Charmonium Production at Forward Rapidity in pp, p-Pb and Pb-Pb Collisions, with ALICE

This contribution focuses on latest ALICE results on charmonium forward production in proton-proton (pp), proton-lead (p-Pb) and lead-lead (Pb-Pb) collisions at the TeV scale. In p-Pb and Pb-Pb collisions, measurements are presented in the form of the charmonium nuclear modification factor (the properly normalized ratio of its production cross section in heavy ion collisions to its pp counterpart) as a function of the charmonium rapidity and transverse momentum. These measurements are compared to available theoretical calculations. Possible interpretations of these results in terms of gluon saturation, initial and final state energy loss, color screening and recombination are also discussed.Comment: 6 pages, 11 figures, Conference Proceedings Large Hadron Collider Physics (LHCP) Conference, 201

THE ECONOMIC CRISIS AND AGRARIAN SUSTAINABILITY: WEAKNESSES AND POTENTIALITIES. CASE STUDY ON GOAT FARMS

International audienceThe objective of this work is to identify the effects (economic, environmental and social) of the economic crisis in agrarian activity at the farm level, focused on farms with the goat livestock of Bravia breed, and to identify the mechanisms/actions/innovations developed by these farms, in order to their survival, as the created opportunities that can sustain them. The methodology focuses on surveys to farmers who hold different levels of livestock heads, in order to measure the evolution of economic, social and environmental indicators before the economic crisis and at the current scenario. The aim is also carry out a SWOT analysis of these systems. In a global view is observed none or little impact of the economic crisis in the studied herds. The high mortality rate, the need of constant labor and the dependence of farmers in farmers' cooperative for most of the purposes are the main weaknesses found on these production systems. Effective responses to these situations reveal themselves as the main opportunities of the activity under study

Identification of gene regulation modules that act in the interaction between cork development and environmental variables

Tese de mestrado, Bioinformática e Biologia Computacional, 2023, Universidade de Lisboa, Faculdade de CiênciasCork oak (Quercus suber) is a mediterranean tree that excels in phellem (cork) production, a valuable raw product with multiple industrial applications. However, increased frequency and severity of drought events, due to climate change, lead to reduced cork oak growth and productivity. This work aimed to integrate different transcriptomics data available for this species to predict a gene co-expression network, and identify candidate regulatory modules of phellem development and assess their regulation by drought. The co-expression network was built using as guides a group of genes differentially expressed in phellem from plants exposed to drought conditions. Based on gene-to-gene co-expression links, transcription factor (TF)-target gene interactions were further predicted and reinforced using functional data available in the model plant A. thaliana. The generated network highlighted predominantly genes negatively regulated under drought, particularly gene modules related to cell division and differentiation (e.g. cell wall development). From the multiple interactions established by co-expression involving 27 TFs, 118 had been already identified in A. thaliana by experimental methods. Additionally, the specific binding sites predicted for 21 TFs were found in the promoters of 144 co-expressed genes. This demonstrated that the predicted co-expression network could, to some extent, predict candidate TF-target interactions. From the highlighted TFs, MYB93 and NAC43 were, respectively, integrated in two modules showing a concerted downregulation in phellem, in response to drought. Additionally, DREB1B TF and co-expressed targets are hypothesized as being involved in a adaptive response to drought by maintaining cellular homeostasis. Overall, the present work unveiled new regulatory gene modules of interest using stateof- the-art machine learning and data mining approaches, with predicted role in phellem development, and described their expression trend in response to drought. The selected candidate transcription factors will be further experimentally validated to reinforce the obtained in silico predictions. This will be an important contribution for the development of future strategies to screen cork oak plants for improved resilience and/or productivity, in response to adverse external conditions

Robotic Exoskeleton Hand with Pneumatic Actuators

With modern developments of smart portable devices and miniaturization of technologies, society has been provided with computerized assistance for almost every daily activity but the physical aspects have been frequently ne-glected. It is currently possible to make robots that process information thru neural networks, that identify and mimic facial expressions and that replace manual labour in assembly plants, getting ever closer to skills associated to human beings. In spite of these technological advances being kept close to they remain separate of humans, replacing or providing assistance with other pe-ripheral tasks, not generally adopting a direct physical symbiotic user assis-tance path. In this dissertation a robotic exoskeleton hand will be described that al-lows for human-machine bidirectional interaction making it possible to provide physical activities with the electromechanical assistance similarly. This system is designed to mimic the human hands functionalities and biomechanical struc-ture, as well sensing and controlling systems. A partial prototype was also built, using components easily acquired in the market, as a proof of concept

Science and technology in Africa : a bibliometric and patent analysis

Mestrado Economia e Gestão de Ciência, Tecnologia e InovaçãoIt is known that Africa's R&D has been fragile. However, the analysis of bibliometric data indicates that Africa has relative distinguish behaviours on publication (2,51% of world output in 2011) and patent production (0,25% of total PCT Applications in 2011). Regarding research output there was a turning point around 2004, when the continent's output was yet to reach 15,000 publications annually. Since that year African publications have grown faster than the world average, with its number more than duplicating until now. These advances are overshadowed by the fact the continent’s production is still highly concentrated (South Africa and Egypt). Concerning scientific specialization, the results indicate that the overall Africa’s specialization is not too different of the world pattern with the exception of Agricultural Sciences, which are relatively more important in Africa. An important finding is that, at the nation level, higher level of specialization and English language colonial legacy seems to lead to better results on “scientific impact”. Other relevant result is that there seems to be a non-linear dynamics between publication output and patent output. The more a country publishes in WoS publications, the more it is able to transform scientific information into technological inventions. Finally, as demonstrated, in a way, by our cluster analysis, Africa is too complex to follow one set of S&T policies. Each country must evaluate what already exists and, with a realistic vision (Lundvall, 2009), develop their knowledge frontiers to respond to local circumstances and opportunities.Historicamente, a I&D em África tem sido diminuta. No entanto, a análise de dados bibliométricos indica que África tem comportamentos distintos em relação à produção científica (2,51% da produção mundial em 2011) e aos pedidos internacionais de patentes (0,25% do total em 2011). Relativamente à produção científica, houve um ponto de viragem em 2004, quando a produção total do continente não ultrapassava as 15000 publicações anuais. Desde esse ano o crescimento anual tem sido mais rápido que a média mundial. Estes avanços são ofuscados pelo facto da produção do continente ser ainda altamente concentrada (África do Sul e Egito). Quando o à especialização científica, a única área científica onde África apresenta maior diferenciação é em “Ciências Agrárias”. Um resultado importante, ao nível dos países, é que maiores níveis de especialização e a existência da língua inglesa como língua colonial, parecem levar a publicações com maior "impacto científico". Outra conclusão relevante é que parece haver uma dinâmica não-linear entre o número de publicações de um país e o número de pedidos PCT. Quanto maior o nível de publicação de um país na WoS, maior parece ser a capacidade dos agentes em transformar a informação científica em invenções tecnológicas. Finalmente, a nossa análise de clusters demonstrou, que África é muito complexa para seguir um conjunto único de políticas de C&T. Cada país deve avaliar as suas características e, com uma visão realista (Lundvall, 2009), desenvolver as suas fronteiras de conhecimento para responder às circunstâncias e oportunidades locais

Lantipéptidos em Archaea: o caso de estudo de Haloferax mediterranei

Mestrado em Biologia Molecular e CelularOs produtos naturais são ainda hoje a maior fonte de descoberta de novas moléculas. Os lantipéptidos são um grupo de produtos naturais que pertencem à família de péptidos sintetizados pelos ribossomas e sujeitos a modificações pós-traducionais (RiPPs). Estas modificações incluem a desidratação de Ser e Thr e a ciclização entre estes aminoácidos desidratados e a Cys, dando origem aos característicos anéis de lantionina (Lan) e/ou metilantionina (MeLan). Estas reações são catalisadas por diferentes tipos de enzimas (LanB, LanM, LanKC e LanL), que constituem a base da classificação destes péptidos. Estas proteínas são codificadas em várias espécies de bactérias e possuem homólogos tanto no domínio Eukarya como no domínio Archaea. Os objectivos deste trabalho foram: i) identificar os clusters de lantipéptidos presentes no genomas de Archaea, recorrendo a bases de dados públicas, ii) caracterizar os clusters identificados e, por último, iii) identificar os padrões de desidratação e ciclização dos lantipéptidos encontrados em Haloferax mediterranei ATCC 33500. Em Archaea foram detectados apenas genes lanM, que estão confinados aos genomas de organismos pertencentes à classe Halobacteria. Uma procura “manual” in silico na região genómica de cada lanM permitiu identificar a presença de vários genes lanA. A análise da sequência dos lantipéptidos codificados por estes lanAs não identificou motivos conservados, mas permitiu a sua divisão em grupos diferentes. Os clusters que contêm estes genes também codificam proteínas de função desconhecida e transportadores ABC. Nenhum destes transportadores é do tipo SunT (LanT) que estão normalmente associados ao processamento de lantipéptidos modificados por LanMs. Haloferax mediterranei ATCC 33500 foi selecionado para uma caracterização mais aprofundada uma vez que possui três genes lanM: um no cromossoma (medM1) e dois num plasmídeo (medM2 e medM3). Foram construídos três vetores que permitiram a co-expressão dos genes medM e His6-medA em Escherichia coli. Após produção, purificação por IMAC e análise por MALDI-TOF, verificou-se que nenhum dos péptidos foi desidratado. Desta forma, as enzimas MedM não parecem estar funcionais no citoplasma de E. coli, necessitando provavelmente de elevadas concentrações de sal para exercer as suas funções. Desta forma, utilizou-se um outro hospedeiro para expressão heteróloga: a Archaea Haloferax volcanii H1424. Para tal, foram construídos novos vectores de co-expressão baseados no plasmídeo pTA1392, contendo dois promotores (e não apenas um como na versão original). Após transformação de H. volcanii, os péptidos foram produzidos e purificados por IMAC. A análise por MALDI-TOF, não revelou a presença de nenhum dos His6-MedA. Consequentemente, será necessário optimizar os protocolos de produção e/ou purificação destes péptidos de H. volcanii. O sucesso desta optimização permitirá provar a funcionalidade das enzimas MedM e estabelecer um sistema de expressão de natureza halófita que poderá ser útil para o estudo de outros clusters biosintéticos de Archaea. Concluindo, organismos do domínio Archaea, em particular Halobacteria, codificam enzimas envolvidas na biossíntese de lantipéptidos homólogas às encontradas em bactérias. Os lantipéptidos de bactérias normalmente são bacteriocinas. Se os lantipéptidos de Archaea possuírem atividade contra outras Archaea (archaeocinas), poderão ser uma ferramenta valiosa para o desenvolvimento de novos marcadores seletivos. Isto permitirá melhorar as ferramentas existentes para manipulação genética de Archaea.Natural products are to this day the major source of novel molecules. Lanthipeptides are a group of natural products belonging to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). Their modifications include the dehydration of Ser and Thr residues immediately followed by a cyclization reaction between the dehydrated amino acids and Cys to form their characteristic lanthionine (Lan) and/or methyllanthionine (MeLan) rings. These reactions are catalyzed by different types of enzymes (LanB, LanM, LanKC and LanL), that define the classification of lanthipeptides. These proteins are encoded in a wide range of bacterial species and have homologues also in Eukarya and Archaea. The objectives of this work were: i) identify lanthipeptide clusters in the publicly available archaeal genomes, ii) characterize the archaeal lanthipeptide gene clusters and iii) identify the dehydration and cyclization pattern of putative lanthipeptides from Haloferax mediterranei ATCC 33500. Archaea encodes exclusively LanM enzymes (21 lanM genes) and they are confined to organisms of the class Halobacteria. Manual search of the genetic neighborhood of each lanM allowed to identify several lanA genes. The putative lanthipeptides encoded by these lanAs do not share conserved motifs but, based on their sequences, they can be divided into groups. Their gene clusters also encode proteins of unknown function and ABC transporters. None of these transporters are of the SunT-type (LanT) that is classically involved in the processing of LanM-modified lanthipeptides. Haloferax mediterranei ATCC 33500 was selected for further characterization because it has three lanM genes: one on the chromosome (medM1) and two on a plasmid (medM2 e medM3). Three expression vectors were constructed to allow the co-expression of medM and His6-medA genes in Escherichia coli. After production, purification by IMAC and MALDI-ToF analysis, it was found that none of the peptides were dehydrated. This indicates that MedM enzymes are not functional in E. coli cytoplasm. Most probably, their functionality is dependent on high concentrations of salt. Therefore, another heterologous expression host was used: the archaeon Haloferax volcanii H1424. To this purpose, new co-expression vectors were constructed based on the pTA1392 plasmid and containing two promoters, instead of the original one. After transformation of H. volcanii, peptide production, IMAC purification and MALDI-ToF analysis, none of the His6-MedA peptides were identified. Thus, in the future, optimization of the production procedures and/or purification of these peptides from H. volcanii will be needed. This will prove the functionality of MedM enzymes and will establish a system with halofilic nature that can be useful for the investigation of other biosynthetic clusters from Archaea. In conclusion, Archaea, in particular Halobacteria, encode lanthipeptide enzymes that are homologous to those found in Bacteria. In Bacteria, these peptides commonly have antibacterial activity. If archaeal lanthipeptides are archaeocins, these peptides will be a valuable tool for the development of novel selective markers for Archaea. This will be highly relevant to improve the tool-box for the genetic manipulation of Archaea

Synchronic variation in Sri Lanka Portuguese personal pronouns

This paper presents and discusses the instances of synchronic variation attested in the personal pronoun paradigm of modern Sri Lanka Portuguese, an endangered Portuguese-based creole spoken by relatively small communities scattered across Eastern and Northern Sri Lanka. Although Sri Lanka Portuguese has a long history of documentation dating from, at least, the beginning of the 19th century, only a few studies have explicitly reported cases of synchronic variation. This study aims, therefore, to fill that gap, by contributing to the description and explanation of patterns of variation relating to the personal pronoun paradigm as encountered in documentary data collected between 2015 and 2020, over several field trips to the districts of Ampara, Batticaloa, Jaffna, and Trincomalee. The nature of the variation observed in the data ranges from phonetic alternations to strategies of paradigm regularization and stylistic shrinkage, often revealing the effects of diachronic processes of variant competition and substitution. Combining the observed patterns of variation with surveyed linguistic trends of language shift, we propose that obsolescence may be responsible for some of the variability encountered in modern SLP personal pronouns, especially that associated with certain socially- or geographically-defined subsets of the speech community (viz. the younger generations and the speakers from Jaffna) characterized by advanced language loss.info:eu-repo/semantics/acceptedVersio

Automatic cymbal classification

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia InformáticaMost of the research on automatic music transcription is focused on the transcription of pitched instruments, like the guitar and the piano. Little attention has been given to unpitched instruments, such as the drum kit, which is a collection of unpitched instruments. Yet, over the last few years this type of instrument started to garner more attention, perhaps due to increasing popularity of the drum kit in the western music. There has been work on automatic music transcription of the drum kit, especially the snare drum, bass drum, and hi-hat. Still, much work has to be done in order to achieve automatic music transcription of all unpitched instruments. An example of a type of unpitched instrument that has very particular acoustic characteristics and that has deserved almost no attention by the research community is the drum kit cymbals. A drum kit contains several cymbals and usually these are treated as a single instrument or are totally disregarded by automatic music classificators of unpitched instruments. We propose to fill this gap and as such, the goal of this dissertation is automatic music classification of drum kit cymbal events, and the identification of which class of cymbals they belong to. As stated, the majority of work developed on this area is mostly done with very different percussive instruments, like the snare drum, bass drum, and hi-hat. On the other hand, cymbals are very similar between them. Their geometry, type of alloys, spectral and sound traits shows us just that. Thus, the great achievement of this work is not only being able to correctly classify the different cymbals, but to be able to identify such similar instruments, which makes this task even harder