Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

In-service and pre-service teachers' opinion on the use of models in teaching chemistry

The presented study examined the opinion of in-service and prospective chemistry teachers about the importance of usage of molecular and crystal models in secondary-level school practice, and investigated some of the reasons for their (non-) usage. The majority of participants stated that the use of models plays an important role in chemistry education and that they would use them more often if the circumstances were more favourable. Many teachers claimed that three-dimensional (3d) models are still not available in sufficient number at their schools; they also pointed to the lack of available computer facilities during chemistry lessons. The research revealed that, besides the inadequate material circumstances, less than one third of participants are able to use simple (freeware) computer programs for drawing molecular structures and their presentation in virtual space; however both groups of teachers expressed the willingness to improve their knowledge in the subject area. The investigation points to several actions which could be undertaken to improve the current situation.

Jpowder: a Java-based program for the display and examination of powder diffraction data

The ability to display and inspect powder diffraction data quickly and efficiently is a central part of the data analysis process. Whilst many computer programs are capable of displaying powder data, their focus is typically on advanced operations such as structure solution or Rietveld refinement. This article describes a lightweight software package, Jpowder, whose focus is fast and convenient visualization and comparison of powder data sets in a variety of formats from computers with network access. Jpowder is written in Java and uses its associated Web Start technology to allow ‘single-click deployment’ from a web page, http://www.jpowder.org. Jpowder is open source, free and available for use by anyone.

Transdifferential and transintegral calculus

The set of transreal numbers is a superset of the real numbers. It totalises real arithmetic by defining division by zero in terms of three def- inite, non-finite numbers: positive infinity, negative infinity and nullity. Elsewhere, in this proceedings, we extended continuity and limits from the real domain to the transreal domain, here we extended the real derivative to the transreal derivative. This continues to demonstrate that transreal analysis contains real analysis and operates at singularities where real analysis fails. Hence computer programs that rely on computing deriva- tives { such as those used in scientific, engineering and financial applica- tions { are extended to operate at singularities where they currently fail. This promises to make software, that computes derivatives, both more competent and more reliable. We also extended the integration of absolutely convergent functions from the real domain to the transreal domain.

Transreal limits expose category errors in IEEE 754 floating-point arithmetic and in mathematics

The IEEE 754 standard for oating-point arithmetic is widely used in computing. It is based on real arithmetic and is made total by adding both a positive and a negative infinity, a negative zero, and many Not-a-Number (NaN) states. The IEEE infinities are said to have the behaviour of limits. Transreal arithmetic is total. It also has a positive and a negative infinity but no negative zero, and it has a single, unordered number, nullity. We elucidate the transreal tangent and extend real limits to transreal limits. Arguing from this firm foundation, we maintain that there are three category errors in the IEEE 754 standard. Firstly the claim that IEEE infinities are limits of real arithmetic confuses limiting processes with arithmetic. Secondly a defence of IEEE negative zero confuses the limit of a function with the value of a function. Thirdly the definition of IEEE NaNs confuses undefined with unordered. Furthermore we prove that the tangent function, with the infinities given by geometrical con- struction, has a period of an entire rotation, not half a rotation as is commonly understood. This illustrates a category error, confusing the limit with the value of a function, in an important area of applied mathe- matics { trigonometry. We brie y consider the wider implications of this category error. Another paper proposes transreal arithmetic as a basis for floating- point arithmetic; here we take the profound step of proposing transreal arithmetic as a replacement for real arithmetic to remove the possibility of certain category errors in mathematics. Thus we propose both theo- retical and practical advantages of transmathematics. In particular we argue that implementing transreal analysis in trans- floating-point arith- metic would extend the coverage, accuracy and reliability of almost all computer programs that exploit real analysis { essentially all programs in science and engineering and many in finance, medicine and other socially beneficial applications.

The use of ICT by adults with learning disabilities in day and residential services

The use of Information and Communication Technology (ICT) by adults with learning disabilities has been positively promoted over the past decade. More recently, policy statements and guidance from the UK government have underlined the importance of ICT for adults with learning disabilities specifically, as well as for the population in general, through the potential it offers for social inclusion. The aim of the present study was to provide a picture of how ICT is currently being used within one organisation providing specialist services for adults with learning disabilities and more specifically to provide a picture of its use in promoting community participation. Nine day and 14 residential services were visited as part of a qualitative study to answer three main questions: What kinds of computer programs are being used? What are they being used for? Does this differ between day and residential services? Computers and digital cameras were used for a wide range of activities and ‘mainstream’ programs were used more widely than those developed for specific user groups. In day services, ICT was often embedded in wider projects and activities, whilst use in houses was based around leisure interests. In both contexts, ICT was being used to facilitate communication, although this was more linked to within-service activities, rather than those external to service provision.

P-T-Fluid evolution and graphite deposition during retrograde metamorphism in Ribeira Fold Belt, SE Brazil: Oxygen fugacity, fluid inclusions and C-O-H isotopic evidence

Combined fluid inclusion (FI) microthermometry, Raman spectroscopy, X-ray diffraction, C-O-H isotopes and oxygen fugacities of granulites from central Ribeira Fold Belt, SE Brazil, provided the following results: i) Magnetite-Hematite fO(2) estimates range from 10(-11.5) bar (QFM + 1) to 10(-18.3) bar (QFM - 1) for the temperature range of 896 degrees C-656 degrees C, implying fO(2) decrease from metamorphic peak temperatures to retrograde conditions; ii) 5 main types of fluid inclusions were observed: a) CO(2) and CO(2)-N(2) (0-11 mol%) high to medium density (1.01-0.59 g/cm(3)) FI; b) CO(2) and CO(2)-N(2) (0-36 mol%) low density (0.19-0.29 g/cm(3)) FI; c) CO(2) (94-95 mol%)-N(2) (3 mol%)-CH(4) (2-3 mol%)-H(2)O (water phi(v) (25 degrees C) = 0.1) FI; d) low-salinity H(2)O-CO(2) FI; and e) late low-salinity H(2)O FI; iii) Raman analyses evidence two graphite types in khondalites: an early highly ordered graphite (T similar to 450 degrees C) overgrown by a disordered kind (T similar to 330 degrees C); iv) delta(18)O quartz results of 10.3-10.7 parts per thousand, imply high-temperature CO(2) delta(18)O values of 14.4-14.8 parts per thousand, suggesting the involvement of a metamorphic fluid, whereas lower temperature biotite delta(18)O and delta D results of 7.5-8.5 parts per thousand and -54 to -67 parts per thousand respectively imply H(2)O delta(18)O values of 10-11 parts per thousand and delta D(H2O) of -23 to -36 parts per thousand suggesting delta(18)O depletion and increasing fluid/rock ratio from metamorphic peak to retrograde conditions. Isotopic results are compatible with low-temperature H(2)O influx and fO(2) decrease that promoted graphite deposition in retrograde granulites, simultaneous with low density CO(2), CO(2)-N(2) and CO(2)-N(2)-CH(4)-H(2)O fluid inclusions at T = 450-330 degrees C. Graphite delta(13)C results of -10.9 to -11.4 parts per thousand imply CO(2) delta(13)C values of -0.8 to -1.3 parts per thousand suggesting decarbonation of Cambrian marine carbonates with small admixture of lighter biogenic or mantle derived fluids. Based on these results, it is suggested that metamorphic fluids from the central segment of Ribeira Fold Belt evolved to CO(2)-N(2) fluids during granulitic metamorphism at high fO(2), followed by rapid pressure drop at T similar to 400-450 degrees C during late exhumation that caused fO(2) reduction induced by temperature decrease and water influx, turning carbonic fluids into CO(2)-H(2)O (depleting biotite delta(18)O and delta D values), and progressively into H(2)O. When fO(2) decreased substantially by mixture of carbonic and aqueous fluids, graphite deposited forming khondalites. (C) 2010 Elsevier Ltd. All rights reserved.

Mineralogical and microthermometric studies and structural aspects of imperial topaz mineralization in Antonio Pereira, Ouro Preto District (Minas Gerais) - Brazil

The occurrences of imperial topaz in the Antonio Pereira mine, Ouro Preto, Minas Gerais, are associated with the metamorphic carbonate rocks of the Minas Supergroup. The crystals have densities varying from 3.46 to 3.58. The parameters of the unitary cells obtained were: 4.658 to 4.663 angstrom (ao), 8.823 to 8.832 angstrom (b(o)), 8.382 to 8.389 angstrom (c(o)), and 344.65 to 345.46 angstrom 3 (V). The refraction indices presented the following variations: 1.622 to 1.630 (nX), 1.624 to 1.632 (nY), 1.633 to 1.640 (nZ), and 0.008 to 0.011 (B). These properties are coherent with the low fluorine contents obtained (16,48%/17,05wt%). Infrared spectroscopy and microthermometry showed that the fluid inclusions, which represent the mineralizing fluids, are formed by H(2)O (with Ca(2+), Mg(2+) and Na(+)), and CO(2) +/- CH(4). The minimal trapping T-P conditions of 290/320 degrees C and 2,349/2,497bar were obtained for the primary fluid inclusions. The pseudo-secondary fluid inclusions were trapped at conditions of lower temperatures and variable pressures, during the deformation process under local alternating states of stress. The microthermometric studies, the structural analysis and the fluorine contents suggest that the mineralized veins were formed from hydrothermal fluids originated during the Brasiliano tectono-metamorphic event.

Análise dinâmica de vigas assimétricas em curva com parede fina e aberta submetidas a ação de carga móveis

Fundamentalmente, o presente trabalho faz uma análise elástica linear de pontes ou vigas curvas assimétricas de seção transversal aberta e de parede fina, com propriedades físicas, geométricas e raio de curvatura constantes ao longo do eixo baricêntrico. Para tanto, utilizaram-se as equações diferenciais de VLASOV considerando o acoplamento entre as deformações nas direções vertical, transversal, axial de torcão nal. Na solução do sistema de quatro equações com derivadas parciais foi utilizado um apropriado método numérico de integração (Diferenças Finitas Centrais). A análise divide-se, basicamente, em dois tipos: análise DINÂMICA e ESTATICA. Ambas são utilizadas também na determinação do coeficiente de impacto (C.M.D.). A primeira refere-se tanto na determinação das características dinâmicas básicas (frequências naturais e respectivos modos de vibração), como também na determinação da resposta dinâmica da viga, em tensões e deformações, para cargas móveis arbitrárias. Vigas com qualquer combinação das condições de contorno, incluindo bordos rotulados e engastados nas três direções de flexão e na torção, são consideradas. 0s resultados da análise teórica, obtidos pela aplicação de programas computacionais implementados em microcomputador (análise estática) e no computador B-6700 (análise dinâmica), são comparados tanto com os da bibliografia técnica como também com resultados experimentais, apresentando boa correlação.

Estudo de antenas patches de microfita miniaturizadas em banda larga para aplicação em dispositivos móveis e portáteis

This work presents techniques used to design and manufacture microstrip patch antennas for applications in portable and mobile devices. To do so, are evaluated several factors that can influence the performance of microstrip patch antennas. Miniaturization techniques are studied and employed in order to apply this type of antenna in mobile and / or mobile. The theories of microstrip patch antennas are addressed by analyzing characteristics such as constitution, kinds of patches, substrates, feeding methods, analysis methods, the main advantages and disadvantages and others. Techniques for obtaining broadband microstrip patch antennas were surveyed in literature and exemplified mainly by means of simulations and measurements. For simulations of the antennas was used the commercial software . In addition, antenna miniaturization techniques have been studied as a main concern the fundamental limits of antennas with special attention to electrically small antennas because they are directly linked to the microstrip patch antennas. Five design antennas are proposed to demonstrate the effectiveness of techniques used to obtain the microstrip patch antennas broadband and miniaturized for use in mobile devices and/or portable. For this, the proposed antennas were simulated, built and measured. The antennas are proposed to be used in modern systems of wireless communications such as DTV, GPS, IEEE 802.16, IEEE 802.11, etc. The simulations of the antennas were made in business and computer programs. The measured results were obtained with a parser Vector of networks of the Rhode and Schwarz model ZVB 14

Detecção de áreas degradadas na sub-bacia hidrográfica do rio taperoá/pb, utilizando parâmetros físicos dos sensores modis/terra e tm/landsat

This study includes the results of the analysis of areas susceptible to degradation by remote sensing in semi-arid region, which is a matter of concern and affects the whole population and the catalyst of this process occurs by the deforestation of the savanna and improper practices by the use of soil. The objective of this research is to use biophysical parameters of the MODIS / Terra and images TM/Landsat-5 to determine areas susceptible to degradation in semi-arid Paraiba. The study area is located in the central interior of Paraíba, in the sub-basin of the River Taperoá, with average annual rainfall below 400 mm and average annual temperature of 28 ° C. To draw up the map of vegetation were used TM/Landsat-5 images, specifically, the composition 5R4G3B colored, commonly used for mapping land use. This map was produced by unsupervised classification by maximum likelihood. The legend corresponds to the following targets: savanna vegetation sparse and dense, riparian vegetation and exposed soil. The biophysical parameters used in the MODIS were emissivity, albedo and vegetation index for NDVI (NDVI). The GIS computer programs used were Modis Reprojections Tools and System Information Processing Georeferenced (SPRING), which was set up and worked the bank of information from sensors MODIS and TM and ArcGIS software for making maps more customizable. Initially, we evaluated the behavior of the vegetation emissivity by adapting equation Bastiaanssen on NDVI for spatialize emissivity and observe changes during the year 2006. The albedo was used to view your percentage of increase in the periods December 2003 and 2004. The image sensor of Landsat TM were used for the month of December 2005, according to the availability of images and in periods of low emissivity. For these applications were made in language programs for GIS Algebraic Space (LEGAL), which is a routine programming SPRING, which allows you to perform various types of algebras of spatial data and maps. For the detection of areas susceptible to environmental degradation took into account the behavior of the emissivity of the savanna that showed seasonal coinciding with the rainy season, reaching a maximum emissivity in the months April to July and in the remaining months of a low emissivity . With the images of the albedo of December 2003 and 2004, it was verified the percentage increase, which allowed the generation of two distinct classes: areas with increased variation percentage of 1 to 11.6% and the percentage change in areas with less than 1 % albedo. It was then possible to generate the map of susceptibility to environmental degradation, with the intersection of the class of exposed soil with varying percentage of the albedo, resulting in classes susceptibility to environmental degradation

A transcript finishing initiative for closing gaps in the human transcriptome

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST Clusters, mapped against the genomic sequence. Each pair of EST Clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted Set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

TIME-OPTIMAL GEOMAGNETIC ATTITUDE MANEUVERS OF AN AXISYMMETRICAL SPINNING SATELLITE

A formulation used to determine the time-optimal geomagnetic attitude maneuvers subject to dynamic and geometric constraints is proposed in this paper. This was obtained by a direct search procedure based on a control function parametrization method, using linear programming to obtain numerical suboptimal solutions by linear perturbation. Due to its characteristics it can be used in small computers and to generate computer programs of general application. The dynamic modeling, the magnetic torque model and the suboptimal control procedure are presented. Simulation runs have verified the feasibility of the formulation thus derived and have shown a notable improvement in performance.

Determination of the maximum force due to skull impact in fights between sheep of the Ovis aries species

The present article presents a means of determining the maximum impact force between two bodies from the determination of the involved impulse in the impact and the sound emitted by the shock of the bodies during this impact.It also presents a case study applied to the shock between the skulls of male sheep of the Ovis aries species. These animals do not possess horns and dispute the territorial leadership by fighting, during which the skull is used as a weapon of attack, similar to a battering ram.Initially, a revision of basic physics approaching the theory of impulse is made, which shows that the average force during an impact can be obtained by the quantity of movement of the bodies. In its turn, the quantity of movement is obtained through the average speed of approach and the mass of the bodies. The maximum force is obtained from the average force, using the approach of the Force X Time curve with the Sonorous Intensity X Time Curve.In order to study the case of a shock between two sheep, the mass of the bodies was obtained through direct weighing and the average speed of approach obtained indirectly through filming, thus making possible the calculation of the average force. The Sonorous Intensity X Time Curve was obtained through the recording of the sound of the impact during a filmed fight, with later manipulation through computer programs. With this data the maximum force exercised between the skull of the sheep during the impact was obtained, which will be used in later studies.