WebGIS applied to Improve Spatial Knowledge of High School Students

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies

Variation in protein expression levels in cell populations

Dissertation presented to obtain the Ph.D degree in Systems Biology

Regulation of gene expression by SnRK1 kinases and miRNAs during the plant stress response

Dissertation presented to obtain the Ph.D degree in Plant Physiology

Controlling gene expression in enterobacteriaceae: studies on sRNAs and strategies for synthetic biology

Dissertation presented to obtain the Master Degree in Molecular, Genetics and Biomedicine

Interactive spatial decision support for sustainable agroforestry management: a case study in East Kalimantan, Indonesia

Forest managers, stakeholders and investors want to be able to evaluate economic, environmental and social benefits in order to improve the outcomes of their decisions and enhance sustainable forest management. This research developed a spatial decision support system that provides: (1) an approach to identify the most beneficial locations for agroforestry projects based on the biophysical properties and evaluate its economic, social and environmental impact; (2) a tool to inform prospective investors and stakeholders of the potential and opportunities for integrated agroforestry management; (3) a simulation environment that enables evaluation via a dashboard with the opportunity to perform interactive sensitivity analysis for key parameters of the project; (4) a 3D interactive geographic visualization of the economic, environmental and social outcomes, which facilitate understanding and eases planning. Although the tool and methodology presented are generic, a case study was performed in East Kalimantan, Indonesia. For the whole study area, it was simulated the most suitable location for three different plantation schemes: monoculture of timber, a specific recipe (cassava, banana and sugar palm) and different recipes per geographic unit. The results indicate that a mixed cropping plantation scheme, with different recipes applied to the most suitable location returns higher economic, environmental and social benefits.

Learning facial-expression models with crowdsourcing

The computational power is increasing day by day. Despite that, there are some tasks that are still difficult or even impossible for a computer to perform. For example, while identifying a facial expression is easy for a human, for a computer it is an area in development. To tackle this and similar issues, crowdsourcing has grown as a way to use human computation in a large scale. Crowdsourcing is a novel approach to collect labels in a fast and cheap manner, by sourcing the labels from the crowds. However, these labels lack reliability since annotators are not guaranteed to have any expertise in the field. This fact has led to a new research area where we must create or adapt annotation models to handle these weaklylabeled data. Current techniques explore the annotators’ expertise and the task difficulty as variables that influences labels’ correction. Other specific aspects are also considered by noisy-labels analysis techniques. The main contribution of this thesis is the process to collect reliable crowdsourcing labels for a facial expressions dataset. This process consists in two steps: first, we design our crowdsourcing tasks to collect annotators labels; next, we infer the true label from the collected labels by applying state-of-art crowdsourcing algorithms. At the same time, a facial expression dataset is created, containing 40.000 images and respective labels. At the end, we publish the resulting dataset.

Cytokine expression in the duodenal mucosa of patients with visceral leishmaniasis

INTRODUCTION: Visceral leishmaniasis (VL) is a neglected tropical disease with a complex immune response in different organs. This pattern of organ-specific immune response has never been evaluated in the gastrointestinal tract. The aim of this study was to determine the in situ immune response in duodenal biopsies on patients with VL. METHODS: A case-control study was conducted on 13 patients with VL in comparison with nine controls. The immune response was evaluated using immunohistochemistry, for CD4, CD8, CD68, IL-4, IFN-γ, TNF-α and IL-10. Histological findings from the villi, crypts and inflammatory process were analyzed. RESULTS: All the cases of VL presented Leishmania antigens. No antigen was detected in the control group. The villus size was greater in the VL patients (p < 0.05). CD68 (macrophages) and CD4 levels were higher in the VL patients (p < 0.05). No differences in the expression of CD8, TNF-α, IL-10 or IL-4 were demonstrated. The number of cells expressing IFN-γ was lower in the VL patients (p < 0.05). CONCLUSIONS: Low levels of cytokines were found in the gastrointestinal tract of patients with VL. This pattern was not found in other organs affected by the disease. Immunotolerance of this tissue against Leishmania could explain these findings, as occurs with intestinal bacteria.

Immunohistochemical expression of oestrogen and progesterone receptors during experimental acute and chronic murine Schistosomiasis mansoni

INTRODUCTION: The responsibility of Schistosoma mansoni in female infertility is still controversial. This study was conducted to evaluate the effect of acute and chronic schistosomiasis mansoni infection on the endometrium using immunohistochemical analysis of uterine hormone receptor expression. METHODS: Twenty-four nonpregnant swiss albino mice were divided into three groups: control, noninfected; acute; and chronic Schistosoma mansoni infection. Histological sections of uterine specimens were examined by light microscope with an image analyzing system to detect structural histological, estrogen receptor (ER) and progesterone receptor (PR) expression in the endometrium. RESULTS: No secretory phase was detected in the endometrium in acute and chronic Schistosoma infection. Hormone receptor expression (ER and PR) showed statistically significant differences among the groups (p< 0.05), with significant low ER hormone expression in chronic infection, compared to control proliferative, control secretory and acute infection cases, and statistically significant high PR expression in both acute and chronic infection cases compared to the control secretory cases (p< 0.05). CONCLUSIONS: Schistosomiasis mansoni seems to have an important impact on the hormone expression of affected women. Further studies to explore the mechanism of such changes are recommended.

Relating the spatial component and users interests to improve applications based on questions, petitions and participatory processes

Nowadays, participatory processes attending the need for real democracy and transparency in governments and collectives are more needed than ever. Immediate participation through channels like social networks enable people to give their opinion and become pro-active citizens, seeking applications to interact with each other. The application described in this dissertation is a hybrid channel of communication of questions, petitions and participatory processes based on Public Participation Geographic Information System (PPGIS), Participation Geographic Information System (PGIS) and ‘soft’ (subjective data) Geographic Information System (SoftGIS) methodologies. To achieve a new approach to an application, its entire design is focused on the spatial component related with user interests. The spatial component is treated as main feature of the system to develop all others depending on it, enabling new features never seen before in social actions (questions, petitions and participatory processes). Results prove that it is possible to develop a working application mainly using open source software, with the possibility of spatial and subject filtering, visualizing and free download of actions within application. The resulting application empowers society by releasing soft data and defines a new breaking approach, unseen so far.

Spatial analysis of crime evolution in Portugal between 1995 and 2013

The main objective of this survey was to perform descriptive analysis of crime evolution in Portugal between 1995 and 2013. The main focus of this survey was to analyse spatial crime evolution patterns in Portuguese NUTS III regions. Most important crime types have been included into analysis. The main idea was to uncover relation between local patterns and global crime evolution; to define regions which have contributed to global crime evolution of some specific crime types and to define how they have contributed. There were many statistical reports and scientific papers which have analysed some particular crime types, but one global spatial-temporal analysis has not been found. Principal Component Analysis and multidimensional descriptive data analysis technique STATIS have been the base of the analysis. The results of this survey has shown that strong spatial and temporal crime patterns exist. It was possible to describe global crime evolution patterns and to define crime evolution patterns in NUTS III regions. It was possible to define three to four groups of crimes where each group shows similar spatial crime dynamics.

The use of analytical hierarchy process in spatial decision support system for land use management

Geographic information systems give us the possibility to analyze, produce, and edit geographic information. Furthermore, these systems fall short on the analysis and support of complex spatial problems. Therefore, when a spatial problem, like land use management, requires a multi-criteria perspective, multi-criteria decision analysis is placed into spatial decision support systems. The analytic hierarchy process is one of many multi-criteria decision analysis methods that can be used to support these complex problems. Using its capabilities we try to develop a spatial decision support system, to help land use management. Land use management can undertake a broad spectrum of spatial decision problems. The developed decision support system had to accept as input, various formats and types of data, raster or vector format, and the vector could be polygon line or point type. The support system was designed to perform its analysis for the Zambezi river Valley in Mozambique, the study area. The possible solutions for the emerging problems had to cover the entire region. This required the system to process large sets of data, and constantly adjust to new problems’ needs. The developed decision support system, is able to process thousands of alternatives using the analytical hierarchy process, and produce an output suitability map for the problems faced.

Analysis of temporal and spatial variations of forest. A case of study in notheastern Armenia

The forest has a crucial ecological role and the continuous forest loss can cause colossal effects on the environment. As Armenia is one of the low forest covered countries in the world, this problem is more critical. Continuous forest disturbances mainly caused by illegal logging started from the early 1990s had a huge damage on the forest ecosystem by decreasing the forest productivity and making more areas vulnerable to erosion. Another aspect of the Armenian forest is the lack of continuous monitoring and absence of accurate estimation of the level of cuts in some years. In order to have insight about the forest and the disturbances in the long period of time we used Landsat TM/ETM + images. Google Earth Engine JavaScript API was used, which is an online tool enabling the access and analysis of a great amount of satellite imagery. To overcome the data availability problem caused by the gap in the Landsat series in 1988- 1998, extensive cloud cover in the study area and the missing scan lines, we used pixel based compositing for the temporal window of leaf on vegetation (June-late September). Subsequently, pixel based linear regression analyses were performed. Vegetation indices derived from the 10 biannual composites for the years 1984-2014 were used for trend analysis. In order to derive the disturbances only in forests, forest cover layer was aggregated and the original composites were masked. It has been found, that around 23% of forests were disturbed during the study period.

WebGIS applied to improve spatial knowledge of high school students

This research seeks to design and implement a WebGIS application allowing high school students to work with information related to the disciplinary competencies of the competency-teaching model, in Mexico. This paradigm assumes knowledge to be acquired through the application of new technologies and to link it with everyday life situations of students. The WebGIS provides access to maps regarding natural risks in Mexico, e.g. volcanism, seismic activities, or hurricanes; the prototype's user interface was designed with special emphasis on scholar needs for high school students.

Viajar no Feminino – As palavras das Imagens: Viagem de Egéria à Terra Santa, séc. IV

Egéria was a 4th century A.D. nun who undertook a long journey from her homeland, the roman province of Gallaecia, to the Near East. Her itinerary, which described the segment between Mount Sinai and Constantinople, revealed the enthusiasm which graced her original decision to embark on the journey, and the determination with which she faced every stage. She kept a Diary throughout her journey. Probably, it constitutes one of the first known Travel Diaries. Her reports describe her observations and the splendor of the Christian cult sites. Her text is affectionately dedicated to her fellow nuns that remained in the West of the Empire, keeping their uniting bond strong. Our study aims to search all references to visited sites in Egéria’s text, as the information contained therein serves as a precious descriptor of their locations, spatial organization and environment. Egéria visits unique, historical sites, which will influence her writing style. She is, in fact, a pilgrim to a recently created historical site, The Holy Land. Egéria lived during a fundamental historical and artistic Framework, that of the architectural forms of expression of the First Christianity. Her words can be translated into images, as a partitions script, a visualization of lights and ambiences, and a testimonial of places that no longer exist. We hope to see, in Egéria’s written work, the images she observed, for her words are images. We expect a complementary approach among the research methods given by Archeology, composed by Architecture and explained by the sensible text from Egéria’s journey - a religious and artistic journey written from a powerful feminine point of view.

Tool for spatial and dynamic representation of artistic performances

This proposal aims to explore the use of available technologies for video representation of sets and performers in order to serve as support for composition processes and artistic performer rehearsals, while focusing in representing the performer’s body and its movements, and its relation with objects belonging to the three-dimensional space of their performances. This project’s main goal is to design and develop a system that can spatially represent the performer and its movements, by means of capturing processes and reconstruction using a camera device, as well as enhance the three-dimensional space where the performance occurs by allowing interaction with virtual objects and by adding a video component, either for documentary purposes, or for live performances effects (for example, using video mapping video techniques in captured video or projection during a performance).