Efficient, Dependable Storage of Human Genome Sequencing Data

A compreensão do genoma humano impacta várias áreas da vida. Os dados oriundos do genoma humano são enormes pois existem milhões de amostras a espera de serem sequenciadas e cada genoma humano sequenciado pode ocupar centenas de gigabytes de espaço de armazenamento. Os genomas humanos são críticos porque são extremamente valiosos para a investigação e porque podem fornecer informações delicadas sobre o estado de saúde dos indivíduos, identificar os seus dadores ou até mesmo revelar informações sobre os parentes destes. O tamanho e a criticidade destes genomas, para além da quantidade de dados produzidos por instituições médicas e de ciências da vida, exigem que os sistemas informáticos sejam escaláveis, ao mesmo tempo que sejam seguros, confiáveis, auditáveis e com custos acessíveis. As infraestruturas de armazenamento existentes são tão caras que não nos permitem ignorar a eficiência de custos no armazenamento de genomas humanos, assim como em geral estas não possuem o conhecimento e os mecanismos adequados para proteger a privacidade dos dadores de amostras biológicas. Esta tese propõe um sistema de armazenamento de genomas humanos eficiente, seguro e auditável para instituições médicas e de ciências da vida. Ele aprimora os ecossistemas de armazenamento tradicionais com técnicas de privacidade, redução do tamanho dos dados e auditabilidade a fim de permitir o uso eficiente e confiável de infraestruturas públicas de computação em nuvem para armazenar genomas humanos. As contribuições desta tese incluem (1) um estudo sobre a sensibilidade à privacidade dos genomas humanos; (2) um método para detetar sistematicamente as porções dos genomas que são sensíveis à privacidade; (3) algoritmos de redução do tamanho de dados, especializados para dados de genomas sequenciados; (4) um esquema de auditoria independente para armazenamento disperso e seguro de dados; e (5) um fluxo de armazenamento completo que obtém garantias razoáveis de proteção, segurança e confiabilidade a custos modestos (por exemplo, menos de $1/Genoma/Ano), integrando os mecanismos propostos a configurações de armazenamento apropriadasThe understanding of human genome impacts several areas of human life. Data from human genomes is massive because there are millions of samples to be sequenced, and each sequenced human genome may size hundreds of gigabytes. Human genomes are critical because they are extremely valuable to research and may provide hints on individuals’ health status, identify their donors, or reveal information about donors’ relatives. Their size and criticality, plus the amount of data being produced by medical and life-sciences institutions, require systems to scale while being secure, dependable, auditable, and affordable. Current storage infrastructures are too expensive to ignore cost efficiency in storing human genomes, and they lack the proper knowledge and mechanisms to protect the privacy of sample donors. This thesis proposes an efficient storage system for human genomes that medical and lifesciences institutions may trust and afford. It enhances traditional storage ecosystems with privacy-aware, data-reduction, and auditability techniques to enable the efficient, dependable use of multi-tenant infrastructures to store human genomes. Contributions from this thesis include (1) a study on the privacy-sensitivity of human genomes; (2) to detect genomes’ privacy-sensitive portions systematically; (3) specialised data reduction algorithms for sequencing data; (4) an independent auditability scheme for secure dispersed storage; and (5) a complete storage pipeline that obtains reasonable privacy protection, security, and dependability guarantees at modest costs (e.g., less than$1/Genome/Year) by integrating the proposed mechanisms with appropriate storage configurations

Respiratory muscle training with normocapnic hyperpnea improves ventilatory pattern and thoracoabdominal coordination, and reduces oxygen desaturation during endurance exercise testing in COPD patients

Background: Few data are available about the effects of respiratory muscle training with normocapnic hyperpnea (NH) in COPD. The aim is to evaluate the effects of 4 weeks of NH (Spirotiger®) on ventilatory pattern, exercise capacity, and quality of life (QoL) in COPD patients. Methods: Twenty-six COPD patients (three females), ages 49-82 years, were included in this study. Spirometry and maximal inspiratory pressure, St George Respiratory Questionnaire, 6-minute walk test, and symptom-limited endurance exercise test (endurance test to the limit of tolerance [tLim]) at 75%-80% of peak work rate up to a Borg Score of 8-9/10 were performed before and after NH. Patients were equipped with ambulatory inductive plethysmography (LifeShirt®) to evaluate ventilatory pattern and thoracoabdominal coordination (phase angle [PhA]) during tLim. After four supervised sessions, subjects trained at home for 4 weeks 10 minutes twice a day at 50% of maximal voluntary ventilation. The workload was adjusted during the training period to maintain a Borg Score of 5-6/10. Results: Twenty subjects completed the study. After NH, maximal inspiratory pressure significantly increased (81.5±31.6 vs 91.8±30.6 cmH2O, P<0.01); exercise endurance time (+150 seconds, P=0.04), 6-minute walk test (+30 meters, P=0.03), and QoL (-8, P<0.01) all increased. During tLim, the ventilatory pattern changed significantly (lower ventilation, lower respiratory rate, higher tidal volume); oxygen desaturation, PhA, and dyspnea Borg Score were lower for the same work intensity (P<0.01, P=0.02, and P<0.01, respectively; one-way ANOVA). The improvement in tidal volume and oxygen saturation after NH were significantly related (R2=0.65, P<0.01). Conclusion: As expected, NH improves inspiratory muscle performance, exercise capacity, and QoL. New results are significant change in ventilatory pattern, which improves oxygen saturation, and an improvement in thoracoabdominal coordination (lower PhA). These two facts could explain the reduced dyspnea during the endurance test. All these results together may play a role in improving exercise capacity after NH training

The role of translanguaging in ELF advice sessions for asylum seekers

This chapter explores the role of translanguaging in ELF advice practices at a UK charity supporting refugees and asylum seekers. Previous research has highlighted how multilingualism is an essential aspect of ELF (Jenkins 2015) and the role of multilingual resources has received increased attention in the latest conceptualizations and linguistic analysis. However, the contribution and nature of multilingualism in relation to ELF need to be further investigated. This study addresses the role of translanguaging in ELF high stakes environments, such as advice services for refugees and asylum seekers. In this chapter, I first explore the notion of translanguaging, and then explain the linguistic ethnographic approach taken to collect and analyze the data. The qualitative analysis of the data shows the complexity of advice practices in relation to the use of multilingual resources in ELF, and demonstrates how translanguaging can be used for at least three functions, i.e. pedagogical, explanatory and interpersonal

Large eddy simulation with wall-stress model: an application to turbulent compressible channel flow

In questo lavoro di tesi si vuole descrivere la teoria e l'implementazione di un modello di parete basato su un sistema di equazioni differenziali ordinarie applicato alla tecnica di Large Eddy Simulation (LES). Questa tecnica è stata usata per simulare un flusso turbolento compressibile in un canale.ope

Special Section on Critical Pedagogy

The seven articles that constitute this Special Section relate to the area of critical pedagogy. Since Graham Crookes’s anniversary article on critical language pedagogy (2021) the number of submissions concerning this topic has increased exponentially. Given their common theme, I thought it would be a good idea to gather the submissions in a Special Section. Special Sections, unlike Special Issues, are not curated by guest editors and do not aim to be exhaustive representations of the field, but simply draw together studies that contribute in different ways to a certain area, and what follows is a very simple introduction to the area of critical pedagogy. Critical pedagogy is an approach to teaching that aims to develop students’ critical understanding of the world and is based on values of social justice. In fact, most people would say that critical pedagogy is ‘teaching for social justice’. In this approach, teachers are not merely teaching skills, but are engaged in the political and social context and make this relevant for their students. Therefore, the role of the teacher is to raise critical questions, pose problems and facilitate students in addressing the issues that are relevant to them. Classroom content, teaching priorities, and curricula are negotiated anew between the students and the teacher, in a dialogue that is participatory and places the students at the centre. When used for languages, especially English, this approach then challenges the view of the ELT profession as the teaching of linguistic skills detached from reality and makes teaching something intrinsically political (Akbari 2008). Seeing English language teaching as a political activity also requires problematizing any form of dominant knowledge and discourse, even problematizing English and its power in relation to aspects of colonization, discrimination, and oppression. All the papers in this Special Section relate critical pedagogy in different ways—I hope you enjoy reading them

Incursões metodológicas para o estudo da recepção midiática: o caso das migrações contemporâneas desde as perspectivas européia e latino-americana

O texto propõe o levantamento e a discussão de implicações metodológicas para o estudo das migrações contemporâneas como instância de recepção midiática a partir de experiências de pesquisa no contexto europeu (Espanha) e latino-americano (Brasil) e desde diferentes perspectivas qualitativas e quantitativas. Uma primeira implicação diz respeito às fronteiras e inter-relações entre instâncias midiáticas e não midiáticas no marco da noção de ethos midiatizado. Uma segunda faz referência às possibilidades de demarcação, no universo da recepção, das incidências, entre a população imigrante e não imigrante, desse ethos midiatizado sobre as migrações contemporâneas. Uma terceira e última perspectiva aponta para as implicações identitárias das experiências migratórias na configuração de especificidades de lógicas e estratégias de usos das mídias.The work proposes to identify and discuss the methodological implications for the study of contemporary migrations as instances of mediatic reception on the basis of research experience in Europe (Spain) and Latin America (Brazil) and from different qualitative and quantitative perspectives. One first implication refers to frontiers and inter-relations amongst mediatic and non-mediatic instances marks of the notion of mediatised ethos. A Second refers to the possibilities of demarcation in the universe of reception, of the incidence, amongst the immigrant an non-immigrant populations, of this mediatised ethos concerning contemporary migrations. A third and last perspective pays attention to the identity implications of migrationary experiences in the configuration of the specific logics and strategies of media use

ELLIPSIS AS A MARKER OF INTERACTION IN SPOKEN DISCOURSE

In this article, we discuss strategies for interaction in spoken discourse, focusing on ellipsis phenomena in English. The data comes from the VOICE corpus of English as a Lingua Franca, and we analyse education data in the form of seminar and workshop discussions, working group meetings, interviews and conversations. The functions ellipsis carries in the data are Intersubjectivity, where participants develop and maintain an understanding in discourse; Continuers, which are examples of back channel support; Correction, both self- and other-initiated; Repetition; and Comments, which are similar to Continuers but do not have a back channel support function. We see that the first of these, Intersubjectivity, is by far the most popular, followed by Repetitions and Comments. These results are explained as consequences of the nature of the texts themselves, as some are discussions of presentations and so can be expected to contain many Repetitions, for example. The speech event is also an important factor, as events with asymmetrical power relations like interviews do not contain so many Continuers. Our clear conclusion is that the use of ellipsis is a strong marker of interaction in spoken discourse

Género y prostitución en Brasil : narrativas sobre ser prostituta en espacios comunicacionales de Internet

Considerando el debate actual en torno a la temática de la prostitución en el escenario brasileño, el presente trabajo busca mapear y analizar las narrativas acerca de la prostitución y la experiencia de ser prostituta que aparecen en disputa en los espacios comunicacionales, especialmente en Internet. Partimos de la noción conceptual de que las narrativas producen conocimiento sobre la sociedad y que Internet es un espacio relevante en la producción y circulación de ideas que fundamentan el debate público sobre cuestiones de género y sexualidad. En términos metodológicos, el artículo propone un análisis de contenido de las publicaciones acerca del género y la prostitución en espacios de Internet así como de las percepciones de mujeres prostitutas capturadas en un trabajo de campo en el Núcleo de Estudios de la Prostitución, entidad situada en Porto Alegre, Brasil, y vinculada a la Red Brasileña de Prostitutas. El análisis hace evidente que, a pesar de la movilización de un debate público en torno de la prostitución, la experiencia subjetiva de las mujeres prostitutas es poco contemplada y visualizada

Bosnian St. Louis: Between Two Worlds

Presentation and conversation with Bosnian St. Louis authors Patrick McCarthy & Akif Cogo. Reception at 5 pm. Reading at 5:30 pm followed by a discussion and book signing (copies available for purchase courtesy of Left Bank Books). Free and open to the public