Twisted trees and inconsistency of tree estimation when gaps are treated as missing data -- the impact of model mis-specification in distance corrections

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree -- though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data.Comment: 29 pages, 3 figure

ARATA’s response to the NDIA’s assistive technology discussion paper

The Australian Rehabilitation and Assistive Technology Association (ARATA) responds to the NDIA’s AT Discussion Paper, and advocates that roles for all stakeholders must be considered.  • Summary of ARATA\u27s key recommendations arising from the Discussion Paper: 1. Evaluate outcomes from AT provision in trial sites and other systems to inform in the development of procurement and service delivery policy, consumer supports, and continuing professional development. 2. Support practitioners and researchers to validate existing AT service models for use in Australia. 3. Assist ARATA and other key stakeholders to develop a national accreditation system for AT practitioners and suppliers. 4. Investigate and document the roles, activities, and scope of practice of suppliers and peer mentors in AT service delivery, and associated outcomes for AT users. 5. Ensure the coupling of AT devices with appropriate soft technology support for device selection, implementation and review. 6. Investigate the efficacy and potential expansion of existing peer and consumer networking channels. 7. Support research into consumer use of information and decision-making in AT provision. 8. Fund independent AT information services and explore options for facilitating consumer ratings of products and services. 9. Identify AT products not yet available on the Australian market. 10. Fund research into AT development and commercialisation in Australia.&nbsp

A Miniaturized Laser Heterodyne Radiometer for Greenhouse Gas Measurements in the Atmospheric Column

Laser Heterodyne Radiometry is a technique adapted from radio receiver technology has been used to measure trace gases in the atmosphere since the 1960s.By leveraging advances in the telecommunications industry, it has been possible to miniaturize this technology.The mini-LHR (Miniaturized Laser Heterodyne Radiometer) has been under development at NASA Goddard Space flight Center since 2009. This sun-viewing instrument measures carbon dioxide and methane in the atmospheric column and operates in tandem with an AERONET sun photometer producing a simultaneous measure of aerosols. The mini-LHR has been extensively field tested in a range of locations ranging in the continental US as well as Alaska and Hawaii and now operates autonomously with sensitivities of approximately 0.2 ppmv and approximately10 ppbv, for carbon dioxide and methane respectively, for 10 averaged scans under clear sky conditions

Miniaturized Laser Heterodyne Radiometer (LHR) for Measurements of Greenhouse Gases in the Atmospheric Column

This passive laser heterodyne radiometer (LHR) instrument simultaneously measures multiple trace gases in the atmospheric column including carbon dioxide (CO2) and methane (CH4), and resolves their concentrations at different altitudes. This instrument has been designed to operate in tandem with the passive aerosol sensor currently used in AERONET (an established network of more than 450 ground aerosol monitoring instruments worldwide). Because aerosols induce a radiative effect that influences terrestrial carbon exchange, simultaneous detection of aerosols with these key carbon cycle gases offers a uniquely comprehensive measurement approach. Laser heterodyne radiometry is a technique for detecting weak signals that was adapted from radio receiver technology. In a radio receiver, a weak input signal from a radio antenna is mixed with a stronger local oscillator signal. The mixed signal (beat note, or intermediate frequency) has a frequency equal to the difference between the input signal and the local oscillator. The intermediate frequency is amplified and sent to a detector that extracts the audio from the signal. In the LHR instrument described here, sunlight that has undergone absorption by the trace gas is mixed with laser light at a frequency matched to a trace gas absorption feature in the infrared (IR). Mixing results in a beat signal in the RF (radio frequency) region that can be related to the atmospheric concentration. For a one-second integration, the estimated column sensitivities are 0.1 ppmv for CO2, and <1 ppbv for CH4. In addition to producing a standalone ground measurement product, this instrument could be used to calibrate/validate four Earth observing missions: ASCENDS (Active Sensing of CO2 Emissions over Nights, Days, and Seasons), OCO-2 (Orbiting Carbon Observatory), OCO-3, and GOSAT (Greenhouse gases Observational SATellite). The only network that currently measures CO2 and CH4 in the atmospheric column is TCCON (Total Carbon Column Observing Network), and only two of its 16 operational sites are in the United States. TCCON data is used for validation of GOSAT data, and will be used for OCO-2 validation. While these Fourier-transform spectrometers (FTS) can measure the largest range of trace gases, the network is severely limited due to the high cost and extreme size of these instruments (these occupy small buildings and require personnel for operation). The LHR/AERONET instrument offers a significantly smaller (carry-on luggage size) autonomous instrument that can be incorporated into AERONET s much larger (450 instruments) global network

An environment built to include rather than exclude me: Creating inclusive environments for human well-being

Contemporary discourses which challenge the notion of health as the 'absence of disease' are prompting changes in health policy and practice. People with disability have been influential in progressing our understanding of the impact of contextual factors in individual and population health, highlighting the impact of environmental factors on functioning and inclusion. The World Health Organization's (WHO) more holistic definition of health as 'wellbeing' is now applied in frameworks and legislation, and has long been understood in occupational therapy theory. In practice, however, occupational therapists and other professionals often address only local and individual environmental factors to promote wellbeing, within systems and societies that limit equity in population health and restrict inclusion in communities. This paper presents an in-depth analysis of the supports and accommodations identified by a cohort of individuals (n-100) living with disability. A range of environmental facilitators and barriers were identified in peoples' experience of 'inclusive community environs' and found to influence inclusion and wellbeing. The roles and responsibilities of individuals, professionals, and society to enact change in environments are discussed in light of these findings. Recommendations include a focus on the subjective experience of environments, and application of theory from human rights and inclusive economics to address the multiple dimensions and levels of environments in working towards inclusion and wellbeing

Natural, Wearable Game Controllers

Natural, wearable game controllers explores how people interact with games and their potential uses. Since the early days of personal computing video games have been used for more than just fun. Such uses include exploration education, simulation of real world environments and the study of human thought processes (Wolf, 2008). As well as video games being used in a wide variety of settings, there has also been considerable variation in the way we interact with them - from basic mouse and keyboard interaction to the introduction of non-traditional gaming systems such the Nintendo Wii and Microsoft Kinect. These different inputs can be fall within a spectrum of abstract and natural game controllers. This thesis looks at the difference between the two and applies this to the creation of a natural wearable game controller. The aim of this thesis was to create a customised human-computer interface (HCI) input device, using a reliable piece of hardware with accompanying software a user could interact with. Through design experiments a wearable game controller was created in the form of a wrap band. Once the wrap band was developed the next step was to see how it could be used as a game controller. Design experiments were conducted, focusing on integration with a pre-existing game, using it as an exercise assessment tool and developing a specific game which could be used for rehabilitation.The area of rehabilitation gaming is broad so this thesis focuses on Weight Bearing Asymmetry (WBA). This is a condition where a person does not evenly distribute their weight between their feet. This thesis explores a range of hardware and software design experiments to see how wearable technology can be used to create a new way of interacting with video games. It looks at the benefits of using wearable technology and gaming for rehabilitation, it’s limitations and future applications of this technology. The thesis concludes that natural wearable game controllers do have potential real world application in both gaming and rehabilitation

A case study of tri-morbidity

Purpose: The purpose of this paper is to highlight the vulnerability of individuals living with tri-morbidity and the complexity of care required to serve this patient group, moreover to consider how a life course approach may assist. Design/methodology/approach: This paper uses a case study of a death of a young male adult experiencing homelessness and tri-morbidity in the UK and comparison of the mortality data for homeless adults in the UK with the general population. A synopsis of the mental health and health inclusion guidance for vulnerable adults is used. Findings: This paper found the importance of considering a life course approach and the impact of negative life events on individuals living with tri-morbidity and also the role of specialist services to support the complex needs of vulnerable adults including the importance of multi-disciplinary working and holistic care. Research limitations/implications: The research implications of this study are to consider how individuals living with tri-morbidity fit in to evidence-based care. Practical implications: The practical implication is to consider that those living with tri-morbidity have extra-ordinary lives often with a high concentration of negative life events. Therefore, an extra-ordinary approach to care maybe needed to ensure health inequalities are reduced. Social implications: This paper is an important case highlighting health inequalities, specifically mortality, in the homeless population. Originality/value: This paper is an original piece of work, with real cases discussed but anonymised according to guidance on reporting death case reports

Understanding choice in assistive technology service provision: considerations for research methodology

The adoption of choice as a policy principle in disability services reforms warrants research into the practical implications for assistive technology provision. This paper outlines methodological considerations for the investigation of how choice is constructed and experienced in assistive technology provision. It argues for an interpretive approach that considers the interactions between stakeholders and the influence of contextual factors on choices over time. Understanding stakeholders’ interpretations and contextual factors that affect their choice behaviors in AT acquisition will assist the interpretation of AT outcomes. It may also assist in efforts to increase the usability of AT services, develop improved service delivery models, and target policy initiatives to support AT provision practices

Technical behaviours of child sexual exploitation material offenders

An exploration of the technological behaviours of previously convicted child sexual exploitation material (CSEM) offenders provides a foundation for future applied research into deterrence, investigation, and treatment efforts. This study evaluates the technology choices and transitions of individuals previously convicted of CSEM offenses. Based on their inclusion in two sex offender registries, anonymous survey results (n=78) were collected from English-speaking adults within the United States. CSEM offenders chose technologies based on both utility and perceived risk; peer-to-peer and web-browsers were the most common gateway technologies and showed substantial sustained usage; a substantial minority of users never stored CSEM and only viewed it; most respondents used more than one technology to view CSEM; CSEM offenders used more countermeasures than the public but did not use encryption at higher rates; almost all CSEM consumers started viewing adult SEM first; and countermeasures were used primarily to reduce psychological strain (anxiety)