A metabolic system-wide characterisation of the pig: a model for human physiology

The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional 1H and 13C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major interspecies differences observed were in the phase II conjugation of extra-genomic metabolites; the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.

[Global climate] global aerosols [in state of the climate in 2008]

The global mean temperature in 2008 was slightly cooler than that in 2007; however, it still ranks within the 10 warmest years on record. Annual mean temperatures were generally well above average in South America, northern and southern Africa, Iceland, Europe, Russia, South Asia, and Australia. In contrast, an exceptional cold outbreak occurred during January across Eurasia and over southern European Russia and southern western Siberia. There has been a general increase in land-surface temperatures and in permafrost temperatures during the last several decades throughout the Arctic region, including increases of 1° to 2°C in the last 30 to 35 years in Russia. Record setting warm summer (JJA) air temperatures were observed throughout Greenland. The year 2008 was also characterized by heavy precipitation in a number of regions of northern South America, Africa, and South Asia. In contrast, a prolonged and intense drought occurred during most of 2008 in northern Argentina, Paraguay, Uruguay, and southern Brazil, causing severe impacts to agriculture and affecting many communities. The year began with a strong La Niña episode that ended in June. Eastward surface current anomalies in the tropical Pacific Ocean in early 2008 played a major role in adjusting the basin from strong La Niña conditions to ENSO-neutral conditions by July–August, followed by a return to La Niña conditions late in December. The La Niña conditions resulted in far-reaching anomalies such as a cooling in the central tropical Pacific, Arctic Ocean, and the regions extending from the Gulf of Alaska to the west coast of North America; changes in the sea surface salinity and heat content anomalies in the tropics; and total column water vapor, cloud cover, tropospheric temperature, and precipitation patterns typical of a La Niña. Anomalously salty ocean surface salinity values in climatologically drier locations and anomalously fresh values in rainier locations observed in recent years generally persisted in 2008, suggesting an increase in the hydrological cycle. The 2008 Atlantic hurricane season was the 14th busiest on record and the only season ever recorded with major hurricanes each month from July through November. Conversely, activity in the northwest Pacific was considerably below normal during 2008. While activity in the north Indian Ocean was only slightly above average, the season was punctuated by Cyclone Nargis, which killed over 145,000 people; in addition, it was the seventh-strongest cyclone ever in the basin and the most devastating to hit Asia since 1991. Greenhouse gas concentrations continued to rise, increasing by more than expected based on with CO2 the 1979 to 2007 trend. In the oceans, the global mean uptake for 2007 is estimated to be 1.67 Pg-C, about CO2 0.07 Pg-C lower than the long-term average, making it the third-largest anomaly determined with this method since 1983, with the largest uptake of carbon over the past decade coming from the eastern Indian Ocean. Global phytoplankton chlorophyll concentrations were slightly elevated in 2008 relative to 2007, but regional changes were substantial (ranging to about 50%) and followed long-term patterns of net decreases in chlorophyll with increasing sea surface temperature. Ozone-depleting gas concentrations continued to fall globally to about 4% below the peak levels of the 2000–02 period. Total column ozone concentrations remain well below pre-1980, levels and the 2008 ozone hole was unusually large (sixth worst on record) and persistent, with low ozone values extending into the late December period. In fact the polar vortex in 2008 persisted longer than for any previous year since 1979. Northern Hemisphere snow cover extent for the year was well below average due in large part to the record-low ice extent in March and despite the record-maximum coverage in January and the shortest snow cover duration on record (which started in 1966) in the North American Arctic. Limited preliminary data imply that in 2008 glaciers continued to lose mass, and full data for 2007 show it was the 17th consecutive year of loss. The northern region of Greenland and adjacent areas of Arctic Canada experienced a particularly intense melt season, even though there was an abnormally cold winter across Greenland's southern half. One of the most dramatic signals of the general warming trend was the continued significant reduction in the extent of the summer sea-ice cover and, importantly, the decrease in the amount of relatively older, thicker ice. The extent of the 2008 summer sea-ice cover was the second-lowest value of the satellite record (which started in 1979) and 36% below the 1979–2000 average. Significant losses in the mass of ice sheets and the area of ice shelves continued, with several fjords on the northern coast of Ellesmere Island being ice free for the first time in 3,000–5,500 years. In Antarctica, the positive phase of the SAM led to record-high total sea ice extent for much of early 2008 through enhanced equatorward Ekman transport. With colder continental temperatures at this time, the 2007–08 austral summer snowmelt season was dramatically weakened, making it the second shortest melt season since 1978 (when the record began). There was strong warming and increased precipitation along the Antarctic Peninsula and west Antarctica in 2008, and also pockets of warming along coastal east Antarctica, in concert with continued declines in sea-ice concentration in the Amundsen/Bellingshausen Seas. One significant event indicative of this warming was the disintegration and retreat of the Wilkins Ice Shelf in the southwest peninsula area of Antarctica.

Ice internal friction: Standard theoretical perspectives on friction codified, adapted for the unusual rheology of ice, and unified

Sea ice contains flaws including frictional contacts. We aim to describe quantitatively the mechanics of those contacts, providing local physics for geophysical models. With a focus on the internal friction of ice, we review standard micro-mechanical models of friction. The solid's deformation under normal load may be ductile or elastic. The shear failure of the contact may be by ductile flow, brittle fracture, or melting and hydrodynamic lubrication. Combinations of these give a total of six rheological models. When the material under study is ice, several of the rheological parameters in the standard models are not constant, but depend on the temperature of the bulk, on the normal stress under which samples are pressed together, or on the sliding velocity and acceleration. This has the effect of making the shear stress required for sliding dependent on sliding velocity, acceleration, and temperature. In some cases, it also perturbs the exponent in the normal-stress dependence of that shear stress away from the value that applies to most materials. We unify the models by a principle of maximum displacement for normal deformation, and of minimum stress for shear failure, reducing the controversy over the mechanism of internal friction in ice to the choice of values of four parameters in a single model. The four parameters represent, for a typical asperity contact, the sliding distance required to expel melt-water, the sliding distance required to break contact, the normal strain in the asperity, and the thickness of any ductile shear zone.

On the Nusselt number for frazil ice growth—a correction to ”Frazil evolution in channels“ by Lars Hammar and Hung-Tao Shen

The growth (melt) rate of frazil ice is governed by heat transfer away from (towards) the ice crystal, which can be represented by the Nusselt number. We discuss choices for the Nusselt number and turbulent length scale appropriate for frazil ice and note an inaccuracy in the study ”Frazil evolution in channels“ by Lars Hammar and Hung-Tao Shen, which has also led to potentially significant errors in several other papers. We correct this error and suggest an appropriate strategy for determining the Nusselt number applicable to frazil ice growth and melting.

Flow-induced morphological instability of a mushy layer

A morphological instability of a mushy layer due to a forced flow in the melt is analysed. The instability is caused by flow induced in the mushy layer by Bernoulli suction at the crests of a sinusoidally perturbed mush–melt interface. The flow in the mushy layer advects heat away from crests which promotes solidification. Two linear stability analyses are presented: the fundamental mechanism for instability is elucidated by considering the case of uniform flow of an inviscid melt; a more complete analysis is then presented for the case of a parallel shear flow of a viscous melt. The novel instability mechanism we analyse here is contrasted with that investigated by Gilpin et al. (1980) and is found to be more potent for the case of newly forming sea ice.

Frazil dynamics and precipitation in a water column with depth-dependent supercooling

A morphological instability of a mushy layer due to a forced flow in the melt is analysed. The instability is caused by flow induced in the mushy layer by Bernoulli suction at the crests of a sinusoidally perturbed mush–melt interface. The flow in the mushy layer advects heat away from crests which promotes solidification. Two linear stability analyses are presented: the fundamental mechanism for instability is elucidated by considering the case of uniform flow of an inviscid melt; a more complete analysis is then presented for the case of a parallel shear flow of a viscous melt. The novel instability mechanism we analyse here is contrasted with that investigated by Gilpin et al. (1980) and is found to be more potent for the case of newly forming sea ice.

Multiple stationary solutions of an irradiated slab

A mathematical model describing the heat budget of an irradiated medium is introduced. The one-dimensional form of the equations and boundary conditions are presented and analysed. Heat transport at one face of the slab occurs by absorption (and reflection) of an incoming beam of short-wave radiation with a fraction of this radiation penetrating into the body of the slab, a diffusive heat flux in the slab and a prescribed incoming heat flux term. The other face of the slab is immersed in its own melt and is considered to be a free surface. Here, temperature continuity is prescribed and evolution of the surface is determined by a Stefan condition. These boundary conditions are flexible enough to describe a range of situations such as a laser shining on an opaque medium, or the natural environment of polar sea ice or lake ice. A two-stream radiation model is used which replaces the simple Beer’s law of radiation attenuation frequently used for semi-infinite domains. The stationary solutions of the governing equations are sought and it is found that there exists two possible stationary solutions for a given set of boundary conditions and a range of parameter choices. It is found that the existence of two stationary solutions is a direct result of the model of radiation absorption, due to its effect on the albedo of the medium. A linear stability analysis and numerical calculations indicate that where two stationary solutions exist, the solution corresponding to a larger thickness is always stable and the solution corresponding to a smaller thickness is unstable. Numerical simulations reveal that when there are two solutions, if the slab is thinner than the smaller stationary thickness it will melt completely, whereas if the slab is thicker than the smaller stationary thickness it will evolve toward the larger stationary thickness. These results indicate that other mechanisms (e.g. wave-induced agglomeration of crystals) are necessary to grow a slab from zero initial thickness in the parameter regime that yields two stationary solutions.

The effect of a new drag-law parameterization on ice shelf water plume dynamics

A drag law accounting for Ekman rotation adjacent to a flat, horizontal bou ndary is proposed for use in a plume model that is written in terms of the depth-mean velocity. The drag l aw contains a variable turning angle between the mean velocity and the drag imposed by the turbulent bound ary layer. The effect of the variable turning angle in the drag law is studied for a plume of ice shelf wat er (ISW) ascending and turning beneath an Antarctic ice shelf with draft decreasing away from the groundi ng line. As the ISW plume ascends the sloping ice shelf–ocean boundary, it can melt the ice shelf, wh ich alters the buoyancy forcing driving the plume motion. Under these conditions, the typical turning ang le is of order 10° over most of the plume area for a range of drag coefficients (the minus sign arises for th e Southern Hemisphere). The rotation of the drag with respect to the mean velocity is found to be signifi cant if the drag coefficient exceeds 0.003; in this case the plume body propagates farther along and across the b ase of the ice shelf than a plume with the standard quadratic drag law with no turning angle.

Impact of variable atmospheric and oceanic form drag on simulations of Arctic sea ice

Over Arctic sea ice, pressure ridges and floe andmelt pond edges all introduce discrete obstructions to the flow of air or water past the ice and are a source of form drag. In current climate models form drag is only accounted for by tuning the air–ice and ice–ocean drag coefficients, that is, by effectively altering the roughness length in a surface drag parameterization. The existing approach of the skin drag parameter tuning is poorly constrained by observations and fails to describe correctly the physics associated with the air–ice and ocean–ice drag. Here, the authors combine recent theoretical developments to deduce the total neutral form drag coefficients from properties of the ice cover such as ice concentration, vertical extent and area of the ridges, freeboard and floe draft, and the size of floes and melt ponds. The drag coefficients are incorporated into the Los Alamos Sea Ice Model (CICE) and show the influence of the new drag parameterization on the motion and state of the ice cover, with the most noticeable being a depletion of sea ice over the west boundary of the Arctic Ocean and over the Beaufort Sea. The new parameterization allows the drag coefficients to be coupled to the sea ice state and therefore to evolve spatially and temporally. It is found that the range of values predicted for the drag coefficients agree with the range of values measured in several regions of the Arctic. Finally, the implications of the new form drag formulation for the spinup or spindown of the Arctic Ocean are discussed.

The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism

Increased intake of dietary carbohydrate that is fermented in the colon by the microbiota has been reported to decrease body weight, although the mechanism remains unclear. Here we use in vivo11C-acetate and PET-CT scanning to show that colonic acetate crosses the blood–brain barrier and is taken up by the brain. Intraperitoneal acetate results in appetite suppression and hypothalamic neuronal activation patterning. We also show that acetate administration is associated with activation of acetyl-CoA carboxylase and changes in the expression profiles of regulatory neuropeptides that favour appetite suppression. Furthermore, we demonstrate through 13C high-resolution magic-angle-spinning that 13C acetate from fermentation of 13C-labelled carbohydrate in the colon increases hypothalamic 13C acetate above baseline levels. Hypothalamic 13C acetate regionally increases the 13C labelling of the glutamate–glutamine and GABA neuroglial cycles, with hypothalamic 13C lactate reaching higher levels than the ‘remaining brain’. These observations suggest that acetate has a direct role in central appetite regulation.

Pan-Arctic and regional sea ice predictability: initialization month dependence

Seasonal-to-interannual predictions of Arctic sea ice may be important for Arctic communities and industries alike. Previous studies have suggested that Arctic sea ice is potentially predictable but that the skill of predictions of the September extent minimum, initialized in early summer, may be low. The authors demonstrate that a melt season “predictability barrier” and two predictability reemergence mechanisms, suggested by a previous study, are robust features of five global climate models. Analysis of idealized predictions with one of these models [Hadley Centre Global Environment Model, version 1.2 (HadGEM1.2)], initialized in January, May and July, demonstrates that this predictability barrier exists in initialized forecasts as well. As a result, the skill of sea ice extent and volume forecasts are strongly start date dependent and those that are initialized in May lose skill much faster than those initialized in January or July. Thus, in an operational setting, initializing predictions of extent and volume in July has strong advantages for the prediction of the September minimum when compared to predictions initialized in May. Furthermore, a regional analysis of sea ice predictability indicates that extent is predictable for longer in the seasonal ice zones of the North Atlantic and North Pacific than in the regions dominated by perennial ice in the central Arctic and marginal seas. In a number of the Eurasian shelf seas, which are important for Arctic shipping, only the forecasts initialized in July have continuous skill during the first summer. In contrast, predictability of ice volume persists for over 2 yr in the central Arctic but less in other regions.

A Lab-in-a-briefcase for rapid prostate specific antigen (PSA) screening from whole blood

We present a new concept for rapid and fully portable Prostate Specific Antigen (PSA) measurement, termed “Lab-in-a-Briefcase”, which integrates an affordable microfluidic ELISA platform utilising a melt-extruded fluoropolymer Micro Capillary Film (MCF) containing 10 bore, 200 μm internal diameter capillaries, a disposable multi-syringe aspirator (MSA) plus a sample tray pre-loaded with all required immunoassay reagents, and a portable film scanner for colorimetric signal digital quantitation. Each MSA can perform 10 replicate microfluidic immunoassays on 8 samples, allowing 80measurements to be made in less than 15 minutes based on semi-automated operation and norequirement of additional fluid handling equipment. An assay was optimised for measurement of a clinically relevant range of PSA from 0.9 to 60.0 ng/ml in 15 minutes with CVs in the order of 5% based on intra-assay variability when read using a consumer flatbed film scanner. The PSA assay performance in the MSA remained robust in the presence of undiluted or 1:2 diluted human serum or whole blood, and the matrix effect could simply be overcome by extending sample incubation times. The PSA "Lab-in-a-briefcase" is particularly suited to a low-resource health setting where diagnostic labs and automated immunoassay systems are not accessible, by allowing PSA measurement outside the laboratory using affordable equipment.

Development of the Surface Urban Energy and Water balance Scheme (SUEWS) for cold climate cities

The Surface Urban Energy and Water Balance Scheme (SUEWS) is developed to include snow. The processes addressed include accumulation of snow on the different urban surface types: snow albedo and density aging, snow melting and re-freezing of meltwater. Individual model parameters are assessed and independently evaluated using long-term observations in the two cold climate cities of Helsinki and Montreal. Eddy covariance sensible and latent heat fluxes and snow depth observations are available for two sites in Montreal and one in Helsinki. Surface runoff from two catchments (24 and 45 ha) in Helsinki and snow properties (albedo and density) from two sites in Montreal are also analysed. As multiple observation sites with different land-cover characteristics are available in both cities, model development is conducted independent of evaluation. The developed model simulates snowmelt related runoff well (within 19% and 3% for the two catchments in Helsinki when there is snow on the ground), with the springtime peak estimated correctly. However, the observed runoff peaks tend to be smoother than the simulated ones, likely due to the water holding capacity of the catchments and the missing time lag between the catchment and the observation point in the model. For all three sites the model simulates the timing of the snow accumulation and melt events well, but underestimates the total snow depth by 18–20% in Helsinki and 29–33% in Montreal. The model is able to reproduce the diurnal pattern of net radiation and turbulent fluxes of sensible and latent heat during cold snow, melting snow and snow-free periods. The largest model uncertainties are related to the timing of the melting period and the parameterization of the snowmelt. The results show that the enhanced model can simulate correctly the exchange of energy and water in cold climate cities at sites with varying surface cover.

Assessing the sensitivities of a distributed snow model to forcing data resolution

Highly heterogeneous mountain snow distributions strongly affect soil moisture patterns; local ecology; and, ultimately, the timing, magnitude, and chemistry of stream runoff. Capturing these vital heterogeneities in a physically based distributed snow model requires appropriately scaled model structures. This work looks at how model scale—particularly the resolutions at which the forcing processes are represented—affects simulated snow distributions and melt. The research area is in the Reynolds Creek Experimental Watershed in southwestern Idaho. In this region, where there is a negative correlation between snow accumulation and melt rates, overall scale degradation pushed simulated melt to earlier in the season. The processes mainly responsible for snow distribution heterogeneity in this region—wind speed, wind-affected snow accumulations, thermal radiation, and solar radiation—were also independently rescaled to test process-specific spatiotemporal sensitivities. It was found that in order to accurately simulate snowmelt in this catchment, the snow cover needed to be resolved to 100 m. Wind and wind-affected precipitation—the primary influence on snow distribution—required similar resolution. Thermal radiation scaled with the vegetation structure (~100 m), while solar radiation was adequately modeled with 100–250-m resolution. Spatiotemporal sensitivities to model scale were found that allowed for further reductions in computational costs through the winter months with limited losses in accuracy. It was also shown that these modeling-based scale breaks could be associated with physiographic and vegetation structures to aid a priori modeling decisions.

Mesomorphic behaviour in copoly(ester-imide)s of poly(butylene-2,6-naphthalate) (PBN)

Copolycondensation of N,N’-bis(4-hydroxybutyl)-biphenyl-3,4,3',4'-tetracarboxylic diimide at 20 and 25 mol% with bis(4-hydroxybutyl)-2,6-naphthalate produces PBN-based copoly(ester-imide)s that not only crystallise but also form a (smectic) mesophase upon cooling from the melt. Incorporation of 25 mol% imide in PBN causes the glass transition temperature (measured by DSC) to rise from 51 to 74 °C, a significant increase relative to PBN. Furthermore, increased storage- (G'), loss- (G'') and elastic (E) moduli are observed for both copoly(ester-imide)s when compared to PBN itself. Structural analysis of the 20 mol% copolymer by X-ray powder and fibre diffraction, interfaced to computational modelling, suggests a crystal structure related to that of α-PBN, in space group P-1, with cell dimensions a = 4.74, b = 6.38, c = 14.45 Å, α = 106.1, β = 122.1, γ = 97.3°, ρ = 1.37 g cm-3.