Image acquisition and manipulation protocols for CT-PET fusion to improve the accuracy of gross tumour volume localisation for 3D conformal radiotherapy for lung cancer

Aims: To develop clinical protocols for acquiring PET images, performing CT-PET registration and tumour volume definition based on the PET image data, for radiotherapy for lung cancer patients and then to test these protocols with respect to levels of accuracy and reproducibility. Method: A phantom-based quality assurance study of the processes associated with using registered CT and PET scans for tumour volume definition was conducted to: (1) investigate image acquisition and manipulation techniques for registering and contouring CT and PET images in a radiotherapy treatment planning system, and (2) determine technology-based errors in the registration and contouring processes. The outcomes of the phantom image based quality assurance study were used to determine clinical protocols. Protocols were developed for (1) acquiring patient PET image data for incorporation into the 3DCRT process, particularly for ensuring that the patient is positioned in their treatment position; (2) CT-PET image registration techniques and (3) GTV definition using the PET image data. The developed clinical protocols were tested using retrospective clinical trials to assess levels of inter-user variability which may be attributed to the use of these protocols. A Siemens Somatom Open Sensation 20 slice CT scanner and a Philips Allegro stand-alone PET scanner were used to acquire the images for this research. The Philips Pinnacle3 treatment planning system was used to perform the image registration and contouring of the CT and PET images. Results: Both the attenuation-corrected and transmission images obtained from standard whole-body PET staging clinical scanning protocols were acquired and imported into the treatment planning system for the phantom-based quality assurance study. Protocols for manipulating the PET images in the treatment planning system, particularly for quantifying uptake in volumes of interest and window levels for accurate geometric visualisation were determined. The automatic registration algorithms were found to have sub-voxel levels of accuracy, with transmission scan-based CT-PET registration more accurate than emission scan-based registration of the phantom images. Respiration induced image artifacts were not found to influence registration accuracy while inadequate pre-registration over-lap of the CT and PET images was found to result in large registration errors. A threshold value based on a percentage of the maximum uptake within a volume of interest was found to accurately contour the different features of the phantom despite the lower spatial resolution of the PET images. Appropriate selection of the threshold value is dependant on target-to-background ratios and the presence of respiratory motion. The results from the phantom-based study were used to design, implement and test clinical CT-PET fusion protocols. The patient PET image acquisition protocols enabled patients to be successfully identified and positioned in their radiotherapy treatment position during the acquisition of their whole-body PET staging scan. While automatic registration techniques were found to reduce inter-user variation compared to manual techniques, there was no significant difference in the registration outcomes for transmission or emission scan-based registration of the patient images, using the protocol. Tumour volumes contoured on registered patient CT-PET images using the tested threshold values and viewing windows determined from the phantom study, demonstrated less inter-user variation for the primary tumour volume contours than those contoured using only the patient’s planning CT scans. Conclusions: The developed clinical protocols allow a patient’s whole-body PET staging scan to be incorporated, manipulated and quantified in the treatment planning process to improve the accuracy of gross tumour volume localisation in 3D conformal radiotherapy for lung cancer. Image registration protocols which factor in potential software-based errors combined with adequate user training are recommended to increase the accuracy and reproducibility of registration outcomes. A semi-automated adaptive threshold contouring technique incorporating a PET windowing protocol, accurately defines the geometric edge of a tumour volume using PET image data from a stand alone PET scanner, including 4D target volumes.

Influences of age and mechanical stability on volume, microstructure, and mineralization of the fracture callus during bone healing : Is osteoclast activity the key to age-related impaired healing?

Earlier studies have shown that the influence of fixation stability on bone healing diminishes with advanced age. The goal of this study was to unravel the relationship between mechanical stimulus and age on callus competence at a tissue level. Using 3D in vitro micro-computed tomography derived metrics, 2D in vivo radiography, and histology, we investigated the influences of age and varying fixation stability on callus size, geometry, microstructure, composition, remodeling, and vascularity. Compared were four groups with a 1.5-mm osteotomy gap in the femora of Sprague–Dawley rats: Young rigid (YR), Young semirigid (YSR), Old rigid (OR), Old semirigid (OSR). Hypothesis was that calcified callus microstructure and composition is impaired due to the influence of advanced age, and these individuals would show a reduced response to fixation stabilities. Semirigid fixations resulted in a larger ΔCSA (Callus cross-sectional area) compared to rigid groups. In vitro μCT analysis at 6 weeks postmortem showed callus bridging scores in younger animals to be superior than their older counterparts (pb0.01). Younger animals showed (i) larger callus strut thickness (pb0.001), (ii) lower perforation in struts (pb0.01), and (iii) higher mineralization of callus struts (pb0.001). Callus mineralization was reduced in young animals with semirigid fracture fixation but remained unaffected in the aged group. While stability had an influence, age showed none on callus size and geometry of callus. With no differences observed in relative osteoid areas in the callus ROI, old as well as semirigid fixated animals showed a higher osteoclast count (pb0.05). Blood vessel density was reduced in animals with semirigid fixation (pb0.05). In conclusion, in vivo monitoring indicated delayed callus maturation in aged individuals. Callus bridging and callus competence (microstructure and mineralization) were impaired in individuals with an advanced age. This matched with increased bone resorption due to higher osteoclast numbers. Varying fixator configurations in older individuals did not alter the dominant effect of advanced age on callus tissue mineralization, unlike in their younger counterparts. Age-associated influences appeared independent from stability. This study illustrates the dominating role of osteoclastic activity in age-related impaired healing, while demonstrating the optimization of fixation parameters such as stiffness appeared to be less effective in influencing healing in aged individuals.

Pandemic (H1N1) 2009 Influenza Outbreak in Australia: Impact on Emergency Departments.

Executive summary Objective: The aims of this study were to identify the impact of Pandemic (H1N1) 2009 Influenza on Australian Emergency Departments (EDs) and their staff, and to inform planning, preparedness, and response management arrangements for future pandemics, as well as managing infectious patients presenting to EDs in everyday practice. Methods This study involved three elements: 1. The first element of the study was an examination of published material including published statistics. Standard literature research methods were used to identify relevant published articles. In addition, data about ED demand was obtained from Australian Government Department of Health and Ageing (DoHA) publications, with several state health departments providing more detailed data. 2. The second element of the study was a survey of Directors of Emergency Medicine identified with the assistance of the Australasian College for Emergency Medicine (ACEM). This survey retrieved data about demand for ED services and elicited qualitative comments on the impact of the pandemic on ED management. 3. The third element of the study was a survey of ED staff. A questionnaire was emailed to members of three professional colleges—the ACEM; the Australian College of Emergency Nursing (ACEN); and the College of Emergency Nursing Australasia (CENA). The overall response rate for the survey was 18.4%, with 618 usable responses from 3355 distributed questionnaires. Topics covered by the survey included ED conditions during the (H1N1) 2009 influenza pandemic; information received about Pandemic (H1N1) 2009 Influenza; pandemic plans; the impact of the pandemic on ED staff with respect to stress; illness prevention measures; support received from others in work role; staff and others’ illness during the pandemic; other factors causing ED staff to miss work during the pandemic; and vaccination against Pandemic (H1N1) 2009 Influenza. Both qualitative and quantitative data were collected and analysed. Results: The results obtained from Directors of Emergency Medicine quantifying the impact of the pandemic were too limited for interpretation. Data sourced from health departments and published sources demonstrated an increase in influenza-like illness (ILI) presentations of between one and a half and three times the normal level of presentations of ILIs. Directors of Emergency Medicine reported a reasonable level of preparation for the pandemic, with most reporting the use of pandemic plans that translated into relatively effective operational infection control responses. Directors reported a highly significant impact on EDs and their staff from the pandemic. Growth in demand and related ED congestion were highly significant factors causing distress within the departments. Most (64%) respondents established a ‘flu clinic’ either as part of Pandemic (H1N1) 2009 Influenza Outbreak in Australia: Impact on Emergency Departments. the ED operations or external to it. They did not note a significantly higher rate of sick leave than usual. Responses relating to the impact on staff were proportional to the size of the colleges. Most respondents felt strongly that Pandemic (H1N1) 2009 Influenza had a significant impact on demand in their ED, with most patients having low levels of clinical urgency. Most respondents felt that the pandemic had a negative impact on the care of other patients, and 94% revealed some increase in stress due to lack of space for patients, increased demand, and filling staff deficits. Levels of concern about themselves or their family members contracting the illness were less significant than expected. Nurses displayed significantly higher levels of stress overall, particularly in relation to skill-mix requirements, lack of supplies and equipment, and patient and patients’ family aggression. More than one-third of respondents became ill with an ILI. Whilst respondents themselves reported taking low levels of sick leave, respondents cited difficulties with replacing absent staff. Ranked from highest to lowest, respondents gained useful support from ED colleagues, ED administration, their hospital occupational health department, hospital administration, professional colleges, state health department, and their unions. Respondents were generally positive about the information they received overall; however, the volume of information was considered excessive and sometimes inconsistent. The media was criticised as scaremongering and sensationalist and as being the cause of many unnecessary presentations to EDs. Of concern to the investigators was that a large proportion (43%) of respondents did not know whether a pandemic plan existed for their department or hospital. A small number of staff reported being redeployed from their usual workplace for personal risk factors or operational reasons. As at the time of survey (29 October –18 December 2009), 26% of ED staff reported being vaccinated against Pandemic (H1N1) 2009 Influenza. Of those not vaccinated, half indicated they would ‘definitely’ or ‘probably’ not get vaccinated, with the main reasons being the vaccine was ‘rushed into production’, ‘not properly tested’, ‘came out too late’, or not needed due to prior infection or exposure, or due to the mildness of the disease. Conclusion: Pandemic (H1N1) 2009 Influenza had a significant impact on Australian Emergency Departments. The pandemic exposed problems in existing plans, particularly a lack of guidelines, general information overload, and confusion due to the lack of a single authoritative information source. Of concern was the high proportion of respondents who did not know if their hospital or department had a pandemic plan. Nationally, the pandemic communication strategy needs a detailed review, with more engagement with media networks to encourage responsible and consistent reporting. Also of concern was the low level of immunisation, and the low level of intention to accept vaccination. This is a problem seen in many previous studies relating to seasonal influenza and health care workers. The design of EDs needs to be addressed to better manage infectious patients. Significant workforce issues were confronted in this pandemic, including maintaining appropriate staffing levels; staff exposure to illness; access to, and appropriate use of, personal protective equipment (PPE); and the difficulties associated with working in PPE for prolonged periods. An administrative issue of note was the reporting requirement, which created considerable additional stress for staff within EDs. Peer and local support strategies helped ensure staff felt their needs were provided for, creating resilience, dependability, and stability in the ED workforce. Policies regarding the establishment of flu clinics need to be reviewed. The ability to create surge capacity within EDs by considering staffing, equipment, physical space, and stores is of primary importance for future pandemics.

A two-Dimensional finite volume method for variable density flow and solute transport through saturated-unsaturated media

Extensive groundwater withdrawal has resulted in a severe seawater intrusion problem in the Gooburrum aquifers at Bundaberg, Queensland, Australia. Better management strategies can be implemented by understanding the seawater intrusion processes in those aquifers. To study the seawater intrusion process in the region, a two-dimensional density-dependent, saturated and unsaturated flow and transport computational model is used. The model consists of a coupled system of two non-linear partial differential equations. The first equation describes the flow of a variable-density fluid, and the second equation describes the transport of dissolved salt. A two-dimensional control volume finite element model is developed for simulating the seawater intrusion into the heterogeneous aquifer system at Gooburrum. The simulation results provide a realistic mechanism by which to study the convoluted transport phenomena evolving in this complex heterogeneous coastal aquifer.

Migration of breast cancer cells : understanding the roles of volume exclusion and cell-to-cell adhesion

We study MCF-7 breast cancer cell movement in a transwell apparatus. Various experimental conditions lead to a variety of monotone and nonmonotone responses which are difficult to interpret. We anticipate that the experimental results could be caused by cell-to-cell adhesion or volume exclusion. Without any modeling, it is impossible to understand the relative roles played by these two mechanisms. A lattice-based exclusion process random-walk model incorporating agent-to-agent adhesion is applied to the experimental system. Our combined experimental and modeling approach shows that a low value of cell-to-cell adhesion strength provides the best explanation of the experimental data suggesting that volume exclusion plays a more important role than cell-to-cell adhesion. This combined experimental and modeling study gives insight into the cell-level details and design of transwell assays.

A Two-stage information filtering based on rough decision rule and pattern mining

Information Overload and Mismatch are two fundamental problems affecting the effectiveness of information filtering systems. Even though both term-based and patternbased approaches have been proposed to address the problems of overload and mismatch, neither of these approaches alone can provide a satisfactory solution to address these problems. This paper presents a novel two-stage information filtering model which combines the merits of term-based and pattern-based approaches to effectively filter sheer volume of information. In particular, the first filtering stage is supported by a novel rough analysis model which efficiently removes a large number of irrelevant documents, thereby addressing the overload problem. The second filtering stage is empowered by a semantically rich pattern taxonomy mining model which effectively fetches incoming documents according to the specific information needs of a user, thereby addressing the mismatch problem. The experimental results based on the RCV1 corpus show that the proposed twostage filtering model significantly outperforms the both termbased and pattern-based information filtering models.

New insights into Crustal Contributions to Large-volume Rhyolite Generation in the Mid-Tertiary Sierra Madre Occidental Province, Mexico, revealed by U Pb Geochronology

Voluminous (≥3·9 × 105 km3), prolonged (∼18 Myr) explosive silicic volcanism makes the mid-Tertiary Sierra Madre Occidental province of Mexico one of the largest intact silicic volcanic provinces known. Previous models have proposed an assimilation–fractional crystallization origin for the rhyolites involving closed-system fractional crystallization from crustally contaminated andesitic parental magmas, with <20% crustal contributions. The lack of isotopic variation among the lower crustal xenoliths inferred to represent the crustal contaminants and coeval Sierra Madre Occidental rhyolite and basaltic andesite to andesite volcanic rocks has constrained interpretations for larger crustal contributions. Here, we use zircon age populations as probes to assess crustal involvement in Sierra Madre Occidental silicic magmatism. Laser ablation-inductively coupled plasma-mass spectrometry analyses of zircons from rhyolitic ignimbrites from the northeastern and southwestern sectors of the province yield U–Pb ages that show significant age discrepancies of 1–4 Myr compared with previously determined K/Ar and 40Ar/39Ar ages from the same ignimbrites; the age differences are greater than the errors attributable to analytical uncertainty. Zircon xenocrysts with new overgrowths in the Late Eocene to earliest Oligocene rhyolite ignimbrites from the northeastern sector provide direct evidence for some involvement of Proterozoic crustal materials, and, potentially more importantly, the derivation of zircon from Mesozoic and Eocene age, isotopically primitive, subduction-related igneous basement. The youngest rhyolitic ignimbrites from the southwestern sector show even stronger evidence for inheritance in the age spectra, but lack old inherited zircon (i.e. Eocene or older). Instead, these Early Miocene ignimbrites are dominated by antecrystic zircons, representing >33 to ∼100% of the dated population; most antecrysts range in age between ∼20 and 32 Ma. A sub-population of the antecrystic zircons is chemically distinct in terms of their high U (>1000 ppm to 1·3 wt %) and heavy REE contents; these are not present in the Oligocene ignimbrites in the northeastern sector of the Sierra Madre Occidental. The combination of antecryst zircon U–Pb ages and chemistry suggests that much of the zircon in the youngest rhyolites was derived by remelting of partially molten to solidified igneous rocks formed during preceding phases of Sierra Madre Occidental volcanism. Strong Zr undersaturation, and estimations for very rapid dissolution rates of entrained zircons, preclude coeval mafic magmas being parental to the rhyolite magmas by a process of lower crustal assimilation followed by closed-system crystal fractionation as interpreted in previous studies of the Sierra Madre Occidental rhyolites. Mafic magmas were more probably important in providing a long-lived heat and material flux into the crust, resulting in the remelting and recycling of older crust and newly formed igneous materials related to Sierra Madre Occidental magmatism.

Automatic in-bucket volume estimation for dragline operations

This paper presents a method for calculating the in-bucket payload volume on a dragline for the purpose of estimating the material’s bulk density in real-time. Knowledge of the bulk density can provide instant feedback to mine planning and scheduling to improve blasting and in turn provide a more uniform bulk density across the excavation site. Furthermore costs and emissions in dragline operation, maintenance and downstream material processing can be reduced. The main challenge is to determine an accurate position and orientation of the bucket with the constraint of real-time performance. The proposed solution uses a range bearing and tilt sensor to locate and scan the bucket between the lift and dump stages of the dragline cycle. Various scanning strategies are investigated for their benefits in this real-time application. The bucket is segmented from the scene using cluster analysis while the pose of the bucket is calculated using the iterative closest point (ICP) algorithm. Payload points are segmented from the bucket by a fixed distance neighbour clustering method to preserve boundary points and exclude low density clusters introduced by overhead chains and the spreader bar. A height grid is then used to represent the payload from which the volume can be calculated by summing over the grid cells. We show volume calculated on a scaled system with an accuracy of greater than 95 per cent.

Generalised finite volume strategies for simulating transport in strongly orthotropic porous media

In this work two different finite volume computational strategies for solving a representative two-dimensional diffusion equation in an orthotropic medium are considered. When the diffusivity tensor is treated as linear, this problem admits an analytic solution used for analysing the accuracy of the proposed numerical methods. In the first method, the gradient approximation techniques discussed by Jayantha and Turner [Numerical Heat Transfer, Part B: Fundamentals, 40, pp.367–390, 2001] are applied directly to the

Sonic loom (Volume 1)

Sonic Loom is a purpose built classroom tool for teachers and students of drama that will enable them to explore the use of music in live performance in theory and practice. It’s intended as a resource for drama classrooms, to encourage communication and exchange about the way music works on us so we can find new ways we can make it work for us. Working to consciously attend to music and how it’s used, particularly in cinema (as a popular way in to styles of western theatre and live performance) will allow students and teachers to use music in more subtle and complex ways an aid to narrative in performance. Sonic Loom encourages active listening, (aided but not encumbered by traditional musicology) so students (and teachers) can develop a ‘critical ear’ in the transformation and adaptation of music for their own artistic purposes, whether it’s soundtracking existing scene work, or acting as a pre-text for scenes which have yet to be created.

Real-time volume estimation of a dragline payload

This paper presents a method for measuring the in-bucket payload volume on a dragline excavator for the purpose of estimating the material's bulk density in real-time. Knowledge of the payload's bulk density can provide feedback to mine planning and scheduling to improve blasting and therefore provide a more uniform bulk density across the excavation site. This allows a single optimal bucket size to be used for maximum overburden removal per dig and in turn reduce costs and emissions in dragline operation and maintenance. The proposed solution uses a range bearing laser to locate and scan full buckets between the lift and dump stages of the dragline cycle. The bucket is segmented from the scene using cluster analysis, and the pose of the bucket is calculated using the Iterative Closest Point (ICP) algorithm. Payload points are identified using a known model and subsequently converted into a height grid for volume estimation. Results from both scaled and full scale implementations show that this method can achieve an accuracy of above 95%.

Rough sets based reasoning and pattern mining for a two-stage information filtering system

This paper presents a novel two-stage information filtering model which combines the merits of term-based and pattern- based approaches to effectively filter sheer volume of information. In particular, the first filtering stage is supported by a novel rough analysis model which efficiently removes a large number of irrelevant documents, thereby addressing the overload problem. The second filtering stage is empowered by a semantically rich pattern taxonomy mining model which effectively fetches incoming documents according to the specific information needs of a user, thereby addressing the mismatch problem. The experiments have been conducted to compare the proposed two-stage filtering (T-SM) model with other possible "term-based + pattern-based" or "term-based + term-based" IF models. The results based on the RCV1 corpus show that the T-SM model significantly outperforms other types of "two-stage" IF models.

The effect of endotracheal suction on regional tidal ventilation and end-expiratory lung volume

Purpose: To examine the impact of different endotracheal tube (ETT) suction techniques on regional end-expiratory lung volume (EELV) and tidal volume (VT) in an animal model of surfactant-deficient lung injury. Methods: Six 2-week old piglets were intubated (4.0 mm ETT), muscle-relaxed and ventilated, and lung injury was induced with repeated saline lavage. In each animal, open suction (OS) and two methods of closed suction (CS) were performed in random order using both 5 and 8 French gauge (FG) catheters. The pre-suction volume state of the lung was standardised on the inflation limb of the pressure-volume relationship. Regional EELV and VT expressed as a proportion of the impedance change at vital capacity (%ZVCroi) within the anterior and posterior halves of the chest were measured during and for 60 s after suction using electrical impedance tomography. Results: During suction, 5 FG CS resulted in preservation of EELV in the anterior (nondependent) and posterior(dependent) lung compared to the other permutations, but these only reached significance in the anterior regions (p\0.001 repeated-measures ANOVA). VT within the anterior, but not posterior lung was significantly greater during 5FG CS compared to 8 FG CS; the mean difference was 15.1 [95% CI 5.1, 25.1]%ZVCroi. Neither catheter size nor suction technique influenced post-suction regional EELV or VT compared to pre-suction values (repeated-measures ANOVA). Conclusions: ETT suction causes transient loss of EELV and VT throughout the lung. Catheter size exerts a greater influence than suction method, with CS only protecting against derecruitment when a small catheter is used, especially in the non-dependent lung.