Singularity, complexity, and quasi--integrability of rational mappings

We investigate global properties of the mappings entering the description of symmetries of integrable spin and vertex models, by exploiting their nature of birational transformations of projective spaces. We give an algorithmic analysis of the structure of invariants of such mappings. We discuss some characteristic conditions for their (quasi)--integrability, and in particular its links with their singularities (in the 2--plane). Finally, we describe some of their properties {\it qua\/} dynamical systems, making contact with Arnol'd's notion of complexity, and exemplify remarkable behaviours.Comment: Latex file. 17 pages. To appear in CM

Air–sea CO2 exchange and ocean acidification in UK seas and adjacent waters

Ongoing anthropogenic emissions of carbon dioxide (CO2) into the atmosphere are driving a net flux of CO2 into the ocean globally, resulting in a decline in pH called ‘ocean acidification’. Here, we discuss the consequences of this for the seas surrounding the UK from a chemical perspective, focussing on studies published since the previous MCCIP review of ocean acidification research (Williamson et al., 2017). In this reporting cycle, the biological, ecological, and socio-economic impacts of ocean acidification are considered in more detail in separate accompanying MCCIP reviews The atmospheric CO2 concentration continues to increase due to human activities (Le Quéré et al., 2018), increasing the net flux of CO2 into the global ocean, including the North Atlantic and UK continental shelf seas. Such CO2 uptake has the desirable effect of reducing the rate of climate change, but the undesirable result of ocean acidification. Our understanding of the factors that drive high spatial and temporal variability in air-sea CO2 fluxes and seawater pH in UK waters has continued to improve, thanks to observational campaigns both across the entire North-West European continental shelf sea and at specific time–series sites. Key challenges for the future include sustaining time–series observations of near-surface marine carbonate system variables, and of the auxiliary parameters required for their interpretation (e.g. temperature, salinity, and nutrients); developing and deploying new sensor technology for full water-column profiles and pore waters in seafloor sediments; and increasing the spatial and temporal resolution of models sufficiently to capture the complex processes that dominate the marine carbonate system in coastal and shelf sea environments, along with improving how those processes are themselves simulated

Agr quorum sensing influences the Wood-Ljungdahl pathway in Clostridium autoethanogenum

Acetogenic bacteria are capable of fermenting CO2 and carbon monoxide containing waste-gases into a range of platform chemicals and fuels. Despite major advances in genetic engineering and improving these biocatalysts, several important physiological functions remain elusive. Among these is quorum sensing, a bacterial communication mechanism known to coordinate gene expression in response to cell population density. Two putative agr systems have been identified in the genome of Clostridium autoethanogenum suggesting bacterial communication via autoinducing signal molecules. Signal molecule-encoding agrD1 and agrD2 genes were targeted for in-frame deletion. During heterotrophic growth on fructose as a carbon and energy source, single deletions of either gene did not produce an observable phenotype. However, when both genes were simultaneously inactivated, final product concentrations in the double mutant shifted to a 1.5:1 ratio of ethanol:acetate, compared to a 0.2:1 ratio observed in the wild type control, making ethanol the dominant fermentation product. Moreover, CO2 re-assimilation was also notably reduced in both hetero- and autotrophic growth conditions. These findings were supported through comparative proteomics, which showed lower expression of carbon monoxide dehydrogenase, formate dehydrogenase A and hydrogenases in the ∆agrD1∆agrD2 double mutant, but higher levels of putative alcohol and aldehyde dehydrogenases and bacterial micro-compartment proteins. These findings suggest that Agr quorum sensing, and by inference, cell density play a role in carbon resource management and use of the Wood-Ljungdahl pathway as an electron sink

Seasonality and spatial heterogeneity of the surface ocean carbonate system in the northwest European continental shelf

In 2014–5 the UK NERC sponsored an 18 month long Shelf Sea Biogeochemistry research programme which collected over 1500 nutrient and carbonate system samples across the NW European Continental shelf, one of the largest continental shelves on the planet. This involved the cooperation of 10 different Institutes and Universities, using 6 different vessels. Additional carbon dioxide (CO2) data were obtained from the underway systems on three of the research vessels. Here, we present and discuss these data across 9 ecohydrodynamic regions, adapted from those used by the EU Marine Strategy Framework Directive (MSFD). We observed strong seasonal and regional variability in carbonate chemistry around the shelf in relation to nutrient biogeochemistry. Whilst salinity increased (and alkalinity decreased) out from the near-shore coastal waters offshore throughout the year nutrient concentrations varied with season. Spatial and seasonal variations in the ratio of DIC to nitrate concentration were seen that could impact carbon cycling. A decrease in nutrient concentrations and a pronounced under-saturation of surface pCO2 was evident in the spring in most regions, especially in the Celtic Sea. This decrease was less pronounced in Liverpool Bay and to the North of Scotland, where nutrient concentrations remained measurable throughout the year. The near-shore and relatively shallow ecosystems such as the eastern English Channel and southern North Sea were associated with a thermally driven increase in pCO2 to above atmospheric levels in summer and an associated decrease in pH. Non-thermal processes (such as mixing and the remineralisation of organic material) dominated in winter in most regions but especially in the northwest of Scotland and in Liverpool Bay. The large database collected will improve understanding of carbonate chemistry over the North-Western European Shelf in relation to nutrient biogeochemistry, particularly in the context of climate change and ocean acidification

Macdonald Polynomials from Sklyanin Algebras: A Conceptual Basis for the pp-Adics-Quantum Group Connection

We establish a previously conjectured connection between $p$-adics and quantum groups. We find in Sklyanin's two parameter elliptic quantum algebra and its generalizations, the conceptual basis for the Macdonald polynomials, which ``interpolate'' between the zonal spherical functions of related real and $p$\--adic symmetric spaces. The elliptic quantum algebras underlie the $Z_n$\--Baxter models. We show that in the n \air \infty limit, the Jost function for the scattering of {\em first} level excitations in the $Z_n$\--Baxter model coincides with the Harish\--Chandra\--like $c$\--function constructed from the Macdonald polynomials associated to the root system $A_1$. The partition function of the $Z_2$\--Baxter model itself is also expressed in terms of this Macdonald\--Harish\--Chandra\ $c$\--function, albeit in a less simple way. We relate the two parameters $q$ and $t$ of the Macdonald polynomials to the anisotropy and modular parameters of the Baxter model. In particular the $p$\--adic ``regimes'' in the Macdonald polynomials correspond to a discrete sequence of XXZ models. We also discuss the possibility of ``$q$\--deforming'' Euler products.Comment: 25 page

Remote health workforce turnover and retention: What are the policy and practice priorities?

BACKGROUND:Residents of remote communities in Australia and other geographically large countries have comparatively poorer access to high-quality primary health care. To inform ongoing policy development and practice in relation to remote area health service delivery, particularly in remote Indigenous communities, this review synthesizes the key findings of (1) a comprehensive study of workforce turnover and retention in remote Northern Territory (NT) of Australia and (2) a narrative review of relevant international literature on remote and rural health workforce retention strategies. This synthesis provides a valuable summary of the current state of international knowledge about improving remote health workforce retention. MAIN TEXT:Annual turnover rates of NT remote area nurses (148%) and Aboriginal health practitioners (80%) are very high and 12-month stability rates low (48% and 76%, respectively). In remote NT, use of agency nurses has increased substantially. Primary care costs are high and proportional to staff turnover and remoteness. Effectiveness of care decreases with higher turnover and use of short-term staff, such that higher staff turnover is always less cost-effective. If staff turnover in remote clinics were halved, the potential savings would be approximately A$32 million per annum. Staff turnover and retention were affected by management style and effectiveness, and employment of Indigenous staff. Review of the international literature reveals three broad themes: Targeted enrolment into training and appropriate education designed to produce a competent, accessible, acceptable and 'fit-for-purpose' workforce; addressing broader health system issues that ensure a safe and supportive work environment; and providing ongoing individual and family support. Key educational initiatives include prioritising remote origin and Indigenous students for university entry; maximising training in remote areas; contextualising curricula; providing financial, pedagogical and pastoral support; and ensuring clear, supported career pathways and continuing professional development. Health system initiatives include ensuring adequate funding; providing adequate infrastructure including fit-for-purpose clinics, housing, transport and information technology; offering flexible employment arrangements whilst ensuring a good 'fit' between individual staff and the community (especially with regard to cultural skills); optimising co-ordination and management of services that empower staff and create positive practice environments; and prioritising community participation and employment of locals. Individual and family supports include offering tailored financial incentives, psychological support and 'time out'. CONCLUSION:Optimal remote health workforce stability and preventing excessive 'avoidable' turnover mandates alignment of government and health authority policies with both health service requirements and individual health professional and community needs. Supportive underpinning policies include: Strong intersectoral collaboration between the health and education sectors to ensure a fit-for-purpose workforce;A funding policy which mandates the development and implementation of an equitable, needs-based formula for funding remote health services;Policies that facilitate transition to community control, prioritise Indigenous training and employment, and mandate a culturally safe work context; andAn employment policy which provides flexibility of employment conditions in order to be able to offer individually customised retention packages There is considerable extant evidence from around the world about effective retention strategies that contribute to slowing excessive remote health workforce turnover, resulting in significant cost savings and improved continuity of care. The immediate problem comprises an 'implementation gap' in translating empirical research evidence into actions designed to resolve existing problems. If we wish to ameliorate the very high turnover of staff in remote areas, in order to provide an equitable service to populations with arguably the highest health needs, we need political and executive commitment to get the policy settings right and ensure the coordinated implementation of multiple strategies, including better linking existing strategies and 'filling the gaps' where necessary.John Wakerman, John Humphreys, Deborah Russell, Steven Guthridge, Lisa Bourke, Terry Dunbar, Yuejen Zhao, Mark Ramjan, Lorna Murakami-Gold and Michael P. Jone

Computer simulation of recrystallization--III. Influence of a dispersion of fine particles

Two-dimensional Monte Carlo simulations of recrystallization have been carried out in the presence of incoherent and immobile particles for a range of different particle fractions, a range of stored energies and a range of densities of potential nuclei (embryos). For stored energies greater than a critical value (H/J > 1) the recrystallization front can readily pass the particles leading to a random density of particles on the front and a negligible influence of particles on the recrystallization kinetics. At lower stored energies the particles pin the recrystallization front leading to incomplete recrystallization. However at very low particle fractions, when the new grain has grown much larger than the matrix grains, before meeting any particles, the new grains can complete the consumption of the deformed grains giving complete "recrystallization" by a process that appears to be similar to abnormal grain growth. Particles are, as reported previously, very effective at pinning grain boundaries, both of the deformed and recrystallized grains, when boundaries migrate under essentially the driving force of boundary energy alone. Such boundaries show a density of particles that rises rapidly from the random value found at the start of the simulation. As a consequence, particles very strongly inhibit normal grain growth after recrystallization. Such growth can only occur if the as-recrystallized grain size is less than the limiting grain size seen in the absence of recrystallization. Under these circumstances a small increment of grain growth occurs until the grain boundaries once again acquire a higher than random density of particles.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29718/1/0000052.pd

Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

Peer reviewe

Breast cancer risk genes: association analysis in more than 113,000 women

BACKGROUNDGenetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking.METHODSWe used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity.RESULTSProtein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants.CONCLUSIONSThe results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.)Molecular tumour pathology - and tumour geneticsMTG1 - Moleculaire genetica en pathologie van borstkanke