Quality control in public participation assessments of water quality: the OPAL Water Survey

BACKGROUND: Public participation in scientific data collection is a rapidly expanding field. In water quality surveys, the involvement of the public, usually as trained volunteers, generally includes the identification of aquatic invertebrates to a broad taxonomic level. However, quality assurance is often not addressed and remains a key concern for the acceptance of publicly-generated water quality data. The Open Air Laboratories (OPAL) Water Survey, launched in May 2010, aimed to encourage interest and participation in water science by developing a 'low-barrier-to-entry' water quality survey. During 2010, over 3000 participant-selected lakes and ponds were surveyed making this the largest public participation lake and pond survey undertaken to date in the UK. But the OPAL approach of using untrained volunteers and largely anonymous data submission exacerbates quality control concerns. A number of approaches were used in order to address data quality issues including: sensitivity analysis to determine differences due to operator, sampling effort and duration; direct comparisons of identification between participants and experienced scientists; the use of a self-assessment identification quiz; the use of multiple participant surveys to assess data variability at single sites over short periods of time; comparison of survey techniques with other measurement variables and with other metrics generally considered more accurate. These quality control approaches were then used to screen the OPAL Water Survey data to generate a more robust dataset. RESULTS: The OPAL Water Survey results provide a regional and national assessment of water quality as well as a first national picture of water clarity (as suspended solids concentrations). Less than 10 % of lakes and ponds surveyed were ‘poor’ quality while 26.8 % were in the highest water quality band. CONCLUSIONS: It is likely that there will always be a question mark over untrained volunteer generated data simply because quality assurance is uncertain, regardless of any post hoc data analyses. Quality control at all stages, from survey design, identification tests, data submission and interpretation can all increase confidence such that useful data can be generated by public participants

Consequences of fish kills for long-term trophic structure in shallow lakes: implications for theory and restoration

Fish kills are a common occurrence in shallow, eutrophic lakes, but their ecological consequences, especially in the long-term, are poorly understood. We studied the decadal-scale response of two UK shallow lakes to fish kills using a palaeolimnological approach. Eutrophic and turbid Barningham Lake experienced two fish kills in the early 1950s and late 1970s with fish recovering after both events, whereas less eutrophic, macrophyte-dominated Wolterton Lake experienced one kill event in the early 1970s from which fish failed to recover. Our palaeo-data show fish-driven trophic cascade effects across all trophic levels (covering benthic and pelagic species) in both lakes regardless of pre-kill macrophyte coverage and trophic status. In turbid Barningham Lake, similar to long-term studies of biomanipulations in other eutrophic lakes, effects at the macrophyte-level are shown to be temporary after the first kill (c.20 years) and non-existent after the second kill. In plant-dominated Wolterton Lake permanent fish disappearance failed to halt a long-term pattern of macrophyte community change (e.g. loss of charophytes and over-wintering macrophyte species) symptomatic of eutrophication. Important implications for theory and restoration ecology arise from our study. Firstly, our data support ideas of slow eutrophication-driven change in shallow lakes where perturbations are not necessary prerequisites for macrophyte loss. Secondly, the study emphasises a key need for lake managers to reduce external nutrient-loading if sustainable and long-term lake restoration is to be achieved. Our research highlights the enormous potential of multi-indicator palaeolimnology and alludes to an important need to consider potential fish kill signatures when interpreting results

Serious Games Application for Memory Training Using Egocentric Images

Mild cognitive impairment is the early stage of several neurodegenerative diseases, such as Alzheimer's. In this work, we address the use of lifelogging as a tool to obtain pictures from a patient's daily life from an egocentric point of view. We propose to use them in combination with serious games as a way to provide a non-pharmacological treatment to improve their quality of life. To do so, we introduce a novel computer vision technique that classifies rich and non rich egocentric images and uses them in serious games. We present results over a dataset composed by 10,997 images, recorded by 7 different users, achieving 79% of F1-score. Our model presents the first method used for automatic egocentric images selection applicable to serious games.Comment: 11 page

Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum

© 2014 Bachmann et al.; licensee BioMed Central Ltd. Background: Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced.Results: Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations.Conclusions: The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen

Pitfalls of using the risk ratio in meta‐analysis

For meta-analysis of studies that report outcomes as binomial proportions, the most popular measure of effect is the odds ratio (OR), usually analyzed as log(OR). Many meta-analyses use the risk ratio (RR) and its logarithm, because of its simpler interpretation. Although log(OR) and log(RR) are both unbounded, use of log(RR) must ensure that estimates are compatible with study-level event rates in the interval (0, 1). These complications pose a particular challenge for random-effects models, both in applications and in generating data for simulations. As background we review the conventional random-effects model and then binomial generalized linear mixed models (GLMMs) with the logit link function, which do not have these complications. We then focus on log-binomial models and explore implications of using them; theoretical calculations and simulation show evidence of biases. The main competitors to the binomial GLMMs use the beta-binomial (BB) distribution, either in BB regression or by maximizing a BB likelihood; a simulation produces mixed results. Two examples and an examination of Cochrane meta-analyses that used RR suggest bias in the results from the conventional inverse-variance-weighted approach. Finally, we comment on other measures of effect that have range restrictions, including risk difference, and outline further research

Power grip, pinch grip, manual muscle testing or thenar atrophy - which should be assessed as a motor outcome after carpal tunnel decompression? A systematic review

<p>Abstract</p> <p>Background</p> <p>Objective assessment of motor function is frequently used to evaluate outcome after surgical treatment of carpal tunnel syndrome (CTS). However a range of outcome measures are used and there appears to be no consensus on which measure of motor function effectively captures change. The purpose of this systematic review was to identify the methods used to assess motor function in randomized controlled trials of surgical interventions for CTS. A secondary aim was to evaluate which instruments reflect clinical change and are psychometrically robust.</p> <p>Methods</p> <p>The bibliographic databases Medline, AMED and CINAHL were searched for randomized controlled trials of surgical interventions for CTS. Data on instruments used, methods of assessment and results of tests of motor function was extracted by two independent reviewers.</p> <p>Results</p> <p>Twenty-two studies were retrieved which included performance based assessments of motor function. Nineteen studies assessed power grip dynamometry, fourteen studies used both power and pinch grip dynamometry, eight used manual muscle testing and five assessed the presence or absence of thenar atrophy. Several studies used multiple tests of motor function. Two studies included both power and pinch strength and reported descriptive statistics enabling calculation of effect sizes to compare the relative responsiveness of grip and pinch strength within study samples. The study findings suggest that tip pinch is more responsive than lateral pinch or power grip up to 12 weeks following surgery for CTS.</p> <p>Conclusion</p> <p>Although used most frequently and known to be reliable, power and key pinch dynamometry are not the most valid or responsive tools for assessing motor outcome up to 12 weeks following surgery for CTS. Tip pinch dynamometry more specifically targets the thenar musculature and appears to be more responsive. Manual muscle testing, which in theory is most specific to the thenar musculature, may be more sensitive if assessed using a hand held dynamometer – the Rotterdam Intrinsic Handheld Myometer. However further research is needed to evaluate its reliability and responsiveness and establish the most efficient and psychometrically robust method of evaluating motor function following surgery for CTS.</p

Correlation between measures of insulin resistance in fasting and non-fasting blood

<p>Abstract</p> <p>Background</p> <p>Epidemiological investigation of insulin resistance is difficult. Standard measures of insulin resistance require invasive investigations, which are impractical for large-scale studies. Surrogate measures using fasting blood samples have been developed, but even these are difficult to obtain in population-based studies. Measures of insulin resistance have not been validated in non-fasting blood samples. Our objective was to assess the correlations between fasting and non-fasting measures of insulin resistance/sensitivity.</p> <p>Methods</p> <p>Fasting and non-fasting measurements of metabolic function were compared in 30 volunteers (15 male) aged 28 to 48 years. Participants provided a morning blood sample after an overnight fast and a second sample approximately 4 hours after lunch on the same day.</p> <p>Results</p> <p>Non-fasting levels of the adipokines leptin, adiponectin, and leptin:adiponectin ratios were not significantly different and highly correlated with fasting values (r values 0.95, 0.96, and 0.95 respectively, P values < 0.001). There were moderate correlations between fasting and non-fasting estimates of insulin sensitivity using the McAuley (r = 0.60, P = 0.001) and QUICKI formulae (r = 0.39, P = 0.037). The HOMA-IR estimate of insulin resistance was also moderately correlated (r = 0.45, P = 0.016).</p> <p>Conclusions</p> <p>Semi-fasting measures of leptin, adiponectin, and leptin:adiponectin ratios correlate closely with fasting values and are likely to be sufficient for population-based research. Other measures of insulin resistance or sensitivity in semi-fasted blood samples are moderately correlated with values obtained after an overnight fast. These estimates of insulin resistance/sensitivity may also be adequate for many epidemiological studies and would avoid the difficulties of obtaining fasting blood samples.</p

Computer-aided diagnosis for (123I)FP-CIT imaging: impact on clinical reporting

BACKGROUND: For (123I)FP-CIT imaging, a number of algorithms have shown high performance in distinguishing normal patient images from those with disease, but none have yet been tested as part of reporting workflows. This study aims to evaluate the impact on reporters' performance of a computer-aided diagnosis (CADx) tool developed from established machine learning technology. Three experienced (123I)FP-CIT reporters (two radiologists and one clinical scientist) were asked to visually score 155 reconstructed clinical and research images on a 5-point diagnostic confidence scale (read 1). Once completed, the process was then repeated (read 2). Immediately after submitting each image score for a second time, the CADx system output was displayed to reporters alongside the image data. With this information available, the reporters submitted a score for the third time (read 3). Comparisons between reads 1 and 2 provided evidence of intra-operator reliability, and differences between reads 2 and 3 showed the impact of the CADx. RESULTS: The performance of all reporters demonstrated a degree of variability when analysing images through visual analysis alone. However, inclusion of CADx improved consistency between reporters, for both clinical and research data. The introduction of CADx increased the accuracy of the radiologists when reporting (unfamiliar) research images but had less impact on the clinical scientist and caused no significant change in accuracy for the clinical data. CONCLUSIONS: The outcomes for this study indicate the value of CADx as a diagnostic aid in the clinic and encourage future development for more refined incorporation into clinical practice

Living biointerfaces based on non-pathogenic bacteria to direct cell differentiation

Genetically modified Lactococcus lactis, non-pathogenic bacteria expressing the FNIII7-10 fibronectin fragment as a protein membrane have been used to create a living biointerface between synthetic materials and mammalian cells. This FNIII7-10 fragment comprises the RGD and PHSRN sequences of fibronectin to bind α5β1 integrins and triggers signalling for cell adhesion, spreading and differentiation. We used L. lactis strain to colonize material surfaces and produce stable biofilms presenting the FNIII7-10 fragment readily available to cells. Biofilm density is easily tunable and remains stable for several days. Murine C2C12 myoblasts seeded over mature biofilms undergo bipolar alignment and form differentiated myotubes, a process triggered by the FNIII7-10 fragment. This biointerface based on living bacteria can be further modified to express any desired biochemical signal, establishing a new paradigm in biomaterial surface functionalisation for biomedical applications

Perceptions of nurse practitioners by emergency department doctors in Australia

BACKGROUND: The Australian Medical Association is strongly opposed to the nurse practitioner (NP) role with concerns that NPs may become doctor substitutes without the requisite training and education that the medical role demands. Despite this, NPs have been heralded by some as a potential solution to the access block, workforce shortage and increased demand affecting emergency departments (EDs). AIMS: The purpose of this study was to determine the perception of NPs by medical staff working in Australian EDs. METHODS: Semi-structured telephone interviews were conducted with closed and open-ended questions. Participants were drawn from a representative stratified sample of two city, two metropolitan and two provincial hospitals of each State/Territory. RESULTS: A total of 95 doctors from 35 EDs participated in this study including 36 Departmental Directors; 36% of participating Directors indicated having an NP on staff. Doctors were strongly opposed to the statement that NPs could replace either nurses or other prevocational doctors; 71 interviewees commented on the role of NPs in the ED. Thematic analyses revealed polarised views held by doctors. Eight major themes were identified, the most common being that there is a lack of clarity of the NP role definition, their scope of practice and differentiation from the medical role. CONCLUSION: Although ED NPs represent a highly skilled professional group their role is poorly understood by ED doctors. Opposition to the NP role is a significant barrier to the introduction of great numbers of ED NPs as a strategy to overcome the medical workforce shortage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12245-010-0214-8) contains supplementary material, which is available to authorized users