Revealing differences in gene network inference algorithms on the network level by ensemble methods

Motivation: The inference of regulatory networks from large-scale expression data holds great promise because of the potentially causal interpretation of these networks. However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context.

Results: In this article, we conduct a statistical analysis investigating differences and similarities of four network inference algorithms, ARACNE, CLR, MRNET and RN, with respect to local network-based measures. We employ ensemble methods allowing to assess the inferability down to the level of individual edges. Our analysis reveals the bias of these inference methods with respect to the inference of various network components and, hence, provides guidance in the interpretation of inferred regulatory networks from expression data. Further, as application we predict the total number of regulatory interactions in human B cells and hypothesize about the role of Myc and its targets regarding molecular information processing.

Oxytocin effects on neural correlates of self-referential processing

Oxytocin (OT) influences how humans process information about others. Whether OT affects the processing of information about oneself remains unknown. Using a double-blind, placebo-controlled within-subject design, we recorded event-related potentials (ERPs) from adults during trait judgments about oneself and a celebrity and during judgments on word valence, after intranasal OT or placebo administration. We found that OT vs. placebo treatment reduced the differential amplitudes of a fronto-central positivity at 220-280 ms (P2) during self- vs. valence-judgments. OT vs. placebo treatment tended to reduce the differential amplitude of a late positive potential at 520-1000 ms (LPP) during self-judgments but to increase the differential LPP amplitude during other-judgments. OT effects on the differential P2 and LPP amplitudes to self- vs. celebrity-judgments were positively correlated with a measure of interdependence of self-construals. Thus OT modulates the neural correlates of self-referential processing and this effect varies as a function of interdependence.

Attentional bias to food-related visual cues: is there a role in obesity?

The incentive sensitisation model of obesity suggests that modification of the dopaminergic associated reward systems in the brain may result in increased awareness of food-related visual cues present in the current food environment. Having a heightened awareness of these visual food cues may impact on food choices and eating behaviours with those being most aware of or demonstrating greater attention to food-related stimuli potentially being at greater risk of overeating and subsequent weight gain. To date, research related to attentional responses to visual food cues has been both limited and conflicting. Such inconsistent findings may in part be explained by the use of different methodological approaches to measure attentional bias and the impact of other factors such as hunger levels, energy density of visual food cues and individual eating style traits that may influence visual attention to food-related cues outside of weight status alone. This review examines the various methodologies employed to measure attentional bias with a particular focus on the role that attentional processing of food-related visual cues may have in obesity. Based on the findings of this review, it appears that it may be too early to clarify the role visual attention to food-related cues may have in obesity. Results however highlight the importance of considering the most appropriate methodology to use when measuring attentional bias and the characteristics of the study populations targeted while interpreting results to date and in designing future studies.

A Agenda 21 local e o desenvolvimento sustentável em Portugal : que perspetivas?

Assumindo a sociedade atual o paradigma do desenvolvimento sustentável como modelo capaz de garantir uma gestão equilibrada dos recursos atuais que não comprometa o futuro das futuras gerações, é fundamental compreender o instrumento da Agenda 21 Local (A21L), ferramenta saída da Conferência do Rio, em 1992, que se apresenta como uma resposta internacional aos objetivos da sustentabilidade. Ao constituir-se como país signatário da Declaração do Rio, Portugal assumiu o compromisso de cooperar internacionalmente para a aplicação deste instrumento, no esforço comum de unir a proteção do ambiente com o desenvolvimento económico e social. Verifica-se que a resposta de Portugal, em matéria de A21L, foi pouco conseguida, marcada por um arranque ténue, desconcertado e disperso a que acresce o caráter dúbio que caracterizou a natureza dos primeiros processos e que, no quadro internacional, atira Portugal para o grupo de países europeus que mais tardiamente conseguiram responder ao apelo da comunidade internacional no que se refere à implementação de A21L. Neste âmbito, esta dissertação visa aprofundar o conhecimento cientifico sobre este instrumento no quadro das experiências de Agenda 21 Local implementadas no território português. O trabalho procurou examinar os objetivos, características e resultados dos processos de Agenda, dando atenção aos elementos individuais que marcaram cada um e, igualmente, avaliando as repercussões que estes tiveram no todo nacional. O estudo incidiu na dinâmica espaciotemporal das Agendas21L, no território nacional, e na análise integrativa de indicadores físicos, sociais e económicos que permitiram compreender as especificidades e os contrastes verificados nos processos implementados e desenvolvidos. Na investigação não foram, igualmente, negligenciadas questões históricas, políticas e culturais, sabendose da importância que estes vários domínios configuram no caso português. O trabalho contou com uma investigação assente na seguinte metodologia: i) Revisão da literatura e recolha de dados bibliográficos sobre a temática da Agenda 21 Local; ii) Levantamento de informação, através de um inquérito por questionário, dirigido a todas as localidades do País, onde decorrem Agendas 21 Local, a fim de complementar informação já processada; iii) Pesquisa direta de dados no terreno que envolveu a utilização de procedimentos de teor quantitativo (inquérito por questionário) e de teor qualitativo (entrevistas), relativamente ao caso de estudo (Agenda 21 Local de Mindelo); iv) Tratamento e análise dos resultados obtidos através da confrontação da perspetiva teórica com a prática com a consequente elaboração de conclusões fundamentadas pela confrontação dos dados com as hipóteses. Para além de se tratar do caso pioneiro de A21L com início no poder mais próximo do cidadão (respeitando um dos princípios inerentes a este instrumento – o princípio da subsidiariedade), afirmou-se, igualmente, como um caso de referência em matéria de coesão e mobilização dos cidadãos locais para os problemas locais existentes. Os resultados empíricos da investigação identificam uma série de dificuldades que condicionaram o arranque e progresso das A21L. Desde logo, a inabilidade dos poderes políticos locais em trabalharem com um modelo que rompe com as típicas e tradicionais formas pré-concebidas de fazer política, isto é, com as práticas instituídas dos políticos fazerem “política” para os cidadãos e não “com” os cidadãos. O próprio desconhecimento do poder político local quanto à natureza de um processo de A21L que evidenciou inaptidão, impreparação e até embaraço para lidar com este instrumento, resultando na necessidade, na grande maioria dos processos desenvolvidos, de serem acompanhados por entidades externas que cooperaram na sua dinamização. Acresce que a nova dinâmica, subjacente à A21L, que desafia os governos locais a mobilizar a participação generalizada dos cidadãos e apela à participação de novos atores (associações, grupos de interesse, ONG e atores sociais, em geral) para a definição de estratégias de desenvolvimento local, não é totalmente aceite pelos vários poderes locais que, não raras vezes, menosprezam a importância dos cidadãos nos momentos de tomada de decisão. A falta de empenho do governo central, em matéria de sustentabilidade, que negligenciou, numa primeira etapa, a figura do poder central na assessoria às entidades locais cerceou o país da existência de uma campanha nacional para a afirmação deste instrumento. A falta/insuficiência de recursos financeiros como resultante da ausência de apoios estatais e a dificuldade na obtenção de fundos da União Europeia configurou-se como um entrave à promoção dos processos ficando as entidades locais e regionais incapazes de ultrapassar a falta de meios imprescindíveis para o desenvolvimento da A21L. O próprio desconhecimento generalizado dos cidadãos sobre a A21L afigura-se como um estigma ao sucesso de qualquer processo com as caraterísticas de um instrumento A21L visto que a participação dos cidadãos é condição sine qua non para a sua operacionalização. Neste quadro, e olhando o futuro, urge a necessidade das autoridades locais criarem modelos de autofinanciamento capazes de garantir a criação, funcionamento e manutenção de infraestruturas económicas e sociais subjacentes aos programas de A21L, assim como o dever do poder político em reforçar a importância da função da informação e da mobilização dos cidadãos em prole do desenvolvimento sustentável, ações indispensáveis para a execução das políticas inerentes à A21L.

Automatic processing of bidimensional images of ''omic'' expression blobs

In this work, a comprehensive review on automatic analysis of Proteomics and Genomics images is presented. Special emphasis is given to a particularly complex image produced by a technique called Two-Dimensional Gel Electrophoresis (2-DE), with thousands of spots (or blobs). Automatic methods for the detection, segmentation and matching of blob like features are discussed and proposed. In particular, a very robust procedure was achieved for processing 2-DE images, consisting mainly of two steps: a) A very trustworthy new approach for the automatic detection and segmentation of spots, based on the Watershed Transform, without any foreknowledge of spot shape or size, and without user intervention; b) A new method for spot matching, based on image registration, that performs well for either global or local distortions. The results of the proposed methods are compared to state-of-the-art academic and commercial products.

Reestruturação produtiva e desenvolvimento local : o caso do Município de Toledo, Estado do Paraná, Brasil

Tese de doutoramento, Geografia (Planeamento Regional e Urbano), Universidade de Lisboa, Instituto de Geografia e Ordenamento do Território, 2016

A videovigilância no local de trabalho

The emergence of new technologies has introduced significant changes in the citizens life’s. There is a constant evolution of technological means and profound impact of their use in the habits of life of the human being. These new technological media are important tools in labor relations. The working and businesses worlds are increasingly turning to these new technologies, so that the use of video surveillance in the workplace is nowadays common. New technologies in general and the use of video surveillance in workplace in particular are providing ways to allow control of the work performance that are desired by most employers. However, the collection of images in the workplace often collides with the fundamental rights and freedoms of workers, in particular, with the right to privacy. The subject concerns the question of investigating is whether the images collected in workplace can be used as evidence in disciplinary proceedings. In fact, this issue is controversial. Doctrine and jurisprudence defend, at least, two responses for the same question. Those who understand that the evidence may be admitted for not violate any right of the worker, and others who argue that the evidence should not be admitted in disciplinary office. In the Portuguese legal system, there is, even, a new intermediate theory that begins to be defended, that only on certain occasions the evidence may be admitted. The solution to this problem involves the study of employment law and data video surveillance processing. Analysis of workers fundamental rights is fundamental to come to a grounded conclusion.

Regional coronary endothelial function is closely related to local early coronary atherosclerosis in patients with mild coronary artery disease: pilot study.

BACKGROUND: Coronary endothelial function is abnormal in patients with established coronary artery disease and was recently shown by MRI to relate to the severity of luminal stenosis. Recent advances in MRI now allow the noninvasive assessment of both anatomic and functional (endothelial function) changes that previously required invasive studies. We tested the hypothesis that abnormal coronary endothelial function is related to measures of early atherosclerosis such as increased coronary wall thickness. METHODS AND RESULTS: Seventeen arteries in 14 healthy adults and 17 arteries in 14 patients with nonobstructive coronary artery disease were studied. To measure endothelial function, coronary MRI was performed before and during isometric handgrip exercise, an endothelial-dependent stressor, and changes in coronary cross-sectional area and flow were measured. Black blood imaging was performed to quantify coronary wall thickness and indices of arterial remodeling. The mean stress-induced change in cross-sectional area was significantly higher in healthy adults (13.5%±12.8%, mean±SD, n=17) than in those with mildly diseased arteries (-2.2%±6.8%, P<0.0001, n=17). Mean coronary wall thickness was lower in healthy subjects (0.9±0.2 mm) than in patients with coronary artery disease (1.4±0.3 mm, P<0.0001). In contrast to healthy subjects, stress-induced changes in cross-sectional area, a measure of coronary endothelial function, correlated inversely with coronary wall thickness in patients with coronary artery disease (r=-0.73, P=0.0008). CONCLUSIONS: There is an inverse relationship between coronary endothelial function and local coronary wall thickness in patients with coronary artery disease but not in healthy adults. These findings demonstrate that local endothelial-dependent functional changes are related to the extent of early anatomic atherosclerosis in mildly diseased arteries. This combined MRI approach enables the anatomic and functional investigation of early coronary disease.

Visual information processing during conscious and non-conscious face perception

Les stimuli naturels projetés sur nos rétines nous fournissent de l’information visuelle riche. Cette information varie le long de propriétés de « bas niveau » telles que la luminance, le contraste, et les fréquences spatiales. Alors qu’une partie de cette information atteint notre conscience, une autre partie est traitée dans le cerveau sans que nous en soyons conscients. Les propriétés de l’information influençant l’activité cérébrale et le comportement de manière consciente versus non-consciente demeurent toutefois peu connues. Cette question a été examinée dans les deux derniers articles de la présente thèse, en exploitant les techniques psychophysiques développées dans les deux premiers articles. Le premier article présente la boîte à outils SHINE (spectrum, histogram, and intensity normalization and equalization), développée afin de permettre le contrôle des propriétés de bas niveau de l'image dans MATLAB. Le deuxième article décrit et valide la technique dite des bulles fréquentielles, qui a été utilisée tout au long des études de cette thèse pour révéler les fréquences spatiales utilisées dans diverses tâches de perception des visages. Cette technique offre les avantages d’une haute résolution au niveau des fréquences spatiales ainsi que d’un faible biais expérimental. Le troisième et le quatrième article portent sur le traitement des fréquences spatiales en fonction de la conscience. Dans le premier cas, la méthode des bulles fréquentielles a été utilisée avec l'amorçage par répétition masquée dans le but d’identifier les fréquences spatiales corrélées avec les réponses comportementales des observateurs lors de la perception du genre de visages présentés de façon consciente versus non-consciente. Les résultats montrent que les mêmes fréquences spatiales influencent de façon significative les temps de réponse dans les deux conditions de conscience, mais dans des sens opposés. Dans le dernier article, la méthode des bulles fréquentielles a été combinée à des enregistrements intracrâniens et au Continuous Flash Suppression (Tsuchiya & Koch, 2005), dans le but de cartographier les fréquences spatiales qui modulent l'activation de structures spécifiques du cerveau (l'insula et l'amygdale) lors de la perception consciente versus non-consciente des expressions faciales émotionnelles. Dans les deux régions, les résultats montrent que la perception non-consciente s'effectue plus rapidement et s’appuie davantage sur les basses fréquences spatiales que la perception consciente. La contribution de cette thèse est donc double. D’une part, des contributions méthodologiques à la recherche en perception visuelle sont apportées par l'introduction de la boîte à outils SHINE ainsi que de la technique des bulles fréquentielles. D’autre part, des indications sur les « corrélats de la conscience » sont fournies à l’aide de deux approches différentes.

Design and Development of an Adaptable Frame -Based System for Dravidian Language Processing

This work is aimed at building an adaptable frame-based system for processing Dravidian languages. There are about 17 languages in this family and they are spoken by the people of South India.Karaka relations are one of the most important features of Indian languages. They are the semabtuco-syntactic relations between verbs and other related constituents in a sentence. The karaka relations and surface case endings are analyzed for meaning extraction. This approach is comparable with the borad class of case based grammars.The efficiency of this approach is put into test in two applications. One is machine translation and the other is a natural language interface (NLI) for information retrieval from databases. The system mainly consists of a morphological analyzer, local word grouper, a parser for the source language and a sentence generator for the target language. This work make contributios like, it gives an elegant account of the relation between vibhakthi and karaka roles in Dravidian languages. This mapping is elegant and compact. The same basic thing also explains simple and complex sentence in these languages. This suggests that the solution is not just ad hoc but has a deeper underlying unity. This methodology could be extended to other free word order languages. Since the frame designed for meaning representation is general, they are adaptable to other languages coming in this group and to other applications.

Vector-Based Integration of Local and Long-Range Information in Visual Cortex

Integration of inputs by cortical neurons provides the basis for the complex information processing performed in the cerebral cortex. Here, we propose a new analytic framework for understanding integration within cortical neuronal receptive fields. Based on the synaptic organization of cortex, we argue that neuronal integration is a systems--level process better studied in terms of local cortical circuitry than at the level of single neurons, and we present a method for constructing self-contained modules which capture (nonlinear) local circuit interactions. In this framework, receptive field elements naturally have dual (rather than the traditional unitary influence since they drive both excitatory and inhibitory cortical neurons. This vector-based analysis, in contrast to scalarsapproaches, greatly simplifies integration by permitting linear summation of inputs from both "classical" and "extraclassical" receptive field regions. We illustrate this by explaining two complex visual cortical phenomena, which are incompatible with scalar notions of neuronal integration.

Local map update for large scale SLAM

A technique for simultaneous localisation and mapping (SLAM) for large scale scenarios is presented. This solution is based on the use of independent submaps of a limited size to map large areas. In addition, a global stochastic map, containing the links between adjacent submaps, is built. The information in both levels is corrected every time a loop is closed: local maps are updated with the information from overlapping maps, and the global stochastic map is optimised by means of constrained minimisation

Municipio saludable como polo de desarrollo local "diagnóstico situación láctea Macheta"

Este proyecto hace parte de un convenio entre la Gobernación de Cundinamarca y la Universidad del Rosario para desarrollar el proyecto Municipio Saludable como Polo de Desarrollo Local en tres municipios de Cundinamarca: Machetá, Sesquilé y Mesitas de El Colegio. Dicho programa tiene cuatro ejes, de los cuales la Facultad de Administración desarrolla el primer eje que se relaciona con la Generación de empleo e Ingresos. La investigación, objeto de estudio se llevó a cabo en el municipio de Machetá, donde se trabajó el tema lácteo con pequeños productores y se desarrolló el módulo de marco lógico, en el que se llevaron a cabo las siguientes actividades: a) Contacto con la comunidad, visitas periódicas al Municipio. b) Elaboración y aplicación de encuestas a funcionarios de la Alcaldía, vendedores de plaza y productores. c) Procesamiento y análisis de resultados. d) Construcción de árbol de problemas con la comunidad, e) Construcción de árbol de objetivos. f) Socialización con la comunidad. g) Elaboración de estrategias. h) Conclusiones y recomendaciones. Para mejorar las condiciones de vida de los pequeños productores de leche se recomienda la organización de una cooperativa u otro tipo de asociación que les permita ofertar un producto con cantidades, con la calidad que requieren las empresas procesadoras o entrar en un proceso mas elaborado que implica el montaje de un tanque de enfriamiento con capacidad mínima de 3.000 litros/diarios y /o procesar la leche para producir quesos y otros productos derivados de leche. Obtener esto, estabilizaría precios, ingresos y les daría poder de negociación que es algo con lo que no cuentan actualmente los pequeños productores.