Testate amoebae as a hydrological proxy for reconstructing water-table depth in the mires of south-eastern Australia

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordAlthough it is well established that moisture availability in south-eastern Australia has been decreasing through time recently, the driver(s) of this trend are contentious, and our understanding of any drivers is limited by a relatively short historic record. Testate amoebae have been widely used to reconstruct peatland hydrology in the Northern Hemisphere, but in the Southern Hemisphere research is still needed to assess their proficiency as a palaeohydrological proxy and to develop robust transfer functions. Here we examine the ecology of testate amoebae in several high altitude mires in south-eastern Australia and present the first transfer function for the continent. Euglypha tuberculata type, Centropyxis platystoma type and Assulina muscorum were the most common taxa in our modern samples. Water-table depth was the primary environmental variable determining testate amoebae assemblages and therefore transfer functions were developed for this ecological factor. We found that the performance of various all-species and species-pruned transfer functions were statistically robust, with R2 values of around 0.8 and Root Mean Squared Error of Prediction (RMSEP) values of about 7 cm. All cross-validation methods (leave-one-out RMSEP, cluster-bootstrap RMSEP, segment-wise RMSEP and leave-one-site-out RMSEP from all-species and species-pruned transfer functions) suggested that the Modern Analogue Technique (MAT) was the best performing transfer function, with negligible bias evident from un-even sampling and spatial autocorrelation. We also used a new approach to evaluate the importance of taxa and the performance of our transfer functions using species-pruned methods. Our results suggest that the all-species MAT, with an RMSEP of 5.73 and R2 of 0.86, provides the best reconstruction of water-table depth across our sites in south-eastern Australia.Australian National Universit

Forecasting GOES 15 >2 MeV Electron Fluxes From Solar Wind Data and Geomagnetic Indices

The flux of > 2 MeV electrons at geosynchronous orbit is used by space weather forecasters as a key indicator of enhanced risk of damage to spacecraft in low, medium or geosynchronous Earth orbits. We present a methodology that uses the amount of time a single input dataset (solar wind data or geomagnetic indices) exceeds a given threshold to produce deterministic and probabilistic forecasts of the > 2 MeV flux at GEO exceeding 1000 or 10000 cm ‐2 s ‐1 sr ‐1 within up to 10 days. By comparing our forecasts with measured fluxes from GOES 15 between 2014 and 2016, we determine the optimum forecast thresholds for deterministic and probabilistic forecasts by maximising the ROC and Brier Skill Scores respectively. The training dataset gives peak ROC scores of 0.71 to 0.87 and peak Brier Skill Scores of ‐0.03 to 0.32. Forecasts from AL give the highest skill scores for forecasts of up to 6‐days. AL, solar wind pressure or SYM‐H give the highest skill scores over 7‐10 days. Hit rates range over 56‐89% with false alarm rates of 11‐53%. Applied to 2012, 2013 and 2017, our best forecasts have hit rates of 56‐83% and false alarm rates of 10‐20%. Further tuning of the forecasts may improve these. Our hit rates are comparable to those from operational fluence forecasts, that incorporate fluence measurements, but our false alarm rates are higher. This proof‐of‐concept shows that the geosynchronous electron flux can be forecast with a degree of success without incorporating a persistence element into the forecasts

Reconstructing grassland fire history using sedimentary charcoal: Considering count, size and shape

Citation: Leys, B. A., Commerford, J. L., & McLauchlan, K. K. (2017). Reconstructing grassland fire history using sedimentary charcoal: Considering count, size and shape. Plos One, 12(4), 15. doi:10.1371/journal.pone.0176445Fire is a key Earth system process, with 80% of annual fire activity taking place in grassland areas. However, past fire regimes in grassland systems have been difficult to quantify due to challenges in interpreting the charcoal signal in depositional environments. To improve reconstructions of grassland fire regimes, it is essential to assess two key traits: (1) charcoal count, and (2) charcoal shape. In this study, we quantified the number of charcoal pieces in 51 sediment samples of ponds in the Great Plains and tested its relevance as a proxy for the fire regime by examining 13 potential factors influencing charcoal count, including various fire regime components (e.g. the fire frequency, the area burned, and the fire season), vegetation cover and pollen assemblages, and climate variables. We also quantified the width to length (W: L) ratio of charcoal particles, to assess its utility as a proxy of fuel types in grassland environments by direct comparison with vegetation cover and pollen assemblages. Our first conclusion is that charcoal particles produced by grassland fires are smaller than those produced by forest fires. Thus, a mesh size of 120 mu m as used in forested environments is too large for grassland ecosystems. We recommend counting all charcoal particles over 60 mu m in grasslands and mixed grass-forest environments to increase the number of samples with useful data. Second, a W: L ratio of 0.5 or smaller appears to be an indicator for fuel types, when vegetation surrounding the site is before composed of at least 40% grassland vegetation. Third, the area burned within 1060m of the depositional environments explained both the count and the area of charcoal particles. Therefore, changes in charcoal count or charcoal area through time indicate a change in area burned. The fire regimes of grassland systems, including both human and climatic influences on fire behavior, can be characterized by long-term charcoal records

Challenges in Australian policy processes for disinvestment from existing, ineffective health care practices

Background Internationally, many health care interventions were diffused prior to the standard use of assessments of safety, effectiveness and cost-effectiveness. Disinvestment from ineffective or inappropriately applied practices is a growing priority for health care systems for reasons of improved quality of care and sustainability of resource allocation. In this paper we examine key challenges for disinvestment from these interventions and explore potential policy-related avenues to advance a disinvestment agenda. Results We examine five key challenges in the area of policy driven disinvestment: 1) lack of resources to support disinvestment policy mechanisms; 2) lack of reliable administrative mechanisms to identify and prioritise technologies and/or practices with uncertain clinical and cost-effectiveness; 3) political, clinical and social challenges to removing an established technology or practice; 4) lack of published studies with evidence demonstrating that existing technologies/practices provide little or no benefit (highlighting complexity of design) and; 5) inadequate resources to support a research agenda to advance disinvestment methods. Partnerships are required to involve government, professional colleges and relevant stakeholder groups to put disinvestment on the agenda. Such partnerships could foster awareness raising, collaboration and improved health outcome data generation and reporting. Dedicated funds and distinct processes could be established within the Medical Services Advisory Committee and Pharmaceutical Benefits Advisory Committee to, a) identify technologies and practices for which there is relative uncertainty that could be the basis for disinvestment analysis, and b) conduct disinvestment assessments of selected item(s) to address existing practices in an analogous manner to the current focus on new and emerging technology. Finally, dedicated funding and cross-disciplinary collaboration is necessary to build health services and policy research capacity, with a focus on advancing disinvestment research methodologies and decision support tools. Conclusion The potential over-utilisation of less than effective clinical practices and the potential under-utilisation of effective clinical practices not only result in less than optimal care but also fragmented, inefficient and unsustainable resource allocation. Systematic policy approaches to disinvestment will improve equity, efficiency, quality and safety of care, as well as sustainability of resource allocation.Adam G Elshaug, Janet E Hiller, Sean R Tunis and John R Mos

Developmental morphology of cover crop species exhibit contrasting behaviour to changes in soil bulk density, revealed by X-ray computed tomography

Plant roots growing through soil typically encounter considerable structural heterogeneity, and local variations in soil dry bulk density. The way the in situ architecture of root systems of different species respond to such heterogeneity is poorly understood due to challenges in visualising roots growing in soil. The objective of this study was to visualise and quantify the impact of abrupt changes in soil bulk density on the roots of three cover crop species with contrasting inherent root morphologies, viz. tillage radish (Raphanus sativus), vetch (Vicia sativa) and black oat (Avena strigosa). The species were grown in soil columns containing a two-layer compaction treatment featuring a 1.2 g cm-3 (uncompacted) zone overlaying a 1.4 g cm-3 (compacted) zone. Three-dimensional visualisations of the root architecture were generated via X-ray computed tomography, and an automated root-segmentation imaging algorithm. Three classes of behaviour were manifest as a result of roots encountering the compacted interface, directly related to the species. For radish, there was switch from a single tap-root to multiple perpendicular roots which penetrated the compacted zone, whilst for vetch primary roots were diverted more horizontally with limited lateral growth at less acute angles. Black oat roots penetrated the compacted zone with no apparent deviation. Smaller root volume, surface area and lateral growth were consistently observed in the compacted zone in comparison to the uncompacted zone across all species. The rapid transition in soil bulk density had a large effect on root morphology that differed greatly between species, with major implications for how these cover crops will modify and interact with soil structure

Assessment of predicted enzymatic activity of α‐N‐acetylglucosaminidase variants of unknown significance for CAGI 2016

The NAGLU challenge of the fourth edition of the Critical Assessment of Genome Interpretation experiment (CAGI4) in 2016, invited participants to predict the impact of variants of unknown significance (VUS) on the enzymatic activity of the lysosomal hydrolase α‐N‐acetylglucosaminidase (NAGLU). Deficiencies in NAGLU activity lead to a rare, monogenic, recessive lysosomal storage disorder, Sanfilippo syndrome type B (MPS type IIIB). This challenge attracted 17 submissions from 10 groups. We observed that top models were able to predict the impact of missense mutations on enzymatic activity with Pearson's correlation coefficients of up to .61. We also observed that top methods were significantly more correlated with each other than they were with observed enzymatic activity values, which we believe speaks to the importance of sequence conservation across the different methods. Improved functional predictions on the VUS will help population‐scale analysis of disease epidemiology and rare variant association analysis

Disability quotas: past or future policy?

This article considers the issues associated with the use of quota systems for the employment of workers with a disability. It examines the use and experiences of such quotas in Italy, Russia and the United Kingdom. Italy has a long established quota for the employment of such workers, whilst the modern Russian system it is a more recent innovation. In contrast the UK abandoned its quotas in the 1990s. We draw on the experiences of the three countries to consider generally whether the use of quotas is either an acceptable means of encouraging employers to take on disabled workers, or is necessary to achieve this objective

Exhaustive prediction of disease susceptibility to coding base changes in the human genome

<p>Abstract</p> <p>Background</p> <p>Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selection pressure, reflected in their inter-species conservation.</p> <p>Results</p> <p>We propose a method that is not dependant on transcription information to score each coding base in the human genome reflecting the disease probability associated with its mutation. Twelve factors likely to be associated with disease alleles were chosen as the input for a support vector machine prediction algorithm. The analysis yielded 83% sensitivity and 84% specificity in segregating disease like alleles as found in the Human Gene Mutation Database from non-disease like alleles as found in the Database of Single Nucleotide Polymorphisms. This algorithm was subsequently applied to each base within all known human genes, exhaustively confirming that interspecies conservation is the strongest factor for disease association. For each gene, the length normalized average disease potential score was calculated. Out of the 30 genes with the highest scores, 21 are directly associated with a disease. In contrast, out of the 30 genes with the lowest scores, only one is associated with a disease as found in published literature. The results strongly suggest that the highest scoring genes are enriched for those that might contribute to disease, if mutated.</p> <p>Conclusion</p> <p>This method provides valuable information to researchers to identify sensitive positions in genes that have a high disease probability, enabling them to optimize experimental designs and interpret data emerging from genetic and epidemiological studies.</p

Does lumbar spinal degeneration begin with the anterior structures? A study of the observed epidemiology in a community-based population

<p>Abstract</p> <p>Background-</p> <p>Prior studies that have concluded that disk degeneration uniformly precedes facet degeneration have been based on convenience samples of individuals with low back pain. We conducted a study to examine whether the view that spinal degeneration begins with the anterior spinal structures is supported by epidemiologic observations of degeneration in a community-based population.</p> <p>Methods-</p> <p>361 participants from the Framingham Heart Study were included in this study. The prevalences of anterior vertebral structure degeneration (disk height loss) and posterior vertebral structure degeneration (facet joint osteoarthritis) were characterized by CT imaging. The cohort was divided into the structural subgroups of participants with 1) no degeneration, 2) isolated anterior degeneration (without posterior degeneration), 3) combined anterior and posterior degeneration, and 4) isolated posterior degeneration (without anterior structure degeneration). We determined the prevalence of each degeneration pattern by age group < 45, 45-54, 55-64, ≥65. In multivariate analyses we examined the association between disk height loss and the response variable of facet joint osteoarthritis, while adjusting for age, sex, BMI, and smoking.</p> <p>Results-</p> <p>As the prevalence of the no degeneration and isolated anterior degeneration patterns decreased with increasing age group, the prevalence of the combined anterior/posterior degeneration pattern increased. 22% of individuals demonstrated isolated posterior degeneration, without an increase in prevalence by age group. Isolated posterior degeneration was most common at the L5-S1 and L4-L5 spinal levels. In multivariate analyses, disk height loss was independently associated with facet joint osteoarthritis, as were increased age (years), female sex, and increased BMI (kg/m²), but not smoking.</p> <p>Conclusions-</p> <p>The observed epidemiology of lumbar spinal degeneration in the community-based population is consistent with an ordered progression beginning in the anterior structures, for the majority of individuals. However, some individuals demonstrate atypical patterns of degeneration, beginning in the posterior joints. Increased age and BMI, and female sex may be related to the occurrence of isolated posterior degeneration in these individuals.</p

Carbon related defects in irradiated silicon revisited

Electronic structure calculations employing hybrid functionals are used to gain insight into the interaction of carbon (C) atoms, oxygen (O) interstitials, and self-interstitials in silicon (Si). We calculate the formation energies of the C related defects C(i)(Si(I)), C(i)O(i), C(i)C(s), and C(i)O(i)(Si(I)) with respect to the Fermi energy for all possible charge states. The C(i)(Si(I))(2+) state dominates in almost the whole Fermi energy range. The unpaired electron in the C(i)O(i)(+) state is mainly localized on the C interstitial so that spin polarization is able to lower the total energy. The three known atomic configurations of the C(i)C(s) pair are reproduced and it is demonstrated that hybrid functionals yield an improved energetic order for both the A and B-types as compared to previous theoretical studies. Different structures of the C(i)O(i)(Si(I)) cluster result for positive charge states in dramatically distinct electronic states around the Fermi energy and formation energies