Over-parameterised, uncertain 'mathematical marionettes' - How can we best use catchment water quality models? An example of an 80-year catchment-scale nutrient balance

The Integrated Catchment Model of Nitrogen (INCA-N) was applied to the River Lambourn, a Chalk river-system in southern England. The model's abilities to simulate the long-term trend and seasonal patterns in observed stream water nitrate concentrations from 1920 to 2003 were tested. This is the first time a semi-distributed, daily time-step model has been applied to simulate such a long time period and then used to calculate detailed catchment nutrient budgets which span the conversion of pasture to arable during the late 1930s and 1940s. Thus, this work goes beyond source apportionment and looks to demonstrate how such simulations can be used to assess the state of the catchment and develop an understanding of system behaviour. The mass-balance results from 1921, 1922, 1991, 2001 and 2002 are presented and those for 1991 are compared to other modelled and literature values of loads associated with nitrogen soil processes and export. The variations highlighted the problem of comparing modelled fluxes with point measurements but proved useful for identifying the most poorly understood inputs and processes thereby providing an assessment of input data and model structural uncertainty. The modelled terrestrial and instream mass-balances also highlight the importance of the hydrological conditions in pollutant transport. Between 1922 and 2002, increased inputs of nitrogen from fertiliser, livestock and deposition have altered the nitrogen balance with a shift from possible reduction in soil fertility but little environmental impact in 1922, to a situation of nitrogen accumulation in the soil, groundwater and instream biota in 2002. In 1922 and 2002 it was estimated that approximately 2 and 18 kg N ha(-1) yr(-1) respectively were exported from the land to the stream. The utility of the approach and further considerations for the best use of models are discussed. (C) 2008 Elsevier B.V. All rights reserved.

Radiative forcing since preindustrial times due to ozone change in the troposphere and the lower stratosphere

Changes in atmospheric ozone have occurred since the preindustrial era as a result of increasing anthropogenic emissions. Within ACCENT, a European Network of Excellence, ozone changes between 1850 and 2000 are assessed for the troposphere and the lower stratosphere ( up to 30 km) by a variety of seven chemistry-climate models and three chemical transport models. The modeled ozone changes are taken as input for detailed calculations of radiative forcing. When only changes in chemistry are considered ( constant climate) the modeled global-mean tropospheric ozone column increase since preindustrial times ranges from 7.9 DU to 13.8 DU among the ten participating models, while the stratospheric column reduction lies between 14.1 DU and 28.6 DU in the models considering stratospheric chemistry. The resulting radiative forcing is strongly dependent on the location and altitude of the modeled ozone change and varies between 0.25 Wm(-2) and 0.45 Wm(-2) due to ozone change in the troposphere and - 0.123 Wm(-2) and + 0.066 Wm(-2) due to the stratospheric ozone change. Changes in ozone and other greenhouse gases since preindustrial times have altered climate. Six out of the ten participating models have performed an additional calculation taking into account both chemical and climate change. In most models the isolated effect of climate change is an enhancement of the tropospheric ozone column increase, while the stratospheric reduction becomes slightly less severe. In the three climate-chemistry models with detailed tropospheric and stratospheric chemistry the inclusion of climate change increases the resulting radiative forcing due to tropospheric ozone change by up to 0.10 Wm(-2), while the radiative forcing due to stratospheric ozone change is reduced by up to 0.034 Wm(-2). Considering tropospheric and stratospheric change combined, the total ozone column change is negative while the resulting net radiative forcing is positive.

Observation and origin of an interannual salinity anomaly in the Mozambique Channel

A positive salinity anomaly of 0.2 PSU was observed between 50 and 200 m over the years 2000–2001 across the Mozambique Channel at a section at 17°S which was repeated in 2003, 2005, 2006, and 2008. Meanwhile, a moored array is continued from 2003 to 2008. This anomaly was most distinct showing an interannual but nonseasonal variation. The possible origin of the anomaly is investigated using output from three ocean general circulation models (Estimating the Circulation and Climate of the Ocean, Ocean Circulation and Climate Advanced Modeling, and Parallel Ocean Program). The most probable mechanism for the salinity anomaly is the anomalous inflow of subtropical waters caused by a weakening of the northern part of the South Equatorial Current by weaker trade winds. This mechanism was found in all three numerical models. In addition, the numerical models indicate a possible salinization of one of the source water masses to the Mozambique Channel as an additional cause of the anomaly. The anomaly propagated southward into the Agulhas Current and northward along the African coast.

An integrative model of amino acid metabolism in the liver of the lactating dairy cow

The objective of this work was to construct a dynamic model of hepatic amino acid metabolism in the lactating dairy cow that could be parameterized using net flow data from in vivo experiments. The model considers 22 amino acids, ammonia, urea, and 13 energetic metabolites, and was parameterized using a steady-state balance model and two in vivo, net flow experiments conducted with mid-lactation dairy cows. Extracellular flows were derived directly from the observed data. An optimization routine was used to derive nine intracellular flows. The resulting dynamic model was found to be stable across a range of inputs suggesting that it can be perturbed and applied to other physiological states. Although nitrogen was generally in balance, leucine was in slight deficit compared to predicted needs for export protein synthesis, suggesting that an alternative source of leucine (e.g. peptides) was utilized. Simulations of varying glucagon concentrations indicated that an additional 5 mol/d of glucose could be synthesized at the reference substrate concentrations and blood flows. The increased glucose production was supported by increased removal from blood of lactate, glutamate, aspartate, alanine, asparagine, and glutamine. As glucose Output increased, ketone body and acetate release increased while CO2 release declined. The pattern of amino acids appearing in hepatic vein blood was affected by changes in amino acid concentration in portal vein blood, portal blood flow rate and glucagon concentration, with methionine and phenylalanine being the most affected of essential amino acids. Experimental evidence is insufficient to determine whether essential amino acids are affected by varying gluconeogenic demands. (C) 2004 Published by Elsevier Ltd.

Lymph heart in chick - somitic origin, development and embryonic oedema

The lymph heart is a sac-like structure on either side of avian tail. In some adult birds, it empties the lymph from the copulatory organ; however, during embryonic development, it is thought to circulate extra-embryonic lymph. Very little is known about the origin, innervation and the cellular changes it undergoes during development. Using immunohistochemistry and gene expression profiling we show that the musculature of the lymph heart is initially composed solely of striated skeletal muscle but later develops an additional layer composed of smooth myofibroblasts. Chick-quail fate-mapping demonstrates that the lymph heart originates from the hypaxial compartments of somites 34-41. The embryonic lymph heart is transiently innervated by somatic motoneurons with no autonomic input. In comparison to body muscles, the lymph heart has different sensitivity to neuromuscular junction blockers (sensitive only to decamethonium). Furthermore, its abundant bungarotoxin-positive acetylcholinesterase receptors are unique as they completely lack specific acetylcholinesterase activity. Several lines of evidence suggest that the lymph heart may possess an intrinsic pacing mechanism. Finally, we assessed the function of the lymph heart during embryogenesis and demonstrate that it is responsible for preventing embryonic oedema in birds, a role previously thought to be played by body skeletal muscle contractions.

An enhanced microsatellite map of diploid Fragaria

A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. × ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F2 mapping population (FV×FN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes of known function, for comparative mapping purposes within Rosaceae.

Supramolecular beta-sheet and nanofibril formation by self-assembling tripeptides containing an N-terminally located gamma-aminobutyric acid residue

Three terminally protected tripeptides Boc-gamma-Abu-Val-Leu-OMe 1, Boc-gamma-Abu-Leu-Phe-OMe 2 and Boc-gamma-Abu-Val-Tyr-OMe 3 (gamma-Abu = gamma-aminobutyric acid) each containing an N-terminally positioned gamma-aminobutyric acid residue have been synthesized, purified and studied. FT-IR studies of all these peptides revealed that these peptides form intermolecularly hydrogen bonded supramolecular beta-sheet structures. Peptides 1, 2 and 3 adopt extended backbone beta-strand molecular structures in crystals. Crystal packing of all these peptides demonstrates that these beta-strand structures self-assemble to form intermolecularly H-bonded parallel beta-sheet structures. Peptide 3 uses a side chain tyrosyl -OH group as an additional hydrogen bonding functionality in addition to the backbone CONH groups to pack in crystals. Transmission electron microscopic studies of all peptides indicate that they self-assemble to form nanofibrillar structures of an average diameter of 65 nm. These peptide fibrils exhibit amyloid-like behavior as they bind to a physiological dye Congo red and show a characteristic green-gold birefringence under polarizing microscope.

An attempt to extend human sensory capabilities by means of implant technology

In this paper an attempt is described to increase the range of human sensory capabilities by means of implant technology. The key aim is to create an additional sense by feeding signals directly to the human brain, via the nervous system rather than via a presently operable human sense. Neural implant technology was used to directly interface a human nervous system with a computer in a one off trial. The output from active ultrasonic sensors was then employed to directly stimulate the human nervous system. An experimental laboratory set up was used as a test bed to assess the usefulness of this sensory addition.

Non-word repetition in adolescents with Specific Language Impairment and Autism plus Language Impairments: a qualitative analysis

Non-word repetition (NWR) was investigated in adolescents with typical development, Specific Language Impairment (SLI) and Autism Plus language Impairment (ALI) (n = 17, 13, 16, and mean age 14;4, 15;4, 14;8 respectively). The study evaluated the hypothesis that poor NWR performance in both groups indicates an overlapping language phenotype (Kjelgaard & Tager-Flusberg, 2001). Performance was investigated both quantitatively, e.g. overall error rates, and qualitatively, e.g. effect of length on repetition, proportion of errors affecting phonological structure, and proportion of consonant substitutions involving manner changes. Findings were consistent with previous research (Whitehouse, Barry, & Bishop, 2008) demonstrating a greater effect of length in the SLI group than the ALI group, which may be due to greater short-term memory limitations. In addition, an automated count of phoneme errors identified poorer performance in the SLI group than the ALI group. These findings indicate differences in the language profiles of individuals with SLI and ALI, but do not rule out a partial overlap. Errors affecting phonological structure were relatively frequent, accounting for around 40% of phonemic errors, but less frequent than straight Consonant-for-Consonant or vowel-for-vowel substitutions. It is proposed that these two different types of errors may reflect separate contributory mechanisms. Around 50% of consonant substitutions in the clinical groups involved manner changes, suggesting poor auditory-perceptual encoding. From a clinical perspective algorithms which automatically count phoneme errors may enhance sensitivity of NWR as a diagnostic marker of language impairment. Learning outcomes: Readers will be able to (1) describe and evaluate the hypothesis that there is a phenotypic overlap between SLI and Autism Spectrum Disorders (2) describe differences in the NWR performance of adolescents with SLI and ALI, and discuss whether these differences support or refute the phenotypic overlap hypothesis, and (3) understand how computational algorithms such as the Levenshtein Distance may be used to analyse NWR data.

Impact of the quantity and flavonoid content of fruits and vegetables on markers of intake in adults with an increased risk of cardiovascular disease: the FLAVURS Trial

Purpose Limited robust randomised controlled trials investigating fruit and vegetable (F&V) intake in people at risk of cardiovascular disease (CVD) exist. We aimed to design and validate a dietary strategy of increasing flavonoid-rich versus flavonoid-poor F&V consumption on nutrient biomarker profile. Methods A parallel, randomised, controlled, dose–response dietary intervention study. Participants with a CVD relative risk of 1.5 assessed by risk scores were randomly assigned to one of the 3 groups: habitual (control, CT), high-flavonoid (HF) or low-flavonoid (LF) diets. While the CT group (n = 57) consumed their habitual diet throughout, the HF (n = 58) and LF (n = 59) groups sequentially increased their daily F&V intake by an additional 2, 4 and 6 portions for 6-week periods during the 18-week study. Results Compliance to target numbers and types of F&V was broadly met and verified by dietary records, and plasma and urinary biomarkers. Mean (±SEM) number of F&V portions/day consumed by the HF and LF groups at baseline (3.8 ± 0.3 and 3.4 ± 0.3), 6 weeks (6.3 ± 0.4 and 5.8 ± 0.3), 12 weeks (7.0 ± 0.3 and 6.8 ± 0.3) and 18 weeks (7.6 ± 0.4 and 8.1 ± 0.4), respectively, was similar at baseline yet higher than the CT group (3.9 ± 0.3, 4.3 ± 0.3, 4.6 ± 0.4, 4.5 ± 0.3) (P = 0.015). There was a dose-dependent increase in dietary and urinary flavonoids in the HF group, with no change in other groups (P = 0.0001). Significantly higher dietary intakes of folate (P = 0.035), non-starch polysaccharides (P = 0.001), vitamin C (P = 0.0001) and carotenoids (P = 0.0001) were observed in both intervention groups compared with CT, which were broadly supported by nutrient biomarker analysis. Conclusions The success of improving nutrient profile by active encouragement of F&V intake in an intervention study implies the need for a more hands-on public health approach.

The property development industry and sustainable urban brownfield regeneration in England: an analysis of case studies in Thames Gateway and Greater Manchester

The property development industry is a key actor in UK brownfield regeneration projects. UK policy has attempted to interlink ‘sustainable development’ and ‘sustainable brownfield’ policy agendas, which have found an additional focus through the UK government’s ‘Sustainable Communities Plan’, part of a growing international emphasis on sustainable development. This paper examines the emergence of these agendas and related policies, and the role of the property development industry in the regeneration of six differing brownfield sites, based in Thames Gateway and Greater Manchester. Using a conceptual framework, the paper investigates aspects of the sustainability of these projects and highlights key lessons from them for both the UK and overseas. The research is based on structured interviews with a variety of stakeholders, including developers, planners, consultants and community representatives to highlight emerging best practice and related policy implications.

L2 performance and context of language learning: a comparative study of learners in Tehran and London

The importance of learning context has stirred debates in the field of second language acquisition over the past two decades since studying a second language (L2) abroad is believed to provide authentic opportunities that facilitate L2 acquisition and development. The present paper examines whether language performance of learners studying English in a formal language classroom context at home (AH) is different from performance of learners who study English abroad (SA) where they would have to use English for a range of communicative purposes. The data for this comparative study is part of a larger corpus of L2 performance of 100 learners of English, 60 in Tehran and 40 in London, on four oral narrative tasks. The two groups’ performances are compared on a range of different measures of fluency, accuracy, syntactic complexity and lexical diversity. The results of the analyses indicate that learners in the two contexts are very similar with respect to the grammatical accuracy and aspects of the oral fluency of their performance. However, the SA group appears to have benefited from living and studying abroad in producing language of higher syntactic complexity and lexical diversity. These results have significant implications for language teaching in AH contexts.

Motion event cognition and grammatical aspect: evidence from Afrikaans

Research on the relationship between grammatical aspect and motion event construal has posited that speakers of non-aspect languages are more prone to encoding event endpoints than are speakers of aspect languages (e.g., von Stutterheim and Carroll 2011). In the present study, we test this hypothesis by extending this line of inquiry to Afrikaans, a non-aspect language which is previously unexplored in this regard. Motion endpoint behavior among Afrikaans speakers was measured by means of a linguistic retelling task and a non-linguistic similarity judgment task, and then compared with the behavior of speakers of a non-aspect language (Swedish) and speakers of an aspect language (English). Results showed the Afrikaans speakers' endpoint patterns aligned with Swedish patterns, but were significantly different from English patterns. It was also found that the variation among the Afrikaans speakers could be partially explained by taking into account their frequency of use of English, such that those who used English more frequently exhibited an endpoint behavior that was more similar to English speakers. The current study thus lends further support to the hypothesis that speakers of different languages attend differently to event endpoints as a function of the grammatical category of aspect.

Extended optimal estimation techniques for sea surface temperature from the Spinning Enhanced Visible and Infra-Red Imager (SEVIRI)

Sea surface temperature (SST) can be estimated from day and night observations of the Spinning Enhanced Visible and Infra-Red Imager (SEVIRI) by optimal estimation (OE). We show that exploiting the 8.7 μm channel, in addition to the “traditional” wavelengths of 10.8 and 12.0 μm, improves OE SST retrieval statistics in validation. However, the main benefit is an improvement in the sensitivity of the SST estimate to variability in true SST. In a fair, single-pixel comparison, the 3-channel OE gives better results than the SST estimation technique presently operational within the Ocean and Sea Ice Satellite Application Facility. This operational technique is to use SST retrieval coefficients, followed by a bias-correction step informed by radiative transfer simulation. However, the operational technique has an additional “atmospheric correction smoothing”, which improves its noise performance, and hitherto had no analogue within the OE framework. Here, we propose an analogue to atmospheric correction smoothing, based on the expectation that atmospheric total column water vapour has a longer spatial correlation length scale than SST features. The approach extends the observations input to the OE to include the averaged brightness temperatures (BTs) of nearby clear-sky pixels, in addition to the BTs of the pixel for which SST is being retrieved. The retrieved quantities are then the single-pixel SST and the clear-sky total column water vapour averaged over the vicinity of the pixel. This reduces the noise in the retrieved SST significantly. The robust standard deviation of the new OE SST compared to matched drifting buoys becomes 0.39 K for all data. The smoothed OE gives SST sensitivity of 98% on average. This means that diurnal temperature variability and ocean frontal gradients are more faithfully estimated, and that the influence of the prior SST used is minimal (2%). This benefit is not available using traditional atmospheric correction smoothing.

Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample

The self-assembly of proteins and peptides into b-sheet-rich amyloid fibers is a process that has gained notoriety because of its association with human diseases and disorders. Spontaneous self-assembly of peptides into nonfibrillar supramolecular structures can also provide a versatile and convenient mechanism for the bottom-up design of biocompatible materials with functional properties favoring a wide range of practical applications.[1] One subset of these fascinating and potentially useful nanoscale constructions are the peptide nanotubes, elongated cylindrical structures with a hollow center bounded by a thin wall of peptide molecules.[2] A formidable challenge in optimizing and harnessing the properties of nanotube assemblies is to gain atomistic insight into their architecture, and to elucidate precisely how the tubular morphology is constructed from the peptide building blocks. Some of these fine details have been elucidated recently with the use of magic-angle-spinning (MAS) solidstate NMR (SSNMR) spectroscopy.[3] MAS SSNMR measurements of chemical shifts and through-space interatomic distances provide constraints on peptide conformation (e.g., b-strands and turns) and quaternary packing. We describe here a new application of a straightforward SSNMR technique which, when combined with FTIR spectroscopy, reports quantitatively on the orientation of the peptide molecules within the nanotube structure, thereby providing an additional structural constraint not accessible to MAS SSNMR.