A Model To Structure Scientific Information For Decision Makers

Scientific information for decision makers needs to be discoverable and transparent so that decisions are more easily based on scientific evidence. One way to achieve these goals is to specify a robust model that structures this scientific information. This paper presents a model that governs the scientific activities, inputs and products for bioregional assessments (BAs), which provide information on the ecology, hydrology, geology and hydrogeology of a bioregion with explicit assessment of the potential direct, indirect and cumulative impacts of coal seam gas and coal mining development on water resources. This scientific information will be available for all interested parties – including Australian federal and state decision makers, industry and the community – when considering coal seam gas and coal mining developments. This model shows the flow of information – including uncertainty – through a BA; the linkages between disciplines, data and numerical models; and ‘decision points’ which can be used to adaptively manage the BAs. The model is illustrated as a 4-meter-long diagram that specifies: a standard structure and language for products, with codes for ‘chunks’ of content. This ensures consistency when BAs are undertaken in many different bioregions, and also enables moving away from traditional reports (with linear narratives) to modern delivery on multiple channels – ensuring that the information is discoverable a standard structure for on-demand reporting of provenance of scientific datasets – ensuring transparency. This model is useful not only because it documents the logic behind a BA; it also visually communicates the linkages within this interdisciplinary programme, ensuring that the science – and the reported information – is better integrated

On the Nonlocality of the Quantum Channel in the Standard Teleportation Protocol

By exhibiting a violation of a novel form of the Bell-CHSH inequality, Zukowski has recently established that the quantum correlations exploited in the standard perfect teleportation protocol cannot be recovered by any local hidden variables model. Allowing the quantum channel state in the protocol to be given by any density operator of two spin-1/2 particles, we show that a violation of a generalized form of Zukowski's teleportation inequality can only occur if the channel state, considered by itself, violates a Bell-CHSH inequality. On the other hand, although it is sufficient for a teleportation process to have a nonclassical fidelity-defined as a fidelity exceeding 2/3-that the channel state employed violate a Bell-CHSH inequality, we show that such a violation does not imply a violation of Zukowski's teleportation inequality or any of its generalizations. The implication does hold, however, if the fidelity of the teleportation exceeds $2/3(1+1/2\sqrt{2})\approx .90$, suggesting the existence of a regime of nonclassical values of the fidelity, less than .90, for which the standard teleportation protocol can be modelled by local hidden variables.Comment: 9 pages, no figures, submitted to PR

Mining drives extensive deforestation in the Brazilian Amazon

Mining poses significant and potentially underestimated risks to tropical forests worldwide. In Brazil\u27s Amazon, mining drives deforestation far beyond operational lease boundaries, yet the full extent of these impacts is unknown and thus neglected in environmental licensing. Here we quantify mining-induced deforestation and investigate the aspects of mining operations, which most likely contribute. We find mining significantly increased Amazon forest loss up to 70 km beyond mining lease boundaries, causing 11,670 km2 of deforestation between 2005 and 2015. This extent represents 9% of all Amazon forest loss during this time and 12 times more deforestation than occurred within mining leases alone. Pathways leading to such impacts include mining infrastructure establishment, urban expansion to support a growing workforce, and development of mineral commodity supply chains. Mining-induced deforestation is not unique to Brazil; to mitigate adverse impacts of mining and conserve tropical forests globally, environmental assessments and licensing must considered both on- and off-lease sources of deforestation

Toward vicarious calibration of microwave remote-sensing satellites in arid environments

The Soil Moisture and Ocean Salinity (SMOS) satellite marks the commencement of dedicated global surface soil moisture missions, and the first mission to make passive microwave observations at L-band. On-orbit calibration is an essential part of the instrument calibration strategy, but on-board beam-filling targets are not practical for such large apertures. Therefore, areas to serve as vicarious calibration targets need to be identified. Such sites can only be identified through field experiments including both in situ and airborne measurements. For this purpose, two field experiments were performed in central Australia. Three areas are studied as follows: 1) Lake Eyre, a typically dry salt lake; 2) Wirrangula Hill, with sparse vegetation and a dense cover of surface rock; and 3) Simpson Desert, characterized by dry sand dunes. Of those sites, only Wirrangula Hill and the Simpson Desert are found to be potentially suitable targets, as they have a spatial variation in brightness temperatures of <4 K under normal conditions. However, some limitations are observed for the Simpson Desert, where a bias of 15 K in vertical and 20 K in horizontal polarization exists between model predictions and observations, suggesting a lack of understanding of the underlying physics in this environment. Subsequent comparison with model predictions indicates a SMOS bias of 5 K in vertical and 11 K in horizontal polarization, and an unbiased root mean square difference of 10 K in both polarizations for Wirrangula Hill. Most importantly, the SMOS observations show that the brightness temperature evolution is dominated by regular seasonal patterns and that precipitation events have only little impact

Next generation PCR microfluidic system

Stokes Bio, founded in 2005, develops innovative microfluidic technologies. In 2008 in collaboration with Monsanto, an application driven development for a high-throughput instrument in the detection and characterisation of Single Nucleotide Polymorphisms (SNPs) in agricultural crops was initiated. Stokes technology is designed to generate aqueous nanolitre scale droplets of reagents and samples, wrapped in a carrier fluid from standard microtitre plates and to mix them using Stokes Bio’s proprietary liquid bridge mixers. Following mixing the complete assay is transferred in the carrier fluid through the use of a continuous flow system, to a flow through thermal cycler and an optical reading station. This poster summarises results collated using the Stokes Bio genotyping platform currently based in Monsanto. Data will be presented to illustrate the dynamic capabilities of the instrument, highlighting the enhanced sensitivity and reproducibility of PCR in droplet format compared to well-based technologies

Fire regimes and carbon in Australian vegetation

Fires regularly affect many of the world\u27s terrestrial ecosystems, and, as a result, fires mediate the exchange of greenhouse gases (GHG) between the land and the atmosphere at a global scale and affect the capacity of terrestrial ecosystems to store carbon (Bowman et al. 2009). Variations in fire -regimes can therefore potentially affect the global, regional and local carbon balance and, potentially, climate change itself (Bonan 2008). Here we examine how variation in fire regimes (Gill 1975; Bradstock et al. 2002) will potentially affect carbon in fire-prone Australian ecosystems via interactions with the stocks and transfers of carbon that are inherent to all terrestrial ecosystems. There are two key reasons why an appreciation of fire regimes is needed to comprehend the fate of terrestrial carbon. First, the status of terrestrial carbon over time will be a function of the balance between losses (emissions) from individual fires (of differing type, season and intensity), which occur as a result of immediate combustion as well as mortality and longerterm decomposition of dead biomass, and carbon that accumulates during regeneration in the intervals between fires. The length of the interval between fires will determine the amount of biomass that accumulates. Second, fire regimes influence the composition and structure of ecosystems and key processes such as plant mortality and recruitment. Hence, alternative trajectories of vegetation composition and structure that result from differing fire regimes will affect carbon dynamics. We explore these themes and summarise the dynamic aspects of carbon stocks and transfers in relation to fire, present conceptual models of carbon dynamics and fire regimes, and review how variation in fire regimes may affect overall storage potential as a function of fireinduced losses and post-fire uptake in two widespread Australian vegetation types. We then appraise future trends under global change and the likely potential for managing fire regimes for carbon \u27benefits\u27, especially with respect to emissions

Epac1 mediates protein kinase A–independent mechanism of forskolin-activated intestinal chloride secretion

Intestinal Cl− secretion is stimulated by cyclic AMP (cAMP) and intracellular calcium ([Ca2+]i). Recent studies show that protein kinase A (PKA) and the exchange protein directly activated by cAMP (Epac) are downstream targets of cAMP. Therefore, we tested whether both PKA and Epac are involved in forskolin (FSK)/cAMP-stimulated Cl− secretion. Human intestinal T84 cells and mouse small intestine were used for short circuit current (Isc) measurement in response to agonist-stimulated Cl− secretion. FSK-stimulated Cl− secretion was completely inhibited by the additive effects of the PKA inhibitor, H89 (1 µM), and the [Ca2+]i chelator, 1,2-bis-(o-aminophenoxy)-ethane-N,N,N’,N’-tetraacetic acid, tetraacetoxymethyl ester (BAPTA-AM; 25 µM). Both FSK and the Epac activator 8-pCPT-2’-O-Me-cAMP (50 µM) elevated [Ca2+]i, activated Ras-related protein 2, and induced Cl− secretion in intact or basolateral membrane–permeabilized T84 cells and mouse ileal sheets. The effects of 8-pCPT-2’-O-Me-cAMP were completely abolished by BAPTA-AM, but not by H89. In contrast, T84 cells with silenced Epac1 had a reduced Isc response to FSK, and this response was completely inhibited by H89, but not by the phospholipase C inhibitor U73122 or BAPTA-AM. The stimulatory effect of 8-pCPT-2’-O-Me-cAMP on Cl− secretion was not abolished by cystic fibrosis transmembrane conductance (CFTR) inhibitor 172 or glibenclamide, suggesting that CFTR channels are not involved. This was confirmed by lack of effect of 8-pCPT-2’-O-Me-cAMP on whole cell patch clamp recordings of CFTR currents in Chinese hamster ovary cells transiently expressing the human CFTR channel. Furthermore, biophysical characterization of the Epac1-dependent Cl− conductance of T84 cells mounted in Ussing chambers suggested that this conductance was hyperpolarization activated, inwardly rectifying, and displayed a Cl−>Br−>I− permeability sequence. These results led us to conclude that the Epac-Rap-PLC-[Ca2+]i signaling pathway is involved in cAMP-stimulated Cl− secretion, which is carried by a novel, previously undescribed Cl− channel

Applying clinical decision aids for the assessment and management of febrile infants presenting to emergency care in the UK and Ireland: Febrile Infant Diagnostic Assessment and Outcome (FIDO) Study protocol.

INTRODUCTION: Febrile infants 90 days and younger are at risk of invasive bacterial infections (bacteraemia and meningitis) and urinary tract infections. Together this is previously termed serious bacterial infection with an incidence of approximately 10-20%. The National Institute for Health and Care Excellence guidance advocates a cautious approach with most infants requiring septic screening, parenteral broad-spectrum antibiotics and hospital admission. Internationally, variations exist in the approach to febrile infants, with European and North American guidance advocating a tailored approach based on clinical features and biomarker testing. None of the available international clinical decision aids (CDAs) has been validated in the UK and Irish cohorts. The aim of the Febrile Infant Diagnostic Assessment and Outcome (FIDO) Study is to prospectively validate a range of CDAs in a UK and Irish population including CDAs that use procalcitonin testing. METHODS AND ANALYSIS: The FIDO Study is a prospective multicentre mixed-methods cohort study conducted in UK and Irish hospitals. All infants aged 90 days and younger presenting with fever or history of fever (≥38°C) are eligible for inclusion. Infants will receive standard emergency clinical care without delay. Clinical data and blood samples will be collected, and consent will be obtained at the earliest appropriate opportunity using research without prior consent methodology. The performance and cost-effectiveness of CDAs will be assessed. An embedded qualitative study will explore clinician and caregiver views on different approaches to care and perceptions of risk. ETHICS AND DISSEMINATION: This study was reviewed and approved by the Office for Research Ethics Committees Northern Ireland-Health and Social Care Research Ethics Committee B, Public Benefit and Privacy Panel for Health and Social Care Scotland, and Children's Health Ireland Research and Ethics Committee Ireland. The results of this study will be presented at academic conferences and in peer-reviewed publications. TRIAL REGISTRATION NUMBER: NCT05259683

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues