Technical note: Optimizing the deliverability of binary collimation-based SRS treatment for multiple metastases with multiple prescriptions.

intra-arc binary collimation (iABC) is a novel treatment technique in which dynamic conformal arcs are periodically interrupted with binary collimation. It has demonstrated its utility through planning studies for the treatment of multiple metastases. However, the binary collimation approach is idealized in the planning system, while the treatment deliveries must adhere to the physical limitations of the mechanical systems involved [e.

Design optimization of a 1-D array of stemless plastic scintillation detectors.

Background: A stemless plastic scintillation detector (SPSD) is composed of an organic plastic scintillator coupled to an organic photodiode. Previous research has shown that SPSDs are ideally suited to challenging dosimetry measurements such as output factors and profiles in small fields. Lacking from the current literature is a systematic effort to optimize the performance of the photodiode component of the detector.

Serial and parallel organ-at-risk-specific noncoplanar arc optimization for small versus large target volumes in liver SBRT.

Noncoplanar arc optimization has been shown to reduce OAR doses in SRS/SRT and has the potential to reduce doses to OARs in SBRT. Extracranial targets have additional considerations, including large OARs and, in the case of the liver, volume constraints on the healthy liver. Considering pathlengths through OARs that encompass target volumes may lead to specific dose reductions as in the encompassing healthy liver tissue.

Computational drug discovery approaches identify mebendazole as a candidate treatment for autosomal dominant polycystic kidney disease.

Autosomal dominant polycystic kidney disease (ADPKD) is a rare genetic disorder characterised by numerous renal cysts, the progressive expansion of which can impact kidney function and lead eventually to renal failure. Tolvaptan is the only disease-modifying drug approved for the treatment of ADPKD, however its poor side effect and safety profile necessitates the need for the development of new therapeutics in this area. Using a combination of transcriptomic and machine learning computational drug discovery tools, we predicted that a number of existing drugs could have utility in the treatment of ADPKD, and subsequently validated several of these drug predictions in established models of disease.

Neurological outcome following out of hospital cardiac arrest: Evaluation of performance of existing risk prediction models in a UK cohort.

Introduction: Out of hospital cardiac arrest (OHCA) is a common problem. Rates of survival are low and a proportion of survivors are left with an unfavourable neurological outcome. Four models have been developed to predict risk of unfavourable outcome at the time of critical care admission - the Cardiac Arrest Hospital Prognosis (CAHP), MIRACLE, Out of Hospital Cardiac Arrest (OHCA), and Targeted Temperature Management (TTM) models.

Static couch non-coplanar arc selection optimization for lung SBRT treatment planning.

. Non-coplanar arc geometry optimizations that take advantage of beam's eye view (BEV) geometric overlap information have been proven to reduce dose to healthy organs-at-risk (OARs). Recently, a metric called mean arc distance (MAD) has been developed that quantifies the arc geometry sampling of 4space.

Assessing the impact of intrafraction motion correction on PTV margins and target and OAR dosimetry for single-fraction free-breathing lung stereotactic body radiation therapy.

The objective of this research is to investigate intrafraction motion correction on planning target volume (PTV) margin requirements and target and organ-at-risk (OAR) dosimetry in single-fraction lung stereotactic body radiation therapy (SBRT). Sixteen patients (15 with upper lobe lesions, 1 with a middle lobe lesion) were treated with single-fraction lung SBRT. Cone-beam computed tomography (CBCT) images were acquired before the treatment, between the arcs, and after the delivery of the treatment fraction.

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.

Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection.

Evaluation of plan quality and treatment efficiency in cranial stereotactic radiosurgery treatment plans with a variable source-to-axis distance.

Introduction: Radiotherapy deliveries with dynamic couch motions that shorten the source-to-axis distance (SAD) on a C-arm linac have the potential to increase treatment efficiency through the increase of the effective dose rate. In this investigation, we convert clinically deliverable volumetric modulated arc therapy (VMAT) and dynamic conformal arc (DCA) plans for cranial radiosurgery into virtual isocenter plans through implementation of couch trajectories that maintain the target at a shortened but variable SAD throughout treatment.

Materials And Methods: A randomly sampled population of patients treated with cranial radiosurgery from within the last three years were separated into groups with one, two, and three lesions.

Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets.

Region-of-interest intra-arc MV imaging to facilitate sub-mm positional accuracy with minimal imaging dose during treatment deliveries of small cranial lesions.

Purpose: To automate the generation of region-of-interest (ROI) apertures for use with megavoltage imaging for online positional corrections during cranial stereotactic radiosurgery.

Materials And Methods: Digitally reconstructed radiographs (DRRs) were created for a 3D-printed skull phantom at 5 degree gantry angle increments for a three-arc beam arrangement. At each angle, 3000 random rectangular apertures were generated, and 100 shifts on a grid were applied to the anatomy within the frame.

Comparison of anatomically informed class solution template trajectories with patient-specific trajectories for stereotactic radiosurgery and radiotherapy.

Class solution template trajectories are used clinically for efficiency, safety, and reproducibility. The aim was to develop class solutions for single cranial metastases radiotherapy/radiosurgery based on intracranial target positioning and compare to patient-specific trajectories in the context of 4π optimization. Template trajectories were constructed based on the open-source Montreal Neurological Institute (MNI) average brain.

Mean Arc Distance (MAD): a quantity to compare trajectory 4sampling in single target cranial stereotactic radiotherapy.

C-arm linac-based radiotherapy has seen a recent interest in 4methods of delivery using simultaneous rotations of couch and gantry to reduce doses to organs-at-risk (OARs) and increase dose compactness. While many methods use heuristics to generate trajectories that avoid OARs, combined with arbitrary trajectory restrictions to prevent oversampling, a quantity has not yet been developed to succinctly compare sampling of the 4space for candidate trajectories as a surrogate for dosimetric compactness.Evenly spaced sampling points were distributed across a 4sphere centred on isocentre.

Machine learning for contour classification in TG-263 noncompliant databases.

A large volume of medical data are labeled using nonstandardized nomenclature. Although efforts have been made by the American Association of Physicists in Medicine (AAPM) to standardize nomenclature through Task Group 263 (TG-263), there remain noncompliant databases. This work aims to create an algorithm that can analyze anatomical contours in patients with head and neck cancer and classify them into TG-263 compliant nomenclature.

Intra-arc binary collimation with dynamic axes trajectory optimization for the SRS treatment of multiple metastases with multiple prescriptions.

Purpose: This work generates multi-metastases cranial stereotactic radiosurgery/radiotherapy (SRS/SRT) plans using a novel treatment planning technique in which dynamic couch, collimator, and gantry trajectories are used with periodic binary target collimation. The performance of this planning technique is evaluated against conventional volumetric arc therapy (VMAT) planning in terms of various dose and plan quality metrics.

Methods: A 3D cost space (referred to herein as the combined optimization of dynamic axes or CODA cube) was calculated based on an overlap between targets and organs-at-risk (OARs) and uncollimated areas between targets (island blocking) for all combinations of couch, gantry, and collimator angles.

Patient-specific collision zones for 4π trajectory optimized radiation therapy.

Purpose: The 4π methodology determines optimized noncoplanar subarcs for stereotactic radiation therapy that minimize dose to organs-at-risk. Every combination of treatment angle is examined, but some angles are not appropriate as a collision would occur between the gantry and the couch or the gantry and the patient. Those combinations of couch and gantry angles are referred to as collision zones.

Long-read assemblies reveal structural diversity in genomes of organelles - an example with .

Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, , using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure.

Measuring small field profiles and output factors with a stemless plastic scintillator array.

Purpose: To fabricate a 1D stemless plastic scintillation detector (SPSD) array using organic photodiodes and to use the detector to measure small field profiles and output factors.

Methods: An organic photodiode array was fabricated by spin coating a mixture of P3HT and PCBM organic semiconductors onto an ITO-coated glass substrate and depositing aluminum top contacts. Four bulk scintillators of various dimensions were placed on top of the photodiode array.

SBRT of ventricular tachycardia using 4pi optimized trajectories.

Purpose: To investigate the possible advantages of using 4pi-optimized arc trajectories in stereotactic body radiation therapy of ventricular tachycardia (VT-SBRT) to minimize exposure of healthy tissues.

Methods And Materials: Thorax computed tomography (CT) data for 15 patients were used for contouring organs at risk (OARs) and defining realistic planning target volumes (PTVs). A conventional trajectory plan, defined as two full coplanar arcs was compared to an optimized-trajectory plan provided by a 4pi algorithm that penalizes geometric overlap of PTV and OARs in the beam's-eye-view.

Investigating the impacts of intrafraction motion on dosimetric outcomes when treating small targets with virtual cones.

Purpose: Intrafraction patient motion is a well-documented phenomenon in radiation therapy. In stereotactic radiosurgery applications in which target sizes can be very small and dose gradients very steep, patient motion can significantly impact the magnitude and positional accuracy of the delivered dose. This work investigates the impact of intrafraction motion on dose metrics for small targets when treated with a virtual cone.

Full spectroscopic model and trihybrid experimental-perturbative-variational line list for CN.

Accurate line lists are important for the description of the spectroscopic nature of small molecules. While a line list for CN (an important molecule for chemistry and astrophysics) exists, no underlying energy spectroscopic model has been published, which is required to consider the sensitivity of transitions to a variation of the proton-to-electron mass ratio. Here we have developed a Duo energy spectroscopic model as well as a novel hybrid style line list for CN and its isotopologues, combining energy levels that are derived experimentally (Marvel), using the traditional/perturbative approach (Mollist), and the variational approach (from a Duo spectroscopic model using standard ExoMol methodology).

Post-administration dosimetry in yttrium-90 radioembolization through micro-CT imaging of radiopaque microspheres in a porcine renal model.

The purpose of this study is to perform post-administration dosimetry in yttrium-90 radioembolization through micro-CT imaging of radiopaque microsphere distributions in a porcine renal model and explore the impact of spatial resolution of an imaging system on the extraction of specific dose metrics. Following the administration of radiopaque microspheres to the kidney of a hybrid farm pig, the kidney was explanted and imaged with micro-CT. To produce an activity distribution, 400 MBq of yttrium-90 activity was distributed throughout segmented voxels of the embolized vasculature based on an established linear relationship between microsphere concentration and CT voxel value.

Method for the differentiation of radiation-induced photocurrent from total measured current in P3HT/PCBM BHJ photodiodes.

Thin film radiation-detecting diodes fabricated in the laboratory, such as an organic bulk heterojunction, often contain conductive leads, indium tin oxide traces and metallic interconnects which are exposed to the high-energy photon beam during operation. These components generate extraneous radiation-induced currents, that, if not accounted for, will erroneously be attributed to the detector. In commercial devices, these contributions are mitigated by minimizing the size of these components, an approach that is often not feasible in a research lab.