Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to capture more than 90% of sequences in the Greengenes database and with nearly twice the resolution of existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the diversity of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90%) in species-level identification thereby opening up potential application of this approach for clinical microbial characterization.Comment: 17 pages, 2 tables, 2 figures, supplementary materia

THE EFFECT OF STEP WIDTH CONTROL ON LOAD CARRIAGE ECONOMY

The purpose of this study was to assess the influence of step width on load carriage economy. Fifteen healthy volunteers (age = 25 ± 3 years; stature = 1.78 ± 0.07 m; body mass = 73.6 ± 10.1 kg) completed three trials in a randomised order. Each trial differed by load carriage method and involved walking on a force-instrumented at 3km.h-1 with 0, 3, 12 and 20 kg. This protocol was then repeated with step width controlled to each participant’s preferred unloaded width. Relative load carriage economy was measured using the Extra Load Index (ELI). Load carriage economy was significantly worse in the head loading method compared to the other two method with step width uncontrolled (p = 0.02) and controlled (p = 0.02). For the trials where step width was uncontrolled, there was a significant difference in step width from unloaded walking between the different loading methods (p = 0.01) but no significant difference between load mass (p = 0.39). There was no difference in ELI between preferred and controlled step widths. Based on the data presented here, moderate alterations in step width caused by load carriage do not appear to influence load carriage economy

Towards quantum enhanced adversarial robustness in machine learning

Machine learning algorithms are powerful tools for data driven tasks such as image classification and feature detection, however their vulnerability to adversarial examples - input samples manipulated to fool the algorithm - remains a serious challenge. The integration of machine learning with quantum computing has the potential to yield tools offering not only better accuracy and computational efficiency, but also superior robustness against adversarial attacks. Indeed, recent work has employed quantum mechanical phenomena to defend against adversarial attacks, spurring the rapid development of the field of quantum adversarial machine learning (QAML) and potentially yielding a new source of quantum advantage. Despite promising early results, there remain challenges towards building robust real-world QAML tools. In this review we discuss recent progress in QAML and identify key challenges. We also suggest future research directions which could determine the route to practicality for QAML approaches as quantum computing hardware scales up and noise levels are reduced.Comment: 10 Pages, 4 Figure

A comparison of economy and sagittal plane trunk movements among back-, back/front- and head-loading.

It has been suggested that freedom of movement in the trunk could influence load carriage economy. This study aimed to compare the economy and sagittal plane trunk movements associated with three load carriage methods that constrain posture differently. Eighteen females walked at 3 km.h-1 with loads of 0, 3, 6, 9, 12, 15 and 20 kg carried on the back, back/front and head. Load carriage economy was assessed using the Extra Load Index (ELI). Change in sagittal plane trunk forward lean and trunk angle excursion from unloaded to loaded walking were assessed. Results show no difference in economy between methods (p = 0.483), despite differences in the change in trunk forward lean (p = 0.001) and trunk angle excursion (p = 0.021) from unloaded to loaded walking. We conclude that economy is not different among the three methods of load carriage, despite significant differences in sagittal plane trunk movements

Decoupling with unitary approximate two-designs

Consider a bipartite system, of which one subsystem, A, undergoes a physical evolution separated from the other subsystem, R. One may ask under which conditions this evolution destroys all initial correlations between the subsystems A and R, i.e. decouples the subsystems. A quantitative answer to this question is provided by decoupling theorems, which have been developed recently in the area of quantum information theory. This paper builds on preceding work, which shows that decoupling is achieved if the evolution on A consists of a typical unitary, chosen with respect to the Haar measure, followed by a process that adds sufficient decoherence. Here, we prove a generalized decoupling theorem for the case where the unitary is chosen from an approximate two-design. A main implication of this result is that decoupling is physical, in the sense that it occurs already for short sequences of random two-body interactions, which can be modeled as efficient circuits. Our decoupling result is independent of the dimension of the R system, which shows that approximate 2-designs are appropriate for decoupling even if the dimension of this system is large.Comment: Published versio

The Ingredients for Innovation: impacts for practice and the education of health service managers

Background: Innovation is associated with improvement, however, there is little published about the “ingredients” for successful innovation in healthcare, and the skills required of Health Service Managers (HSMs) who facilitate change in their organisations.   Aim: This paper synthesizes the findings of a literature review performed to describe the organizational and contextual factors that enable and sustain innovation in healthcare settings.   Implications for the practice of Health Service Management and curriculum development have been extrapolated as innovation has been identified as a solution to escalating health system demands in a rapidly changing environment.Approach: A literature review used a systematic approach to source articles from the Scopus and Emerald databases over the period of 1993 to February 2016.  Papers were also retrieved from a BMC Health Services Research weekly alert.  Snowballing from relevant articles identified additional and significant papers.  Grey literature, peer-reviewed papers and reports were similarly reviewed to incorporate contemporary perspectives on this topic across the business, health and University sectors, and to facilitate discussion of the skills and competencies for HSMs practice and education in relation to this topic. Context: Innovation is crucial to the sustainability and viability of Australia’s world class health system.  There is potential for innovation to lead to more cost-effective and efficient ways to address the challenges of limited health budgets and increasingly complex morbidities in an ageing population. Main findings: Successful innovation according to the literature, is determined by a complex interaction of determinants including organizational culture, support and resourcing for innovation, leadership and a clear and shared vision.  An organizational culture supportive of innovation includes strong transdisciplinary communication, engaged and invested staff and recognition of the role of innovation in health improvement and outcomes.  A setting that is open to identifying, testing and evaluating initiatives for innovation requires capabilities to establish and maintain the working relationships, team dynamics and to prioritise resourcing to facilitate and sustain new ways of working, services, products or technologies.Recent research on the skills required for health service management employability and career success was also examined and identified the importance of skills such as communication, creativity and problem solving.  These skills are critical and linked to the role of the HSM in accelerating innovation in their organisations.Conclusions: The key ingredients for successful innovation in health were inferred from the literature.  HSMs are well positioned to support innovation as they possess the necessary technical and professional skillsets. The literature suggests that the development of graduate skills in the areas of communication, problem solving, and team work is critical to meet industry needs and for HSMs to enable innovation.Universities educating health service managers strive to ensure that graduates are professionals equipped to lead and manage health services. HSM graduates can foster the organizational and contextual factors that sustain and sanction innovative ideas to flourish and progress to implementation.  Current research advocates that strong industry and higher education collaboration is important to further develop the graduate attributes necessary for innovation.&nbsp

Predicting the public health benefit of vaccinating cattle against Escherichia coli O157

Identifying the major sources of risk in disease transmission is key to designing effective controls. However, understanding of transmission dynamics across species boundaries is typically poor, making the design and evaluation of controls particularly challenging for zoonotic pathogens. One such global pathogen is Escherichia coli O157, which causes a serious and sometimes fatal gastrointestinal illness. Cattle are the main reservoir for E. coli O157, and vaccines for cattle now exist. However, adoption of vaccines is being delayed by conflicting responsibilities of veterinary and public health agencies, economic drivers, and because clinical trials cannot easily test interventions across species boundaries, lack of information on the public health benefits. Here, we examine transmission risk across the cattle–human species boundary and show three key results. First, supershedding of the pathogen by cattle is associated with the genetic marker stx2. Second, by quantifying the link between shedding density in cattle and human risk, we show that only the relatively rare supershedding events contribute significantly to human risk. Third, we show that this finding has profound consequences for the public health benefits of the cattle vaccine. A naïve evaluation based on efficacy in cattle would suggest a 50% reduction in risk; however, because the vaccine targets the major source of human risk, we predict a reduction in human cases of nearly 85%. By accounting for nonlinearities in transmission across the human–animal interface, we show that adoption of these vaccines by the livestock industry could prevent substantial numbers of human E. coli O157 cases

Inter-individual variability in load carriage economy and comparisons between different load conditions.

Equivocal findings exist for the economy associated with load carried close to the body's centre of mass. Individual variation could explain some of the equivocal findings. This research aimed to examine the extent of individual variation in loaded walking economy. Eighteen females carried load on the back, head and split between the front and back. Individual variation in relative load carriage economy (ELI) was primarily assessed using standard deviation, coefficients of variation (CV) and intraclass correlation coefficients (ICC). There was large inter-individual variation in ELI values with highest mean CV's of 16%, 12% and 10% for head-, back- and combined front and back-loading. Mean ELI values were not significantly different between methods. The large amount of individual variation found here suggests future load carriage research should account for individual variation, particularly when considering sample size and when making inferences on the economy associated with different types of load carriage using group mean data

Ethnicity and low wage traps: favouritism, homosocial reproduction and economic marginalization

This article analyses the relationship between cultural difference, social connections and opportunity structures using interview evidence from low-paid workers and managers in local government, the health service, facilities management and housing. Exploring the operation of homosocial reproduction it reveals the double-edged nature of informality and the role of favouritism in particular in perpetuating ethnic advantage and privilege. While demonstrating that uses of homosocial reproduction need to be sensitive to intersections of identities or categories of difference, the article adds further evidence of the persistent gap between equal opportunities policies and practice for ethnic minorities in the United Kingdom labour market. The article concludes that stronger forms of positive action, and even positive discrimination, are needed to address the low pay traps and restricted opportunities of ethnic minority workers

Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions