An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.

Global surveillance of cancer survival 1995–2009: analysis of individual data for 25 676 887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control.

METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75,000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights.

FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease.

INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems.

CD4+ T Cells Targeting Dominant and Cryptic Epitopes from Bacillus anthracis Lethal Factor

Anthrax is an endemic infection in many countries, particularly in the developing world. The causative agent, Bacillus anthracis, mediates disease through the secretion of binary exotoxins. Until recently, research into adaptive immunity targeting this bacterial pathogen has largely focused on the humoral response to these toxins. There is, however, growing recognition that cellular immune responses involving IFNγ producing CD4+ T cells also contribute significantly to a protective memory response. An established concept in adaptive immunity to infection is that during infection of host cells, new microbial epitopes may be revealed, leading to immune recognition of so called 'cryptic' or 'subdominant' epitopes. We analyzed the response to both cryptic and immunodominant T cell epitopes derived from the toxin component lethal factor and presented by a range of HLA-DR alleles. Using IFNγ-ELISpot assays we characterized epitopes that elicited a response following immunization with synthetic peptide and the whole protein and tested their capacities to bind purified HLA-DR molecules in vitro. We found that DR1 transgenics demonstrated T cell responses to a greater number of domain III cryptic epitopes than other HLA-DR transgenics, and that this pattern was repeated with the immunodominant epitopes, as a greater proportion of these epitopes induced a T cell response when presented within the context of the whole protein. Immunodominant epitopes LF457-476 and LF467-487 were found to induce a T cell response to the peptide, as well as to the whole native LF protein in DR1 and DR15, but not in DR4 transgenics. The analysis of Domain I revealed the presence of several unique cryptic epitopes all of which showed a strong to moderate relative binding affinity to HLA-DR4 molecules. However, none of the cryptic epitopes from either domain III or I displayed notably high binding affinities across all HLA-DR alleles assayed. These responses were influenced by the specific HLA alleles presenting the peptide, and imply that construction of future epitope string vaccines which are immunogenic across a wide range of HLA alleles could benefit from a combination of both cryptic and immunodominant anthrax epitopes.

Introducing the CTA concept

The Cherenkov Telescope Array (CTA) is a new observatory for very high-energy (VHE) gamma rays. CTA has ambitions science goals, for which it is necessary to achieve full-sky coverage, to improve the sensitivity by about an order of magnitude, to span about four decades of energy, from a few tens of GeV to above 100 TeV with enhanced angular and energy resolutions over existing VHE gamma-ray observatories. An international collaboration has formed with more than 1000 members from 27 countries in Europe, Asia, Africa and North and South America. In 2010 the CTA Consortium completed a Design Study and started a three-year Preparatory Phase which leads to production readiness of CTA in 2014. In this paper we introduce the science goals and the concept of CTA, and provide an overview of the project. © 2013 Elsevier B.V. All rights reserved.

Seven key actions to eradicate rheumatic heart disease in Africa: the Addis Ababa communiqué

Acute rheumatic fever (ARF) and rheumatic heart disease (RHD) remain major causes of heart failure, stroke and death among African women and children, despite being preventable and imminently treatable. From 21 to 22 February 2015, the Social Cluster of the Africa Union Commission (AUC) hosted a consultation with RHD experts convened by the Pan-African Society of Cardiology (PASCAR) in Addis Ababa, Ethiopia, to develop a 'roadmap' of key actions that need to be taken by governments to eliminate ARF and eradicate RHD in Africa. Seven priority areas for action were adopted: (1) create prospective disease registers at sentinel sites in affected countries to measure disease burden and track progress towards the reduction of mortality by 25% by the year 2025, (2) ensure an adequate supply of high-quality benzathine penicillin for the primary and secondary prevention of ARF/RHD, (3) improve access to reproductive health services for women with RHD and other non-communicable diseases (NCD), (4) decentralise technical expertise and technology for diagnosing and managing ARF and RHD (including ultrasound of the heart), (5) establish national and regional centres of excellence for essential cardiac surgery for the treatment of affected patients and training of cardiovascular practitioners of the future, (6) initiate national multi-sectoral RHD programmes within NCD control programmes of affected countries, and (7) foster international partnerships with multinational organisations for resource mobilisation, monitoring and evaluation of the programme to end RHD in Africa. This Addis Ababa communiqué has since been endorsed by African Union heads of state, and plans are underway to implement the roadmap in order to end ARF and RHD in Africa in our lifetime.

Characteristics, complications, and gaps in evidence-based interventions in rheumatic heart disease: the Global Rheumatic Heart Disease Registry (the REMEDY study)

AIMS: Rheumatic heart disease (RHD) accounts for over a million premature deaths annually; however, there is little contemporary information on presentation, complications, and treatment.

METHODS AND RESULTS: This prospective registry enrolled 3343 patients (median age 28 years, 66.2% female) presenting with RHD at 25 hospitals in 12 African countries, India, and Yemen between January 2010 and November 2012. The majority (63.9%) had moderate-to-severe multivalvular disease complicated by congestive heart failure (33.4%), pulmonary hypertension (28.8%), atrial fibrillation (AF) (21.8%), stroke (7.1%), infective endocarditis (4%), and major bleeding (2.7%). One-quarter of adults and 5.3% of children had decreased left ventricular (LV) systolic function; 23% of adults and 14.1% of children had dilated LVs. Fifty-five percent (n = 1761) of patients were on secondary antibiotic prophylaxis. Oral anti-coagulants were prescribed in 69.5% (n = 946) of patients with mechanical valves (n = 501), AF (n = 397), and high-risk mitral stenosis in sinus rhythm (n = 48). However, only 28.3% (n = 269) had a therapeutic international normalized ratio. Among 1825 women of childbearing age (12-51 years), only 3.6% (n = 65) were on contraception. The utilization of valvuloplasty and valve surgery was higher in upper-middle compared with lower-income countries.

CONCLUSION: Rheumatic heart disease patients were young, predominantly female, and had high prevalence of major cardiovascular complications. There is suboptimal utilization of secondary antibiotic prophylaxis, oral anti-coagulation, and contraception, and variations in the use of percutaneous and surgical interventions by country income level.

Numerical considerations for the implementation of a comprehensive composite damage model

A comprehensive continuum damage mechanics model [1] had been developed to capture the detailed
behaviour of a composite structure under a crushing load. This paper explores some of the difficulties
encountered in the implementation of this model and their mitigation. The use of reduced integration
element and a strain softening model both negatively affect the accuracy and stability of the
simulation. Damage localisation effects demanded an accurate measure of characteristic length. A
robust algorithm for determining the characteristic length was implemented. Testing showed that this
algorithm produced marked improvements over the use of the default characteristic length provided
by Abaqus. Zero-energy or hourglass modes, in reduced integration elements, led to reduced
resistance to bending. This was compounded by the strain softening model, which led to the formation
of elements with little resistance to deformation that could invert if left unchecked. It was shown,
through benchmark testing, that by deleting elements with excess distortions and controlling the mesh
using inbuilt distortion/hourglass controls, these issues can be alleviated. These techniques
contributed significantly to the viability and usability of the damage model.

Validation of a 3D damage model for predicting the response of composite structures under crushing loads

A 3D intralaminar continuum damage mechanics based material model, combining damage mode interaction and material nonlinearity, was developed to predict the damage response of composite structures undergoing crush loading. This model captures the structural response without the need for calibration of experimentally determined material parameters. When used in the design of energy absorbing composite structures, it can reduce the dependence on physical testing. This paper validates this model against experimental data obtained from the literature and in-house testing. Results show that the model can predict the force response of the crushed composite structures with good accuracy. The simulated energy absorption in each test case was within 12% of the experimental value. Post-crush deformation and the damage morphologies, such as ply splitting, splaying and breakage, were also accurately reproduced. This study establishes the capability of this damage model for predicting the responses of composite structures under crushing loads.

Motivation à apprendre des élèves et modèle d'autorité de l'enseignant étude du lien au travers des perceptions d'élèves de troisième d'enseignement agricole

Cette thèse s'inscrit dans le cadre d'une thématique d'interrelation recherche-formation-pratique. Elle a pour objectif principal d'étudier le lien entre les perceptions motivationnelles à apprendre d'élèves de troisième d'enseignement agricole et leur perception du modèle d'autorité de l'enseignant. Son caractère novateur repose sur l'interculturalité des approches utilisées: la motivation à apprendre empruntée aux études nord-américaines et le modèle d'autorité de l'enseignant empruntée aux études françaises. L'étape de recension des écrits nous a permis de préparer le terrain à un questionnaire de type quantitatif. Il comprend deux sections sur les modèles d'autorité (autoritaire et d'autorité) et trois sections sur les perceptions motivationnelles (valeur, sentiment de compétence et contrôlabilité) en lien avec deux matières: français et STP (sciences et techniques professionnelles). À la suite de cette investigation, les entrevues menées ont permis de découvrir deux cas de figure non envisagés au départ. Le premier est qu'un enseignant de tendance autoritaire sur l'axe relationnel n'altère pas la perception de la valeur de la matière si celui-ci autonomise et responsabilise les élèves et s'il est impliqué dans leur réussite. Il en est de même si cela rejoint les buts éloignés des élèves (brevet, projet personnel ou professionnel). Enfin, il ressort des résultats un troisième modèle d'autorité de l'enseignant inattendu qu'est l'enseignant manquant d'autorité. Il fait apparaître le besoin des élèves d'avoir un enseignant cadrant sur l'axe relationnel afin de contenir les apprentissages. Même si les apprentissages sont variés et novateurs et que l'enseignant est disponible et explique bien ses cours, ils ne sont pas suffisants pour motiver les élèves rencontrés. Il semble que le cadre donné par l'enseignant les sécurise, donne de la fiabilité à l'enseignant et de la valeur à la matière même s'il est de tendance autoritaire.

L'inscription des référents culturels : étude de l'intertextualité dans vingt premiers romans québécois de l'extrême contemporain

La scène littéraire québécoise accorde, depuis les années 2000, une attention grandissante à la relève. Critiques, chercheurs et journalistes braquent tour à tour leur projecteur sur les primo-romanciers, contribuant ainsi à les placer dans une catégorie à part des autres auteurs. Or, la publication d'un premier roman est une étape décisive dans l'établissement de la crédibilité intellectuelle d'un auteur. Pour cette raison, il est tenté d'écrire une oeuvre reflétant l'ensemble de son projet d'écriture et, par extension, l'essentiel de ses influences culturelles. Dans le but de comprendre ces influences formant la mémoire culturelle d'un écrivain, mais aussi de voir si un groupe de romanciers d'âge semblable partagent certaines d'entre elles, cette étude se penche sur vingt premiers romans québécois publiés entre 2000 et 2010. À l'aide du concept d'intertextualité et d'une analyse quantitative, elle tente plus exactement de relever et d'interroger les référents culturels observables dans ces textes et d'en faire ressortir les plus répandus. Ce mémoire vise donc, dans un premier temps, à tracer un portrait global des intertextes culturels mis en place dans les premiers romans du corpus afin de comprendre l'usage qu'en font les primo-romanciers et d'orienter la suite de la recherche. Dans un deuxième temps, elle s'intéresse à trois média desquels les écrivains tirent leurs référents, soit l'audiovisuel (comprenant le cinéma et la télévision), la musique et la littérature, et cherche à décrire de quoi est composée la mémoire culturelle des écrivains du corpus.

Entomofauna associated with the olive tree in southern Portugal

Since 2004 several studies have been carried out in order to identify the main insect species that usually inhabiting the olive ecosystem. The field trials have taken place in two olive groves, one situated in Olhão and the other one in Loulé, both in Algarve and also under Integrated Pest Management (IPM). The sampling techniques used differ according to their purpose (sticky traps, pheromone traps, pitfall traps and samples of aerial parts of the trees such as inflorescences, leaves, fruits and branches). Results showed that the main insect pests of olive tree in southern Portugal were the olive fruit fly Bactrocera oleae Gmelin (Diptera: Tephritidae) and the olive moth Prays oleae Bernard (Lepidoptera: Hyponeumetidae). Other insect pests were also found in our olive groves namely the olive psyllid Euphyllura olivina Costa (Homoptera: Psyllidae), the olive dark beetle Phloeotribus scarabaeoides Bernard (Coleoptera: Curculionidae), the mediterranean black scale Saissetia oleae (Olivier) (Homoptera: Coccidae) and the olive thrip Liothripes oleae Costa (Thysanoptera: Phlaeothripidae). Concerning the auxiliary insects that were found in our olives groves they belong to the following orders and families: Diptera (Syrphidae), Coleoptera (Carabidae, Coccinelidae and Staphylinidae), Hemiptera (Anthocoridae and Miridae), Neuroptera (Chrysopidae) and Hymenoptera (Braconidae, Encyrtidae, Eulophidae, Formicidae and Trichogrammatidae).

A tradução da Peregrinaçam de Fernão Mendes Pinto em Espanha, França, Inglaterra e Alemanha no século XVII

Este trabalho de investigação comparativista insere-se no âmbito das relações entretecidas pelos Estudos de Tradução e a Literatura Comparada, nomeadamente no que respeita ao conceito de tradução literária na Europa Ocidental do século XVII. Trata-se de um estudo intercultural, atendendo a que a tradução promove a mudança cultural decorrente de um processo de transferência intercultural com implicações literárias e ideológicas. Os textos que constituíram o nosso objeto de trabalho são a Peregrinaçam de Fernão Mendes Pinto (1614) e as primeiras traduções completas ou parciais para espanhol (1620), da autoria de Francisco de Herrera Maldonado, para francês (1628), de Bernard Figuier, para inglês (1653), de Henry Cogan, e para alemão (1671), dos editores Henrich e Dietrich Boom. No decorrer da análise comparativa, procurámos demonstrar o grau de (in)fidelidade de cada tradução, estabelecendo paralelismos e realçando os procedimentos tradutológicos adotados em cada versão, os quais revelam, claramente, contactos entre si e/ou condicionalismos culturais e ideológicos implícitos. Estudámos o modo como cada tradução adaptou a obra original ao gosto e aos códigos linguísticos e literários do seu público-alvo. No desenvolvimento do nosso trabalho, tivemos em mente os códigos tradutológicos do século XVII em Espanha, França, Inglaterra e Alemanha, em virtude de o nosso corpus ser constituído por textos publicados no decorrer desse período. Como metodologia de trabalho, delimitámos cinco momentos narrativos, no interior dos quais foram encontradas e analisadas comparativamente passagens consideradas exemplificativas das principais técnicas tradutivas características de cada texto e das inter-relações estabelecidas entre eles. Por fim, um outro objetivo nosso consistiu na avaliação do significado e da relevância da receção da tradução- -adaptação desta obra portuguesa naqueles contextos de chegada (no momento imediato e para além dele).