SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Characterizing the signal pattern of a four-cylinder diesel engine using acoustic emission and vibration analysis

Condition monitoring of diesel engines can prevent unpredicted engine failures and the associated consequence. This paper presents an experimental study of the signal characteristics of a 4-cylinder diesel engine under various loading conditions. Acoustic emission, vibration and in-cylinder pressure signals were employed to study the effectiveness of these techniques for condition monitoring and identifying symptoms of incipient failures. An event driven synchronous averaging technique was employed to average the quasi-periodic diesel engine signal in the time domain to eliminate or minimize the effect of engine speed and amplitude variations on the analysis of condition monitoring signal. It was shown that acoustic emission (AE) is a better technique than vibration method for condition monitor of diesel engines due to its ability to produce high quality signals (i.e., excellent signal to noise ratio) in a noisy diesel engine environment. It was found that the peak amplitude of AE RMS signals correlating to the impact-like combustion related events decreases in general due to a more stable mechanical process of the engine as the loading increases. A small shift in the exhaust valve closing time was observed as the engine load increases which indicates a prolong combustion process in the cylinder (to produce more power). On the contrary, peak amplitudes of the AE RMS attributing to fuel injection increase as the loading increases. This can be explained by the increase fuel friction caused by the increase volume flow rate during the injection. Multiple AE pulses during the combustion process were identified in the study, which were generated by the piston rocking motion and the interaction between the piston and the cylinder wall. The piston rocking motion is caused by the non-uniform pressure distribution acting on the piston head as a result of the non-linear combustion process of the engine. The rocking motion ceased when the pressure in the cylinder chamber stabilized.

Narratives of complexity : an ethnographic exploration of resilience and wellbeing among single refugee women in Brisbane

This study aimed to explore resilience and wellbeing among a group of eight refugee women originating from several countries (mainly African) and living in Brisbane, most of whom were single mothers. To challenge mostly quantitative and gender-blind explorations of mental health concepts among refugee groups, the project sought an emic and contextual understanding of resilience and wellbeing. Established perspectives, while useful, tend to overlook the complexities of refugee mental health experiences and can neglect the dense nature of individual stories. The purpose of my study was to contest relatively simplistic narratives of mental health constructs that tend to dominate migrant and refugee studies and influence practice paradigms in the human services field. In this ethnographic exploration of mental health constructs conducted in 2008 and 2009, the use of in-depth interviews, participant observations, and visual ethnographic elements provided an opportunity for refugee women to tell their own stories. The participants’ unique narratives of pre- and post-migration experiences, shaped by specific gender, age, social, cultural and political aspects prevailing in their lives, yielded ‘thick’ ethnographic description (Geertz, 1973) of their social worlds. The findings explored in this study, namely language issues, the impact of community dynamics, and the single status of refugee women, clearly demonstrate that mental health constructs are fluid, multifaceted and complex in reality. In fact, language, community dynamics, and being a single mother, represented both opportunities and barriers in the lives of participants. In some contexts, these factors were conducive to resilience and wellbeing, while in other circumstances, these three elements acted as a hindrance to positive mental health outcomes. There are multiple dimensions to the findings, signifying that the social worlds of refugee women cannot be simplified using set definitions and neat notions of resilience and wellbeing. Instead, the intricacies and complexities embedded in the mundane of the everyday highlight novel conceptualisations of resilience and wellbeing. Based on the particular circumstances of single refugee mothers, whose experiences differ from that of married women, this thesis presents novel articulations of mental health constructs, as an alternative view to existing trends in the literature on refugee issues. Rich and multi-dimensional meanings associated with the socio-cultural determinants of mental health emerged in the process. This thesis’ findings highlight a significant gap in diasporic studies as well as simplistic assumptions about refugee women’s resettlement experiences. Single refugee women’s distinct issues are so complex and dense, that a contextual approach is critical to yield accurate depictions of their circumstances. It is therefore essential to understand refugee lived experiences within broader socio-political contexts to truly appreciate the depth of these narratives. In this manner, critical aspects salient to refugee journeys can inform different understandings of resilience, wellbeing and mental health, and shape contemporary policy and human service practice paradigms.

Experimentally induced diesel engine injector faults and some preliminary acoustic emission signal observations

Diesel engine fuel injector faults can lead to reduced power, increased fuel consumption and greater exhaust emission levels and if left unchecked, can eventually lead to premature engine failure. This paper provides an overview of the Diesel, or compression ignition combustion process, and of the two basic fuel injector nozzle designs used in Diesel engines, namely, the pintle-type and hole-type nozzles. Also described are some common faults associated with these two types of fuel injector nozzles and the techniques previously used to experimentally simulate these faults. This paper also presents a recent experimental campaign undertaken using two different diesel engines whereby various fuel injector nozzle faults were induced into the engines. The first series of tests was undertaken using a turbo-charged 5.9 litre; Cummins Diesel engine whist the second series of tests was undertaken using a naturally aspirated 4 cylinder, 2.216 litre, Perkins Diesel engine. Data corresponding to different injector fault conditions was captured using in-cylinder pressure, and acoustic emission transducers along with both crank-angle encoder and top-dead centre reference signals. Using averaged in-cylinder pressure signals, it was possible to qualify the severity of the faults whilst averaged acoustic emission signals were in turn, used as the basis for wavelets decomposition. Initial observations from this signal decomposition are also presented and discussed.

Aircraft emission reduction through multi-disciplinary flight path optimisation

There is worldwide interest in reducing aircraft emissions. The difficulty of reducing emissions including water vapour, carbon dioxide (CO2) and oxides of nitrogen (NOx) is mainly due from the fact that a commercial aircraft is usually designed for a particular optimal cruise altitude but may be requested or required to operate and deviate at different altitude and speeds to archive a desired or commanded flight plan, resulting in increased emissions. This is a multi- disciplinary problem with multiple trade-offs such as optimising engine efficiency, minimising fuel burnt, minimise emissions while maintaining aircraft separation and air safety. This project presents the coupling of an advanced optimisation technique with mathematical models and algorithms for aircraft emission reduction through flight optimisation. Numerical results show that the method is able to capture a set of useful trade-offs between aircraft range and NOx, and mission fuel consumption and NOx. In addition, alternative cruise operating conditions including Mach and altitude that produce minimum NOx and CO2 (minimum mission fuel weight) are suggested.

A study on acoustic emission signal propagation of a small size multi-cylinder diesel engine

Acoustic emission has been found effective in offering earlier fault detection and improving identification capabilities of faults. However, the sensors are inherently uncalibrated. This paper presents a source to sensor paths calibration technique which can lead to diagnosis of faults in a small size multi-cylinder diesel engine. Preliminary analysis of the acoustic emission (AE) signals is outlined, including time domain, time-frequency domain, and the root mean square (RMS) energy. The results reveal how the RMS energy of a source propagates to the adjacent sensors. The findings lead to allocate the source and estimate its inferences to the adjacent sensor, and finally help to diagnose the small size diesel engines by minimising the crosstalk from multiple cylinders.

Aerial SLAM with a single camera using visual expectation

Micro aerial vehicles (MAVs) are a rapidly growing area of research and development in robotics. For autonomous robot operations, localization has typically been calculated using GPS, external camera arrays, or onboard range or vision sensing. In cluttered indoor or outdoor environments, onboard sensing is the only viable option. In this paper we present an appearance-based approach to visual SLAM on a flying MAV using only low quality vision. Our approach consists of a visual place recognition algorithm that operates on 1000 pixel images, a lightweight visual odometry algorithm, and a visual expectation algorithm that improves the recall of place sequences and the precision with which they are recalled as the robot flies along a similar path. Using data gathered from outdoor datasets, we show that the system is able to perform visual recognition with low quality, intermittent visual sensory data. By combining the visual algorithms with the RatSLAM system, we also demonstrate how the algorithms enable successful SLAM.

Accurately simulating the production of radiotherapy portal images using non-zero beam angles

In this study, the delivery and portal imaging of one square-field and one conformal radiotherapy treatment was simulated using the Monte Carlo codes BEAMnrc and DOSXYZnrc. The treatment fields were delivered to a humanoid phantom from different angles by a 6 MV photon beam linear accelerator, with an amorphous-silicon electronic portal imaging device (a-Si EPID) used to provide images of the phantom generated by each field. The virtual phantom preparation code CTCombine was used to combine a computed-tomography-derived model of the irradiated phantom with a simple, rectilinear model of the a-Si EPID, at each beam angle used in the treatment. Comparison of the resulting experimental and simulated a-Si EPID images showed good agreement, within \[gamma](3%, 3 mm), indicating that this method may be useful in providing accurate Monte Carlo predictions of clinical a-Si EPID images, for use in the verification of complex radiotherapy treatments.

Single crystal Raman spectroscopy of selected arsenite, antimonite and hydroxyantimonate minerals

This thesis concentrates on the characterisation of selected arsenite, antimonite, and hydroxyantimonate minerals based on their vibrational spectra. A number of natural arsenite and antimonite minerals were studied by single crystal Raman spectroscopy in order to determine the contribution of bridging and terminal oxygen atoms to the vibrational spectra. A series of natural hydrated antimonate minerals was also compared and contrasted using single crystal Raman spectroscopy to determine the contribution of the isolated antimonate ion. The single crystal data allows each band in the spectrum to be assigned to a symmetry species. The contribution of bridging and terminal oxygen atoms in the case of the arsenite and antimonite minerals was determined by factor group analysis, the results of which are correlated with the observed symmetry species. In certain cases, synthetic analogues of a mineral and/or synthetic compounds isostructural or related to the mineral of interest were also prepared. These synthetic compounds are studied by non-oriented Raman spectroscopy to further aid band assignments of the minerals of interest. Other characterisation techniques include IR spectroscopy, SEM and XRD. From the single crystal data, it was found that good separation between different symmetry species is observed for the minerals studied.

Infrared transmission and emission spectroscopic study of selected Chinese palygorskites

Infrared and infrared emission spectroscopy were used to analyze the difference in structure and thermal behavior of two Chinese palygorskites. The position of the main bands identified in the infrared spectra of the palygorskites studied is similar for these two Chinese samples, but there are some differences in their intensity, which is significant. This discrepancy is attributed to various geological environments in different regions and the existence of impurities. The infrared emission spectra clearly show the structural changes and dehydroxylation of the palygorskites when the temperature is raised. The dehydration of the palygorskites is followed by the loss of intensity of the OH stretching vibration bands in the region 3600-3200 cm-1. Dehydroxylation is followed by the decrease in intensity in the bands between 3700 and 3550 cm-1. Dehydration of pure palygorskite was completed by 600 °C. Partial loss of coordinated water was observed at 400 °C. Infrared emission spectroscopy is an effective method to determine the stability of the mineral.