Stochastic amplitude-modulated stretching of Rabbit flexor digitorum profundus tendons reduces stiffness compared to Cyclic Loading but does not affect Tenocyte Metabolism

Background It has been demonstrated that frequency modulation of loading influences cellular response and metabolism in 3D tissues such as cartilage, bone and intervertebral disc. However, the mechano-sensitivity of cells in linear tissues such as tendons or ligaments might be more sensitive to changes in strain amplitude than frequency. Here, we hypothesized that tenocytes in situ are mechano-responsive to random amplitude modulation of strain. Methods We compared stochastic amplitude-modulated versus sinusoidal cyclic stretching. Rabbit tendon were kept in tissue-culture medium for twelve days and were loaded for 1h/day for six of the total twelve culture days. The tendons were randomly subjected to one of three different loading regimes: i) stochastic (2 – 7% random strain amplitudes), ii) cyclic_RMS (2–4.42% strain) and iii) cyclic_high (2 - 7% strain), all at 1 Hz and for 3,600 cycles, and one unloaded control. Results At the end of the culture period, the stiffness of the “stochastic” group was significantly lower than that of the cyclic_RMS and cyclic_high groups (both, p < 0.0001). Gene expression of eleven anabolic, catabolic and inflammatory genes revealed no significant differences between the loading groups. Conclusions We conclude that, despite an equivalent metabolic response, stochastically stretched tendons suffer most likely from increased mechanical microdamage, relative to cyclically loaded ones, which is relevant for tendon regeneration therapies in clinical practice.

USE OF HIDDEN MARKOV MODELS FOR QTL MAPPING

An important aspect of the QTL mapping problem is the treatment of missing genotype data. If complete genotype data were available, QTL mapping would reduce to the problem of model selection in linear regression. However, in the consideration of loci in the intervals between the available genetic markers, genotype data is inherently missing. Even at the typed genetic markers, genotype data is seldom complete, as a result of failures in the genotyping assays or for the sake of economy (for example, in the case of selective genotyping, where only individuals with extreme phenotypes are genotyped). We discuss the use of algorithms developed for hidden Markov models (HMMs) to deal with the missing genotype data problem.

A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data

Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number (Olshen {\it et~al}, 2004). The algorithm tests for change-points using a maximal $t$-statistic with a permutation reference distribution to obtain the corresponding $p$-value. The number of computations required for the maximal test statistic is $O(N^2),$ where $N$ is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster. algorithm. Results: We present a hybrid approach to obtain the $p$-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analysis of array CGH data from a breast cancer cell line to show the impact of the new approaches on the analysis of real data. Availability: An R (R Development Core Team, 2006) version of the CBS algorithm has been implemented in the ``DNAcopy'' package of the Bioconductor project (Gentleman {\it et~al}, 2004). The proposed hybrid method for the $p$-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.

Dynamic changes of cardiac conduction during rapid pacing

Slow conduction and unidirectional conduction block (UCB) are key mechanisms of reentry. Following abrupt changes in heart rate, dynamic changes of conduction velocity (CV) and structurally determined UCB may critically influence arrhythmogenesis. Using patterned cultures of neonatal rat ventricular myocytes grown on microelectrode arrays, we investigated the dynamics of CV in linear strands and the behavior of UCB in tissue expansions following an abrupt decrease in pacing cycle length (CL). Ionic mechanisms underlying rate-dependent conduction changes were investigated using the Pandit-Clark-Giles-Demir model. In linear strands, CV gradually decreased upon a reduction of CL from 500 ms to 230-300 ms. In contrast, at very short CLs (110-220 ms), CV first decreased before increasing again. The simulations suggested that the initial conduction slowing resulted from gradually increasing action potential duration (APD), decreasing diastolic intervals, and increasing postrepolarization refractoriness, which impaired Na(+) current (I(Na)) recovery. Only at very short CLs did APD subsequently shorten again due to increasing Na(+)/K(+) pump current secondary to intracellular Na(+) accumulation, which caused recovery of CV. Across tissue expansions, the degree of UCB gradually increased at CLs of 250-390 ms, whereas at CLs of 180-240 ms, it first increased and subsequently decreased. In the simulations, reduction of inward currents caused by increasing intracellular Na(+) and Ca(2+) concentrations contributed to UCB progression, which was reversed by increasing Na(+)/K(+) pump activity. In conclusion, CV and UCB follow intricate dynamics upon an abrupt decrease in CL that are determined by the interplay among I(Na) recovery, postrepolarization refractoriness, APD changes, ion accumulation, and Na(+)/K(+) pump function.

Pasture Conditions at the Initiation of Grazing to Optimize Forage Productivity: A Progress Report

To determine environmental, soil, and sward effects at the initiation of cattle grazing in the spring on seasonal (forage accumulated during the grazing season) and cumulative (seasonal + initial forage mass) forage accumulation (FA), 15 commercial cow-calf producers from southern Iowa were selected by historical initial grazing date. At grazing initiation, twelve .25-m2 samples were hand-clipped from each pasture and sward heights (SH) measured with a falling plane meter (4.8 kg/m2) to determine initial forage mass. At each location, soil temperature and load bearing capacity (LBC) were measured and a soil sample was collected to measure pH and moisture, P, and K concentrations. Cumulative degree-days (base=3.85°C) and precipitation at grazing initiation were calculated from NOAA records. At the beginning of each month, at least three grazing exclosures were placed on each grazed pasture to determine monthly FA. SH in each exclosure was recorded, and a .25-m2 forage sample was hand-clipped proximate to each exclosure. At the end of each month, SH was recorded and .25-m2 hand-clipped forage samples from inside exclosures were obtained. In linear regressions, cumulative and seasonal SH increased with greater soil P (r2=.5049 and .5417), soil K (r2=.4675 and .4397), and initial forage mass (r2=.1984 and .2801). Seasonal SH increased with earlier initial grazing dates (r2=.1996) and less accumulated degree-days (r2=.2364). Cumulative and seasonal FA increased with earlier initial grazing dates (r2=.2106 and .3744), lower soil temperatures (r2=.2617 and.2874), and greater soil P (r2=.3489 and .2598). Cumulative FA increased with greater soil K (r2=.4675). In quadratic regressions, cumulative and seasonal SH were correlated to soil P (r2=.6310 and .5310) and soil K (r2=.5095 and.4401). Cumulative and seasonal FA were correlated to degree days (r2=.3630 and.4013) and initial grazing date (r2=.3425 and .4088). Cumulative FA was correlated to soil P (r2=.3539), and seasonal FA was correlated to soil moisture (r2=.3688).

Geological and hydrological histories of the Argyre province, Mars

The geologic history of the multi-ringed Argyre impact basin and surroundings has been reconstructed on the basis of geologic mapping and relative-age dating of rock materials and structures. The impact formed a primary basin, rim materials, and a complex basement structural fabric including faults and valleys that are radial and concentric about the primary basin, as well as structurally-controlled local basins. Since its formation, the basin has been a regional catchment for volatiles and sedimentary materials as well as a dominant influence on the flow of surface ice, debris flows, and groundwater through and over its basement structures. The basin is interpreted to have been occupied by lakes, including a possible Mediterranean-sized sea that formed in the aftermath of the Argyre impact event The hypothesized lakes froze and diminished through time, though liquid water may have remained beneath the ice cover and sedimentation may have continued for some time. At its deepest, the main Argyre lake may have taken more than a hundred thousand years to freeze to the bottom even absent any heat source besides the Sun, but with impact-induced hydrothermal heat, geothermal heat flow due to long-lived radioactivities in early martian history, and concentration of solutes in sub-ice brine, liquid water may have persisted beneath thick ice for many millions of years. Existence of an ice-covered sea perhaps was long enough for life to originate and evolve with gradually colder and more hypersaline conditions. The Argyre rock materials, diverse in origin and emplacement mechanisms, have been modified by impact, magmatic, eolian, fluvial, lacustrine, glacial, periglacial, alluvial, colluvial, and tectonic processes. Post-impact adjustment of part of the impact-generated basement structural fabric such as concentric faults is apparent. Distinct basin-stratigraphic units are interpreted to be linked to large-scale geologic activity far from the basin, including growth of the Tharsis magmatic-tectonic complex and the growth into southern middle latitudes of south polar ice sheets. Along with the migration of surface and sub-surface volatiles towards the central part of the primaiy basin, the substantial difference in elevation with respect to the surrounding highlands and Tharsis and the Thaumasia highlands result in the trapping of atmospheric volatiles within the basin in the form of fog and regional or local precipitation, even today. In addition, the impact event caused long-term (millions of years) hydrothermal activity, as well as deep-seated basement structures that have tapped the internal heat of Mars, as conduits, for far greater time, possibly even today. This possibility is raised by the observation of putative open-system pingos and nearby gullies that occur in linear depressions with accompanying systems of faults and fractures. Long-term water and heat energy enrichment, complemented by the interaction of the nutrient-enriched primordial crustal and mantle materials favorable to life excavated to the surface and near-surface environs through the Argyre impact event, has not only resulted in distinct geomorphology, but also makes the Argyre basin a potential site of exceptional astrobiological significance. (C) 2015 Elsevier Inc. All rights reserved.

Índices de calidad de sitio de Populus nigra ‘Italica’ en plantaciones lineales en el noroeste de Chubut

En el noroeste del Chubut, los álamos se encuentran establecidos en cortinas de protección en predios de pastoreo o donde se cultivan pasturas y forrajes en secano. El Populus nigra ‘Italica’ es el clon más difundido en plantaciones lineales, ubicadas en diferentes calidades de sitio. No existen antecedentes sobre crecimiento en altura e Índice de Sitio en la zona. Se seleccionaron ocho sitios de muestreo, donde fueron apeados 24 árboles dominantes, a los que se les realizó análisis fustal. Con los pares de datos de edad-altura, resultantes del análisis de fuste de los árboles muestra, se ajustó el modelo de Chapman-Richards mediante técnicas de regresión no lineal. Se construyó una familia de curvas de crecimiento en altura, según la metodología de curva guía. Las curvas de Índice de Sitio, basadas en altura y edad, se construyeron mediante deducción matemática a partir de la función de crecimiento en altura, tomándose como edad de referencia 25 años a la altura del pecho. Se definieron cinco calidades de sitio, con un rango de 4 metros, con Índices de Sitio comprendidos entre 19 y 35 m.

Effects of light and elevated pCO2 on the growth and photochemical efficiency of Acropora cervicornis

The effects of light and elevated pCO2 on the growth and photochemical efficiency of the critically endangered staghorn coral, Acropora cervicornis, were examined experimentally. Corals were subjected to high and low treatments of CO2 and light in a fully crossed design and monitored using 3D scanning and buoyant weight methodologies. Calcification rates, linear extension, as well as colony surface area and volume of A. cervicornis were highly dependent on light intensity. At pCO2 levels projected to occur by the end of the century from ocean acidification (OA), A. cervicornis exhibited depressed calcification, but no change in linear extension. Photochemical efficiency (F v /F m ) was higher at low light, but unaffected by CO2. Amelioration of OA-depressed calcification under high-light treatments was not observed, and we suggest that the high-light intensity necessary to reach saturation of photosynthesis and calcification in A. cervicornis may limit the effectiveness of this potentially protective mechanism in this species. High CO2 causes depressed skeletal density, but not linear extension, illustrating that the measurement of extension by itself is inadequate to detect CO2 impacts. The skeletal integrity of A. cervicornis will be impaired by OA, which may further reduce the resilience of the already diminished populations of this endangered species.

Responses of three tropical seagrass species to CO2 enrichment

Increased atmospheric carbon dioxide leads to ocean acidification and carbon dioxide (CO2) enrichment of seawater. Given the important ecological functions of seagrass meadows, understanding their responses to CO2 will be critical for the management of coastal ecosystems. This study examined the physiological responses of three tropical seagrasses to a range of seawater pCO2 levels in a laboratory. Cymodocea serrulata, Halodule uninervis and Thalassia hemprichii were exposed to four different pCO2 treatments (442-1204 µatm) for 2 weeks, approximating the range of end-of-century emission scenarios. Photosynthetic responses were quantified using optode-based oxygen flux measurements. Across all three species, net productivity and energetic surplus (PG:R) significantly increased with a rise in pCO2 (linear models, P < 0.05). Photosynthesis-irradiance curve-derived photosynthetic parameters-maximum photosynthetic rates (P max) and efficiency (alpha) also increased as pCO2 increased (linear models, P < 0.05). The response for productivity measures was similar across species, i.e. similar slopes in linear models. A decrease in compensation light requirement (Ec) with increasing pCO2 was evident in C. serrulata and H. uninervis, but not in T. hemprichii. Despite higher productivity with pCO2 enrichment, leaf growth rates in C. serrulata did not increase, while those in H. uninervis and T. hemprichii significantly increased with increasing pCO2 levels. While seagrasses can be carbon-limited and productivity can respond positively to CO2 enrichment, varying carbon allocation strategies amongst species suggest differential growth response between species. Thus, future increase in seawater CO2 concentration may lead to an overall increase in seagrass biomass and productivity, as well as community changes in seagrass meadows.

A new class of symbolic abstract neural nets

Starting from the way the inter-cellular communication takes place by means of protein channels and also from the standard knowledge about neuron functioning, we propose a computing model called a tissue P system, which processes symbols in a multiset rewriting sense, in a net of cells similar to a neural net. Each cell has a finite state memory, processes multisets of symbol-impulses, and can send impulses (?excitations?) to the neighboring cells. Such cell nets are shown to be rather powerful: they can simulate a Turing machine even when using a small number of cells, each of them having a small number of states. Moreover, in the case when each cell works in the maximal manner and it can excite all the cells to which it can send impulses, then one can easily solve the Hamiltonian Path Problem in linear time. A new characterization of the Parikh images of ET0L languages are also obtained in this framework.

Rational invariants on the space of all structures of algebras on a two-dimensional vector space

Rational invariants on the space of all structures of algebras on a two-dimensional vector space

Further Applications of P-Adaptive Boundary Elements

In previous BEM Conferences , the concepts, developments and organisation of the p-adaptive philosophy have been presented by the authors, as well as some interesting features of the hierarchisation of the solution, accuracy estimates and numerical computations optimization. This current paper is devoted to presenting some new developments and aplications in linear elastostatics, with emphasis on: a ) Efficient computation of influence coefficients, b) Efficient evaluation of the residuals by taking advantage of the hierarchy of the interpolation functions and e) New results regarding estimators and convergence ratios.In addition, several practical examples will be shown and discussed in order to point out the advantages of the method .

An Architecture forRepresenting Biological Processes based on Networks of Bio-inspired Processors

n this paper we propose the use of Networks of Bio-inspired Processors (NBP) to model some biological phenomena within a computational framework. In particular, we propose the use of an extension of NBP named Network Evolutionary Processors Transducers to simulate chemical transformations of substances. Within a biological process, chemical transformations of substances are basic operations in the change of the state of the cell. Previously, it has been proved that NBP are computationally complete, that is, they are able to solve NP complete problems in linear time, using massively parallel computations. In addition, we propose a multilayer architecture that will allow us to design models of biological processes related to cellular communication as well as their implications in the metabolic pathways. Subsequently, these models can be applied not only to biological-cellular instances but, possibly, also to configure instances of interactive processes in many other fields like population interactions, ecological trophic networks, in dustrial ecosystems, etc.

Discussion of “Initial Pore Pressure from Vertical Surface Loads” by Jacobo Bielak (September, 1982)

The author presents a very interesting application of the ideas developed by Scott to determine the initial pore pressure in excess of the hydrostatic pore pressure in linear, elastic, homogeneous and isotropic soil-skeleton. Scott demonstrates that under vertical surface loads the problem is governed by Laplace's equation. Nevertheless the writers' think that it could be interesting to state clearly the conditions under which this analogy can be applied.

Análisis de elementos viga-columna en régimen no lineal con deformación por cortante

El hormigón estructural sigue siendo sin duda uno de los materiales más utilizados en construcción debido a su resistencia, rigidez y flexibilidad para diseñar estructuras. El cálculo de estructuras de hormigón, utilizando vigas y vigas-columna, es complejo debido a los fenómenos de acoplamiento entre esfuerzos y al comportamiento no lineal del material. Los modelos más empleados para su análisis son el de Bernoulli-Euler y el de Timoshenko, indicándose en la literatura la conveniencia de usar el segundo cuando la relación canto/luz no es pequeña o los elementos están fuertemente armados. El objetivo fundamental de esta tesis es el análisis de elementos viga y viga-columna en régimen no lineal con deformación por cortante, aplicando el concepto de Pieza Lineal Equivalente (PLE). Concepto éste que consiste básicamente en resolver el problema de una pieza en régimen no lineal, transformándolo en uno lineal equivalente, de modo que ambas piezas tengan la misma deformada y los mismos esfuerzos. Para ello, se hizo en primer lugar un estudio comparado de: las distintas propuestas que aplican la deformación por cortante, de los distintos modelos constitutivos y seccionales del hormigón estructural y de los métodos de cálculo no lineal aplicando el método de elementos finitos (MEF). Teniendo en cuenta que la resolución del problema no lineal se basa en la resolución de sucesivos problemas lineales empleando un proceso de homotopía, los problemas lineales de la viga y viga-columna de Timoshenko, se resuelven mediante MEF, utilizando soluciones nodalmente exactas (SNE) y acción repartida equivalente de cualquier orden. Se obtiene así, con muy pocos elementos finitos, una excelente aproximación de la solución, no sólo en los nodos sino en el interior de los elementos. Se introduce el concepto PLE para el análisis de una barra, de material no lineal, sometida a acciones axiales, y se extiende el mismo para el análisis no lineal de vigas y vigas-columna con deformación por cortante. Cabe señalar que para estos últimos, la solución de una pieza en régimen no lineal es igual a la de una en régimen lineal, cuyas rigideces son constantes a trozos, y donde además hay que añadir momentos y cargas puntuales ficticias en los nodos, así como, un momento distribuido ficticio en toda la pieza. Se han desarrollado dos métodos para el análisis: uno para problemas isostáticos y otro general, aplicable tanto a problemas isostáticos como hiperestáticos. El primero determina de entrada la PLE, realizándose a continuación el cálculo por MEF-SNE de dicha pieza, que ahora está en régimen lineal. El general utiliza una homotopía que transforma de manera iterativa, unas leyes constitutivas lineales en las leyes no lineales del material. Cuando se combina con el MEF, la pieza lineal equivalente y la solución del problema original quedan determinadas al final de todo el proceso. Si bien el método general es un procedimiento próximo al de Newton- Raphson, presenta sobre éste la ventaja de permitir visualizar las deformaciones de la pieza en régimen no lineal, de manera tanto cualitativa como cuantitativa, ya que es posible observar en cada paso del proceso la modificación de rigideces (a flexión y cortante) y asimismo la evolución de las acciones ficticias. Por otra parte, los resultados obtenidos comparados con los publicados en la literatura, indican que el concepto PLE ofrece una forma directa y eficiente para analizar con muy buena precisión los problemas asociados a vigas y vigas-columna en las que por su tipología los efectos del cortante no pueden ser despreciados. ABSTRACT The structural concrete clearly remains the most used material in construction due to its strength, rigidity and structural design flexibility. The calculation of concrete structures using beams and beam-column is complex as consequence of the coupling phenomena between stresses and of its nonlinear behaviour. The models most commonly used for analysis are the Bernoulli-Euler and Timoshenko. The second model is strongly recommended when the relationship thickness/span is not small or in case the elements are heavily reinforced. The main objective of this thesis is to analyse the beam and beam-column elements with shear deformation in nonlinear regime, applying the concept of Equivalent Linear Structural Element (ELSE). This concept is basically to solve the problem of a structural element in nonlinear regime, transforming it into an equivalent linear structural element, so that both elements have the same deformations and the same stresses. Firstly, a comparative study of the various proposals of applying shear deformation, of various constitutive and sectional models of structural concrete, and of the nonlinear calculation methods (using finite element methods) was carried out. Considering that the resolution of nonlinear problem is based on solving the successive linear problem, using homotopy process, the linear problem of Timoshenko beam and beam-columns is resolved by FEM, using the exact nodal solutions (ENS) and equivalent distributed load of any order. Thus, the accurate solution approximation can be obtained with very few finite elements for not only nodes, but also for inside of elements. The concept ELSE is introduced to analyse a bar of nonlinear material, subjected to axial forces. The same bar is then used for other nonlinear beam and beam-column analysis with shear deformation. It is noted that, for the last analyses, the solution of a structural element in nonlinear regime is equal to that of linear regime, in which the piecewise-stiffness is constant, the moments and fictitious point loads need to be added at nodes of each element, as well as the fictitious distributed moment on element. Two methods have been developed for analysis: one for isostatic problem and other more general, applicable for both isostatic and hiperstatic problem. The first method determines the ELSE, and then the calculation of this piece is performed by FEM-ENS that now is in linear regime. The general method uses the homotopy that transforms iteratively linear constitutive laws into nonlinear laws of material. When combined with FEM, the ELSE and the solution of the original problem are determined at the end of the whole process. The general method is well known as a procedure closed to Newton-Raphson procedure but presents an advantage that allows displaying deformations of the piece in nonlinear regime, in both qualitative and quantitative way. Since it is possible to observe the modification of stiffness (flexural and shear) in each step of process and also the evolution of the fictitious actions. Moreover, the results compared with those published in the literature indicate that the ELSE concept offers a direct and efficient way to analyze with very good accuracy the problems associated with beams and beams columns in which, by typology, the effects of shear cannot be neglected.