PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth-death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open-source command-line Python program available at http://sourceforge.net/projects/pyrate/.

A feature-based object-oriented expert system to model and support product design

In this paper a computer program to model and support product design is presented. The product is represented through a hierarchical structure that allows the user to navigate across the product’s components, and it aims at facilitating each step of the detail design process. A graphical interface was also developed, which shows visually to the user the contents of the product structure. Features are used as building blocks for the parts that compose the product, and object-oriented methodology was used as a means to implement the product structure. Finally, an expert system was also implemented, whose knowledge base rules help the user design a product that meets design and manufacturing requirements.

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

A policy model for secure information flow

When a computer program requires legitimate access to confidential data, the question arises whether such a program may illegally reveal sensitive information. This paper proposes a policy model to specify what information flow is permitted in a computational system. The security definition, which is based on a general notion of information lattices, allows various representations of information to be used in the enforcement of secure information flow in deterministic or nondeterministic systems. A flexible semantics-based analysis technique is presented, which uses the input-output relational model induced by an attacker's observational power, to compute the information released by the computational system. An illustrative attacker model demonstrates the use of the technique to develop a termination-sensitive analysis. The technique allows the development of various information flow analyses, parametrised by the attacker's observational power, which can be used to enforce what declassification policies.

Confinement and soliton solutions in the SL(3) Toda model coupled to matter fields

We consider an integrable conformally invariant two-dimensional model associated to the affine Kac-Moody algebra sl3(ℂ). It possesses four scalar fields and six Dirac spinors. The theory does not possesses a local Lagrangian since the spinor equations of motion present interaction terms which are bilinear in the spinors. There exists a submodel presenting an equivalence between a U(1) vector current and a topological current, which leads to a confinement of the spinors inside the solitons. We calculate the one-soliton and two-soliton solutions using a procedure which is a hybrid of the dressing and Hirota methods. The soliton masses and time delays due to the soliton interactions are also calculated. We give a computer program to calculate the soliton solutions. © 2002 Published by Elsevier Science B.V.

Model to design drip hose lateral line using two spacing between emitters

The use of non-pressure compensating drip hose in horticultural and annual cycle fruits is growing in Brazil. In this case, the challenge for designers is getting longer lateral lines with high values of uniformity. The objective of this study was to develop a model to design longer lateral lines using non-pressure compensating drip hose. Using the developed model, the hypotheses to be evaluated were: a) the use of two different spacing between emitters in the same lateral line allows longer length; b) it is possible to get longer lateral lines using high values of pressure variation in the lateral lines since the distribution uniformity stays below allowable limits. A computer program was developed in Delphi based on the model developed and it is able to design lateral lines in level using non-pressure compensating drip hose. The input data are: desired distribution uniformity (DU); initial and final pressure in the lateral line; coefficients of relationship between emitter discharge and pressure head; hose internal diameter; pipe cross-sectional area with the dripper; and roughness coefficient for the Hazen-Williams equation. The program allows calculate the lateral line length with three possibilities: selecting two spacing between emitters and defining the exchange point; using two pre-established spacing between emitters and calculating the length of each section with different spacing; using one emitter spacing. Results showed that the use of two sections with different spacing between drippers in the lateral line didn't allow longer length but got better uniformity when compared with lateral line with one spacing between emitters. The adoption of two spacing increased the flow rate per meter in the final section which represented approximately 80% of the lateral line total length and this justifies their use. The software allowed DU above 90% with pressure head variation of 40% and the use of two spacing between emitters. The developed model/software showed to be accurate, easy to handle and useful for lateral line design using non-pressure compensating drip hose.

Desenvolvimento de um sistema computacional para tratamento de dados meteorológicos no setor de agroenergia

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Sistema de controle de escoamento de gás natural em dutos de distribuição com detecção de vazamentos utilizando redes neurais

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelo Matemático para redimensionamento de motores elétricos trifásicos superdimensionados

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Content and English Language Integrated Learning: The use of Moodle in Aircraft Maintenance Training Programs

The aim of this work is to develop a prototype of an e-learning environment that can foster Content and Language Integrated Learning (CLIL) for students enrolled in an aircraft maintenance training program, which allows them to obtain a license valid in all EU member states. Background research is conducted to retrace the evolution of the field of educational technology, analyzing different learning theories – behaviorism, cognitivism, and (socio-)constructivism – and reflecting on how technology and its use in educational contexts has changed over time. Particular attention is given to technologies that have been used and proved effective in Computer Assisted Language Learning (CALL). Based on the background research and on students’ learning objectives, i.e. learning highly specialized contents and aeronautical technical English, a bilingual approach is chosen, three main tools are identified – a hypertextbook, an exercise creation activity, and a discussion forum – and the learning management system Moodle is chosen as delivery medium. The hypertextbook is based on the technical textbook written in English students already use. In order to foster text comprehension, the hypertextbook is enriched by hyperlinks and tooltips. Hyperlinks redirect students to webpages containing additional information both in English and in Italian, while tooltips show Italian equivalents of English technical terms. The exercise creation activity and the discussion forum foster interaction and collaboration among students, according to socio-constructivist principles. In the exercise creation activity, students collaboratively create a workbook, which allow them to deeply analyze and master the contents of the hypertextbook and at the same time create a learning tool that can help them, as well as future students, to enhance learning. In the discussion forum students can discuss their individual issues, content-related, English-related or e-learning environment-related, helping one other and offering instructors suggestions on how to improve both the hypertextbook and the workbook based on their needs.

Temporal lobe white matter asymmetry and language laterality in epilepsy patients.

Recent studies using diffusion tensor imaging (DTI) have advanced our knowledge of the organization of white matter subserving language function. It remains unclear, however, how DTI may be used to predict accurately a key feature of language organization: its asymmetric representation in one cerebral hemisphere. In this study of epilepsy patients with unambiguous lateralization on Wada testing (19 left and 4 right lateralized subjects; no bilateral subjects), the predictive value of DTI for classifying the dominant hemisphere for language was assessed relative to the existing standard-the intra-carotid Amytal (Wada) procedure. Our specific hypothesis is that language laterality in both unilateral left- and right-hemisphere language dominant subjects may be predicted by hemispheric asymmetry in the relative density of three white matter pathways terminating in the temporal lobe implicated in different aspects of language function: the arcuate (AF), uncinate (UF), and inferior longitudinal fasciculi (ILF). Laterality indices computed from asymmetry of high anisotropy AF pathways, but not the other pathways, classified the majority (19 of 23) of patients using the Wada results as the standard. A logistic regression model incorporating information from DTI of the AF, fMRI activity in Broca's area, and handedness was able to classify 22 of 23 (95.6%) patients correctly according to their Wada score. We conclude that evaluation of highly anisotropic components of the AF alone has significant predictive power for determining language laterality, and that this markedly asymmetric distribution in the dominant hemisphere may reflect enhanced connectivity between frontal and temporal sites to support fluent language processes. Given the small sample reported in this preliminary study, future research should assess this method on a larger group of patients, including subjects with bi-hemispheric dominance.

Coupled model of initiation and propagation of corrosion in reinforced concrete

Corrosion of reinforcing steel in concrete due to chloride ingress is one of the main causes of the deterioration of reinforced concrete structures. Structures most affected by such a corrosion are marine zone buildings and structures exposed to de-icing salts like highways and bridges. Such process is accompanied by an increase in volume of the corrosión products on the rebarsconcrete interface. Depending on the level of oxidation, iron can expand as much as six times its original volume. This increase in volume exerts tensile stresses in the surrounding concrete which result in cracking and spalling of the concrete cover if the concrete tensile strength is exceeded. The mechanism by which steel embedded in concrete corrodes in presence of chloride is the local breakdown of the passive layer formed in the highly alkaline condition of the concrete. It is assumed that corrosion initiates when a critical chloride content reaches the rebar surface. The mathematical formulation idealized the corrosion sequence as a two-stage process: an initiation stage, during which chloride ions penetrate to the reinforcing steel surface and depassivate it, and a propagation stage, in which active corrosion takes place until cracking of the concrete cover has occurred. The aim of this research is to develop computer tools to evaluate the duration of the service life of reinforced concrete structures, considering both the initiation and propagation periods. Such tools must offer a friendly interface to facilitate its use by the researchers even though their background is not in numerical simulation. For the evaluation of the initiation period different tools have been developed: Program TavProbabilidade: provides means to carry out a probability analysis of a chloride ingress model. Such a tool is necessary due to the lack of data and general uncertainties associated with the phenomenon of the chloride diffusion. It differs from the deterministic approach because it computes not just a chloride profile at a certain age, but a range of chloride profiles for each probability or occurrence. Program TavProbabilidade_Fiabilidade: carries out reliability analyses of the initiation period. It takes into account the critical value of the chloride concentration on the steel that causes breakdown of the passive layer and the beginning of the propagation stage. It differs from the deterministic analysis in that it does not predict if the corrosion is going to begin or not, but to quantifies the probability of corrosion initiation. Program TavDif_1D: was created to do a one dimension deterministic analysis of the chloride diffusion process by the finite element method (FEM) which numerically solves Fick’second Law. Despite of the different FEM solver already developed in one dimension, the decision to create a new code (TavDif_1D) was taken because of the need to have a solver with friendly interface for pre- and post-process according to the need of IETCC. An innovative tool was also developed with a systematic method devised to compare the ability of the different 1D models to predict the actual evolution of chloride ingress based on experimental measurements, and also to quantify the degree of agreement of the models with each others. For the evaluation of the entire service life of the structure: a computer program has been developed using finite elements method to do the coupling of both service life periods: initiation and propagation. The program for 2D (TavDif_2D) allows the complementary use of two external programs in a unique friendly interface: • GMSH - an finite element mesh generator and post-processing viewer • OOFEM – a finite element solver. This program (TavDif_2D) is responsible to decide in each time step when and where to start applying the boundary conditions of fracture mechanics module in function of the amount of chloride concentration and corrosion parameters (Icorr, etc). This program is also responsible to verify the presence and the degree of fracture in each element to send the Information of diffusion coefficient variation with the crack width. • GMSH - an finite element mesh generator and post-processing viewer • OOFEM – a finite element solver. The advantages of the FEM with the interface provided by the tool are: • the flexibility to input the data such as material property and boundary conditions as time dependent function. • the flexibility to predict the chloride concentration profile for different geometries. • the possibility to couple chloride diffusion (initiation stage) with chemical and mechanical behavior (propagation stage). The OOFEM code had to be modified to accept temperature, humidity and the time dependent values for the material properties, which is necessary to adequately describe the environmental variations. A 3-D simulation has been performed to simulate the behavior of the beam on both, action of the external load and the internal load caused by the corrosion products, using elements of imbedded fracture in order to plot the curve of the deflection of the central region of the beam versus the external load to compare with the experimental data.

Diseño de separadores mediante aplicación informática = Computer Application for Sepators Design

Programa informático desarrollado en plataforma EXCEL (VBA) y dirigido al diseño de Separadores de dos y tres fases, verticales y horizontales. El programa de ordenador o aplicación tiene la capacidad de determinar las propiedades físicas del fluido, utilizando diferentes correlaciones sobre la base del “Black Oil Model”, con dichas propiedades el Programa predice el tipo de flujo presente. Si el tipo de flujo es “Slug Flow” el programa determinara las dimensiones del “Slug catcher” necesario. Bajo las condiciones de funcionamiento existentes el programa diseñará el separador elegido: dos o tres fases, vertical u horizontal. Por último, la aplicación informática estimará el coste del equipo. Abstract Computer program developed in EXCEL (VBA) platform and aimed for the design of Two-Phase, Three-Phase, Vertical or Horizontal Separators. The computer Program or Application has the capability to determine the fluid physical properties utilizing different correlations on the basis of the Black Oil Model, with those Properties the Program will predict the Flow Regime present. If the flow regime is Slug Flow the program will determine the necessary slug catcher dimensions. Under certain operational conditions the program will design the selected: Two-Phase or Three-Phase, Vertical or Horizontal Separator. Finally the computer Application will estimate the cost of the equipment.

An Ecological Model for Predicting Behaviour of Mediterranean Shrublands

In order to build dynamic models for prediction and management of degraded Mediterranean forest areas was necessary to build MARIOLA model, which is a calculation computer program. This model includes the following subprograms. 1) bioshrub program, which calculates total, green and woody shrubs biomass and it establishes the time differences to calculate the growth. 2) selego program, which builds the flow equations from the experimental data. It is based on advanced procedures of statistical multiple regression. 3) VEGETATION program, which solves the state equations with Euler or Runge-Kutta integration methods. Each one of these subprograms can act as independent or as linked programs.

A numerical model for predicting shoreline changes /

A mathematical model for long-term, three-dimensional shoreline evolution is developed. The combined effects of variations of sea level; wave refraction and diffraction; loss of sand by density currents during storms, by rip currents, and by wind; bluff erosion and berm accretion; effects of manmade structures such as long groin or navigational structures; and beach nourishment are all taken into account. A computer program is developed with various subroutines which permit modification as the state-of-the-art progresses. The program is applied to a test case at Holland Harbor, Michigan. (Author).