Cross-shelf flow forced by daily variable winds in the presence of a cape

Tese de doutoramento, Ciências Geofísicas e da Geoinformação (Oceanografia), Universidade de Lisboa, Faculdade de Ciências, 2018This thesis intends to contribute to the knowledge of the nearshore circulation in the vicinity of a cape under daily variable wind conditions. Throughout this study, several different tools were used to understand the diurnal variability of the circulation, with special emphasis on the cross-shelf transport in the leeside of the cape. In-situ data collected near Cape Sines, on the southwestern coast of Portugal, during three summers, indicated that the wind was consistently favourable to upwelling with recurrent sea breeze-like diurnal variability. Current data collected by an ADCP in the leeside of the cape during events of strong diurnal variability of the wind showed that the average day of the cross-shelf circulation consisted of three distinct periods: a morning period with a 3-layer structure with onshore velocities at mid-depth, a mid-day period where the flow is reversed and has a 2-layer structure with onshore velocities at the surface and offshore flow below, and, lastly, in the evening, a 2-layer flow with intensified offshore velocities at the surface and onshore flow at the bottom. A simplified 2D numerical model hinted at the fact that the cross shelf flow reversal which occurred at mid-day was forced by the local acceleration of the along-shelf velocity. A numerical modelling experiment exclusively forced by winds simulated successfully most of the circulation at a location consistent with the ADCP, especially the mid-day reversal and the evening’s upwelling-type structure. This supported the hypothesis that the observed crossshelf circulation at diurnal timescales was dominantly wind-driven. Analysing a set of modelling experiments with simplified topography and wind forcing helped to clarify the dynamics behind the ocean circulation around the cape, indicating that the cross-shelf flow reversal resulted as a response to the rapid change of the wind magnitude at mid-day. The fact that the wind diurnally undergoes relaxation and intensification strongly affects the cross-shelf circulation, promoting surface onshore transport in the leeside of the cape

Generation of an integration-free induced pluripotent stem cell line (CSC-43) from a patient with sporadic Parkinson's disease

An induced pluripotent stem cell (iPSC) line was generated from a 36-year-old patient with sporadic Parkinson's disease (PD). Skin fibroblasts were reprogrammed using the non-integrating Sendai virus technology to deliver OCT3/4, SOX2, c-MYC and KLF4 factors. The generated cell line (CSC-43) exhibits expression of common pluripotency markers, in vitro differentiation into three germ layers and normal karyotype. This iPSC line can be used to study the mechanisms underlying the development of PD.‘Cell Line and DNA Biobank from Patients affected by Genetic Diseases’ (Istituto G. Gaslini, Genova, Italy) and the Parkinson Institute Biobank, members of the Telethon Network of Genetic Biobanks (http://biobanknetwork.telethon.it; project no. GTB12001) funded by Telethon Italy, for providing fibroblasts samples. This work was supported by the Strategic Research Environment MultiPark at Lund University, the strong research environment BAGADILICO (grant 349-2007-8626), the Swedish Parkinson Foundation (Parkinsonfonden, grant 889/16), the Swedish Research Council (grant 2015-03684 to LR) and Finnish Cultural Foundation (grant 00161167 to YP). We also acknowledge the Portuguese Foundation for Science and Technologyinfo:eu-repo/semantics/publishedVersio

Generation of an induced pluripotent stem cell line (CSC-44) from a Parkinson's disease patient carrying a compound heterozygous mutation (c.823C>T and EX6 del) in the PARK2 gene

Mutations in the PARK2 gene, which encodes PARKIN, are the most frequent cause of autosomal recessive Parkinson's disease (PD). We report the generation of an induced pluripotent stem cell (iPSC) line from a 78-year-old patient carrying a compound heterozygous mutation (c.823C>T and EX6del) in the PARK2 gene. Skin fibroblasts were reprogrammed using the non-integrating Sendai virus technology to deliver OCT3/4, SOX2, c-MYC and KLF4 factors. The generated cell line CSC-44 exhibits expression of common pluripotency markers, in vitro differentiation into the three germ layers and normal karyotype. This iPSC line can be used to explore the association between PARK2 mutations and PD.‘Cell Line and DNA Biobank from Patients affected by Genetic Diseases’ (Istituto G. Gaslini, Genova, Italy) and the ‘Parkinson Institute Biobank, members of the Telethon Network of Genetic Biobanks (http://biobanknetwork.telethon.it; project no. GTB12001) funded by Telethon Italy, for providing fibroblasts samples. This work was supported by the Strategic Research Environment MultiPark at Lund University and the strong research environment BAGADILICO (grant 349-2007-8626), the Swedish Parkinson Foundation (Parkinsonfonden; grant 889/16), the Swedish Research Council (grant 2015-03684 to LR) and Finnish Cultural Foundation (grant 00161167 to YP). We also acknowledge the Portuguese Foundation for Science and Technology for the doctoral fellowshipinfo:eu-repo/semantics/publishedVersio

Evaluation of SMOS L4 Sea Surface Salinity Product in the Western Iberian Coast

Special issue Moving Forward on Remote Sensing of Sea Surface Salinity.-- 24 pages, 14 figures, supplementary materials https://www.mdpi.com/article/10.3390/rs14020423/s1.-- Data Availability Statement: Data sharing not applicableSalinity is one of the oldest parameters being measured in oceanography and one of the most important to study in the context of climate change. However, its quantification by satellite remote sensing has been a relatively recent achievement. Currently, after over ten years of data gathering, there are still many challenges in quantifying salinity from space, especially when it is intended for coastal environments study. That is mainly due to the spatial resolution of the available products. Recently, a new higher resolution (5 km) L4 SMOS sea surface salinity (SSS) product was developed by the Barcelona Expert Center (BEC). In this study, the quality of this product was tested along the Western Iberian Coast through its comparison with in situ observations and modelled salinity estimates (CMEMS IBI Ocean Reanalysis system). Moreover, several parameters such as the temperature and depth of in situ measurements were tested to identify the variables or processes that induced higher errors in the product or influenced its performance. Lastly, a seasonal and interannual analysis was conducted considering data between 2011 to 2019 to test the product as a potential tool for long-term studies. The results obtained in the present analysis showed a high potential of using the L4 BEC SSS SMOS product in extended temporal and spatial analyses along the Portuguese coast. A good correlation between the satellite and the in situ datasets was observed, and the satellite dataset showed lower errors in retrieving coastal salinities than the oceanic model. Overall, the distance to the coast and the closest rivers were the factors that most influenced the quality of the product. The present analysis showed that great progress has been made in deriving coastal salinity over the years and that the SMOS SSS product is a valuable contribution to worldwide climatological studies. In addition, these results reinforce the need to continue developing satellite remote sensing products as a global and cost-effective methodology for long-term studiesThis work was conducted within the framework of the project AQUIMAR—Marine Knowledge Supporting Aquaculture (MAR-02.01.01-FEAMP-0107), funded by the Mar 2020—Operational Program Mar2020. B.B. was funded by a grant from Mar2020 under AQUIMAR project and also by a PhD grant awarded by Fundação para a Ciência e a Tecnologia (FCT) within the scope of the MIT Portugal Program. A.C.B. was funded by FCT through the Scientific Employment Stimulus Programme (CEECIND/0095/2017). A.T. was funded by Project SARDINHA2020 (MAR-01.04.02-FEAMP-0009), funded by the Operational Program Mar2020. This work benefited from the Infrastructure CoastNet (http://geoportal.coastnet.pt, accessed on 30 September 2021), funded by FCT and the European Regional Development Fund (FEDER), through LISBOA2020 and ALENTEJO2020 regional operational programs, in the framework of the National Roadmap of Research Infrastructures of strategic relevance (PINFRA/22128/2016). This study also received further support from FCT through MARE’s strategic program (UID/MAR/04292/2019). This work represents a contribution to CSIC Thematic Interdisciplinary Platform PTI Teledetect, with the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). This publication was also funded by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement N810139: Project Portugal Twinning for Innovation and Excellence in Marine Science and Earth Observation—PORTWIMSPeer reviewe

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

Estimativas de transporte na parte oriental da Corrente dos Açores

Tese de mestrado, Ciências Geofísicas (Oceanografia), Universidade de Lisboa, Faculdade de Ciências, 2009Circulation patterns of the eastern part of the Azores Current are investigated through estimates of current velocities and volume transports using two sets of data: ARGO hydrographic data and also an absolute dynamic topography (ADT) product resulting from merging ARGO data with Altimetry data. Calculations of velocity fields are made considering the flow in geostrophic balance and estimates of transport along the Azores Current are presented. The circulation structures obtained are compared and related with the β- plume theory, which says that the Azores Current may be forced by the entrainment of Central Waters by the denser Mediterranean outflow, forming a cyclonic recirculation at the surface layer. For this reason, special emphasis is given to the area of the Gulf of Cadiz. The surface velocity fields obtained are compared with surface drifter buoys database (SVP), and transport and velocity results are compared with previous studies made in the study region. The three data sets (ARGO, ADT and SVP) show a structure similar to the β- plume, previously found by the models, in the Gulf of Cadiz. It is possible to observe the flow entering the Gulf of Cadiz, circulating cyclonically and returning in a northwestward direction, creating a cyclonic cell similar to that predicted by the β-plume theory. The estimates of transport made in this work are within the range of values obtained by previous studies in the region.São estudados os padrões de circulação da zona oriental da Corrente dos Açores através de estimativas de velocidades de corrente e de transporte utilizando dois tipos de volumes de dados: dados hidrográficos ARGO e dados resultantes da junção de dados ARGO com altimetria que resultam num produto de topografia dinâmica absoluta (ADT). São calculados campos de velocidade e o transporte ao longo da corrente dos Açores, considerando o escoamento em equilíbrio geostrófico. As estruturas de circulação obtidas são, então, comparadas e relacionadas com a teoria da pluma-β, que indica que a corrente dos Açores pode ter como forçamento a intrusão de Água Mediterrânea no Oceano Atlântico, e que essa troca de massa no Estreito de Gibraltar formaria uma recirculação ciclónica à superfície. Por essa razão foi dado especial ênfase à zona do Golfo de Cádis. Os campos de velocidade obtidos à superfície são comparados com resultados obtidos por bóias derivantes à superfície (SVP) e os resultados de transporte e velocidade comparados com estudos previamente feitos nesta região. Verifica-se que os três conjuntos de dados (ARGO, ADT e SVP) revelam uma estrutura semelhante à pluma-β, anteriormente observada nos modelos, na zona do Golfo de Cádis. Observa-se o escoamento da Corrente dos Açores a entrar no Golfo de Cádis, a circular ciclonicamente e a dirigir-se para fora do Golfo numa direcção para noroeste, gerando uma célula ciclónica, semelhante à prevista pela teoria da pluma-β. Os valores de transporte calculados neste trabalho estão dentro do intervalo de valores estimados por estudos previamente feitos nesta região

Immunoglobulin G4 Related-Disease: A Rare Presentation With Secondary Hypereosinophilic Syndrome and Eosinophilic Ascites

Immunoglobulin G4 related-disease (IgG4-RD) is a multisystemic immune-mediated fibroinflammatory disease, with a strong predilection for salivary and lacrimal glands, pancreas, biliary tree, lungs, kidneys, aorta, and retroperitoneum. In the case of pancreatic involvement, it manifests as autoimmune pancreatitis. Patients with IgG4-RD usually have mild to moderate eosinophilia in the peripheral blood, however, they may present a secondary hypereosinophilic syndrome (HES). Although there are cases described with severe eosinophilia (> 5,000/µL), the 2019 American College of Rheumatology/European League Against Rheumatism classification criteria for IgG4-RD considers peripheral eosinophilia above 3,000/µL as an exclusion criterion, although stating that assessment for the presence of exclusion criteria should be individualized depending on a patient's clinical scenario. Here, we describe the clinical case of a 30-year-old woman who presented with chronic diarrhea and abdominal pain. The diagnostic workup revealed eosinophilic ascites, severe peripheral blood eosinophilia (> 5,000/µL), IgG4 elevation (> 2 × upper normal limit), and also diffuse swelling in the body and pancreatic tail (computed tomography (CT) scan). There was a prompt response to corticosteroid therapy with clinical resolution and continued remission under therapy. The patient was diagnosed with IgG4-RD with secondary HES, explaining the gastrointestinal tract and peritoneum damage in the form of enterocolitis and ascites. Exclusion of alternative diagnosis was made.info:eu-repo/semantics/publishedVersio

Estudo Geral - Methodology to develop an excel tool aiming at estimating the heating energy demands of the AHUs

In many secondary schools in Portugal, indoor air quality is currently assured by mechanical ventilation. In some cases, Air Handling Units (AHUs) are used to supply fresh air at the rooms conditions. Once in the classrooms, thermal loads are suppressed by terminal units, e.g. hot water radiators (used for heating conditions, at 20 ºC). Some heating capacity is also due to a differential temperature between the outdoor air entering the AHU and the supply air into the room. Based upon these considerations and specifically for air-supplying at room conditions, the authors developed an excel tool, aiming at estimating the heating energy demands of the AHUs serving classrooms during an entire scholar year, i.e. the integration of the computed heating transfer rate over the considered period of time. This working file includes the integration of an ‘Energy Plus’ weather file that may vary according to the building site. Therefore, the energy estimations account on the supplied air temperature differential, between the outside air temperature and the desired temperature of the supplied air during the occupancy period. A detailed description of the methodology developed to build this tool – which is mostly rooted on The 2013 ASHRAE Handbook of Fundamentals (Chapter 1) [1] – is next presented