Vertical structure and physical processes of the Madden-Julian oscillation: Linking hindcast fidelity to simulated diabatic heating and moistening

Many theories for the Madden-Julian oscillation (MJO) focus on diabatic processes, particularly the evolution of vertical heating and moistening. Poor MJO performance in weather and climate models is often blamed on biases in these processes and their interactions with the large-scale circulation. We introduce one of three components of a model-evaluation project, which aims to connect MJO fidelity in models to their representations of several physical processes, focusing on diabatic heating and moistening. This component consists of 20-day hindcasts, initialised daily during two MJO events in winter 2009-10. The 13 models exhibit a range of skill: several have accurate forecasts to 20 days' lead, while others perform similarly to statistical models (8-11 days). Models that maintain the observed MJO amplitude accurately predict propagation, but not vice versa. We find no link between hindcast fidelity and the precipitation-moisture relationship, in contrast to other recent studies. There is also no relationship between models' performance and the evolution of their diabatic-heating profiles with rain rate. A more robust association emerges between models' fidelity and net moistening: the highest-skill models show a clear transition from low-level moistening for light rainfall to mid-level moistening at moderate rainfall and upper-level moistening for heavy rainfall. The mid-level moistening, arising from both dynamics and physics, may be most important. Accurately representing many processes may be necessary, but not sufficient for capturing the MJO, which suggests that models fail to predict the MJO for a broad range of reasons and limits the possibility of finding a panacea.

Sialic acids in biological and therapeutic processes: opportunities and challenges

It is now well documented that carbohydrates play multiple roles in biological processes, and hence are interesting targets for chemical biology and medicinal chemistry programmes. This review focuses on a subset of carbohydrates, specifically sialic acid containing carbohydrates. It highlights their occurrence and diversity, and presents evidence for their roles in a range of biological pathways. It illustrates that they are targets for novel medicinal chemistry strategies for a range of therapeutic areas, including cancer and immunity. Case studies highlight opportunities and challenges in this area, and sialic acid based drugs that have entered clinical practice, and are promising candidates for future disease intervention schemes, are discussed. The review concludes by highlighting perspectives and emerging roles for these targets.

What controls the vertical distribution of aerosol? Relationships between process sensitivity in HadGEM3–UKCA and inter-model variation from AeroCom Phase II

The vertical profile of aerosol is important for its radiative effects, but weakly constrained by observations on the global scale, and highly variable among different models. To investigate the controlling factors in one particular model, we investigate the effects of individual processes in HadGEM3–UKCA and compare the resulting diversity of aerosol vertical profiles with the inter-model diversity from the AeroCom Phase II control experiment. In this way we show that (in this model at least) the vertical profile is controlled by a relatively small number of processes, although these vary among aerosol components and particle sizes. We also show that sufficiently coarse variations in these processes can produce a similar diversity to that among different models in terms of the global-mean profile and, to a lesser extent, the zonal-mean vertical position. However, there are features of certain models' profiles that cannot be reproduced, suggesting the influence of further structural differences between models. In HadGEM3–UKCA, convective transport is found to be very important in controlling the vertical profile of all aerosol components by mass. In-cloud scavenging is very important for all except mineral dust. Growth by condensation is important for sulfate and carbonaceous aerosol (along with aqueous oxidation for the former and ageing by soluble material for the latter). The vertical extent of biomass-burning emissions into the free troposphere is also important for the profile of carbonaceous aerosol. Boundary-layer mixing plays a dominant role for sea salt and mineral dust, which are emitted only from the surface. Dry deposition and below-cloud scavenging are important for the profile of mineral dust only. In this model, the microphysical processes of nucleation, condensation and coagulation dominate the vertical profile of the smallest particles by number (e.g. total CN  >  3 nm), while the profiles of larger particles (e.g. CN  >  100 nm) are controlled by the same processes as the component mass profiles, plus the size distribution of primary emissions. We also show that the processes that affect the AOD-normalised radiative forcing in the model are predominantly those that affect the vertical mass distribution, in particular convective transport, in-cloud scavenging, aqueous oxidation, ageing and the vertical extent of biomass-burning emissions.

The release of silicon from amorphous silica and rice straw in Sri Lankan soils

Silicon release from rice straw and amorphous silica when shaken in solution with five Sri Lankan soils was studied indirectly using sorption isotherms and changes in concentration and directly using straw in dialysis bags examined using electron microscopy. The aim was to further our understanding of the processes and factors affecting the release of straw-Si in soils and its availability to rice. The soils (alfisols and ultisols) shaken with 0.1 M NaCl (5 g per 125 mL for 250 days) produced concentrations of 1 - 4 mg L-1 of monosilicic acid-Si. Amorphous silica added to these suspensions (36.5 mg, containing 17 mg Si) raised the concentrations to 20 - 40 mg L-1, and added rice straw (0.5 g, containing 17 mg Si) gave 10 - 25 mg L-1. Sorption isotherms (7 days equilibrations) were used to calculate from the concentrations the amounts of Si released ( 24 - 38% and 8 - 21%, respectively). Both materials gave about 40 mg L-1 of monosilicic acid-Si plus 30 mg L-1 of disilicic acid-Si when shaken in solution alone (5 g per 125 mL). Straw in dialysis bags ( 0.5 g per 25 mL in 0.1 M NaCl) was shaken in soil suspension ( 5 g per 100 mL) for 60 days. Similar concentrations and releases were measured to those obtained above. About one fifth of the mass of straw was lost by decomposition in the first 15 days. A chloroform treatment prevented decomposition, but Si release was unaffected. Disintegration continued throughout the experiments, with phytoliths being exposed and dissolved. Compared to the rate of release from straw into solution without soil, the release of Si into soil suspensions was increased during the first 20 days by adsorption on the soil, but was then reduced probably through the effect of Fe and Al on the phytolith surfaces. The extent of this blocking effect varied between soils and was not simply related to soil pH.

A geomatics-based approach for the derivation of the spatial distribution of sediment transport processes in periglacial mountain environments

Within this paper modern techniques such as satellite image analysis and tools provided by geographic information systems (GIS.) are exploited in order to extend and improve existing techniques for mapping the spatial distribution of sediment transport processes. The processes of interest comprise mass movements such as solifluction, slope wash, dirty avalanches and rock- and boulder falls. They differ considerably in nature and therefore different approaches for the derivation of their spatial extent are required. A major challenge is addressing the differences between the comparably coarse resolution of the available satellite data (Landsat TM/ETM+, 30 in x 30 m) and the actual scale of sediment transport in this environment. A three-stepped approach has been developed which is based on the concept of Geomorphic Process Units (GPUs): parameterization, process area delineation and combination. Parameters include land cover from satellite data and digital elevation model derivatives. Process areas are identified using a hierarchical classification scheme utilizing thresholds and definition of topology. The approach has been developed for the Karkevagge in Sweden and could be successfully transferred to the Rabotsbekken catchment at Okstindan, Norway using similar input data. Copyright (C) 2008 John Wiley & Sons, Ltd.

Dust production and the release of iron oxides resulting from the aeolian abrasion of natural dune sands

Global dust trajectories indicate that significant quantities of aeolian-transported iron oxides originate in contemporary dryland areas. One potential source is the iron-rich clay coatings that characterize many sand-sized particles in desert dunefields. This paper uses laboratory experiments to determine the rate at which these coatings can be removed from dune sands by aeolian abrasion. The coatings impart a red colour to the grains to which previous researchers have assigned variable geomorphological significance. The quantities or iron removed during a 120 hour abrasion experiment are small (99 mg kg(-1)) and difficult to detect by eye; however, high resolution spectroscopy clearly indicates that ferric oxides are released during abrasion and the reflectance of the particles alters. One of the products of aeolian abrasion is fine particles (<10 mum diameter) with the potential for long distance transport. Copyright (C) 2004 John Wiley Sons, Ltd.

The effect of aqueous diffusion on the fractionation of chlorine and bromine stable isotopes

Diffusive isotopic fractionation factors are important in order to understand natural processes and have practical application in radioactive waste storage and carbon dioxide sequestration. We determined the isotope fractionation factors and the effective diffusion coefficients of chloride and bromide ions during aqueous diffusion in polyacrylamide gel. Diffusion was determined as functions of temperature, time and concentration. The effect of temperature is relatively large on the diffusion coefficient (D) but only small on isotope fractionation. For chlorine, the ratio, D-35cl/D-37cl varied from 1.00128 +/- 0.00017 (1 sigma) at 2 degrees C to 1.00192 +/- 0.00015 at 80 degrees C. For bromine, D-79Br/D-81Br varied from 1.00098 +/- 0.00009 at 2 degrees C to 1.0064 +/- 0.00013 at 21 degrees C and 1.00078 +/- 0.00018 (1 sigma) at 80 degrees C. There were no significant effects on the isotope fractionation due to concentration. The lack of sensitivity of the diffusive isotope fractionation to anything at the most common temperatures (0 to 30 C) makes it particularly valuable for application to understanding processes in geological environments and an important natural tracer in order to understand fluid transport processes. (C) 2009 Elsevier Ltd. All rights reserved.

Catchment-scale modelling of flow and nutrient transport in the Chalk unsaturated zone

The unsaturated zone exerts a major control on the delivery of nutrients to Chalk streams, yet flow and transport processes in this complex, dual-porosity medium have remained controversial. A major challenge arises in characterising these processes, both at the detailed mechanistic level and at an appropriate level for inclusion within catchment-scale models for nutrient management. The lowland catchment research (LOCAR) programme in the UK has provided a unique set of comprehensively instrumented groundwater-dominated catchments. Of these, the Pang and Lambourn, tributaries of the Thames near Reading, have been a particular focus for research into subsurface processes and surface water-groundwater interactions. Data from LOCAR and other sources, along with a new dual permeability numerical model of the Chalk, have been used to explore the relative roles of matrix and fracture flow within the unsaturated zone and resolve conflicting hypotheses of response. From the improved understanding gained through these explorations, a parsimonious conceptualisation of the general response of flow and transport within the Chalk unsaturated zone was formulated. This paper summarises the modelling and data findings of these explorations, and describes the integration of the new simplified unsaturated zone representation with a catchment-scale model of nutrients (INCA), resulting in a new model for catchment-scale flow and transport within Chalk systems: INCA-Chalk. This model is applied to the Lambourn, and results, including hindcast and forecast simulations, are presented. These clearly illustrate the decadal time-scales that need to be considered in the context of nutrient management and the EU Water Framework Directive. (C) 2007 Elsevier B.V. All rights reserved.

The role of calcite and gypsum in the leaching of potassium in a sandy soil

Pulses of potassium (K+) applied to columns of repacked calcium (Ca2+) saturated soil were leached with distilled water or calcium chloride (CaCl2) solutions of various concentrations at a rate of 12 mm h(-1). With increased Ca2+ concentration, the rate of movement of K+ increased, as did the concentration of K+ in the displaced pulse, which was less dispersed. The movement of K+ in calcite-amended soil leached with water was at a similar rate to that of the untreated soil leached with 1 mM CaCl2, and in soil containing gypsum, movement was similar to that leached with 15 mM CaCl2. The Ca2+ concentrations in the leachates were about 0.4 and 15 mM respectively the expected values for the dissolution of the two amendments. Soil containing native K+ was leached with distilled water or CaCl2 solutions. The amount of K+ leached increased as Ca2+ concentration increased, with up to 34% of the exchangeable K+ being removed in five pore volumes of 15 mM CaCl2. Soil amended with calcite and leached with water lost K+ at a rate between that for leaching the unamended soil with 1 mM CaCl2 and that with water. Soil containing gypsum and leached with water lost K+ at a similar rate to unamended soil leached with 15 mM CaCl2. The presence of Ca2+ in irrigation water and of soil minerals able to release Ca2+ are of importance in determining the amounts of K+ leached from soils. The LEACHM model predicted approximately the displacement of K+, and was more accurate with higher concentrations of displacing solution. The shortcomings of this model are its inability to account for rate-controlled processes and the assumption that K+:Ca2+ exchange during leaching can be described using a constant adsorption coefficient. As a result, the pulse is predicted to appear a little earlier and the following edge has less of a tail than chat measured. In practical agriculture, the model will be more useful in soils containing gypsum or leached with saline water than in either calcareous or non-calcareous soils leached with rainwater.

Assessing the sources and magnitude of diurnal nitrate variability in the San Joaquin River (California) with an in-situ optical nitrate sensor and dual nitrate isotopes

We investigated diurnal nitrate (NO3-) concentration variability in the San Joaquin River using an in situ optical NO3- sensor and discrete sampling during a 5-day summer period characterized by high algal productivity. Dual NO3- isotopes (delta N-15(NO3) and delta O-18(NO3)) and dissolved oxygen isotopes (delta O-18(DO)) were measured over 2 days to assess NO3- sources and biogeochemical controls over diurnal time-scales. Concerted temporal patterns of dissolved oxygen (DO) concentrations and delta O-18(DO) were consistent with photosynthesis, respiration and atmospheric O-2 exchange, providing evidence of diurnal biological processes independent of river discharge. Surface water NO3- concentrations varied by up to 22% over a single diurnal cycle and up to 31% over the 5-day study, but did not reveal concerted diurnal patterns at a frequency comparable to DO concentrations. The decoupling of delta N-15(NO3) and delta O-18(NO3) isotopes suggests that algal assimilation and denitrification are not major processes controlling diurnal NO3- variability in the San Joaquin River during the study. The lack of a clear explanation for NO3- variability likely reflects a combination of riverine biological processes and time-varying physical transport of NO3- from upstream agricultural drains to the mainstem San Joaquin River. The application of an in situ optical NO3- sensor along with discrete samples provides a view into the fine temporal structure of hydrochemical data and may allow for greater accuracy in pollution assessment.

Use of bone meal amendments to immobilise Pb, Zn and Cd in soil: A leaching column study

The aim of this study is to test the stabilisation of metals in contaminated soils via the formation of low-solubility metal phosphates. Bone apatite, in the form of commercially available bone meal, was tested as a phosphate source on a mine waste contaminated made-ground with high levels of Pb, Zn and Cd. Triplicate leaching columns were set up at bone meal to soil ratios of 1:25 and 1:10, in addition to unamended controls, and were run for 18 months. The columns were irrigated daily with a synthetic rain solution at pH of 2, 3, and 4.4. After 100 days, the leachate Pb, Zn and Cd concentrations of all amended columns were significantly reduced. For 1:10 treatments, release of these metals was suppressed throughout the trial. For 1:25 treatments, Zn and Cd concentrations in the leachates began to increase after 300 days. DTPA and water extractions showed that Pb and Cd were more strongly held in the amended soils. This study concludes that the complexity of soil processes and the small quantities of metals sequestered precluded determination of a metal immobilisation mechanism. (c) 2006 Elsevier Ltd. All rights reserved.

Evolution of late glacial ice-marginal lakes on the northwestern Canadian Shield and their influence on the location of the Dubawnt Lake palaeo-ice stream

During deglaciation of the North American Laurentide Ice Sheet large proglacial lakes developed in positions where proglacial drainage was impeded by the ice margin. For some of these lakes, it is known that subsequent drainage had an abrupt and widespread impact on North Atlantic Ocean circulation and climate, but less is known about the impact that the lakes exerted on ice sheet dynamics. This paper reports palaeogeographic reconstructions of the evolution of proglacial lakes during deglaciation across the northwestern Canadian Shield, covering an area in excess of 1,000,000 km(2) as the ice sheet retreated some 600 km. The interactions between proglacial lakes and ice sheet flow are explored, with a particular emphasis on whether the disposition of lakes may have influenced the location of the Dubawnt Lake ice stream. This ice stream falls outside the existing paradigm for ice streams in the Laurentide Ice Sheet because it did not operate over fined-grained till or lie in a topographic trough. Ice margin positions and a digital elevation model are utilised to predict the geometry and depth of proglacial takes impounded at the margin at 30-km increments during deglaciation. Palaeogeographic reconstructions match well with previous independent estimates of lake coverage inferred from field evidence, and results suggest that the development of a deep lake in the Thelon drainage basin may have been influential in initiating the ice stream by inducing calving, drawing down ice and triggering fast ice flow. This is the only location alongside this sector of the ice sheet where large (>3000 km(2)), deep lakes (similar to120 m) are impounded for a significant length of time and exactly matches the location of the ice stream. It is speculated that the commencement of calving at the ice sheet margin may have taken the system beyond a threshold and was sufficient to trigger rapid motion but that once initiated, calving processes and losses were insignificant to the functioning of the ice stream. It is thus concluded that proglacial lakes are likely to have been an important control on ice sheet dynamics during deglaciation of the Laurentide Ice Sheet. (C) 2004 Elsevier B.V. All rights reserved.

Mineral and geochemical characterization of a leptic aluandic soil and a thapto aluandic-ferralsol developed on trachytes in Mount Bambouto (Cameroon volcanic line)

Mineral and geochemical investigations were carried out on soil samples and fresh rock (trachytes) from two selected soil profiles (TM profile on leptic aluandic soils and TL profile on thapto aluandic-ferralsols) from Mount Bambouto to better understand geochemical processes and mineral paragenesis involved in the development of soils in this environment. In TM profile, the hydrated halloysites and goethite occur in the weathered saprolite boulders of BC horizon while dehydrated halloysite, gibbsite and goethite dominate the soils matrices of BC and A horizons. In TL profile, the dehydrated halloysites and goethite are the most abundant secondary minerals in the weathered saprolites of C and BC horizons while gibbsite, hematite and kaolinite occur in the soil matrices of BC, B and A horizons. The highest gibbsite content is in the platy nodules of B horizon. In both soil profiles, organo-metal complexes (most likely of AI and Fe) are present in the surface A horizon. Geochemically, between the fresh rock and the weathered saprolites in both soils, SiO2, K2O, CaO, Na2O and MgO contents decrease strongly while Fe2O3 and Al2O3 tend to accumulate. The molar ratio of SiO2/Al2O3 (Ki) and the sum of Ca, Mg, K and Na ions (TRB) also decreases abruptly between fresh rocks and the weathered saprolites, but increases significantly at the soil surface. The TM profile shows intense Al enrichment whereas the TL profile highlights enrichment in both AI and Fe as the weathering progresses upwards. Both soil profiles are enriched in Ni, Cu, Ba and Co and depleted in U, Th, Ta, Hf, Y, Sr, Pb, Zr and Zn relative to fresh rock. They also show a relatively low fractionation of the rare earth elements (REE: La, Nd, Sm, Eu, Tb, Yb and Lu), except for Ce which tends to be enriched in soils compared to CI chondrite. All these results give evidence of intense hydrolysis at soil deep in Mount Bambouto resulting in the formation of halloysite which progressively transforms into gibbsite and/or dehydrated halloysite. At the soil surface, the prominent pedogenetic process refers to andosolization with formation of organo-metal complexes. In TL profile, the presence of kaolinite in soil matrices BC and B horizons is consistent with ferralitization at soil deep. In conclusion, soil forming processes in Mount Bambouto are strongly influenced by local climate: (i) in the upper mountain (>2000 m), the fresh, misty and humid climate favors andosolization; whereas (ii) in the middle lands (1700-2000 m) with a relatively dry climate, both andosolization at the soil surface and ferralitization at soil deep act together. (C) 2009 Elsevier B.V. All rights reserved.

The release of silicon from amorphous silica and rice straw in Sri Lankan soils

Silicon release from rice straw and amorphous silica when shaken in solution with five Sri Lankan soils was studied indirectly using sorption isotherms and changes in concentration and directly using straw in dialysis bags examined using electron microscopy. The aim was to further our understanding of the processes and factors affecting the release of straw-Si in soils and its availability to rice. The soils (alfisols and ultisols) shaken with 0.1 M NaCl (5 g per 125 mL for 250 days) produced concentrations of 1 - 4 mg L-1 of monosilicic acid-Si. Amorphous silica added to these suspensions (36.5 mg, containing 17 mg Si) raised the concentrations to 20 - 40 mg L-1, and added rice straw (0.5 g, containing 17 mg Si) gave 10 - 25 mg L-1. Sorption isotherms (7 days equilibrations) were used to calculate from the concentrations the amounts of Si released ( 24 - 38% and 8 - 21%, respectively). Both materials gave about 40 mg L-1 of monosilicic acid-Si plus 30 mg L-1 of disilicic acid-Si when shaken in solution alone (5 g per 125 mL). Straw in dialysis bags ( 0.5 g per 25 mL in 0.1 M NaCl) was shaken in soil suspension ( 5 g per 100 mL) for 60 days. Similar concentrations and releases were measured to those obtained above. About one fifth of the mass of straw was lost by decomposition in the first 15 days. A chloroform treatment prevented decomposition, but Si release was unaffected. Disintegration continued throughout the experiments, with phytoliths being exposed and dissolved. Compared to the rate of release from straw into solution without soil, the release of Si into soil suspensions was increased during the first 20 days by adsorption on the soil, but was then reduced probably through the effect of Fe and Al on the phytolith surfaces. The extent of this blocking effect varied between soils and was not simply related to soil pH.

Modelling monsoons: understanding and predicting current and future behaviour

The global monsoon system is so varied and complex that understanding and predicting its diverse behaviour remains a challenge that will occupy modellers for many years to come. Despite the difficult task ahead, an improved monsoon modelling capability has been realized through the inclusion of more detailed physics of the climate system and higher resolution in our numerical models. Perhaps the most crucial improvement to date has been the development of coupled ocean-atmosphere models. From subseasonal to interdecadal time scales, only through the inclusion of air-sea interaction can the proper phasing and teleconnections of convection be attained with respect to sea surface temperature variations. Even then, the response to slow variations in remote forcings (e.g., El Niño—Southern Oscillation) does not result in a robust solution, as there are a host of competing modes of variability that must be represented, including those that appear to be chaotic. Understanding the links between monsoons and land surface processes is not as mature as that explored regarding air-sea interactions. A land surface forcing signal appears to dominate the onset of wet season rainfall over the North American monsoon region, though the relative role of ocean versus land forcing remains a topic of investigation in all the monsoon systems. Also, improved forecasts have been made during periods in which additional sounding observations are available for data assimilation. Thus, there is untapped predictability that can only be attained through the development of a more comprehensive observing system for all monsoon regions. Additionally, improved parameterizations - for example, of convection, cloud, radiation, and boundary layer schemes as well as land surface processes - are essential to realize the full potential of monsoon predictability. A more comprehensive assessment is needed of the impact of black carbon aerosols, which may modulate that of other anthropogenic greenhouse gases. Dynamical considerations require ever increased horizontal resolution (probably to 0.5 degree or higher) in order to resolve many monsoon features including, but not limited to, the Mei-Yu/Baiu sudden onset and withdrawal, low-level jet orientation and variability, and orographic forced rainfall. Under anthropogenic climate change many competing factors complicate making robust projections of monsoon changes. Absent aerosol effects, increased land-sea temperature contrast suggests strengthened monsoon circulation due to climate change. However, increased aerosol emissions will reflect more solar radiation back to space, which may temper or even reduce the strength of monsoon circulations compared to the present day. Precipitation may behave independently from the circulation under warming conditions in which an increased atmospheric moisture loading, based purely on thermodynamic considerations, could result in increased monsoon rainfall under climate change. The challenge to improve model parameterizations and include more complex processes and feedbacks pushes computing resources to their limit, thus requiring continuous upgrades of computational infrastructure to ensure progress in understanding and predicting current and future behaviour of monsoons.