First insights into the impacts of benthic cyanobacterial mats on fish herbivory functions on a nearshore coral reef

Benthic cyanobacterial mats (BCMs) are becoming increasingly common on coral reefs. In Fiji, blooms generally occur in nearshore areas during warm months but some are starting to prevail through cold months. Many fundamental knowledge gaps about BCM proliferation remain, including their composition and how they influence reef processes. This study examined a seasonal BCM bloom occurring in a 17-year-old no-take inshore reef area in Fiji. Surveys quantified the coverage of various BCM-types and estimated the biomass of key herbivorous fish functional groups. Using remote video observations, we compared fish herbivory (bite rates) on substrate covered primarily by BCMs (> 50%) to substrate lacking BCMs (< 10%) and looked for indications of fish (opportunistically) consuming BCMs. Samples of different BCM-types were analysed by microscopy and next-generation amplicon sequencing (16S rRNA). In total, BCMs covered 51 ± 4% (mean ± s.e.m) of the benthos. Herbivorous fish biomass was relatively high (212 ± 36 kg/ha) with good representation across functional groups. Bite rates were significantly reduced on BCM-dominated substratum, and no fish were unambiguously observed consuming BCMs. Seven different BCM-types were identified, with most containing a complex consortium of cyanobacteria. These results provide insight into BCM composition and impacts on inshore Pacific reefs

A first step toward uncovering the truth about weight tuning in deformable image registration

Deformable image registration is currently predominantly solved by optimizing a weighted linear combination of objectives. Successfully tuning the weights associated with these objectives is not trivial, leading to trial-and-error approaches. Such an approach assumes an intuitive interplay between weights, optimization objectives, and target registration errors. However, it is not known whether this always holds for existing registration methods. To investigate the interplay between weights, optimization objectives, and registration errors, we employ multi-objective optimization. Here, objectives of interest are optimized simultaneously, causing a set of multiple optimal solutions to exist, called the optimal Pareto front. Our medical application is in breast cancer and includes the challenging prone-supine registration problem. In total, we studied the interplay in three different ways. First, we ran many random linear combinations of objectives using the well-known registration software elastix. Second, since the optimization algorithms used in registration are typically of a local-search nature, final solutions may not always form a Pareto front. We therefore employed a multi-objective evolutionary algorithm that finds weights that correspond to registration outcomes that do form a Pareto front. Third, we examined how the interplay differs if a true multi-objective (i.e., weight-free) image registration method is used. Results indicate that a trial-and-error weight-adaptation approach can be successful for the easy prone to prone breast image registration case, due to the absence of many local optima. With increasing problem difficulty the use of more advanced approaches can be of value in finding and selecting the optimal registration outcomes

On the usefulness of gradient information in multi-objective deformable image registration using a B-spline-based dual-dynamic transformation model: comparison of three optimization algorithms

The use of gradient information is well-known to be highly useful in single-objective optimization-based image registration methods. However, its usefulness has not yet been investigated for deformable image registration from a multi-objective optimization perspective. To this end, within a previously introduced multi-objective optimization framework, we use a smooth B-spline-based dual-dynamic transformation model that allows us to derive gradient information analytically, while still being able to account for large deformations. Within the multi-objective framework, we previously employed a powerful evolutionary algorithm (EA) that computes and advances multiple outcomes at once, resulting in a set of solutions (a so-called Pareto front) that represents efficient trade-offs between the objectives. With the addition of the B-spline-based transformation model, we studied the usefulness of gradient information in multiobjective deformable image registration using three different optimization algorithms: the (gradient-less) EA, a gradientonly algorithm, and a hybridization of these two. We evaluated the algorithms to register highly deformed images: 2D MRI slices of the breast in prone and supine positions. Results demonstrate that gradient-based multi-objective optimization significantly speeds up optimization in the initial stages of optimization. However, allowing sufficient computational resources, better results could still be obtained with the EA. Ultimately, the hybrid EA found the best overall approximation of the optimal Pareto front, further indicating that adding gradient-based optimization for multiobjective optimization-based deformable image registration can indeed be beneficial

Diversifying Multi-Objective Gradient Techniques and their Role in Hybrid Multi-Objective Evolutionary Algorithms for Deformable Medical Image Registration

Gradient methods and their value in single-objective, real-valued optimization are well-established. As such, they play a key role in tackling real-world, hard optimization problems such as deformable image registration (DIR). A key question is to which extent gradient techniques can also play a role in a multi-objective approach to DIR. We therefore aim to exploit gradient information within an evolutionary-algorithm-based multi-objective optimization framework for DIR. Although an analytical description of the multi-objective gradient (the set of all Pareto-optimal improving directions) is available, it is nontrivial how to best choose the most appropriate direction per solution because these directions are not necessarily uniformly distributed in objective space. To address this, we employ a Monte-Carlo method to obtain a discrete, spatially-uniformly distributed approximation of the set of Pareto-optimal improving directions. We then apply a diversification technique in which each solution is associated with a unique direction from this set based on its multi- as well as single-objective rank. To assess its utility, we compare a state-of-the-art multi-objective evolutionary algorithm with three different hybrid versions thereof on several benchmark problems and two medical DIR problems. Results show that the diversification strategy successfully leads to unbiased improvement, helping an adaptive hybrid scheme solve all problems, but the evolutionary algorithm remains the most powerful optimization method, providing the best balance between proximity and diversity

Development and operation of a pixel segmented liquid-filled linear array for radiotherapy quality assurance

A liquid isooctane (C$_{8}$H$_{18}$) filled ionization linear array for radiotherapy quality assurance has been designed, built and tested. The detector consists of 128 pixels, each of them with an area of 1.7 mm $\times$ 1.7 mm and a gap of 0.5 mm. The small pixel size makes the detector ideal for high gradient beam profiles like those present in Intensity Modulated Radiation Therapy (IMRT) and radiosurgery. As read-out electronics we use the X-Ray Data Acquisition System (XDAS) with the Xchip developed by the CCLRC. Studies concerning the collection efficiency dependence on the polarization voltage and on the dose rate have been made in order to optimize the device operation. In the first tests we have studied dose rate and energy dependences, and signal reproducibility. Dose rate dependence was found lower than 2.5 % up to 5 Gy min$^{-1}$, and energy dependence lower than 2.1 % up to 20 cm depth in solid water. Output factors and penumbras for several rectangular fields have been measured with the linear array and were compared with the results obtained with a 0.125 cm$^{3}$ air ionization chamber and radiographic film, respectively. Finally, we have acquired profiles for an IMRT field and for a virtual wedge. These profiles have also been compared with radiographic film measurements. All the comparisons show a good correspondence. Signal reproducibility was within a 2% during the test period (around three months). The device has proved its capability to verify on-line therapy beams with good spatial resolution and signal to noise ratio.Comment: 16 pages, 12 figures Submitted to Phys. Med. Bio

Focused VHEE (very high energy electron) beams and dose delivery for radiotherapy applications

From Springer Nature via Jisc Publications RouterHistory: received 2021-04-21, accepted 2021-06-10, registration 2021-06-23, pub-electronic 2021-07-07, online 2021-07-07, collection 2021-12Publication status: PublishedFunder: Engineering and Physical Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000266; Grant(s): EPZ EPSRC PHYSICS DTP 2018-2023Funder: Science and Technology Facilities Council; doi: http://dx.doi.org/10.13039/501100000271; Grant(s): IAA 2015Abstract: This paper presents the first demonstration of deeply penetrating dose delivery using focused very high energy electron (VHEE) beams using quadrupole magnets in Monte Carlo simulations. We show that the focal point is readily modified by linearly changing the quadrupole magnet strength only. We also present a weighted sum of focused electron beams to form a spread-out electron peak (SOEP) over a target region. This has a significantly reduced entrance dose compared to a proton-based spread-out Bragg peak (SOBP). Very high energy electron (VHEE) beams are an exciting prospect in external beam radiotherapy. VHEEs are less sensitive to inhomogeneities than proton and photon beams, have a deep dose reach and could potentially be used to deliver FLASH radiotherapy. The dose distributions of unfocused VHEE produce high entrance and exit doses compared to other radiotherapy modalities unless focusing is employed, and in this case the entrance dose is considerably improved over existing radiations. We have investigated both symmetric and asymmetric focusing as well as focusing with a range of beam energies

Dosimetric uncertainties related to the elasticity of bladder and rectal walls: Adenocarcinoma of the prostate

Purpose. - Radiotherapy is an important treatment for prostate cancer.During treatment sessions, bladder and rectal repletion is difficult to quantify and cannot be measured with a single and initial CT scan acquisition. Some methods, such as image-guided radiation therapy and dose-guided radiation therapy, aimto compensate thismissing information through periodic CT acquisitions. The aimis to adapt patient's position, beam configuration or prescribed dose for a dosimetric compliance. Methods. -We evaluated organmotion (and repletion) for 54 patients after having computed the original ballistic on a new CT scan acquisition. A new delineation was done on the prostate, bladder and rectum to determine the newdisplacements and define organ dosesmistakes (equivalent uniformdose, average dose and dose-volume histograms). Results. - The new CT acquisitions confirmed that bladder and rectal volumes were not constant during sessions. Some cases showed that previously validated treatment plan became unsuitable. A proposed solution is to correct dosimetries when bladder volume modifications are significant. The result is an improvement for the stability of bladder doses, D50 error is reduced by 25.3%, mean dose error by 5.1% and equivalent uniform dose error by 2.6%. For the rectum this method decreases errors by only 1%. This process can reduce the risk of mismatch between the initial scan and following treatment sessions. Conclusion. - For the proposedmethod, the cone-beamCT is necessary to properly position the isocenter and to quantify bladder and rectal volume variation and deposited doses. The dosimetries are performed in the event that bladder (or rectum) volume modification limits are exceeded. To identify these limits, we have calculated that a tolerance of 10% for the equivalent uniformdose (compared to the initial value of the first dosimetry), this represents 11% of obsolete dosimetries for the bladder, and 4% for the rectum

The influence of BRAF and KRAS mutation status on the association between aspirin use and survival after colon cancer diagnosis

Background: Use of aspirin after diagnosis of colon cancer has been associated with improved survival. Identification of cancer subtypes that respond to aspirin treatment may help develop personalized treatment regimens. The aim of this study was to investigate the influence of BRAF and KRAS mutation status on the association between aspirin use and overall survival after colon cancer diagnosis. Methods: A random selection of 599 patients with colon cancer were analyzed, selected from the Eindhoven Cancer Registry, and BRAF and KRAS mutation status was determined. Data on aspirin use (80 mg) were obtained from the PHARMO Database Network. Parametric survival models with exponential (Poisson) distribution were used. Results: Aspirin use after colon cancer diagnosis was associated with improved overall survival in wild-type BRAF tumors, adjusted rate ratio (RR) of 0.60 (95% CI 0.44-0.83). In contrast, aspirin use in BRAF mutated tumors was not associated with an improved survival (RR 1.11, 95% CI 0.57-2.16). P-value for interaction was non-significant. KRAS mutational status did not differentiate in the association between aspirin use and survival. Conclusion: Low-dose aspirin use after colon cancer diagnosis was associated with improved survival in BRAF wild-type tumors only. However, the large confidence interval of the rate ratio for the use of aspirin in patients with BRAF mutation does not rule out a possible benefit. These results preclude BRAF and KRAS mutation status to be used as a marker for individualized treatment with aspirin, if aspirin becomes regular adjuvant treatment for colon cancer patients in the future