Computer-assisted polyp matching between optical colonoscopy and CT colonography: a phantom study

Potentially precancerous polyps detected with CT colonography (CTC) need to be removed subsequently, using an optical colonoscope (OC). Due to large colonic deformations induced by the colonoscope, even very experienced colonoscopists find it difficult to pinpoint the exact location of the colonoscope tip in relation to polyps reported on CTC. This can cause unduly prolonged OC examinations that are stressful for the patient, colonoscopist and supporting staff. We developed a method, based on monocular 3D reconstruction from OC images, that automatically matches polyps observed in OC with polyps reported on prior CTC. A matching cost is computed, using rigid point-based registration between surface point clouds extracted from both modalities. A 3D printed and painted phantom of a 25 cm long transverse colon segment was used to validate the method on two medium sized polyps. Results indicate that the matching cost is smaller at the correct corresponding polyp between OC and CTC: the value is 3.9 times higher at the incorrect polyp, comparing the correct match between polyps to the incorrect match. Furthermore, we evaluate the matching of the reconstructed polyp from OC with other colonic endoluminal surface structures such as haustral folds and show that there is a minimum at the correct polyp from CTC. Automated matching between polyps observed at OC and prior CTC would facilitate the biopsy or removal of true-positive pathology or exclusion of false-positive CTC findings, and would reduce colonoscopy false-negative (missed) polyps. Ultimately, such a method might reduce healthcare costs, patient inconvenience and discomfort.Comment: This paper was presented at the SPIE Medical Imaging 2014 conferenc

Radiation pressure-driven plasma surface dynamics in ultra-intense laser pulse interactions with ultra-thin foils

The dynamics of the plasma critical density surface in an ultra-thin foil target irradiated by an ultra-intense ( ∼ 6 × 1020 Wcm−2 ) laser pulse is investigated experimentally and via 2D particle-in- cell simulations. Changes to the surface motion are diagnosed as a function of foil thickness. The experimental and numerical results are compared with hole-boring and light-sail models of radi- ation pressure acceleration, to identify the foil thickness range for which each model accounts for the measured surface motion. Both the experimental and numerical results show that the onset of relativistic self-induced transparency, in the thinnest targets investigated, limits the velocity of the critical surface, and thus the e ff ectiveness of radiation pressure acceleration

CT colonography: external clinical validation of an algorithm for computer-assisted prone and supine registration

Purpose To perform external validation of a computer-assisted registration algorithm for prone and supine computed tomographic (CT) colonography and to compare the results with those of an existing centerline method. Materials and Methods All contributing centers had institutional review board approval; participants provided informed consent. A validation sample of CT colonographic examinations of 51 patients with 68 polyps (6–55 mm) was selected from a publicly available, HIPAA compliant, anonymized archive. No patients were excluded because of poor preparation or inadequate distension. Corresponding prone and supine polyp coordinates were recorded, and endoluminal surfaces were registered automatically by using a computer algorithm. Two observers independently scored three-dimensional endoluminal polyp registration success. Results were compared with those obtained by using the normalized distance along the colonic centerline (NDACC) method. Pairwise Wilcoxon signed rank tests were used to compare gross registration error and McNemar tests were used to compare polyp conspicuity. Results Registration was possible in all 51 patients, and 136 paired polyp coordinates were generated (68 polyps) to test the algorithm. Overall mean three-dimensional polyp registration error (mean ± standard deviation, 19.9 mm ± 20.4) was significantly less than that for the NDACC method (mean, 27.4 mm ± 15.1; P = .001). Accuracy was unaffected by colonic segment (P = .76) or luminal collapse (P = .066). During endoluminal review by two observers (272 matching tasks, 68 polyps, prone to supine and supine to prone coordinates), 223 (82%) polyp matches were visible (120° field of view) compared with just 129 (47%) when the NDACC method was used (P < .001). By using multiplanar visualization, 48 (70%) polyps were visible after scrolling ± 15 mm in any multiplanar axis compared with 16 (24%) for NDACC (P < .001). Conclusion Computer-assisted registration is more accurate than the NDACC method for mapping the endoluminal surface and matching the location of polyps in corresponding prone and supine CT colonographic acquisitions

Influence of laser polarization on collective electron dynamics in ultraintense laser-foil interactions

The collective response of electrons in an ultrathin foil target irradiated by an ultraintense laser pulse is investigated experimentally and via 3D particle-in-cell simulations. It is shown that if the target is sufficiently thin that the laser induces significant radiation pressure, but not thin enough to become relativistically transparent to the laser light, the resulting relativistic electron beam is elliptical, with the major axis of the ellipse directed along the laser polarization axis. When the target thickness is decreased such that it becomes relativistically transparent early in the interaction with the laser pulse, diffraction of the transmitted laser light occurs through a so called 'relativistic plasma aperture', inducing structure in the spatial-intensity profile of the beam of energetic electrons. It is shown that the electron beam profile can be modified by variation of the target thickness and degree of ellipticity in the laser polarization

Towards optical polarization control of laser-driven proton acceleration in foils undergoing relativistic transparency

Control of the collective response of plasma particles to intense laser light is intrinsic to relativistic optics, the development of compact laser-driven particle and radiation sources, as well as investigations of some laboratory astrophysics phenomena. We recently demonstrated that a relativistic plasma aperture produced in an ultra-thin foil at the focus of intense laser radiation can induce diffraction, enabling polarization-based control of the collective motion of plasma electrons. Here we show that under these conditions the electron dynamics are mapped into the beam of protons accelerated via strong charge-separation-induced electrostatic fields. It is demonstrated experimentally and numerically via 3D particle-in-cell simulations that the degree of ellipticity of the laser polarization strongly influences the spatial-intensity distribution of the beam of multi-MeV protons. The influence on both sheath accelerated and radiation pressure accelerated protons is investigated. This approach opens up new routes to control laser-driven ion sources

Endoluminal surface registration for CT colonography using Haustral Fold Matching

Computed Tomographic (CT) colonography is a technique used for the detection of bowel cancer or potentially precancerous polyps. The procedure is performed routinely with the patient both prone and supine to differentiate fixed colonic pathology from mobile faecal residue. Matching corresponding locations is difficult and time consuming for radiologists due to colonic deformations that occur during patient repositioning. We propose a novel method to establish correspondence between the two acquisitions automatically. The problem is first simplified by detecting haustral folds using a graph cut method applied to a curvature-based metric applied to a surface mesh generated from segmentation of the colonic lumen. A virtual camera is used to create a set of images that provide a metric for matching pairs of folds between the prone and supine acquisitions. Image patches are generated at the fold positions using depth map renderings of the endoluminal surface and optimised by performing a virtual camera registration over a restricted set of degrees of freedom. The intensity difference between image pairs, along with additional neighbourhood information to enforce geometric constraints over a 2D parameterisation of the 3D space, are used as unary and pair-wise costs respectively, and included in a Markov Random Field (MRF) model to estimate the maximum a-posteriori fold labelling assignment. The method achieved fold matching accuracy of 96.0% and 96.1% in patient cases with and without local colonic collapse. Moreover, it improved upon an existing surface-based registration algorithm by providing an initialisation. The set of landmark correspondences is used to non-rigidly transform a 2D source image derived from a conformal mapping process on the 3D endoluminal surface mesh. This achieves full surface correspondence between prone and supine views and can be further refined with an intensity based registration showing a statistically significant improvement (p<0.001p<0.001), and decreasing mean error from 11.9mm11.9mm to 6.0mm6.0mm measured at 1743 reference points from 17 CTC datasets

Imaging biomarker roadmap for cancer studies.

Imaging biomarkers (IBs) are integral to the routine management of patients with cancer. IBs used daily in oncology include clinical TNM stage, objective response and left ventricular ejection fraction. Other CT, MRI, PET and ultrasonography biomarkers are used extensively in cancer research and drug development. New IBs need to be established either as useful tools for testing research hypotheses in clinical trials and research studies, or as clinical decision-making tools for use in healthcare, by crossing 'translational gaps' through validation and qualification. Important differences exist between IBs and biospecimen-derived biomarkers and, therefore, the development of IBs requires a tailored 'roadmap'. Recognizing this need, Cancer Research UK (CRUK) and the European Organisation for Research and Treatment of Cancer (EORTC) assembled experts to review, debate and summarize the challenges of IB validation and qualification. This consensus group has produced 14 key recommendations for accelerating the clinical translation of IBs, which highlight the role of parallel (rather than sequential) tracks of technical (assay) validation, biological/clinical validation and assessment of cost-effectiveness; the need for IB standardization and accreditation systems; the need to continually revisit IB precision; an alternative framework for biological/clinical validation of IBs; and the essential requirements for multicentre studies to qualify IBs for clinical use.Development of this roadmap received support from Cancer Research UK and the Engineering and Physical Sciences Research Council (grant references A/15267, A/16463, A/16464, A/16465, A/16466 and A/18097), the EORTC Cancer Research Fund, and the Innovative Medicines Initiative Joint Undertaking (grant agreement number 115151), resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and European Federation of Pharmaceutical Industries and Associations (EFPIA) companies' in kind contribution

Crop Updates 2002 - Geraldton

This session covers twenty seven papers from different authors: 1. Taking the Why out of Wyalkatchem – the new widely adapted wheat variety, Steve Penny Jr, Department of Agriculture 2. Future wheat varieties, Robin Wilson, Iain Barclay,Robyn McLean, Robert Loughman, Jenny Garlinge, Bill Lambe, Neil Venn and Peter Clarke Department of Agriculture 3. Maximising wheat variety performance through agronomic management, Wal Anderson, Raffaele Del Cima, James Bee, Darshan Sharma, Sheena Lyon, Melaine Kupsch, Mohammad Amjad, Pam Burgess, Veronika Reck, Brenda Shackley, Ray Tugwell, Bindi Webb and Steve Penny Jr Department of Agriculture 4. Cereal rust update 2002 – a new stem rust on Camm wheat, Robert Loughman1and Robert Park2 1Department of Agriculture, 2University of Sydney 5. Influence of nutrition and environmental factors on seed vigour in wheat, Darshan Sharma, Wal Anderson and Daya Patabendige, Department of Agriculture 6. Cereal aphids and direct feeding damage to cereals, Phil Michael, Department of Agriculture 7. A decision support system for control of aphids and BYDV in cereal crops, Debbie Thackray, Jenny Hawkes and Roger Jones, Department of Agriculture and Centre for Legumes in Mediterranean Agriculture 8. Summary of 2001 weather and seasonal prospects for 2002, David Stephens, Department of Agriculture 9. Towards a management package for grain protein in lupins, Bob French, Senior Research Officer, Department of Agriculture 10. Lupin genotypes respond differently to potash, Bob French and Laurie Wahlsten, Senior Research Officer and Technical Officer, Department of Agriculture 11. Time of harvest for improved seed yield of pulses, G. Riethmuller and B. French, Department of Agriculture 12. Comparing the phosphorus requirement of field pea and wheat, M. Bolland and P. White, Department of Agriculture Western Australia 13. Field pea variety evaluation, T. Khan, Department of Agriculture Western Australia 14. Diamondback moth (DBM) in canola, Kevin Walden, Department of Agriculture 15. WA blackleg resistance ratings on canola varieties for 2002, Ravjit Khangura, Martin J. Barbetti and Graham Walton, Department of Agriculture 16. The effect of single or multiple spray treatments on the control of Diamondback moth (Plutella xylostella) and yield of canola at Wongan Hills, Françoise Berlandier, Paul Carmody and Christiaan Valentine, Department of Agriculture 17. Perennial pastures in annual cropping systems: Lucerne and beyond, Roy Latta and Keith Devenish, Department of Agriculture 18. Nutrition in 2002: Decisions to be made as a result of last season, Bill Bowden,Department of Agriculture 19. Profitability of deep banding lime, Michael O\u27Connell, Chris Gazey and David Gartner, Department of Agriculture 20. Economic comparisons of farming systems for the medium rainfall northern sandplain, Caroline Peek and David Rogers, Department of Agriculture 21. The use of Twist Fungus as a biosecurity measure against Annual Ryegrass Toxicity (ARGT), Greg Shea, GrainGuard Coordinator and George Yan, Biological and Resource Technology 22. Major outcomes from IWM demonstration sites, Alexandra Douglas, Department of Agriculture 23. Understanding the weed seed bank life of important agricultural weeds, Sally Peltzer and Paul Matson, Department of Agriculture 24. Seeding rate, row spacing and herbicides for weed control, David Minkey, Department of Agriculture 25. Improving weed control in grazed pastures using legumes with low palatability, Clinton Revell and Giles Glasson, Department of Agriculture, Dean Thomas, Faculty of Agriculture, University of Western Australia 26. Group F resistant wild radish: What’s new? Aik Cheam1, Siew Lee1and Mike Clarke2, 1Department of Agriculture WA, 2Aventis Crop Science 27. Knockdown herbicides do not reliably kill small grass weeds, Peter Newman and Glenn Adam, Department of Agricultur

Imaging biomarker roadmap for cancer studies.

Imaging biomarkers (IBs) are integral to the routine management of patients with cancer. IBs used daily in oncology include clinical TNM stage, objective response and left ventricular ejection fraction. Other CT, MRI, PET and ultrasonography biomarkers are used extensively in cancer research and drug development. New IBs need to be established either as useful tools for testing research hypotheses in clinical trials and research studies, or as clinical decision-making tools for use in healthcare, by crossing 'translational gaps' through validation and qualification. Important differences exist between IBs and biospecimen-derived biomarkers and, therefore, the development of IBs requires a tailored 'roadmap'. Recognizing this need, Cancer Research UK (CRUK) and the European Organisation for Research and Treatment of Cancer (EORTC) assembled experts to review, debate and summarize the challenges of IB validation and qualification. This consensus group has produced 14 key recommendations for accelerating the clinical translation of IBs, which highlight the role of parallel (rather than sequential) tracks of technical (assay) validation, biological/clinical validation and assessment of cost-effectiveness; the need for IB standardization and accreditation systems; the need to continually revisit IB precision; an alternative framework for biological/clinical validation of IBs; and the essential requirements for multicentre studies to qualify IBs for clinical use.Development of this roadmap received support from Cancer Research UK and the Engineering and Physical Sciences Research Council (grant references A/15267, A/16463, A/16464, A/16465, A/16466 and A/18097), the EORTC Cancer Research Fund, and the Innovative Medicines Initiative Joint Undertaking (grant agreement number 115151), resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and European Federation of Pharmaceutical Industries and Associations (EFPIA) companies' in kind contribution

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements