Just-in-time Hardware generation for abstracted reconfigurable computing

This thesis addresses the use of reconfigurable hardware in computing platforms, in order to harness the performance benefits of dedicated hardware whilst maintaining the flexibility associated with software. Although the reconfigurable computing concept is not new, the low level nature of the supporting tools normally used, together with the consequent limited level of abstraction and resultant lack of backwards compatibility, has prevented the widespread adoption of this technology. In addition, bandwidth and architectural limitations, have seriously constrained the potential improvements in performance. A review of existing approaches and tools flows is conducted to highlight the current problems being faced in this field. The objective of the work presented in this thesis is to introduce a radically new approach to reconfigurable computing tool flows. The runtime based tool flow introduces complete abstraction between the application developer and the underlying hardware. This new technique eliminates the ease of use and backwards compatibility issues that have plagued the reconfigurable computing concept, and could pave the way for viable mainstream reconfigurable computing platforms. An easy to use, cycle accurate behavioural modelling system is also presented, which was used extensively during the early exploration of new concepts and architectures. Some performance improvements produced by the new reconfigurable computing tool flow, when applied to both a MIPS based embedded platform, and the Cray XDl, are also presented. These results are then analyzed and the hardware and software factors affecting the performance increases that were obtained are discussed, together with potential techniques that could be used to further increase the performance of the system. Lastly a heterogenous computing concept is proposed, in which, a computer system, containing multiple types of computational resource is envisaged, each having their own strengths and weaknesses (e.g. DSPs, CPUs, FPGAs). A revolutionary new method of fully exploiting the potential of such a system, whilst maintaining scalability, backwards compatibility, and ease of use is also presented

Optimal weak lensing tomography for CFHTLenS

Weak gravitational lensing is a powerful astronomical tool for constraining cosmological parameters that is entering its prime. Lensing occurs because gravitational fields deflect light rays and measuring this deflection through a statistic known as cosmic shear allows us to directly measure the properties of dark matter and dark energy on large scales. In principle, gravitational lensing is a clean probe of the cosmology of the Universe, as it depends on gravity alone and not on incomplete astrophysical models or approximations. In practice, however, there are several factors that limit the accuracy and precision of lensing measurements. These include accurate measurement of galaxy shapes, correctly accounting for distortions to galaxy images due to the point spread function of the telescope, the presence of intrinsic alignments (IAs) of galaxy shapes due to physical processes, and inaccuracies in commonly-used galaxy photometric redshift information. These effects may all introduce systematic errors in lensing measurements which must be carefully accounted for to ensure that cosmological constraints from lensing are unbiased and as precise as possible. The Canada-France-Hawaii-Telescope Lensing Survey (CFHTLenS) is the largest weak lensing survey completed to date, covering 154 square degrees of the sky in 5 optical bands, with photometric redshift information for every survey galaxy. With lensing measurements from more galaxies than ever before, the statistical uncertainties on parameter estimates will be the lowest ever achieved from weak lensing. If left unaccounted for, sources of systematic error would dominate over the statistical uncertainty, potentially biasing parameter estimates catastrophically. A technique known as tomography in which galaxies are sorted into bins based on their redshift can help constrain cosmological parameters more precisely. This is because utilising the redshifts of survey galaxies retains cosmological information that would otherwise be lost, such as the behaviour of dark energy and the growth of structure over time. Tomography, however, increases the demand for systematics-free galaxy catalogues as the technique is strongly sensitive to the IA signal and photometric redshift errors. Therefore, future lensing analyses will require a more sophisticated treatment of these effects to extract maximal information from the lensing signal. A thorough understanding of the error on lensing measurements is necessary in order to produce meaningful cosmological constraints. One of the key features of cosmic shear is that it is highly correlated over di erent angular scales, meaning that error estimates must take into account the covariance of the data over different angular scales, and in the case of tomography, between different redshift bins. The behaviour and size of the (inverse) covariance matrix is one of the limiting factors in such a cosmological likelihood analysis, so constructing an accurate, unbiased estimate of the covariance matrix inverse is essential to cosmic shear analysis. This thesis presents work to optimise tomographic weak lensing analysis and achieve the tightest parameter constraints possible for a CFHTLenS-like survey. N-body simulations and Gaussian shear fields incorporating an IA model (known as the `non-linear alignment' model) with a free parameter are used to estimate fully tomographic covariance matrices of cosmic shear for CFHTLenS. We simultaneously incorporate for the first time the error contribution expected from the non-linear alignment model for IAs and realistic photometric redshift uncertainties as measured from the CFHTLenS. We find that non-Gaussian simulations that incorporate nonlinearity on small scales are needed to ensure the covariance is not underestimated, and that the covariance matrix is shot-noise dominated for almost all tomographic correlations. The number of realisations of the simulations used to estimate the covariance places a hard limit on the maximum number of tomographic bins that one can use in an analysis. Given the available number of lines of sight generated from CFHTLenS-like simulations, we find that up to ~ 15 tomographic bins may be utilised in a likelihood analysis. The estimated tomographic covariance matrices are used in a least-squares likelihood analysis in order to find the combination of both angular and tomographic bins that gives the tightest constraints on some key cosmological parameters. We find that the optimum binning is somewhat degenerate, with around 6 tomographic and 8 angular bins being optimal, and limited by the available number of realisations of the simulations used to estimate the covariance. We also investigate the bias on best- t parameter estimates that occurs if IAs or photometric redshift errors are neglected. With our choice of IA model, the effect of neglecting IAs on the best- t cosmological parameters is not significant for a CFHTLenS-like survey, although this may not be true if the IA signal differs substantially from the model, or for future wide-field surveys with much smaller statistical uncertainties. Similarly, neglecting photometric redshift errors does not result in significant bias, although we apply similar caveats. Finally, we apply the results of this optimisation to the CFHTLenS cosmic shear data, performing a preliminary analysis of the shear correlation function to produce both 2D and optimal tomographic cosmological constraints. From 6-bin tomography, we constrain the matter density parameter Ωm = 0:419+0:123-0:090, the amplitude of the matter power spectrum σ8 = 0:623+0:101 -0:084 and the amplitude parameter of the non-linear alignment model, A = -1:161+1:163 -0:597. We perform this analysis to test the validity and limitations of the optimal binning on real data and find that 6-bin tomography improves parameter constraints considerably, albeit not as much as when performed on simulated data. This analysis represents an important step in the development of techniques to optimise the recovery of lensing information and hence cosmological constraints, while simultaneously accounting for potential sources of bias in shear analysis

Adaptive dose escalated radiotherapy in oropharyngeal cancers: a treatment planning feasibility study

Background: A significant proportion of patients with poor prognosis squamous cell cancer of the oropharynx relapse loco-regionally despite radical (chemo)radiotherapy. If a predictive biomarker for disease control can be identified during treatment then individualised and adaptive treatment strategies may be employed. The aim of this study is to assess the feasibility of adaptive and dose-escalated RT to the gross tumour volume without increasing surrounding planning target volume doses and maintaining clinically acceptable organs at risk doses. Materials and methods: Twenty representative patients with poor prognosis locally advanced OPSCC who were known to have relapsed post RT, were re-planned retrospectively using Eclipse TPS v15.5, RapidPlan™ and multi-criteria optimisation. In our centre, PTV65 is treated with 65 Gy in 30 fractions while areas at risk of containing microscopic disease (PTV54) are treated synchronously to 54 Gy in 30 fractions. The original clinical plans were re-optimised to act as controls (Group I). These plans were split into two plans of 15 fractions each, with the latter 15 fractions used to escalate the dose to the GTV to 73 Gy (Group II) and 82 Gy (Group III). Plan sums were created for the total 30 fractions to record plan evaluation parameters along with assessments of plan deliverability. Results: For all groups, the dose coverage at D98% and D50% for the PTVs were comparable. The D2% dose levels for PTV65-GTV increased. All dose levels associated with PTV54 remained largely unaffected by the dose escalation regimens. Conformity indices for PTV65 and PTVAll (PTV65 plus PTV54) reveal comparable target volume coverage across all three groups. Despite the GTV being escalated by 12.3% and 26.2% in groups II and III, the volume of GTV receiving > 84 Gy was considerably less than 1.75 cc. While OAR doses increased for the escalated groups, these increases were not clinically significant. Conclusion: This planning feasibility study exploring RapidPlan™ combined with multi-criteria optimisation has demonstrated that doses to the GTV may be escalated without increasing PTV65-GTV, PTV54 or OAR doses considerably, suggesting an interventional clinical trial using this approach would be feasible

The impact of COVID-19 on radiotherapy services in Scotland, UK: a population-based study

Aims: The effect of the COVID-19 pandemic on cancer radiotherapy services is largely unknown. The aim of the present study was to investigate the impact of the resultant contingency plans on radiotherapy cancer services in Scotland. Materials and methods: Detailed data of radiotherapy activity at our centre were collected from 1 April 2019 to 31 March 2021. Differences in mean weekly radiotherapy courses, dose and fractionation patterns and treatment intent were compared with corresponding pre-pandemic months for all treatment sites. Qualitative data were collected for a subgroup of radical radiotherapy patients. Results: Total radiotherapy courses decreased from 6968 to 6240 (–10%) compared with the previous year, prior to the pandemic. Average weekly radiotherapy courses delivered were 134 (standard deviation ±13), decreasing by 10% to 120 ([AQ1]standard deviation 15) (Welch’s t-test, P < 0.001). The greatest decrease in new start treatment courses was observed from May to August 2020 (–7.7%, –24.0%, –16.7% and –18.7%) compared with the corresponding months in 2019. A significant reduction was seen for female patients <70 years (–16%) compared with females >70 years (–8%) or their male counterparts (–7% and –6%, respectively). By diagnosis, the largest reductions between pre- and post-pandemic levels were for anal (–26%), breast (–18%) and prostate (–14%) cancer. Contrarily, a significant increase was found for bladder (28%) and oesophageal (11%) cancers. Conclusions: Over the first 12 months of the COVID-19 pandemic, radiotherapy activity significantly decreased compared with the 12 months prior. Due to issued guidance, the use of hypofractionated regimens increased, contributing to the reduction in treatments for some tumour sites. An increase in other tumour sites can probably be attributed to the reduction or cancellation of surgical interventions. These results will inform our understanding of the indirect consequences of the pandemic on radiotherapy services

Lifetime measurements of N ≃ 20 phosphorus isotopes using the AGATA γ-ray tracking spectrometer

International audienceLifetimes of excited states of the phosphorus isotopes 1533,34,35,36P have been measured by using the differential recoil-distance method. The isotopes of phosphorus were populated in binary grazing reactions initiated by a beam of S36 ions of energy 225 MeV incident on a thin Pb208 target mounted in the Cologne plunger apparatus. The combination of the PRISMA magnetic spectrometer and an early implementation of the AGATA γ-ray tracking array was used to detect γ rays in coincidence with projectile-like nuclear species. Lifetime measurements of populated states were made within the range from about 1 to 100 ps. The number of states for which lifetime measurements were possible was limited by statistics. For P33, lifetime limits were determined for the first 3/2+ and 5/2+ states at 1431 and 1848 keV, respectively; the results are compared with previous published lifetime values. The lifetime of the first 2+ state of P34 at 429 keV was determined and compared with earlier measurements. For P35, the states for which lifetimes, or lifetime limits, were determined were those at 2386, 3860, 4101, and 4493 keV, with Jπ values of 3/2+, 5/2+, 7/21−, and 7/22−, respectively. There have been no previous published lifetimes for states in this nucleus. A lifetime was measured for the stretched π(1f7/2)⊗ν(1f7/2)Jπ=(7+) state of P36 at 5212 keV and a lifetime limit was established for the stretched π(1d3/2)⊗ν(1f7/2)Jπ=(5−) state at 2030 keV. There are no previously published lifetimes for states of P36. Measured lifetime values were compared with the results of state-of-the-art shell-model calculations based on the PSDPF effective interaction. In addition, measured branching ratios, published mixing ratios, and electromagnetic transition rates, where available, have been compared with shell-model values. In general, there is good agreement between experiment and the shell model; however there is evidence that the shell-model values of the M1 transition rates for the 3/21+→1/2+ (ground state) and 5/21+→3/21+ transitions in P33 underestimate the experimental values by a factor between 5 and 10. In P35 there are some disagreements between experimental and shell-model values of branching ratios for the first and second excited 7/2− states. In particular, there is a serious disagreement for the decay characteristics of the second 7/2− state at 4493 keV, for which the shell-model counterpart lies at 4754 keV. In this case, the shell-model competing electromagnetic decay branches are dominated by E1 and M1 transitions

Direct observation of the Ba 114 → Xe 110 → Te 106 → Sn 102 triple α -decay chain using position and time correlations

The triple α-decay chain 114Ba → 110Xe → 106Te → 102Sn has been directly observed for the first time, following the 58Ni(58Ni ,2n) reaction. Implantation of 114Ba nuclei into a double-sided silicon-strip detector has allowed their α decays to be correlated in position and time with the α decays of the daughter (110Xe) and granddaughter (106Te) nuclei. In total, 17 events have been assigned to the 114Ba → 110Xe → 106Te → 102Sn triple α-decay chain. The energy of the 114Ba α decay has been measured to be Eα = 3480(20) keV, which is 70 keV higher than the previously measured value, and the half-life of 114Ba has been measured with improved accuracy, to be 380+190 −110 ms. A revised Q12C value of 19 035(45) keV for 114Ba is presented.peerReviewe

Effects of a high-dose 24-h infusion of tranexamic acid on death and thromboembolic events in patients with acute gastrointestinal bleeding (HALT-IT): an international randomised, double-blind, placebo-controlled trial

Background: Tranexamic acid reduces surgical bleeding and reduces death due to bleeding in patients with trauma. Meta-analyses of small trials show that tranexamic acid might decrease deaths from gastrointestinal bleeding. We aimed to assess the effects of tranexamic acid in patients with gastrointestinal bleeding. Methods: We did an international, multicentre, randomised, placebo-controlled trial in 164 hospitals in 15 countries. Patients were enrolled if the responsible clinician was uncertain whether to use tranexamic acid, were aged above the minimum age considered an adult in their country (either aged 16 years and older or aged 18 years and older), and had significant (defined as at risk of bleeding to death) upper or lower gastrointestinal bleeding. Patients were randomly assigned by selection of a numbered treatment pack from a box containing eight packs that were identical apart from the pack number. Patients received either a loading dose of 1 g tranexamic acid, which was added to 100 mL infusion bag of 0·9% sodium chloride and infused by slow intravenous injection over 10 min, followed by a maintenance dose of 3 g tranexamic acid added to 1 L of any isotonic intravenous solution and infused at 125 mg/h for 24 h, or placebo (sodium chloride 0·9%). Patients, caregivers, and those assessing outcomes were masked to allocation. The primary outcome was death due to bleeding within 5 days of randomisation; analysis excluded patients who received neither dose of the allocated treatment and those for whom outcome data on death were unavailable. This trial was registered with Current Controlled Trials, ISRCTN11225767, and ClinicalTrials.gov, NCT01658124. Findings: Between July 4, 2013, and June 21, 2019, we randomly allocated 12 009 patients to receive tranexamic acid (5994, 49·9%) or matching placebo (6015, 50·1%), of whom 11 952 (99·5%) received the first dose of the allocated treatment. Death due to bleeding within 5 days of randomisation occurred in 222 (4%) of 5956 patients in the tranexamic acid group and in 226 (4%) of 5981 patients in the placebo group (risk ratio [RR] 0·99, 95% CI 0·82–1·18). Arterial thromboembolic events (myocardial infarction or stroke) were similar in the tranexamic acid group and placebo group (42 [0·7%] of 5952 vs 46 [0·8%] of 5977; 0·92; 0·60 to 1·39). Venous thromboembolic events (deep vein thrombosis or pulmonary embolism) were higher in tranexamic acid group than in the placebo group (48 [0·8%] of 5952 vs 26 [0·4%] of 5977; RR 1·85; 95% CI 1·15 to 2·98). Interpretation: We found that tranexamic acid did not reduce death from gastrointestinal bleeding. On the basis of our results, tranexamic acid should not be used for the treatment of gastrointestinal bleeding outside the context of a randomised trial