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The pBR322 plasmid DNA was irradiated with 35 MeV electrons, 228 MeV protons and 300 kVp X-rays to quantify DNA damage and make comparisons of DNA damage between radiation modalities. Plasmid was irradiated in a medium containing hydroxyl radical scavengers in varying concentrations. This altered the amount of indirect hydroxyl-mediated DNA damage, to create an environment that is more closely associated with a biological cell. We show that increasing hydroxyl scavenger concentration significantly reduced post-irradiation DNA damage to pBR322 plasmid DNA consistently and equally with three radiation modalities. At low scavenging capacities, irradiation with both 35 MeV electrons and 228 MeV protons resulted in increased DNA damage per dose compared with 300 kVp X-rays. We quantify both single-strand break (SSB) and double-strand break (DSB) induction between the modalities as a ratio of yields relative to X-rays, referred to as relative biological effectiveness (RBE). RBESSB values of 1.16 ± 0.15 and 1.18 ± 0.08 were calculated for protons and electrons, respectively, in a low hydroxyl scavenging environment containing 1 mM Tris–HCl for SSB induction. In higher hydroxyl scavenging capacity environments (above 1.1 × 106 s−1), no significant differences in DNA damage induction were found between radiation modalities when using SSB induction as a measure of RBE. Considering DSB induction, significant differences were only found between X-rays and 35 MeV electrons, with an RBEDSB of 1.72 ± 0.91 for 35 MeV electrons, indicating that electrons result in significantly more SSBs and DSBs per unit of dose than 300 kVp X-rays.

Micronucleus (MN) formation is routinely used as a biodosimeter for radiation exposures and has historically been used as a measure of DNA damage in cells. Strongly correlating with dose, MN are also suggested to indicate radiation quality, differentiating between particle and photon irradiation. The “gold standard” for measuring MN formation is Fenech’s cytokinesis-block micronucleus (CBMN) cytome assay, which uses the cytokinesis blocking agent cytochalasin-B. Here, we present a comprehensive analysis of the literature investigating MN induction trends in vitro, collating 193 publications, with 2476 data points. Data were collected from original studies that used the CBMN assay to quantify MN in response to ionizing radiation in vitro. Overall, the meta-analysis showed that individual studies mostly have a linear increase of MN with dose [85% of MN per cell (MNPC) datasets and 89% of percentage containing MN (PCMN) datasets had an R2 greater than 0.90]. However, there is high variation between studies, resulting in a low R2 when data are combined (0.47 for MNPC datasets and 0.60 for PCMN datasets). Particle type, species, cell type, and cytochalasin-B concentration were suggested to influence MN frequency. However, variation in the data meant that the effects could not be strongly correlated with the experimental parameters investigated. There is less variation between studies when comparing the PCMN rather than the number of MNPC. Deviation from CBMN protocol specified timings did not have a large effect on MN induction. However, further analysis showed less variation between studies following Fenech’s protocol closely, which provided more reliable results. By limiting the cell type and species as well as only selecting studies following the Fenech protocol, R2 was increased to 0.64 for both measures. We therefore determine that due to variation between studies, MN are currently a poor predictor of radiation-induced DNA damage and make recommendations for futures studies assessing MN to improve consistency between datasets.

Immunofluorescent tagging of DNA double-strand break (DSB) markers, such as γ-H2AX and other DSB repair proteins, are powerful tools in understanding biological consequences following irradiation. However, whilst the technique is widespread, there are many uncertainties related to its ability to resolve and reliably deduce the number of foci when counting using microscopy. We present a new tool for simulating radiation-induced foci in order to evaluate microscope performance within in silico immunofluorescent images. Simulations of the DSB distributions were generated using Monte Carlo track-structure simulation. For each DSB distribution, a corresponding DNA repair process was modelled and the un-repaired DSBs were recorded at several time points. Corresponding microscopy images for both a DSB and (γ-H2AX) fluorescent marker were generated and compared for different microscopes, radiation types and doses. Statistically significant differences in miscounting were found across most of the tested scenarios. These inconsistencies were propagated through to repair kinetics where there was a perceived change between radiation-types. These changes did not reflect the underlying repair rate and were caused by inconsistencies in foci counting. We conclude that these underlying uncertainties must be considered when analysing images of DNA damage markers to ensure differences observed are real and are not caused by non-systematic miscounting.

Background: Clinical data suggest that the relative biological effectiveness (RBE) in proton therapy (PT) varies with linear energy transfer (LET). However, LET calculations are neither standardized nor available in clinical routine. Here, the status of LET calculations among European PT institutions and their comparability are assessed. Materials and methods: Eight European PT institutions used suitable treatment planning systems with their center-specific beam model to create treatment plans in a water phantom covering different field arrangements and fulfilling commonly agreed dose objectives. They employed their locally established LET simulation environments and procedures to determine the corresponding LET distributions. Dose distributions D 1.1 and D RBE assuming constant and variable RBE, respectively, and LET were compared among the institutions. Inter-center variability was assessed based on dose- and LET-volume-histogram parameters. Results: Treatment plans from six institutions fulfilled all clinical goals and were eligible for common analysis. D 1.1 distributions in the target volume were comparable among PT institutions. However, corresponding LET values varied substantially between institutions for all field arrangements, primarily due to differences in LET averaging technique and considered secondary particle spectra. Consequently, D RBE using non-harmonized LET calculations increased inter-center dose variations substantially compared to D 1.1 and significantly in mean dose to the target volume of perpendicular and opposing field arrangements (p < 0.05). Harmonizing LET reporting (dose-averaging, all protons, LET to water or to unit density tissue) reduced the inter-center variability in LET to the order of 10–15% within and outside the target volume for all beam arrangements. Consequentially, inter-institutional variability in D RBE decreased to that observed for D 1.1. Conclusion: Harmonizing the reported LET among PT centers is feasible and allows for consistent multi-centric analysis and reporting of tumor control and toxicity in view of a variable RBE. It may serve as basis for harmonized variable RBE dose prescription in PT.

FLASH radiotherapy is a rapidly developing field which promises improved normal tissue protection compared to conventional irradiation and no compromise on tumour control. The transient hypoxic state induced by the depletion of oxygen at high dose rates provides one possible explanation. However, studies have mostly focused on uniform fields of dose and there is a lack of investigation into the spatial and temporal variation of dose from proton pencil-beam scanning (PBS). A model of oxygen reaction and diffusion in tissue has been extended to simulate proton PBS delivery and its impact on oxygen levels. This provides a tool to predict oxygen effects from various PBS treatments, and explore potential delivery strategies. Here we present a number of case applications to demonstrate the use of this tool for FLASH-related investigations. We show that levels of oxygen depletion could vary significantly across a large parameter space for PBS treatments, and highlight the need for in silico models such as this to aid in the development and optimisation of FLASH radiotherapy.

Simple Summary When cells are irradiated, their DNA can become damaged, this causes different types of repair processes to try and fix the DNA breaks. One of the most lethal types of DNA damage is double-strand breaks (DSBs). This work models the most used DSB repair process called Non-Homologous End Joining (NHEJ) and includes both its resection-independent and resection-dependent pathways. The models produced are benchmarked against experimental normal and deficient cell-types across a wide range of radiation qualities. We compare two approaches of modelling, the first is where the DSBs can repair in parallel and the second is where the DSBs repair is entwined. We find that it is necessary to consider both the resection-independent and resection-dependent pathways as entwined to produce a model which robustly matches experimental work. Through better modelling of NHEJ repair, it can improve our understanding of radiation response which has potential in biological optimisation for radiotherapy. Abstract Mechanistic in silico models can provide insight into biological mechanisms and highlight uncertainties for experimental investigation. Radiation-induced double-strand breaks (DSBs) are known to be toxic lesions if not repaired correctly. Non-homologous end joining (NHEJ) is the major DSB-repair pathway available throughout the cell cycle and, recently, has been hypothesised to consist of a fast and slow component in G0/G1. The slow component has been shown to be resection-dependent, requiring the nuclease Artemis to function. However, the pathway is not yet fully understood. This study compares two hypothesised models, simulating the action of individual repair proteins on DSB ends in a step-by-step manner, enabling the modelling of both wild-type and protein-deficient cell systems. Performance is benchmarked against experimental data from 21 cell lines and 18 radiation qualities. A model where resection-dependent and independent pathways are entirely separated can only reproduce experimental repair kinetics with additional restraints on end motion and protein recruitment. However, a model where the pathways are entwined was found to effectively fit without needing additional mechanisms. It has been shown that DaMaRiS is a useful tool when analysing the connections between resection-dependent and independent NHEJ repair pathways and robustly matches with experimental results from several sources.

Developments in the genome organisation field has resulted in the recent methodology to infer spatial conformations of the genome directly from experimentally measured genome contacts (Hi-C data). This provides a detailed description of both intra- and inter-chromosomal arrangements. Chromosomal intermingling is an important driver for radiation-induced DNA mis-repair. Which is a key biological endpoint of relevance to the fields of cancer therapy (radiotherapy), public health (biodosimetry) and space travel. For the first time, we leverage these methods of inferring genome organisation and couple them to nano-dosimetric radiation track structure modelling to predict quantities and distribution of DNA damage within cell-type specific geometries. These nano-dosimetric simulations are highly dependent on geometry and are benefited from the inclusion of experimentally driven chromosome conformations. We show how the changes in Hi-C contract maps impact the inferred geometries resulting in significant differences in chromosomal intermingling. We demonstrate how these differences propagate through to significant changes in the distribution of DNA damage throughout the cell nucleus, suggesting implications for DNA repair fidelity and subsequent cell fate. We suggest that differences in the geometric clustering for the chromosomes between the cell-types are a plausible factor leading to changes in cellular radiosensitivity. Furthermore, we investigate changes in cell shape, such as flattening, and show that this greatly impacts the distribution of DNA damage. This should be considered when comparing in vitro results to in vivo systems. The effect may be especially important when attempting to translate radiosensitivity measurements at the experimental in vitro level to the patient or human level., Author summary We have used a technique which allows us to understand how parts of our DNA are organised within a cell nucleus. This technique has previously shown differences in the organisation between different cell-types. In this study, we show that these differences produce significant change in the way our DNA is damaged when exposed to radiation. This is important to understand as one of the primary ways we treat cancer is using radiotherapy. However, whilst we attempt to target the cancer with radiation, some healthy tissue also receives radiation. It is the radiation delivered to the healthy tissue which limits how much radiation we can safely give to the cancer without causing significant side effects in patients. To know how much radiation we can give, over time, we have learnt generally safe amounts of radiation that can be given to healthy tissue. Even so, sometimes patients will still have worse side effects than what we would have predicted. If we want to further improve our treatments and patient safety, we need to better understand how this safe limit varies between each patient. The first step in to fully understanding this process comes from a better understanding of how different cell-types are affected by radiation, which is partly driven by DNA organisation, shown in this work.

The monolithic silicon telescope technology allows to produce solid state microdosimeters. A detector constituted by a matrix of pixels (2 μm in thickness) coupled with a deeper stage (about 500 μm in thickness) was designed, developed and characterized by comparing its response against Tissue Equivalent Proportional Counters (TEPCs) in different irradiation fields, showing promising results. Each pixel of the ΔE stage is a thin diode of 9 μm in diameter delimited by a guard ring of 14 μm in diameter. The aim of this work is the study of the charge collection efficiency of the single pixel of the silicon microdosimeter by irradiating a prototype at the micro-beam facility of the Ion Beam Center - IBC of the University of Surrey. Different light ions were exploited (protons, lithium ions and carbon ions) and scanned on different positions on and around a single pixel of the detector. The results show that the charge generated by events on the sensitive region of the ΔE stage is completely collected, while a charge collection efficiency lower than one characterizes the region between the central pixel and its guard ring. The guard ring delimits properly the sensitive region: no signals arise from events outside the 14 μm in diameter ring. Nevertheless, the microdosimetric distributions of the different charged particles highlight a minor distortion in terms of the absorbed dose. This latter result justifies the good agreement with TEPCs in terms of microdosimetric distributions in different hadrons beams described in previous works.

After radiation exposure, one of the critical processes for cellular survival is the repair of DNA double strand breaks. The pathways involved in this response are complex in nature and involve many individual steps that act across different time scales, all of which combine to produce an overall behaviour. It is therefore experimentally challenging to unambiguously determine the mechanisms involved and how they interact whilst maintaining strict control of all confounding variables. In silico methods can provide further insight into results produced by focused experimental investigations through testing of the hypotheses generated. Such computational testing can asses competing hypotheses by investigating their effects across all time scales concurrently, highlighting areas where further experimental work can have the most significance. We describe the construction of a mechanistic model by combination of several hypothesised mechanisms reported in the literature and supported by experiment. Compatibility of these mechanisms was tested by fitting simulation to results reported in the literature. To avoid over-fitting, we used an approach of sequentially testing individual mechanisms within this pathway. We demonstrate that using this approach the model is capable of reproducing published protein kinetics and overall repair trends. This provides evidence supporting the feasibility of the proposed mechanisms and revealed how they interact to produce an overall behaviour. Furthermore, we show that the assumed motion of individual double strand break ends plays a crucial role in determining overall system behaviour.

The strong in vitro evidence that proton Relative Biological Effectiveness (RBE) varies with Linear Energy Transfer (LET) has led to an interest in applying LET within treatment planning. However, there is a lack of consensus on LET definition, Monte Carlo (MC) parameters or clinical methodology. This work aims to investigate how common variations of LET definition may affect potential clinical applications. MC simulations (GATE/GEANT4) were used to calculate absorbed dose and different types of LET for a simple Spread Out Bragg Peak (SOBP) and for four clinical PBT plans covering a range of tumour sites. Variations in the following LET calculation methods were considered: (i) averaging (dose-averaged LET (LETd) & track-averaged LET); (ii) scoring (LETd to water, to medium and to mass density); (iii) particle inclusion (LETd to all protons, to primary protons and to particles); (iv) MC settings (hit type and Maximum Step Size (MSS)). LET distributions were compared using: qualitative comparison, LET Volume Histograms (LVHs), single value criteria (maximum and mean values) and optimised LET-weighted dose models. Substantial differences were found between LET values in averaging, scoring and particle type. These differences depended on the methodology, but for one patient a difference of ∼100% was observed between the maximum LETd for all particles and maximum LETd for all protons within the brainstem in the high isodose region (4 keV μm−1 and 8 keV μm−1 respectively). An RBE model using LETd including heavier ions was found to predict substantially different LET-weighted dose compared to those using other LET definitions. In conclusion, the selection of LET definition may affect the results of clinical metrics considered in treatment planning and the results of an RBE model. The authors’ advocate for the scoring of dose-averaged LET to water for primary and secondary protons using a random hit type and automated MSS.

Ionising radiation can induce giant-nucleated cells (GCs) in the progeny of irradiated populations, as demonstrated in various cellular systems. Most in vitro studies have utilised quiescent cancerous or normal cell lines but it is not clear whether radiation-induced GCs persist in the progeny of normal replicated cells. In the current work we show persistent induction of GCs in the progeny of normal human-diploid skin fibroblasts (AG1522). These cells were originally irradiated with a single equivalent clinical dose of 0.2, 1 or 2 Gy of either X-ray or proton irradiation and maintained in an active state for various post-irradiation incubation interval times before they were replated for GC analysis. The results demonstrate that the formation of GCs in the progeny of X-ray or proton irradiated cells was increased in a dose-dependent manner when measured 7 days after irradiation and this finding is in agreement with that reported for the AG1522 cells using other radiation qualities. For the 1 Gy X-ray doses it was found that the GC yield increased continually with time up to 21 days post-irradiation. These results can act as benchmark data for such work and may have important implications for studies aimed at evaluating the efficacy of radiation therapy and in determining the risk of delayed effects particularly when applying protons.

Following radiation induced DNA damage, several repair pathways are activated to help preserve genome integrity. Double Strand Breaks (DSBs), which are highly toxic, have specified repair pathways to address them. The main repair pathways used to resolve DSBs are Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). Cell cycle phase determines the availability of HR, but the repair choice between pathways in the G2 phases where both HR and NHEJ can operate is not clearly understood. This study compares several in silico models of repair choice to experimental data published in the literature, each model representing a different possible scenario describing how repair choice takes place. Competitive only scenarios, where initial protein recruitment determines repair choice, are unable to fit the literature data. In contrast, the scenario which uses a more entwined relationship between NHEJ and HR, incorporating protein co-localisation and RNF138-dependent removal of the Ku/DNA-PK complex, is better able to predict levels of repair similar to the experimental data. Furthermore, this study concludes that co-localisation of the Mre11-Rad50-Nbs1 (MRN) complexes, with initial NHEJ proteins must be modeled to accurately depict repair choice.

There has been a recent revival of interest in the FLASH effect, after experiments have shown normal tissue sparing capabilities of ultra-high-dose-rate radiation with no compromise on tumour growth restraint. A model has been developed to investigate the relative importance of a number of fundamental parameters considered to be involved in the oxygen depletion paradigm of induced radioresistance. An example eight-dimensional parameter space demonstrates the conditions under which radiation may induce sufficient depletion of oxygen for a diffusion-limited hypoxic cellular response. Initial results support experimental evidence that FLASH sparing is only achieved for dose rates on the order of tens of Gy s−1 or higher, for a sufficiently high dose, and only for tissue that is slightly hypoxic at the time of radiation. We show that the FLASH effect is the result of a number of biological, radiochemical and delivery parameters. Also, the threshold dose for a FLASH effect occurring would be more prominent when the parameterisation was optimised to produce the maximum effect. The model provides a framework for further FLASH-related investigation and experimental design. An understanding of the mechanistic interactions producing an optimised FLASH effect is essential for its translation into clinical practice.

Vertical Microbeams (VMB) are used to irradiate individual cells with low MeV energy ions. The irradiation of cells using VMBs requires cells to be removed from an incubator; this can cause physiological changes to cells because of the lower CO2 concentration, temperature and relative humidity outside of the incubator. Consequently, for experiments where cells require irradiation and observation for extended time periods, it is important to provide a controlled environment. The highly customised nature of the microscopes used on VMB systems means that there are no commercially available environmentally controlled microscope systems for VMB systems. The Automated Microbeam Observation Environment for Biological Analysis (AMOEBA) is a highly flexible modular environmental control system used to create incubator conditions on the end of a VMB. The AMOEBA takes advantage of the recent “maker” movement to create an open source control system that can be easily configured by the user to fit their control needs even beyond VMB applications. When applied to the task of controlling cell medium temperature, CO2 concentration and relative humidity on VMBs it creates a stable environment that allows cells to multiply on the end of a VMB over a period of 36 h, providing a low-cost (costing less than $2700 to build), customisable alternative to commercial time-lapse microscopy systems. AMOEBA adds the potential of VMBs to explore the long-term effects of radiation on single cells opening up new research areas for VMBs.

Gold nanoparticles have been proven as potential radiosensitizer when combined with protons. Initially the radiosensitization effect was attributed to the physical interactions of radiation with the gold and the production of secondary electrons that induce DNA damage. However, emerging data challenge this hypothesis, supporting the existence of alternative or supplementary radiosensitization mechanisms. In this work we incorporate a realistic cell model with detailed DNA geometry and a realistic gold nanoparticle biodistribution based on experimental data. The DNA single and double strand breaks, and damage complexity are counted under various scenarios of different gold nanoparticle size, biodistribution and concentration, and proton energy. The locality of the effect, i.e. the existence of higher damage at a location close to the gold distribution, is also addressed by investigating the DNA damage at a chromosomal territory. In all the cases we do not observe any significant increase in the single/double strand break yield or damage complexity in the presence of gold nanoparticles under proton irradiation; nor there is a locality to the effect. Our results show for the first time that the physical interactions of protons with the gold nanoparticles should not be considered directly responsible for the observed radiosensitization effect. The model used only accounts for DNA damage from direct interactions, whilst considering the indirect effect, and it is possible the radiosensitization effect to be due to other physical effects, although we consider that possibility unlikely. Our conclusion suggests that other mechanisms might have greater contribution to the radiosensitization effect and further investigation should be conducted.

Gold nanoparticles (GNPs) have been shown to sensitize cancer cells to x-ray radiation, particularly at kV energies where photoelectric interactions dominate and the high atomic number of gold makes a large difference to x-ray absorption. Protons have a high cross-section for gold at a large range of relevant clinical energies, and so potentially could be used with GNPs for increased therapeutic effect.Here, we investigate the contribution of secondary electron emission to cancer cell radiosensitization and investigate how this parameter is affected by proton energy and a free radical scavenger. We simulate the emission from a realistic cell phantom containing GNPs after traversal by protons and x-rays with different energies. We find that with a range of proton energies (1-250 MeV) there is a small increase in secondaries compared to a much larger increase with x-rays. Secondary electrons are known to produce toxic free radicals. Using a cancer cell line in vitro we find that a free radical scavenger has no protective effect on cells containing GNPs irradiated with 3 MeV protons, while it does protect against cells irradiated with x-rays. We conclude that GNP generated free radicals are a major cause of radiosensitization and that there is likely to be much less dose enhancement effect with clinical proton beams compared to x-rays.

It is well known that broad beam irradiation with heavy ions leads to variation in the number of hit(s) received by each cell as the distribution of particles follows the Poisson statistics. Although the nucleus area will determine the number of hit(s) received for a given dose, variation amongst its irradiated cell population is generally not considered. In this work, we investigate the effect of the nucleus area's distribution on the survival fraction. More specifically, this work aims to explain the deviation, or tail, which might be observed in the survival fraction at high irradiation doses. For this purpose, the nucleus area distribution was added to the beam Poisson statistics and the Linear-Quadratic model in order to fit the experimental data. As shown in this study, nucleus size variation, and the associated Poisson statistics, can lead to an upward survival trend after broad beam irradiation. The influence of the distribution parameters (mean area and standard deviation) was studied using a normal distribution, along with the Linear-Quadratic model parameters (α and β). Finally, the model proposed here was successfully tested to the survival fraction of LN18 cells irradiated with a 85 keV µm(- 1) carbon ion broad beam for which the distribution in the area of the nucleus had been determined.

A "broadbeam" facility is demonstrated for the vertical microbeam at Surrey's Ion Beam Centre, validating the new technique used by Barazzuol et al. (Radiat Res 177:651-662, 2012). Here, droplets with a diameter of about 4 mm of 15,000 mammalian cells in suspension were pipetted onto defined locations on a 42-mm-diameter cell dish with each droplet individually irradiated in "broadbeam" mode with 2 MeV protons and 4 MeV alpha particles and assayed for clonogenicity. This method enables multiple experimental data points to be rapidly collected from the same cell dish. Initially, the Surrey vertical beamline was designed for the targeted irradiation of single cells with single counted ions. Here, the benefits of both targeted single-cell and broadbeam irradiations being available at the same facility are discussed: in particular, high-throughput cell irradiation experiments can be conducted on the same system as time-intensive focused-beam experiments with the added benefits of fluorescent microscopy, cell recognition and time-lapse capabilities. The limitations of the system based on a 2 MV tandem accelerator are also discussed, including the uncertainties associated with particle Poisson counting statistics, spread of linear energy transfer in the nucleus and a timed dose delivery. These uncertainties are calculated with Monte Carlo methods. An analysis of how this uncertainty affects relative biological effect measurements is made and discussed. © 2013 Springer-Verlag Berlin Heidelberg.

As a part of a systematic study on mechanisms involved in physical cancer therapies, this work investigated response of mammalian cells to ultra-low-dose ion beam irradiation. The ion beam irradiation was performed using the recently completed nanobeam facility at the Surrey Ion Beam Centre. A scanning focused vertical ion nano-beam was applied to irradiate Chinese hamster V79 cells. The V79 cells were irradiated in two different beam modes, namely, focused single ion beam and defocused scanning broad ion beam of 3.8-MeV protons. The single ion beam was capable of irradiating a single cell with a precisely controlled number of the ions to extremely low doses. After irradiation and cell incubation, the number of surviving colonies as a function of the number of the irradiating ions was measured for the cell survival fraction curve. A lower survival for the single ion beam irradiation than that of the broad beam case implied the hypersensitivity and bystander effect. The ion-beam-induced cell survival curves were compared with that from 300-kV X-ray irradiation. Theoretical studies indicated that the cell death in single ion irradiation mainly occurred in the cell cycle phases of cell division and intervals between the cell division and the DNA replication. The success in the experiment demonstrated the Surrey vertical nanobeam successfully completed.

Charged particle therapy is increasingly becoming a valuable tool in cancer treatment, mainly due to the favorable interaction of particle radiation with matter. Its application is still limited due, in part, to lack of data regarding the radiosensitivity of certain cell lines to this radiation type, especially to high-linear energy transfer (LET) particles. From the earliest days of radiation biology, the clonogenic survival assay has been used to provide radiation response data. This method produces reliable data but it is not optimized for high-throughput microbeam studies with high-LET radiation where high levels of cell killing lead to a very low probability of maintaining cells’ clonogenic potential. A new method, therefore, is proposed in this paper, which could potentially allow these experiments to be conducted in a high-throughput fashion. Cells are seeded in special polypropylene dishes and bright-field illumination provides cell visualization. Digital images are obtained and cell detection is applied based on corner detection, generating individual cell targets as x–y points. These points in the dish are then irradiated individually by a micron field size high-LET microbeam. Post-irradiation, time-lapse imaging follows cells’ response. All irradiated cells are tracked by linking trajectories in all time-frames, based on finding their nearest position. Cell divisions are detected based on cell appearance and individual cell temporary corner density. The number of divisions anticipated is low due to the high probability of cell killing from high-LET irradiation. Survival curves are produced based on cell’s capacity to divide at least four to five times. The process is repeated for a range of doses of radiation. Validation shows the efficiency of the proposed cell detection and tracking method in finding cell divisions.

High-linear energy transfer radiation offers superior biophysical properties over conventional radiotherapy and may have a great potential for treating radioresistant tumors, such as glioblastoma. However, very little pre-clinical data exists on the effects of high-LET radiation on glioblastoma cell lines and on the concomitant application of chemotherapy. This study investigates the in vitro effects of temozolomide in combination with low-energy protons and α particles. Cell survival, DNA damage and repair, and cell growth were examined in four human glioblastoma cell lines (LN18, T98G, U87 and U373) after treatment with either X rays, protons (LET 12.91 keV/μm), or α particles (LET 99.26 keV/μm) with or without concurrent temozolomide at clinically-relevant doses of 25 and 50 μM. The relative biological effectiveness at 10% survival (RBE(10)) increased as LET increased: 1.17 and 1.06 for protons, and 1.84 and 1.68 for α particles in the LN18 and U87 cell lines, respectively. Temozolomide administration increased cell killing in the O(6)-methylguanine DNA methyltransferase-methylated U87 and U373 cell lines. In contrast, temozolomide provided no therapeutic enhancement in the methylguanine DNA methyltransferase-unmethylated LN18 and T98G cell lines. In addition, the residual number of γ-H2AX foci at 24 h after treatment with radiation and concomitant temozolomide was found to be lower than or equal to that expected by DNA damage with either of the individual treatments. Kinetics of foci disappearance after X-ray and proton irradiation followed similar time courses; whereas, loss of γ-H2AX foci after α particle irradiation occurred at a slower rate than that by low-LET radiation (half-life 12.51-16.87 h). The combination of temozolomide with different radiation types causes additive rather than synergistic cytotoxicity. Nevertheless, particle therapy combined with chemotherapy may offer a promising alternative with the additional benefit of superior biophysical properties. It is also possible that new fractionation schedules could be designed to exploit the change in DNA repair kinetics when MGMT-methylated cells respond to high-LET radiation.

Purpose In proton therapy precise knowledge of the beam range is essential to guarantee the treatment’s efficacy and to avoid unnecessary toxicities. Over a fractionated course of treatment anatomical changes can severely impact the delivered dose distribution from that planned; evaluation of these changes on a fraction-by-fraction basis is essential. We report the first results of a new method to determine proton beam range in three dimensions, for pencil-beam scanning systems, with an uncertainty below 3 mm. Methods The range is determined through the reconstruction of the origin of prompt gamma (PG) rays emitted from nuclear de-excitations following proton bombardment. PG emission is almost instantaneous and is characterised by a high-production rate. The prototype system is comprised of 16 symmetrically-spaced LaBr3(Ce) detectors, in a spherical design. Initially the position reconstruction capability of the detector system was examined using Geant4 simulations. To determine the PG-rays emission positions in 3D, the information recorded by each detector is fed into a reconstruction algorithm, developed in the MATLAB environment. The development, testing and laboratory validation of the algorithm has been conducted using a sealed 60 Co source. Furthermore the algorithm has been employed to investigate, by means of Geant4 simulations, how the system performs with a proton pencil beam at different clinical energies. In the simulations a water phantom with 2-cm thick body materials slabs embedded inside has been modelled. Results Preliminary simulation results show that for an ideal detector system the reconstruction algorithm is capable of determining the source position to within 1 mm in the 3D space. The algorithm is also able of discriminating between multiple sources with a relative separation of 0.15 mm. A good agreement has been observed between the dose and the prompt-gamma distribution from a proton pencil beam impinging the different phantoms at all the employed clinical energies. Conclusions Proof-of-principle for the reconstruction algorithm with a sealed 60 Co source has been obtained. The response of the system with a clinical proton beam has been evaluated, by means on Monte Carlo simulations. The next stage is to test the system with a proton beam experimentally.

This paper evaluates the lens aberrations in microbeam and nanobeam systems caused by stray DC magnetic fields. Stray DC fields are far less influential on focussed beam spots than stray AC fields, but in order to achieve good beam-spot resolution the beamline must be aligned to the stray DC fields in the laboratory. The relative thickness of the optical elements compared to the curvature of the beam in such fields causes aberration where the beam axis differs from the optical axis of the lens system. In this paper numerical ray tracing has been used to study the influence of stray DC magnetic fields on beam resolution at the sub-micron level using typical field strengths for the Earth’s magnetic field as a case study.

In proton beam therapy precise knowledge of the proton beam range is essential to guarantee the treatment’s efficacy and to avoid unnecessary toxicities. Unlike photon beams, protons stop inside the patient’s body, therefore a direct detection of the distal fall-off is impossible. One technique to determine the beam range is to detect the prompt gamma (PG) rays emitted from the nuclei de-exciting following proton bombardment [1] . PG emission is almost instantaneous and has a high-production rate. The aim of this project is to develop a new method, based on an optimized PG detector system, which can achieve 3D range determination with an uncertainty of no more than 2 mm. The presented method is based on the detection of discrete gamma-rays. As a first step, the position reconstruction capability of the PG detector system was examined by means of Geant4 simulations. The prototype system is comprised of 12 LaBr 3 (Ce) detectors. The information recorded by each individual detector is fed into a reconstruction algorithm to determine the gamma-ray emission point in 3 dimensions. The development of the algorithm, proof-of-principle and simulation validation, have all been conducted using a sealed 60 Co source. Our simulations demonstrate that an ideal detector system with the current reconstruction algorithm is capable of determining the source position with sub-millimetre accuracy. Having obtained proof-of-principle for the reconstruction algorithm the next stage is to investigate how implementing a realistic detector system affects the reconstruction performance. In addition, the ability of the detector system to discriminate between multiple sources in different positions is under evaluation.

Proton beam writing (PBW) is a direct write technique that employs a focused MeV proton beam which is scanned in a pre-determined pattern over a target material which is subsequently electrochemically etched or chemically developed. By changing the energy of the protons the range of the protons can be changed. The ultimate depth of the structure is determined by the range of the protons in the material and this allows structures to be formed to different depths. PBW has been successfully employed on etchable glasses, polymers and semiconductor materials such as silicon (Si) and gallium arsenide (GaAs). This study reports on PBW in p–type GaAs and compares experimental results with computer simulations using the Atlas© semiconductor device package from SILVACO. It has already been proven that hole transport is required for the electrochemical etching of GaAs using Tiron (4,5-dihydroxy-m-benzenedisulfonic acid, di-sodium salt). PBW in GaAs results in carrier removal in the irradiated regions and consequently minimal hole transport (in these regions) during electrochemical etching. As a result the irradiated regions are significantly more etch resistant than the non-irradiated regions. This allows high aspect ratio structures to be formed.

Since the construction of the first ion microprobe at Harwell in the early 1970s, there has been a steady improvement in the resolution of ion microprobes. However, in recent years the rate of improvement has slowed dramatically, with few systems able routinely to achieve resolutions less than 1 μm. There are many reasons for this lack of progress relating both to engineering at the nanometer scale and to fundamental physics. One crucial factor in the achievement of sub-micrometer resolution is the beam optical performance of the focusing system. This requires a high demagnification to permit the use of larger object apertures giving lower slit scattering, but this usually results in a correspondingly large aberration. We are investigating the use of two-stage lens systems with an intermediate focus. Such systems are capable of far greater demagnification than single-stage systems, but the challenge is to find a two-stage system with an acceptable ratio between demagnification and aberration. This paper presents preliminary the results of a systematic survey of two-stage lenses for nanobeam design. The scope of the survey is bounded by a number of practical limitations for nanobeam design. The survey encompasses systems of up to 8 quadrupole lenses and 4 independent power supplies arranged as two groups of up to four lenses constrained to form an intermediate image. The parameter space for this survey is vast, and even restricting the quadrupole lengths to those commercially available and to the 9 m beam length available in our laboratory, several million system geometries have been considered. A matrix-based beam optics software package has been developed which surveys the parameter space to determine the optimum value of a figure of merit based on the ratio of demagnification to spherical aberration. This uses the analytical approximations for spherical aberration in quadrupole lenses derived by Dymnikov et al. [A.D. Dymnikov, T.Ya. Fishkova, S.Ya. Yavor, Nucl. Instr. and Meth. 37 (1965) 268]. The performance of selected systems with good figures of merits have been further investigated using numerical raytracing software and the results are presented.

Automatic cell detection in bright-field illumination microscopy is challenging due to cells' inherent optical properties. Applications including individual cell microbeam irradiation demand minimisation of additional cell stressing factors, so contrast-enhancing fluorescence microscopy should be avoided. Additionally, the use of optically non-homogeneous substrates amplifies the problem. This research focuses on the design of a method for automatic cell detection on polypropylene substrate, suitable for microbeam irradiation. In order to fulfil the relative requirements, the Harris corner detector was employed to detect apparent cellular features. These features-corners were clustered based on a dual-clustering technique according to the density of their distribution across the image. Weighted centroids were extracted from the clusters of corners and constituted the targets for irradiation. The proposed method identified more than 88% of the 1,738 V79 Chinese hamster cells examined. Moreover, a processing time of 2.6 s per image fulfilled the requirements for a near real-time cell detection-irradiation system.

This report describes how proton beam writing can be used to produce direct write, high resolution three dimensional structures on the nano and micron scales in semiconductor materials such as p-type (1 0 0) bulk silicon and gallium arsenide. The lattice damage caused by the proton irradiation increases the electrical resistance of the semiconductors resulting in a raised structure of the scanned area after an electrochemical etch. Advances in this field over the past few years and its relevance to future technology mean that it is now a powerful contender for direct write technology for future nodes 45 nm and below.

Investigations using MeV protons for lithography applications are being performed at the Ion Beam Centre of the University of Surrey, UK. High aspect ratio three dimensional structures have been produced by protons in gallium arsenide (GaAs) and Poly(methyl methacrylate) (PMMA). Structures produced in PMMA require significantly lower fluences than GaAs and behave positively to etching, whereas GaAs shows a negative behaviour. Variable fluence studies on GaAs show a transition from low to high aspect ratio three dimensional structures as the fluence increases.

Gold nanoparticles (GNPs) have shown a potential as a radiosensitizer in radiotherapy. The radiosensitization effect is thought to be linked to the increased dose deposition around the GNP. Monte Carlo simulations have been implemented for the calculation of the dose distributions around the GNPs and have been used for the calculation of the dose enhancement. They have also been imported to radiobiological models to predict biological endpoints. This work assessed the implications of different physical interaction models on the dose distribution and dose enhancement of GNPs surrounded by water under proton irradiation. The Penelope and Livermore physical interaction model implementation of the Geant4 simulation toolkit were compared considering the following parameters: (i) GNP size, (ii) proton energy, and (iii) alternative physics model parameters in the gold or water medium. We found that neither the dose distribution nor the dose enhancement is sensitive to the model selection after the first 100 nm from the GNP surface. Within the first 100 nm the Livermore models calculated a higher dose, attributed to a higher production of low energy secondary electrons inside the GNP.

One of the fundamental limitations in the performance of MeV ion microbeam focusing systems is the effect of ion scattering at the edges of the object aperture. As the aperture is reduced in the search for smaller spot sizes, the fraction of scattered to unscattered beam increases. The scattered beam contains lower energy particles which can be transmitted through the system to create a halo of over-focused particles surrounding the final image. Removal of this halo is critical to achieving small spot sizes, especially in single ion applications. In this paper, we discuss the use of a Wien filter (crossed magnetic and electrostatic fields) to deflect the reduced energy scattered particles and ensure that only ions with the correct energy are accepted into the lens. This paper reviews the beam optics of Wien filter systems and presents calculations of the parameters required to obtain useful energy dispersion.

The potential that laser based particle accelerators offer to solve sizing and cost issues arising with conventional proton therapy has generated great interest in the understanding and development of laser ion acceleration, and in investigating the radiobiological effects induced by laser accelerated ions. Laser-driven ions are produced in bursts of ultra-short duration resulting in ultra-high dose rates, and an investigation at Queen's University Belfast was carried out to investigate this virtually unexplored regime of cell rdaiobiology. This employed the TARANIS terawatt laser producing protons in the MeV range for proton irradiation, with dose rates exceeding 109 Gys-1 on a single exposure. A clonogenic assay was implemented to analyse the biological effect of proton irradiation on V79 cells, which, when compared to data obtained with the same cell line irradiated with conventionally accelerated protons, was found to show no significant difference. A Relative Biological effectiveness of 1.4±0.2 at 10 % Survival Fraction was estimated from a comparison with a 225 kVp X-ray source. © 2013 SPIE.

The ultrashort duration of laser-driven multi-MeV ion bursts offers the possibility of radiobiological studies at extremely high dose rates. Employing the TARANIS Terawatt laser at Queen's University, the effect of proton irradiation at MeV-range energies on live cells has been investigated at dose rates exceeding 109Gy/s as a single exposure. A clonogenic assay showed consistent lethal effects on V-79 live cells, which, even at these dose rates, appear to be in line with previously published results employing conventional sources. A Relative Biological Effectiveness (RBE) of 1.4±0.2 at 10% survival is estimated from a comparison with a 225 kVp X-ray source.

Laser-driven proton and ion acceleration is an area of increasing research interest given the recent development of short pulse-high intensity lasers. Several groups have reported experiments to understand whether a laser-driven beam can be applied for radiobiological purposes and in each of these, the method to obtain dose and spectral analysis was slightly different. The difficulty with these studies is that the very large instantaneous dose rate is a challenge for commonly used dosimetry techniques, so that other more sophisticated procedures need to be explored. This paper aims to explain a method for obtaining the energetic spectrum and the dose of a laser-driven proton beam irradiating a cell dish used for radiobiology studies. The procedure includes the use of a magnet to have charge and energy separation of the laser-driven beam, Gafchromic films to have information on dose and partially on energy, and a Monte Carlo code to expand the measured data in order to obtain specific details of the proton spectrum on the cells. Two specific correction factors have to be calculated: one to take into account the variation of the dose response of the films as a function of the proton energy and the other to obtain the dose to the cell layer starting from the dose measured on the films. This method, particularly suited to irradiation delivered in a single laser shot, can be applied in any other radiobiological experiment performed with laser-driven proton beams, with the only condition that the initial proton spectrum has to be at least roughly known. The method was tested in an experiment conducted at Queen's University of Belfast using the TARANIS laser, where the mean energy of the protons crossing the cells was between 0.9 and 5 MeV, the instantaneous dose rate was estimated to be close to 10(9) Gy s(-1) and doses between 0.8 and 5 Gy were delivered to the cells in a single laser shot. The combination of the applied corrections modified the initial estimate of dose by up to 40%.

A single-ended HVEE® 3.5 MV Singletron electrostatic accelerator has been installed since October 2005 at the Centre d’Etudes Nucleaires de Bordeaux-Gradignan (CENBG) in France. This facility is equipped with a microbeam line dedicated to ion beam analysis (scanning transmission ion microscopy – STIM, particle induced X-ray emission – PIXE, Rutherford back scattering) and cellular irradiation in single event mode. A high demagnification nanobeam line will be installed on the same facility in the near future. This paper focuses on the simulation of the microbeam and nanobeam lines performances using the Geant4 Monte Carlo simulation toolkit. Comparisons with experimental data collected on the microbeam line are presented.

For many years the only ray-tracing software available with sufficient precision for the design of quadrupole microbeam focusing systems has been OXRAY and its successor TRAX, developed at Oxford in the 1980s. With the current interest in pushing the beam diameter into the nanometre region, this software has become dated and more importantly the precision at small displacements may not be sufficient and new simulation tools are required. Two candidates for this are Zgoubi, developed at CEA as a general beam line design tool and the CERN simulation program Geant in its latest version Geant4. In order to use Geant4 new quadrupole field modules have been developed and implemented. In this paper the capabilities of the three codes TRAX, Zgoubi and Geant4 are reviewed. Comparisons of ray-tracing calculations in a high demagnification quadrupole probe-forming system for the sub-micron region are presented.

Inductively coupled plasma mass spectrometry (ICP-MS) was used to quantify the total amount of trace elements in retina from adult male Sprague-Dawley rats (n = 6). Concentration of trace elements within individual retinal areas in frozen sections of the fellow eye was established with the use of two methodologies: (1) particle-induced X-ray emission (PIXE) in combination with 3D depth profiling with Rutherford backscattering spectrometry (RBS) and (2) synchrotron X-ray fluorescence (SXRF) microscopy. The most abundant metal in the retina was zinc, followed by iron and copper. Nickel, manganese, chromium, cobalt, selenium and cadmium were present in very small amounts. The PIXE and SXRF analysis yielded a non-homogenous pattern distribution of metals in the retina. Relatively high levels of zinc were found in the inner part of the photoreceptor inner segments (RIS)/outer limiting membrane (OLM), inner nuclear layer and plexiform layers. Iron was found to accumulate in the retinal pigment epithelium/choroid layer and RIS/OLM. Copper in turn, was localised primarily in the RIS/OLM and plexiform layers. The trace elements iron, copper, and zinc exist in different amounts and locations in the rat retina.

Relative Biological Effectiveness (RBE), the ratio of doses between radiation modalities to produce the same biological endpoint, is a controversial and important topic in proton therapy. A number of phenomenological models incorporate variable RBE as a function of Linear Energy Transfer (LET), though a lack of mechanistic description limits their applicability. In this work we take a different approach, using a track structure model employing fundamental physics and chemistry to make predictions of proton and photon induced DNA damage, the first step in the mechanism of radiation-induced cell death. We apply this model to a proton therapy clinical case showing, for the first time, predictions of DNA damage on a patient treatment plan. Our model predictions are for an idealised cell and are applied to an ependymoma case, at this stage without any cell specific parameters. By comparing to similar predictions for photons, we present a voxel-wise RBE of DNA damage complexity. This RBE of damage complexity shows similar trends to the expected RBE for cell kill, implying that damage complexity is an important factor in DNA repair and therefore biological effect.

This paper presents the first plasmid DNA irradiations carried out with Very High Energy Electrons (VHEE) over 100–200 MeV at the CLEAR user facility at CERN to determine the Relative Biological Effectiveness (RBE) of VHEE. DNA damage yields were measured in dry and aqueous environments to determine that ~ 99% of total DNA breaks were caused by indirect effects, consistent with other published measurements for protons and photons. Double-Strand Break (DSB) yield was used as the biological endpoint for RBE calculation, with values found to be consistent with established radiotherapy modalities. Similarities in physical damage between VHEE and conventional modalities gives confidence that biological effects of VHEE will also be similar—key for clinical implementation. Damage yields were used as a baseline for track structure simulations of VHEE plasmid irradiation using GEANT4-DNA. Current models for DSB yield have shown reasonable agreement with experimental values. The growing interest in FLASH radiotherapy motivated a study into DSB yield variation with dose rate following VHEE irradiation. No significant variations were observed between conventional and FLASH dose rate irradiations, indicating that no FLASH effect is seen under these conditions.

Objectives: High-energy Proton Beam Therapy (PBT) commenced in England in 2018 and NHS England commissions PBT for 1.5% of patients receiving radical radiotherapy. We sought expert opinion on the level of provision. Methods: Invitations were sent to 41 colleagues working in PBT, most at one UK centre, to contribute by completing a spreadsheet. 39 responded: 23 (59%) completed the spreadsheet; 16 (41%) declined, arguing that clinical outcome data are lacking, but joined six additional site-specialist oncologists for two consensus meetings. The spreadsheet was pre-populated with incidence data from Cancer Research UK and radiotherapy use data from the National Cancer Registration and Analysis Service. ‘Mechanisms of Benefit’ of reduced growth impairment, reduced toxicity, dose escalation and reduced second cancer risk were examined. Results: The most reliable figure for percentage of radical radiotherapy patients likely to benefit from PBT was that agreed by 95% of the 23 respondents at 4.3%, slightly larger than current provision. The median was 15% (range 4–92%) and consensus median 13%. The biggest estimated potential benefit was from reducing toxicity, median benefit to 15% (range 4–92%), followed by dose escalation median 3% (range 0 to 47%); consensus values were 12 and 3%. Reduced growth impairment and reduced second cancer risk were calculated to benefit 0.5% and 0.1%. Conclusions: The most secure estimate of percentage benefit was 4.3% but insufficient clinical outcome data exist for confident estimates. The study supports the NHS approach of using the evidence base and developing it through randomised trials, non-randomised studies and outcomes tracking. Advances in knowledge: Less is known about the percentage of patients who may benefit from PBT than is generally acknowledged. Expert opinion varies widely. Insufficient clinical outcome data exist to provide robust estimates. Considerable further work is needed to address this, including international collaboration; much is already underway but will take time to provide mature data.