NMR structure and backbone dynamics of a concatemer of epidermal growth factor homology modules of the human low-density lipoprotein receptor

The ligand-binding region of the low-density lipoprotein (LDL) receptor is formed by seven N-terminal, imperfect, cysteine-rich (LB) modules. This segment is followed by an epidermal growth factor precursor homology domain with two N-terminal, tandem, EGF-like modules that are thought to participate in LDL binding and recycling of the endocytosed receptor to the cell surface. EGF-A and the concatemer, EGF-AB, of these modules were expressed in Escherichia coli. Correct protein folding of EGF-A and the concatemer EGF-AB was achieved in the presence or absence of calcium ions, in contrast to the LB modules, which require them for correct folding. Homonuclear and heteronuclear H-1-N-15 NMR spectroscopy at 17.6 T was used to determine the three-dimensional structure of the concatemer. Both modules are formed by two pairs of short, anti-parallel beta -strands. In the concatemer, these modules have a fixed relative orientation, stabilized by calcium ion-binding and hydrophobic interactions at the interface. N-15 longitudinal and transverse relaxation rates, and {H-1}-N-15 heteronuclear NOEs were used to derive a model-free description of the backbone dynamics of the molecule. The concatemer appears relatively rigid, particularly near the calcium ion-binding site at the module interface, with an average generalized order parameter of 0.85 +/- 0.11. Some mutations causing familial hypercholesterolemia may now be rationalized. Mutations of D41, D43 and E44 in the EGF-B calcium ion-binding region may affect the stability of the linker and thus the orientation of the tandem modules. The diminutive core also provides little structural stabilization, necessitating the presence of disulfide bonds. The structure and dynamics of EGF-AB contrast with the N-terminal LB modules, which require calcium ions both for folding to form the correct disulfide connectivities and for maintenance of the folded structure, and are connected by highly mobile linking peptides. (C) 2001 Academic Press.

Solid-state NMR structure determination of melittin in a lipid environment

Solid-state C-13 NMR spectroscopy was used to investigate the three-dimensional structure of melittin as lyophilized powder and in ditetradecylphosphatidylcholine (DTPC) membranes. The distance between specifically labeled carbons in analogs [1-C-13]Gly3-[2-C-13]Ala4, [1-C-13]Gly3-[2-C-13]Leu6, [1-C-13]Leu13-[2-C-13]Ala15, [2-C-13]Leu13-[1-C-13]Ala15, and [1-C-13]Leu13-[2-C-13]Leu16 was measured by rotational resonance. As expected, the internuclear distances measured in [1-C-13]Gly3-[2-C-13]Ala4 and [1-C-13]Gly3-[2-C-13]Leu6 were consistent with alpha -helical structure in the N-terminus irrespective of environment. The Internuclear distances measured in [1-C-13]Leu13-[2-C-13]Ala15, [2-C-13]Leu13-[1-C-13]Ala15, and [1-C-13]Leu13-[2-C-13]Leu16 revealed, via molecular modeling, some dependence upon environment for conformation in the region of the bend in helical structure induced by Pro14. A slightly larger interhelical angle between the N- and C-terminal helices was indicated for peptide in dry or hydrated gel state DTPC (139 degrees -145 degrees) than in lyophilized powder (121 degrees -139 degrees) or crystals (129 degrees). The angle, however, is not as great as deduced for melittin in aligned bilayers of DTPC in the liquid-crystalline state (similar to 160 degrees) (R. Smith, F. Separovic, T. J. Milne, A. Whittaker, F. M. Bennett, B. A. Cornell, and A. Makriyannis, 1994, J. Mol, Biol 241:456-466). The study illustrates the utility of rotational resonance in determining local structure within peptide-lipid complexes.

Quantum criticality

We investigate the theory of quantum fluctuations in non-equilibrium systems having large critical fluctuations. This allows us to treat the limits imposed by nonlinearities to quantum squeezing and noise reduction, and also to envisage future tests of quantum theory in regions of macroscopic quantum fluctuations. A long-term objective of this research is to identify suitable physical systems in which macroscopic 'Schrodinger cat'-like behaviour may be observed. We investigate two systems in particular of much current experimental interest, namely the degenerate parametric oscillator near threshold, and the evaporatively cooled (BEC). We compare the results obtained in the positive-P representation, as a fully quantum mechanical calculation, with the truncated Wigner phase space equation, also known as semi-classical theory. We show when these results agree and differ in calculations taken beyond the linearized approximation. In the region where the largest quantum fluctuations and Schrodinger cat-like behaviour might be expected, we find that the quantum predictions correspond very closely to the semi-classical theory. Nature abhors observing a Schrodinger car.

Tidal effects on groundwater dynamics in unconfined aquifers

The variation of seawater level resulting from tidal fluctuations is usually neglected in regional groundwater flow studies. Although the tidal oscillation is damped near the shoreline, there is a quasi-steady-slate rise in the mean water-table position, which may have an influence on regional groundwater flow. In this paper the effects of tidal fluctuations on groundwater hydraulics are investigated using a variably saturated numerical model that includes the effects of a realistic mild beach slope, seepage face and the unsaturated zone. In particular the impact of these factors on the velocity field in the aquifer is assessed. Simulations show that the tidal fluctuation has substantial consequences for the local velocity field in the vicinity of the exit face, which affects the nearshore migration of contaminant in coastal aquifers. An overheight in the water table as a result of the tidal fluctuation is observed anti this has a significant effect on groundwater discharge to the sea when the landward boundary condition is a constant water level. The effect of beach slope is very significant and simplifying the problem by considering a vertical beach face causes serious errors in predicting the water-table position and the groundwater flux. For media with a high effective capillary fringe, the moisture retained above the water table is important in determining the effects of the tidal fluctuations. Copyright (C) 2001 John Wiley & Sons, Ltd.

Advances in application of climate prediction in agriculture

Agricultural ecosystems and their associated business and government systems are diverse and varied. They range from farms, to input supply businesses, to marketing and government policy systems, among others. These systems are dynamic and responsive to fluctuations in climate. Skill in climate prediction offers considerable opportunities to managers via its potential to realise system improvements (i.e. increased food production and profit and/or reduced risks). Realising these opportunities, however, is not straightforward as the forecasting skill is imperfect and approaches to applying the existing skill to management issues have not been developed and tested extensively. While there has been much written about impacts of climate variability, there has been relatively little done in relation to applying knowledge of climate predictions to modify actions ahead of likely impacts. However, a considerable body of effort in various parts of the world is now being focused on this issue of applying climate predictions to improve agricultural systems. In this paper, we outline the basis for climate prediction, with emphasis on the El Nino-Southern Oscillation phenomenon, and catalogue experiences at field, national and global scales in applying climate predictions to agriculture. These diverse experiences are synthesised to derive general lessons about approaches to applying climate prediction in agriculture. The case studies have been selected to represent a diversity of agricultural systems and scales of operation. They also represent the on-going activities of some of the key research and development groups in this field around the world. The case studies include applications at field/farm scale to dryland cropping systems in Australia, Zimbabwe, and Argentina. This spectrum covers resource-rich and resource-poor farming with motivations ranging from profit to food security. At national and global scale we consider possible applications of climate prediction in commodity forecasting (wheat in Australia) and examine implications on global wheat trade and price associated with global consequences of climate prediction. In cataloguing these experiences we note some general lessons. Foremost is the value of an interdisciplinary systems approach in connecting disciplinary Knowledge in a manner most suited to decision-makers. This approach often includes scenario analysis based oil simulation with credible models as a key aspect of the learning process. Interaction among researchers, analysts and decision-makers is vital in the development of effective applications all of the players learn. Issues associated with balance between information demand and supply as well as appreciation of awareness limitations of decision-makers, analysts, and scientists are highlighted. It is argued that understanding and communicating decision risks is one of the keys to successful applications of climate prediction. We consider that advances of the future will be made by better connecting agricultural scientists and practitioners with the science of climate prediction. Professions involved in decision making must take a proactive role in the development of climate forecasts if the design and use of climate predictions are to reach their full potential. (C) 2001 Elsevier Science Ltd. All rights reserved.

Riddling and invariance for discontinuous maps preserving Lebesgue measure

In this paper we use the mixture of topological and measure-theoretic dynamical approaches to consider riddling of invariant sets for some discontinuous maps of compact regions of the plane that preserve two-dimensional Lebesgue measure. We consider maps that are piecewise continuous and with invertible except on a closed zero measure set. We show that riddling is an invariant property that can be used to characterize invariant sets, and prove results that give a non-trivial decomposion of what we call partially riddled invariant sets into smaller invariant sets. For a particular example, a piecewise isometry that arises in signal processing (the overflow oscillation map), we present evidence that the closure of the set of trajectories that accumulate on the discontinuity is fully riddled. This supports a conjecture that there are typically an infinite number of periodic orbits for this system.

Spatial and temporal patterns in Australian wheat yield and their relationship with ENSO

Spatial and temporal variability in wheat production in Australia is dominated by rainfall occurrence. The length of historical production records is inadequate, however, to analyse spatial and temporal patterns conclusively. In this study we used modelling and simulation to identify key spatial patterns in Australian wheat yield, identify groups of years in the historical record in which spatial patterns were similar, and examine association of those wheat yield year groups with indicators of the El Nino Southern Oscillation (ENSO). A simple stress index model was trained on 19 years of Australian Bureau of Statistics shire yield data (1975-93). The model was then used to simulate shire yield from 1901 to 1999 for all wheat-producing shires. Principal components analysis was used to determine the dominating spatial relationships in wheat yield among shires. Six major components of spatial variability were found. Five of these represented near spatially independent zones across the Australian wheatbelt that demonstrated coherent temporal (annual) variability in wheat yield. A second orthogonal component was required to explain the temporal variation in New South Wales. The principal component scores were used to identify high- and low-yielding years in each zone. Year type groupings identified in this way were tested for association with indicators of ENSO. Significant associations were found for all zones in the Australian wheatbelt. Associations were as strong or stronger when ENSO indicators preceding the wheat season (April-May phases of the Southern Oscillation Index) were used rather than indicators based on classification during the wheat season. Although this association suggests an obvious role for seasonal climate forecasting in national wheat crop forecasting, the discriminatory power of the ENSO indicators, although significant, was not strong. By examining the historical years forming the wheat yield analog sets within each zone, it may be possible to identify novel climate system or ocean-atmosphere features that may be causal and, hence, most useful in improving seasonal forecasting schemes.

Photosynthetic responses of the coral Montipora digitata to cold temperature stress

Coral bleaching events have become more frequent and widespread, largely due to elevated sea surface temperatures. Global climate change could lead to increased variability of sea surface temperatures, through influences on climate systems, e.g. El Nino Southern Oscillation (ENSO). Field observations in 1999, following a strong ENSO, revealed that corals bleached in winter after unusually cold weather. To explore the basis for these observations, the photosynthetic responses of the coral species Montipora digitata Studer were investigated in a series of temperature and light experiments. Small replicate coral colonies were exposed to ecologically relevant lower temperatures for varying durations and under light regimes that ranged from darkness to full sunlight. Photosynthetic efficiency was analyzed using a pulse amplitude modulated (PAM) fluorometer (F-0, F-m, F-v/F-m), and chlorophyll a (chl a) content and symbiotic dinoflagellate density were analyzed with spectrophotometry and microscopy, respectively. Cold temperature stress had a negative impact on M digitata colonies indicated by decreased photosynthetic efficiency (F-v/F-m), loss of symbiotic dinoflagellates and changes in photosynthetic pigment concentrations. Corals in higher light regimes were more susceptible to cold temperature stress, Moderate cold stress resulted in photoacclimatory responses, but severe cold stress resulted in photodamage, bleaching and increased mortality. Responses to cold temperature stress of M digitata appeared similar to that observed in corals exposed to warmer than normal temperatures, suggesting a common mechanism. The results of this study suggest that corals and coral reefs may also be impacted by exposure to cold as well as warm temperature extremes as climate change occurs.

Hemodynamic and ventilatory effects of manual respiratory physiotherapy techniques of chest clapping, vibration, and shaking in an animal model

Chest clapping, vibration, and shaking were studied in 10 physiotherapists who applied these techniques on an anesthetized animal model. Hemodynamic variables (such as heart rate, blood pressure, pulmonary artery pressure, and right atrial pressure) were measured during the application of these techniques to verify claims of adverse events. In addition, expired tidal volume and peak expiratory flow rate were measured to ascertain effects of these techniques. Physiotherapists in this study applied chest clapping at a rate of 6.2 +/- 0.9 Hz, vibration at 10.5 +/- 2.3 Hz, and shaking at 6.2 +/- 2.3 Hz. With the use of these rates, esophageal pressure swings of 8.8 +/- 5.0, 0.7 +/- 0.3, and 1.4 +/- 0.7 mmHg resulted from clapping, vibration, and shaking respectively. Variability in rates and forces generated by these techniques was 80% of variance in shaking force (P = 0.003). Application of these techniques by physiotherapists was found to have no significant effects on hemodynamic and most ventilatory variables in this study. From this study, we conclude that chest clapping, vibration, and shaking 1) can be consistently performed by physiotherapists; 2) are significantly related to physiotherapists' characteristics, particularly clinical experience; and 3) caused no significant hemodynamic effects.

Learning the dynamics of embedded clauses

Recent work by Siegelmann has shown that the computational power of recurrent neural networks matches that of Turing Machines. One important implication is that complex language classes (infinite languages with embedded clauses) can be represented in neural networks. Proofs are based on a fractal encoding of states to simulate the memory and operations of stacks. In the present work, it is shown that similar stack-like dynamics can be learned in recurrent neural networks from simple sequence prediction tasks. Two main types of network solutions are found and described qualitatively as dynamical systems: damped oscillation and entangled spiraling around fixed points. The potential and limitations of each solution type are established in terms of generalization on two different context-free languages. Both solution types constitute novel stack implementations - generally in line with Siegelmann's theoretical work - which supply insights into how embedded structures of languages can be handled in analog hardware.

Influence of hysteresis on tidal capillary fringe dynamics in a well-sorted sand

Nielsen and Perrochet [Adv. Water Resour. 23 (2000) 503] presented experimental data for cyclic water movement in the vadose zone above an oscillating watertable. The response of the watertable to cyclic forcing was characterised by the ratios of the forcing head to watertable amplitudes and their associated phase lag. They found that their non-hysteretic Richards' equation model failed to represent the observed behaviour of these parameters. This paper explores the effect on the simulated capillary fringe dynamics (in terms of these parameters) of including varying degrees of hysteresis in the moisture retention curve used in a numerical model of their experiment. It is clear that hysteresis can indeed account for observed discrepancies between simulation and experiment and that the effect of hysteresis varies with the frequency of oscillation. The use of a single-valued mean retention curve, as advocated by some authors, fails to provide a match between the simulated and observed behaviour of the Nielsen and Perrochet parameters, but is shown to be adequate for predicting time-averaged soil moisture profiles. (C) 2003 Elsevier Ltd. All rights reserved.

Water table waves in an unconfined aquifer: Experiments and modeling

[1] Comprehensive measurements are presented of the piezometric head in an unconfined aquifer during steady, simple harmonic oscillations driven by a hydrostatic clear water reservoir through a vertical interface. The results are analyzed and used to test existing hydrostatic and nonhydrostatic, small-amplitude theories along with capillary fringe effects. As expected, the amplitude of the water table wave decays exponentially. However, the decay rates and phase lags indicate the influence of both vertical flow and capillary effects. The capillary effects are reconciled with observations of water table oscillations in a sand column with the same sand. The effects of vertical flows and the corresponding nonhydrostatic pressure are reasonably well described by small-amplitude theory for water table waves in finite depth aquifers. That includes the oscillation amplitudes being greater at the bottom than at the top and the phase lead of the bottom compared with the top. The main problems with respect to interpreting the measurements through existing theory relate to the complicated boundary condition at the interface between the driving head reservoir and the aquifer. That is, the small-amplitude, finite depth expansion solution, which matches a hydrostatic boundary condition between the bottom and the mean driving head level, is unrealistic with respect to the pressure variation above this level. Hence it cannot describe the finer details of the multiple mode behavior close to the driving head boundary. The mean water table height initially increases with distance from the forcing boundary but then decreases again, and its asymptotic value is considerably smaller than that previously predicted for finite depth aquifers without capillary effects. Just as the mean water table over-height is smaller than predicted by capillarity-free shallow aquifer models, so is the amplitude of the second harmonic. In fact, there is no indication of extra second harmonics ( in addition to that contained in the driving head) being generated at the interface or in the interior.

Determinação do momento crítico de flambagem lateral com distorção em vigas mistas contínuas de aço e concreto com perfis de alma senoidal

As vigas mistas de aço e concreto estão sendo largamente utilizadas em construções de edifícios e pontes. Ao se combinar o aço com o concreto obtêm-se estruturas mais econômicas, uma vez que se tira proveito das melhores características de cada material. Nas regiões de momento negativo de uma viga mista contínua, a mesa inferior e parte da alma estão comprimidas, se a alma do perfil não tiver rigidez suficiente para evitar a flexão lateral, ela distorcerá gerando um deslocamento lateral e um giro na mesa comprimida, caracterizando um modo de flambagem denominado flambagem lateral com distorção (FLD). O procedimento de verificação à FLD da EN 1994-1-1:2004 originou o método de cálculo da ABNT NBR 8800:2008, entretanto a EN 1994-1-1:2004 não fornece expressão para o cálculo do momento crítico elástico, enquanto a ABNT NBR 8800:2008 prescreve uma formulação proposta por Roik, Hanswille e Kina (1990) desenvolvida para vigas mistas com perfis de alma plana. Embora as normas prescrevam um método de verificação à FLD para vigas mistas com perfis de alma plana, poucos estudos têm sido feitos sobre esse estado-limite. Além disso, tanto a ABNT NBR 8800:2008 quanto as normas internacionais não abordam perfis de alma senoidal. Neste trabalho, foram implementadas análises de flambagem elástica, com auxílio do software ANSYS 14.0 (2011), em modelos de elementos finitos que retratem o comportamento à FLD de vigas mistas de aço e concreto com perfis de alma plana e senoidal. Os modelos numéricos foram constituídos pelo perfil de aço, por uma mola rotacional que restringe parcialmente o giro da mesa superior e uma restrição ao deslocamento lateral, ao longo de todo o comprimento da viga. Os resultados numéricos são comparados com os obtidos pelas formulações de Roik, Hanswille e Kina (1990) e de Hanswille (2002), adaptadas para levar em consideração a corrugação da alma do perfil de aço. Para avaliação das formulações supracitadas e da consistência da modelagem numérica adotada, o momento crítico elástico foi determinado para vigas mistas com perfis de aço de alma plana. Como resultado, um método para o cálculo do momento crítico elástico de vigas mistas de alma senoidal é proposto.

Elaboração e análise de extrato hidrossolúvel de gergelim (Sesamum indicum)

O objetivo do presente estudo foi elaborar e caracterizar um extrato hidrossolúvel à base de gergelim para ser usado como possível substituto do leite de vaca e extrato de soja. Foi proposto um modelo de cinética de absorção de água durante a etapa de maceração no qual estimou o tempo ideal de batimento do gergelim macerado e se essa etapa influencia no rendimento do produto. Posteriormente com o objetivo de saber a influência do tempo de batimento (0,45 min a 14,55 min) e a concentração do extrato (1,925% a 23,07%) foram avaliadas através de um delineamento composto central rotacional (DCCR), ou seja, um delineamento 22 incluindo 4 ensaios nas condições axiais e 5 repetições no ponto central, totalizando 13 experimentos. Para todos os ensaios do delineamento realizou-se análises de viscosidade, cor, sólidos solúveis totais e rendimento. As mesmas análises foram realizadas em amostras comerciais de leite de vaca e extrato hidrossolúvel de soja com o intuito de comparação. Após a realização dessa etapa foi possível à seleção de algumas amostras para elaboração do extrato hidrossolúvel de gergelim e então realizou-se análises físico-químicas (proteína, cinzas, lipídios, carboidratos) e determinou-se a capacidade antioxidante por ABTS e teor de compostos fenólicos de tais amostras. Quanto à análise de rendimento não houve diferença significativa da quantidade de extrato obtido em diferentes temperaturas de maceração pelo teste de Tukey (p> 0,05). O DCCR foi realizado no programa Statistica e selecionaram-se os ensaios 1, 2, 6, 7, PC (ponto central) que foram as amostras que mais se assemelharam com as amostras comerciais estudadas. Nessas amostras realizou-se as análises físico-químicas além de capacidade antioxidante e compostos fenólicos. O conteúdo de sólidos totais na amostra 6 foi superior as demais amostras, diferindo estatisticamente das demais amostras (p> 0,05). Já para o teor de lipídios, cinzas e proteínas encontrados nas amostras 6 e PC foram maiores que as demais amostras, enquanto a amostra 7 exibiu o menor teor de lipídios e proteínas, considerando que o teor de cinzas das amostras 1, 2 e 7 foram estatisticamente iguais. O teor de carboidratos calculado por diferença foi superior nas amostras 1, 2 e 7 e com o menor valor na amostra 6. Os valores de capacidade antioxidante e compostos fenólicos não se diferenciaram estatisticamente entre si ao nível de 5% de probabilidade. Concluiu-se portanto que a etapa de maceração não influenciou no rendimento do produto final. A partir das análises físico-químicas pode-se concluir que o extrato hidrossolúvel de gergelim em determinadas amostras apresentou um melhor desempenho quanto ao valor nutricional comparado ao extrato de soja.

Identification of tsunami-induced deposits using numerical modeling and rock magnetism techniques: A study case of the 1755 Lisbon tsunami in Algarve, Portugal

Storm- and tsunami-deposits are generated by similar depositional mechanisms making their discrimination hard to establish using classic sedimentologic methods. Here we propose an original approach to identify tsunami-induced deposits by combining numerical simulation and rock magnetism. To test our method, we investigate the tsunami deposit of the Boca do Rio estuary generated by the 1755 earthquake in Lisbon which is well described in the literature. We first test the 1755 tsunami scenario using a numerical inundation model to provide physical parameters for the tsunami wave. Then we use concentration (MS. SIRM) and grain size (chi(ARM), ARM, B1/2, ARM/SIRM) sensitive magnetic proxies coupled with SEM microscopy to unravel the magnetic mineralogy of the tsunami-induced deposit and its associated depositional mechanisms. In order to study the connection between the tsunami deposit and the different sedimentologic units present in the estuary, magnetic data were processed by multivariate statistical analyses. Our numerical simulation show a large inundation of the estuary with flow depths varying from 0.5 to 6 m and run up of similar to 7 m. Magnetic data show a dominance of paramagnetic minerals (quartz) mixed with lesser amount of ferromagnetic minerals, namely titanomagnetite and titanohematite both of a detrital origin and reworked from the underlying units. Multivariate statistical analyses indicate a better connection between the tsunami-induced deposit and a mixture of Units C and D. All these results point to a scenario where the energy released by the tsunami wave was strong enough to overtop and erode important amount of sand from the littoral dune and mixed it with reworked materials from underlying layers at least 1 m in depth. The method tested here represents an original and promising tool to identify tsunami-induced deposits in similar embayed beach environments.