Probabilistic reasoning with a bayesian DNA device based on strand displacement

We present a computing model based on the DNA strand displacement technique which performs Bayesian inference. The model will take single stranded DNA as input data, representing the presence or absence of a specific molecular signal (evidence). The program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different DNA complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded DNA species whose relative proportion represents the application of Bayes? Law: the conditional probability of the disease given the signal. The models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro.

Load displacement in grape harvesters: Discrete Element Analysis.

Dynamic weighing of the hopper in grape harvesters is affected by a number of factors. One of them is the displacement of the load inside the hopper as a consequence of the terrain topography. In this work, the weight obtained by a load cell in a grape harvester has been analysed and quantified using the discrete element method (DEM). Different models have been developed considering different scenarios for the terrain.

Increasing the accuracy of positive displacement meters for the measurement of volume in liquid hydrocarbon logistics

Accuracy in the liquid hydrocarbons custody transfer is mandatory because it has a great economic impact. By far the most accurate meter is the positive displacement (PD) meter. Increasing such an accuracy may adversely affect the cost of the custody transfer, unless simple models are developed in order to lower the cost, which is the purpose of this work. PD meter consists of a fixed volume rotating chamber. For each turn a pulse is counted, hence, the measured volume is the number of pulses times the volume of the chamber. It does not coincide with the real volume, so corrections have to be made. All the corrections are grouped by a meter factor. Among corrections highlights the slippage flow. By solving the Navier-Stokes equations one can find an analytical expression for this flow. It is neither easy nor cheap to apply straightforward the slippage correction; therefore we have made a simple model where slippage is regarded as a single parameter with dimension of time. The model has been tested for several PD meters. In our careful experiments, the meter factor grows with temperature at a constant pace of 8?10?5?ºC?1. Be warned

Modelling Human Displacement through Movement Surfaces.

This paper introduces a new approach for predicting people displacement by means of movementsurfaces. These surfaces can allow the simulation of a person?s movement through the use of semanticmovement concepts such as those making up the environment, the people who are moving, eventsthat describe a human activity, and time of occurrences. In order to represent this movement we havetransformed the trajectory of a person or group of persons into a raindrop path over a surface. As araindrop flows over a surface looking for the maximum slopes, people flow over the landscapelooking for the maximum utility. The movement surfaces are the response to a chained succession of events describing the way a person moves from one destination to another passing through the mostaffine trajectory to his interest. The three construction phases of this modelling approach (exploration,reasoning and prediction) are presented in this paper. The model was implemented in Protégé and aJava application was developed to generate the movement surface based on a recreational scenario.The results had shown the opportunity to apply our approach to optimise the accessibility of recreational areas according to the preferences of the users of that location.

Arquitecturas desplazadas. Rafael Bergamín y las arquitecturas del exilio español en Venezuela

El siglo XX ha sido el siglo de los desplazamientos. Una ingente cantidad de personas fueron forzadas por motivos políticos, o se vieron obligadas por motivos económicos, a abandonar sus territorios de origen, generando un distanciamiento que en la mayoría de los casos resultaría irrecuperable. Las penurias vividas en Europa, las oportunidades que se abrían en países americanos, o la presión ejercida por los regímenes totalitarios, llevaron a un buen número de profesionales, artistas e intelectuales europeos a territorio americano. El presente trabajo se propone indagar sobre una de esas migraciones que se establecieron en Latinoamérica en la primera mitad del siglo XX: la de los arquitectos españoles que se vieron forzados al exilio. Para ello se busca poner en evidencia no sólo sus aportaciones sino también la influencia que ejerció en su obra la cultura de los países de adopción. Venezuela recibió gran parte del contingente de arquitectos españoles desplazados como consecuencia de la Guerra Civil. Tras México fue el país que mayor número acogió. La llegada de dichos exiliados coincidió con el momento en que la sociedad venezolana, de base agrícola y comercial, pasaría a evidenciar el impacto de la revolución petrolera. Así pues, dicha llegada supuso no sólo la dramática pérdida del mundo previo, implícita en todo exilio, sino el arribo a una sociedad en profundo proceso de cambio. En ambos casos se trataba de “mundos que se desvanecen”. Se propone la asunción de la obra de dichos profesionales como una arquitectura desplazada. Un desplazamiento que se produce en dos sentidos: por un lado, se trata de un desplazamiento físico, por otro, la palabra desplazada habla también de la condición secundaria que adquiere la arquitectura ante el drama vital y de supervivencia que afectó a los exiliados. Así pues, a un desplazamiento físico, verificable, se une un desplazamiento en cuanto al nivel de importancia y de atención asignado a la arquitectura. El trabajo comprende una introducción, cuatro capítulos, y un epílogo, a modo de conclusión. A lo largo de dichos capítulos se conjugan el enfoque individual en la obra de uno de estos arquitectos desterrados, Rafael Bergamín, y la visión “coral” de diversas trayectorias vitales que enfrentaron un destino común. Se elige la figura de Bergamín como eje de desarrollo debido a la presencia significativa que tuvo su obra tanto en España como en Venezuela, y por la caracterización de la misma como obra construida en colaboración. La introducción, “Exilios arquitectónicos”, muestra el sustrato estructural, la fundamentación y la metodología empleada, incluyendo “problematizaciones” sobre el exilio arquitectónico. El primer capítulo, “Memoria de partida”, da cuenta de la formación y actuación, durante la preguerra, de los arquitectos españoles que saldrían al exilio. Se introduce un esquema de base generacional y se revela un panorama para nada unívoco. El segundo capítulo, “Guerra y salida al exilio”, aborda la actuación de dichos arquitectos durante la contienda bélica así como la posterior dispersión general del exilio. El tercer capítulo, “Construir desde lo que se desvanece. Arquitectos del exilio español en Venezuela”, propone diversos presupuestos conceptuales en torno al tema del desplazamiento en la arquitectura, revisando la adscripción disciplinar y profesional de los arquitectos españoles exiliados en Venezuela. El cuarto capítulo, “El regreso”, versa sobre el recorrido final de estos arquitectos. Como marco general, se revisa su itinerario de regreso o, en muchos casos, la imposibilidad de retorno. Por último, se dispone la fuente de los diversos documentos de archivos y repositorios, así como el aparato bibliográfico y referencial, empleados en la investigación. Tres anexos se adjuntan al corpus del trabajo. El primero presenta documentos inéditos, hallados durante el pertinente proceso de investigación; el segundo, dibujos de Bergamín, básicamente de las primeras décadas del siglo XX: caricaturas, anuncios y trabajos de la Escuela; el tercero, un esbozo biográfico de los arquitectos del exilio español. ABSTRACT The 20th Century has been the century of displacements. An enormous number of people were forced to leave their homelands for political or economic reasons, which generated a gap that in most of the cases would be unrecoverable. The hardships that people had to endure in Europe, the opportunities that emerged in American countries, or the pressure exerted by totalitarian regimes drove a good number of European professionals, artists and intellectuals to American territory. This research study is intended to investigate one of those migrations that settled in Latin America during the first half of the 20th century: the one of the Spanish architects that were forced into exile. To achieve this, an attempt was made to expose not only their contributions but also the influence that the culture of the countries which welcomed them exerted in their work. Venezuela received a large portion of Spanish architects who were displaced as a consequence of the Civil War. After Mexico, it was the country that sheltered the greatest number of persons. The arrival of these exiled Spanish architects coincided with the moment in which the Venezuelan society – based on agriculture and commerce – would witness the impact of the revolution of the oil industry. Thus, their arrival supposed not only experiencing the dramatic loss of their previous world – implicit in the notion of the exile – but also settling in a society going through a profound change process. In both cases it was about “two worlds that were vanishing.” The assumption of these architects’ work is regarded as a displaced architecture. A displacement that takes place in two ways: on one hand, there was a physical displacement, and on the other hand, the word displaced also talks about the second place that architecture is given when confronted with the urgent drama of survival that affected the exiled community. Hence, a physical, verifiable displacement is combined with a displacement that has to do with the importance and the attention given to architecture. This research study encompasses an introduction, four chapters, and an epilogue as a conclusion. Throughout the chapters, the individual approach to the work of one of these exiled architects, Rafael Bergamín, runs in parallel to an overall view of various other architects’ career paths that faced a common destiny. The work of the architect Bergamín was chosen as the center of this research study due to the significant presence that his work had in Spain as well as in Venezuela, and because its main characteristic was that it was built in collaboration with other architects. The introduction, “Architectural exiles”, shows the structural contextualization, the explanatory thesis statement and the methodology used, including “problematizations” about the architectural exile. The first chapter, “Memory of departure”, contains the academic background and performance during the pre-war time of the Spanish architects that would go into exile. An outline based on different generations and revealing an unambiguous perspective is introduced. The second chapter, “War and departure into exile”, tackles the performance of the Spanish architects during the war, as well as the following general diaspora into exile. The third chapter, “Building from what vanishes. Architects of the Spanish exile in Venezuela”, proposes various conceptual assumptions concerning the topic of displacement in architecture according to the doctrine and professional affiliations of the Spanish architects exiled in Venezuela. The fourth chapter, “The return”, deals with the end of these architects’ careers. As a general framework, their itineraries to return, or in many cases, the impossibility of returning, are reviewed. Finally, the sources to the various documents of files and repositories, as well as the bibliographical references consulted for the research, are provided. Three annexes have been attached to this research study. The first annex contains unpublished documents found during the research process; the second includes Bergamín’s drawings, basically from the first decades of the 20th century, such as, caricatures, advertisements and assignments done when he was a university student; and the third annex presents a biographical outline of the architects of the Spanish exile.

A large displacement structural analysis of a pipeline subjected to gravity and buoyancy forces

A nonlinear analysis of an elastic tube subjected to gravity forces and buoyancy pressure is carried out. An update lagrangian formulation is used. The structural analysis efficiency in terms of computer time and accuracy, has been improved when load stiffness matrices have been introduced. In this way the follower forces characteristics such as their intensity and direction changes can be well represented. A sensitivity study of different involved variables on the final deformed pipeline shape is carried out.

Uncertainty in optical bio-sensors due to the spectral displacement of the interference modes of the transduction signal. Incertidumbre en bio-sensores ópticos asociada al desplazamiento espectral de los modos de interferencia de la señal de transducción

The analysis of the interference modes has an increasing application, especially in the field of optical biosensors. In this type of sensors, the displacement Δν of the interference modes of the transduction signal is observed when a particular biological agent is placed over the biosensor. In order to measure this displacement, the position of a maximum (or a minimum) of the signal must be detected before and after placing the agent over the sensor. A parameter of great importance for this kind of sensors is the period Pν of the signal, which is inversely proportional to the optical thickness h0 of the sensor in the absence of the biological agent. The increase of this period improves the sensitivity of the sensor but it worsens the detection of the maximum. In this paper, authors analyze the propagation of uncertainties in these sensors when using least squares techniques for the detection of the maxima (or minima) of the signal. Techniques described in supplement 2 of the ISO-GUM Guide are used. The result of the analysis allows a metrological educated answer to the question of which is the optimal period Pν of the signal. El análisis del comportamiento de los modos de interferencia tiene una aplicación cada vez más amplia, especialmente en el campo de los biosensores ópticos. En este tipo de sensores se observa el desplazamiento Δν de los modos de interferencia de la señal de transducción al reconocer un de-terminado agente biológico. Para medir ese desplazamiento se debe detectar la posición de un máximo o mínimo de la señal antes y después de dicho desplazamiento. En este tipo de biosensores un parámetro de gran importancia es el periodo Pν de la señal el cual es inversamente proporcional al espesor óptico h0 del sensor en ausencia de agente biológico. El aumento de dicho periodo mejora la sensibilidad del sensor pero parece dificultar la detección del mínimo o máximo. Por tanto, su efecto sobre la incertidumbre del resultado de la medida presenta dos efectos contrapuestos: la mejora de la sensibilidad frente a la dificultad creciente en la detección del mínimo ó máximo. En este trabajo, los autores analizan la propagación de incertidumbres en estos sensores utilizando herramientas de ajuste por MM.CC. para la detección de los mínimos o máximos de la señal y técnicas de propagación de incertidumbres descritas en el suplemento 2 de la Guía ISO-GUM. El resultado del análisis permite dar una respuesta, justificada desde el punto de vista metrológico, de en que condiciones es conveniente o no aumentar el periodo Pν de la señal.

Forced Response of Mistuned Bladed Disks: Quantitative Validation of the Asymptotic Description

The effect of small mistuning in the forced response of a bladed disk is analyzed using a recently introduced methodology: the asymptotic mistuning model. The asymptotic mistuning model is an extremely reduced, simplified model that is derived directly from the full formulation of the mistuned bladed disk using a consistent perturbative procedure based on the relative smallness of the mistuning distortion. A detailed description of the derivation of the asymptotic mistuning model for a realistic bladed disk configuration is presented. The asymptotic mistuning model results for several different mistuning patterns and forcing conditions are compared with those from a high-resolution finite element model. The asymptotic mistuning model produces quantitatively accurate results, and, probably more relevant, it gives precise information about the factors (tuned modes and components of the mistuning pattern) that actually play a role in the vibrational forced response of mistuned bladed disks.

Pararotor dynamics: center of mass displacement from the blade plane—analytical approach

The pararotor is a biology-inspired decelerator device based on the autorotation of a rotary wing whose main purpose is to guide a load descent into a certain atmosphere. This paper focuses on a practical approach to the general dynamic stability of a pararotor whose center of mass is displaced from the blade plane. The analytical study departs from the motion equations of pararotor flight, considering the center of mass displacement from the blade plane, studied over a number of simplifying hypotheses that allows determining the most important influences to flight behavior near equilibrium. Two practical indexes are developed to characterize the stability of a pararotor in terms of geometry, inertia, and the aerodynamic characteristics of the device. Based on these two parameters, a stability diagram can be defined upon which stability regions can be identified. It was concluded that the ability to reach stability conditions depends mainly on a limited number of parameters associated with the pararotor configuration: the relationship between moments of inertia, the position of the blades, the planform shape (associated with the blade aerodynamic coefficients and blade area), and the vertical distance between the center of mass and the blade plane. These parameters can be evaluated by computing practical indexes to determine stability behavior.

The forced oscillations of submerged bodies

The increasing use of very light structures in aerospace applications are given rise to the need of taking into account the effects of the surrounding media in the motion of a structure (as for instance, in modal testing of solar panels or antennae) as it is usually performed in the motion of bodies submerged in water in marine applications. New methods are in development aiming at to determine rigid-body properties (the center of mass position and inertia properties) from the results of oscillations tests (at low frequencies during modal testing, by exciting the rigid-body modes only) by using the equations of the rigid-body dynamics. As it is shown in this paper, the effect of the surrounding media significantly modifies the oscillation dynamics in the case of light structures and therefore this effect should be taken into account in the development of the above-mentioned methods. The aim of the paper is to show that, if a central point exists for the aerodynamic forces acting on the body, the motion equations for the small amplitude rotational and translational oscillations can be expressed in a form which is a generalization of the motion equations for a body in vacuum, thus allowing to obtain a physical idea of the motion and aerodynamic effects and also significantly simplifying the calculation of the solutions and the interpretation of the results. In the formulation developed here the translational oscillations and the rotational motion around the center of mass are decoupled, as is the case for the rigid-body motion in vacuum, whereas in the classical added mass formulation the six motion equations are coupled. Also in this paper the nonsteady motion of small amplitude of a rigid body submerged in an ideal, incompressible fluid is considered in order to define the conditions for the existence of the central point in the case of a three-dimensional body. The results here presented are also of interest in marine applications.

The role of enzyme distortion in the single displacement mechanism of family 19 chitinases

By using molecular dynamics simulations, we have examined the binding of a hexaNAG substrate and two potential hydrolysis intermediates (an oxazoline ion and an oxocarbenium ion) to a family 19 barley chitinase. We find the hexaNAG substrate binds with all sugars in a chair conformation, unlike the family 18 chitinase which causes substrate distortion. Glu 67 is in a position to protonate the anomeric oxygen linking sugar residues D and E whereas Asn 199 serves to hydrogen bond with the C2′ N-acetyl group of sugar D, thus preventing the formation of an oxazoline ion intermediate. In addition, Glu 89 is part of a flexible loop region allowing a conformational change to occur within the active site to bring the oxocarbenium ion intermediate and Glu 89 closer by 4–5 Å. A hydrolysis product with inversion of the anomeric configuration occurs because of nucleophilic attack by a water molecule that is coordinated by Glu 89 and Ser 120. Issues important for the design of inhibitors specific to family 19 chitinases over family 18 chitinases also are discussed.

Architectural specificity in chromatin structure at the TATA box in vivo: Nucleosome displacement upon β-phaseolin gene activation

Extensive studies of the β-phaseolin (phas) gene in transgenic tobacco have shown that it is highly active during seed embryogenesis but is completely silent in leaf and other vegetative tissues. In vivo footprinting revealed that the lack of even basal transcriptional activity in vegetative tissues is associated with the presence of a nucleosome that is rotationally positioned with base pair precision over three phased TATA boxes present in the phas promoter. Positioning is sequence-dependent because an identical rotational setting is obtained upon nucleosome reconstitution in vitro. A comparison of DNase I and dimethyl sulfate footprints in vivo and in vitro strongly suggests that this repressive chromatin architecture is remodeled concomitant with gene activation in the developing seed. This leads to the disruption of histone-mediated DNA wrapping and the assembly of the TATA boxes into a transcriptionally competent nucleoprotein complex.

Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

The semiempirical PM3 method, calibrated against ab initio HF/6–31+G(d) theory, has been used to elucidate the reaction of 1,2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO− with DCE; (ii) the structures of the transition states in the gas-phase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal/mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.

Character displacement in some Cnemidophorus lizards revisited: A phylogenetic analysis

Ecological studies have demonstrated the role of competition in structuring communities; however, the importance of competition as a vehicle for evolution by natural selection and speciation remains unresolved. Study systems of insular faunas have provided several well known cases where ecological character displacement, coevolution of competitors leading to increased morphological separation, is thought to have occurred (e.g., anoline lizards and geospizine finches). Whiptail lizards (genus Cnemidophorus) from the islands of the Sea of Cortez and the surrounding mainland demonstrate a biogeographic pattern of morphological variation suggestive of character displacement. Two species of Cnemidophorus occur on the Baja peninsula, one relatively large (Cnemidophorus tigris) and one smaller (Cnemidophorus hyperythrus). Oceanic islands in the Sea of Cortez contain only single species, five of six having sizes intermediate to both species found on the Baja peninsula. On mainland Mexico C. hyperythrus is absent, whereas C. tigris is the smaller species in whiptail guilds. Here we construct a phylogeny using nucleotide sequences of the cytochrome b gene to infer the evolutionary history of body size change and historical patterns of colonization in the Cnemidophorus system. The phylogenetic analysis indicates that (i) oceanic islands have been founded at least five times from mainland sources by relatives of either C. tigris or C. hyperythrus, (ii) there have been two separate instances of character relaxation on oceanic islands for C. tigris, and (iii) there has been colonization of the oceanic island Cerralvo with retention of ancestral size for Cnemidophorus ceralbensis, a relative of C. hyperythrus. Finally, the phylogenetic analysis reveals potential cryptic species within mainland populations of C. tigris.

Voltage-induced membrane displacement in patch pipettes activates mechanosensitive channels

The patch-clamp technique allows currents to be recorded through single ion channels in patches of cell membrane in the tips of glass pipettes. When recording, voltage is typically applied across the membrane patch to drive ions through open channels and to probe the voltage-sensitivity of channel activity. In this study, we used video microscopy and single-channel recording to show that prolonged depolarization of a membrane patch in borosilicate pipettes results in delayed slow displacement of the membrane into the pipette and that this displacement is associated with the activation of mechanosensitive (MS) channels in the same patch. The membrane displacement, ≈1 μm with each prolonged depolarization, occurs after variable delays ranging from tens of milliseconds to many seconds and is correlated in time with activation of MS channels. Increasing the voltage step shortens both the delay to membrane displacement and the delay to activation. Preventing depolarization-induced membrane displacement by applying positive pressure to the shank of the pipette or by coating the tips of the borosilicate pipettes with soft glass prevents the depolarization-induced activation of MS channels. The correlation between depolarization-induced membrane displacement and activation of MS channels indicates that the membrane displacement is associated with sufficient membrane tension to activate MS channels. Because membrane tension can modulate the activity of various ligand and voltage-activated ion channels as well as some transporters, an apparent voltage dependence of a channel or transporter in a membrane patch in a borosilicate pipette may result from voltage-induced tension rather than from direct modulation by voltage.