The Effect of High-Dose Radiation Therapy on Healthy Vertebral Bone Density.

Objective Increased rates of insufficiency fractures are reported after radiation therapy without well-defined causality. Here, we conduct a cross-sectional study on the density change of a non-lesioned vertebral bone after irradiation relative to a control bone in patients with spinal metastases. Methods Patients were identified who received radiation therapy for spinal metastases to a region, including an adjacent vertebra without identifiable malignancy on pre-treatment CT. Every patient had an untreated vertebra of a similar type available as a control. A Hounsfield-density calibration curve was used to measure the vertebral body density before and after treatment. Analysis of covariance was used to model vertebral bone density changes with respect to treatment status. Significance was established as p < 0.05. Results We identified 36 patients who fit the study criteria. The irradiated healthy bone received a median dose of 30 Gy. The median biologically effective dose (BED) was 60 Gy (α/ß = 3) and 39 Gy (α/ß = 10). Median follow-up imaging intervals between pre-treatment and follow-up CT scans was 13.4 months. Levene's test was used to confirm the equality of error variance assumption of ANCOVA (p = 0.093). The mean change in the density of the irradiated vertebral bone was -3.59% (95% CI = -8.51% - 1.32%, p = 0.149). Conclusions We found no significant change in vertebral bone density attributable to radiation treatment. Further work is needed to elucidate if increased fracture rates after radiation are due to factors other than bone density.

Lumbar Ganglioneuroma Presenting With Scoliosis.

Ganglioneuromas are rare, benign tumors arising from the sympathetic nervous system. The presentation of the tumor is variable and may be associated with scoliosis. Few reports of ganglioneuroma associated with scoliosis- exist and most involve the thoracic spine. Here, we present a 13-year-old female with scoliosis who was found to have a lumbar ganglioneuroma. The patient was treated with a subtotal resection and lumbar spinal fusion to correct her scoliosis in a single-stage operation. The patient's symptoms and scoliosis markedly improved following treatment without any complications. Additionally, we conducted an up-to-date literature review of ganglioneuromas associated with scoliosis that have been published in the last 20 years. We discuss variations in clinical presentation and surgical approach.

Bone Density Changes Following Radiotherapy to Vertebral Metastases.

Introduction Patients have increasing longevity and time for bone healing following radiotherapy (RT) for treatment of bone metastases (BM). Attempts to assess the treatment response of bone metastases have been either limited or heavily subjective. Our goal was to try to quantitate cancer-involved bone changes after RT using changes in bone mineral density (BMD) from computer tomographic (CT) imaging. Methods Retrospectively, 117 spinal metastases were identified that received RT with follow-up CT scans >9 months following CT simulation. Contoured volumes included: the metastasis (gross tumor volume; GTV); the involved vertebra (gross bone volume; GBV); a total lytic volume (Lyt); a dominant lytic volume (Domlyt); a control volume, and the nearest uninvolved, unirradiated vertebra (control bone volume; CBV). The Hounsfield-density calibration curve was used to measure the density of these volumes before and after treatment. Results Whether using raw or control-adjusted changes, the absolute and percent change in density of the GBV, GTV, Lyt, and Domlyt volumes all significantly increased (each p<0.0001). The increase in the density of Domlyt volumes was greater than that of Lyt volumes (p=0.0465), which were greater than GTV (p=0.0065), which were greater than GBV (p<0.0001). On multivariate analysis, only the biologically effective dose (BED) dose significantly correlated with GTV density change (p=0.0175). K means clustering created groups by initial lesion size, GTV, or GBV density. A significant difference in GTV density change was not detected between any groups. Conclusion Increases in BMD are associated with healing regardless of lesion size or initial density. A prospective study to determine whether long-term control is related to early density measurements is needed.

Vargas: heuristic-free alignment for assessing linear and graph read aligners.

MOTIVATION: Read alignment is central to many aspects of modern genomics. Most aligners use heuristics to accelerate processing, but these heuristics can fail to find the optimal alignments of reads. Alignment accuracy is typically measured through simulated reads; however, the simulated location may not be the (only) location with the optimal alignment score. RESULTS: Vargas implements a heuristic-free algorithm guaranteed to find the highest-scoring alignment for real sequencing reads to a linear or graph genome. With semiglobal and local alignment modes and affine gap and quality-scaled mismatch penalties, it can implement the scoring functions of commonly used aligners to calculate optimal alignments. While this is computationally intensive, Vargas uses multi-core parallelization and vectorized (SIMD) instructions to make it practical to optimally align large numbers of reads, achieving a maximum speed of 456 billion cell updates per second. We demonstrate how these 'gold standard' Vargas alignments can be used to improve heuristic alignment accuracy by optimizing command-line parameters in Bowtie 2, BWA-maximal exact match and vg to align more reads correctly. AVAILABILITY AND IMPLEMENTATION: Source code implemented in C++ and compiled binary releases are available at https://github.com/langmead-lab/vargas under the MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fast, compact, autonomous holographic adaptive optics.

We present a closed-loop adaptive optics system based on a holographic sensing method. The system uses a multiplexed holographic recording of the response functions of each actuator in a deformable mirror. By comparing the output intensity measured in a pair of photodiodes, the absolute phase can be measured over each actuator location. From this a feedback correction signal is applied to the input beam without need for a computer. The sensing and correction is applied to each actuator in parallel, so the bandwidth is independent of the number of actuator. We demonstrate a breadboard system using a 32-actuator MEMS deformable mirror capable of operating at over 10 kHz without a computer in the loop.