High performance data processing

Dissertação de mestrado em Informatics EngeneeringÀ medida que as aplicações atingem uma maior quantidade de utilizadores, precisam de processar uma crescente quantidade de pedidos. Para além disso, precisam de muitas vezes satisfazer pedidos de utilizadores de diferentes partes do globo, onde as latências de rede têm um impacto significativo no desempenho em instalações monolíticas. Portanto, distribuição é uma solução muito procurada para melhorar a performance das camadas aplicacional e de dados. Contudo, distribuir dados não é uma tarefa simples se pretendemos assegurar uma forte consistência. Isto leva a que muitos sistemas de base de dados dependam de protocolos de sincronização pesados, como two-phase commit, consenso distribuído, bloqueamento distribuído, entre outros, enquanto que outros sistemas dependem em consistência fraca, não viável para alguns casos de uso. Esta tese apresenta o design, implementação e avaliação de duas soluções que têm como objetivo reduzir o impacto de assegurar garantias de forte consistência em sistemas de base de dados, especialmente aqueles distribuídos pelo globo. A primeira é o Primary Semi-Primary, uma arquitetura de base de dados distribuída com total replicação que permite que as réplicas evoluam independentemente, para evitar que os clientes precisem de esperar que escritas precedentes que não geram conflitos sejam propagadas. Apesar das réplicas poderem processar tanto leituras como escritas, melhorando a escalabilidade, o sistema continua a oferecer garantias de consistência forte, através do envio da certificação de transações para um nó central. O seu design é independente de modelos de dados, mas a sua implementação pode tirar partido do controlo de concorrência nativo oferecido por algumas base de dados, como é mostrado na implementação usando PostgreSQL e o seu Snapshot Isolation. Os resultados apresentam várias vantagens tanto em ambientes locais como globais. A segunda solução são os Multi-Record Values, uma técnica que particiona dinâmicamente valores numéricos em múltiplos registros, permitindo que escritas concorrentes possam executar com uma baixa probabilidade de colisão, reduzindo a taxa de abortos e/ou contenção na adquirição de locks. Garantias de limites inferiores, exigido por objetos como saldos bancários ou inventários, são assegurados por esta estratégia, ao contrário de muitas outras alternativas. O seu design é também indiferente do modelo de dados, sendo que as suas vantagens podem ser encontradas em sistemas SQL e NoSQL, bem como distribuídos ou centralizados, tal como apresentado na secção de avaliação.As applications reach an wider audience that ever before, they must process larger and larger amounts of requests. In addition, they often must be able to serve users all over the globe, where network latencies have a significant negative impact on monolithic deployments. Therefore, distribution is a well sought-after solution to improve performance of both applicational and database layers. However, distributing data is not an easy task if we want to ensure strong consistency guarantees. This leads many databases systems to rely on expensive synchronization controls protocols such as two-phase commit, distributed consensus, distributed locking, among others, while other systems rely on weak consistency, unfeasible for some use cases. This thesis presents the design, implementation and evaluation of two solutions aimed at reducing the impact of ensuring strong consistency guarantees on database systems, especially geo-distributed ones. The first is the Primary Semi-Primary, a full replication distributed database architecture that allows different replicas to evolve independently, to avoid that clients wait for preceding non-conflicting updates. Al though replicas can process both reads and writes, improving scalability, the system still ensures strong consistency guarantees, by relaying transactions’ certifications to a central node. Its design is independent of the underlying data model, but its implementation can take advantage of the native concurrency control offered by some systems, as is exemplified by an implementation using PostgreSQL and its Snapshot Isolation. The results present several advantages in both throughput and response time, when comparing to other alternative architectures, in both local and geo-distributed environments. The second solution is the Multi-Record Values, a technique that dynami cally partitions numeric values into multiple records, allowing concurrent writes to execute with low conflict probability, reducing abort rate and/or locking contention. Lower limit guarantees, required by objects such as balances or stocks, are ensure by this strategy, unlike many other similar alternatives. Its design is also data model agnostic, given its advantages can be found in both SQL and NoSQL systems, as well as both centralized and distributed database, as presented in the evaluation section

The influence of laser power and scan speed on the dimensional accuracy of Ti6Al4V thin-walled parts manufactured by selective laser melting

Laser Powder Bed Fusion (LPBF) technologies such as Selective Laser Melting (SLM) are being increasingly considered as viable production routes. This paradigm change demands an in-depth understanding of the fabrication process and variables, as previous studies have shown that energy density calculation alone is insufficient, because parts fabricated using similar energy density, but using different combinations of parameters, can display significantly different properties and dimensions. Thin-walled parts are particularly influenced by processing parameters; in this sense, this study explores the influence of laser power and scan speed on the dimensions of Ti6Al4V thin-walled tubes. Predictive models for manufacturing Ti6Al4V thin-walled tubes were developed using Response Surface Methodology (RSM), and the most influential (single and combined) factors were determined using Analysis of Variance (ANOVA). Three models were obtained: for the wall melt zone thickness, the total wall thickness, and the hole width.FCT (Fundação para a Ciência e a Tecnologia) through the project PTDC/EME-EME/1442/2020 (Add2MechBio) and POCI-01-0247-FEDER-024533 (Add-Additive–Add additive manufacturing to Portuguese industry). Acknowledgments to the project CICECO-Aveiro Institute of Materials, UIDB/50011/2020, UIDP/50011/2020, and LA/P/0006/2020, financed by national funds through the FCT/MEC (PIDDAC)

WNT6 is a novel oncogenic prognostic biomarker in human glioblastoma

Glioblastoma (GBM) is a universally fatal brain cancer, for which novel therapies targeting specific underlying oncogenic events are urgently needed. While the WNT pathway has been shown to be frequently activated in GBM, constituting a potential therapeutic target, the relevance of WNT6, an activator of this pathway, remains unknown. Methods: WNT6 protein and mRNA levels were evaluated in GBM. WNT6 levels were silenced or overexpressed in GBM cells to assess functional effects in vitro and in vivo. Phospho-kinase arrays and TCF/LEF reporter assays were used to identify WNT6-signaling pathways, and significant associations with stem cell features and cancer-related pathways were validated in patients. Survival analyses were performed with Cox regression and Log-rank tests. Meta-analyses were used to calculate the estimated pooled effect. Results: We show that WNT6 is significantly overexpressed in GBMs, as compared to lower-grade gliomas and normal brain, at mRNA and protein levels. Functionally, WNT6 increases typical oncogenic activities in GBM cells, including viability, proliferation, glioma stem cell capacity, invasion, migration, and resistance to temozolomide chemotherapy. Concordantly, in in vivo orthotopic GBM mice models, using both overexpressing and silencing models, WNT6 expression was associated with shorter overall survival, and increased features of tumor aggressiveness. Mechanistically, WNT6 contributes to activate typical oncogenic pathways, including Src and STAT, which intertwined with the WNT pathway may be critical effectors of WNT6-associated aggressiveness in GBM. Clinically, we establish WNT6 as an independent prognostic biomarker of shorter survival in GBM patients from several independent cohorts. Conclusion: Our findings establish WNT6 as a novel oncogene in GBM, opening opportunities to develop more rational therapies to treat this highly aggressive tumor.FCT - Foundation for Science and Technology (PTDC/SAU-GMG/113795/2009 and IF/00601/2012 to B.M.C.; SFRH/BD/92786/2013 to C.S.G.; SFRH/BD/88121/2012 to J.V.C.; SFRH/BD/81042/2011 to M.P.; SFRH/BD/93443/2013 to S.Q.) and Fundação Calouste Gulbenkian (B.M.C.), by FEDER funds through the Operational Programme Competitiveness Factors - COMPETE and National Funds through FCT under the project POCI-01-0145-FEDER-007038; by the project NORTE-01-0145-FEDER-000013 and NORTE-01-0246-FEDER-000012, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF); and by the project NORTE-01-0145-FEDER-000023, supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)info:eu-repo/semantics/publishedVersio

uma análise transversal

Publisher Copyright: Copyright © Ordem dos Médicos 2022.Introduction: Pre-exposure prophylaxis (PrEP) has gained relevance as a method of prevention for HIV in certain people and settings. Following the publication of the guideline on PrEP prescribing in Portugal, we aimed to assess the knowledge of Portuguese Medical Students about PrEP. Material and Methods: An online survey was sent to Medical students of Portuguese Medical Schools. We conducted a descriptive analysis of the results and an analytic cross-sectional study to identify factors associated with “knowing about PrEP”, “having had one class about PrEP” and “identifying eligible groups correctly”. Results: Of the 796 students that responded to the survey, 64.6% were aware of what PrEP is. Of these, 34.44% acquired this knowledge during their training. Out of the total amount of respondents, 4.77% could identify correctly and completely the eligible groups for PrEP. As the training years went by, the probability of being aware of PrEP, having had one class about PrEP, and identifying the eligible groups correctly, increased. Of the sixth-year students, 43.48% had had one class about PrEP and among the students that were aware of PrEP, 28% identified what the eligible groups were. After adjusting for the school year, we found differences between Medical Schools regarding the outcomes. The association between the different ways of knowing about PrEP and the ability to correctly identify eligible groups for PrEP was not statistically significant. Conclusion: The differences between Medical Schools could be harmonized through changes in the medical curricula that would allow for this topic to be addressed more often.publishersversionpublishe

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

COOPEDU IV — Cooperação e Educação de Qualidade

O quarto Congresso Internacional de Cooperação e Educação-IV COOPEDU, organizado pelo Centro de Estudos Internacionais (CEI) do Instituto Universitário de Lisboa e pela Escola Superior de Educação e Ciências Sociais do Instituto Politécnico de Leiria decorreu nos dias 8 e 9 de novembro de 2018, subordinado à temática Cooperação e Educação de Qualidade. Este congresso insere-se numa linha de continuidade de intervenção por parte das duas instituições organizadoras e dos elementos coordenadores e este ano beneficiou do financiamento do Instituto Camões, obtido através de um procedimento concursal, que nos permitiu contar com a participação presencial de elementos dos Países Africanos de Língua Portuguesa, fortemente implicados nas problemáticas da Educação e da Formação. Contou também com a participação do Instituto Camões e da Fundação Calouste Gulbenkian, entidades que sistematizaram a sua intervenção nos domínios da cooperação na área da educação nos últimos anos. A opção pela temática da qualidade pareceu aos organizadores pertinente e actual. Com efeito os sistemas educativos dos países que constituem a Comunidade de países de língua portuguesa têm implementado várias reformas mas em vários domínios mantem-se a insatisfação de responsáveis políticos, pedagogos, técnicos sociais face aos resultados obtidos. Aliás o caminho de procura da Qualidade é interminável porque vai a par da aposta na exigência e na promoção da cidadania e responsabilidade social. As comunicações que agora se publicam estão organizadas em dois eixos: o das Políticas da Educação e Formação e o das dimensões em que se traduzem essas políticas. Neste último eixo encontramos fios condutores para agregarmos as comunicações apresentadas

Integrated monitoring of mola mola behaviour in space and time

Over the last decade, ocean sunfish movements have been monitored worldwide using various satellite tracking methods. This study reports the near-real time monitoring of finescale (< 10 m) behaviour of sunfish. The study was conducted in southern Portugal in May 2014 and involved satellite tags and underwater and surface robotic vehicles to measure both the movements and the contextual environment of the fish. A total of four individuals were tracked using custom-made GPS satellite tags providing geolocation estimates of fine-scale resolution. These accurate positions further informed sunfish areas of restricted search (ARS), which were directly correlated to steep thermal frontal zones. Simultaneously, and for two different occasions, an Autonomous Underwater Vehicle (AUV) videorecorded the path of the tracked fish and detected buoyant particles in the water column. Importantly, the densities of these particles were also directly correlated to steep thermal gradients. Thus, both sunfish foraging behaviour (ARS) and possibly prey densities, were found to be influenced by analogous environmental conditions. In addition, the dynamic structure of the water transited by the tracked individuals was described by a Lagrangian modelling approach. The model informed the distribution of zooplankton in the region, both horizontally and in the water column, and the resultant simulated densities positively correlated with sunfish ARS behaviour estimator (r(s) = 0.184, p < 0.001). The model also revealed that tracked fish opportunistically displace with respect to subsurface current flow. Thus, we show how physical forcing and current structure provide a rationale for a predator's finescale behaviour observed over a two weeks in May 2014

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).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

Descriptive statistics of the encountered environment.

<p>Mean and standard deviation (s.d.) for each environmental feature are presented.</p