Assembling networks of microbial genomes using linear programming

<p>Abstract</p> <p>Background</p> <p>Microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. Assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem.</p> <p>Results</p> <p>We have developed a new approach that uses linear programming to find between-genome relationships, by treating tables of genetic affinities (here, represented by transformed BLAST e-values) as an optimization problem. Validation trials on simulated data demonstrate the effectiveness of the approach in recovering and representing vertical and lateral relationships among genomes. Application of the technique to a set comprising <it>Aquifex aeolicus </it>and 75 other thermophiles showed an important role for large genomes as 'hubs' in the gene sharing network, and suggested that genes are preferentially shared between organisms with similar optimal growth temperatures. We were also able to discover distinct and common genetic contributors to each sequenced representative of genus <it>Pseudomonas</it>.</p> <p>Conclusions</p> <p>The linear programming approach we have developed can serve as an effective inference tool in its own right, and can be an efficient first step in a more-intensive phylogenomic analysis.</p

Effect of technique and transfer board use on the performance of wheelchair transfers

Transferring to and from the wheelchair seat is a necessary skill for many wheelchair users who wish to be independent of their everyday life. The performance of wheelchair transfers has been associated with the risk of falling and developing upper limb injuries. Both present a risk to the independence of the individual. Previous studies on wheelchair transfers have focused mainly on the analysis of sitting transfers performed by individuals with spinal cord injury, which only represent a small portion of the wider wheelchair users' population. The purpose of this study is to investigate the effect of different transferring techniques (sitting, standing) and transfer board use on the ground reaction forces under the hands during transfer performance and transfer quality measured using the transfer assessment instrument (TAI). Sitting transfers displayed generally higher peak and mean reaction forces underneath both leading and trailing hands compared with the other techniques, but the difference was only significant between sitting and standing transfers. Standing transfers had significantly lower TAI scores compared with sitting transfer, potentially indicating a decreased level of safety associated with their performance. Transfer boards were only partially effective in reducing the weight born by the upper limbs and they caused only a minor reduction in the overall TAI score in comparison to sitting transfers

Expressive haptics for enhanced usability of mobile interfaces in situations of impairments

Designing for situational awareness could lead to better solutions for disabled people, likewise, exploring the needs of disabled people could lead to innovations that can address situational impairments. This in turn can create non-stigmatising assistive technology for disabled people from which eventually everyone could benefit. In this paper, we investigate the potential for advanced haptics to compliment the graphical user interface of mobile devices, thereby enhancing user experiences of all people in some situations (e.g. sunlight interfering with interaction) and visually impaired people. We explore technical solutions to this problem space and demonstrate our justification for a focus on the creation of kinaesthetic force feedback. We propose initial design concepts and studies, with a view to co-create delightful and expressive haptic interactions with potential users motivated by scenarios of situational and permanent impairments.Comment: Presented at the CHI'19 Workshop: Addressing the Challenges of Situationally-Induced Impairments and Disabilities in Mobile Interaction, 2019 (arXiv:1904.05382

PRET Printer: Development and Evaluation of a Passive Refreshable Tactile Printer

While audio-based interfaces make information accessible to people with visual impairments, some information, such as diagrams, graphs, and charts, can be better interpreted tactilely. We introduce a new Passive Refreshable Tactile (PRET) Printer concept. Using off-the-shelf components of a laser engraver and the nascent Tacilia technology, the prototype enables the creation of refreshable tactile graphics. By leveraging Pixel Art as a rendering process, we enhance the diversity of image production on this medium. We contribute technical specifications, open-source files to make the PRET printer and a qualitative evaluation of the concept by tactile learners. The prototype facilitates rapid and cost-effective development of refreshable tactile media, crucial for improving comprehension. The work builds upon existing research, furthering the groundwork to address the needs of tactile learners worldwide and establishing a foundation for further innovation and development in this domain

Assistive Technology (AT), for What?

Amartya Sen’s seminal Tanner lecture: Equality of What? began a contestation on social justice and human wellbeing that saw a new human development paradigm emerge—the capability approach (CA)—which has been influential ever since. Following interviews with leading global assistive technology (AT) stakeholders, and users, this paper takes inspiration from Sen’s core question and posits, AT for what? arguing that AT should be understood as a mechanism to achieve the things that AT users’ value. Significantly, our research found no commonly agreed operational global framework for (disability) justice within which leading AT stakeholders were operating. Instead, actors were loosely aligned through funding priorities and the CRPD. We suggest that this raises the possibility for (welcome and needed) incoming actors to diverge from efficiently designed collective action, due to perverse incentives enabled by unanchored interventions. The Global Report on Assistive Technology (GReAT) helps, greatly! However, we find there are still vital gaps in coordination; as technology advances, and AT proliferates, no longer can the device-plus-service approach suffice. Rather, those of us interested in human flourishing might explore locating AT access within an operational global framework for disability justice, which recognizes AT as a mechanism to achieve broader aims, linked to people’s capabilities to choose what they can do and be

Nose Heat: Exploring Stress-induced Nasal Thermal Variability through Mobile Thermal Imaging

Automatically monitoring and quantifying stress-induced thermal dynamic information in real-world settings is an extremely important but challenging problem. In this paper, we explore whether we can use mobile thermal imaging to measure the rich physiological cues of mental stress that can be deduced from a person's nose temperature. To answer this question we build i) a framework for monitoring nasal thermal variable patterns continuously and ii) a novel set of thermal variability metrics to capture a richness of the dynamic information. We evaluated our approach in a series of studies including laboratory-based psychosocial stress-induction tasks and real-world factory settings. We demonstrate our approach has the potential for assessing stress responses beyond controlled laboratory settings

Exploring Information Needs for Tracking to Support Using Wheelchairs in Everyday Life

Past research on wheelchair user tracking technologies has emphasized physical activity support, upper body pain alleviation, and accessibility mapping. However, little is known about what information users consider important in tracking to support their daily use of wheelchairs. To address this gap, we took a holistic view through an online survey (53 responses) and discovered the overall need to track beyond accessibility and physical activities, including a keen interest in monitoring 'wheelchair health', social causes, and concerns regarding data accountability for policy change. Our study contributes by delineating the unmet information needs in wheelchair tracking and advocating for more research interests to develop and design tracking tools in Human-Computer Interactions (HCI) that enrich the everyday experiences of wheelchair users

Mapping Assistive Technology Start-ups

Assistive technology (AT) is the application of organised knowledge and skills related to assistive products, systems and services designed to maintain or improve an individ-ual’s functioning and independence, thereby promoting their well-being [1]. We can enable life-changing differences in millions of lives worldwide using and enabling ac-cess to assistive technology. However, with all the incredible innovation, development and distribution of assistive products, there is still a significant gap between design and awareness to access and use of assistive products [2]. This was corroborated through our project to understand the met and unmet needs of AT through a country-capacity assessment [3]. As a part of this project, we carried out 5 focus group discussions with AT Users, policy stakeholders, AT developers, providers and those that work in AT distribution and support (n=31). We explored their experiences of providing and ac-cessing AT, including procurement strategies, adoption of new technologies and provi-sion pathways. Overall, we found that there is still a substantial knowledge gap in as-sistive products, how to access products and funding for needed products. These dis-cussions also enlightened us that word-of-mouth and peer networks are the main ave-nues through which knowledge of assistive products is shared. Difficulties in keeping up with the expanding innovative landscape was raised as a key concern