Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Lost in translation (and rotation) : rapid extrinsic calibration for 2D and 3D LIDARs

This paper describes a novel method for determining the extrinsic calibration parameters between 2D and 3D LIDAR sensors with respect to a vehicle base frame. To recover the calibration parameters we attempt to optimize the quality of a 3D point cloud produced by the vehicle as it traverses an unknown, unmodified environment. The point cloud quality metric is derived from Rényi Quadratic Entropy and quantifies the compactness of the point distribution using only a single tuning parameter. We also present a fast approximate method to reduce the computational requirements of the entropy evaluation, allowing unsupervised calibration in vast environments with millions of points. The algorithm is analyzed using real world data gathered in many locations, showing robust calibration performance and substantial speed improvements from the approximations.

Frank-starling control of a left ventricular assist device

A physiological control system was developed for a rotary left ventricular assist device (LVAD) in which the target pump flow rate (LVADQ) was set as a function of left atrial pressure (LAP), mimicking the Frank-Starling mechanism. The control strategy was implemented using linear PID control and was evaluated in a pulsatile mock circulation loop using a prototyped centrifugal pump by varying pulmonary vascular resistance to alter venous return. The control strategy automatically varied pump speed (2460 to 1740 to 2700 RPM) in response to a decrease and subsequent increase in venous return. In contrast, a fixed-speed pump caused a simulated ventricular suction event during low venous return and higher ventricular volumes during high venous return. The preload sensitivity was increased from 0.011 L/min/mmHg in fixed speed mode to 0.47L/min/mmHg, a value similar to that of the native healthy heart. The sensitivity varied automatically to maintain the LAP and LVADQ within a predefined zone. This control strategy requires the implantation of a pressure sensor in the left atrium and a flow sensor around the outflow cannula of the LVAD. However, appropriate pressure sensor technology is not yet commercially available and so an alternative measure of preload such as pulsatility of pump signals should be investigated.

Self-calibration of wireless cameras with restricted degrees of freedom

This paper presents an approach for the automatic calibration of low-cost cameras which are assumed to be restricted in their freedom of movement to either pan or tilt movements. Camera parameters, including focal length, principal point, lens distortion parameter and the angle and axis of rotation, can be recovered from a minimum set of two images of the camera, provided that the axis of rotation between the two images goes through the camera’s optical center and is parallel to either the vertical (panning) or horizontal (tilting) axis of the image. Previous methods for auto-calibration of cameras based on pure rotations fail to work in these two degenerate cases. In addition, our approach includes a modified RANdom SAmple Consensus (RANSAC) algorithm, as well as improved integration of the radial distortion coefficient in the computation of inter-image homographies. We show that these modifications are able to increase the overall efficiency, reliability and accuracy of the homography computation and calibration procedure using both synthetic and real image sequences

Assessing of circuit breaker restrike risks using computer simulation and wavelet analysis

A breaker restrike is an abnormal arcing phenomenon, leading to a possible breaker failure. Eventually, this failure leads to interruption of the transmission and distribution of the electricity supply system until the breaker is replaced. Before 2008, there was little evidence in the literature of monitoring techniques based on restrike measurement and interpretation produced during switching of capacitor banks and shunt reactor banks in power systems. In 2008 a non-intrusive radiometric restrike measurement method and a restrike hardware detection algorithm were developed by M.S. Ramli and B. Kasztenny. However, the limitations of the radiometric measurement method are a band limited frequency response as well as limitations in amplitude determination. Current restrike detection methods and algorithms require the use of wide bandwidth current transformers and high voltage dividers. A restrike switch model using Alternative Transient Program (ATP) and Wavelet Transforms which support diagnostics are proposed. Restrike phenomena become a new diagnostic process using measurements, ATP and Wavelet Transforms for online interrupter monitoring. This research project investigates the restrike switch model Parameter „A. dielectric voltage gradient related to a normal and slowed case of the contact opening velocity and the escalation voltages, which can be used as a diagnostic tool for a vacuum circuit-breaker (CB) at service voltages between 11 kV and 63 kV. During current interruption of an inductive load at current quenching or chopping, a transient voltage is developed across the contact gap. The dielectric strength of the gap should rise to a point to withstand this transient voltage. If it does not, the gap will flash over, resulting in a restrike. A straight line is fitted through the voltage points at flashover of the contact gap. This is the point at which the gap voltage has reached a value that exceeds the dielectric strength of the gap. This research shows that a change in opening contact velocity of the vacuum CB produces a corresponding change in the slope of the gap escalation voltage envelope. To investigate the diagnostic process, an ATP restrike switch model was modified with contact opening velocity computation for restrike waveform signature analyses along with experimental investigations. This also enhanced a mathematical CB model with the empirical dielectric model for SF6 (sulphur hexa-fluoride) CBs at service voltages above 63 kV and a generalised dielectric curve model for 12 kV CBs. A CB restrike can be predicted if there is a similar type of restrike waveform signatures for measured and simulated waveforms. The restrike switch model applications are used for: computer simulations as virtual experiments, including predicting breaker restrikes; estimating the interrupter remaining life of SF6 puffer CBs; checking system stresses; assessing point-on-wave (POW) operations; and for a restrike detection algorithm development using Wavelet Transforms. A simulated high frequency nozzle current magnitude was applied to an Equation (derived from the literature) which can calculate the life extension of the interrupter of a SF6 high voltage CB. The restrike waveform signatures for a medium and high voltage CB identify its possible failure mechanism such as delayed opening, degraded dielectric strength and improper contact travel. The simulated and measured restrike waveform signatures are analysed using Matlab software for automatic detection. Experimental investigation of a 12 kV vacuum CB diagnostic was carried out for the parameter determination and a passive antenna calibration was also successfully developed with applications for field implementation. The degradation features were also evaluated with a predictive interpretation technique from the experiments, and the subsequent simulation indicates that the drop in voltage related to the slow opening velocity mechanism measurement to give a degree of contact degradation. A predictive interpretation technique is a computer modeling for assessing switching device performance, which allows one to vary a single parameter at a time; this is often difficult to do experimentally because of the variable contact opening velocity. The significance of this thesis outcome is that it is a non-intrusive method developed using measurements, ATP and Wavelet Transforms to predict and interpret a breaker restrike risk. The measurements on high voltage circuit-breakers can identify degradation that can interrupt the distribution and transmission of an electricity supply system. It is hoped that the techniques for the monitoring of restrike phenomena developed by this research will form part of a diagnostic process that will be valuable for detecting breaker stresses relating to the interrupter lifetime. Suggestions for future research, including a field implementation proposal to validate the restrike switch model for ATP system studies and the hot dielectric strength curve model for SF6 CBs, are given in Appendix A.

Videogame control device impact on the play experience

New types of control devices for videogames have emerged and expanded the demographics of the game playing public, yet little is known about which populations of gamers prefer which style of interaction and why. This paper presents data from a study that seeks to clarify the influence the control interface has on the play experience. Three commercial control devices were categorised using an existing typology, according to how the interface maps physical control inputs with the virtual gameplay actions. The devices were then used in a within-groups experimental design aimed at measuring differences in play experience across 64 participants. Descriptive analysis is undertaken on the performance, play experience and preference results for each device. Potential explanations for these results are discussed, as well as the direction of future work.

An assessment tool for selection of appropriate daylighting solutions for buildings in tropical and subtropical regions : Validation using radiance simulation

A new decision-making tool that will assist designers in the selection of appropriate daylighting solutions for buildings in tropical locations has been previously proposed by the authors. Through an evaluation matrix that prioritizes the parameters that best respond to the needs of tropical climates (e.g. reducing solar gain and protection from glare) the tool determines the most appropriate devices for specific climate and building inputs. The tool is effective in demonstrating the broad benefits and limitations of the different daylight strategies for buildings in the tropics. However for thorough analysis and calibration of the tool, validation is necessary. This paper presents a first step in the validation process. RADIANCE simulations were conducted to compare simulation performance with the performance predicted by the tool. To this end, an office building case study in subtropical Brisbane, Australia, and five different daylighting devices including openings, light guiding systems and light transport systems were simulated. Illuminance, light uniformity, daylight penetration and glare analysis were assessed for each device. The results indicate the tool can appropriately rank and recommend daylighting strategies based on specific building inputs for tropical and subtropical regions, making it a useful resource for designers.

Efficacy of oral or intrauterine device-delivered progestin in patients with complex endometrial hyperplasia with atypia or early endometrial adenocarcinoma : a meta-analysis and systematic review of the literature

Objectives: To investigate the efficacy of progestin treatment to achieve pathological complete response (pCR) in patients with complex atypical endometrial hyperplasia (CAH) or early endometrial adenocarcinoma (EC). Methods: A systematic search identified 3245 potentially relevant citations. Studies containing less than ten eligible CAH or EC patients in either oral or intrauterine treatment arm were excluded. Only information from patients receiving six or more months of treatment and not receiving other treatments was included. Weighted proportions of patients achieving pCR were calculated using R software. Results: Twelve studies met the selection criteria. Eleven studies reported treatment of patients with oral (219 patients, 117 with CAH, 102 with grade 1 Stage I EC) and one reported treatment of patients with intrauterine progestin (11 patients with grade 1 Stage IEC). Overall, 74% (95% confidence interval [CI] 65-81%) of patients with CAH and 72% (95% CI 62-80%) of patients with grade 1 Stage I EC achieved a pCR to oral progestin. Disease progression while on oral treatment was reported for 6/219 (2.7%), and relapse after initial complete response for 32/159 (20.1%) patients. The weighted mean pCR rate of patients with grade 1 Stage I EC treated with intrauterine progestin from one prospective pilot study and an unpublished retrospective case series from the Queensland Centre of Gynaecologic Oncology (QCGC) was 68% (95% CI 45- 86%). Conclusions: There is a lack of high quality evidence for the efficacy of progestin in CAH or EC. The available evidence however suggests that treatment with oral or intrauterine progestin is similarly effective. The risk of progression during treatment is small but longer follow-up is required. Evidence from prospective controlled clinical trials is warranted to establish how the efficacy of progestin for the treatment of CAH and EC can be improved further.

An investigation into factors affecting electron density calibration for a megavoltage cone-beam CT system

There is a growing interest in the use of megavoltage cone-beam computed tomography (MV CBCT) data for radiotherapy treatment planning. To calculate accurate dose distributions, knowledge of the electron density (ED) of the tissues being irradiated is required. In the case of MV CBCT, it is necessary to determine a calibration-relating CT number to ED, utilizing the photon beam produced for MV CBCT. A number of different parameters can affect this calibration. This study was undertaken on the Siemens MV CBCT system, MVision, to evaluate the effect of the following parameters on the reconstructed CT pixel value to ED calibration: the number of monitor units (MUs) used (5, 8, 15 and 60 MUs), the image reconstruction filter (head and neck, and pelvis), reconstruction matrix size (256 by 256 and 512 by 512), and the addition of extra solid water surrounding the ED phantom. A Gammex electron density CT phantom containing EDs from 0.292 to 1.707 was imaged under each of these conditions. The linear relationship between MV CBCT pixel value and ED was demonstrated for all MU settings and over the range of EDs. Changes in MU number did not dramatically alter the MV CBCT ED calibration. The use of different reconstruction filters was found to affect the MV CBCT ED calibration, as was the addition of solid water surrounding the phantom. Dose distributions from treatment plans calculated with simulated image data from a 15 MU head and neck reconstruction filter MV CBCT image and a MV CBCT ED calibration curve from the image data parameters and a 15 MU pelvis reconstruction filter showed small and clinically insignificant differences. Thus, the use of a single MV CBCT ED calibration curve is unlikely to result in any clinical differences. However, to ensure minimal uncertainties in dose reporting, MV CBCT ED calibration measurements could be carried out using parameter-specific calibration measurements.

Intravascular device-related research : future priority areas for cancer nursing

The majority of cancer nurses have to manage intravascular devices (IVDs) on a daily basis, thus placing nurses in the strongest position to generate and use best available evidence to inform this area of practice and to ensure that patients are receiving the best care available. Our literature clearly reflects that cancer nurses are concerned about complications associated with IVDs (eg, extravasation,1 IVD-related bloodstream infection [IVD-BSI],2,3 and thrombosis4). Although enormous attention is given to this area, a number of nursing practices are not sufficiently based on empirical evidence.5,6 Nurses need to set goals and priorities for future research and investments. Priority areas for future research are suggested here for your consideration.

Applicability of the polysulphone horizontal calibration to differently inclined dosimeters

Polysulphone (PS) dosimetry has been a widely used technique for more than 30 years to quantify the erythemally effective UV dose received by anatomic sites (personal exposure). The calibration of PS dosimeters is an important issue as their spectral response is different from the erythemal action spectrum. It is performed exposing a set of PS dosimeters on a horizontal plane and measuring the UV doses received by dosimeters using calibrated spectroradiometers or radiometers. In this study, data collected during PS field campaigns (from 2004 to 2006), using horizontal and differently inclined dosimeters, were analyzed to provide some considerations on the transfer of the horizontal calibration to differently inclined dosimeters, as anatomic sites usually are. The role of sky conditions, of the angle of incidence between the sun and the normal to the slope, and of the type of surrounding surface on the calibration were investigated. It was concluded that PS horizontal calibrations apply to differently inclined dosimeters for incidence angles up to approximately 70 degrees and for surfaces excluding ones with high albedo. Caution should be used in the application of horizontal calibrations for cases of high-incidence angle and/or high albedo surfaces.

Context-aware device self-configuration using self-organizing maps

Modern mobile computing devices are versatile, but bring the burden of constant settings adjustment according to the current conditions of the environment. While until today, this task has to be accomplished by the human user, the variety of sensors usually deployed in such a handset provides enough data for autonomous self-configuration by a learning, adaptive system. However, this data is not fully available at certain points in time, or can contain false values. Handling potentially incomplete sensor data to detect context changes without a semantic layer represents a scientific challenge which we address with our approach. A novel machine learning technique is presented - the Missing-Values-SOM - which solves this problem by predicting setting adjustments based on context information. Our method is centered around a self-organizing map, extending it to provide a means of handling missing values. We demonstrate the performance of our approach on mobile context snapshots, as well as on classical machine learning datasets.

A prospective window into medical device-related pressure ulcers in intensive care

Objective: To determine the prevalence, severity, location, etiology, treatment, and healing of medical device-related pressure ulcers in intensive care patients for up to 7 days. Design: Prospective repeated measures study. Setting and participants: Patients in 6 intensive care units of 2 major medical centers, one each in Australia and the United States, were screened 1 day per month for 6 months. Those with device-related ulcers were followed daily up to 7 days. Outcome measures: Device-related ulcer prevalence, pain, infection, treatment, healing. Results: 15/483 patients had device-related ulcers and 9/15 with 11 ulcers were followed beyond screening. Their mean age was 60.5 years, most were men, over-weight, and at increased pressure ulcer risk. Endotracheal and nasogastric tubes were the cause of most device-related ulcers. Repositioning was the most frequent treatment. 4/11 ulcers healed within the 7 day observation period. Conclusion: Device-related ulcer prevalence was 3.1%, similar to that reported in the limited literature available, indicating an ongoing problem. Systematic assessment and repositioning of devices are the mainstays of care. We recommend continued prevalence determination and that nurses remain vigilant to prevent device-related ulcers, especially in patients with nasogastric and endotracheal tubes.