acquisition method). Another method is for real-space imaging measurements that significantly reduces total acquisition time (scanning acquisition method). We provide several examples of these methods that clearly indicate higher accuracy in k-space mapping as well as higher efficiency in real-space imaging, and thus improved throughput of high-resolution APRES microscopy.

Defining TP53 pioneering capabilities with competitive nucleosome binding assays.

Accurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a TF binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest TP53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how TP53 binds to nucleosomal DNA. To comprehensively examine TP53 nucleosome binding, we competitively bound TP53 to multiple in vitro–formed nucleosomes containing a high- or low-affinity TP53 TFBS located at differing translational and rotational positions within the nucleosome. Stable TP53–nucleosome complexes were isolated and quantified using next-generation sequencing. Our results demonstrate TP53 binding is limited to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. Binding site affinity only affects TP53 binding for TFBSs located at the same nucleosomal positions; otherwise, nucleosome position takes precedence. Furthermore, TP53 has strong nonspecific nucleosome binding facilitating its interaction with chromatin. Our in vitro findings were confirmed by examining TP53-induced binding in a cell line model, showing induced binding at nucleosome edges flanked by a nucleosome-free region. Overall, our results suggest that the pioneering capabilities of TP53 are driven by nonspecific nucleosome binding with specific binding at nucleosome edges.

Nonlinear Vision-Based Observer for Visual Servo Control of an Aerial Robot in Global Positioning System Denied Environments

This paper presents a nonlinear vision-based observer to estimate 3D translational position and velocity of a quadrotor aerial robot for closed-loop, position-based, visual-servo control in global positioning system (GPS)-denied environments. The method allows for motion control in areas where GPS signals are weak or absent, for example, inside of a building. Herein, the robot uses a low-cost on-board camera to observe at least two feature points fixed in the world frame to self-localize for feedback control, without constraints on the altitude of the robot. The nonlinear observer described takes advantage of the geometry of the perspective projection and is designed to update the translational position and velocity in real-time by exploiting visual information and information from an inertial measurement unit. One key advantage of the algorithm is it does not require constraints or assumptions on the altitude and initial estimation errors. Two new controllers based on the backstepping technique that take advantage of the estimator's output are described and implemented for trajectory tracking. The Lyapunov method is used to show asymptotic stability of the closed-loop system. Simulation and experimental results from an indoor environment where GPS localization is not available are presented to demonstrate feasibility and validate the performance of the observer and control system for hovering and tracking a circular trajectory defined in the world frame.

A unified computational framework for modeling genome-wide nucleosome landscape

Nucleosomes form the fundamental building blocks of eukaryotic chromatin, and previous attempts to understand the principles governing their genome-wide distribution have spurred much interest and debate in biology. In particular, the precise role of DNA sequence in shaping local chromatin structure has been controversial. This paper rigorously quantifies the contribution of hitherto-debated sequence features—including G+C content, 10.5 bp periodicity, and poly(dA:dT) tracts—to three distinct aspects of genome-wide nucleosome landscape: occupancy, translational positioning and rotational positioning. Our computational framework simultaneously learns nucleosome number and nucleosome-positioning energy from genome-wide nucleosome maps. In contrast to other previous studies, our model can predict both in vitro and in vivo nucleosome maps in Saccharomyces cerevisiae. We find that although G+C content is the primary determinant of MNase-derived nucleosome occupancy, MNase digestion biases may substantially influence this GC dependence. By contrast, poly(dA:dT) tracts are seen to deter nucleosome formation, regardless of the experimental method used. We further show that the 10.5 bp nucleotide periodicity facilitates rotational but not translational positioning. Applying our method to in vivo nucleosome maps demonstrates that, for a subset of genes, the regularly-spaced nucleosome arrays observed around transcription start sites can be partially recapitulated by DNA sequence alone. Finally, in vivo nucleosome occupancy derived from MNase-seq experiments around transcription termination sites can be mostly explained by the genomic sequence. Implications of these results and potential extensions of the proposed computational framework are discussed.

A proposed method for linear accelerator photon beam steering using EPID.

Beam steering is the process of calibrating the angle and translational position with which a linear accelerator's (linac's) electron beam strikes the x‐ray target with respect to the collimator rotation axis. The shape of the dose profile is highly dependent on accurate beam steering and is essential for ensuring correct delivery of the radiotherapy treatment plan. Traditional methods of beam steering utilize a scanning water tank phantom that makes the process user‐dependent. This study is the first to provide a methodology for both beam angle steering and beam translational position steering based on EPID imaging of the beam and does not require a phantom. Both the EPID‐based beam angle steering and beam translational steering methods described have been validated against IC Profiler measurement. Wide field symmetry agreement was found between the EPID and IC Profiler to within 0.06 ± 0.14% (1 SD) and 0.32 ± 0.11% (1 SD) for flattened and flattening‐filter‐free (FFF) beams, respectively. For a 1.1% change in symmetry measured by IC Profiler the EPID method agreed to within 0.23%. For beam translational position steering, the EPID method agreed with IC Profiler method to within 0.03 ± 0.05 mm (1 SD) at isocenter. The EPID‐based methods presented are quick to perform, simple, accurate and could easily be integrated with the linac, potentially via the MPC application. The methods have the potential to remove user variability and to standardize the process of beam steering throughout the radiotherapy community.

Collision Risk Mitigation of Varian TrueBeam Linear Accelerator With Supplemental Live-View Cameras

BackgroundNoncoplanar radiation therapy techniques such as 4π have potential dosimetric advantages but introduce complexities in treatment delivery that increase the risk for collision. Direct or remote visual confirmation of clearance is a safeguard against collisions of the gantry, couch, and patient. With our institution’s Varian TrueBeam system, we identified configurations that cannot be visualized with the included closed-circuit television cameras. At our practice, electronic, portal imaging device (EPID) collision risk also exists because of the routine deployment to capture exit-dose images for treatment quality assurance. We propose a simple, cost-effective solution using network cameras to help eliminate blind spots that permits safe, noncoplanar arrangements with an EPID-acquired exit dose. Methods and materialsTwo Panasonic cameras were installed overhead while a third Panasonic camera was mounted onto the pedestal to monitor the couch undersurface. Live views from each camera were accessed with a web-based client. The EPID and gantry were visually assessed at 52 couch and gantry rotational angle configurations at 6 couch translational positions. Visibility was compared for the standard and supplemental camera setups at each configuration (χ2 test). ResultsOf the 294 assessable couch-gantry configurations, the standard camera setup had limited visibility of either gantry or EPID for 146 configurations compared with 72 configurations with additional cameras (51% blind-spot reduction; P < .01). An 87% blind-spot reduction was observed for our laterally centered, cranial-based, couch translational position (P < .01). ConclusionsThe supplemental cameras were simple, effective additions for collision detection, especially for noncoplanar radiation therapy with EPID-acquired, exit-dose imaging. Over half of the assessable noncoplanar configurations had blind spots using standard cameras, which was reduced to <25% with additional cameras. In practice, there were almost no blind spots for patients with brain tumors who were treated with our templated beam arrangements. Using live-view camera feeds, vault re-entry to visually confirm clearance was reduced approximately 10-fold, which increased the treatment efficiency. In the most recent 12 months, no collision or near-collision events have been reported.

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens.

We have adapted the yeast 2-hybrid assay to simultaneously uncover dozens of transient and static protein interactions within a single screen utilizing high-throughput short-read DNA sequencing. The resulting sequence datasets can not only track what genes in a population that are enriched during selection for positive yeast 2-hybrid interactions, but also give detailed information about the relevant subdomains of proteins sufficient for interaction. Here, we describe a full suite of stand-alone software programs that allow non-experts to perform all the bioinformatics and statistical steps to process and analyze DNA sequence fastq files from a batch yeast 2-hybrid assay. The processing steps covered by these software include: 1) mapping and counting sequence reads corresponding to each candidate protein encoded within a yeast 2-hybrid prey library; 2) a statistical analysis program that evaluates the enrichment profiles; and 3) tools to examine the translational frame and position within the coding region of each enriched plasmid that encodes the interacting proteins of interest.

A Load Transportation Nonlinear Control Strategy Using a Tilt-Rotor UAV

This paper proposes a nonlinear control strategy to solve the trajectory tracking problem of a tilt-rotor Unmanned Aerial Vehicle (UAV) when transporting a suspended load. For the present study, the aim of the control system is to track a desired trajectory of the aircraft with load’s swing-free, even in the presence of external disturbances, parametric uncertainties, unmodeled dynamics, and noisy position measurements with lower sampling frequency than the controller. The whole system modeling is obtained through the Euler-Lagrange formulation considering the dynamics of the tilt-rotor UAV coupled to the suspended load. As for the nonlinear control strategy, an inner-loop control is designed based on input-output feedback linearization combined with the dynamic extension approach to stabilize the attitude and altitude of the UAV assuming nonlinearities, while an outer-loop control law is designed for guiding the aircraft with reduced load swing. The linearized dynamics are controlled using linear mixed H2/H∞ controllers with pole placement constraints. The solution is compared to two simpler control systems: the first one considers the load as a disturbance to the system but does not avoid its swing; the second one is a previous academic result with a three-level cascade strategy. Finally, in order to deal with the problem of position estimation in presence of unknown disturbances and noisy measurements with low sampling frequency, a Linear Kalman Filter with Unknown Inputs is designed for estimating both the aircraft’s translational position and translational disturbances. Simulation results are carried out to corroborate the proposed control strategy.

Plug-and-Play Approach for Preparing Chromatin Containing Site-Specific DNA Modifications: The Influence of Chromatin Structure on Base Excision Repair.

The genomic DNA of eukaryotic cells exists in the form of chromatin, the structure of which controls the biochemical accessibility of the underlying DNA to effector proteins. In order to gain an in depth molecular understanding of how chromatin structure regulates DNA repair, detailed in vitro biochemical and biophysical studies are required. However, because of challenges associated with reconstituting nucleosome arrays containing site-specifically positioned DNA modifications, such studies have been limited to the use of mono- and dinucleosomes as model in vitro substrates, which are incapable of folding into native chromatin structures. To address this issue, we developed a straightforward and general approach for assembling chemically defined oligonucleosome arrays (i.e., designer chromatin) containing site-specifically modified DNA. Our method takes advantage of nicking endonucleases to excise short fragments of unmodified DNA, which are subsequently replaced with synthetic oligonucleotides containing the desired modification. Using this approach, we prepared several oligonucleosome substrates containing precisely positioned 2'-deoxyuridine (dU) residues and examined the efficiency of base excision repair (BER) within several distinct chromatin architectures. We show that, depending on the translational position of the lesion, the combined catalytic activities of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) can be either inhibited by as much as 20-fold or accelerated by more than 5-fold within compact chromatin (i.e., the 30 nm fiber) relative to naked DNA. Moreover, we demonstrate that digestion of dU by UDG/APE1 proceeds much more rapidly in mononucleosomes than in compacted nucleosome arrays, thereby providing the first direct evidence that internucleosome interactions play an important role in regulating BER within higher-order chromatin structures. Overall, this work highlights the value of performing detailed biochemical studies on precisely modified chromatin substrates in vitro and provides a robust platform for investigating DNA modifications in chromatin biology.

2234 Developing the future translational science workforce at the University of Iowa

2234 Developing the future translational science workforce at the University of Iowa

Positioning error and expanding margins of planning target volume with kilovoltage cone beam computed tomography for prostate cancer radiotherapy

ObjectiveIn this study, prostate cancer patients were treated with image-guided radiotherapy (IGRT). The translational positioning errors were discussed to provide the basis for determining margins of the planning target volume (PTV).MethodsThirty prostate cancer patients were treated with radical radiotherapy using the IGRT system. Patients were placed in the supine position and underwent kilovoltage cone beam computed tomography (KVCBCT) scans before radiotherapy. A total of 447 images were acquired. The translational positioning errors were obtained in three linear directions which were X (left-to-right), Y (superior-to-inferior) and Z (anterior-to-posterior) axes (denoted as Lx, Ly and Lz) through the contrast between images adjusted with gray and manual registrations and the planning CT images. Rotational errors were denoted as Rx, Ry and Rz.ResultsUncorrected translational errors Lx, Ly and Lz in the 251 positioning images were all higher than those after correction, and the differences were all statistically significant (P=0.000, 0.037 and 0.004, respectively). For rotational errors Rx, Ry and Rz, only Rx had a significant difference before and after correction (P=0.044). Before correction, PTV margins in the X, Y and Z directions were 0.61, 0.78 and 0.41 cm, respectively; after correction, these were 0.17, 0.12 and 0.17 cm, respectively.ConclusionKVCBCT can be applied to measure positioning errors in prostate cancer radiotherapy and correct these errors in real time through the 6° robotic patient positioning system, in order to improve patient positioning accuracy. The application of IGRT with KVCBCT may reduce PTV margins.

Correct Assessment of Acetabular Component Orientation in Total Hip Arthroplasty From Plane Radiographs

BackgroundCorrect positioning of the cup is an important factor in total hip arthroplasty. Assessing its position from a plain anteroposterior pelvic radiograph is known to be hampered by systemic errors. This study focuses on developing a correction method to adjust for these potential sources of error and to eliminate them based on a 3D geometric analysis. MethodsComputed tomography scans of 113 (66 male, 47 female) pelvices were reconstructed and virtually projected onto a plain radiograph with varying rotational and translational positions. Thus cup inclination and anteversion as measured on a 2D-radiograph and in the 3D environment were correlated. Projected offset of the symphysis from the mid-sacrum served as a mean to measure pelvic right/left-rotation. Pelvic tilt was determined from the projected height of the contour of the small pelvis. Correction formulas were verified by projecting a gimbal-mounted artificial pelvis with a cup implanted in a known position. ResultsWe found gender-specific formulas that correct for malrotated and off-centered radiographs. Applying these formulas cup inclination was assessed as close as 1.3° (±1.90°) to the true 3D value and cup anteversion as close as 1° (±1.91°) although deviations between directly measured plain values and corrected values rose up to 18°. ConclusionInherent effects of central projection and malrotations due to pelvic tilt, pelvic rotation, and noncentered radiographs are corrected. Evaluation of radiographic inclination and anteversion of acetabular cups from plain 2D-radiographs show improved precision. Real values are approached better than 1.3° when applying our correction formulas.

Generalized shift-rotation absolute measurement method for high-numerical-aperture spherical surfaces with global optimized wavefront reconstruction algorithm.

In this paper, a generalized shift-rotation absolute measurement method is proposed to measure the absolute surface shape of high-numerical-aperture spherical surfaces. Based on the wavefront difference method, the high order misalignment aberrations can be removed from the measurements. Our generalized shift-rotation absolute measurement process only needs one rotational measurement position and one translational measurement position. A wavefront reconstruction method based on the self-adaptive differential evolution algorithm is proposed to calculate the Zernike polynomials coefficient ai of the absolute surface shape Wtest(x,y), the rotation angle Δθ, the translation δx along the x axis, and the translation δy along the y axis. The translation error and rotation error in other absolute measurement methods are avoided using our generalized shift-rotation absolute measurement method. Experimental absolute results of the test surface and reference surface are given and the difference of reference surface shapes between two testings in experiments is 0.12 nm root mean square.

Subluxation of knees in TKA - a neglected fact? An in vitro study.

Aims and Objectives:Correct implant alignment is a well known factor for good functional results and increased implant survival after total knee arthroplasty (TKA). However, in present studies only coronal, sagittal and rotational alignment parameters have been considered, while translational parameters, the relative position between the femur and the tibia in medio-lateral, ventro-dorsal and proximo-distal direction are widely neglected. Due to variable mediolateral, proximodistal and ventrodorsal component placement in TKA, we hypothesised changed relative positions between the femoral and tibial bone resulting in a subluxation of knees after TKA.Materials and Methods:In nine Thiel embalmed whole body cadavers without any history of orthopaedic surgeries, fracutres and osteoarthritis, the relative positions between the femoral and tibial bones were measured between 0 and 90° of flexion before and after TKA (DePuy PFC Sigma, CR, fixed bearing) by means of a navigation system (Brainlab 2.6, Feldkirchen). To compare femoral positions before and after TKA, a paired t-test was used. A two-sided p-value of <0.05 was considered statistically significant.Results:In full extension, the femoral bones shifted 5.7 mm laterally(SD 4.0, p=0.003), and 2.7 proximally (SD 3.1, p=0.030), which decreased up to 90° of flexion to a lateral shift of 3.7 mm (SD 3.5, p=0.006) and proximal shift of 0.9 mm (SD 1.6, p=0.144). The femoral bones were located more dorsal in extension (2.8 mm dorsally (SD 4.8, p=0.113) which changed to a more ventral position in flexion (2.8 mm, SD 4.2, p=0.077).Conclusion:In the present setting, total knee arthroplasty resulted in significant changes of translational positions between the femoral and tibial bones, thus subluxation of knees. Major reasons for that might be a non centered placement of tibial or femoral implants, symmetric implants which do not respect individual anatomy, operative techniques, and large steps between two component sizes. Subluxation might cause an altered tension of the ligaments and consequently change tibiofemoral or patellar kinematics or tensioning of the periarticular soft tissue resulting in pain. However, clinical trials are necessary to evaluate clinical impact of the presented results.

Dynamic virtual simulation of the occurrence and severity of edge loading in hip replacements associated with variation in the rotational and translational surgical position

Variation in the surgical positioning of total hip replacement can result in edge loading of the femoral head on the rim of the acetabular cup. Previous work has reported the effect of edge loading on the wear of hip replacement bearings with a fixed level of dynamic biomechanical hip separation. Variations in both rotational and translational surgical positioning of the hip joint replacement combine to influence both the biomechanics and the tribology including the severity of edge loading, the amount of dynamic separation, the force acting on the rim of the cup and the resultant wear and torque acting on the cup. In this study, a virtual model of a hip joint simulator has been developed to predict the effect of variations in some surgical positioning (inclination and medial-lateral offset) on the level of dynamic separation and the contact force of the head acting on the rim as a measure of severity of edge loading. The level of dynamic separation and force acting on the rim increased with increased translational mismatch between the centres of the femoral head and the acetabular cup from 0 to 4 mm and with increased cup inclination angle from 45° to 65°. The virtual model closely replicated the dynamics of the experimental hip simulator previously reported, which showed similar dynamic biomechanical trends, with the highest level of separation being found with a mismatch of 4 mm between the centres of the femoral head and acetabular cup and 65° cup inclination angle.

The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler

Chromatin remodelers are ATP-dependent enzymes that are critical for reorganizing and repositioning nucleosomes in concert with many basic cellular processes. For the chromodomain helicase DNA-binding protein 1 (Chd1) remodeler, nucleosome sliding has been shown to depend on the DNA flanking the nucleosome, transcription factor binding at the nucleosome edge, and the presence of the histone H2A/H2B dimer on the entry side. Here, we report that Chd1 is also sensitive to the sequence of DNA within the nucleosome and slides nucleosomes made with the 601 Widom positioning sequence asymmetrically. Kinetic and equilibrium experiments show that poly(dA:dT) tracts perturb remodeling reactions if within one and a half helical turns of superhelix location 2 (SHL2), where the Chd1 ATPase engages nucleosomal DNA. These sequence-dependent effects do not rely on the Chd1 DNA-binding domain and are not due to differences in nucleosome affinity. Using site-specific cross-linking, we show that internal poly(dA:dT) tracts do not block the engagement of the ATPase motor with SHL2, yet they promote multiple translational positions of DNA with respect to both Chd1 and the histone core. We speculate that Chd1 senses the sequence-dependent response of DNA as the remodeler ATPase perturbs the duplex at SHL2. These results suggest that the sequence sensitivity of histones and remodelers occur at unique segments of DNA on the nucleosome, allowing them to work together or in opposition to determine nucleosome positions throughout the genome.

Transformation of spatiotemporal dynamics in the macaque vestibular system from otolith afferents to cortex.

Sensory signals undergo substantial recoding when neural activity is relayed from sensors through pre-thalamic and thalamic nuclei to cortex. To explore how temporal dynamics and directional tuning are sculpted in hierarchical vestibular circuits, we compared responses of macaque otolith afferents with neurons in the vestibular and cerebellar nuclei, as well as five cortical areas, to identical three-dimensional translational motion. We demonstrate a remarkable spatio-temporal transformation: otolith afferents carry spatially aligned cosine-tuned translational acceleration and jerk signals. In contrast, brainstem and cerebellar neurons exhibit non-linear, mixed selectivity for translational velocity, acceleration, jerk and position. Furthermore, these components often show dissimilar spatial tuning. Moderate further transformation of translation signals occurs in the cortex, such that similar spatio-temporal properties are found in multiple cortical areas. These results suggest that the first synapse represents a key processing element in vestibular pathways, robustly shaping how self-motion is represented in central vestibular circuits and cortical areas.

Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution

UV-induced DNA lesions are important contributors to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. Genome-wide profiling of repair activity in UV irradiated cells has revealed significant variations in repair kinetics across the genome, not only among large chromatin domains, but also at individual transcription factor binding sites. Here we report that there is also a striking but predictable variation in initial UV damage levels across a eukaryotic genome. We used a new high-throughput sequencing method, known as CPD-seq, to precisely map UV-induced cyclobutane pyrimidine dimers (CPDs) at single-nucleotide resolution throughout the yeast genome. This analysis revealed that individual nucleosomes significantly alter CPD formation, protecting nucleosomal DNA with an inward rotational setting, even though such DNA is, on average, more intrinsically prone to form CPD lesions. CPD formation is also inhibited by DNA-bound transcription factors, in effect shielding important DNA elements from UV damage. Analysis of CPD repair revealed that initial differences in CPD damage formation often persist, even at later repair time points. Furthermore, our high-resolution data demonstrate, to our knowledge for the first time, that CPD repair is significantly less efficient at translational positions near the dyad of strongly positioned nucleosomes in the yeast genome. These findings define the global roles of nucleosomes and transcription factors in both UV damage formation and repair, and have important implications for our understanding of UV-induced mutagenesis in human cancers.

TH‐AB‐201‐07: Filmless Treatment Localization QA for the CyberKnife System

Purpose:Accuray recommends daily evaluation of the treatment localization and delivery systems (TLS/TDS) of the CyberKnife. The vendor‐provided solution is a Winston‐Lutz‐type test that evaluates film shadows from an orthogonal beam pair (known as AQA). Since film‐based techniques are inherently inefficient and potentially inconsistent and uncertain, this study explores a method which provides a comparable test with greater efficiency, consistency, and certainty. This test uses the QAStereoChecker (QASC, Standard Imaging, Inc., Middleton, WI), a high‐resolution flat‐panel detector with coupled fiducial markers for automated alignment. Fiducial tracking is used to achieve high translational and rotational position accuracy.Methods:A plan is generated delivering five circular beams, with varying orientation and angular incidence. Several numeric quantities are calculated for each beam: eccentricity, centroid location, area, major‐axis length, minor‐axis length, and orientation angle. Baseline values were acquired and repeatability of baselines analyzed. Next, errors were induced in the path calibration of the CK, and the test repeated. A correlative study was performed between the induced errors and quantities measured using the QASC. Based on vendor recommendations, this test should be able to detect a TLS/TDS offset of 0.5mm.Results:Centroid shifts correlated well with induced plane‐perpendicular offsets (p &lt; 0.01). Induced vertical shifts correlated best with the absolute average deviation of eccentricities (p &lt; 0.05). The values of these metrics which correlated with the threshold of 0.5mm induced deviation were used as individual pass/fail criteria. These were then used to evaluate induced offsets which shifted the CK in all axes (a clinically‐realistic offset), with a total offset of 0.5mm. This test provided high and specificity and sensitivity.Conclusion:From setup to analysis, this filmless TLS/TDS test requires 4 minutes, as opposed to 15–20 minutes for film‐based methods. The techniques introduced can potentially isolate errors in individual joints of the CK robot.Spectrum Medical Physics, LLC of Greenville, SC has a consulting contract with Standard Imaging of Middleton, WI