Styx grid services: lightweight middleware for efficient scientific workflows

The service-oriented approach to performing distributed scientific research is potentially very powerful but is not yet widely used in many scientific fields. This is partly due to the technical difficulties involved in creating services and workflows and the inefficiency of many workflow systems with regard to handling large datasets. We present the Styx Grid Service, a simple system that wraps command-line programs and allows them to be run over the Internet exactly as if they were local programs. Styx Grid Services are very easy to create and use and can be composed into powerful workflows with simple shell scripts or more sophisticated graphical tools. An important feature of the system is that data can be streamed directly from service to service, significantly increasing the efficiency of workflows that use large data volumes. The status and progress of Styx Grid Services can be monitored asynchronously using a mechanism that places very few demands on firewalls. We show how Styx Grid Services can interoperate with with Web Services and WS-Resources using suitable adapters.

A visual language for the collaborative visualization of integrated conceptual models in product development scenarios

In various industrial and scientific fields, conceptual models are derived from real world problem spaces to understand and communicate containing entities and coherencies. Abstracted models mirror the common understanding and information demand of engineers, who apply conceptual models for performing their daily tasks. However, most standardized models in Process Management, Product Lifecycle Management and Enterprise Resource Planning lack of a scientific foundation for their notation. In collaboration scenarios with stakeholders from several disciplines, tailored conceptual models complicate communication processes, as a common understanding is not shared or implemented in specific models. To support direct communication between experts from several disciplines, a visual language is developed which allows a common visualization of discipline-specific conceptual models. For visual discrimination and to overcome visual complexity issues, conceptual models are arranged in a three-dimensional space. The visual language introduced here follows and extends established principles of Visual Language science.

Why is there no genetics in phylogenetics : misconceptions, clarification and solutions

Fundamental misconceptions regarding some basic phylogenetic terminology are presented in this opinion piece. An attempt is made to point out why these misconceptions exist and what may be causing the misapplication of terminology. Clarification is providing via basic definitions and simple explanations. Differences between the scientific fields of genetics and population genetics are discussed. The appropriate use of terminology is advocated and alternative terms are proposed to eliminate one potential source of confusion. It is suggested we use 'sequence data' instead of molecular data and 'non-sequence data' instead of morphological data in the field of phylogenetics and systematics.

Neuroimaging and genetics: Exploring, searching, and finding

This issue on the genetics of brain imaging phenotypes is a celebration of the happy marriage between two of science's highly interesting fields: neuroscience and genetics. The articles collected here are ample evidence that a good deal of synergy exists in this marriage. A wide selection of papers is presented that provide many different perspectives on how genes cause variation in brain structure and function, which in turn influence behavioral phenotypes (including psychopathology). They are examples of the many different methodologies in contemporary genetics and neuroscience research. Genetic methodology includes genome-wide association (GWA), candidate-gene association, and twin studies. Sources of data on brain phenotypes include cortical gray matter (GM) structural/volumetric measures from magnetic resonance imaging (MRI); white matter (WM) measures from diffusion tensor imaging (DTI), such as fractional anisotropy; functional- (activity-) based measures from electroencephalography (EEG), and functional MRI (fMRI). Together, they reflect a combination of scientific fields that have seen great technological advances, whether it is the single-nucleotide polymorphism (SNP) array in genetics, the increasingly high-resolution MRI imaging, or high angular resolution diffusion imaging technique for measuring WM connective properties.

Untersuchungen zur Fachsprache der Ökologie und des Umweltschutzes im Deutschen und Finnischen : Bezeichnungsvarianten unter einem geschichtlichen, lexikographischen, morphologischen und linguistisch-pragmatischen Aspekt

The work integrates research in the language and terminology of various fields with lexicography, etymology, semantics, word formation, and pragmatics. Additionally, examination of German and Finnish provides the work with perspective of contrastive linguistics and the translation of texts in specialized fields. The work is an attempt to chart the language, vocabulary, different textual types, and essential communication-connected features of this special field. The study is primary concerned with internal communication within the field of ecology, but it also provides a comparison of the public discussion of environmental issues in Germany and Finland. The work attempts to use textual signs to provide a picture of the literary communication used on the different vertical levels in the central text types within the field. The dictionaries in the fields of environmental issues and ecology for the individual text types are examined primarily from the perspective of their quantity and diversity. One central point of the work is to clarify and collect all of the dictionaries in the field that have been compiled thus far in which German and/or Finnish ware included. Ecology and environmental protection are closely linked not only to each other but also to many other scientific fields. Consequently, the language of the environmental field has acquired an abundance of influences and vocabulary from the language of the special fields close to it as well as from that of politics and various areas of public administration. The work also demonstrates how the popularization of environmental terminology often leads to semantic distortion. Traditionally, scientific texts have used the smallest number of expressions, the purpose of which is to appeal to or influence the behavior of the text recipient. Particularly in Germany, those who support or oppose measures to protect the environment have long been making concerted efforts to represent their own views in the language that they use. When discussing controversial issues competing designations for the same referent or concept are used in accordance with the interest group to which the speaker belongs. One of the objectives of the study is to sensitize recipients of texts to notice the euphemistic expressions that occur in German and Finnish texts dealing with issues that are sensitive from the standpoint of environmental policy. One particular feature of the field is the wealth and large number of variants designating the same entry or concept. The terminological doublets formed by words of foreign origin and their German or Finnish language equivalents are quite typical of the field. Methods of corpus linguistics are used to determine the reasons for the large number of variant designations as well as their functionality.

The first cut is the deepest: Repeated interactions of co-authorship and academic productivity in Nobel laureate teams

Despite much in-depth investigation of factors influencing the co-authorship evolution in various scientific fields, our knowledge about how efficiency or creativity is linked to the longevity of collaborative relationships remains very limited. We explore what Nobel laureates’ co-authorship patterns reveal about the nature of scientific collaborations looking at the intensity and success of scientific collaborations across fields and across laureates’ collaborative lifecycles in physics, chemistry, and physiology/medicine. We find that more collaboration with the same researcher is actually no better for advancing creativity: publications produced early in a sequence of repeated collaborations with a given coauthor tend to be published better and cited more than papers that come later in the collaboration with the same coauthor. Our results indicate that scientific collaboration involves conceptual complementarities that may erode over a sequence of repeated interactions.

Monte Carlo Simulations of Molecular Clusters in Nucleation

A better understanding of the limiting step in a first order phase transition, the nucleation process, is of major importance to a variety of scientific fields ranging from atmospheric sciences to nanotechnology and even to cosmology. This is due to the fact that in most phase transitions the new phase is separated from the mother phase by a free energy barrier. This barrier is crossed in a process called nucleation. Nowadays it is considered that a significant fraction of all atmospheric particles is produced by vapor-to liquid nucleation. In atmospheric sciences, as well as in other scientific fields, the theoretical treatment of nucleation is mostly based on a theory known as the Classical Nucleation Theory. However, the Classical Nucleation Theory is known to have only a limited success in predicting the rate at which vapor-to-liquid nucleation takes place at given conditions. This thesis studies the unary homogeneous vapor-to-liquid nucleation from a statistical mechanics viewpoint. We apply Monte Carlo simulations of molecular clusters to calculate the free energy barrier separating the vapor and liquid phases and compare our results against the laboratory measurements and Classical Nucleation Theory predictions. According to our results, the work of adding a monomer to a cluster in equilibrium vapour is accurately described by the liquid drop model applied by the Classical Nucleation Theory, once the clusters are larger than some threshold size. The threshold cluster sizes contain only a few or some tens of molecules depending on the interaction potential and temperature. However, the error made in modeling the smallest of clusters as liquid drops results in an erroneous absolute value for the cluster work of formation throughout the size range, as predicted by the McGraw-Laaksonen scaling law. By calculating correction factors to Classical Nucleation Theory predictions for the nucleation barriers of argon and water, we show that the corrected predictions produce nucleation rates that are in good comparison with experiments. For the smallest clusters, the deviation between the simulation results and the liquid drop values are accurately modelled by the low order virial coefficients at modest temperatures and vapour densities, or in other words, in the validity range of the non-interacting cluster theory by Frenkel, Band and Bilj. Our results do not indicate a need for a size dependent replacement free energy correction. The results also indicate that Classical Nucleation Theory predicts the size of the critical cluster correctly. We also presents a new method for the calculation of the equilibrium vapour density, surface tension size dependence and planar surface tension directly from cluster simulations. We also show how the size dependence of the cluster surface tension in equimolar surface is a function of virial coefficients, a result confirmed by our cluster simulations.

Monte Carlo simulations of molecular clusters in nucleation

A better understanding of the limiting step in a first order phase transition, the nucleation process, is of major importance to a variety of scientific fields ranging from atmospheric sciences to nanotechnology and even to cosmology. This is due to the fact that in most phase transitions the new phase is separated from the mother phase by a free energy barrier. This barrier is crossed in a process called nucleation. Nowadays it is considered that a significant fraction of all atmospheric particles is produced by vapor-to liquid nucleation. In atmospheric sciences, as well as in other scientific fields, the theoretical treatment of nucleation is mostly based on a theory known as the Classical Nucleation Theory. However, the Classical Nucleation Theory is known to have only a limited success in predicting the rate at which vapor-to-liquid nucleation takes place at given conditions. This thesis studies the unary homogeneous vapor-to-liquid nucleation from a statistical mechanics viewpoint. We apply Monte Carlo simulations of molecular clusters to calculate the free energy barrier separating the vapor and liquid phases and compare our results against the laboratory measurements and Classical Nucleation Theory predictions. According to our results, the work of adding a monomer to a cluster in equilibrium vapour is accurately described by the liquid drop model applied by the Classical Nucleation Theory, once the clusters are larger than some threshold size. The threshold cluster sizes contain only a few or some tens of molecules depending on the interaction potential and temperature. However, the error made in modeling the smallest of clusters as liquid drops results in an erroneous absolute value for the cluster work of formation throughout the size range, as predicted by the McGraw-Laaksonen scaling law. By calculating correction factors to Classical Nucleation Theory predictions for the nucleation barriers of argon and water, we show that the corrected predictions produce nucleation rates that are in good comparison with experiments. For the smallest clusters, the deviation between the simulation results and the liquid drop values are accurately modelled by the low order virial coefficients at modest temperatures and vapour densities, or in other words, in the validity range of the non-interacting cluster theory by Frenkel, Band and Bilj. Our results do not indicate a need for a size dependent replacement free energy correction. The results also indicate that Classical Nucleation Theory predicts the size of the critical cluster correctly. We also presents a new method for the calculation of the equilibrium vapour density, surface tension size dependence and planar surface tension directly from cluster simulations. We also show how the size dependence of the cluster surface tension in equimolar surface is a function of virial coefficients, a result confirmed by our cluster simulations.

Virtual Reconstruction of the Ancient State of a Ruined Church

Contributed to: 4th International Conference, EuroMed 2012, Limassol, Cyprus, October 29 – November 3, 2012.

Using the system dynamics paradigm in teaching and learning technological university subjets

2nd International Conference on Education and New Learning Technologies

Orientar espíritos; formar cidadãos: o saneamento da nação em Cartilhas de Higiene (1920/1930).

Este estudo possui o interesse em ampliar as discussões, no campo da história da educação, sobre o uso de cartilhas como dispositivos por meio dos quais se procurou pôs em circulação, no espaço escolar, os ideais higiênicos, cuja aquisição permitiria a construção de uma vida vista como saudável e feliz. As cartilhas analisadas são: Cartilha de Higiene, de 1922, de Antônio de Almeida Júnior, médico e educador, conhecido por ter tido envolvimento no Movimento da Escola Nova; e Cartilha de Higiene, de 1936, de Renato Kehl, médico e defensor da eugenia no Brasil. As obras em questão foram produzidas em um cenário em que proliferaram intervenções oriundas do campo médico, entre outros campos científicos, com vistas à conformação da sociedade brasileira em bases modernas. Pretende-se analisar esses livros, valorizando sua dimensão de objeto cultural, explorando o caráter prescritivo de que se revestem, dirigido às crianças, em vários aspectos de sua vida escolar e doméstica, e ainda as representações produzidas sobre infância, família, escola e saúde.

A criação da Associação Brasileira de Obstetrizes e Enfermeiros Obstetras (ABENFO) e sua participação no Movimento de Humanização do Parto e Nascimento (1989-2002)

Este estudo, de natureza histórico-social, tem como objeto a criação da Associação Brasileira de Obstetrizes e Enfermeiros Obstetras (ABENFO) e suas estratégias no Movimento de Humanização do Parto e Nascimento Brasileiro (1989-2002). A delimitação temporal do estudo abrange o período de 1989 a 2002. Os objetivos da pesquisa são: analisar a transição da Associação Brasileira de Obstetrizes (ABO) para Associação Brasileira de Obstetrizes e Enfermeiros Obstetras (ABENFO); analisar as estratégias elaboradas pela ABENFO para a atualização do habitus das agentes; analisar o fortalecimento do Movimento de Humanização do Parto e Nascimento empreendido pela ABENFO. O estudo apoia-se teoricamente nos conceitos desenvolvidos pelo sociólogo Pierre Bourdieu e utilizou o método da história oral temática. Na análise, houve a articulação de documentos escritos e depoimentos orais à luz do referencial teórico. Os resultados da pesquisa evidenciam que, no processo de surgimento da ABENFO, houve um período de aproximações de agentes que durou aproximadamente 15 anos. A primeira aproximação foi entre parteiras/obstetrizes e as enfermeiras no campo sindical; a segunda aproximação de agentes, desta vez pelo habitus profissional, foi de enfermeiras de saúde pública e enfermeiras obstétricas no campo hospitalar e científico; e a terceira aproximação foi entre as parteiras/obstetrizes com as enfermeiras obstétricas. Após essas aproximações, a enfermeira obstétrica assumiu a diretoria provisória da ABO, realizando, em seguida, a transição para a ABENFO. Após a transição, a ABENFO nacional consolidou-se como representante das enfermeiras obstétricas e obstetrizes. Em seguida, foi necessário criar estratégias para atualizar o habitus das agentes, tais como: Estratégias de fortalecimento da Associação no campo político da Enfermagem e da Saúde da Mulher; Estratégias de ampliação da sua representação nacional entre enfermeiras obstétricas; Estratégias para divulgação do capital social da ABENFO. Dentre as estratégias de divulgação, aconteceram três Congressos Brasileiros de Enfermagem Obstétrica e Neonatal (COBEONS) que fortaleceram o Movimento de Humanização do Parto e Nascimento, pois neste espaço circulou o capital sociocultural do movimento social entre as associadas, levando aos mesmos uma atualização do seu habitus, e, por outro lado, fortalecendo o Movimento por meio do reconhecimento. Portanto, o fortalecimento do processo de humanização do parto e nascimento brasileiro confirmou a hipótese de que a criação da ABENFO possibilitou a elaboração de estratégias que impulsionaram a atualização do habitus das agentes. Este estudo foi esclarecedor, na medida em que favoreceu a compreensão das circunstâncias de criação da ABENFO e sua participação como a única representante das enfermeiras obstétricas e obstetrizes no Movimento de Humanização do Parto e Nascimento, além de demonstrar o quanto estas agentes contribuíram para a sua consolidação.

Understanding university academics' internal and external knowledge interactions in different disciplines: evidence from university in South Korea

Most of the literature on the role of universities in innovation assumes that academics¡¯ knowledge interacts only with industry and knowledge transfer occurs only or mainly in the technological and scientific fields. We question these assumptions, suggesting academics¡¯ internal and external knowledge interact across disciplines. Using national survey data, this paper tries to show the heterogeneity of university teachers¡¯ knowledge interactions across wider disciplines. Also, this paper explores the patterns of university academics¡¯ internal knowledge interactions with other academics within academia and the university academics¡¯ external knowledge interactions with industry, such as small and medium enterprises (SMEs) and major Korean firms, Chaebols. We found that there are heterogeneities of academics¡¯ knowledge interactions across the disciplines.

Diagnóstico Molecular na era da sequenciação de 3ª geração e da PCR digital

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Porfirinas e Terapia Fotodinâmica em Neoplasias

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas