Dosimetric characteristics of a new linear accelerator under gated operation.

Respiratory gated radiotherapy may allow reduction of the treatment margins, thus sparing healthy tissue and/or allowing dose escalation to the tumor. However, current commissioning and quality assurance of linear accelerators do not include evaluation of gated delivery. The purpose of this study is to test gated photon delivery of a Siemens ONCOR Avant-Garde linear accelerator. Dosimetric characteristics for gated and nongated delivery of 6-MV and 15-MV photons were compared for the range of doses, dose rates, and for several gating regimes. Dose profiles were also compared using Kodak EDR2 and X-Omat V films for 6-MV and 15-MV photons for several dose rates and gating regimes. Results showed that deviation is less than or equal to 0.6% for all dose levels evaluated with the exception of the lowest dose delivered at 25 MU at an unrealistically high gating frequency of 0.5 Hz. At 400 MU, dose profile deviations along the central axes in in-plane and cross-plane directions within 80% of the field size are below 0.7%. No unequivocally detectable dose profile deviation was observed for 50 MU. Based on the comparison with widely accepted standards for conventional delivery, our results indicate that this LINAC is well suited for gated delivery of nondynamic fields

Four-dimensional Cone Beam CT Reconstruction and Enhancement using a Temporal Non-Local Means Method

Four-dimensional Cone Beam Computed Tomography (4D-CBCT) has been developed to provide respiratory phase resolved volumetric imaging in image guided radiation therapy (IGRT). Inadequate number of projections in each phase bin results in low quality 4D-CBCT images with obvious streaking artifacts. In this work, we propose two novel 4D-CBCT algorithms: an iterative reconstruction algorithm and an enhancement algorithm, utilizing a temporal nonlocal means (TNLM) method. We define a TNLM energy term for a given set of 4D-CBCT images. Minimization of this term favors those 4D-CBCT images such that any anatomical features at one spatial point at one phase can be found in a nearby spatial point at neighboring phases. 4D-CBCT reconstruction is achieved by minimizing a total energy containing a data fidelity term and the TNLM energy term. As for the image enhancement, 4D-CBCT images generated by the FDK algorithm are enhanced by minimizing the TNLM function while keeping the enhanced images close to the FDK results. A forward-backward splitting algorithm and a Gauss-Jacobi iteration method are employed to solve the problems. The algorithms are implemented on GPU to achieve a high computational efficiency. The reconstruction algorithm and the enhancement algorithm generate visually similar 4D-CBCT images, both better than the FDK results. Quantitative evaluations indicate that, compared with the FDK results, our reconstruction method improves contrast-to-noise-ratio (CNR) by a factor of 2.56~3.13 and our enhancement method increases the CNR by 2.75~3.33 times. The enhancement method also removes over 80% of the streak artifacts from the FDK results. The total computation time is ~460 sec for the reconstruction algorithm and ~610 sec for the enhancement algorithm on an NVIDIA Tesla C1060 GPU card.Comment: 20 pages, 3 figures, 2 table

Progress in rational methods of cryoprotection in macromolecular crystallography

Measurements of the average thermal contractions (294→72 K) of 26 different cryosolutions are presented and discussed in conjunction with other recent advances in the rational design of protocols for cryogenic cooling in macromolecular crystallography

Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector

Observations of the dose-rate effect in continuous X-ray diffraction data acquisition at room temperature are presented

Temperature-dependent macromolecular X-ray crystallography

The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed

Preparation of Group I Introns for Biochemical Studies and Crystallization Assays by Native Affinity Purification

The study of functional RNAs of various sizes and structures requires efficient methods for their synthesis and purification. Here, 23 group I intron variants ranging in length from 246 to 341 nucleotides—some containing exons—were subjected to a native purification technique previously applied only to shorter RNAs (<160 nucleotides). For the RNAs containing both exons, we adjusted the original purification protocol to allow for purification of radiolabeled molecules. The resulting RNAs were used in folding assays on native gel electrophoresis and in self-splicing assays. The intron-only RNAs were subjected to the regular native purification scheme, assayed for folding and employed in crystallization screens. All RNAs that contained a 3′ overhang of one nucleotide were efficiently cleaved off from the support and were at least 90% pure after the non-denaturing purification. A representative subset of these RNAs was shown to be folded and self-splicing after purification. Additionally, crystals were grown for a 286 nucleotide long variant of the Clostridium botulinum intron. These results demonstrate the suitability of the native affinity purification method for the preparation of group I introns. We hope these findings will stimulate a broader application of this strategy to the preparation of other large RNA molecules

Increasing the X-ray Diffraction Power of Protein Crystals by Dehydration: The Case of Bovine Serum Albumin and a Survey of Literature Data

Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 Å, b = 44.72 Å, c = 140.18 Å, β = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 Å to 3.2 Å, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals

Radiation damage in macromolecular crystallography: what is it and why should we care?

The basic causes of the radiation damage inflicted on macromolecular crystals during diffraction experiments are summarized, as well as the current state of research which attempts to understand and to mitigate it