Implementation for spatial data of the shared nearest neighbour with metric data structures

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Effects of Spatial Pattern of GreenSpace on Land Surface Temperature: A case study on Oasis City Aksu, northwest China

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

UJI Navigation Network, Development of a pedestrian spatial network within the University Jaume I of Castellón (Spain)

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

Participatory mapping in the design process of a spatial data infrastructure SDI: a case study in the Biosphere Reserve Rio Platano (Honduras)

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

Extracting temporal and spatial distributions information about marine mucilage phenomenon based on Modis satellite images; a case study of the Tyrrhenian and the Adriatic Sea, 2010-2012

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

The influence of consumption vocabulary on the encoding and retrieval of haptic information

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Interactive acquisition of spatial information from images for multimedia applications

Dissertação para obtenção do Grau de Doutor em Informática

Using GIS to map the spatial and temporal occurrence of cholera epidemic in Camaroon

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

Spatial Patterns and Irregularities of the electoral data: general elections in Canada

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

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

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.

Transcriptional regulation of the mannosyltransferase-encoding gene pigm in inherited glycosylphosphatidylinositol (GPI) deficiency

RESUMO:O glicosilfosfatidilinositol (GPI) é um complexo glicolipídico utlizado por dezenas de proteínas, o qual medeia a sua ancoragem à superfície da célula. Proteínas de superfície celular ancoradas a GPI apresentam várias funções essenciais para a manutenção celular. A deficiência na síntese de GPI é o que caracteriza principalmente a deficiência hereditária em GPI, um grupo de doenças autossómicas raras que resultam de mutações nos genes PIGA, PIGL, PIGM, PIGV, PIGN, PIGO e PIGT, os quais sao indispensáveis para a biossíntese do GPI. Uma mutação pontual no motivo rico em GC -270 no promotor de PIGM impede a ligação do factor de transcrição (FT) Sp1 à sua sequência de reconhecimento, impondo a compactação da cromatina, associada à hipoacetilação de histonas, e consequentemente, impedindo a transcrição de PIGM. Desta forma, a adição da primeira manose ao GPI é comprometida, a síntese de GPI diminui assim como as proteínas ligadas a GPI à superficie das células. Pacientes com Deficiência Hereditária em GPI-associada a PIGM apresentam trombose e epilesia, e ausência de hemólise intravascular e anemia, sendo que estas duas últimas características definem a Hemoglobinúria Paroxística Nocturna (HPN), uma doença rara causada por mutações no gene PIGA. Embora a mutação que causa IGD seja constitutiva e esteja presente em todos os tecidos, o grau de deficiência em GPI varia entre células do mesmo tecido e entre células de tecidos diferentes. Por exemplo nos granulócitos e linfócitos B a deficiência em GPI é muito acentuada mas nos linfócitos T, fibroblastos, plaquetas e eritrócitos é aproximadamente normal, daí a ausência de hemólise intravascular. Os eventos transcricionais que estão na base da expressão diferencial da âncora GPI nas células hematopoiéticas são desconhecidos e constituem o objectivo geral desta tese. Em primeiro lugar, os resultados demonstraram que os níveis de PIGM mRNA variam entre células primárias hematopoiéticas normais. Adicionalmente, a configuração dos nucleossomas no promotor de PIGM é mais compacta em células B do que em células eritróides e tal está correlacionado com os níveis de expressão de PIGM, isto é, inferior nas células B. A presença de vários motivos de ligação para o FT específico da linhagem megacariocítica-eritróide GATA-1 no promotor de PIGM sugeriu que GATA-1 desempenha um papel regulador na sua transcrição. Os resultados mostraram que muito possivelmente GATA-1 desempenha um papel repressor em vez de activador da expressão de PIGM. Resultados preliminares sugerem que KLF1, um factor de transcrição restritamente eritróide, regula a transcrição de PIGM independentemente do motivo -270GC. Em segundo lugar, a investigação do papel dos FTs Sp demonstrou que Sp1 medeia directamente a transcrição de PIGM em ambas as células B e eritróide. Curiosamente, ao contrário do que acontece nas células B, em que a transcrição de PIGM requer a ligação do FT geral Sp1 ao motivo -270GC, nas células eritróides Sp1 regula a transcrição de PIGM ao ligar-se a montante e não ao motivo -270GC. Para além disso, demonstrou-se que Sp2 não é um regulador directo da transcrição de PIGM quer nas células B quer nas células eritróides. Estes resultados explicam a ausência de hemólise intravascular nos doentes com IGD associada a PIGM, uma das principais características que define a HPN. Por último, resultados preliminares mostraram que a repressão da transcrição de PIGM devida à mutação patogénica -270C>G está associada com a diminuição da frequência de interacções genómicas em cis entre PIGM e os seus genes “vizinhos”, sugerindo adicionalmente que a regulação de PIGM e desses genes é partilhada. No seu conjunto, os resultados apresentados nesta tese contribuem para o conhecimento do controlo transcricional de um gene housekeeping, específico-detecido, por meio de FTs genéricos e específicos de linhagem.-------------ABSTRACTC: Glycosylphosphatidylinositol (GPI) is a complex glycolipid used by dozens of proteins for cell surface anchoring. GPI-anchored proteins have various functions that are essential for the cellular maintenance. Defective GPI biosynthesis is the hallmark of inherited GPI deficiency (IGD), a group of rare autosomal diseases caused by mutations in PIGA, PIGL, PIGM, PIGV, PIGN, PIGO and PIGT, all genes indispensable for GPI biosynthesis. A point mutation in the -270GC-rich box in the core promoter of PIGM disrupts binding of the transcription factor (TF) Sp1 to it, imposing nucleosome compaction associated with histone hypoacetylation, thus abrogating transcription of PIGM. As a consequence of PIGM transcriptional repression, addition of the first mannose residue onto the GPI core and thus GPI production are impaired; and expression of GPI-anchored proteins on the surface of cells is severely impaired. Patients with PIGM-associated IGD suffer from life-threatening thrombosis and epilepsy but not intravascular haemolysis and anaemia, two defining features of paroxysmal nocturnal haemoglobinuria (PNH), a rare disease caused by somatic mutations in PIGA. Although the disease-causing mutation in IGD is constitutional and present in all tissues, the degree of GPI deficiency is variable and differs between cells of the same and of different tissues. Accordingly, GPI deficiency is severe in granulocytes and B cells but mild in T cells, fibroblasts, platelets and erythrocytes, hence the lack of intravascular haemolysis.The transcriptional events underlying differential expression of GPI in the haematopoietic cells of PIG-M-associated IGD are not known and constitute the general aim of this thesis. Firstly, I found that PIGM mRNA levels are variable amongst normal primary haematopoietic cells. In addition, the nucleosome configuration in the promoter of PIGM is more compacted in B cells than in erythroid cells and this correlated with the levels of PIGM mRNA expression, i.e., lower in B cells. The presence of several binding sites for GATA-1, a mega-erythroid lineage-specific transcription factor (TF), at the PIGM promoter suggested that GATA-1 has a role on PIGM transcription. My results showed that GATA-1 in erythroid cells is most likely a repressor rather than an activator of PIGM expression. Preliminary data suggested that KLF1, an erythroid-specific TF, regulates PIGM transcription but independently of the -270GC motif. Secondly, investigation of the role of the Sp TFs showed that Sp1 directly mediates PIGM transcriptional regulation in both B and erythroid cells. However, unlike in B cells in which active PIGM transcription requires binding of the generic TF Sp1 to the -270GC-rich box, in erythroid cells, Sp1 regulates PIGM transcription by binding upstream of but not to the -270GC-rich motif. Additionally, I showed that Sp2 is not a direct regulator of PIGM transcription in B and erythroid cells. These findings explain lack of intravascular haemolysis in PIGM-associated IGD, a defining feature of PNH. Lastly, preliminary work shows that transcriptional repression of PIG-M by the pathogenic -270C>G mutation is associated with reduced frequency of in cis genomic interactions between PIGM and its neighbouring genes, suggesting a shared regulatory link between these genes and PIGM. Altogether, the results presented in this thesis provide novel insights into tissuespecific transcriptional control of a housekeeping gene by lineage-specific and generic TFs.

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.