Segmentation of cone-beam CT using a hidden Markov random field with informative priors

Cone-beam computed tomography (CBCT) has enormous potential to improve the accuracy of treatment delivery in image-guided radiotherapy (IGRT). To assist radiotherapists in interpreting these images, we use a Bayesian statistical model to label each voxel according to its tissue type. The rich sources of prior information in IGRT are incorporated into a hidden Markov random field model of the 3D image lattice. Tissue densities in the reference CT scan are estimated using inverse regression and then rescaled to approximate the corresponding CBCT intensity values. The treatment planning contours are combined with published studies of physiological variability to produce a spatial prior distribution for changes in the size, shape and position of the tumour volume and organs at risk. The voxel labels are estimated using iterated conditional modes. The accuracy of the method has been evaluated using 27 CBCT scans of an electron density phantom. The mean voxel-wise misclassification rate was 6.2\%, with Dice similarity coefficient of 0.73 for liver, muscle, breast and adipose tissue. By incorporating prior information, we are able to successfully segment CBCT images. This could be a viable approach for automated, online image analysis in radiotherapy.

Evaluation of MegaVoltage Cone Beam CT image quality with an unmodified Elekta Precise Linac and EPID : a feasibility study

In order to increase the accuracy of patient positioning for complex radiotherapy treatments various 3D imaging techniques have been developed. MegaVoltage Cone Beam CT (MVCBCT) can utilise existing hardware to implement a 3D imaging modality to aid patient positioning. MVCBCT has been investigated using an unmodified Elekta Precise linac and 15 iView amorphous silicon electronic portal imaging device (EPID). Two methods of delivery and acquisition have been investigated for imaging an anthropomorphic head phantom and quality assurance phantom. Phantom projections were successfully acquired and CT datasets reconstructed using both acquisition methods. Bone, tissue and air were 20 clearly resolvable in both phantoms even with low dose (22 MU) scans. The feasibility of MegaVoltage Cone beam CT was investigated using a standard linac, amorphous silicon EPID and a combination of a free open source reconstruction toolkit as well as custom in-house software written in Matlab. The resultant image quality has 25 been assessed and presented. Although bone, tissue and air were resolvable 2 in all scans, artifacts are present and scan doses are increased when compared with standard portal imaging. The feasibility of MVCBCT with unmodified Elekta Precise linac and EPID has been considered as well as the identification of possible areas for future development in artifact correction techniques to 30 further improve image quality.

CTCombine : rotating and combining CT data with an accurate detector model to simulate radiotherapy portal imaging at non-zero beam angles

Established Monte Carlo user codes BEAMnrc and DOSXYZnrc permit the accurate and straightforward simulation of radiotherapy experiments and treatments delivered from multiple beam angles. However, when an electronic portal imaging detector (EPID) is included in these simulations, treatment delivery from non-zero beam angles becomes problematic. This study introduces CTCombine, a purpose-built code for rotating selected CT data volumes, converting CT numbers to mass densities, combining the results with model EPIDs and writing output in a form which can easily be read and used by the dose calculation code DOSXYZnrc...

Resonance of graphene nanoribbons doped with nitrogen and boron : a molecular dynamics study

Based on its enticing properties, graphene has been envisioned with applications in the area of electronics, photonics, sensors, bioapplications and others. To facilitate various applications, doping has been frequently used to manipulate the properties of graphene. Despite a number of studies conducted on doped graphene regarding its electrical and chemical properties, the impact of doping on the mechanical properties of graphene has been rarely discussed. A systematic study of the vibrational properties of graphene doped with nitrogen and boron is performed by means of a molecular dynamics simulation. The influence from different density or species of dopants has been assessed. It is found that the impacts on the quality factor, Q, resulting from different densities of dopants vary greatly, while the influence on the resonance frequency is insignificant. The reduction of the resonance frequency caused by doping with boron only is larger than the reduction caused by doping with both boron and nitrogen. This study gives a fundamental understanding of the resonance of graphene with different dopants, which may benefit their application as resonators.

Photon beam dose distributions for patients with implanted temporary tissue expanders

This study examines the effects of temporary tissue expanders (TTEs) on the dose distributions of photon beams in breast cancer radiotherapy treatments. EBT2 radiochromic film and ion chamber measurements were taken to quantify the attenuation and backscatter effects of the inhomogeneity. Results illustrate that the internal magnetic port present in a tissue expander causes a dose reduction of approximately 25% in photon tangent fields immediately downstream of the implant. It was also shown that the silicone elastomer shell of the tissue expander reduced the dose to the target volume by as much as 8%. This work demonstrates the importance for an accurately modelled high-density implant in the treatment planning system for post-mastectomy breast cancer patients.

An external field prior for the hidden Potts model with application to cone-beam computed tomography

In images with low contrast-to-noise ratio (CNR), the information gain from the observed pixel values can be insufficient to distinguish foreground objects. A Bayesian approach to this problem is to incorporate prior information about the objects into a statistical model. A method for representing spatial prior information as an external field in a hidden Potts model is introduced. This prior distribution over the latent pixel labels is a mixture of Gaussian fields, centred on the positions of the objects at a previous point in time. It is particularly applicable in longitudinal imaging studies, where the manual segmentation of one image can be used as a prior for automatic segmentation of subsequent images. The method is demonstrated by application to cone-beam computed tomography (CT), an imaging modality that exhibits distortions in pixel values due to X-ray scatter. The external field prior results in a substantial improvement in segmentation accuracy, reducing the mean pixel misclassification rate for an electron density phantom from 87% to 6%. The method is also applied to radiotherapy patient data, demonstrating how to derive the external field prior in a clinical context.

Multi-rotor with suspended load: System dynamics and control toolbox

There is an increasing demand for Unmanned Aerial Systems (UAS) to carry suspended loads as this can provide significant benefits to several applications in agriculture, law enforcement and construction. The load impact on the underlying system dynamics should not be neglected as significant feedback forces may be induced on the vehicle during certain flight manoeuvres. The constant variation in operating point induced by the slung load also causes conventional controllers to demand increased control effort. Much research has focused on standard multi-rotor position and attitude control with and without a slung load. However, predictive control schemes, such as Nonlinear Model Predictive Control (NMPC), have not yet been fully explored. To this end, we present a novel controller for safe and precise operation of multi-rotors with heavy slung load in three dimensions. The paper describes a System Dynamics and Control Simulation Toolbox for use with MATLAB/SIMULINK which includes a detailed simulation of the multi-rotor and slung load as well as a predictive controller to manage the nonlinear dynamics whilst accounting for system constraints. It is demonstrated that the controller simultaneously tracks specified waypoints and actively damps large slung load oscillations. A linear-quadratic regulator (LQR) is derived and control performance is compared. Results show the improved performance of the predictive controller for a larger flight envelope, including aggressive manoeuvres and large slung load displacements. The computational cost remains relatively small, amenable to practical implementations.

Determining reverse salient types and evolutionary dynamics of technology systems with performance disparities

Technological system evolution is marked by the uneven evolution of constituent sub-systems. Subsequently, system evolution is hampered by the resulting state of unevenness, or reverse salience, which results from the presence of the sub-system that delivers the lowest level of performance with respect to other sub-systems, namely, the reverse salient. In this paper, we develop absolute and proportional performance gap measures of reverse salience and, in turn, derive a typology of reverse salients that distinguishes alternative dynamics of change in the evolving system. We subsequently demonstrate the applicability of the measures and the typology through an illustrative empirical study of the PC (personal computer) technological system that functions as a gaming platform. Our empirical analysis demonstrates that patterns of temporal dynamics can be distinguished with the measurement of reverse salience, and that distinct paths of technological system evolution can be identified as different types of reverse salients emerge over time.

MegaVoltage Cone Beam Computed Tomography with a standard medical linear accelerator

Accurate patient positioning is vital for improved clinical outcomes for cancer treatments using radiotherapy. This project has developed Mega Voltage Cone Beam CT using a standard medical linear accelerator to allow 3D imaging of the patient position at treatment time with no additional hardware required. Providing 3D imaging functionality at no further cost allows enhanced patient position verification on older linear accelerators and in developing countries where access to new technology is limited.

Spatiotemporal transmission dynamics of hemorrhagic fever with renal syndrome in China, 2005-2012

Background Hemorrhagic fever with renal syndrome (HFRS) is a rodent-borne disease caused by many serotypes of hantaviruses. In China, HFRS has been recognized as a severe public health problem with 90% of the total reported cases in the world. This study describes the spatiotemporal dynamics of HFRS cases in China and identifies the regions, time, and populations at highest risk, which could help the planning and implementation of key preventative measures. Methods Data on all reported HFRS cases at the county level from January 2005 to December 2012 were collected from Chinese Center for Disease Control and Prevention. Geographic Information System-based spatiotemporal analyses including Local Indicators of Spatial Association and Kulldorff's space-time scan statistic were performed to detect local high-risk space-time clusters of HFRS in China. In addition, cases from high-risk and low-risk counties were compared to identify significant demographic differences. Results A total of 100,868 cases were reported during 2005–2012 in mainland China. There were significant variations in the spatiotemporal dynamics of HFRS. HFRS cases occurred most frequently in June, November, and December. There was a significant positive spatial autocorrelation of HFRS incidence during the study periods, with Moran's I values ranging from 0.46 to 0.56 (P<0.05). Several distinct HFRS cluster areas were identified, mainly concentrated in northeastern, central, and eastern of China. Compared with cases from low-risk areas, a higher proportion of cases were younger, non-farmer, and floating residents in high-risk counties. Conclusions This study identified significant space-time clusters of HFRS in China during 2005–2012 indicating that preventative strategies for HFRS should be particularly focused on the northeastern, central, and eastern of China to achieve the most cost-effective outcomes.

Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

CXCL-8 (Interleukin 8) is a CXC chemokine with a central role in the human immune response. We have undertaken extensive in silico analyses to elucidate the interactions of CXCL-8 with its various binding partners, which are crucial for its biological function. Sequence and structure analyses showed that residues in the thirdq β-sheet and basic residues in the heparin binding site are highly variable, while residues in the second β-sheet are highly conserved. Molecular dynamics simulations in aqueous solution of dimeric CXCL-8 have been performed with starting geometries from both X-ray and NMR structures showed shearing movements between the two antiparallel C-terminal helices. Dynamic conservation analyses of these simulations agreed with experimental data indicating that structural differences between the two structures at quaternary level arise from changes in the secondary structure of the N-terminal loop, the 310-helix, the 30s, 40s, and 50s loops and the third β-sheet, resulting in a different interhelical separation. Nevertheless, the observation of these different states indicates that CXCL-8 has the potential to undergo conformational changes, and it seems likely that this feature is relevant to the mode of binding of glycosaminoglycan (GAG) mimetics such as cyclitols. Simulations of the receptor peptide fragment−CXCL-8 complex identified several specific interactions of the receptor peptide with CXCL-8 that could be exploited in the structure-based design of competitive peptides and nonpeptidic molecules targeting CXCL-8 for combating inflammatory diseases. Simulations of the CXCL-8 dimer complexed with a 24-mer heparin fragment and of the CXCL-8−receptor peptide complex revealed that Arg60, Lys64, and Arg68 in the dimer bind to cyclitols in a horseshoe pattern, defining a region which is spatially distinct from the receptor binding site. There appears to be an optimum number of sulfates and an optimum length of alkyl spacers required for the interaction of cyclitol inhibitors with the dimeric form of CXCL-8. Calculation of the binding affinities of cyclitol inhibitors reflected satisfactorily the ranking of experimentally determined inhibitory potencies. The findings of these molecular modeling studies will help in the search for inhibitors which can modulate various CXCL-8 biological activities and serve as an excellent model system to study CXC-inhibitor interactions.