Pooled biological specimens for human biomonitoring of environmental chemicals : opportunities and limitations

Biomonitoring has become the ‘gold standard’ in assessing chemical exposures, and plays an important role in risk assessment. The pooling of biological specimens – combining multiple individual specimens into a single sample – can be used in biomonitoring studies to monitor levels of exposure and identify exposure trends, or to identify susceptible populations in a cost-effective manner. Pooled samples provide an estimate of central tendency, and may also reveal information about variation within the population. The development of a pooling strategy requires careful consideration of the type and number of samples collected, the number of pools required, and the number of specimens to combine per pool in order to maximize the type and robustness of the data. Creative pooling strategies can be used to explore exposure-outcome associations, and extrapolation from other larger studies can be useful in identifying elevated exposures in specific individuals. The use of pooled specimens is advantageous as it saves significantly on analytical costs, may reduce the time and resources required for recruitment, and in certain circumstances, allows quantification of samples approaching the limit of detection. In addition, use of pooled samples can provide population estimates while avoiding ethical difficulties that may be associated with reporting individual results.

Social media and journalism during times of crisis

Around lunchtime on 22 February 2011, the New Zealand city of Christchurch – the country’s second largest city – was hit by a magnitude 6.3 earthquake. Built on a geological faultline, like Los Angeles and Tokyo, Christchurch is no stranger to tremors; indeed, it had experienced a magnitude 7.1 quake just months before, in September 2010, and technically, this new earthquake was no more than an aftershock of the earlier tremor. That earlier quake had caused significant structural damage, but no fatalities, but the February earthquake was different: with its epicentre located no more than ten kilometres from the Christchurch city centre, at a depth of only five kilometres, it proved considerably more destructive – and it affected buildings whose structural integrity had already been severely compromised by the September quake, in the middle of a weekday when schools and city offices would have been fully occupied. While the full death toll has yet to be determined, it is estimated at close to 200.

A multi-scaling approach to predict hydraulic damage of poromaterials

The purpose of this paper is to introduce the concept of hydraulic damage and its numerical integration. Unlike the common phenomenological continuum damage mechanics approaches, the procedure introduced in this paper relies on mature concepts of homogenization, linear fracture mechanics, and thermodynamics. The model is applied to the problem of fault reactivation within resource reservoirs. The results show that propagation of weaknesses is highly driven by the contrasts of properties in porous media. In particular, it is affected by the fracture toughness of host rocks. Hydraulic damage is diffused when it takes place within extended geological units and localized at interfaces and faults.

"The Stratified Record upon Which We Set Our Feet" : The Spatial Turn and the Multilayering of History, Geography, and Geology

In Thomas Mann’s tetralogy of the 1930s and 1940s, Joseph and His Brothers, the narrator declares history is not only “that which has happened and that which goes on happening in time,” but it is also “the stratified record upon which we set our feet, the ground beneath us.” By opening up history to its spatial, geographical, and geological dimensions Mann both predicts and encapsulates the twentieth-century’s “spatial turn,” a critical shift that divested geography of its largely passive role as history’s “stage” and brought to the fore intersections between the humanities and the earth sciences. In this paper, I draw out the relationships between history, narrative, geography, and geology revealed by this spatial turn and the questions these pose for thinking about the disciplinary relationship between geography and the humanities. As Mann’s statement exemplifies, the spatial turn itself has often been captured most strikingly in fiction, and I would argue nowhere more so than in Graham Swift’s Waterland (1983) and Anne Michaels’s Fugitive Pieces (1996), both of which present space, place, and landscape as having a palpable influence on history and memory. The geographical/geological line that runs through both Waterland and Fugitive Pieces continues through Tim Robinson’s non-fictional, two-volume “topographical” history Stones of Aran. Robinson’s Stones of Aran—which is not history, not geography, and not literature, and yet is all three—constructs an imaginative geography that renders inseparable geography, geology, history, memory, and the act of writing.

The "Shackleton Site" (IODP Site U1385) on the Iberian Margin

Nick Shackleton’s research on piston cores from the Iberian margin highlighted the importance of this region for providing high-fidelity records of millennial-scale climate variability, and for correlating climate events from the marine environment to polar ice cores and European terrestrial sequences. During the Integrated Ocean Drilling Program (IODP) Expedition 339, we sought to extend the Iberian margin sediment record by drilling with the D/V JOIDES Resolution. Five holes were cored at Site U1385 using the advanced piston corer (APC) system to a maximum depth of ∼ 155.9 m below sea floor (m b.s.f.). Immediately after the expedition, cores from all holes were analyzed by core scanning X-ray fluorescence (XRF) at 1 cm spatial resolution. Ca/Ti data were used to accurately correlate from hole-to-hole and construct a composite spliced section, containing no gaps or disturbed intervals to 166.5 m composite depth (mcd). A low-resolution (20 cm sample spacing) oxygen isotope record confirms that Site U1385 contains a continuous record of hemipelagic sedimentation from the Holocene to 1.43 Ma (Marine Isotope Stage 46). The sediment profile at Site U1385 extends across the middle Pleistocene transition (MPT) with sedimentation rates averaging ∼ 10 cm kyr−1. Strongprecession cycles in colour and elemental XRF signals provide a powerful tool for developing an orbitally tuned reference timescale. Site U1385 is likely to become an important type section for marine–ice–terrestrial core correlations and the study of orbital- and millennial-scale climate variability.

Setting water quality objectives for the health of freshwater fish

An important responsibility of the Environment Protection Authority, Victoria, is to set objectives for levels of environmental contaminants. To support the development of environmental objectives for water quality, a need has been identified to understand the dual impacts of concentration and duration of a contaminant on biota in freshwater streams. For suspended solids contamination, information reported by Newcombe and Jensen [ North American Journal of Fisheries Management , 16(4):693--727, 1996] study of freshwater fish and the daily suspended solids data from the United States Geological Survey stream monitoring network is utilised. The study group was requested to examine both the utility of the Newcombe and Jensen and the USA data, as well as the formulation of a procedure for use by the Environment Protection Authority Victoria that takes concentration and duration of harmful episodes into account when assessing water quality. The extent to which the impact of a toxic event on fish health could be modelled deterministically was also considered. It was found that concentration and exposure duration were the main compounding factors on the severity of effects of suspended solids on freshwater fish. A protocol for assessing the cumulative effect on fish health and a simple deterministic model, based on the biology of gill harm and recovery, was proposed. References D. W. T. Au, C. A. Pollino, R. S. S Wu, P. K. S. Shin, S. T. F. Lau, and J. Y. M. Tang. Chronic effects of suspended solids on gill structure, osmoregulation, growth, and triiodothyronine in juvenile green grouper epinephelus coioides . Marine Ecology Press Series , 266:255--264, 2004. J.C. Bezdek, S.K. Chuah, and D. Leep. Generalized k-nearest neighbor rules. Fuzzy Sets and Systems , 18:237--26, 1986. E. T. Champagne, K. L. Bett-Garber, A. M. McClung, and C. Bergman. {Sensory characteristics of diverse rice cultivars as influenced by genetic and environmental factors}. Cereal Chem. , {81}:{237--243}, {2004}. S. G. Cheung and P. K. S. Shin. Size effects of suspended particles on gill damage in green-lipped mussel perna viridis. Marine Pollution Bulletin , 51(8--12):801--810, 2005. D. H. Evans. The fish gill: site of action and model for toxic effects of environmental pollutants. Environmental Health Perspectives , 71:44--58, 1987. G. C. Grigg. The failure of oxygen transport in a fish at low levels of ambient oxygen. Comp. Biochem. Physiol. , 29:1253--1257, 1969. G. Holmes, A. Donkin, and I.H. Witten. {Weka: A machine learning workbench}. In Proceedings of the Second Australia and New Zealand Conference on Intelligent Information Systems , volume {24}, pages {357--361}, {Brisbane, Australia}, {1994}. {IEEE Computer Society}. D. D. Macdonald and C. P. Newcombe. Utility of the stress index for predicting suspended sediment effects: response to comments. North American Journal of Fisheries Management , 13:873--876, 1993. C. P. Newcombe. Suspended sediment in aquatic ecosystems: ill effects as a function of concentration and duration of exposure. Technical report, British Columbia Ministry of Environment, Lands and Parks, Habitat Protection branch, Victoria, 1994. C. P. Newcombe and J. O. T. Jensen. Channel suspended sediment and fisheries: A synthesis for quantitative assessment of risk and impact. North American Journal of Fisheries Management , 16(4):693--727, 1996. C. P. Newcombe and D. D. Macdonald. Effects of suspended sediments on aquatic ecosystems. North American Journal of Fisheries Management , 11(1):72--82, 1991. K. Schmidt-Nielsen. Scaling. Why is animal size so important? Cambridge University Press, NY, 1984. J. S. Schwartz, A. Simon, and L. Klimetz. Use of fish functional traits to associate in-stream suspended sediment transport metrics with biological impairment. Environmental Monitoring and Assessment , 179(1--4):347--369, 2011. E. Al Shaw and J. S. Richardson. Direct and indirect effects of sediment pulse duration on stream invertebrate assemb ages and rainbow trout ( Oncorhynchus mykiss ) growth and survival. Canadian Journal of Fish and Aquatic Science , 58:2213--2221, 2001. P. Tiwari and H. Hasegawa. {Demand for housing in Tokyo: A discrete choice analysis}. Regional Studies , {38}:{27--42}, {2004}. Y. Tramblay, A. Saint-Hilaire, T. B. M. J. Ouarda, F. Moatar, and B Hecht. Estimation of local extreme suspended sediment concentrations in california rivers. Science of the Total Environment , 408:4221--

Breaking time-inversion invariance through decoherence : energetic consequences for attosecond neutron scattering

Nuclei and electrons in condensed matter and/or molecules are usually entangled, due to the prevailing (mainly electromagnetic) interactions. However, the "environment" of a microscopic scattering system (e.g. a proton) causes ultrafast decoherence, thus making atomic and/or nuclear entanglement e®ects not directly accessible to experiments. However, our neutron Compton scattering experiments from protons (H-atoms) in condensed systems and molecules have a characteristic collisional time about 100|1000 attoseconds. The quantum dynamics of an atom in this ultrashort, but ¯nite, time window is governed by non-unitary time evolution due to the aforementioned decoherence. Unexpectedly, recent theoretical investigations have shown that decoherence can also have the following energetic consequences. Disentangling two subsystems A and B of a quantum system AB is tantamount to erasure of quantum phase relations between A and B. This erasure is widely believed to be an innocuous process, which e.g. does not a®ect the energies of A and B. However, two independent groups proved recently that disentangling two systems, within a su±ciently short time interval, causes increase of their energies. This is also derivable by the simplest Lindblad-type master equation of one particle being subject to pure decoherence. Our neutron-proton scattering experiments with H2 molecules provide for the first time experimental evidence of this e®ect. Our results reveal that the neutron-proton collision, leading to the cleavage of the H-H bond in the attosecond timescale, is accompanied by larger energy transfer (by about 2|3%) than conventional theory predicts. Preliminary results from current investigations show qualitatively the same e®ect in the neutron-deuteron Compton scattering from D2 molecules. We interpret the experimental findings by treating the neutron-proton (or neutron-deuteron) collisional system as an entangled open quantum system being subject to fast decoherence caused by its "environment" (i.e., two electrons plus second nucleus of H2 or D2). The presented results seem to be of generic nature, and may have considerable consequences for various processes in condensed matter and molecules, e.g. in elementary chemical reactions.

Accessibility of pores in coal to methane and carbon dioxide

Fluid–solid interactions in natural and engineered porous solids underlie a variety of technological processes, including geological storage of anthropogenic greenhouse gases, enhanced coal bed methane recovery, membrane separation, and heterogeneous catalysis. The size, distribution and interconnectivity of pores, the chemical and physical properties of the solid and fluid phases collectively dictate how fluid molecules migrate into and through the micro- and meso-porous media, adsorb and ultimately react with the solid surfaces. Due to the high penetration power and relatively short wavelength of neutrons, smallangle neutron scattering (SANS) as well as ultra small-angle scattering (USANS) techniques are ideally suited for assessing the phase behavior of confined fluids under pressure as well as for evaluating the total porosity in engineered and natural porous systems including coal. Here we demonstrate that SANS and USANS can be also used for determining the fraction of the pore volume that is actually accessible to fluids as a function of pore sizes and study the fraction of inaccessible pores as a function of pore size in three coals from the Illinois Basin (USA) and Bowen Basin (Australia). Experiments were performed at CO2 and methane pressures up to 780 bar, including pressures corresponding to zero average contrast condition (ZAC), which is the pressure where no scattering from the accessible pores occurs. Scattering curves at the ZAC were compared with the scattering from same coals under vacuum and analysed using a newly developed approach that shows that the volume fraction of accessible pores in these coals varies between �90% in the macropore region to �30% in the mesopore region and the variation is distinctive for each of the examined coals. The developed methodology may be also applied for assessing the volume of accessible pores in other natural underground formations of interest for CO2 sequestration, such as saline aquifers as well as for estimating closed porosity in engineered porous solids of technological importance.

Indications of energetic consequences of decoherence at short times for scattering from open quantum systems

Decoherence of quantum entangled particles is observed in most systems, and is usually caused by system-environment interactions. Disentangling two subsystems A and B of a quantum systemAB is tantamount to erasure of quantum phase relations between A and B. It is widely believed that this erasure is an innocuous process, which e.g. does not affect the energies of A and B. Surprisingly, recent theoretical investigations by different groups showed that disentangling two systems, i.e. their decoherence, can cause an increase of their energies. Applying this result to the context of neutronCompton scattering from H2 molecules, we provide for the first time experimental evidence which supports this prediction. The results reveal that the neutron-proton collision leading to the cleavage of the H-H bond in the sub-femtosecond timescale is accompanied by larger energy transfer (by about 3%) than conventional theory predicts. It is proposed to interpreted the results by considering the neutron-proton collisional system as an entangled open quantum system being subject to decoherence owing to the interactions with the “environment” (i.e., two electrons plus second proton of H2).

Small angle X-ray scattering mapping and kinetics study of sub-critical CO2 sorption by two Australian coals

Time- and position-resolved synchrotron small angle X-ray scattering data were acquired from samples of two Australian coal seams: Bulli seam (Bulli 4, Ro=1.42%, Sydney Basin), which naturally contains CO2 and Baralaba seam (Ro=0.67%, Bowen Basin), a potential candidate for sequestering CO2. This experimental approach has provided unique, pore-size-specific insights into the kinetics of CO2 sorption in the micro- and small mesopores (diameter 5 to 175 Å) and the density of the sorbed CO2 at reservoir-like conditions of temperature and hydrostatic pressure. For both samples, at pressures above 5 bar, the density of CO2 confined in pores was found to be uniform, with no densification in near-wall regions. In the Bulli 4 sample, CO2 first flooded the slit pores between polyaromatic sheets. In the pore-size range analysed, the confined CO2 density was close to that of the free CO2. The kinetics data are too noisy for reliable quantitative analysis, but qualitatively indicate faster kinetics in mineral-matter-rich regions. In the Baralaba sample, CO2 preferentially invaded the smallest micropores and the confined CO2 density was up to five times that of the free CO2. Faster CO2 sorption kinetics was found to be correlated with higher mineral matter content but, the mineral-matter-rich regions had lower-density CO2 confined in their pores. Remarkably, the kinetics was pore-size dependent, being faster for smaller pores. These results suggest that injection into the permeable section of an interbedded coal-clastic sequence could provide a viable combination of reasonable injectivity and high sorption capacity.

A derivation of high-frequency asymptotic values of 3D added mass and damping based on properties of the Cummins' equation

This brief paper provides a novel derivation of the known asymptotic values of three-dimensional (3D) added mass and damping of marine structures in waves. The derivation is based on the properties of the convolution terms in the Cummins's Equation as derived by Ogilvie. The new derivation is simple and no approximations or series expansions are made. The results follow directly from the relative degree and low-frequency asymptotic properties of the rational representation of the convolution terms in the frequency domain. As an application, the extrapolation of damping values at high frequencies for the computation of retardation functions is also discussed.

A combined neutralization-reionization mass spectrometric and theoretical study of oxyallyl and other elusive [C3,H4,O] neutrals

Five different anionic [C3′H4′O]•- isomers, i.e. the radical anions of acrolein, acetyl carbene, formyl methyl carbene, methoxy vinylidene, and oxyallyl are generated in an ion beam mass spectrometer and subjected to neutralization-reionization (NR) mass spectrometric experiments including neutral and ion decomposition difference (NIDD) mass spectrometry; the latter allows for the examination of the neutrals' unimolecular reactivity. Further, the anionic, the singlet and triplet neutral, and the cationic [C3′H4′O] •-/0/•+ potentialenergy surfaces are calculated at the B3LYP/6-311++G(d,p) level of theory. For some species, notably the singlet state of oxyallyl, the theoretical treatment is complemented by G2, CASSCF, and MR-CI calculations. Theory and experiment are in good agreement in that at the neutral stage (i) acrolein does not react within the μsec timescale, (ii) acetyl and formyl methyl carbenes isomerize to methyl ketene, (iii) methoxy vinylidene rearranges to methoxy acetylene, (iv) singlet 1A1 oxyallyl undergoes ring closure to cyclopropanone, and (v) triplet 3B2 oxyallyl may have a lifetime sufficient to survive a NR experiment.

Estimating present day extreme total water level exceedance probabilities around the Australian coastline

The occurrence of extreme water level events along low-lying, highly populated and/or developed coastlines can lead to devastating impacts on coastal infrastructure. Therefore it is very important that the probabilities of extreme water levels are accurately evaluated to inform flood and coastal management and for future planning. The aim of this study was to provide estimates of present day extreme total water level exceedance probabilities around the whole coastline of Australia, arising from combinations of mean sea level, astronomical tide and storm surges generated by both extra-tropical and tropical storms, but exclusive of surface gravity waves. The study has been undertaken in two main stages. In the first stage, a high-resolution (~10 km along the coast) hydrodynamic depth averaged model has been configured for the whole coastline of Australia using the Danish Hydraulics Institute’s Mike21 modelling suite of tools. The model has been forced with astronomical tidal levels, derived from the TPX07.2 global tidal model, and meteorological fields, from the US National Center for Environmental Prediction’s global reanalysis, to generate a 61-year (1949 to 2009) hindcast of water levels. This model output has been validated against measurements from 30 tide gauge sites around Australia with long records. At each of the model grid points located around the coast, time series of annual maxima and the several highest water levels for each year were derived from the multi-decadal water level hindcast and have been fitted to extreme value distributions to estimate exceedance probabilities. Stage 1 provided a reliable estimate of the present day total water level exceedance probabilities around southern Australia, which is mainly impacted by extra-tropical storms. However, as the meteorological fields used to force the hydrodynamic model only weakly include the effects of tropical cyclones the resultant water levels exceedance probabilities were underestimated around western, northern and north-eastern Australia at higher return periods. Even if the resolution of the meteorological forcing was adequate to represent tropical cyclone-induced surges, multi-decadal periods yielded insufficient instances of tropical cyclones to enable the use of traditional extreme value extrapolation techniques. Therefore, in the second stage of the study, a statistical model of tropical cyclone tracks and central pressures was developed using histroic observations. This model was then used to generate synthetic events that represented 10,000 years of cyclone activity for the Australia region, with characteristics based on the observed tropical cyclones over the last ~40 years. Wind and pressure fields, derived from these synthetic events using analytical profile models, were used to drive the hydrodynamic model to predict the associated storm surge response. A random time period was chosen, during the tropical cyclone season, and astronomical tidal forcing for this period was included to account for non-linear interactions between the tidal and surge components. For each model grid point around the coast, annual maximum total levels for these synthetic events were calculated and these were used to estimate exceedance probabilities. The exceedance probabilities from stages 1 and 2 were then combined to provide a single estimate of present day extreme water level probabilities around the whole coastline of Australia.

Multivariate statistical analysis of hydrochemical data to assess alluvial aquifer–stream connectivity during drought and flood : Cressbrook Creek, southeast Queensland, Australia

A catchment-scale multivariate statistical analysis of hydrochemistry enabled assessment of interactions between alluvial groundwater and Cressbrook Creek, an intermittent drainage system in southeast Queensland, Australia. Hierarchical cluster analyses and principal component analysis were applied to time-series data to evaluate the hydrochemical evolution of groundwater during periods of extreme drought and severe flooding. A simple three-dimensional geological model was developed to conceptualise the catchment morphology and the stratigraphic framework of the alluvium. The alluvium forms a two-layer system with a basal coarse-grained layer overlain by a clay-rich low-permeability unit. In the upper and middle catchment, alluvial groundwater is chemically similar to streamwater, particularly near the creek (reflected by high HCO3/Cl and K/Na ratios and low salinities), indicating a high degree of connectivity. In the lower catchment, groundwater is more saline with lower HCO3/Cl and K/Na ratios, notably during dry periods. Groundwater salinity substantially decreased following severe flooding in 2011, notably in the lower catchment, confirming that flooding is an important mechanism for both recharge and maintaining groundwater quality. The integrated approach used in this study enabled effective interpretation of hydrological processes and can be applied to a variety of hydrological settings to synthesise and evaluate large hydrochemical datasets.

Multi-stage collapse events in the South Soufrière Hills, Montserrat as recorded in marine sediment cores

We present new evidence for sector collapses of the South Soufrière Hills (SSH) edifice, Montserrat during the mid-Pleistocene. High-resolution geophysical data provide evidence for sector collapse, producing an approximately 1 km3 submarine collapse deposit to the south of SSH. Sedimentological and geochemical analyses of submarine deposits sampled by sediment cores suggest that they were formed by large multi-stage flank failures of the subaerial SSH edifice into the sea. This work identifies two distinct geochemical suites within the SSH succession on the basis of trace-element and Pb-isotope compositions. Volcaniclastic turbidites in the cores preserve these chemically heterogeneous rock suites. However, the subaerial chemostratigraphy is reversed within the submarine sediment cores. Sedimentological analysis suggests that the edifice failures produced high-concentration turbidites and that the collapses occurred in multiple stages, with an interval of at least 2 ka between the first and second failure. Detailed field and petrographical observations, coupled with SEM image analysis, shows that the SSH volcanic products preserve a complex record of magmatic activity. This activity consisted of episodic explosive eruptions of andesitic pumice, probably triggered by mafic magmatic pulses and followed by eruptions of poorly vesiculated basaltic scoria, and basaltic lava flows.