Identification of evidence-based biospecimen quality-control tools

Control of biospecimen quality that is linked to processing is one of the goals of biospecimen science. Consensus is lacking, however, regarding optimal sample quality-control (QC) tools (ie, markers and assays). The aim of this review was to identify QC tools, both for fluid and solid-tissue samples, based on a comprehensive and critical literature review. The most readily applicable tools are those with a known threshold for the preanalytical variation and a known reference range for the QC analyte. Only a few meaningful markers were identified that meet these criteria, such as CD40L for assessing serum exposure at high temperatures and VEGF for assessing serum freeze-thawing. To fully assess biospecimen quality, multiple QC markers are needed. Here we present the most promising biospecimen QC tools that were identified.

Seed-based biclustering of gene expression data

Background Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns: (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. Conclusions This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

How should Australia regulate voluntary euthanasia and assisted suicide?

This paper invites consideration of how Australia should regulate voluntary euthanasia and assisted suicide. We have attempted to pose this question as neutrally as possible, acknowledging that both prohibition and legalisation of such conduct involve decisions about regulation. We begin by charting the wider field of law at the end of life, before considering the repeated, but ultimately unsuccessful, attempts at law reform in Australia. The situation in Australia is contrasted with permissive jurisdictions overseas where voluntary euthanasia and/or assisted suicide are lawful. We consider the arguments for and against legalisation of such conduct along with the available empirical evidence as to what happens in practice both in Australia and overseas. The paper concludes by outlining a framework for deliberating on how Australia should regulate voluntary euthanasia and assisted suicide. We ask a threshold question of whether such conduct should be criminal acts (as they presently are), the answer to which then leads to a range of possible regulatory options.

Validity and use of the UV index : Report from the UVI working group, Schloss Hohenkammer, Germany, 5-7 December 2011

The adequacy of the UV Index (UVI), a simple measure of ambient solar ultraviolet (UV) radiation, has been questioned on the basis of recent scientific data on the importance of vitamin D for human health, the mutagenic capacity of radiation in the UVA wavelength, and limitations in the behavioral impact of the UVI as a public awareness tool. A working group convened by ICNIRP and WHO met to assess whether modifications of the UVI were warranted and to discuss ways of improving its effectiveness as a guide to healthy sun-protective behavior. A UV Index greater than 3 was confirmed as indicating ambient UV levels at which harmful sun exposure and sunburns could occur and hence as the threshold for promoting preventive messages. There is currently insufficient evidence about the quantitative relationship of sun exposure, vitamin D, and human health to include vitamin D considerations in sun protection recommendations. The role of UVA in sunlight-induced dermal immunosuppression and DNA damage was acknowledged, but the contribution of UVA to skin carcinogenesis could not be quantified precisely. As ambient UVA and UVB levels mostly vary in parallel in real life situations, any minor modification of the UVI weighting function with respect to UVA-induced skin cancer would not be expected to have a significant impact on the UV Index. Though it has been shown that the UV Index can raise awareness of the risk of UV radiation to some extent, the UVI does not appear to change attitudes to sun protection or behavior in the way it is presently used. Changes in the UVI itself were not warranted based on these findings, but rather research testing health behavior models, including the roles of self-efficacy and self-affirmation in relation to intention to use sun protection among different susceptible groups, should be carried out to develop more successful strategies toward improving sun protection behavior. Health Phys. 103(3):301-306; 2012

Towards equity in the futures market : curriculum as a condition of access

This article provides a consideration of the problem of equity in education. In the first part of the discussion, the author draws on philosophical and sociological literatures to consider what equity means and its implications for education. Drawing on work by Burbules, Lord & Sherman, she looks to curriculum as a condition of access and the importance of learning support structures in bringing about equitable educational outcomes, conceived in terms of Amy Gutmanns’s democratic threshold. The paper offers a conceptual-theoretical model for thinking about the resourcing and curricular requirements for equity in contemporary liberal democratic societies, contrasting the social and economic policy mixes employed by governments situated at different points along a liberty/equality continuum.

Low vitamin B12 levels among newly-arrived refugees from Bhutan, Iran and Afghanistan : a multicentre Australian study

Background: Vitamin B12 deficiency is prevalent in many countries of origin of refugees. Using a threshold of 5% above which a prevalence of low Vitamin B12 is indicative of a population health problem, we hypothesised that Vitamin B12 deficiency exceeds this threshold among newly-arrived refugees resettling in Australia, and is higher among women due to their increased risk of food insecurity. This paper reports Vitamin B12 levels in a large cohort of newly arrived refugees in five Australian states and territories. Methods: In a cross-sectional descriptive study, we collected Vitamin B12, folate and haematological indices on all refugees(n = 916; response rate 94% of eligible population) who had been in Australia for less than one year, and attended one of the collaborating health services between July 2010 and July 2011. Results: 16.5% of participants had Vitamin B12 deficiency (,150 pmol/L). One-third of participants from Iran and Bhutan, and one-quarter of participants from Afghanistan had Vitamin B12 deficiency. Contrary to our hypothesis, low Vitamin B12 levels were more prevalent in males than females. A higher prevalence of low Vitamin B12 was also reported in older age groups in some countries. The sensitivity of macrocytosis in detecting Vitamin B12 deficiency was only 4.6%. Conclusion: Vitamin B12 deficiency is an important population health issue in newly-arrived refugees from many countries. All newly-arrived refugees should be tested for Vitamin B12 deficiency. Ongoing research should investigate causes,treatment, and ways to mitigate food insecurity, and the contribution of such measures to enhancing the health of the refugee communities.

The association between objectively measured neighbourhood features and walking for transport in mid-aged adults

The aim of this paper is to examine the association between a range of objectively measured neighbourhood features and the likelihood of mid-aged adults walking for transport. Increased walking for transport would bring multiple benefits, including improved population and environmental health. As part of the baseline HABITAT study, 10,745 residents of Brisbane, Australia, aged 40–65 years, from 200 neighbourhoods were asked about the time they spent walking for transport. Walking data were collected by mail survey and the physical environmental features of neighbourhoods were compiled using a geographic information systems database. Walking for transport was categorised into four levels and the association between walking and each neighbourhood characteristic was examined using multilevel multinomial models. A number of threshold trends were evident; for example, off-road bikeways were consistently associated with walking between 60 and 150 min per week. Living within 500 m of public transit was also an important predictor but only for those who walked for less than 150 min per week. Interventions targeting these neighbourhood characteristics may lead to improved environmental quality, lower rates of overweight and obesity and associated chromic disease.

A model for enhancing assessment and teaching practice at the coalface : Insights from a Fellow-In-Residence engagement program

Australian universities are currently engaging with new governmental policies and regulations that require them to demonstrate enhanced quality and accountability in teaching and research. The development of national academic standards for learning outcomes in higher education is one such instance of this drive for excellence. These discipline-specific standards articulate the minimum, or Threshold Learning Outcomes, to be addressed by higher education institutions so that graduating students can demonstrate their achievement to their institutions, accreditation agencies, and industry recruiters. This impacts not only on the design of Engineering courses (with particular emphasis on pedagogy and assessment), but also on the preparation of academics to engage with these standards and implement them in their day-to-day teaching practice on a micro level. This imperative for enhanced quality and accountability in teaching is also significant at a meso level, for according to the Australian Bureau of Statistics, about 25 per cent of teachers in Australian universities are aged 55 and above and more than 54 per cent are aged 45 and above (ABS, 2006). A number of institutions have undertaken recruitment drives to regenerate and enrich their academic workforce by appointing capacity-building research professors and increasing the numbers of early- and mid-career academics. This nationally driven agenda for quality and accountability in teaching permeates also the micro level of engineering education, since the demand for enhanced academic standards and learning outcomes requires both a strong advocacy for a shift to an authentic, collaborative, outcomes-focused education and the mechanisms to support academics in transforming their professional thinking and practice. Outcomes-focused education means giving greater attention to the ways in which the curriculum design, pedagogy, assessment approaches and teaching activities can most effectively make a positive, verifiable difference to students’ learning. Such education is authentic when it is couched firmly in the realities of learning environments, student and academic staff characteristics, and trustworthy educational research. That education will be richer and more efficient when staff works collaboratively, contributing their knowledge, experience and skills to achieve learning outcomes based on agreed objectives. We know that the school or departmental levels of universities are the most effective loci of changes in approaches to teaching and learning practices in higher education (Knight & Trowler, 2000). Heads of Schools are being increasingly entrusted with more responsibilities - in addition to setting strategic directions and managing the operational and sometimes financial aspects of their school, they are also expected to lead the development and delivery of the teaching, research and other academic activities. Guiding and mentoring individuals and groups of academics is one critical aspect of the Head of School’s role. Yet they do not always have the resources or support to help them mentor staff, especially the more junior academics. In summary, the international trend in undergraduate engineering course accreditation towards the demonstration of attainment of graduate attributes poses new challenges in addressing academic staff development needs and the assessment of learning. This paper will give some insights into the conceptual design, implementation and empirical effectiveness to date, of a Fellow-In-Residence Engagement (FIRE) program. The program is proposed as a model for achieving better engagement of academics with contemporary issues and effectively enhancing their teaching and assessment practices. It will also report on the program’s collaborative approach to working with Heads of Schools to better support academics, especially early-career ones, by utilizing formal and informal mentoring. Further, the paper will discuss possible factors that may assist the achievement of the intended outcomes of such a model, and will examine its contributions to engendering an outcomes-focussed thinking in engineering education.

ECMO : the clinician’s view

Background: Extra corporeal membrane oxygenation (ECMO) is a complex rescue therapy used to provide cardiac and/or respiratory support for critically ill patients who have failed maximal conventional medical management. ECMO is based on a modified cardiopulmonary bypass (CPB) circuit, and can provide cardiopulmonary support for up-to several months. It can be used in a veno venous configuration for isolated respiratory failure, (VV-ECMO), or in a veno arterial configuration (VA-ECMO) where support is necessary for cardiac +/- respiratory failure. The ECMO circuit consists of five main components: large bore cannulae (access cannulae) for drainage of the venous system, and return cannulae to either the venous (in VV-ECMO) or arterial (in VA ECMO) system. An oxygenator, with a vast surface area of hollow filaments, allows addition of oxygen and removal of carbon dioxide; a centrifugal blood pump allows propulsion of blood through the circuit at upto 10 L/minute; a control module and a thermoregulatory unit, which allows for exact temperature control of the extra corporeal blood. Methods: The first successful use of ECMO for ARDS in adults occurred in 1972, and its use has become more commonplace over the last 30 years, supported by the improvement in design and biocompatibility of the equipment, which has reduced the morbidity associated with this modality. Whilst the use of ECMO in neonatal population has been supported by numerous studies, the evidence upon which ECMO was integrated into adult practice was substantially less robust. Results: Recent data, including the CESAR study (Conventional Ventilatory Support versus Extra corporeal membrane oxygenation for Severe Respiratory failure) has added a degree of evidence to the role of ECMO in such a patient population. The CESAR study analysed 180 patients, and confirmed that ECMO was associated with an improved rate of survival. More recently, ECMO has been utilized in numerous situations within the critical care area, including support in high-risk percutaneous interventions in cardiac catheter lab; the operating room, emergency department, as well in specialized inter-hospital retrieval services. The increased understanding of the risk:benefit profile of ECMO, along with a reduction in morbidity associated with its use will doubtless lead to a substantial rise in the utilisation of this modality. As with all extra-corporeal circuits, ECMO opposes the basic premises of the mammalian inflammation and coagulation cascade where blood comes into foreign circulation, both these cascades are activated. Anti-coagulation is readily dealt with through use of agents such as heparin, but the inflammatory excess, whilst less macroscopically obvious, continues un-abated. Platelet consumption and neutrophil activation occur rapidly, and the clinician is faced with balancing the need of anticoagulation for the circuit, against haemostasis in an acutely bleeding patient. Alterations in pharmacokinetics may result in inadequate levels of disease modifying therapeutics, such as antibiotics, hence paradoxically delaying recovery from conditions such as pneumonia. Key elements of nutrition and the innate immune system maysimilarly be affected. Summary: This presentation will discuss the basic features of ECMO to the nonspecialist, and review the clinical conundrum faced by the team treating these most complex cases.

Temporal dynamics of rod and cone photoreceptor interactions under mesopic illumination

Purpose: Photoreceptor interactions reduce the temporal bandwidth of the visual system under mesopic illumination. The dynamics of these interactions are not clear. This study investigated cone-cone and rod-cone interactions when the rod (R) and three cone (L, M, S) photoreceptor classes contribute to vision via shared post-receptoral pathways. Methods: A four-primary photostimulator independently controlled photoreceptor activity in human observers. To determine the temporal dynamics of receptoral (L, S, R) and post-receptoral (LMS, LMSR, +L-M) pathways (5 Td, 7° eccentricity) in Experiment 1, ON-pathway sensitivity was assayed with an incremental probe (25ms) presented relative to onset of an incremental sawtooth conditioning pulse (1000ms). To define the post-receptoral pathways mediating the rod stimulus, Experiment 2 matched the color appearance of increased rod activation (30% contrast, 25-1000ms; constant cone excitation) with cone stimuli (variable L+M, L/L+M, S/L+M; constant rod excitation). Results: Cone-cone interactions with luminance stimuli (LMS, LMSR, L-cone) reduced Weber contrast sensitivity by 13% and the time course of adaptation was 23.7±1ms (μ±SE). With chromatic stimuli (+L-M, S), cone pathway sensitivity was also reduced and recovery was slower (+L-M 8%, 2.9±0.1ms; S 38%, 1.5±0.3ms). Threshold patterns at ON-conditioning pulse onset were monophasic for luminance and biphasic for chromatic stimuli. Rod-rod interactions increased sensitivity(19%) with a recovery time of 0.7±0.2ms. Compared to cone-cone interactions, rod-cone interactions with luminance stimuli reduced sensitivity to a lesser degree (5%) with faster recovery (42.9±0.7ms). Rod-cone interactions were absent with chromatic stimuli. Experiment 2 showed that rod activation generated luminance (L+M) signals at all durations, and chromatic signals (L/L+M, S/L+M) for durations >75ms. Conclusions: Temporal dynamics of cone-cone interactions are consistent with contrast sensitivity loss in the MC pathway for luminance stimuli and chromatically opponent responses in the PC and KC pathway with chromatic stimuli. Rod-cone interactions limit contrast sensitivity loss during dynamic illumination changes and increase the speed of mesopic light adaptation. The change in relative weighting of the temporal rod signal within the major post-receptoral pathways modifies the sensitivity and dynamics of photoreceptor interactions.

Fast exact nearest neighbour matching in high dimensions using d-D Sort

Data structures such as k-D trees and hierarchical k-means trees perform very well in approximate k nearest neighbour matching, but are only marginally more effective than linear search when performing exact matching in high-dimensional image descriptor data. This paper presents several improvements to linear search that allows it to outperform existing methods and recommends two approaches to exact matching. The first method reduces the number of operations by evaluating the distance measure in order of significance of the query dimensions and terminating when the partial distance exceeds the search threshold. This method does not require preprocessing and significantly outperforms existing methods. The second method improves query speed further by presorting the data using a data structure called d-D sort. The order information is used as a priority queue to reduce the time taken to find the exact match and to restrict the range of data searched. Construction of the d-D sort structure is very simple to implement, does not require any parameter tuning, and requires significantly less time than the best-performing tree structure, and data can be added to the structure relatively efficiently.

Sediment-transport (wind) experiments in zero gravity

The carousel wind tunnel (CWT) can be a significant tool for the determination of the nature and magnitude of interparticlar forces at threshold of motion. By altering particle and drum surface electrical properties and/or by applying electric potential difference across the inner and outer drums, it should be possible to separate electrostatic effects from other forces of cohesion. Besides particle trajectory and bedform analyses, suggestions for research include particle aggregation in zero and sub-gravity environments, effect of suspension-saltation ratio on soil abrasion, and the effects of shear and shear free turbulence on particle aggregation as applied to evolution of solar nebula.

ActiGraph GT3X determined variations in “free-living” standing, lying, and sitting duration among sedentary adults

Background Overweight and obesity has become a serious public health problem in many parts of the world. Studies suggest that making small changes in daily activity levels such as “breaking-up” sedentary time (i.e., standing) may help mitigate the health risks of sedentary behavior. The aim of the present study was to examine time spent in standing (determined by count threshold), lying, and sitting postures (determined by inclinometer function) via the ActiGraph GT3X among sedentary adults with differing weight status based on body mass index (BMI) categories. Methods Participants included 22 sedentary adults (14 men, 8 women; mean age 26.5 ± 4.1 years). All subjects completed the self-report International Physical Activity Questionnaire to determine time spent sitting over the previous 7 days. Participants were included if they spent seven or more hours sitting per day. Postures were determined with the ActiGraph GT3X inclinometer function. Participants were instructed to wear the accelerometer for 7 consecutive days (24 h a day). BMI was categorized as: 18.5 to <25 kg/m2 as normal, 25 to <30 kg/m2 as overweight, and ≥30 kg/m2 as obese. Results Participants in the normal weight (n = 10) and overweight (n = 6) groups spent significantly more time standing (after adjustment for moderate-to-vigorous intensity physical activity and wear-time) (6.7 h and 7.3 h respectively) and less time sitting (7.1 h and 6.9 h respectively) than those in obese (n = 6) categories (5.5 h and 8.0 h respectively) after adjustment for wear-time (p < 0.001). There were no significant differences in standing and sitting time between normal weight and overweight groups (p = 0.051 and p = 0.670 respectively). Differences were not significant among groups for lying time (p = 0.55). Conclusion This study described postural allocations standing, lying, and sitting among normal weight, overweight, and obese sedentary adults. The results provide additional evidence for the use of increasing standing time in obesity prevention strategies.

Adaptive metering algorithm for electronic commercial vehicle preclearance systems

This paper presents an adaptive metering algorithm for enhancing the electronic screening (e-screening) operation at truck weight stations. This algorithm uses a feedback control mechanism to control the level of truck vehicles entering the weight station. The basic operation of the algorithm allows more trucks to be inspected when the weight station is underutilized by adjusting the weight threshold lower. Alternatively, the algorithm restricts the number of trucks to inspect when the station is overutilized to prevent queue spillover. The proposed control concept is demonstrated and evaluated in a simulation environment. The simulation results demonstrate the considerable benefits of the proposed algorithm in improving overweight enforcement with minimal negative impacts on nonoverweighed trucks. The test results also reveal that the effectiveness of the algorithm improves with higher truck participation rates in the e-screening program.

Scoring-thresholding pattern based text classifier

A big challenge for classification on text is the noisy of text data. It makes classification quality low. Many classification process can be divided into two sequential steps scoring and threshold setting (thresholding). Therefore to deal with noisy data problem, it is important to describe positive feature effectively scoring and to set a suitable threshold. Most existing text classifiers do not concentrate on these two jobs. In this paper, we propose a novel text classifier with pattern-based scoring that describe positive feature effectively, followed by threshold setting. The thresholding is based on score of training set, make it is simple to implement in other scoring methods. Experiment shows that our pattern-based classifier is promising.