Micro-scale habitat associations of woody plants in a neotropical cloud forest

Species?habitat associations may contribute to the maintenance of species richness in tropical forests, but previous research has been conducted almost exclusively in lowland forests and has emphasized the importance of topography and edaphic conditions. Is the distribution of woody plant species in a Peruvian cloud forest determined by microhabitat conditions? What is the role of environmental characteristics and forest structure in habitat partitioning in a tropical cloud forest? We examined species?habitat associations in three 1-ha plots using the torus-translation method. We used three different criteria to define habitats for habitat partitioning analyses, based on microtopography, forest structure and both sets of factors. The number of species associated either positively or negatively with each habitat was assessed. Habitats defined on the basis of environmental conditions and forest structure discriminated a greater number of positive and negative associations at the scale of our analyses in a tropical cloud forest. Both topographic conditions and forest structure contribute to small-scale microhabitat partitioning of woody plant species in a Peruvian tropical cloud forest. Nevertheless, canopy species were most correlated with the distribution of environmental variables, while understorey species displayed associations with forest structure.

Small-scale variation of vegetation in a mixed forest understorey is partly controlled by the effect of overstory composition on litter accumulation

We investigated how richness and composition of vascular plant species in the understory of a mixed hardwood forest stand varied with respect to the abundance and composition of the overstory. The stand is in central Spain and represents the southernmost range of distribution of several tree and herbaceous species in Europe. Understory species were identified in 46 quadrats (0.25 m2) where variables litter depth and light availability were measured. In addition, we estimated tree density, basal area, and percent basal area by tree species within 6-m-radius areas around each plot. Species richness and composition were studied using path analysis and scale-dependent geostatistical methods, respectively. We found that the relative abundance of certain trees species in the overstory was more important than total overstory abundance in explaining understory species richness. Richness decreased as soil litter depth increased, and soil litter increased as the relative proportion of Fagus sylvatica in the overstory increased, which accounted for a negative, indirect effect of Fagus sylvatica on richness. Regarding understory species composition, we found that some species distributed preferentially below certain tree species. For example, Melica uniflora was most frequent below Fagus sylvatica and Quercus petraea while the increasing proportion of Q. pyrenaica in the overstory favored the presence of Cruciata glabra, Arenaria montana, Prunus avium, Conopodium bourgaei, Holcus mollis, Stellaria media and Galium aparine in the understory. Overall, these results emphasize the importance of individual tree species in controlling the assemblage and richness of understory species in mixed stands. We conclude that soil litter accumulation is one way through which overstory composition shapes the understory community.

Large scale multiphysics modeling of neurites

Situado en el límite entre Ingeniería, Informática y Biología, la mecánica computacional de las neuronas aparece como un nuevo campo interdisciplinar que potencialmente puede ser capaz de abordar problemas clínicos desde una perspectiva diferente. Este campo es multiescala por naturaleza, yendo desde la nanoescala (como, por ejemplo, los dímeros de tubulina) a la macroescala (como, por ejemplo, el tejido cerebral), y tiene como objetivo abordar problemas que son complejos, y algunas veces imposibles, de estudiar con medios experimentales. La modelización computacional ha sido ampliamente empleada en aplicaciones Neurocientíficas tan diversas como el crecimiento neuronal o la propagación de los potenciales de acción compuestos. Sin embargo, en la mayoría de los enfoques de modelización hechos hasta ahora, la interacción entre la célula y el medio/estímulo que la rodea ha sido muy poco explorada. A pesar de la tremenda importancia de esa relación en algunos desafíos médicos—como, por ejemplo, lesiones traumáticas en el cerebro, cáncer, la enfermedad del Alzheimer—un puente que relacione las propiedades electrofisiológicas-químicas y mecánicas desde la escala molecular al nivel celular todavía no existe. Con ese objetivo, esta investigación propone un marco computacional multiescala particularizado para dos escenarios respresentativos: el crecimiento del axón y el acomplamiento electrofisiológicomecánico de las neuritas. En el primer caso, se explora la relación entre los constituyentes moleculares del axón durante su crecimiento y sus propiedades mecánicas resultantes, mientras que en el último, un estímulo mecánico provoca deficiencias funcionales a nivel celular como consecuencia de sus alteraciones electrofisiológicas-químicas. La modelización computacional empleada en este trabajo es el método de las diferencias finitas, y es implementada en un nuevo programa llamado Neurite. Aunque el método de los elementos finitos es también explorado en parte de esta investigación, el método de las diferencias finitas tiene la flexibilidad y versatilidad necesaria para implementar mode los biológicos, así como la simplicidad matemática para extenderlos a simulaciones a gran escala con un coste computacional bajo. Centrándose primero en el efecto de las propiedades electrofisiológicas-químicas sobre las propiedades mecánicas, una versión adaptada de Neurite es desarrollada para simular la polimerización de los microtúbulos en el crecimiento del axón y proporcionar las propiedades mecánicas como función de la ocupación de los microtúbulos. Después de calibrar el modelo de crecimiento del axón frente a resultados experimentales disponibles en la literatura, las características mecánicas pueden ser evaluadas durante la simulación. Las propiedades mecánicas del axón muestran variaciones dramáticas en la punta de éste, donde el cono de crecimiento soporta las señales químicas y mecánicas. Bansándose en el conocimiento ganado con el modelo de diferencias finitas, y con el objetivo de ir de 1D a 3D, este esquema preliminar pero de una naturaleza innovadora allana el camino a futuros estudios con el método de los elementos finitos. Centrándose finalmente en el efecto de las propiedades mecánicas sobre las propiedades electrofisiológicas- químicas, Neurite es empleado para relacionar las cargas mecánicas macroscópicas con las deformaciones y velocidades de deformación a escala microscópica, y simular la propagación de la señal eléctrica en las neuritas bajo carga mecánica. Las simulaciones fueron calibradas con resultados experimentales publicados en la literatura, proporcionando, por tanto, un modelo capaz de predecir las alteraciones de las funciones electrofisiológicas neuronales bajo cargas externas dañinas, y uniendo lesiones mecánicas con las correspondientes deficiencias funcionales. Para abordar simulaciones a gran escala, aunque otras arquitecturas avanzadas basadas en muchos núcleos integrados (MICs) fueron consideradas, los solvers explícito e implícito se implementaron en unidades de procesamiento central (CPU) y unidades de procesamiento gráfico (GPUs). Estudios de escalabilidad fueron llevados acabo para ambas implementaciones mostrando resultados prometedores para casos de simulaciones extremadamente grandes con GPUs. Esta tesis abre la vía para futuros modelos mecánicos con el objetivo de unir las propiedades electrofisiológicas-químicas con las propiedades mecánicas. El objetivo general es mejorar el conocimiento de las comunidades médicas y de bioingeniería sobre la mecánica de las neuronas y las deficiencias funcionales que aparecen de los daños producidos por traumatismos mecánicos, como lesiones traumáticas en el cerebro, o enfermedades neurodegenerativas como la enfermedad del Alzheimer. ABSTRACT Sitting at the interface between Engineering, Computer Science and Biology, Computational Neuron Mechanics appears as a new interdisciplinary field potentially able to tackle clinical problems from a new perspective. This field is multiscale by nature, ranging from the nanoscale (e.g., tubulin dimers) to the macroscale (e.g., brain tissue), and aims at tackling problems that are complex, and sometime impossible, to study through experimental means. Computational modeling has been widely used in different Neuroscience applications as diverse as neuronal growth or compound action potential propagation. However, in the majority of the modeling approaches done in this field to date, the interactions between the cell and its surrounding media/stimulus have been rarely explored. Despite of the tremendous importance of such relationship in several medical challenges—e.g., traumatic brain injury (TBI), cancer, Alzheimer’s disease (AD)—a bridge between electrophysiological-chemical and mechanical properties of neurons from the molecular scale to the cell level is still lacking. To this end, this research proposes a multiscale computational framework particularized for two representative scenarios: axon growth and electrophysiological-mechanical coupling of neurites. In the former case, the relation between the molecular constituents of the axon during its growth and its resulting mechanical properties is explored, whereas in the latter, a mechanical stimulus provokes functional deficits at cell level as a consequence of its electrophysiological-chemical alterations. The computational modeling approach chosen in this work is the finite difference method (FDM), and was implemented in a new program called Neurite. Although the finite element method (FEM) is also explored as part of this research, the FDM provides the necessary flexibility and versatility to implement biological models, as well as the mathematical simplicity to extend them to large scale simulations with a low computational cost. Focusing first on the effect of electrophysiological-chemical properties on the mechanical proper ties, an adaptation of Neurite was developed to simulate microtubule polymerization in axonal growth and provide the axon mechanical properties as a function of microtubule occupancy. After calibrating the axon growth model against experimental results available in the literature, the mechanical characteristics can be tracked during the simulation. The axon mechanical properties show dramatic variations at the tip of the axon, where the growth cone supports the chemical and mechanical signaling. Based on the knowledge gained from the FDM scheme, and in order to go from 1D to 3D, this preliminary yet novel scheme paves the road for future studies with FEM. Focusing then on the effect of mechanical properties on the electrophysiological-chemical properties, Neurite was used to relate macroscopic mechanical loading to microscopic strains and strain rates, and simulate the electrical signal propagation along neurites under mechanical loading. The simulations were calibrated against experimental results published in the literature, thus providing a model able to predict the alteration of neuronal electrophysiological function under external damaging load, and linking mechanical injuries to subsequent acute functional deficits. To undertake large scale simulations, although other state-of-the-art architectures based on many integrated cores (MICs) were considered, the explicit and implicit solvers were implemented for central processing units (CPUs) and graphics processing units (GPUs). Scalability studies were done for both implementations showing promising results for extremely large scale simulations with GPUs. This thesis opens the avenue for future mechanical modeling approaches aimed at linking electrophysiological- chemical properties to mechanical properties. Its overarching goal is to enhance the bioengineering and medical communities knowledge on neuronal mechanics and functional deficits arising from damages produced by direct mechanical insults, such as TBI, or neurodegenerative evolving illness, such as AD.

Incorporating small-scale farmers into sustainable supply chains: the Manobi case

Increased globalization and outsourcing to developing countries is fostering the interest in supply chain sustainability. From the academic point of view, while environmental impacts of supply chains have been largely analysed, the research on social issues has been scattered and fragmented. This paper thereby sets out to close this gap. We have identified an emerging sphere of knowledge at the interface between sustainable supply chain management, business strategy and international development literature, which seeks to propose innovative strategies for poverty alleviation. The incorporation of impoverished farmers into supply chains is presented here as one of those strategies, and illustrated through a case study on the integration of these farmers in the Senegalese horticulture supply chain.

On the generative equations of fractal self-similarity in granular media and the related PSD models

The physical appearance of granular media suggests the existence of geometrical scale invariance. The paper discuss how this physico-empirical property can be mathematically encoded leading to different generative models: a smooth one encoded by a differential equation and another encoded by an equation coming from a measure theoretical property.

Latent hardening size effect in small-scale plasticity

We aim at understanding the multislip behaviour of metals subject to irreversible deformations at small-scales. By focusing on the simple shear of a constrained single-crystal strip, we show that discrete Dislocation Dynamics (DD) simulations predict a strong latent hardening size effect, with smaller being stronger in the range [1.5 µm, 6 µm] for the strip height. We attempt to represent the DD pseudo-experimental results by developing a flow theory of Strain Gradient Crystal Plasticity (SGCP), involving both energetic and dissipative higher-order terms and, as a main novelty, a strain gradient extension of the conventional latent hardening. In order to discuss the capability of the SGCP theory proposed, we implement it into a Finite Element (FE) code and set its material parameters on the basis of the DD results. The SGCP FE code is specifically developed for the boundary value problem under study so that we can implement a fully implicit (Backward Euler) consistent algorithm. Special emphasis is placed on the discussion of the role of the material length scales involved in the SGCP model, from both the mechanical and numerical points of view.

Latent hardening size effect in small-scale plasticity

We aim at understanding the multislip behaviour of metals subject to irreversible deformations at small-scales. By focusing on the simple shear of a constrained single-crystal strip, we show that discrete Dislocation Dynamics (DD) simulations predict a strong latent hardening size effect, with smaller being stronger in the range [1.5 µm, 6 µm] for the strip height. We attempt to represent the DD pseudo-experimental results by developing a flow theory of Strain Gradient Crystal Plasticity (SGCP), involving both energetic and dissipative higher-order terms and, as a main novelty, a strain gradient extension of the conventional latent hardening. In order to discuss the capability of the SGCP theory proposed, we implement it into a Finite Element (FE) code and set its material parameters on the basis of the DD results. The SGCP FE code is specifically developed for the boundary value problem under study so that we can implement a fully implicit (Backward Euler) consistent algorithm. Special emphasis is placed on the discussion of the role of the material length scales involved in the SGCP model, from both the mechanical and numerical points of view.

Use of the energy-release rate in a 2 scale damage analysis of a bonded joint

Stress singularities appear at the extremities of an adhesive bond. They can produce a damage mechanism that we assimilate in this Note to a crack. The energy release rate permits to characterize its evolution. But a very refined mesh would be necessary for a real structure. Using an asymptotic method based on the small thickness of the bond a limit model with a different local behaviour is suggested. It leads to an approximation of the energy release rate

Visual grading of large cross section structural timber of Pinus sylvestris L. according to UNE 56544:2007 standard

Large cross section structural timber have been used in many structures over long periods of time and still make up an important part of the market due to its mechanical properties. Furthermore, it is frequent its employment in new construction site. It involves the need for a visual grading standard for timber used in construction according to the quality assessment. The material has to satisfy the requirements according to the currently regulations. UNE 56544 is the Spanish visual grading standard for coniferous structural timber. The 2007 version defined a new visual grade in the standard for large section termed Structural Large Timber (MEG). This research checks the new visual grading and consists of 116 structural size specimens of sawn coniferous timber of Scotch pine (Pinus sylvestris L.) from Segovia, Spain. The pieces had a cross section of 150 by 200 mm. They were visually graded according to UNE 56544:2007. Also, mechanical properties have been obtained according to standard EN 408. The results show very low output with an excessive percentage of rejected pieces (33%). The main reasons for the rejection of pieces are fissures and twist

On the onset of turbulence in natural convection on inclined plates

The problem of determination of the turbulence onset in natural convection on heated inclined plates in an air environment has been experimentally revisited. The transition has been detected by using hot wire velocity measurements. The onset of turbulence has been considered to take place where velocity fluctuations (measured through turbulence intensity) start to grow. Experiments have shown that the onset depends not only on the Grashof number defined in terms of the temperature difference between the heated plate and the surrounding air. A correlation between dimensionless Grashof and Reynolds numbers has been obtained, fitting quite well the experimental data.

Comparison of turbulence models for the computational fluid dynamics simulation of wind turbine wakes in the atmospheric boundary layer

An elliptic computational fluid dynamics wake model based on the actuator disk concept is used to simulate a wind turbine, approximated by a disk upon which a distribution of forces, defined as axial momentum sources, is applied on an incoming non-uniform shear flow. The rotor is supposed to be uniformly loaded with the exerted forces estimated as a function of the incident wind speed, thrust coefficient and rotor diameter. The model is assessed in terms of wind speed deficit and added turbulence intensity for different turbulence models and is validated from experimental measurements of the Sexbierum wind turbine experiment.

Involutivity of the Hamilton-Cartan equations of a second-order Lagrangian admitting a first-order Hamiltonian formalism

Involutivity of the Hamilton-Cartan equations of a second-order Lagrangian admitting a first-order Hamiltonian formalism

Cálculo de la recarga natural en grandes áreas, en función de la litología y la precipitación = Calculation of natural recharge in large areas, as a function of lithology and rainfall

En una región amplia como España se demuestra —mediante inferencias estadísticas sobre una muestra completa de 875 manantiales en los que se conoce su caudal medio y la litología de su área de alimentación y que han sido agrupados en regiones de distinta pluviometría— que la recarga media anual es una fracción fija de la precipitación media para cada litología. Se han establecido así unas tasas de recarga respecto de la precipitación para seis grupos litológicos de diferente permeabilidad: arenas, gravas y formaciones aluviales en general, 8.3%; conglomerados, 5.6%; areniscas, 7.3%; calizas y dolomías, 34.3%; margas, margocalizas, limos y arcillas, 3.3%; otras rocas, 1.3%. Teniendo en cuenta la representatividad de España, la cual tiene una gran variabilidad de litología, pluviometría, topografía, etcétera, estas tasas de recarga respecto de la precipita-ción son probablemente valores cuasi universales que pueden ser utilizados para estimar la recarga media o los recursos hídricos subterráneos medios de regiones amplias en cualquier parte del mundo, salvo en regiones especiales, como las que tienen permafrost, por ejemplo. En todo caso, estas tasas de recarga podrían ser retocadas para cada región según sus particulares características. Los datos de precipitación y litología son muy corrientes, por lo que el método puede ser ampliamente utilizado para completar balances hidráulicos.In a region as large as Spain, annual mean recharge is shown to be a fixed proportion of the mean rainfall for each lithology. This determination is based on statistical inferences from a complete sample of 875 springs for which mean flow and catchment areas are known and which have been grouped into distinct rainfall regions. Recharge rates have thus been established with respect to rainfall for six lithological groups with different permeability: sands, gravels and generally alluvial formations, 8.3%; conglomerates, 5.6%; sandstones, 7.3%; limestone and dolomite 34.3%; marls, marly limestones, silts and clays, 3.3%; and hard rocks, 1.3%. Considering the representativeness of Spain, which is large in size and has a highly varied lithology, topography and rainfall, these recharge rates for rainfall are probably quasi-universal values that can be used to estimate average recharge or average groundwater resources of large regions in any part of the world (except in special cases such as areas with permafrost, for example). For any case, these recharge rates can be adapted to each region according to its particular characteristics. Rainfall and lithology data are very common, and so the method can be widely used to calculate hydraulic balances.

Performance metrics for small-signal stability assessment of DC-distributed power-system-architecture comparisons

The objective of this paper is to provide performance metrics for small-signal stability assessment of a given system architecture. The stability margins are stated utilizing a concept of maximum peak criteria (MPC) derived from the behavior of an impedance-based sensitivity function. For each minor-loop gain defined at every system interface, a single number to state the robustness of stability is provided based on the computed maximum value of the corresponding sensitivity function. In order to compare various power-architecture solutions in terms of stability, a parameter providing an overall measure of the whole system stability is required. The selected figure of merit is geometric average of each maximum peak value within the system. It provides a meaningful metrics for system comparisons: the best system in terms of robust stability is the one that minimizes this index. In addition, the largest peak value within the system interfaces is given thus detecting the weakest point of the system in terms of robustness.

Deriving the full-reducing Krivine machine from the small-step operational semantics of normal order

We derive by program transformation Pierre Crégut s full-reducing Krivine machine KN from the structural operational semantics of the normal order reduction strategy in a closure-converted pure lambda calculus. We thus establish the correspondence between the strategy and the machine, and showcase our technique for deriving full-reducing abstract machines. Actually, the machine we obtain is a slightly optimised version that can work with open terms and may be used in implementations of proof assistants.