Geometric evaluations of CT and MRI based deep learning segmentation for brain OARs in radiotherapy.

Objective. Deep-learning auto-contouring (DL-AC) promises standardisation of organ-at-risk (OAR) contouring, enhancing quality and improving efficiency in radiotherapy. No commercial models exist for OAR contouring based on brain magnetic resonance imaging (MRI). We trained and evaluated computed tomography (CT) and MRI OAR autosegmentation models in RayStation. To ascertain clinical usability, we investigated the geometric impact of contour editing before training on model quality. Approach. Retrospective glioma cases were randomly selected for training (n = 32, 47) and validation (n = 9, 10) for MRI and CT, respectively. Clinical contours were edited using international consensus (gold standard) based on MRI and CT. MRI models were trained (i) using the original clinical contours based on planning CT and rigidly registered T1-weighted gadolinium-enhanced MRI (MRIu), (ii) as (i), further edited based on CT anatomy, to meet international consensus guidelines (MRIeCT), and (iii) as (i), further edited based on MRI anatomy (MRIeMRI). CT models were trained using: (iv) original clinical contours (CTu) and (v) clinical contours edited based on CT anatomy (CTeCT). Auto-contours were geometrically compared to gold standard validation contours (CTeCT or MRIeMRI) using Dice Similarity Coefficient, sensitivity, and mean distance to agreement. Models' performances were compared using paired Student's t-testing. Main results. The edited autosegmentation models successfully generated more segmentations than the unedited models. Paired t-testing showed editing pituitary, orbits, optic nerves, lenses, and optic chiasm on MRI before training significantly improved at least one geometry metric. MRI-based DL-AC performed worse than CT-based in delineating the lacrimal gland, whereas the CT-based performed worse in delineating the optic chiasm. No significant differences were found between the CTeCT and CTu except for optic chiasm. Significance. T1w-MRI DL-AC could segment all brain OARs except the lacrimal glands, which cannot be easily visualized on T1w-MRI. Editing contours on MRI before model training improved geometric performance. MRI DL-AC in RT may improve consistency, quality and efficiency but requires careful editing of training contours

The benefit of MR-only radiotherapy treatment planning for anal and rectal cancers: A planning study

Introduction: Limited evidence exists showing the benefit of magnetic resonance (MR)-only radiotherapy treatment planning for anal and rectal cancers. This study aims to assess the impact of MR-only planning on target volumes (TVs) and treatment plan doses to organs at risks (OARs) for anal and rectal cancers versus a computed tomography (CT)-only pathway. Materials and methods: Forty-six patients (29 rectum and 17 anus) undergoing preoperative or radical external beam radiotherapy received CT and T2 MR simulation. TV and OARs were delineated on CT and MR, and volumetric arc therapy treatment plans were optimized independently (53.2 Gy/28 fractions for anus, 45 Gy/25 fractions for rectum). Further treatment plans assessed gross tumor volume (GTV) dose escalation. Differences in TV volumes and OAR doses, in terms of Vx Gy (organ volume (%) receiving x dose (Gy)), were assessed. Results: MR GTV and primary planning TV (PTV) volumes systematically reduced by 13 cc and 98 cc (anus) and 44 cc and 109 cc (rectum) respectively compared to CT volumes. Statistically significant OAR dose reductions versus CT were found for bladder and uterus (rectum) and bladder, penile bulb, and genitalia (anus). With GTV boosting, statistically significant dose reductions were found for sigmoid, small bowel, vagina, and penile bulb (rectum) and vagina (anus). Conclusion: Our findings provide evidence that the introduction of MR (whether through MR-only or CT-MR pathways) to radiotherapy treatment planning for anal and rectal cancers has the potential to improve treatments. MR-related OAR dose reductions may translate into less treatment-related toxicity for patients or greater ability to dose escalate

Patient position verification in magnetic-resonance imaging only radiotherapy of anal and rectal cancers

Background and Purpose: Magnetic resonance (MR)-only treatment pathways require either the MR-simulation or synthetic-computed tomography (sCT) as an alternative reference image for cone beam computed tomography (CBCT) patient position verification. This study assessed whether using T2 MR or sCT as CBCT reference images introduces systematic registration errors as compared to CT for anal and rectal cancers. Materials and Methods: A total of 32 patients (18 rectum,14 anus) received pre-treatment CT- and T2 MR- simulation. Routine treatment CBCTs were acquired. sCTs were generated using a validated research model. The local clinical registration protocol, using a grey-scale registration algorithm, was performed for 216 CBCTs using CT, MR and sCT as the reference image. Linear mixed effects modelling identified systematic differences between modalities. Results: Systematic translation and rotation differences to CT for MR were −0.3 to + 0.3 mm and −0.1 to 0.4° for anal cancers and −0.4 to 0.0 mm and 0.0 to 0.1° for rectal cancers, and for sCT were −0.4 to + 0.8 mm, −0.1 to 0.2° for anal cancers and −0.6 to + 0.2 mm, −0.1 to + 0.1° for rectal cancers. Conclusions: T2 MR or sCT can successfully be used as reference images for anal and rectal cancer CBCT position verification with systematic differences to CT <±1 mm and <±0.5°. Clinical enabling of alternative modalities as reference images by vendors is required to reduce challenges associated with their use

Costing conservation: an expert appraisal of the pollinator habitat benefits of England’s entry level stewardship

Pollination services provided by insects play a key role in English crop production and wider ecology. Despite growing evidence of the negative effects of habitat loss on pollinator populations, limited policy support is available to reverse this pressure. One measure that may provide beneficial habitat to pollinators is England’s entry level stewardship agri-environment scheme. This study uses a novel expert survey to develop weights for a range of models which adjust the balance of Entry Level Stewardship options within the current area of spending. The annual costs of establishing and maintaining these option compositions were estimated at £59.3–£12.4 M above current expenditure. Although this produced substantial reduction in private cost:benefit ratios, the benefits of the scheme to pollinator habitat rose by 7–140 %; significantly increasing the public cost:benefit ratio. This study demonstrates that the scheme has significant untapped potential to provide good quality habitat for pollinators across England, even within existing expenditure. The findings should open debate on the costs and benefits of specific entry level stewardship management options and how these can be enhanced to benefit both participants and biodiversity more equitably

Evaluation of integrin αvβ6 cystine knot PET tracers to detect cancer and idiopathic pulmonary fibrosis.

Advances in precision molecular imaging promise to transform our ability to detect, diagnose and treat disease. Here, we describe the engineering and validation of a new cystine knot peptide (knottin) that selectively recognizes human integrin αvβ6 with single-digit nanomolar affinity. We solve its 3D structure by NMR and x-ray crystallography and validate leads with 3 different radiolabels in pre-clinical models of cancer. We evaluate the lead tracer's safety, biodistribution and pharmacokinetics in healthy human volunteers, and show its ability to detect multiple cancers (pancreatic, cervical and lung) in patients at two study locations. Additionally, we demonstrate that the knottin PET tracers can also detect fibrotic lung disease in idiopathic pulmonary fibrosis patients. Our results indicate that these cystine knot PET tracers may have potential utility in multiple disease states that are associated with upregulation of integrin αvβ6

Spatial analysis of anthropogenic river disturbance at regional and continental scales: identifying the wild rivers of Australia

A method for assessing anthropogenic river disturbance is described. The grid-based spatial modeling procedure computes indices of disturbance for individual stream sections. These indices rank streams along a continuum from near-pristine to severely disturbed. The method couples geographical data, recording the extent and intensity of human activities known to impact on river condition, with a Digital Elevation Model (DEM) used for drainage analysis. It was developed to produce the first nation-wide assessment of river disturbance from which Australia's least disturbed or 'wild' rivers were identified. A national summary of the extent and the potential impact of human activities is presented, calculated from the disturbance index values computed for more than 1.5 × 106 stream sections with a total length of over 3 × 106 km. Index values close to the undisturbed end of the continuum are rare, especially among large rivers. Most of the least disturbed streams are predicted to lie within the monsoonal tropical north or the arid/semi-arid center of the continent. The disturbance indices generated provide a comprehensive and consistent characterization of river and catchment disturbance that has applications beyond the identification of wild rivers. These include identification of priorities for rehabilitation and restoration; development of systematic survey strategies for aquatic, riparian and estuarine biota and identification of reserve networks for river systems. However, these applications depend on validating the correlation between river disturbance indices and intensively sampled physical and biological indicators of river condition

The nature of Northern Australia: Natural values, ecological processes and future prospects

Northern Australia stands out as one of the largest natural areas remaining on Earth- alongside such global treasures as the Amazon rainforests, the boreal conifer forests of Alaska and Canada, and the polar wilderness of Antarctica. Nature remains in abundance in ‘the North.’ Its intact tropical savannas, rainforests, and free flowing rivers provide a basis for much of the economic activity and the quality of life for residents of the area. The Nature of Northern Australia details the latest science on the Northern environment. With increasing debate over the future of Australia’s often forgotten North, this is a timely examination of its environmental significance, the ecological processes that make it function, and the economies that are compatible with maintaining healthy communities and people and healthy country into the future

Bioclim: the first species distribution modelling package, its early applications and relevance to most current MaxEnt studies

Aim: Interest in species distribution models (SDMs) and related niche studies has increased dramatically in recent years, with several books and reviews being prepared since 2000. The earliest SDM studies are dealt with only briefly even in the books. Consequently, many researchers are unaware of when the first SDM software package (bioclim) was developed and how a broad range of applications using the package was explored within the first 8 years following its release. The purpose of this study is to clarify these early developments and initial applications, as well as to highlight bioclim's continuing relevance to current studies. Location: Mainly Australia and New Zealand, but also some global applications. Methods: We outline the development of the bioclim package, early applications (1984-1991) and its current relevance. Results: bioclim was the first SDM package to be widely used. Early applications explored many of the possible uses of SDMs in conservation biogeography, such as quantifying the environmental niche of species, identifying areas where a species might be invasive, assisting conservation planning and assessing the likely impacts of climate change on species distributions. Main conclusions: Understanding this pioneering work is worthwhile as bioclim was for many years one of the leading SDM packages and remains widely used. Climate interpolation methods developed for bioclim were used to create the WorldClim database, the most common source of climate data for SDM studies, and bioclim variables are used in about 76% of recent published MaxEnt analyses of terrestrial ecosystems. Also, some of the bioclim studies from the late 1980s, such as measuring niche (both realized and fundamental) and assessing possible impacts of climate change, are still highly relevant to key conservation biogeography issues