ICGE: an R package for detecting relevant clusters and atypical units in gene expression

Background: Gene expression technologies have opened up new ways to diagnose and treat cancer and other diseases. Clustering algorithms are a useful approach with which to analyze genome expression data. They attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. An important problem associated with gene classification is to discern whether the clustering process can find a relevant partition as well as the identification of new genes classes. There are two key aspects to classification: the estimation of the number of clusters, and the decision as to whether a new unit (gene, tumor sample ... ) belongs to one of these previously identified clusters or to a new group. Results: ICGE is a user-friendly R package which provides many functions related to this problem: identify the number of clusters using mixed variables, usually found by applied biomedical researchers; detect whether the data have a cluster structure; identify whether a new unit belongs to one of the pre-identified clusters or to a novel group, and classify new units into the corresponding cluster. The functions in the ICGE package are accompanied by help files and easy examples to facilitate its use. Conclusions: We demonstrate the utility of ICGE by analyzing simulated and real data sets. The results show that ICGE could be very useful to a broad research community.

An agent-based multi-scale wind generation model

(EuroPES 2009)

Energy Functions And Basic Equations For Ferroelectrics

Energy functions (or characteristic functions) and basic equations for ferroelectrics in use today are given by those for ordinary dielectrics in the physical and mechanical communications. Based on these basic equations and energy functions, the finite element computation of the nonlinear behavior of the ferroelectrics has been carried out by several research groups. However, it is difficult to process the finite element computation further after domain switching, and the computation results are remarkably deviating from the experimental results. For the crack problem, the iterative solution of the finite element calculation could not converge and the solutions for fields near the crack tip oscillate. In order to finish the calculation smoothly, the finite element formulation should be modified to neglect the equivalent nodal load produced by spontaneous polarization gradient. Meanwhile, certain energy functions for ferroelectrics in use today are not compatible with the constitutive equations of ferroelectrics and need to be modified. This paper proposes a set of new formulae of the energy functions for ferroelectrics. With regard to the new formulae of the energy functions, the new basic equations for ferroelectrics are derived and can reasonably explain the question in the current finite element analysis for ferroelectrics.

High Order Multi-Moment Constrained Finite Volume Method. Part I: Basic Formulation

A new high-order finite volume method based on local reconstruction is presented in this paper. The method, so-called the multi-moment constrained finite volume (MCV) method, uses the point values defined within single cell at equally spaced points as the model variables (or unknowns). The time evolution equations used to update the unknowns are derived from a set of constraint conditions imposed on multi kinds of moments, i.e. the cell-averaged value and the point-wise value of the state variable and its derivatives. The finite volume constraint on the cell-average guarantees the numerical conservativeness of the method. Most constraint conditions are imposed on the cell boundaries, where the numerical flux and its derivatives are solved as general Riemann problems. A multi-moment constrained Lagrange interpolation reconstruction for the demanded order of accuracy is constructed over single cell and converts the evolution equations of the moments to those of the unknowns. The presented method provides a general framework to construct efficient schemes of high orders. The basic formulations for hyperbolic conservation laws in 1- and 2D structured grids are detailed with the numerical results of widely used benchmark tests. (C) 2009 Elsevier Inc. All rights reserved.

Relationship between the basic morphometric measurements and growth pattern of Heterotis niloticus from River Kaduna floodplain

A total of 61 specimens of Heterotis niloticus were evaluated by linear regression and correlation. The specimens had mean standard length of 27.09 plus or minus 4.73cm, total length of 33-49cm, mean weight of 2445,108.3g, mean snout length of 48 plus or minus 0.86cm, mean eye diameter of 1.30 plus or minus 0.15cm, mean head length of 6.29 plus or minus 1.75cm. There was a strong relationship between the length and the weight, the eye diameter and the standard length, snout length and the standard length, head length and the standard length, snout length and the weight, head length and the weight (P<0.05). But the correlation of the eye diameters and the weight was insignificant (P>0.05). The growth pattern analysis depicts that the growth was negatively allometric with a b value of 1.16

Reproduction in Gammarus (Crustacea, Amphipoda): basic processes

Research on the basic reproduction processes of Gammarus is summarized and reviewed, reproductive strategies in males and females being left to two later papers. The author describes the reproductive systems, the development of eggs (oocytes) in the ovaries, courtship and precopulatory amplexus, mating and the production of sperms, egg laying, mortality and diapause.

As práticas de saúde do enfermeiro e do agente comunitário de saúde na visita domiciliar da Estratégia Saúde da Família

Esta pesquisa teve como objetivo conhecer os sentidos atribuídos pelos enfermeiros e agentes comunitários de saúde da Estratégia Saúde da Família do município do Rio de Janeiro/RJ acerca das práticas de saúde desenvolvidas na visita domiciliar. É um estudo descritivo, de natureza qualitativa e teve como abordagem metodológica a hermenêutica-dialética. O cenário foi a cidade do Rio de Janeiro/RJ, em duas Unidades Básicas de Saúde da Família (UBSF) da Área Programática 3.1. Os sujeitos foram 08 enfermeiros e 07 agentes comunitários de saúde (ACSs) atuantes nas UBSF selecionadas. A coleta de dados foi realizada entre janeiro e março de 2010, por meio de entrevistas semi-estruturadas e para a avaliação dos resultados utilizou-se a técnica de análise de conteúdo proposta por Bardin. A partir dos resultados alcançados foi possível elaborar três categorias de estudo: a primeira trata das práticas de saúde do enfermeiro e do ACS na Estratégia Saúde da Família (ESF); a segunda aborda a visita domiciliar do enfermeiro e do ACS, a qual inclui subcategorias sobre o trabalho em equipe na visita domiciliar, as dificuldades na realização da visita domiciliar, o planejamento da visita domiciliar, o vínculo entre enfermeiro, ACS e família na visita domiciliar e a interação profissional do enfermeiro e do ACS na visita domiciliar; a última categoria trata dos sentidos atribuídos pelos enfermeiros e ACSs acerca das práticas de saúde desenvolvidas na visita domiciliar, as quais incluem subcategorias sobre as práticas de saúde do enfermeiro e do ACS na visita domiciliar e as opiniões sobre a visita domiciliar. Com a análise dos dados constatou-se que os enfermeiros e os ACS's desenvolvem diversas práticas de saúde na ESF, com destaque para as práticas de cuidado. As práticas de cuidado do enfermeiro na visita domiciliar estão voltadas para a investigação das necessidades de saúde e realização das atividades assistenciais. Já as do ACS estão voltadas para a identificação de demandas. A escuta ativa, a observação da estrutura física, da alimentação e das relações familiares e a educação em saúde são as principais práticas de cuidado realizadas em conjunto por estes profissionais na visita domiciliar. O percentual de visitas domiciliares semanais do enfermeiro está abaixo do esperado, sendo que a principal justificativa para este baixo índice é a sobrecarga de trabalho na UBSF. Ficou evidente que a interação profissional entre enfermeiro e ACS na visita domiciliar é pequena, pois diversas vezes, o ACS está presente na visita domiciliar do enfermeiro apenas como acompanhante. Por fim, pode-se constatar que o cuidado desenvolvido por enfermeiros e por ACSs é distinto. A prática de cuidado que o enfermeiro desenvolve na visita domiciliar é específica, destinada às famílias com prioridades de saúde e a que o ACS desenvolve é mais ampla, voltada para todas as famílias da microárea. Estas conclusões demonstram a necessidade de estimular enfermeiros e ACSs a (re)pensarem as práticas de saúde desenvolvidas na visita domiciliar, bem como a compreenderem e discutirem seus papéis e a interação nesta atividade.

Magnetic behavior of basic iron(III) compounds. I. Magnetic behavior of the basic iron sulphates and basic iron chromate. II. Magnetic behavior of delta ferric oxide hydroxide

I. The thermomagnetic behavior and infrared spectroscopic features of KFe₃(SO₄)₂(OH)₆ (jarosite), (H₃O)Fe₃(SO₄)₂ (OH)₆ (hydronium jarosite), KFe₃(CrO₄)₂ (OH)₆, Fe(OH)SO₄ (basic iron sulfate), and Fe(OH)CrO₄ (basic iron chromate) are reported. Fe(OH)CrO₄ and KFe₃(CrO₄)₂ (OH)₆ are shown to be weak ferro magnets with Curie temperatures of 73 and 71 °K, respectively. This unusual magnetic behavior is rationalized in terms of the ionic spin configurations of the phases. Exchange coupling through chromate bridging groups is shown to be weak.

II. The magnetic behavior and the influence of preparative history on the magnetic behavior of δFeO(OH) is reported. δFeO(OH) is shown to be a fine-particulate, uniaxial, magnetic species. Magnetization data for this species are shown to be consistent with the existence of magnetically inactive layers surrounding magnetic particles.

A vivência do processo de menopausa para mulheres: uma contribuição para a enfermagem

Estima-se que, no ano de 2025, 23% da população total dos países desenvolvidos estarão com mais de 60 anos, evidenciando-se assim o envelhecimento gradativo do contingente populacional destes países. Deste modo, é perceptível o contingente de mulheres que estarão vivenciando a fase da menopausa com seus efeitos biológicos, psicológicos e sociais. As mudanças hormonais e fisiológicas que acontecem nas mulheres durante a fase da menopausa, acompanhadas pela desvalorização estética do corpo e por toda uma sintomatologia física e psíquica, têm sido interpretadas como perda da feminilidade, sinalizando o envelhecimento inevitável e a finitude. No entanto, muitos dos desconfortos que as mulheres vivenciam nesta fase não se devem às mudanças biológicas, mas ao seu processo de socialização, caracterizando a influência de gênero. Neste contexto, este trabalho teve como objeto o estudo da influência da relação de gênero na vivência e no significado do processo da menopausa, tendo como objetivos: descrever a vivência da menopausa a partir da perspectiva de mulheres que a vivenciam e identificar as particularidades relacionadas ao gênero diretamente envolvidas na experiência da menopausa a partir da perspectiva das mulheres. Para desenvolvimento do trabalho foi utilizada abordagem qualitativa de natureza descritiva com vinte mulheres de idade entre 45 e 55 anos que apresentavam menopausa espontânea e eram clientes das Unidades Básicas de Saúde da cidade de Curitibanos-SC, no período de 1 a 15 de outubro de 2009. Para a coleta de dados foi utilizado um roteiro de entrevista semi-estruturada com uma questão norteadora: Fale-me como é para você estar vivenciando a menopausa. A interpretação e análise foram feitas através de análise de conteúdo do tipo temática descritas por Bardin. Nas narrativas, identificaram-se categorias que foram integradas em quatro temas principais: 1- Vivenciando a Menopausa, 2- Identificando Transformações no Corpo e na Vida, 3- Cuidando de Si, 4- Buscando Informações/Influências e Construindo Conhecimento. Foi possível identificar nessas categorias que as mulheres trazem o conceito de que a fase da menopausa é uma doença, e relacionam essa fase com envelhecimento e declínio físico, a qual traz grandes sofrimentos, o que demonstra a influência de gênero no vivenciar desta fase. As entrevistadas explicitaram em suas falas diversos sintomas que as incomodavam e interferiam em suas atividades diárias e na sua maneira de ser, repercutindo muitas vezes no seu comportamento familiar e profissional. O conhecimento sobre a menopausa, neste grupo de mulheres, foi construído ao longo de suas vidas e reflete as suas realidades culturais e sociais, deixando evidente a escassez de fontes de informação e os tabus relacionados com relação à fase da menopausa. Este estudo contribui com a geração de conhecimentos levando em consideração os efeitos que a influência de gênero pode ter na vivência e percepção da menopausa, desmistificando-a para que a vivência das mulheres durante esse período não seja condicionada por estereótipos e crenças relacionadas ao gênero.

A computer-aided investigation of motion detection units in the fly

This work deals with two related areas: processing of visual information in the central nervous system, and the application of computer systems to research in neurophysiology.

Certain classes of interneurons in the brain and optic lobes of the blowfly Calliphora phaenicia were previously shown to be sensitive to the direction of motion of visual stimuli. These units were identified by visual field, preferred direction of motion, and anatomical location from which recorded. The present work is addressed to the questions: (1) is there interaction between pairs of these units, and (2) if such relationships can be found, what is their nature. To answer these questions, it is essential to record from two or more units simultaneously, and to use more than a single recording electrode if recording points are to be chosen independently. Accordingly, such techniques were developed and are described.

One must also have practical, convenient means for analyzing the large volumes of data so obtained. It is shown that use of an appropriately designed computer system is a profitable approach to this problem. Both hardware and software requirements for a suitable system are discussed and an approach to computer-aided data analysis developed. A description is given of members of a collection of application programs developed for analysis of neuro-physiological data and operated in the environment of and with support from an appropriate computer system. In particular, techniques developed for classification of multiple units recorded on the same electrode are illustrated as are methods for convenient graphical manipulation of data via a computer-driven display.

By means of multiple electrode techniques and the computer-aided data acquisition and analysis system, the path followed by one of the motion detection units was traced from open optic lobe through the brain and into the opposite lobe. It is further shown that this unit and its mirror image in the opposite lobe have a mutually inhibitory relationship. This relationship is investigated. The existence of interaction between other pairs of units is also shown. For pairs of units responding to motion in the same direction, the relationship is of an excitatory nature; for those responding to motion in opposed directions, it is inhibitory.

Experience gained from use of the computer system is discussed and a critical review of the current system is given. The most useful features of the system were found to be the fast response, the ability to go from one analysis technique to another rapidly and conveniently, and the interactive nature of the display system. The shortcomings of the system were problems in real-time use and the programming barrier—the fact that building new analysis techniques requires a high degree of programming knowledge and skill. It is concluded that computer system of the kind discussed will play an increasingly important role in studies of the central nervous system.

The interactions of basic proteins and DNA

I. ELECTROPHORESIS OF THE NUCLEIC ACIDS

A zone electrophoresis apparatus using ultraviolet optics has been constructed to study nucleic acids at concentrations less than 0.004%. Native DNA has a mobility about 15% higher than denatured DNA over a range of conditions. Otherwise, the electrophoretic mobility is independent of molecular weight, base composition or source. DNA mobilities change in the expected way with pH but the fractional change in mobility is less than the calculated change in charge. A small decrease in mobility accompanies an increase in ionic strength. RNA’s from various sources have mobilities slightly lower than denatured DNA except for s-RNA which travels slightly faster. The important considerations governing the mobility of nucleic acids appear to be the nature of the hydrodynamic segment, and the binding of counterions. The differences between electrophoresis and sedimentation stem from the fact that all random coil polyelectrolytes are fundamentally free draining in electrophoresis.

II. THE CYTOCHROME C/DNA COMPLEX

The basic protein, cytochrome c, has been complexed to DNA. Up to a cytochrome:DNA mass ratio of 2, a single type of complex is formed. Dissociation of this complex occurs between 0.05F and 0.1F NaCl. The complexing of cytochrome to DNA causes a slight increase in the melting temperature of the DNA, and a reduction of the electrophoretic mobility proportional to the decrease in net charge. Above a cytochrome:DNA mass ratio of 2.5, a different type of complex is formed. The results suggest that complexes such as are formed in the Kleinschmidt technique of electron microscopy would not exist in bulk solution and are exclusively film phenomena.

III. STUDIES OF THE ELECTROPHORESIS AND MELTING BEHAVIOUR OF NUCLEOHISTONES

Electrophoresis studies on reconstituted nucleohistones indicate that the electrophoretic mobility for these complexes is a function of the net charge of the complex. The mobility is therefore dependent on the charge density of the histone complexing the DNA, as well as on the histone/DNA ratio. It is found that the different histones affect the transition from native to denatured DNA in different ways. It appears that histone I is exchanging quite rapidly between DNA molecules in 0.01 F salt, while histone II is irreversibly bound. Histone III-IV enhances the capacity of non-strand separated denatured DNA to reanneal. Studies on native nucleoproteins indicate that there are no gene-sized uncomplexed DNA regions in any preparations studied.

IV. THE DISSOCIATION OF HISTONE FROM CALF THYMUS CROMATIN

Calf thymus nucleoprotein was treated with varying concentrations of NaCl. The identity of the histones associated and dissociated from the DNA at each salt concentration was determined by gel electrophoresis. It was found that there is no appreciable histone dissociation below 0.4 F NaCl. The lysine rich histones dissociate between 0.4 and 0.5 F NaCl. Their dissociation is accompanies by a marked increase in the solubility of the chromatin. The moderately lysine rich histones dissociate mainly between 0.8 and 1.1 F NaCl. There are two arginine rich histone components: the first dissociates between 0.8 F and 1.1 F NaCl, but the second class is the very last to be dissociated from the DNA (dissociation beginning at 1.0 F NaCl). By 2.0 F NaCl, essentially all the histones are dissociated.

The properties of the extracted nucleoprotein were studied. The electrophoretic mobility increases and the melting temperature decreases as more histones are dissociated from the DNA. A comparison with the dissociation of histones from DNA in NaClO₄ shows that to dissociate the same class of histones, the concentration of NaCl required is twice that of NaClO₄.