Pattern based software development

Tese de Doutoramento em InformáticaSeveral types of approaches support the software development process. Special interest should be paid to model driven development methodologies, of which Model Driven Architecture (MDA) is a main example. The usage of software models in these methodologies improves the quality of the produced solutions. On the one hand, models are formal artifacts to represent the software to develop. On the other hand, models represented in computable formats are amenable to the application of systematic transformation techniques, in order to produce other models or source code as output. The architectural models used in the MDA are derived from requirement specifications, and are achieved through manual processes. The negative effects of manual transformation steps are well known, since they are susceptible to interpretation errors and subjectivity. Errors resulting from this process are propagated through all of the development process, and reflected in the produced solutions. Since requirement models specify the system to be developed, naturally, they should not be disconnected from the development process itself. Formalizing requirement specifications in computable formats would enable their operationalization. Such would provide the possibility to analyze and manipulate them, and also to perform a requirement patterns inference process. Requirement patterns represent well known solutions for recurring problems, and their nature provides architectural hints. If software patterns can be derived from the requirement patterns, then through the composition of the resulting software patterns, architectural models can be achieved. As a result, requirements models will be better integrated into the MDA chain, thus extending the advantages of the MDA to requirement models, providing a software development process which starts from requirements and through rigorous transformations results in software solutions. This work presents an approach that aims to provide such an integration of requirements models into theMDA. The approach starts with the formalization of software requirements in a controlled natural language. The requirements are then transformed into an intermediary representation (namely, an ontology), with support for information extraction. Such makes it possible to perform requirement pattern inference, in order to understand, at a higher level of abstraction, the features required in the software solution. Associating the requirement patterns with software patterns, makes it possible to instantiate and compose such patterns, in order to produce architectural artifacts as output. The presented approach is supported by a tool, designed to support the several steps of the approach. Furthermore, the tool provides the required automation level to produce the architectural models. Two validation studies and a case study in the eCommerce domain are also presented, in order to illustrate the viability of both the tool and the approach.Diferentes tipos de abordagens suportam o processo de desenvolvimento de software. Especial interesse deve ser dado às metodologias baseadas em modelos, das quais a Model Driven Architecture (MDA) é um exemplo relevante. O uso de modelos de software nestas metodologias melhora a qualidade das soluções obtidas. Por um lado, os modelos são artefactos formais para representar o software a ser desenvolvido. Por outro lado, os modelos representados em formatos computáveis podem ser manipulados utilizando técnicas de transformação sistemáticas, de modo a obter como resultado outros modelos, ou código fonte. Os modelos arquitecturais usados na MDA derivam das especificações de requisitos, sendo obtidos através de processos manuais. O impacto negativo da aplicação de transformações manuais é bem conhecido, uma vez que estas são suscetíveis a erros de interpretação e subjectividade. Os erros resultantes deste processo são propagados através do processo de desenvolvimento, e reflectem-se nas soluções produzidas. Uma vez que os modelos de requisitos especificam os sistemas a desenvolver, naturalmente, estes não devem estar desligados do processo de desenvolvimento. A formalização dos modelos de requisitos em formatos computáveis possibilitaria a sua operacionalização. Tal forneceria a capacidade de analisar e manipular os modelos, e também suportaria a inferência de padrões de requisitos. Padrões de requisitos representam soluções bem conhecidas, para problemas recorrentes, e a sua natureza fornece indicações arquitecturais. Se for possível obter padrões de software, através de padrões de requisitos, então através de um processo de composição de padrões de software, é possível obter modelos arquitecturais. Como resultado, os padrões de requisitos podem ser integrados na cadeia MDA, estendendo assim as vantagens desse processo aos modelos de requisitos, e obtendo um processo de desenvolvimento que inicia nos requisitos, e fornece transformações rigorosas que levam a soluções de software. Este trabalho apresenta uma abordagem que tem como objectivo fornecer tal integração de modelos de requisitos, na MDA. A abordagem inicia com a formalização de requisitos de software numa linguagem natural controlada. Os requisitos são então transformados numa representação intermedia (nomeadamente, uma ontologia), com suporte para extração de informação. Tal fornece a possibilidade de efetuar inferência de padrões de requisitos, de modo a perceber, a um alto nível de abstração, as funcionalidades necessárias nas soluções de software. Associando os padrões de requisitos com padrões de software, é possível instanciar e compor esses padrões, de modo a obter artefactos arquitecturais. A abordagem apresentada ´e suportada por uma ferramenta, desenhada para suportar os diferentes passos da abordagem. Para além disso, a ferramenta fornece a automação necessária para produzir os modelos arquiteturais. São também apresentados dois estudos de validação e um caso de estudo na área de e-Commerce, de modo a ilustrar a viabilidade da abordagem e da ferramenta

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

MODELLING THE POTENTIAL DISTRIBUTION AND RICHNESS OF CETACEANS IN THE AZORES FROM FISHERIES OBSERVER PROGRAM DATA

Marine spatial planning and ecological research call for high-resolution species distribution data. However, those data are still not available for most marine large vertebrates. The dynamic nature of oceanographic processes and the wide-ranging behavior of many marine vertebrates create further difficulties, as distribution data must incorporate both the spatial and temporal dimensions. Cetaceans play an essential role in structuring and maintaining marine ecosystems and face increasing threats from human activities. The Azores holds a high diversity of cetaceans but the information about spatial and temporal patterns of distribution for this marine megafauna group in the region is still very limited. To tackle this issue, we created monthly predictive cetacean distribution maps for spring and summer months, using data collected by the Azores Fisheries Observer Programme between 2004 and 2009. We then combined the individual predictive maps to obtain species richness maps for the same period. Our results reflect a great heterogeneity in distribution among species and within species among different months. This heterogeneity reflects a contrasting influence of oceanographic processes on the distribution of cetacean species. However, some persistent areas of increased species richness could also be identified from our results. We argue that policies aimed at effectively protecting cetaceans and their habitats must include the principle of dynamic ocean management coupled with other area-based management such as marine spatial planning

Analysis of atmospheric vertical profiles in the presence of desert dust aerosols

The present work aims at studying a very recent episode of desert dust transport that affected Iberia in mid May 2015. The dust aerosols were detected over Évora, where a varied set of instrumentation for aerosol measurements is installed, including: a CIMEL sunphotometer integrated in AERONET, a Raman Lidar and a TEOM monitor, as well as ceilometer and a microwave radiometer (profiler). The aerosol occurrence, detected using the columnar, vertically-resolved and in situ measurements, was characterized by a fairly high aerosol optical thickness that reached a value of 1.0 at 440 nm and showed mass concentration peaks at the surface of the order of 100 μg/m3. Subsequently, the tropospheric vertical profiles of humidity and temperature obtained with the passive microwave (MW) radiometer are analysed in order to distinguish possible modifications that can be connected with the transport of desert dust. Modelling results are also examined and the total, SW and LW radiative forcings are investigated, taking into account the different vertical profiles obtained during the desert dust occurrence. It is found that the differences in the atmospheric profiles mostly affect the LW radiative forcing, with an underestimation of about 30% when the actual vertical profile is not considered

Nearly 20 years of satellite remote sensing at CGE

The first steps in satellite remote sensing at CGE were made in 1993, in the first years in close cooperation with the Remote Sensing Division of the Institute of Meteorology. The interest in the study of the atmospheric and surface properties using satellite images was first introduced in CGE by Ana Maria Silva and as a first year Master student, the first author here willingly accepted the challenge of developing her Master thesis on this unknown but rather appealing subject. Since then satellite remote sensing has greatly evolved with the launch of satellites with improved capabilities. CGE has taken advantage of these advancements to explore new methodologies applied not only to the atmospheric characterization, but also to land and water surfaces. Since the beginning of the 2000s the research group contributing to the development of satellite remote sensing at CGE has increased, including several eager students

SUMO E3 ligase SIZ1 connects sumoylation and reactive oxygen species homeostasis processes in Arabidopsis

International audienceAbstract The ubiquitin-like modifying peptide SMALL UBIQUITIN-LIKE MODIFIER (SUMO) has become a known modulator of the plant response to multiple environmental stimuli. A common feature of many of these external stresses is the production of reactive oxygen species (ROS). Taking into account that SUMO conjugates rapidly accumulate in response to an external oxidative stimulus, it is likely that ROS and sumoylation converge at the molecular and regulatory levels. In this study, we explored the SUMO–ROS relationship, using as a model the Arabidopsis (Arabidopsis thaliana) null mutant of the major SUMO-conjugation enhancer, the E3 ligase SAP AND MIZ 1 (SIZ1). We showed that SIZ1 is involved in SUMO conjugate increase when primed with both exogenous and endogenous ROS. In siz1, seedlings were sensitive to oxidative stress imposition, and mutants accumulated different ROS throughout development. We demonstrated that the deregulation in hydrogen peroxide and superoxide homeostasis, but not of singlet O2 (1O2), was partially due to SA accumulation in siz1. Furthermore, transcriptomic analysis highlighted a transcriptional signature that implicated siz1 with 1O2 homeostasis. Subsequently, we observed that siz1 displayed chloroplast morphological defects and altered energy dissipation activity and established a link between the chlorophyll precursor protochlorophyllide and deregulation of PROTOCHLOROPHYLLIDE OXIDOREDUCTASE A (PORA), which is known to drive overproduction of 1O2. Ultimately, network analysis uncovered known and additional associations between transcriptional control of PORA and SIZ1-dependent sumoylation. Our study connects sumoylation, and specifically SIZ1, to the control of chloroplast functions and places sumoylation as a molecular mechanism involved in ROS homeostatic and signaling events

Induction of a hyperanxious state by antenatal dexamethasone: a case for less detrimental natural corticosteroids

Background: Synthetic glucocorticoids are commonly prescribed during pregnancy, despite a lack of systematic investigations of their potential impact on the developing brain and neurological and behavioral performance. Methods: Neuroendocrine parameters and behavior in the adult offspring of pregnant Wistar rats treated antenatally with either dexamethasone (DEX) or corticosterone (CORT) were monitored; DEX (.1 mg/kg and 1 mg/kg) and CORT (25 mg/kg) were given to pregnant rat dams on gestation days 18 and 19. Results: Despite normal basal levels of corticosterone, the adult offspring of mothers given DEX or CORT displayed abnormal responses in the dexamethasone-suppression test. Neither treatment influenced spatial memory performance, but both DEX and CORT facilitated development of depressionlike behavior following chronic stress. The latter finding demonstrates that high-dose antenatal corticotherapy can impair the organism’s resilience to stress in adulthood. Interestingly, comparison of the progeny of CORT-treated and DEX-treated mothers revealed that the latter were more anxious. Conclusions: Since DEX and CORT differ in their affinity for glucocorticoid and mineralocorticoid receptors and corticosteroidbinding globulin, our findings emphasize the need to consider the pharmacologic properties of antenatal corticotherapies and demonstrate the potential long-term benefits of ligands that can bind to both receptors

Portuguese recommendations for the use of methotrexate in the treatment of rheumatoid arthritis

Objectives:To develop Portuguese evidence-based recommendations for the use of methotrexate (MTX) in daily clinical practice in rheumatic disorders. Methods:The Portuguese project was integrated in the multinational 3E Initiative (Evidence, Expertise, Exchange) 2007-2008 where a total of 751 rheumatologists from 17 countries have participated. Ten clinical questions concerning the use of MTX in rheumatic diseases were formulated and the Portuguese group added three more questions. A systematic literature search in Medline, Embase, Cochrane Library and 2005-2007 ACR/EULAR meeting abstracts was conducted. Selected articles were systematically reviewed and the evidence was appraised according to the Oxford Levels of Evidence. In Portugal, a national meeting was held in Obidos on February 15 th and 16 th, 2008, involving 50 rheumatologists who discussed and voted by Dephi method the recommendations. Finally, the agreement among the rheumatologists and the potential impact on their clinical practice was assessed. Results: Thirteen national key recommendations on the use of MTX were formulated: work-up before starting MTX, optimal dosage and route of administration, use of folic acid, monitoring, management of hepatotoxicity, long-term safety, mono versus combination therapy, management in the perioperative period, during infections, before/during pregnancy and after clinical remission, screening and treatment of tuberculosis and the role of MTX as a steroid-sparing agent in rheumatic diseases. Discussion: The Portuguese recommendations for the use of MTX in daily clinical practice were developed, which are evidence-based and supported by a panel of 50 rheumatologists, enhancing their validity and practical use. This project was integrated in a multinational initiative that led to the recent publication of ten multinational recommendations which differ from ours in some specific aspects.publishersversionpublishe