Analysis of the static and dynamic behaviour of hydraulic fills

En la actualidad existe un gran conocimiento en la caracterización de rellenos hidráulicos, tanto en su caracterización estática, como dinámica. Sin embargo, son escasos en la literatura estudios más generales y globales de estos materiales, muy relacionados con sus usos y principales problemáticas en obras portuarias y mineras. Los procedimientos semi‐empíricos para la evaluación del efecto silo en las celdas de cajones portuarios, así como para el potencial de licuefacción de estos suelos durantes cargas instantáneas y terremotos, se basan en estudios donde la influencia de los parámetros que los rigen no se conocen en gran medida, dando lugar a resultados con considerable dispersión. Este es el caso, por ejemplo, de los daños notificados por el grupo de investigación del Puerto de Barcelona, la rotura de los cajones portuarios en el Puerto de Barcelona en 2007. Por estos motivos y otros, se ha decidido desarrollar un análisis para la evaluación de estos problemas mediante la propuesta de una metodología teórico‐numérica y empírica. El enfoque teórico‐numérico desarrollado en el presente estudio se centra en la determinación del marco teórico y las herramientas numéricas capaces de solventar los retos que presentan estos problemas. La complejidad del problema procede de varios aspectos fundamentales: el comportamiento no lineal de los suelos poco confinados o flojos en procesos de consolidación por preso propio; su alto potencial de licuefacción; la caracterización hidromecánica de los contactos entre estructuras y suelo (camino preferencial para el flujo de agua y consolidación lateral); el punto de partida de los problemas con un estado de tensiones efectivas prácticamente nulo. En cuanto al enfoque experimental, se ha propuesto una metodología de laboratorio muy sencilla para la caracterización hidromecánica del suelo y las interfaces, sin la necesidad de usar complejos aparatos de laboratorio o procedimientos excesivamente complicados. Este trabajo incluye por tanto un breve repaso a los aspectos relacionados con la ejecución de los rellenos hidráulicos, sus usos principales y los fenómenos relacionados, con el fin de establecer un punto de partida para el presente estudio. Este repaso abarca desde la evolución de las ecuaciones de consolidación tradicionales (Terzaghi, 1943), (Gibson, English & Hussey, 1967) y las metodologías de cálculo (Townsend & McVay, 1990) (Fredlund, Donaldson and Gitirana, 2009) hasta las contribuciones en relación al efecto silo (Ranssen, 1985) (Ravenet, 1977) y sobre el fenómeno de la licuefacción (Casagrande, 1936) (Castro, 1969) (Been & Jefferies, 1985) (Pastor & Zienkiewicz, 1986). Con motivo de este estudio se ha desarrollado exclusivamente un código basado en el método de los elementos finitos (MEF) empleando el programa MATLAB. Para ello, se ha esablecido un marco teórico (Biot, 1941) (Zienkiewicz & Shiomi, 1984) (Segura & Caron, 2004) y numérico (Zienkiewicz & Taylor, 1989) (Huerta & Rodríguez, 1992) (Segura & Carol, 2008) para resolver problemas de consolidación multidimensional con condiciones de contorno friccionales, y los correspondientes modelos constitutivos (Pastor & Zienkiewicz, 1986) (Fiu & Liu, 2011). Asimismo, se ha desarrollado una metodología experimental a través de una serie de ensayos de laboratorio para la calibración de los modelos constitutivos y de la caracterización de parámetros índice y de flujo (Castro, 1969) (Bahda 1997) (Been & Jefferies, 2006). Para ello se han empleado arenas de Hostun como material (relleno hidráulico) de referencia. Como principal aportación se incluyen una serie de nuevos ensayos de corte directo para la caracterización hidromecánica de la interfaz suelo – estructura de hormigón, para diferentes tipos de encofrados y rugosidades. Finalmente, se han diseñado una serie de algoritmos específicos para la resolución del set de ecuaciones diferenciales de gobierno que definen este problema. Estos algoritmos son de gran importancia en este problema para tratar el procesamiento transitorio de la consolidación de los rellenos hidráulicos, y de otros efectos relacionados con su implementación en celdas de cajones, como el efecto silo y la licuefacciones autoinducida. Para ello, se ha establecido un modelo 2D axisimétrico, con formulación acoplada u‐p para elementos continuos y elementos interfaz (de espesor cero), que tratan de simular las condiciones de estos rellenos hidráulicos cuando se colocan en las celdas portuarias. Este caso de estudio hace referencia clara a materiales granulares en estado inicial muy suelto y con escasas tensiones efectivas, es decir, con prácticamente todas las sobrepresiones ocasionadas por el proceso de autoconsolidación (por peso propio). Por todo ello se requiere de algoritmos numéricos específicos, así como de modelos constitutivos particulares, para los elementos del continuo y para los elementos interfaz. En el caso de la simulación de diferentes procedimientos de puesta en obra de los rellenos se ha requerido la modificacion de los algoritmos empleados para poder así representar numéricamente la puesta en obra de estos materiales, además de poder realizar una comparativa de los resultados para los distintos procedimientos. La constante actualización de los parámetros del suelo, hace también de este algoritmo una potente herramienta que permite establecer un interesante juego de perfiles de variables, tales como la densidad, el índice de huecos, la fracción de sólidos, el exceso de presiones, y tensiones y deformaciones. En definitiva, el modelo otorga un mejor entendimiento del efecto silo, término comúnmente usado para definir el fenómeno transitorio del gradiente de presiones laterales en las estructuras de contención en forma de silo. Finalmente se incluyen una serie de comparativas entre los resultados del modelo y de diferentes estudios de la literatura técnica, tanto para el fenómeno de las consolidaciones por preso propio (Fredlund, Donaldson & Gitirana, 2009) como para el estudio del efecto silo (Puertos del Estado, 2006, EuroCódigo (2006), Japan Tech, Stands. (2009), etc.). Para concluir, se propone el diseño de un prototipo de columna de decantación con paredes friccionales, como principal propuesta de futura línea de investigación. Wide research is nowadays available on the characterization of hydraulic fills in terms of either static or dynamic behavior. However, reported comprehensive analyses of these soils when meant for port or mining works are scarce. Moreover, the semi‐empirical procedures for assessing the silo effect on cells in floating caissons, and the liquefaction potential of these soils during sudden loads or earthquakes are based on studies where the underlying influence parameters are not well known, yielding results with significant scatter. This is the case, for instance, of hazards reported by the Barcelona Liquefaction working group, with the failure of harbor walls in 2007. By virtue of this, a complex approach has been undertaken to evaluate the problem by a proposal of numerical and laboratory methodology. Within a theoretical and numerical scope, the study is focused on the numerical tools capable to face the different challenges of this problem. The complexity is manifold; the highly non‐linear behavior of consolidating soft soils; their potentially liquefactable nature, the significance of the hydromechanics of the soil‐structure contact, the discontinuities as preferential paths for water flow, setting “negligible” effective stresses as initial conditions. Within an experimental scope, a straightforward laboratory methodology is introduced for the hydromechanical characterization of the soil and the interface without the need of complex laboratory devices or cumbersome procedures. Therefore, this study includes a brief overview of the hydraulic filling execution, main uses (land reclamation, filled cells, tailing dams, etc.) and the underlying phenomena (self‐weight consolidation, silo effect, liquefaction, etc.). It comprises from the evolution of the traditional consolidation equations (Terzaghi, 1943), (Gibson, English, & Hussey, 1967) and solving methodologies (Townsend & McVay, 1990) (Fredlund, Donaldson and Gitirana, 2009) to the contributions in terms of silo effect (Ranssen, 1895) (Ravenet, 1977) and liquefaction phenomena (Casagrande, 1936) (Castro, 1969) (Been & Jefferies, 1985) (Pastor & Zienkiewicz, 1986). The novelty of the study lies on the development of a Finite Element Method (FEM) code, exclusively formulated for this problem. Subsequently, a theoretical (Biot, 1941) (Zienkiewicz and Shiomi, 1984) (Segura and Carol, 2004) and numerical approach (Zienkiewicz and Taylor, 1989) (Huerta, A. & Rodriguez, A., 1992) (Segura, J.M. & Carol, I., 2008) is introduced for multidimensional consolidation problems with frictional contacts and the corresponding constitutive models (Pastor & Zienkiewicz, 1986) (Fu & Liu, 2011). An experimental methodology is presented for the laboratory test and material characterization (Castro 1969) (Bahda 1997) (Been & Jefferies 2006) using Hostun sands as reference hydraulic fill. A series of singular interaction shear tests for the interface calibration is included. Finally, a specific model algorithm for the solution of the set of differential equations governing the problem is presented. The process of consolidation and settlements involves a comprehensive simulation of the transient process of decantation and the build‐up of the silo effect in cells and certain phenomena related to self‐compaction and liquefaction. For this, an implementation of a 2D axi‐syimmetric coupled model with continuum and interface elements, aimed at simulating conditions and self‐weight consolidation of hydraulic fills once placed into floating caisson cells or close to retaining structures. This basically concerns a loose granular soil with a negligible initial effective stress level at the onset of the process. The implementation requires a specific numerical algorithm as well as specific constitutive models for both the continuum and the interface elements. The simulation of implementation procedures for the fills has required the modification of the algorithm so that a numerical representation of these procedures is carried out. A comparison of the results for the different procedures is interesting for the global analysis. Furthermore, the continuous updating of the model provides an insightful logging of variable profiles such as density, void ratio and solid fraction profiles, total and excess pore pressure, stresses and strains. This will lead to a better understanding of complex phenomena such as the transient gradient in lateral pressures due to silo effect in saturated soils. Interesting model and literature comparisons for the self‐weight consolidation (Fredlund, Donaldson, & Gitirana, 2009) and the silo effect results (Puertos del Estado (2006), EuroCode (2006), Japan Tech, Stands. (2009)). This study closes with the design of a decantation column prototype with frictional walls as the main future line of research.

Analysis of the railway track as a spatially periodic structure

This article presents a new and computationally efficient method of analysis of a railway track modelled as a continuous beam of 2N spans supported by elastic vertical springs. The main feature of this method is its important reduction in computational effort with respect to standard matrix methods of structural analysis. In this article, the whole structure is considered to be a repetition of a single one. The analysis presented is applied to a simple railway track model, i.e. to a repetitive beam supported on vertical springs (sleepers). The proposed method of analysis is based on the general theory of spatially periodic structures. The main feature of this theory is the possibility to apply Discrete Fourier Transform (DFT) in order to reduce a large system of q(2N + 1) linear stiffness equilibrium equations to a set of 2N + 1 uncoupled systems of q equations each. In this way, a dramatic reduction of the computational effort of solving the large system of equations is achieved. This fact is particularly important in the analysis of railway track structures, in which N is a very large number (around several thousands), and q = 2, the vertical displacement and rotation, is very small. The proposed method allows us to easily obtain the exact solution given by Samartín [1], i.e. the continuous beam railway track response. The comparison between the proposed method and other methods of analysis of railway tracks, such as Lorente de Nó and Zimmermann-Timoshenko, clearly shows the accuracy of the obtained results for the proposed method, even for low values of N. In addition, identical results between the proposed and the Lorente methods have been found, although the proposed method seems to be of simpler application and computationally more efficient than the Lorente one. Small but significative differences occur between these two methods and the one developed by Zimmermann-Timoshenko. This article also presents a detailed sensitivity analysis of the vertical displacement of the sleepers. Although standard matrix methods of structural analysis can handle this railway model, one of the objectives of this article is to show the efficiency of DFT method with respect to standard matrix structural analysis. A comparative analysis between standard matrix structural analysis and the proposed method (DFT), in terms of computational time, input, output and also software programming, will be carried out. Finally, a URL link to a MatLab computer program list, based on the proposed method, is given

Code assessment and modelling for Design Basis Accident Analysis of the European sodium fast reactor design. Part I: System description, modelling and benchmarking

The new reactor concepts proposed in the Generation IV International Forum (GIF) are conceived to improve the use of natural resources, reduce the amount of high-level radioactive waste and excel in their reliability and safe operation. Among these novel designs sodium fast reactors (SFRs) stand out due to their technological feasibility as demonstrated in several countries during the last decades. As part of the contribution of EURATOM to GIF the CP-ESFR is a collaborative project with the objective, among others, to perform extensive analysis on safety issues involving renewed SFR demonstrator designs. The verification of computational tools able to simulate the plant behaviour under postulated accidental conditions by code-to-code comparison was identified as a key point to ensure reactor safety. In this line, several organizations employed coupled neutronic and thermal-hydraulic system codes able to simulate complex and specific phenomena involving multi-physics studies adapted to this particular fast reactor technology. In the “Introduction” of this paper the framework of this study is discussed, the second section describes the envisaged plant design and the commonly agreed upon modelling guidelines. The third section presents a comparative analysis of the calculations performed by each organisation applying their models and codes to a common agreed transient with the objective to harmonize the models as well as validating the implementation of all relevant physical phenomena in the different system codes.

Dynamic analysis of translational shells

In this paper a dynamic analysis of transnational shells is presented. The general linear shell theory is used in conjunction with additional shallow and curved plate approximations. In order to apply some type of extended Levy solution, the shell is assumed to be limited by a rectangular plan form, with two opposite edges simply supported (gable boundary conditions). First, the shells free vibrations are studied in the usual way, obtaining for each Fourier term the natural frequencies as solutions of a transcendental equation. However, solving these equations arises enormous computational difficulties. This paper deals specifically with this problem, trying to reduce its dimension by a discretization procedure. In the shell dynamic characteristics, namely the mass. The shell mass is lumped along a family of coordinate lines. Therefore, the natural frequencies for each harmonic term can be found from the solution of a typical matrix eigenvalues problem and standard numerical techniques can be applied. The shell response to forced vibrations, particularly to earthquake excitation, can be determined by using conventional procedure either in the time or in the frequency domain. Finally, extending the above procedure, any system of translational shells under dynamic loading can be studied. Then, by using matrix methods, a general computer program is written and applied to some illustrative examples. Numerical results has been obtained in two cases: circular cylindrical shell and box girder bridge.

Systematic analysis of the decoding delay in multiview video

We present a framework for the analysis of the decoding delay in multiview video coding (MVC). We show that in real-time applications, an accurate estimation of the decoding delay is essential to achieve a minimum communication latency. As opposed to single-view codecs, the complexity of the multiview prediction structure and the parallel decoding of several views requires a systematic analysis of this decoding delay, which we solve using graph theory and a model of the decoder hardware architecture. Our framework assumes a decoder implementation in general purpose multi-core processors with multi-threading capabilities. For this hardware model, we show that frame processing times depend on the computational load of the decoder and we provide an iterative algorithm to compute jointly frame processing times and decoding delay. Finally, we show that decoding delay analysis can be applied to design decoders with the objective of minimizing the communication latency of the MVC system.

Dynamic analysis of translational shells

This paper presents a Levy-type solution for the natural frequencies of translational shells. A computer program in FORTRAN IV language corresponding to this solution is described. This direct solution is compared with some indirect solutions utilising Galerkin and Rayleigh methods. An extension to the study of forced vibrations is outlined.

Automated wordlength optimization framework for multi-source statistical interval-based analysis of nonlinear systems with control-flow structures

El uso de aritmética de punto fijo es una opción de diseño muy extendida en sistemas con fuertes restricciones de área, consumo o rendimiento. Para producir implementaciones donde los costes se minimicen sin impactar negativamente en la precisión de los resultados debemos llevar a cabo una asignación cuidadosa de anchuras de palabra. Encontrar la combinación óptima de anchuras de palabra en coma fija para un sistema dado es un problema combinatorio NP-hard al que los diseñadores dedican entre el 25 y el 50 % del ciclo de diseño. Las plataformas hardware reconfigurables, como son las FPGAs, también se benefician de las ventajas que ofrece la aritmética de coma fija, ya que éstas compensan las frecuencias de reloj más bajas y el uso más ineficiente del hardware que hacen estas plataformas respecto a los ASICs. A medida que las FPGAs se popularizan para su uso en computación científica los diseños aumentan de tamaño y complejidad hasta llegar al punto en que no pueden ser manejados eficientemente por las técnicas actuales de modelado de señal y ruido de cuantificación y de optimización de anchura de palabra. En esta Tesis Doctoral exploramos distintos aspectos del problema de la cuantificación y presentamos nuevas metodologías para cada uno de ellos: Las técnicas basadas en extensiones de intervalos han permitido obtener modelos de propagación de señal y ruido de cuantificación muy precisos en sistemas con operaciones no lineales. Nosotros llevamos esta aproximación un paso más allá introduciendo elementos de Multi-Element Generalized Polynomial Chaos (ME-gPC) y combinándolos con una técnica moderna basada en Modified Affine Arithmetic (MAA) estadístico para así modelar sistemas que contienen estructuras de control de flujo. Nuestra metodología genera los distintos caminos de ejecución automáticamente, determina las regiones del dominio de entrada que ejercitarán cada uno de ellos y extrae los momentos estadísticos del sistema a partir de dichas soluciones parciales. Utilizamos esta técnica para estimar tanto el rango dinámico como el ruido de redondeo en sistemas con las ya mencionadas estructuras de control de flujo y mostramos la precisión de nuestra aproximación, que en determinados casos de uso con operadores no lineales llega a tener tan solo una desviación del 0.04% con respecto a los valores de referencia obtenidos mediante simulación. Un inconveniente conocido de las técnicas basadas en extensiones de intervalos es la explosión combinacional de términos a medida que el tamaño de los sistemas a estudiar crece, lo cual conlleva problemas de escalabilidad. Para afrontar este problema presen tamos una técnica de inyección de ruidos agrupados que hace grupos con las señales del sistema, introduce las fuentes de ruido para cada uno de los grupos por separado y finalmente combina los resultados de cada uno de ellos. De esta forma, el número de fuentes de ruido queda controlado en cada momento y, debido a ello, la explosión combinatoria se minimiza. También presentamos un algoritmo de particionado multi-vía destinado a minimizar la desviación de los resultados a causa de la pérdida de correlación entre términos de ruido con el objetivo de mantener los resultados tan precisos como sea posible. La presente Tesis Doctoral también aborda el desarrollo de metodologías de optimización de anchura de palabra basadas en simulaciones de Monte-Cario que se ejecuten en tiempos razonables. Para ello presentamos dos nuevas técnicas que exploran la reducción del tiempo de ejecución desde distintos ángulos: En primer lugar, el método interpolativo aplica un interpolador sencillo pero preciso para estimar la sensibilidad de cada señal, y que es usado después durante la etapa de optimización. En segundo lugar, el método incremental gira en torno al hecho de que, aunque es estrictamente necesario mantener un intervalo de confianza dado para los resultados finales de nuestra búsqueda, podemos emplear niveles de confianza más relajados, lo cual deriva en un menor número de pruebas por simulación, en las etapas iniciales de la búsqueda, cuando todavía estamos lejos de las soluciones optimizadas. Mediante estas dos aproximaciones demostramos que podemos acelerar el tiempo de ejecución de los algoritmos clásicos de búsqueda voraz en factores de hasta x240 para problemas de tamaño pequeño/mediano. Finalmente, este libro presenta HOPLITE, una infraestructura de cuantificación automatizada, flexible y modular que incluye la implementación de las técnicas anteriores y se proporciona de forma pública. Su objetivo es ofrecer a desabolladores e investigadores un entorno común para prototipar y verificar nuevas metodologías de cuantificación de forma sencilla. Describimos el flujo de trabajo, justificamos las decisiones de diseño tomadas, explicamos su API pública y hacemos una demostración paso a paso de su funcionamiento. Además mostramos, a través de un ejemplo sencillo, la forma en que conectar nuevas extensiones a la herramienta con las interfaces ya existentes para poder así expandir y mejorar las capacidades de HOPLITE. ABSTRACT Using fixed-point arithmetic is one of the most common design choices for systems where area, power or throughput are heavily constrained. In order to produce implementations where the cost is minimized without negatively impacting the accuracy of the results, a careful assignment of word-lengths is required. The problem of finding the optimal combination of fixed-point word-lengths for a given system is a combinatorial NP-hard problem to which developers devote between 25 and 50% of the design-cycle time. Reconfigurable hardware platforms such as FPGAs also benefit of the advantages of fixed-point arithmetic, as it compensates for the slower clock frequencies and less efficient area utilization of the hardware platform with respect to ASICs. As FPGAs become commonly used for scientific computation, designs constantly grow larger and more complex, up to the point where they cannot be handled efficiently by current signal and quantization noise modelling and word-length optimization methodologies. In this Ph.D. Thesis we explore different aspects of the quantization problem and we present new methodologies for each of them: The techniques based on extensions of intervals have allowed to obtain accurate models of the signal and quantization noise propagation in systems with non-linear operations. We take this approach a step further by introducing elements of MultiElement Generalized Polynomial Chaos (ME-gPC) and combining them with an stateof- the-art Statistical Modified Affine Arithmetic (MAA) based methodology in order to model systems that contain control-flow structures. Our methodology produces the different execution paths automatically, determines the regions of the input domain that will exercise them, and extracts the system statistical moments from the partial results. We use this technique to estimate both the dynamic range and the round-off noise in systems with the aforementioned control-flow structures. We show the good accuracy of our approach, which in some case studies with non-linear operators shows a 0.04 % deviation respect to the simulation-based reference values. A known drawback of the techniques based on extensions of intervals is the combinatorial explosion of terms as the size of the targeted systems grows, which leads to scalability problems. To address this issue we present a clustered noise injection technique that groups the signals in the system, introduces the noise terms in each group independently and then combines the results at the end. In this way, the number of noise sources in the system at a given time is controlled and, because of this, the combinato rial explosion is minimized. We also present a multi-way partitioning algorithm aimed at minimizing the deviation of the results due to the loss of correlation between noise terms, in order to keep the results as accurate as possible. This Ph.D. Thesis also covers the development of methodologies for word-length optimization based on Monte-Carlo simulations in reasonable times. We do so by presenting two novel techniques that explore the reduction of the execution times approaching the problem in two different ways: First, the interpolative method applies a simple but precise interpolator to estimate the sensitivity of each signal, which is later used to guide the optimization effort. Second, the incremental method revolves on the fact that, although we strictly need to guarantee a certain confidence level in the simulations for the final results of the optimization process, we can do it with more relaxed levels, which in turn implies using a considerably smaller amount of samples, in the initial stages of the process, when we are still far from the optimized solution. Through these two approaches we demonstrate that the execution time of classical greedy techniques can be accelerated by factors of up to ×240 for small/medium sized problems. Finally, this book introduces HOPLITE, an automated, flexible and modular framework for quantization that includes the implementation of the previous techniques and is provided for public access. The aim is to offer a common ground for developers and researches for prototyping and verifying new techniques for system modelling and word-length optimization easily. We describe its work flow, justifying the taken design decisions, explain its public API and we do a step-by-step demonstration of its execution. We also show, through an example, the way new extensions to the flow should be connected to the existing interfaces in order to expand and improve the capabilities of HOPLITE.

Comparative Analysis of Firms’ Participation in National and International Programmes to Support Innovation

Innovation is a process that faces several market failure situations. For this reason and for being considered one of the main drivers of economic growth, a large number of governmental and supranational policies are designed to foster technological progress. Along with these policies, there is an increasing concern with their continuous evaluation aiming at providing valuable feedback for these program?s adaptation and adequacy to the firm?s needs. The paper develops an evaluation of the influence of innovation-focused programs in firm¿s innovation and economic performance by means of a comparative analysis of the results obtained by Spanish firms that have participated in R&D national programmes and those achieved by Spanish firms participating in EUREKA international program. Findings show that the programmes were effective in achieving their objective of promoting technological innovation but, as regards the economic effects, the results were less conclusive since some differences were observed depending on the programme. The EUREKA companies displayed better behaviour, with positive differences in their returns on assets and labour productivity. The results also confirm the importance of designing more detailed and rigorous evaluation processes, taking into account the risk variable, in order to draw a more realistic picture of the impact of national and international programmes.

Molecular analysis of CaMnt1p, a mannosyl transferase important for adhesion and virulence of Candida albicans

There is an immediate need for identification of new antifungal targets in opportunistic pathogenic fungi like Candida albicans. In the past, efforts have focused on synthesis of chitin and glucan, which confer mechanical strength and rigidity upon the cell wall. This paper describes the molecular analysis of CaMNT1, a gene involved in synthesis of mannoproteins, the third major class of macromolecule found in the cell wall. CaMNT1 encodes an α-1,2-mannosyl transferase, which adds the second mannose residue in a tri-mannose oligosaccharide structure which represents O-linked mannan in C. albicans. The deduced amino acid sequence suggests that CaMnt1p is a type II membrane protein residing in a medial Golgi compartment. The absence of CaMnt1p reduced the ability of C. albicans cells to adhere to each other, to human buccal epithelial cells, and to rat vaginal epithelial cells. Both heterozygous and homozygous Camnt1 null mutants of C. albicans showed strong attenuation of virulence in guinea pig and mouse models of systemic candidosis, which, in guinea pigs, could be attributed to a decreased ability to reach and/or adhere internal organs. Therefore, correct CaMnt1p-mediated O-linked mannosylation of proteins is critical for adhesion and virulence of C. albicans.

Analysis of the role of the Spitzenkörper in fungal morphogenesis by computer simulation of apical branching in Aspergillus niger

High-resolution video microscopy, image analysis, and computer simulation were used to study the role of the Spitzenkörper (Spk) in apical branching of ramosa-1, a temperature-sensitive mutant of Aspergillus niger. A shift to the restrictive temperature led to a cytoplasmic contraction that destabilized the Spk, causing its disappearance. After a short transition period, new Spk appeared where the two incipient apical branches emerged. Changes in cell shape, growth rate, and Spk position were recorded and transferred to the fungus simulator program to test the hypothesis that the Spk functions as a vesicle supply center (VSC). The simulation faithfully duplicated the elongation of the main hypha and the two apical branches. Elongating hyphae exhibited the growth pattern described by the hyphoid equation. During the transition phase, when no Spk was visible, the growth pattern was nonhyphoid, with consecutive periods of isometric and asymmetric expansion; the apex became enlarged and blunt before the apical branches emerged. Video microscopy images suggested that the branch Spk were formed anew by gradual condensation of vesicle clouds. Simulation exercises where the VSC was split into two new VSCs failed to produce realistic shapes, thus supporting the notion that the branch Spk did not originate by division of the original Spk. The best computer simulation of apical branching morphogenesis included simulations of the ontogeny of branch Spk via condensation of vesicle clouds. This study supports the hypothesis that the Spk plays a major role in hyphal morphogenesis by operating as a VSC—i.e., by regulating the traffic of wall-building vesicles in the manner predicted by the hyphoid model.

Genetic analysis of calcium spiking responses in nodulation mutants of Medicago truncatula

The symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti results in the formation of nitrogen-fixing nodules on the roots of the host plant. The early stages of nodule formation are induced by bacteria via lipochitooligosaccharide signals known as Nod factors (NFs). These NFs are structurally specific for bacterium–host pairs and are sufficient to cause a range of early responses involved in the host developmental program. Early events in the signal transduction of NFs are not well defined. We have previously reported that Medicago sativa root hairs exposed to NF display sharp oscillations of cytoplasmic calcium ion concentration (calcium spiking). To assess the possible role of calcium spiking in the nodulation response, we analyzed M. truncatula mutants in five complementation groups. Each of the plant mutants is completely Nod− and is blocked at early stages of the symbiosis. We defined two genes, DMI1 and DMI2, required in common for early steps of infection and nodulation and for calcium spiking. Another mutant, altered in the DMI3 gene, has a similar mutant phenotype to dmi1 and dmi2 mutants but displays normal calcium spiking. The calcium behavior thus implies that the DMI3 gene acts either downstream of calcium spiking or downstream of a common branch point for the calcium response and the later nodulation responses. Two additional mutants, altered in the NSP and HCL genes, which show root hair branching in response to NF, are normal for calcium spiking. This system provides an opportunity to use genetics to study ligand-stimulated calcium spiking as a signal transduction event.

Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning Ache to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by Ache and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse–human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations

rSNP_Guide is a novel curated database system for analysis of transcription factor (TF) binding to target sequences in regulatory gene regions altered by mutations. It accumulates experimental data on naturally occurring site variants in regulatory gene regions and site-directed mutations. This database system also contains the web tools for SNP analysis, i.e., active applet applying weight matrices to predict the regulatory site candidates altered by a mutation. The current version of the rSNP_Guide is supplemented by six sub-databases: (i) rSNP_DB, on DNA–protein interaction caused by mutation; (ii) SYSTEM, on experimental systems; (iii) rSNP_BIB, on citations to original publications; (iv) SAMPLES, on experimentally identified sequences of known regulatory sites; (v) MATRIX, on weight matrices of known TF sites; (vi) rSNP_Report, on characteristic examples of successful rSNP_Tools implementation. These databases are useful for the analysis of natural SNPs and site-directed mutations. The databases are available through the Web, http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/.

Biochemical Analysis of Plant Protection Afforded by a Nonpathogenic Endophytic Mutant of Colletotrichum magna1

A nonpathogenic mutant of Colletotrichum magna (path-1) was previously shown to protect watermelon (Citrullus lanatus) and cucumber (Cucumis sativus) seedlings from anthracnose disease elicited by wild-type C. magna. Disease protection was observed in stems of path-1-colonized cucurbits but not in cotyledons, indicating that path-1 conferred tissue-specific and/or localized protection. Plant biochemical indicators of a localized and systemic (peroxidase, phenylalanine ammonia-lyase, lignin, and salicylic acid) “plant-defense” response were investigated in anthracnose-resistant and -susceptible cultivars of cucurbit seedlings exposed to four treatments: (1) water (control), (2) path-1 conidia, (3) wild-type conidia, and (4) challenge conditions (inoculation into path-1 conidia for 48 h and then exposure to wild-type conidia). Collectively, these analyses indicated that disease protection in path-1-colonized plants was correlated with the ability of these plants to mount a defense response more rapidly and to equal or greater levels than plants exposed to wild-type C. magna alone. Watermelon plants colonized with path-1 were also protected against disease caused by Colletotrichum orbiculare and Fusarium oxysporum. A model based on the kinetics of plant-defense activation is presented to explain the mechanism of path-1-conferred disease protection.

Correlates of Program Completion in Juvenile Diversion

The current study evaluated the State Juvenile Diversion Program, managed by the District Attorney’s (DA) office in Denver Colorado. The purpose of this study was to review factors, which potentially contribute to success or failure in diversion. Research in diversion programing typically focuses on recidivism rates, but fails to examine which factors contribute to program completion. The analysis was conducted using data from 57 juveniles who entered the DA diversion program in 2015. This represents the majority of juveniles in the diversion program rather than a sample. The current study confirmed prior research findings that those juveniles who do not successfully complete a diversion program are more likely to reoffend. Additionally, the factors which were significantly correlated with successful completion of the diversion program were grade point average (GPA) and number of municipal tickets. The number of behavior reports in school before and after the Diversion program was significantly lower for both groups. Non-significant findings are also discussed as they may help guide future research.