The df: A proposed data format standard

A standard is proposed describing a portable format for electronic exchange of data in the physical sciences. Writing scientific data in a standard format has three basic advantages: portability; the ability to use metadata to aid in interpretation of the data (understandability); and reusability. An improperly formulated standard format tends towards four disadvantages: (1) it can be inflexible and fail to allow the user to express his data as needed; (2) reading and writing such datasets can involve high overhead in computing time and storage space; (3) the format may be accessible only on certain machines using certain languages; and (4) under some circumstances it may be uncertain whether a given dataset actually conforms to the standard. A format was designed which enhances these advantages and lessens the disadvantages. The fundamental approach is to allow the user to make her own choices regarding strategic tradeoffs to achieve the performance desired in her local environment. The choices made are encoded in a specific and portable way in a set of records. A fully detailed description and specification of the format is given, and examples are used to illustrate various concepts. Implementation is discussed

Polybridge Technical Report

This study examined the physical and chemical properties of a novel, fully-recirculated prawn and polychaete production system that incorporated polychaete-assisted sand filters (PASF). The aims were to assess and demonstrate the potential of this system for industrialisation, and to provide optimisations for wastewater treatment by PASF. Two successive seasons were studied at commercially-relevant scales in a prototype system constructed at the Bribie Island Research Centre in Southeast Queensland. The project produced over 5.4 tonnes of high quality black tiger prawns at rates up to 9.9 tonnes per hectare, with feed conversion of up to 1.1. Additionally, the project produced about 930 kg of high value polychaete biomass at rates up to 1.5 kg per square metre of PASF, with the worms feeding predominantly on waste nutrients. Importantly, this closed production system demonstrated rapid growth of healthy prawns at commercially relevant production levels, using methods that appear feasible for application at large scale. Deeper (23 cm) PASF beds provided similar but more reliable wastewater treatment efficacies compared with shallower (13 cm) beds, but did not demonstrate significantly greater polychaete productivity than (easier to harvest) shallow beds. The nutrient dynamics associated with seasonal and tidal operations of the system were studied in detail, providing technical and practical insights into how PASF could be optimised for the mitigation of nutrient discharge. The study also highlighted some of the other important advantages of this integrated system, including low sludge production, no water discharge during the culture phase, high ecosystem health, good prospects for biosecurity controls, and the sustainable production of a fishery-limited resource (polychaetes) that may be essential for the expansion of prawn farming industries throughout the world. Regarding nutrient discharge from this prototype mariculture system, when PASF was operating correctly it proved feasible to have no water (or nutrient) discharge during the entire prawn growing season. However, the final drain harvest and emptying of ponds that is necessary at the end of the prawn farming season released 58.4 kg ha-1 of nitrogen and 6 kg ha-1 of phosphorus (in Season 2). Whilst this is well below (i.e., one-third to one-half of) the current load-based licencing conditions for many prawn farms in Australia, the levels of nitrogen and chlorophyll a in the ponds remained higher than the more-stringent maximum limits at the Bribie Island study site. Zero-net-nutrient discharge was not achieved, but waste nutrients were low where 5.91 kg of nitrogen and 0.61 kg of phosphorus was discharged per tonne of prawns produced. This was from a system that deployed PASF at 14.4% of total ponded farm area which treated an average of 5.8% of pond water daily and did not use settlement ponds or other natural or artificial water remediation systems. Four supplemental appendices complement this research by studying several additional aspects that are central to the industrialisation of PASF. The first details an economic model and decision tool which allows potential users to interactively assess construction and operational variables of PASF at different scales. The second provides the qualitative results of a prawn maturation trial conducted collaboratively with the Commonwealth Scientific and Industrial Research Organisation (CSIRO) to assess dietary inclusions of PASF-produced worms. The third provides the reproductive results from industry-based assessments of prawn broodstock produced using PASF. And the fourth appendix provides detailed elemental and nutritional analyses of bacterial biofilm produced by PASF and assesses its potential to improve the growth of prawns in recirculated culture systems

Approximate Well-supported Nash Equilibria below Two-thirds

In an epsilon-Nash equilibrium, a player can gain at most epsilon by changing his behaviour. Recent work has addressed the question of how best to compute epsilon-Nash equilibria, and for what values of epsilon a polynomial-time algorithm exists. An epsilon-well-supported Nash equilibrium (epsilon-WSNE) has the additional requirement that any strategy that is used with non-zero probability by a player must have payoff at most epsilon less than the best response. A recent algorithm of Kontogiannis and Spirakis shows how to compute a 2/3-WSNE in polynomial time, for bimatrix games. Here we introduce a new technique that leads to an improvement to the worst-case approximation guarantee

Variability of Irreversible Poleward Transport in the Lower Stratosphere

The ascent and descent of the Brewer-Dobson circulation plays a large role in determining the distributions of many constituents in the extratropical lower stratosphere. However, relatively fast, quasi-horizontal transport out of the tropics and polar regions also significantly contribute to determining these distributions. The tropical tape recorder signal assures that there must be outflow from the tropics into the extratropical lower stratosphere. The phase of the quasi-biennial oscillation (QBO) and state of the polar vortex are known to modulate the transport from the tropical and polar regions, respectively. In this study we examine multiple years of ozone distributions in the extratropical lower stratosphere observed by the Aura Microwave Limb Sounder (MLS) and the Aura High Resolution Dynamic Limb Sounder (HIRDLS). The distributions are compared with analyses of irreversible, meridional isentropic transport. We show that there is considerable year-to-year seasonal variability in the amount of irreversible transport from the tropics, which is related to both the phase of the QBO and the state of the polar vortex. The reversibility of the transport is consistent with the number of observed breaking waves. The variability of the atmospheric index of refraction in the lower stratosphere is shown to be significantly correlated with the wave breaking and amount of irreversible transport. Finally, we will show that the seasonal extratropical stratosphere to troposphere transport of ozone can be substantially modulated by the amount of irreversible meridional transport in the lower stratosphere and we investigate how observable these differences are in data of tropospheric ozone

Polybridge Season 3: Ecosystem effects of polychaete-assisted sand filters

This study is an extension of research undertaken in the first two seasons of the Polybridge Project (2013-2016: for results see Palmer et al., 2016), which sought to investigate operational aspects of polychaete-assisted sand filters (PASF) when deployed for scaled prawn farm recirculation at the Bribie Island Research Centre (BIRC). The aims of the present work were to assess its functionality with increased organic loading rates provided by higher prawn stocking densities than previously trialled, and to assess the ecological effects on this integrated farming system when using PASF to initially fill ponds for a range of biosecurity purposes. Using prawn postlarval stocking densities in excess of 44 m-2, prawn production of up to 12 tonnes ha-1 was achieved without discharge of any wastewater during the production season (2015-16). However, the average production for the two ponds was 9.4 tonnes ha-1, which was lower than in the previous season (9.9 tonnes ha-1 in 2014/15) which used a lower prawn stocking density (37.5 postlarvae m-2). The prawns and worms produced were again healthy and of high commercial quality and value, but slower prawn growth (particularly after 140 d) and lower worm survival limited overall production in the fully-recirculated system. There were also several concerning aspects to this closed-system approach that need to be highlighted. Firstly, nutrient levels in the pond waters rose to particularly high levels, and some of the more toxic parameters, such as ammonia, reached critical levels that could be considered dangerous for routine prawn culture operations. Worm production in the PASF beds also suffered from the very rich wastewaters in the integrated system, and the capacity of PASF to filter water via percolation was limited by excessive sand clogging and a build-up of organic matter on the upper surface of the sand beds. The resultant excessive anoxic conditions created in the sand beds appeared to reduce worm productivity which, in turn, reduced their sand cleansing actions, for an overall lower functionality in terms of nutrient (and particularly nitrogen) removal rates. Alternatively, within the confines of the overall study, there were no significant deleterious effects on worm production or nutrient removal efficacies from using the PASF beds to initially fill the prawn production pond. The apparent effect of this on pond plankton communities was: 1) to slow the development of copepod populations; and 2) change the assemblage of algal species in the first few weeks after filling. This slower development of natural feed organisms in the PASF-filled pond may have provided lower survival of the particularly-young (PL 13) prawn seedstock used to stock the pond. Importantly however, there may be several potential remedies to this issue. These include management for a longer period for bloom development after fill and before stocking, and assuming a greater reliance on artificial feeds more suited to small prawns. As expected, this pond-fill strategy appeared to beneficially help exclude some problematic algal species, and greatly reduced barnacle fouling, though tube worm fouling did not appear overly affected. The project successfully demonstrated a third successive season of zero-water discharge from an integrated prawn/ worm production system, though ultimately, the water in ponds with some residual nutrients were discharged. The expansion of prawn farming in Australia is limited by nutrient discharge issues, and biosecurity measures are also of increasing interest to this industry. In this legacy project, polychaete-assisted sand filters are further demonstrated to hold potential for biosecurity controls whilst minimising nutrient discharge

The evolution of embryonic creek systems in a recently inundated large open coast managed realignment site

Managed realignment (MR) schemes are being implemented to compensate for the degradation of coastal habitats. However, evidence suggests that MR sites have lower biodiversity than anticipated, which has been linked to poor drainage. Despite creek networks playing an important role in enhancing site drainage in natural intertidal environments, there remains a shortage of data on the formation and evolution of creeks within MR sites. This study evaluates creek development at the Medmerry Managed Realignment Site, UK. Creek development is investigated using differential global positioning system(dGPS) data, supported by sedimentological analyses and a high-resolution digital surface model (DSM) derived from images taken using a small unmanned aerial vehicle. Measurements indicated that creeks will develop relatively quickly, but are influenced by differences in the sub-surface sedimentological conditions. A suitable level of agreement was found between the DSM and dGPS measurements, demonstrating the appropriateness of this method to study creek development within intertidal environments at a higher resolution than traditional surveying techniques. These results are used to propose the collapseof sub-surface piping as the primary creek formation mechanism. Findings are discussed in terms of increasing the success of MR schemes and enhancing site design to maximise the ecosystem services provided

Direct observations of the kinetics of migrating T-cells suggest active retention by endothelial cells with continual bidirectional migration.

The kinetics and regulatory mechanisms of T-cell migration through endothelium have not been fully defined. In experimental filter-based assays in vitro, transmigration of lymphocytes takes hours, compared to minutes in vivo. We cultured endothelial cell (EC) monolayers on filters, solid substrates or collagen gels, and treated them with tumour necrosis factor-α (TNF), interferon-γ (IFN), or both, prior to analysis of lymphocyte migration in the presence or absence of flow. Peripheral blood lymphocytes (PBL), CD4+ cells or CD8+ cells, took many hours to migrate through EC-filter constructs for all cytokine treatments. However, direct microscopic observations of EC-filters which had been mounted in a flow chamber showed that PBL crossed the endothelial monolayer in minutes and were highly motile in the subendothelial space. Migration through EC was also observed on clear plastic, with or without flow. After brief settling without flow, PBL and isolated CD3+ or CD4+ cells all crossed EC in minutes, but the numbers of migrated cells varied little with time. Close observation revealed that lymphocytes continuously migrated back and forth across endothelium. Under flow, migration kinetics and the proportions migrating back and forth were little altered. On collagen gels, PBL again crossed EC in minutes and migrated back and forth, but showed little penetration of the gel over hours.In contrast, neutrophils migrated efficiently through EC and into gels. These observations suggest a novel model for lymphoid migration, in which endothelial cells support migration but retain lymphocytes (as opposed to neutrophils), and additional signal(s) are required for onward migration

When Will the Antarctic Ozone Hole Recover?

The Antarctic ozone hole demonstrates large-scale, man-made affects on our atmosphere. Surface observations now show that human produced ozone depleting substances (ODSs) are declining. The ozone hole should soon start to diminish because of this decline. Herein we demonstrate an ozone hole parametric model. This model is based upon: 1) a new algorithm for estimating C1 and Br levels over Antarctica and 2) late-spring Antarctic stratospheric temperatures. This parametric model explains 95% of the ozone hole area s variance. We use future ODS levels to predict ozone hole recovery. Full recovery to 1980 levels will occur in approximately 2068. The ozone hole area will very slowly decline over the next 2 decades. Detection of a statistically significant decrease of area will not occur until approximately 2024. We further show that nominal Antarctic stratospheric greenhouse gas forced temperature change should have a small impact on the ozone hole

A mixed effect model for bivariate meta-analysis of diagnostic test accuracy studies using a copula representation of the random effects distribution

Diagnostic test accuracy studies typically report the number of true positives, false positives, true negatives and false negatives. There usually exists a negative association between the number of true positives and true negatives, because studies that adopt less stringent criterion for declaring a test positive invoke higher sensitivities and lower specificities. A generalized linear mixed model (GLMM) is currently recommended to synthesize diagnostic test accuracy studies. We propose a copula mixed model for bivariate meta-analysis of diagnostic test accuracy studies. Our general model includes the GLMM as a special case and can also operate on the original scale of sensitivity and specificity. Summary receiver operating characteristic curves are deduced for the proposed model through quantile regression techniques and different characterizations of the bivariate random effects distribution. Our general methodology is demonstrated with an extensive simulation study and illustrated by re-analysing the data of two published meta-analyses. Our study suggests that there can be an improvement on GLMM in fit to data and makes the argument for moving to copula random effects models. Our modelling framework is implemented in the package CopulaREMADA within the open source statistical environment R