MethDB—a public database for DNA methylation data

Methylation of cytosine in the 5 position of the pyrimidine ring is a major modification of the DNA in most organisms. In eukaryotes, the distribution and number of 5-methylcytosines (5mC) along the DNA is heritable but can also change with the developmental state of the cell and as a response to modifications of the environment. While DNA methylation probably has a number of functions, scientific interest has recently focused on the gene silencing effect methylation can have in eukaryotic cells. In particular, the discovery of changes in the methylation level during cancer development has increased the interest in this field. In the past, a vast amount of data has been generated with different levels of resolution ranging from 5mC content of total DNA to the methylation status of single nucleotides. We present here a database for DNA methylation data that attempts to unify these results in a common resource. The database is accessible via WWW (http://www.methdb.de). It stores information about the origin of the investigated sample and the experimental procedure, and contains the DNA methylation data. Query masks allow for searching for 5mC content, species, tissue, gene, sex, phenotype, sequence ID and DNA type. The output lists all available information including the relative gene expression level. DNA methylation patterns and methylation profiles are shown both as a graphical representation and as G/A/T/C/5mC-sequences or tables with sequence positions and methylation levels, respectively.

Effects of temporal association on recognition memory

The influence of temporal association on the representation and recognition of objects was investigated. Observers were shown sequences of novel faces in which the identity of the face changed as the head rotated. As a result, observers showed a tendency to treat the views as if they were of the same person. Additional experiments revealed that this was only true if the training sequences depicted head rotations rather than jumbled views; in other words, the sequence had to be spatially as well as temporally smooth. Results suggest that we are continuously associating views of objects to support later recognition, and that we do so not only on the basis of the physical similarity, but also the correlated appearance in time of the objects.

Functional organization of the hippocampal memory system

In humans declarative or explicit memory is supported by the hippocampus and related structures of the medial temporal lobe working in concert with the cerebral cortex. This paper reviews our progress in developing an animal model for studies of cortical–hippocampal interactions in memory processing. Our findings support the view that the cortex maintains various forms of memory representation and that hippocampal structures extend the persistence and mediate the organization of these codings. Specifically, the parahippocampal region, through direct and reciprocal interconnections with the cortex, is sufficient to support the convergence and extended persistence of cortical codings. The hippocampus itself is critical to the organization cortical representations in terms of relationships among items in memory and in the flexible memory expression that is the hallmark of declarative memory.

Lesion-induced reorganization in the brainstem is not completely expressed in somatosensory cortex.

Electrophysiological and neuroanatomical methods were used to determine the extent to which neonatal forelimb removal altered the organization of the cuneate nucleus and representations of the fore- and hindlimbs in the primary somatosensory cortex of adult rats. Neonatal forelimb removal resulted in invasion of the cuneate nucleus by sciatic nerve primary afferents and development of cuneothalamic projection neurons with split receptive fields that included both the hindlimb and forelimb stump. Mapping in the primary somatosensory cortex of the neonatally manipulated adult rats demonstrated abnormalities, but the major change observed in the cuneate nucleus was demonstrable at only a few (5%) cortical recording sites in the remaining stump representation and there were none at all in the hindlimb representation. These results suggest that lesion-induced brainstem reorganization may be functionally suppressed at either the thalamic or cortical level.

El análisis de co-citas como método de investigación en Bibliotecología y Ciencia de la Información

Se muestra aquí la pertinencia y utilidad del análisis de co-citas como método de investigación en Bibliotecología y Ciencia de la Información (BCI), mediante un análisis bibliométrico y una revisión del contenido de los principales trabajos publicados sobre este tema. Se analiza el tamaño y evolución de la literatura, la tipología documental y las temáticas de las revistas donde se publican las principales contribuciones. Se mencionan algunos de los métodos y técnicas más utilizados para analizar y visualizar las estructuras de conocimiento de dominios científicos, y se presentan algunos de los modelos de mapas propuestos. Se describen algunas de las aplicaciones y posibles usos de los resultados de estos análisis y, finalmente, se mencionan sus principales ventajas y limitaciones

Informações de suporte ao escalonamento de workflows científicos para a execução em plataformas de computação em nuvem

A ciência tem feito uso frequente de recursos computacionais para execução de experimentos e processos científicos, que podem ser modelados como workflows que manipulam grandes volumes de dados e executam ações como seleção, análise e visualização desses dados segundo um procedimento determinado. Workflows científicos têm sido usados por cientistas de várias áreas, como astronomia e bioinformática, e tendem a ser computacionalmente intensivos e fortemente voltados à manipulação de grandes volumes de dados, o que requer o uso de plataformas de execução de alto desempenho como grades ou nuvens de computadores. Para execução dos workflows nesse tipo de plataforma é necessário o mapeamento dos recursos computacionais disponíveis para as atividades do workflow, processo conhecido como escalonamento. Plataformas de computação em nuvem têm se mostrado um alternativa viável para a execução de workflows científicos, mas o escalonamento nesse tipo de plataforma geralmente deve considerar restrições específicas como orçamento limitado ou o tipo de recurso computacional a ser utilizado na execução. Nesse contexto, informações como a duração estimada da execução ou limites de tempo e de custo (chamadas aqui de informações de suporte ao escalonamento) são importantes para garantir que o escalonamento seja eficiente e a execução ocorra de forma a atingir os resultados esperados. Este trabalho identifica as informações de suporte que podem ser adicionadas aos modelos de workflows científicos para amparar o escalonamento e a execução eficiente em plataformas de computação em nuvem. É proposta uma classificação dessas informações, e seu uso nos principais Sistemas Gerenciadores de Workflows Científicos (SGWC) é analisado. Para avaliar o impacto do uso das informações no escalonamento foram realizados experimentos utilizando modelos de workflows científicos com diferentes informações de suporte, escalonados com algoritmos que foram adaptados para considerar as informações inseridas. Nos experimentos realizados, observou-se uma redução no custo financeiro de execução do workflow em nuvem de até 59% e redução no makespan chegando a 8,6% se comparados à execução dos mesmos workflows sendo escalonados sem nenhuma informação de suporte disponível.

Las maquetas como material didáctico para la enseñanza y aprendizaje de la lectura e interpretación de planos en la ingeniería

Utilizamos las maquetas como herramientas auxiliares para proyectar y mostrar proyectos de ingeniería, pero también pueden ser un excelente material didáctico para la enseñanza y aprendizaje de la lectura, interpretación y realización de los planos que definen un proyecto o sus diferentes elementos. En este trabajo se refiere la experiencia realizada por los autores con los alumnos de Ingeniería Técnica de Obras Públicas dentro de la unidad de Interpretación de Planos de la asignatura de Sistemas de Representación. La dificultad que los alumnos de la materia tienen para interpretar el lenguaje, códigos y convenciones de la expresión gráfica está entre los motivos por los que se ha utilizado las maquetas como método de representación tridimensional que permite hacer comprensibles y fácilmente interpretadas las características constructivas de los diferentes elementos y las operaciones necesarias para pasar de la representación a la realización de la unidad de obra. En la comunicación se describe la actividad realizada con los alumnos, la selección de las unidades a representar, la elaboración de las maquetas y planos, poniendo especial acento en la concordancia entre la representación gráfica y el modelo tridimensional. Asimismo se han analizado las capacidades didácticas de uno de los trabajos realizados por los alumnos así como la evaluación y conclusiones de la experiencia realizada.

Construction of Intelligent Virtual Worlds Using a Grammatical Framework

The potential of integrating multiagent systems and virtual environments has not been exploited to its whole extent. This paper proposes a model based on grammars, called Minerva, to construct complex virtual environments that integrate the features of agents. A virtual world is described as a set of dynamic and static elements. The static part is represented by a sequence of primitives and transformations and the dynamic elements by a series of agents. Agent activation and communication is achieved using events, created by the so-called event generators. The grammar defines a descriptive language with a simple syntax and a semantics, defined by functions. The semantics functions allow the scene to be displayed in a graphics device, and the description of the activities of the agents, including artificial intelligence algorithms and reactions to physical phenomena. To illustrate the use of Minerva, a practical example is presented: a simple robot simulator that considers the basic features of a typical robot. The result is a functional simple simulator. Minerva is a reusable, integral, and generic system, which can be easily scaled, adapted, and improved. The description of the virtual scene is independent from its representation and the elements that it interacts with.

3D model reconstruction using neural gas accelerated on GPU

In this work, we propose the use of the neural gas (NG), a neural network that uses an unsupervised Competitive Hebbian Learning (CHL) rule, to develop a reverse engineering process. This is a simple and accurate method to reconstruct objects from point clouds obtained from multiple overlapping views using low-cost sensors. In contrast to other methods that may need several stages that include downsampling, noise filtering and many other tasks, the NG automatically obtains the 3D model of the scanned objects. To demonstrate the validity of our proposal we tested our method with several models and performed a study of the neural network parameterization computing the quality of representation and also comparing results with other neural methods like growing neural gas and Kohonen maps or classical methods like Voxel Grid. We also reconstructed models acquired by low cost sensors that can be used in virtual and augmented reality environments for redesign or manipulation purposes. Since the NG algorithm has a strong computational cost we propose its acceleration. We have redesigned and implemented the NG learning algorithm to fit it onto Graphics Processing Units using CUDA. A speed-up of 180× faster is obtained compared to the sequential CPU version.

Commonplace book of John Holyoke, 1662 - May 1663

This unbound commonplace book was kept by John Holyoke during 1662 and 1663. The volume contains chiefly religious quotations and sermon notes (possibly of sermons preached by Holyoke himself), in English, Latin and Greek. Both ends of the volume were used to begin writing: the front page reads “Johannes Holyoke, adjunctu occupatu, May-1663” and the rear page reads “Johannes Holyoke [illegible] 1662.” The texts do not follow a straight tête-bêche model, where one text is upside down in relation to the other; rather, the texts change direction several times within the volume. The volume also includes part of letter sent to Holyoke’s grandfather Pynchon, September 16, 16?? [date illegible], as well as a series of alphabetically arranged quotations.

Student essay composed by Curtis Guild, 1795

Two-page handwritten essay written in English by Curtis Guild when he was an undergraduate at Harvard College. The essay is titled with a quote in Latin from Virgil, "Omnis in Ascanio cari stat cura parentis," that translates as, “All the fond Parent’s Care centers in Ascanio.” The essay begins, “The machinery of man is wonderful…” and discusses parental affection. The essay is signed “C Guild” and dated May 7, 1795.

A criatividade como competência essencial no desenvolvimento progressivo do aluno em artes visuais

Relatório da Prática de Ensino Supervisionada, Mestrado em Ensino das Artes Visuais, Universidade de Lisboa, Instituto de Educação, 2016

Selfmapping : o mapa colaborativo como medium de visualização espácio-temporal

THE MAP AS A COLLABORATIVE MEDIUM FOR SPATIO-TEMPORAL VISUALIZATION This dissertation focuses on the relationship between maps and spatio-temporal data visualization. It is divided into two components: theoretical framework and practical approach. The study begins by questioning the role of the map in today’s digital society and particularly its role in visualization, and finishes with the conceptualization and development of an interactive dot map that visualizes data from Instagram and Twitter. Nowadays, geographic information is no longer produced just by experts, but also by ordinary people that are able to participate in data creation and exchange. The Web 2.0 lies in the heart of this change, where social media represent a significant tool for producing geotagged content, allowing its users to share their location and to spatially reference their publications. Furthermore, amateur mapmaking and neogeography have benefited from the emergence of several new devices that enable the creation of digital maps that are interactive, adaptable and easily shared on the Web. This study adopts a descriptive approach calling upon the diverse aspects of the map and its evolution as a medium for visualizing geotagged data, highlighting collaborative mapping as an emerging subject area that is of mandatory future research. Relevant projects are also analyzed in order to identify trends and different approaches for visualizing social media data in its spatial context, intended to support the project’s conceptualization, development and evaluation. The created map demonstrates how spatial knowledge and perception of place are now redefined by the contributions of individuals; it also shows how that activity produces new sources of geographic information, forcing the development of new techniques and approaches that allow an adequate exploration of content and visualization methods of the contemporary map

Galeria de espelhos: figuras da representação em François Truffaut

Esta dissertação consiste numa análise de quatro filmes de François Truffaut, nomeadamente La mariée était en noir (1968), La sirène du Mississipi (1969), L’histoire d’Adèle H. (1975) e La chambre verte (1978). O meu estudo centra-se nalgumas figuras pertencentes a sistemas de representação, que ocupam posições de relevo nas narrativas e na imagética destes filmes. Assim, considero o tratamento dado a fotografias, pinturas, desenhos ou esculturas no quadro maior da imagem fílmica, e atento na caracterização de certas personagens enquanto, elas mesmas, propiciadoras de uma reflexão acerca da imagem. Finalmente, procuro repensar o modo como, associando esse trabalho sobre objectos representativos a um pensamento sobre a morte, Truffaut formula uma meditação sobre o cinema enquanto arte intimamente relacionada com a noção de fantasma.

A relação inconsciente-consciente na produção do pensamento consciente

Tese de mestrado, Psicologia (Ciência Cognitiva), Universidade de Lisboa, Faculdade de Psicologia, Faculdade de Letras, Faculdade de Ciências, Faculdade de Medicina, 2016