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.

Geometría de presas bóveda

Se presenta en este artículo un programa para cálculo mediante ordenador, de utilización frecuente en el Departamento de Estudios Experimentales de Presas del Labo¬ratorio Central. Este programa se refiere a presas bóvedas asimétricas de tres centros y determina: a) el replanteo geométrico de las mismas para su construcción en modelo reducido. b) la posición -punto de aplicación y dirección- de las cargas puntuales equivalentes a las acciones de peso propio y presión hidrostática, que se introducen en el modelo median¬te gatos hidráulicos. c) la directriz de la presa, dato necesario para un posible cálculo estático posterior. This paper presents a computer program currently used in the Department of Experimental Studies of Dams in the Laboratorio Central. This program concerns asymmetric arch dams of three centers and it determines: a) The geometrical definition of the arch dams for the scaled model construction. b) The position, acting point and direction of the punctual loads equivalent to the actions of self-weight and water pressure, which are applied to the model by means of hydraulic jacks. c) The middle surface of the dam, which later would be introduced for a stress analy¬sis of the dam itself

Certificación energética mediante la herramienta CE3X y rehabilitación energética de una vivienda unifamiliar

El siguiente proyecto lleva a cabo un estudio sobre la eficiencia energética en una vivienda unifamiliar basándose en la legislación actual europea y española. Para empezar se obtendrá la calificación energética del inmueble mediante el programa informático de la opción simplificada CE3X. A continuación se proporcionará un estudio con las medidas de mejora más adecuadas para mejorar la eficiencia energética de la vivienda, las medidas que se llevarán a cabo serán: la mejora de la envolvente térmica, mejorando el aislamiento de la fachada y la sustitución de ventanas, la instalación de una caldera de biomasa y la instalación de un sistema de colectores solares para cubrir la demanda de calefacción y ACS. Para finalizar se realiza un presupuesto de las medidas de mejoras propuestas, así como un análisis económico y una planificación y programación temporal. ABSTRACT The object of this Project is to carry out a study on the energy efficiency of a single family home in accordance with the present European and Spanish legislation. The first step is to obtain the home energy efficiency by means of a CE3X computer program. The second step is a study with the most appropriate improvement measures is provided in order to improve the home energy efficiency. The measures to be carried out will be as follows: improving the heat insulation, as well as, the facade heat insulation and replacing the windows, installing a biomass heating system and a solar collector in order to satisfy the heating and domestic hot water (DHW) demands. Finally a budget with the proposed improvement measures is made as well as a financial analysis and a time planning and programming of the project.

Emotion transplantation through adaptation in HMM-based speech synthesis

This paper proposes an emotion transplantation method capable of modifying a synthetic speech model through the use of CSMAPLR adaptation in order to incorporate emotional information learned from a different speaker model while maintaining the identity of the original speaker as much as possible. The proposed method relies on learning both emotional and speaker identity information by means of their adaptation function from an average voice model, and combining them into a single cascade transform capable of imbuing the desired emotion into the target speaker. This method is then applied to the task of transplanting four emotions (anger, happiness, sadness and surprise) into 3 male speakers and 3 female speakers and evaluated in a number of perceptual tests. The results of the evaluations show how the perceived naturalness for emotional text significantly favors the use of the proposed transplanted emotional speech synthesis when compared to traditional neutral speech synthesis, evidenced by a big increase in the perceived emotional strength of the synthesized utterances at a slight cost in speech quality. A final evaluation with a robotic laboratory assistant application shows how by using emotional speech we can significantly increase the students’ satisfaction with the dialog system, proving how the proposed emotion transplantation system provides benefits in real applications.

Aprendizaje integrado en arquitectura con modelos virtuales : implementación de metodología BIM en la docencia universitaria

Los procesos de diseño y construcción en Arquitectura han mostrado un desarrollo de optimización históricamente muy deficiente cuando se compara con las restantes actividades típicamente industriales. La aspiración constante a una industrialización efectiva, tanto en aras de alcanzar mayores cotas de calidad así como de ahorro de recursos, recibe hoy una oportunidad inmejorable desde el ámbito informático: el Building Information Modelling o BIM. Lo que en un inicio puede parecer meramente un determinado tipo de programa informático, en realidad supone un concepto de “proceso” que subvierte muchas rutinas hoy habituales en el desarrollo de proyectos y construcciones arquitectónicas. La inclusión y desarrollo de datos ligados al proyecto, desde su inicio hasta el fin de su ciclo de vida, conlleva la oportunidad de crear una realidad virtual dinámica y actualizable, que por añadidura posibilita su ensayo y optimización en todos sus aspectos: antes y durante su ejecución, así como vida útil. A ello se suma la oportunidad de transmitir eficientemente los datos completos de proyecto, sin apenas pérdidas o reelaboración, a la cadena de fabricación, lo que facilita el paso a una industrialización verdaderamente significativa en edificación. Ante una llamada mundial a la optimización de recursos y el interés indudable de aumentar beneficios económicos por medio de la reducción del factor de incertidumbre de los procesos, BIM supone un opción de mejora indudable, y así ha sido reconocido a través de la inminente implantación obligatoria por parte de los gobiernos (p. ej. Gran Bretaña en 2016 y España en 2018). La modificación de procesos y roles profesionales que conlleva la incorporación de BIM resulta muy significativa y marcará el ejercicio profesional de los futuros graduados en las disciplinas de Arquitectura, Ingeniería y Construcción (AEC por sus siglas en inglés). La universidad debe responder ágilmente a estas nuevas necesidades incorporando esta metodología en la enseñanza reglada y aportando una visión sinérgica que permita extraer los beneficios formativos subyacentes en el propio marco BIM. En este sentido BIM, al aglutinar el conjunto de datos sobre un único modelo virtual, ofrece un potencial singularmente interesante. La realidad tridimensional del modelo, desarrollada y actualizada continuamente, ofrece al estudiante una gestión radicalmente distinta de la representación gráfica, en la que las vistas parciales de secciones y plantas, tan complejas de asimilar en los inicios de la formación universitaria, resultan en una mera petición a posteriori, para ser extraída según necesidad del modelo virtual. El diseño se realiza siempre sobre el propio modelo único, independientemente de la vista de trabajo elegida en cada momento, permaneciendo los datos y sus relaciones constructivas siempre actualizados y plenamente coherentes. Esta descripción condensada de características de BIM preconfiguran gran parte de las beneficios formativos que ofrecen los procesos BIM, en especial, en referencia al desarrollo del diseño integrado y la gestión de la información (incluyendo TIC). Destacan a su vez las facilidades en comprensión visual de elementos arquitectónicos, sistemas técnicos, sus relaciones intrínsecas así como procesos constructivos. A ello se une el desarrollo experimental que la plataforma BIM ofrece a través de sus software colaborativos: la simulación del comportamiento estructural, energético, económico, entre otros muchos, del modelo virtual en base a los datos inherentes del proyecto. En la presente tesis se describe un estudio de conjunto para explicitar tanto las cualidades como posibles reservas en el uso de procesos BIM, en el marco de una disciplina concreta: la docencia de la Arquitectura. Para ello se ha realizado una revisión bibliográfica general sobre BIM y específica sobre docencia en Arquitectura, así como analizado las experiencias de distintos grupos de interés en el marco concreto de la enseñanza de la en Arquitectura en la Universidad Europea de Madrid. El análisis de beneficios o reservas respecto al uso de BIM se ha enfocado a través de la encuesta a estudiantes y la entrevista a profesionales AEC relacionados o no con BIM. Las conclusiones del estudio permiten sintetizar una implantación de metodología BIM que para mayor claridad y facilidad de comunicación y manejo, se ha volcado en un Marco de Implantación eminentemente gráfico. En él se orienta sobre las acciones docentes para el desarrollo de competencias concretas, valiéndose de la flexibilidad conceptual de los Planes de Estudio en el contexto del Espacio Europeo de Educación Superior (Declaración de Bolonia) para incorporar con naturalidad la nueva herramienta docente al servicio de los objetivos formativo legalmente establecidos. El enfoque global del Marco de Implementación propuesto facilita la planificación de acciones formativas con perspectiva de conjunto: combinar los formatos puntuales o vehiculares BIM, establecer sinergias transversales y armonizar recursos, de modo que la metodología pueda beneficiar tanto la asimilación de conocimientos y habilidades establecidas para el título, como el propio flujo de aprendizaje o learn flow BIM. Del mismo modo reserva, incluso visualmente, aquellas áreas de conocimiento en las que, al menos en la planificación actual, la inclusión de procesos BIM no se considera ventajosa respecto a otras metodologías, o incluso inadecuadas para los objetivos docentes establecidos. Y es esta última categorización la que caracteriza el conjunto de conclusiones de esta investigación, centrada en: 1. la incuestionable necesidad de formar en conceptos y procesos BIM desde etapas muy iniciales de la formación universitaria en Arquitectura, 2. los beneficios formativos adicionales que aporta BIM en el desarrollo de competencias muy diversas contempladas en el currículum académico y 3. la especificidad del rol profesional del arquitecto que exigirá una implantación cuidadosa y ponderada de BIM que respete las metodologías de desarrollo creativo tradicionalmente efectivas, y aporte valor en una reorientación simbiótica con el diseño paramétrico y fabricación digital que permita un diseño finalmente generativo. ABSTRACT The traditional architectural design and construction procedures have proven to be deficient where process optimization is concerned, particularly when compared to other common industrial activities. The ever‐growing strife to achieve effective industrialization, both in favor of reaching greater quality levels as well as sustainable management of resources, has a better chance today than ever through a mean out of the realm of information technology, the Building Information Modelling o BIM. What may initially seem to be merely another computer program, in reality turns out to be a “process” concept that subverts many of today’s routines in architectural design and construction. Including and working with project data from the very beginning to the end of its full life cycle allows for creating a dynamic and updatable virtual reality, enabling data testing and optimizing throughout: before and during execution, all the way to the end of its lifespan. In addition, there is an opportunity to transmit complete project data efficiently, with hardly any loss or redeveloping of the manufacture chain required, which facilitates attaining a truly significant industrialization within the construction industry. In the presence of a world‐wide call for optimizing resources, along with an undeniable interest in increasing economic benefits through reducing uncertainty factors in its processes, BIM undoubtedly offers a chance for improvement as acknowledged by its imminent and mandatory implementation on the part of governments (for example United Kingdom in 2016 and Spain in 2018). The changes involved in professional roles and procedures upon incorporating BIM are highly significant and will set the course for future graduates of Architecture, Engineering and Construction disciplines (AEC) within their professions. Higher Education must respond to such needs with swiftness by incorporating this methodology into their educational standards and providing a synergetic vision that focuses on the underlying educational benefits inherent in the BIM framework. In this respect, BIM, in gathering data set under one single virtual model, offers a uniquely interesting potential. The three‐dimensional reality of the model, under continuous development and updating, provides students with a radically different graphic environment, in which partial views of elevation, section or plan that tend characteristically to be difficult to assimilate at the beginning of their studies, become mere post hoc requests to be ordered when needed directly out the virtual model. The design is always carried out on the sole model itself, independently of the working view chosen at any particular moment, with all data and data relations within construction permanently updated and fully coherent. This condensed description of the features of BIM begin to shape an important part of the educational benefits posed by BIM processes, particularly in reference to integrated design development and information management (including ITC). At the same time, it highlights the ease with which visual understanding is achieved regarding architectural elements, technology systems, their intrinsic relationships, and construction processes. In addition to this, there is the experimental development the BIM platform grants through its collaborative software: simulation of structural, energetic, and economic behavior, among others, of the virtual model according to the data inherent to the project. This doctoral dissertation presents a broad study including a wide array of research methods and issues in order to specify both the virtues and possible reservations in the use of BIM processes within the framework of a specific discipline: teaching Architecture. To do so, a literature review on BIM has been carried out, specifically concerning teaching in the discipline of Architecture, as well as an analysis of the experience of different groups of interest delimited to Universidad Europea de Madrid. The analysis of the benefits and/or limitations of using BIM has been approached through student surveys and interviews with professionals from the AEC sector, associated or not, with BIM. Various diverse educational experiences are described and academic management for experimental implementation has been analyzed. The conclusions of this study offer a synthesis for a Framework of Implementation of BIM methodology, which in order to reach greater clarity, communication ease and user‐friendliness, have been posed in an eminently graphic manner. The proposed framework proffers guidance on teaching methods conducive to the development of specific skills, taking advantage of the conceptual flexibility of the European Higher Education Area guidelines based on competencies, which naturally facilitate for the incorporation of this new teaching tool to achieve the educational objectives established by law. The global approach of the Implementation Framework put forth in this study facilitates the planning of educational actions within a common perspective: combining exceptional or vehicular BIM formats, establishing cross‐disciplinary synergies, and sharing resources, so as to purport a methodology that contributes to the assimilation of knowledge and pre‐defined competencies within the degree program, and to the flow of learning itself. At the same time, it reserves, even visually, those areas of knowledge in which the use of BIM processes is not considered necessarily an advantage over other methodologies, or even inadequate for the learning outcomes established, at least where current planning is concerned. It is this last category which characterizes the research conclusions as a whole, centering on: 1. The unquestionable need for teaching BIM concepts and processes in Architecture very early on, in the initial stages of higher education; 2. The additional educational benefits that BIM offers in a varied array of competency development within the academic curriculum; and 3. The specific nature of the professional role of the Architect, which demands a careful and balanced implementation of BIM that respects the traditional teaching methodologies that have proven effective and creative, and adds value by a symbiotic reorientation merged with parametric design and digital manufacturing so to enable for a finally generative design.

DETERMINAÇÃO DAS FORMAS DO ARCO DENTÁRIO INFERIOR NA OCLUSÃO NORMAL NATURAL

Com a finalidade de determinar as formas do arco dentário inferior de maior incidência na oclusão normal natural, utilizou-se um método matemático associado ao emprego de uma função polinomial, o qual foi aplicado a 63 modelos de arcadas inferiores selecionados a partir de 6118 adolescentes. Todos os indivíduos eram portadores de dentição permanente, incluindo os segundos molares, e oclusão normal natural. Em cada dente foi fixada uma esfera de vidro, que teve a função de simular o acessório do aparelho ortodôntico, sendo utilizada na medição das distâncias entre o centro da imagem dessas esferas aos eixos x e y. Após a digitalização dos modelos de gesso, as imagens foram plotadas em um programa de computador, a fim de se obterem a função polinomial de sexto grau e o gráfico dessa função para os 126 segmentos de curva, originados das secções das imagens em lado direito e esquerdo. A seguir organizaram-se esses segmentos, de acordo com as características da curvatura anterior dos arcos dentários, em oito grupos diferentes de formas, que receberam as denominações de Forma A, Forma B, Forma C, Forma D, Forma E, Forma F, Forma G, Forma H. Cada grupo foi, então, dividido em três subgrupos, conforme os tamanhos pequeno, médio e grande. Os resultados indicaram 23 formas representativas do arco dentário inferior e uma forma média para a oclusão normal natural.

DETERMINAÇÃO DAS FORMAS DO ARCO DENTÁRIO INFERIOR NA OCLUSÃO NORMAL NATURAL

Com a finalidade de determinar as formas do arco dentário inferior de maior incidência na oclusão normal natural, utilizou-se um método matemático associado ao emprego de uma função polinomial, o qual foi aplicado a 63 modelos de arcadas inferiores selecionados a partir de 6118 adolescentes. Todos os indivíduos eram portadores de dentição permanente, incluindo os segundos molares, e oclusão normal natural. Em cada dente foi fixada uma esfera de vidro, que teve a função de simular o acessório do aparelho ortodôntico, sendo utilizada na medição das distâncias entre o centro da imagem dessas esferas aos eixos x e y. Após a digitalização dos modelos de gesso, as imagens foram plotadas em um programa de computador, a fim de se obterem a função polinomial de sexto grau e o gráfico dessa função para os 126 segmentos de curva, originados das secções das imagens em lado direito e esquerdo. A seguir organizaram-se esses segmentos, de acordo com as características da curvatura anterior dos arcos dentários, em oito grupos diferentes de formas, que receberam as denominações de Forma A, Forma B, Forma C, Forma D, Forma E, Forma F, Forma G, Forma H. Cada grupo foi, então, dividido em três subgrupos, conforme os tamanhos pequeno, médio e grande. Os resultados indicaram 23 formas representativas do arco dentário inferior e uma forma média para a oclusão normal natural.

AVALIAÇÃO DAS ALTERAÇÕES DO SORRISO EM INDIVÍDUOS SUBMETIDOS À EXPANSÃO RÁPIDA DA MAXILA

O objetivo deste estudo foi avaliar as possíveis alterações das características horizontais, verticais, de simetria e do arco do sorriso de pacientes com atresia maxilar submetidos à expansão rápida da maxila. A amostra consistiu de 81 fotografias extra-bucais do sorriso máximo de 27 pacientes com idade média de 10 anos e 3 meses. Foram realizadas fotografias do sorriso máximo nos períodos: inicial (antes da instalação do aparelho expansor); 3 meses após a fixação do parafuso expansor; 6 meses após a fixação do parafuso expansor. Para a calibragem e análise das fotografias foi utilizado o programa CEFX 2001 CDT. Os pontos fotométricos e as medidas a serem analisadas foram escolhidos após revisão da literatura do sorriso realizada. Para avaliar as alterações no sorriso durante as fases, foi utilizada a análise de variância ANOVA, com nível de significância de 5%. A expansão rápida da maxila promoveu aumento estatisticamente significante da dimensão transversal do sorriso; aumento da quantidade de exposição dos incisivos centrais e laterais superiores; manutenção da simetria entre os lados direito e esquerdo e da falta de paralelismo entre a curvatura das bordas dos incisivos superiores com a curvatura do lábio inferior (arco do sorriso).(AU)

AVALIAÇÃO DAS ALTERAÇÕES DO SORRISO EM INDIVÍDUOS SUBMETIDOS À EXPANSÃO RÁPIDA DA MAXILA

O objetivo deste estudo foi avaliar as possíveis alterações das características horizontais, verticais, de simetria e do arco do sorriso de pacientes com atresia maxilar submetidos à expansão rápida da maxila. A amostra consistiu de 81 fotografias extra-bucais do sorriso máximo de 27 pacientes com idade média de 10 anos e 3 meses. Foram realizadas fotografias do sorriso máximo nos períodos: inicial (antes da instalação do aparelho expansor); 3 meses após a fixação do parafuso expansor; 6 meses após a fixação do parafuso expansor. Para a calibragem e análise das fotografias foi utilizado o programa CEFX 2001 CDT. Os pontos fotométricos e as medidas a serem analisadas foram escolhidos após revisão da literatura do sorriso realizada. Para avaliar as alterações no sorriso durante as fases, foi utilizada a análise de variância ANOVA, com nível de significância de 5%. A expansão rápida da maxila promoveu aumento estatisticamente significante da dimensão transversal do sorriso; aumento da quantidade de exposição dos incisivos centrais e laterais superiores; manutenção da simetria entre os lados direito e esquerdo e da falta de paralelismo entre a curvatura das bordas dos incisivos superiores com a curvatura do lábio inferior (arco do sorriso).(AU)

Selection of Gβ Subunits with Point Mutations That Fail to Activate Specific Signaling Pathways In Vivo: Dissecting Cellular Responses Mediated by a Heterotrimeric G Protein in Dictyostelium discoideum

In Dictyostelium discoideum, a unique Gβ subunit is required for a G protein–coupled receptor system that mediates a variety of cellular responses. Binding of cAMP to cAR1, the receptor linked to the G protein G2, triggers a cascade of responses, including activation of adenylyl cyclase, gene induction, actin polymerization, and chemotaxis. Null mutations of the cAR1, Gα2, and Gβ genes completely impair all these responses. To dissect specificity in Gβγ signaling to downstream effectors in living cells, we screened a randomly mutagenized library of Gβ genes and isolated Gβ alleles that lacked the capacity to activate some effectors but retained the ability to regulate others. These mutant Gβ subunits were able to link cAR1 to G2, to support gene expression, and to mediate cAMP-induced actin polymerization, and some were able to mediate to chemotaxis toward cAMP. None was able to activate adenylyl cyclase, and some did not support chemotaxis. Thus, we separated in vivo functions of Gβγ by making point mutations on Gβ. Using the structure of the heterotrimeric G protein displayed in the computer program CHAIN, we examined the positions and the molecular interactions of the amino acids substituted in each of the mutant Gβs and analyzed the possible effects of each replacement. We identified several residues that are crucial for activation of the adenylyl cyclase. These residues formed an area that overlaps but is not identical to regions where bovine Gtβγ interacts with its regulators, Gα and phosducin.

Intron positions correlate with module boundaries in ancient proteins

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of “linker regions” that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-Å modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters and show that, as the diameter varies, significant peaks of correlation appear for module diameters centered at 21.7, 27.6, and 32.9 Å. These preferred module diameters roughly correspond to predicted exon sizes of 15, 22, and 30 residues. Thus, there are significant correlations between introns, modules, and a quantized pattern of the lengths of polypeptide chains, which is the prediction of the “Exon Theory of Genes.”

GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

The release of vast quantities of DNA sequence data by large-scale genome and expressed sequence tag (EST) projects underlines the necessity for the development of efficient and inexpensive ways to link sequence databases with temporal and spatial expression profiles. Here we demonstrate the power of linking cDNA sequence data (including EST sequences) with transcript profiles revealed by cDNA-AFLP, a highly reproducible differential display method based on restriction enzyme digests and selective amplification under high stringency conditions. We have developed a computer program (GenEST) that predicts the sizes of virtual transcript-derived fragments (TDFs) of in silico-digested cDNA sequences retrieved from databases. The vast majority of the resulting virtual TDFs could be traced back among the thousands of TDFs displayed on cDNA-AFLP gels. Sequencing of the corresponding bands excised from cDNA-AFLP gels revealed no inconsistencies. As a consequence, cDNA sequence databases can be screened very efficiently to identify genes with relevant expression profiles. The other way round, it is possible to switch from cDNA-AFLP gels to sequences in the databases. Using the restriction enzyme recognition sites, the primer extensions and the estimated TDF size as identifiers, the DNA sequence(s) corresponding to a TDF with an interesting expression pattern can be identified. In this paper we show examples in both directions by analyzing the plant parasitic nematode Globodera rostochiensis. Various novel pathogenicity factors were identified by combining ESTs from the infective stage juveniles with expression profiles of ∼4000 genes in five developmental stages produced by cDNA-AFLP.

The evolution of coloration and toxicity in the poison frog family (Dendrobatidae)

The poison frogs (family Dendrobatidae) are terrestrial anuran amphibians displaying a wide range of coloration and toxicity. These frogs generally have been considered to be aposematic, but relatively little research has been carried out to test the predictions of this hypothesis. Here we use a comparative approach to test one prediction of the hypothesis of aposematism: that coloration will evolve in tandem with toxicity. Recently, we developed a phylogenetic hypothesis of the evolutionary relationships among representative species of poison frogs, using sequences from three regions of mitochondrial DNA. In our analysis, we use that DNA-based phylogeny and comparative analysis of independent contrasts to investigate the correlation between coloration and toxicity in the poison frog family (Dendrobatidae). Information on the toxicity of different species was obtained from the literature. Two different measures of the brightness and extent of coloration were used. (i) Twenty-four human observers were asked to rank different photos of each different species in the analysis in terms of contrast to a leaf-littered background. (ii) Color photos of each species were scanned into a computer and a computer program was used to obtain a measure of the contrast of the colors of each species relative to a leaf-littered background. Comparative analyses of the results were carried out with two different models of character evolution: gradual change, with branch lengths proportional to the amount of genetic change, and punctuational change, with all change being associated with speciation events. Comparative analysis using either method or model indicated a significant correlation between the evolution of toxicity and coloration across this family. These results are consistent with the hypothesis that coloration in this group is aposematic.

Highly specific protein sequence motifs for genome analysis

We present a method for discovering conserved sequence motifs from families of aligned protein sequences. The method has been implemented as a computer program called emotif (http://motif.stanford.edu/emotif). Given an aligned set of protein sequences, emotif generates a set of motifs with a wide range of specificities and sensitivities. emotif also can generate motifs that describe possible subfamilies of a protein superfamily. A disjunction of such motifs often can represent the entire superfamily with high specificity and sensitivity. We have used emotif to generate sets of motifs from all 7,000 protein alignments in the blocks and prints databases. The resulting database, called identify (http://motif.stanford.edu/identify), contains more than 50,000 motifs. For each alignment, the database contains several motifs having a probability of matching a false positive that range from 10−10 to 10−5. Highly specific motifs are well suited for searching entire proteomes, while generating very few false predictions. identify assigns biological functions to 25–30% of all proteins encoded by the Saccharomyces cerevisiae genome and by several bacterial genomes. In particular, identify assigned functions to 172 of proteins of unknown function in the yeast genome.

Computation of Surface Electrical Potentials of Plant Cell Membranes : Correspondence to Published Zeta Potentials from Diverse Plant Sources

A Gouy-Chapman-Stern model has been developed for the computation of surface electrical potential (ψ0) of plant cell membranes in response to ionic solutes. The present model is a modification of an earlier version developed to compute the sorption of ions by wheat (Triticum aestivum L. cv Scout 66) root plasma membranes. A single set of model parameters generates values for ψ0 that correlate highly with published ζ potentials of protoplasts and plasma membrane vesicles from diverse plant sources. The model assumes ion binding to a negatively charged site (R− = 0.3074 μmol m−2) and to a neutral site (P0 = 2.4 μmol m−2) according to the reactions R− + IΖ ⇌ RIΖ−1 and P0 + IΖ ⇌ PIΖ, where IΖ represents an ion of charge Ζ. Binding constants for the negative site are 21,500 m−1 for H+, 20,000 m−1 for Al3+, 2,200 m−1 for La3+, 30 m−1 for Ca2+ and Mg2+, and 1 m−1 for Na+ and K+. Binding constants for the neutral site are 1/180 the value for binding to the negative site. Ion activities at the membrane surface, computed on the basis of ψ0, appear to determine many aspects of plant-mineral interactions, including mineral nutrition and the induction and alleviation of mineral toxicities, according to previous and ongoing studies. A computer program with instructions for the computation of ψ0, ion binding, ion concentrations, and ion activities at membrane surfaces may be requested from the authors.