lattice: Easy construction of professional graphs for agricultural research in R environment

This paper shows how to apply the lattice package of R to create effective scientific graphs. The readers will learn basic notions of the package and ways to work with it in an easy way. The R code the paper provides will help them create various graphs, including a scatter plot, a box plot, a density plot, and a bar plot; with a little work, the code can be changed to make other graphs. The paper emphasizes the trellis display, a useful but still undervalued technique in scientific visualization.

lattice: Easy construction of professional graphs for agricultural research in R environment

This paper shows how to apply the lattice package of R to create effective scientific graphs. The readers will learn basic notions of the package and ways to work with it in an easy way. The R code the paper provides will help them create various graphs, including a scatter plot, a box plot, a density plot, and a bar plot; with a little work, the code can be changed to make other graphs. The paper emphasizes the trellis display, a useful but still undervalued technique in scientific visualization.(AU)

Effects of the bull on conception rate of dairy cows in different seasons and according to AI type

Background: Reproductive efficiency is one of the most important factors affecting the performance dairy cattle, and fixedtime artificial insemination (TAI) is an important biotechnology factor employed in bovine livestock. The achievement of satisfactory results in TAI protocols depends of several factors, such as health and body condition, milk yield, environmental temperatures, ovulation time, semen manipulation, as well as semen quality. The goal of this study was to evaluate the conception rate of heifers and multiparous cows based on different Holstein bulls used for artificial insemination (AI). The effects of the type of management AI, animal category, and season of the year were also examined.Materials, Methods & Results: A three-year database on the reproductive management of a dairy farm was formed. All the cows and heifers were of the Holstein breed, in semi-intensive nutritional management, milked twice a day, and received a total mix ration. After 45 days in milk, when cows were observed twice daily with estrus signs, posterior artificial insemination occurred 12 h after estrus visualization was made. However, cows that were not observed in estrus were submitted to a timed artificial insemination (TAI). In this study, these fixed factors were considered: bulls utilized for the AI (totalizing 10 animals with at least 100 inseminations in each season, denoted by the letter B and a number - B1, B2, B3, B4, B5, B6, B7, B8, B9, B10); the season of the insemination (spring/summer being from November to April and autumn/winter from May to October), category animal (heifers, animals that never have been calved, or multiparous, animals that have already given birth more than once), and the type of AI (which included TAI using a protocol for synchronization, but cows having not necessarily shown estrus signs at the AI; ETAI: using protocol of synchronization, cows showing estrus signs at the AI;[...]

Effects of the bull on conception rate of dairy cows in different seasons and according to AI type

Background: Reproductive efficiency is one of the most important factors affecting the performance dairy cattle, and fixedtime artificial insemination (TAI) is an important biotechnology factor employed in bovine livestock. The achievement of satisfactory results in TAI protocols depends of several factors, such as health and body condition, milk yield, environmental temperatures, ovulation time, semen manipulation, as well as semen quality. The goal of this study was to evaluate the conception rate of heifers and multiparous cows based on different Holstein bulls used for artificial insemination (AI). The effects of the type of management AI, animal category, and season of the year were also examined.Materials, Methods & Results: A three-year database on the reproductive management of a dairy farm was formed. All the cows and heifers were of the Holstein breed, in semi-intensive nutritional management, milked twice a day, and received a total mix ration. After 45 days in milk, when cows were observed twice daily with estrus signs, posterior artificial insemination occurred 12 h after estrus visualization was made. However, cows that were not observed in estrus were submitted to a timed artificial insemination (TAI). In this study, these fixed factors were considered: bulls utilized for the AI (totalizing 10 animals with at least 100 inseminations in each season, denoted by the letter B and a number - B1, B2, B3, B4, B5, B6, B7, B8, B9, B10); the season of the insemination (spring/summer being from November to April and autumn/winter from May to October), category animal (heifers, animals that never have been calved, or multiparous, animals that have already given birth more than once), and the type of AI (which included TAI using a protocol for synchronization, but cows having not necessarily shown estrus signs at the AI; ETAI: using protocol of synchronization, cows showing estrus signs at the AI;[...](AU)

s size with AFM

Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described.

s size with AFM

Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described.

Basic principles of graphing data

Data visualization is a very important aspect of data analysis and of presentation. Focusing on the latter, this paper discusses various elements of constructing graphs for publications. Bad and good graphs are compared, and a checklist with graphical elements to be used while creating graphs is proposed.

A visualização de dados é um aspecto importante da análise de dados e de sua apresentação. Nesse ponto de vista enfocam-se vários elementos da construção de gráficos para publicações. Gráficos ruins e bons são comparados, e uma lista de checagem de elementos de composição gráfica é proposta para ser utilizada durante a confecção de gráficos.

Basic principles of graphing data

Data visualization is a very important aspect of data analysis and of presentation. Focusing on the latter, this paper discusses various elements of constructing graphs for publications. Bad and good graphs are compared, and a checklist with graphical elements to be used while creating graphs is proposed.

A visualização de dados é um aspecto importante da análise de dados e de sua apresentação. Nesse ponto de vista enfocam-se vários elementos da construção de gráficos para publicações. Gráficos ruins e bons são comparados, e uma lista de checagem de elementos de composição gráfica é proposta para ser utilizada durante a confecção de gráficos.

Radiographie avaliation of prostatic conditions and prostatectomy simplification in dog / Avaliação radiográfica das condições prostáticas e simplificação da técnica da prostatectomia em cão

The author valves the conditions of the prostate and primordially of the urethra, across contrastic urethocistography with hyorosoluble iodate compounds. To presents modification in the technica of prostatectomy, primordially when the perineal hernia reduction, proposing of the departure of the orgasm in parallel layers without attain it. Was studied 3 experimental cases and 6 dogs that carrier prostatic pathology, and from thence was selecting the material that was utilize for document, both before and after the surgery

Avalia-se as condições da próstata, e principalmente uretra, através da uretrocistografia contrastada com compostos iodados hidrossolúveis. Apresenta modificação na técnica da prostatectomia principalmente quando da redução da hérnia perineal, propondo a retirada do órgão em camadas paralelas à uretra sem atingi-la. Foram estudados 3 casos experimentais e 6 de cães portadores de patologia prostática dos quais foi selecionado o material utilizado para documentação, tanto antes como depois da cirurgia.

Radiographie avaliation of prostatic conditions and prostatectomy simplification in dog / Avaliação radiográfica das condições prostáticas e simplificação da técnica da prostatectomia em cão

The author valves the conditions of the prostate and primordially of the urethra, across contrastic urethocistography with hyorosoluble iodate compounds. To presents modification in the technica of prostatectomy, primordially when the perineal hernia reduction, proposing of the departure of the orgasm in parallel layers without attain it. Was studied 3 experimental cases and 6 dogs that carrier prostatic pathology, and from thence was selecting the material that was utilize for document, both before and after the surgery

Avalia-se as condições da próstata, e principalmente uretra, através da uretrocistografia contrastada com compostos iodados hidrossolúveis. Apresenta modificação na técnica da prostatectomia principalmente quando da redução da hérnia perineal, propondo a retirada do órgão em camadas paralelas à uretra sem atingi-la. Foram estudados 3 casos experimentais e 6 de cães portadores de patologia prostática dos quais foi selecionado o material utilizado para documentação, tanto antes como depois da cirurgia.

Modelagem numérica em mapa temático: sítios florestais

The objective of this work was to utilize programs of geoprocessing and treatment of images, considerated to be well-knowm and easily operated, for numerical modelling of a thematical map. This modelling is carried out from feeding a digital base bank, for forest planning and cadaster. More specifically, a methodology that uses the numerical modelling for tridimensional visualization of a layer of geoindicated forest sites has been designed to permit the crossing (superposition) with other layers, also, related to the forest area. The following materiais have been used in order to reach the goals: a map of natural sites in the National Forest of Passo fundo, hardware (microcomputer, ink jet printer, table scanner), software (Idrisi 4.1 and Aldus PhotoStyler 2.0). The employed methodology based geoindication for posterior numerical modelling and tridimensional visualization of the different site represented in the plannimetrical map of the National Forest of Passo fundo. As a result, representative archives about the employed methodology were obtainde to help in identifying, through different heights, the site where the most adequated species to their natural characteristics can be implanted, showing, the viability of the application of the present methodology in forest.

O presente trabalho tem por objetivo a utilização de programas de geoprocessamento e de tratamento de imagens, considerados de domínio público e de fácil operacionalidade, para modelagem numérica de um mapa temático. Esta modelagem é feita a partir da alimentação de um banco de dados digitais, para fins de planejamento e cadastro florestal. Mais especificamente, criou-se uma metodologia que utiliza a modelagem numérica para a visualização tridimensional de um plano de informação de sítios florestais georeferenciados, que permite o cruzamento (sobreposição) com outros planos de informações, também georeferenciados, de interesse na área florestal. Foram utilizados os seguintes materiais: mapa de sítios naturais da Floresta Nacional de Passo Fundo, microcomputador, impressora, scanner de mesa, os softwares Idrisi 4.1 e Aldus PhotoStyler 2.0. A metodologia empregada baseou-se na digitalização, por varredura ótica, do mapa de sítios naturais existentes, sua edição de cores e georeferenciamento, para posterior modelagem numérica e visualização tridimensional dos diferentes sítios representados no mapa planimétrico da Floresta Nacional de Passo Fundo. Como resultado, obteve-se arquivos, que possibilitaram a identificação, através das diferentes alturas, dos sítios onde podem ser implantadas espécies mais adequadas às suas características naturais, demonstrando a viabilidade da aplicação da presente metodologia no planejamento florestal.

A system for generating virtual seeds

Seed analysts need to identify seeds, and seed catalogs are used as a reference to accomplish this task. Conventional seed catalogs supply two-dimensional photographs and hand-drawn diagrams. In this study, a new, three-dimensional representation of seeds is developed to supplement these traditional photographs and drawings. QuickTime VR is a promising method for viewing three-dimensional objects on a computer screen. It permits manipulation of an object by rotating and viewing it from any pre-specified angle at an interactive speed, allowing the viewer the sense of examining a hand-held object. In this study, QuickTime VR object movies of seeds were created as interactive "movies" of seeds that can be rotated and scaled to give the viewer the sensation of examining actual seeds. This approach allows the examination of virtual seeds from any angle, permitting more accurate identification of seeds by seed analysts.

Os analistas precisam identificar as sementes e utilizam como referência catálogos específicos. Os catálogos geralmente apresentam fotografias bidimensionais e diagramas manuais. Neste estudo, foi desenvolvida uma nova representação tridimensional das sementes como suplementação aos materiais de apoio tradicionais. "QuickTime VR" é um método promissor para a visualização de objetos em três dimensões na tela do computador, permitindo a movimentação de um objeto através da rotação e visualização, em ângulos pré definidos em uma velocidade interativa. No "QuickTime VR" foram criadas imagens interativas que podem ser rotacionadas e dimensionadas dando ao observador a sensação de estar examinando a própria semente. Este procedimento permite o exame de "sementes virtuais" sob qualquer ângulo, permitindo aos analistas de sementes uma identificação mais detalhada.

Modelagem numérica em mapa temático: sítios florestais

The objective of this work was to utilize programs of geoprocessing and treatment of images, considerated to be well-knowm and easily operated, for numerical modelling of a thematical map. This modelling is carried out from feeding a digital base bank, for forest planning and cadaster. More specifically, a methodology that uses the numerical modelling for tridimensional visualization of a layer of geoindicated forest sites has been designed to permit the crossing (superposition) with other layers, also, related to the forest area. The following materiais have been used in order to reach the goals: a map of natural sites in the National Forest of Passo fundo, hardware (microcomputer, ink jet printer, table scanner), software (Idrisi 4.1 and Aldus PhotoStyler 2.0). The employed methodology based geoindication for posterior numerical modelling and tridimensional visualization of the different site represented in the plannimetrical map of the National Forest of Passo fundo. As a result, representative archives about the employed methodology were obtainde to help in identifying, through different heights, the site where the most adequated species to their natural characteristics can be implanted, showing, the viability of the application of the present methodology in forest.

O presente trabalho tem por objetivo a utilização de programas de geoprocessamento e de tratamento de imagens, considerados de domínio público e de fácil operacionalidade, para modelagem numérica de um mapa temático. Esta modelagem é feita a partir da alimentação de um banco de dados digitais, para fins de planejamento e cadastro florestal. Mais especificamente, criou-se uma metodologia que utiliza a modelagem numérica para a visualização tridimensional de um plano de informação de sítios florestais georeferenciados, que permite o cruzamento (sobreposição) com outros planos de informações, também georeferenciados, de interesse na área florestal. Foram utilizados os seguintes materiais: mapa de sítios naturais da Floresta Nacional de Passo Fundo, microcomputador, impressora, scanner de mesa, os softwares Idrisi 4.1 e Aldus PhotoStyler 2.0. A metodologia empregada baseou-se na digitalização, por varredura ótica, do mapa de sítios naturais existentes, sua edição de cores e georeferenciamento, para posterior modelagem numérica e visualização tridimensional dos diferentes sítios representados no mapa planimétrico da Floresta Nacional de Passo Fundo. Como resultado, obteve-se arquivos, que possibilitaram a identificação, através das diferentes alturas, dos sítios onde podem ser implantadas espécies mais adequadas às suas características naturais, demonstrando a viabilidade da aplicação da presente metodologia no planejamento florestal.

A system for generating virtual seeds

Seed analysts need to identify seeds, and seed catalogs are used as a reference to accomplish this task. Conventional seed catalogs supply two-dimensional photographs and hand-drawn diagrams. In this study, a new, three-dimensional representation of seeds is developed to supplement these traditional photographs and drawings. QuickTime VR is a promising method for viewing three-dimensional objects on a computer screen. It permits manipulation of an object by rotating and viewing it from any pre-specified angle at an interactive speed, allowing the viewer the sense of examining a hand-held object. In this study, QuickTime VR object movies of seeds were created as interactive "movies" of seeds that can be rotated and scaled to give the viewer the sensation of examining actual seeds. This approach allows the examination of virtual seeds from any angle, permitting more accurate identification of seeds by seed analysts.

Os analistas precisam identificar as sementes e utilizam como referência catálogos específicos. Os catálogos geralmente apresentam fotografias bidimensionais e diagramas manuais. Neste estudo, foi desenvolvida uma nova representação tridimensional das sementes como suplementação aos materiais de apoio tradicionais. "QuickTime VR" é um método promissor para a visualização de objetos em três dimensões na tela do computador, permitindo a movimentação de um objeto através da rotação e visualização, em ângulos pré definidos em uma velocidade interativa. No "QuickTime VR" foram criadas imagens interativas que podem ser rotacionadas e dimensionadas dando ao observador a sensação de estar examinando a própria semente. Este procedimento permite o exame de "sementes virtuais" sob qualquer ângulo, permitindo aos analistas de sementes uma identificação mais detalhada.