CATARINA 2012-Leg 1 - CTD-O2 Data report

The CATARINA Leg1 cruise was carried out from June 22 to July 24 2012 on board the B/O Sarmiento de Gamboa, under the scientific supervision of Aida Rios (CSIC-IIM). It included the occurrence of the OVIDE hydrological section that was performed in June 2002, 2004, 2006, 2008 and 2010, as part of the CLIVAR program (name A25) ), and under the supervision of Herlé Mercier (CNRSLPO). This section begins near Lisbon (Portugal), runs through the West European Basin and the Iceland Basin, crosses the Reykjanes Ridge (300 miles north of Charlie-Gibbs Fracture Zone, and ends at Cape Hoppe (southeast tip of Greenland). The objective of this repeated hydrological section is to monitor the variability of water mass properties and main current transports in the basin, complementing the international observation array relevant for climate studies. In addition, the Labrador Sea was partly sampled (stations 101-108) between Greenland and Newfoundland, but heavy weather conditions prevented the achievement of the section south of 53°40’N. The quality of CTD data is essential to reach the first objective of the CATARINA project, i.e. to quantify the Meridional Overturning Circulation and water mass ventilation changes and their effect on the changes in the anthropogenic carbon ocean uptake and storage capacity. The CATARINA project was mainly funded by the Spanish Ministry of Sciences and Innovation and co-funded by the Fondo Europeo de Desarrollo Regional. The hydrological OVIDE section includes 95 surface-bottom stations from coast to coast, collecting profiles of temperature, salinity, oxygen and currents, spaced by 2 to 25 Nm depending on the steepness of the topography. The position of the stations closely follows that of OVIDE 2002. In addition, 8 stations were carried out in the Labrador Sea. From the 24 bottles closed at various depth at each stations, samples of sea water are used for salinity and oxygen calibration, and for measurements of biogeochemical components that are not reported here. The data were acquired with a Seabird CTD (SBE911+) and an SBE43 for the dissolved oxygen, belonging to the Spanish UTM group. The software SBE data processing was used after decoding and cleaning the raw data. Then, the LPO matlab toolbox was used to calibrate and bin the data as it was done for the previous OVIDE cruises, using on the one hand pre and post-cruise calibration results for the pressure and temperature sensors (done at Ifremer) and on the other hand the water samples of the 24 bottles of the rosette at each station for the salinity and dissolved oxygen data. A final accuracy of 0.002°C, 0.002 psu and 0.04 ml/l (2.3 umol/kg) was obtained on final profiles of temperature, salinity and dissolved oxygen, compatible with international requirements issued from the WOCE program.

Mulheres negras e (in)visibilidade : imaginários sobre a intersecção de raça e gênero no cinema brasileiro (1999-2009)

Tese (doutorado)—Universidade de Brasília, Faculdade de Comunicação, Programa de Pós-Graduação em Comunicação, 2016.

Weakly-constrained codes for suppression of patterning effects in digital communications

We propose weakly-constrained stream and block codes with tunable pattern-dependent statistics and demonstrate that the block code capacity at large block sizes is close to the the prediction obtained from a simple Markov model published earlier. We demonstrate the feasibility of the code by presenting original encoding and decoding algorithms with a complexity log-linear in the block size and with modest table memory requirements. We also show that when such codes are used for mitigation of patterning effects in optical fibre communications, a gain of about 0.5dB is possible under realistic conditions, at the expense of small redundancy (≈10%). © 2010 IEEE

Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum

mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density

Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.

De la lecture à la production verbale écrite, et réciproquement

L’objectif du chapitre consiste à dresser un bilan des acquis concernant les relations entre lecture-compréhension et écriture-rédaction. Deux approches sont envisagées. La première s’appuie sur des évaluations globales des dimensions relatives dites au bas niveau (au code : écriture et décodage) et des dimensions de haut niveau (compréhension et production textuelle). Elle met en évidence des relations fortes entre les premières, mais plutôt faibles entre les secondes. La seconde approche procède à la mise en relation entre composantes des deux activités : lexique (en lecture et en production), syntaxe, structure des textes, etc. Elle fait apparaître une plus grande complexité des relations et une relative indépendance des composantes. Elle conduit à reposer la question des impacts respectifs et réciproques de la lecture-compréhension sur l’écriture-rédaction. Elle amène à s’interroger sur ce que seraient les effets d’une pratique accordant une priorité à la production plutôt qu’à la lecture-compréhension et à rechercher les modalités d’intervention visant à améliorer l’une à partir de l’autre, et réciproquement.

Élucidation et identification des différents interacteurs impliqués dans le mécanisme de régulation du LDLR par la protéine PCSK9

Résumé : Les maladies cardiovasculaires représentent la principale cause de mortalité mondiale, soit le tiers des décès annuels selon l’Organisation mondiale de la Santé. L’hypercholestérolémie, caractérisée par une élévation des niveaux plasmatiques de lipoprotéines de faible densité (LDL), est l’un des facteurs de risque majeur pour les maladies cardiovasculaires. La proprotéine convertase subtilisine/kexine type 9 (PCSK9) joue un rôle essentiel dans l’homéostasie du cholestérol sanguin par la régulation des niveaux protéiques du récepteur LDL (LDLR). PCSK9 est capable de se lier au LDLR et favorise l’internalisation et la dégradation du récepteur dans les lysosomes. L’inhibition de PCSK9 s’avère une cible thérapeutique validée pour le traitement de l’hypercholestérolémie et la prévention des maladies cardiovasculaires. Par contre, plusieurs mécanismes responsables de la régulation et la dégradation du complexe PCSK9-LDLR n’ont pas encore été complètement caractérisés comme la régulation par la protéine annexin A2 (AnxA2), un inhibiteur endogène de PCSK9. De plus, plusieurs évidences suggèrent la présence d’une ou plusieurs protéines, encore inconnues, impliquées dans le mécanisme d’action de PCSK9. Celles-ci pourraient réguler l’internalisation et le transport du complexe PCSK9-LDLR vers les lysosomes. Les objectifs de cette thèse sont de mieux définir le rôle et l’impact de l’AnxA2 sur la protéine PCSK9 en plus d’identifier de nouveaux partenaires d’interactions de PCSK9 pour mieux caractériser son mécanisme d’action sur la régulation des niveaux de LDLR. Nous avons démontré que l’inhibition de PCSK9 par l’AnxA2 extracellulaire s’effectue via sa liaison aux domaines M1+M2 de la région C-terminale de PCSK9 et nous avons mis en évidence les premières preuves d’un contrôle intracellulaire de l’AnxA2 sur la traduction de l’ARNm de PCSK9. Nos résultats révèlent une liaison de l’AnxA2 à l’ARN messager de PCSK9 qui cause une répression traductionnelle. Nous avons également identifié la protéine glypican-3 (GPC3) comme un nouveau partenaire d’interaction extracellulaire avec le PCSK9 et intracellulaire avec le complexe PCSK9-LDLR dans le réticulum endoplasmique des cellules HepG2 et Huh7. Nos études démontrent que GPC3 réduit l’activité extracellulaire de PCSK9 en agissant comme un compétiteur du LDLR pour la liaison avec PCSK9. Une meilleure compréhension des mécanismes de régulation et de dégradation du complexe PCKS9-LDLR permettra de mieux évaluer l’impact et l’efficacité des inhibiteurs de la protéine PCSK9.

The teaching of reading English in a foreign language in Libyan universities: methods and models

This study focuses on the learning and teaching of Reading in English as a Foreign Language (REFL), in Libya. The study draws on an action research process in which I sought to look critically at students and teachers of English as a Foreign Language (EFL) in Libya as they learned and taught REFL in four Libyan research sites. The Libyan EFL educational system is influenced by two main factors: the method of teaching the Holy-Quran and the long-time ban on teaching EFL by the former Libyan regime under Muammar Gaddafi. Both of these factors have affected the learning and teaching of REFL and I outline these contextual factors in the first chapter of the thesis. This investigation, and the exploration of the challenges that Libyan university students encounter in their REFL, is supported by attention to reading models. These models helped to provide an analytical framework and starting point for understanding the many processes involved in reading for meaning and in reading to satisfy teacher instructions. The theoretical framework I adopted was based, mainly and initially, on top-down, bottom-up, interactive and compensatory interactive models. I drew on these models with a view to understanding whether and how the processes of reading described in the models could be applied to the reading of EFL students and whether these models could help me to better understand what was going on in REFL. The diagnosis stage of the study provided initial data collected from four Libyan research sites with research tools including video-recorded classroom observations, semi-structured interviews with teachers before and after lesson observation, and think-aloud protocols (TAPs) with 24 students (six from each university) in which I examined their REFL reading behaviours and strategies. This stage indicated that the majority of students shared behaviours such as reading aloud, reading each word in the text, articulating the phonemes and syllables of words, or skipping words if they could not pronounce them. Overall this first stage indicated that alternative methods of teaching REFL were needed in order to encourage ‘reading for meaning’ that might be based on strategies related to eventual interactive reading models adapted for REFL. The second phase of this research project was an Intervention Phase involving two team-teaching sessions in one of the four stage one universities. In each session, I worked with the teacher of one group to introduce an alternative method of REFL. This method was based on teaching different reading strategies to encourage the students to work towards an eventual interactive way of reading for meaning. A focus group discussion and TAPs followed the lessons with six students in order to discuss the 'new' method. Next were two video-recorded classroom observations which were followed by an audio-recorded discussion with the teacher about these methods. Finally, I conducted a Skype interview with the class teacher at the end of the semester to discuss any changes he had made in his teaching or had observed in his students' reading with respect to reading behaviour strategies, and reactions and performance of the students as he continued to use the 'new' method. The results of the intervention stage indicate that the teacher, perhaps not surprisingly, can play an important role in adding to students’ knowledge and confidence and in improving their REFL strategies. For example, after the intervention stage, students began to think about the title, and to use their own background knowledge to comprehend the text. The students employed, also, linguistic strategies such as decoding and, above all, the students abandoned the behaviour of reading for pronunciation in favour of reading for meaning. Despite the apparent efficacy of the alternative method, there are, inevitably, limitations related to the small-scale nature of the study and the time I had available to conduct the research. There are challenges, too, related to the students’ first language, the idiosyncrasies of the English language, the teacher training and continuing professional development of teachers, and the continuing political instability of Libya. The students’ lack of vocabulary and their difficulties with grammatical functions such as phrasal and prepositional verbs, forms which do not exist in Arabic, mean that REFL will always be challenging. Given such constraints, the ‘new’ methods I trialled and propose for adoption can only go so far in addressing students’ difficulties in REFL. Overall, the study indicates that the Libyan educational system is underdeveloped and under resourced with respect to REFL. My data indicates that the teacher participants have received little to no professional developmental that could help them improve their teaching in REFL and skills in teaching EFL. These circumstances, along with the perennial problem of large but varying class sizes; student, teacher and assessment expectations; and limited and often poor quality resources, affect the way EFL students learn to read in English. Against this background, the thesis concludes by offering tentative conclusions; reflections on the study, including a discussion of its limitations, and possible recommendations designed to improve REFL learning and teaching in Libyan universities.

A leitura no processo ensino aprendizagem em escolas da rede particular, na 4ª série do ensino fundamental em Belém do Pará: Uma busca para além decodificação

O presente estudo está baseado na Metodologia fenomenológica, com pesquisa bibliográfica e de campo. Apresenta como objetivo geral, analisar como se desenvolve o processo de ensino e aprendizagem de leitura, assim como, os estímulos e a prática do ato de ler em alunos de tenra idade em escolas particulares de Belém do Pará, em turmas da 4a Serie, do Ensino Fundamental. Tendo como objetivos específicos averiguar o ponto principal de indagação está centrado na questão se a leitura prática é apenas o desenvolvimento dos códigos linguísticos aprendidos, ou buscar não somente o processo de decodificar, sem considerar os aspectos mais abrangentes como a interpretação do texto, direcionado para o leitor ativo e atuante na compreensão das ideias do autor. Tal questionamento a respeito do processo de aprendizagem da leitura em nível fundamental das escolas particulares de Belém do Pará foi perguntado por meio de pesquisas de campo, a professores, alunos e para a coordenação, utilizando como instrumento de coleta de dados, questionário com perguntas abertas e fechadas de opinião entrevistas e grupos focais. No decorrer deste estudo, nota-se que para formar leitores mirins, serão exigidos alguns requisitos importantes, como a escolha de bons livros e atividades norteadoras de estimulação em classe e até mesmo fora dela. Afim de que principalmente o aluno em fase inicial de aprendizagem, seja e sinta-se preparado e ainda, conscientizado da importância da leitura para o seu questionamento crítico, como cidadão do futuro. Para tanto, fatores que interferem no processo de leitura, tais como: títulos variados, histórias que versem a respeito do imaginário cultural, textos direcionados ao público infantil, que despertem o interesse do alunado, além de apenas lei os códigos linguísticos na aquisição do texto, sem obtenção dos critérios interpretativos, que este possa evocar. A leitura é tida pela sociedade em geral, como um fator que pode levar o individuo a descobertas de novos patamares e horizontes sociais, mas somente indo além do mecanismo na apresentação dos textos cm sala de aula, é que o professor poderá atingir os níveis de compreensão integral do sistema escrito. Ensinando a ler, com elementos fundamentais para a iniciação de leitura interpretativa e proficiente no ensino fundamental. ABSTRACT: The present study is based upon the Phenomenological Methodology, with field and bibliographic research. It presents as a main objective the analysis on how the teaching and learning educational process develop upon the reading skills, as well as the encouragement and practice of reading in students of young ages in private schools in Belém, state of Pará (Brazil), in fourth grade groups, in elementary school. Having set specific goals, the search is centered in the practical reading ability matter, and if such ability is of linguistic code development solely learned or the search of not only the decoding process, without taking in consideration the broadening aspects, such as text comprehension, targeting the active reader especially when it comes to the author's ideas. Such discussion regarding the reading learning process in elementary levels in private schools in Belém, state of Para (Brazil) is questioned by field research, teachers, students and the coordination, using as data collecting instruments, questionnaires with open and closed questions, interviews and focal groups. Along the study, regarding the formation of young readers, it requires some aspects, such as, the choice of good titles and in-class stimulating activities or even outdoor ones, so the students - especially the ones in the initial phase of learning- are and feel prepared and even conscious of the importance of the reading for their critical thinking- as a future citizen. Therefore, the factors that may interfere in the reading process, for instance, varied titles, stories that verse towards the cultural imaginary, texts directed to the young public, that awaken the interest of the student body, beyond the linguistic codes acquired in the texts, not obtaining the interpreting criteria that it might evoke. The reading is, by the society, a fundamental factor that might lead the human being to discovering new standards and social horizons, but only going further the typical mechanisms in presenting the texts in class, is when the teacher may reach the whole levels of comprehension of the written system, teaching how to read, with fundamental elements to the initial reading in elementary school.

Modellbucher editi e inediti: dispositivi decodificatori della prassi teatrale brechtiana

I Modellbücher di Bertolt Brecht e del Berliner Ensemble si configurano come elementi dal carattere duplice e controverso, in bilico fra lo statuto di exempla per i futuri allestitori e quello di dispositivi interni al lavoro dell’ensemble, risultanti dinamiche della processualità scenica. L’interesse per la fotografia e il montaggio, che in Brecht assume molteplici forme – dando vita, ad esempio, ad opere come L’Abicí della guerra – si colloca al centro della composizione di tali strumenti, veri e propri esempi di assemblaggio di frammenti scenici. I Modellbücher trovano la propria ragion d’essere entro le dinamiche della regia brechtiana, di cui si prestano a tradurre le pratiche. La tesi indaga lo statuto dei Modellbücher, facendo riferimento alla storia degli studi e all’indagine archivistica condotta presso il Bertolt-Brecht-Archiv di Berlino fra 2018 e 2019.

La Bukowina e la "letteratura etnografica" di lingua tedesca

La Bukowina è una regione dell’impero asburgico ricordata come “eccezionale” per la compresenza e la tolleranza fra etnie, nonché per l’accoglienza unica della lingua tedesca. Questa narrazione proviene e dai nostalgici ricordi delle ultime generazioni di abitanti del luogo, che in seguito hanno vissuto la fine del “mondo di ieri”; e da un discorso propagandistico della Corona. La presente ricerca si propone di illustrare il paesaggio culturale della Bukowina nonché le reali modalità con cui la cultura dell’imperatore si insinuò nella regione. Nel decodificare il rapporto di superiorità con cui il tedesco si affacciava agli altri popoli – investigato con l’ausilio dei postcolonial studies –, il progetto propone come materia di studio un fenomeno letterario in voga a cavallo tra XIX e XX secolo, la “letteratura etnografica”, ispirato dall’affascinante molteplicità della Bukowina, nonché da una disciplina accademica che in quegli anni attirava molti studiosi e curiosi: l’etnografia. Questo tipo di letteratura si esprime attraverso diversi generi letterari, che spesso condividono il tratto della frammentarietà. Tra queste opere, la presente analisi si sofferma su tre esempi che mostrano un progressivo allontanamento dal metodo “scientifico” della disciplina etnografica, illustrando l’ampiezza dell’insieme “letteratura etnografica”: "Die Völkergruppen der Bukowina" (1884) di Ludwig Adolf Staufe Simiginowicz; "Aus Halb-Asien" (1876-1888) di Karl Emil Franzos; "Maghrebinische Geschichten" (1953), di Gregor von Rezzori.

Predicting corticospinal excitability from pre-TMS EEG using convolutional neural networks

The amplitude of motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) of the primary motor cortex (M1) shows a large variability from trial to trial, although MEPs are evoked by the same repeated stimulus. A multitude of factors is believed to influence MEP amplitudes, such as cortical, spinal and motor excitability state. The goal of this work is to explore to which degree the variation in MEP amplitudes can be explained by the cortical state right before the stimulation. Specifically, we analyzed a dataset acquired on eleven healthy subjects comprising, for each subject, 840 single TMS pulses applied to the left M1 during acquisition of electroencephalography (EEG) and electromyography (EMG). An interpretable convolutional neural network, named SincEEGNet, was utilized to discriminate between low- and high-corticospinal excitability trials, defined according to the MEP amplitude, using in input the pre-TMS EEG. This data-driven approach enabled considering multiple brain locations and frequency bands without any a priori selection. Post-hoc interpretation techniques were adopted to enhance interpretation by identifying the more relevant EEG features for the classification. Results show that individualized classifiers successfully discriminated between low and high M1 excitability states in all participants. Outcomes of the interpretation methods suggest the importance of the electrodes situated over the TMS stimulation site, as well as the relevance of the temporal samples of the input EEG closer to the stimulation time. This novel decoding method allows causal investigation of the cortical excitability state, which may be relevant for personalizing and increasing the efficacy of therapeutic brain-state dependent brain stimulation (for example in patients affected by Parkinson’s disease).

Performance Analysis of Topological Quantum Error Correcting Codes

In the last few years there has been a great development of techniques like quantum computers and quantum communication systems, due to their huge potentialities and the growing number of applications. However, physical qubits experience a lot of nonidealities, like measurement errors and decoherence, that generate failures in the quantum computation. This work shows how it is possible to exploit concepts from classical information in order to realize quantum error-correcting codes, adding some redundancy qubits. In particular, the threshold theorem states that it is possible to lower the percentage of failures in the decoding at will, if the physical error rate is below a given accuracy threshold. The focus will be on codes belonging to the family of the topological codes, like toric, planar and XZZX surface codes. Firstly, they will be compared from a theoretical point of view, in order to show their advantages and disadvantages. The algorithms behind the minimum perfect matching decoder, the most popular for such codes, will be presented. The last section will be dedicated to the analysis of the performances of these topological codes with different error channel models, showing interesting results. In particular, while the error correction capability of surface codes decreases in presence of biased errors, XZZX codes own some intrinsic symmetries that allow them to improve their performances if one kind of error occurs more frequently than the others.

Motor Unit Spike Trains Recontruction from sEMG Signals for Gesture Classification on a Low-Power Processing Platform

Hand gesture recognition based on surface electromyography (sEMG) signals is a promising approach for the development of intuitive human-machine interfaces (HMIs) in domains such as robotics and prosthetics. The sEMG signal arises from the muscles' electrical activity, and can thus be used to recognize hand gestures. The decoding from sEMG signals to actual control signals is non-trivial; typically, control systems map sEMG patterns into a set of gestures using machine learning, failing to incorporate any physiological insight. This master thesis aims at developing a bio-inspired hand gesture recognition system based on neuromuscular spike extraction rather than on simple pattern recognition. The system relies on a decomposition algorithm based on independent component analysis (ICA) that decomposes the sEMG signal into its constituent motor unit spike trains, which are then forwarded to a machine learning classifier. Since ICA does not guarantee a consistent motor unit ordering across different sessions, 3 approaches are proposed: 2 ordering criteria based on firing rate and negative entropy, and a re-calibration approach that allows the decomposition model to retain information about previous sessions. Using a multilayer perceptron (MLP), the latter approach results in an accuracy up to 99.4% in a 1-subject, 1-degree of freedom scenario. Afterwards, the decomposition and classification pipeline for inference is parallelized and profiled on the PULP platform, achieving a latency < 50 ms and an energy consumption < 1 mJ. Both the classification models tested (a support vector machine and a lightweight MLP) yielded an accuracy > 92% in a 1-subject, 5-classes (4 gestures and rest) scenario. These results prove that the proposed system is suitable for real-time execution on embedded platforms and also capable of matching the accuracy of state-of-the-art approaches, while also giving some physiological insight on the neuromuscular spikes underlying the sEMG.