Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Best practice in the management of mild-to-moderately active ulcerative colitis and achieving maintenance of remission using mesalazine.

Optimizing treatment goals in ulcerative colitis requires recognizing the needs of patients. It is increasingly recognized that adapting treatment strategies aligned with patient needs can improve patient compliance and consequently minimize relapse rates. Tailoring of treatment strategies can improve not only patient quality of life, and decrease the number harmed by adverse events from more potent drugs, but can also save valuable healthcare costs by avoiding high-cost treatment interventions associated with acute ulcerative colitis. This review will consider several elements of mesalazine management from the patient perspective based on a range of clinical and patient-focused evidence. By highlighting patient preferences in disease management it is envisaged that this review will aid physicians to optimize treatment decisions with the different mesalazine preparations available.

Nouvelle procédure civile et espace judiciaire européen: actes du colloque de Lausanne du 27 janvier 2012

Nouveaux cahiers de linguistique française 30 Département de linguistique, Université de Genève Antoine AUCHLIN, Présentation Tim ROHRER et Mary Jean VIGNONE, The Bankers Go to Washington: Theory and Method in Conceptual Metaphor Analysis, Napoleon KATSOS et Chris CUMMINS, Scalar implicature : Theory, processing and acquisition, Jacques MOESCHLER, Pourquoi le sens est-il structuré ? Une approche vériconditionelle de la signification linguistique et du sens pragmatique, Joanna BLOCHOWIAK, Les questions enchâssant les verbes d'attitude dans le contexte d'explications, Cristina GRISOT et Bruno CARTONI, Une description bilingue des temps verbaux : étude contrastive en corpus, Jacques MOESCHLER, Cristina GISOT et Bruno CARTONI, Jusqu'où les temps verbaux sont-ils procéduraux ? Hasmik JIVANIAN, Relations causales épistémiques : Focalisation de parce que et contrefactualité, Cosmina-Maria HODOROAGA, Les traits démonstratifs de la citation, Maíra AVELAR MIRANDA, L'intégration entre gestes et prosodie : une vision incarnée, Tea PRSIR, L'étude du discours représenté dans le cadre de l'intégration expérientielle, Jean-Philippe GOLDMAN et Yves SCHERRER, Création automatique de dictionnaires bilingues d'entités nommées grâce à Wikipédia.

Expression of prox1, lymphatic endothelial nuclear transcription factor, in Kaposiform hemangioendothelioma and tufted angioma.

Kaposiform hemangioendothelioma (KHE) and tufted angioma (TA) are rare tumors mainly occurring in early childhood. Our recent results showed that ectopic overexpression of human Prox1 gene, a lymphatic endothelial nuclear transcription factor, promoted an aggressive behavior in 2 murine models of KHE. This dramatic Prox1-induced phenotype prompted us to investigate immunohistochemical staining pattern of Prox1, podoplanin (D2-40), LYVE-1, and Prox1/CD34 as well as double immunofluorescent staining pattern of LYVE-1/CD31 in KHE and TA, compared with other pediatric vascular tumors. For this purpose, we examined 75 vascular lesions: KHE (n=18), TA (n=13), infantile hemangioma (n=13), pyogenic granuloma (n=18), and granulation tissue (n=13). Overall, KHE and TA shared an identical endothelial immunophenotype: the neoplastic spindle cells were Prox1, podoplanin, LYVE-1, CD31, and CD34, whereas endothelial cells within glomeruloid foci were Prox1, podoplanin, LYVE-1, CD31, and CD34. The lesional cells of all infantile hemangiomas and pyogenic granulomas were negative for Prox1 in the presence of positive internal control. These findings provide immunophenotypic evidence to support a preexisting notion that KHE and TA are closely related, if not identical. Overall, our results show, for the first time, that Prox1 is an immunohistochemical biomarker helpful in confirming the diagnosis of KHE/TA and in distinguishing it from infantile hemangioma and pyogenic granuloma.

Bladder cancer documentation of causes: multilingual questionnaire, 'bladder cancer doc'

There is a considerable discrepancy between the number of identified occupational-related bladder cancer cases and the estimated numbers particularly in emerging nations or less developed countries where suitable approaches are less or even not known. Thus, within a project of the World Health Organisation Collaborating Centres in Occupational Health, a questionnaire of the Dortmund group, applied in different studies, was translated into more than 30 languages (Afrikaans, Arabic, Bengali, Chinese, Czech, Dutch, English, Finnish, French, Georgian, German, Greek, Hindi, Hungarian, Indonesian, Italian, Japanese, Kannada, Kazakh, Kirghiz, Korean, Latvian, Malay, Persian (Farsi), Polish, Portuguese, Portuguese/Brazilian, Romanian, Russian, Serbo-Croatian, Slovak, Spanish, Spanish/Mexican, Tamil, Telugu, Thai, Turkish, Urdu, Vietnamese). The bipartite questionnaire asks for relevant medical information in the physician's part and for the occupational history since leaving school in the patient's part. Furthermore, this questionnaire is asking for intensity and frequency of certain occupational and non-occupational risk factors. The literature regarding occupations like painter, hairdresser or miner and exposures like carcinogenic aromatic amines, azo dyes, or combustion products is highlighted. The questionnaire is available on www.ifado.de/BladderCancerDoc.

The association between alcohol screening scores and health status in male veterans.

OBJECTIVES: Alcohol use is associated with self-reported health status. However, little is known about the concurrent association between alcohol screening scores and patient perception of health. We evaluated this association in a sample of primarily older male veterans.METHODS: This secondary, cross-sectional analysis included male general medicine outpatients from 7 VA medical centers who returned mailed questionnaires. Screening scores from the Alcohol Use Disorders Identification Test Consumption (AUDIT-C) questionnaire were divided into 6 categories (0, 1­3, 4­5, 6­7, 8­9, and 10­12). Outcomes included scores on the 8 subscales and 2 component scores of the 36-item Short Form Health Survey (SF-36). Unadjusted and adjusted linear regression models were fit to characterize the association between AUDIT-C categories and SF-36 scores. Models were adjusted for demographic characteristics, smoking, and site?both alone and in combination with 14 self-reported comorbid conditions.RESULTS: Male respondents (n = 24,531; mean age = 63.6 years) represented 69% of those surveyed with the SF-36. After adjustment, a quadratic (inverted U-shaped) relationship was demonstrated between AUDIT-C categories and all SF-36 scores such that patients with AUDIT-C scores 4­5 or 6­7 reported the highest health status, and patients with AUDIT-C scores 0, 8­9, and =10 reported the lowest health status.CONCLUSIONS: Across all measures of health status, patients with the most severe alcohol misuse had significantly poorer health status than those who screened positive for alcohol misuse at mild or moderate levels of severity. The relatively good health status reported by patients with mild-moderate alcohol misuse might interfere with clinicians' acceptance and adoption of guidelines recommending that they counsel these patients about their drinking.

Cost-effectiveness of opportunistic versus organised mammography screening in Switzerland

BACKGROUND: Various centralised mammography screening programmes have shown to reduce breast cancer mortality at reasonable costs. However, mammography screening is not necessarily cost-effective in every situation. Opportunistic screening, the predominant screening modality in several European countries, may under certain circumstances be a cost-effective alternative. In this study, we compared the cost-effectiveness of both screening modalities in Switzerland. METHODS: Using micro-simulation modelling, we predicted the effects and costs of biennial mammography screening for 50-69 years old women between 1999 and 2020, in the Swiss female population aged 30-70 in 1999. A sensitivity analysis on the test sensitivity of opportunistic screening was performed. RESULTS: Organised mammography screening with an 80% participation rate yielded a breast cancer mortality reduction of 13%. Twenty years after the start of screening, the predicted annual breast cancer mortality was 25% lower than in a situation without screening. The 3% discounted cost-effectiveness ratio of organised mammography screening was euro11,512 per life year gained. Opportunistic screening with a similar participation rate was comparably effective, but at twice the costs: euro22,671-24,707 per life year gained. This was mainly related to the high costs of opportunistic mammography and frequent use of imaging diagnostics in combination with an opportunistic mammogram. CONCLUSION: Although data on the performance of opportunistic screening are limited, both opportunistic and organised mammography screening seem effective in reducing breast cancer mortality in Switzerland. However, for opportunistic screening to become equally cost-effective as organised screening, costs and use of additional diagnostics should be reduced.

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.

BACKGROUND: Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global contribution of conserved non-coding sequences to the transcriptional regulation of human genes is currently unknown. Deeply conserved elements shared between humans and teleost fish predominantly flank genes active during morphogenesis and are enriched for positive transcriptional regulatory elements. However, such deeply conserved elements account for <1% of the conserved non-coding sequences in the human genome, which are predominantly mammalian. RESULTS: We explored the regulatory potential of a large sample of these 'common' conserved non-coding sequences using a variety of classic assays, including chromatin remodeling, and enhancer/repressor and promoter activity. When tested across diverse human model cell types, we find that the fraction of experimentally active conserved non-coding sequences within any given cell type is low (approximately 5%), and that this proportion increases only modestly when considered collectively across cell types. CONCLUSIONS: The results suggest that classic assays of cis-regulatory potential are unlikely to expose the functional potential of the substantial majority of mammalian conserved non-coding sequences in the human genome.

Histoire discursive du "cinéma-vérité" : techniques, controverses, historiographie (1960-1970)

Histoire discursive du « cinéma-vérité ». Techniques, controverses, historiographie (1960-1970) retrace l'histoire du succès et de la disgrâce du label « cinéma vérité » en France qui, entre 1960 - date à laquelle Edgar Morin publie son essai programmatique « Pour un nouveau "cinéma vérité" » dans France Observateur - et 1964-65 - moment où la notion commence à perdre en popularité - sert de bannière à un mouvement cinématographique supposé renouveler les rapports entre cinéma et réalité. Une vingtaine de films - comme Chronique d'un été de Jean Rouch et Edgar Morin, Primary de Richard Leacock et Robert Drew, Les Inconnus de la terre ou Regard sur la folie de Mario Ruspoli, Hitler, connais pas de Bertrand Blier, Le Chemin de la mauvaise route de Jean Herman, Le Joli Mai de Chris Marker, La Punition de Jean Rouch ou Pour la Suite du monde de Michel Brault et Pierre Perrault - revendiquent cette étiquette ou y sont associés par la presse hexagonale qui y consacre des centaines d'articles. En effet, la sortie en salles de ces « films-vérité » provoque en France de virulentes controverses qui interrogent aussi bien l'éthique de ces projets où les personnes filmées sont supposées révéler une vérité intime face à la caméra, le statut artistique de ces réalisations, ou l'absence d'un engagement politique marqué des « cinéastes-vérité » devant les questions abordées par les protagonistes (par exemple la Guerre d'Algérie, la jeunesse française, la politique internationale). L'hypothèse à la base de cette recherche est que la production cinématographique qui se réclame du « cinéma-vérité » se caractérise par une étroite corrélation entre film et discours sur le film. D'une part car la première moitié de la décennie est marquée par de nombreuses rencontres entre les « cinéastes vérité », les critiques ou les constructeurs de caméras légères et de magnétophones synchrones ; rencontres qui contribuent à accentuer et à médiatiser les dissensions au sein du mouvement. D'autre part car la particularité de nombreux projets est d'inclure dans le film des séquences méta-discursives où les participants, les réalisateurs ou des experts débattent de la réussite du tournage. Ce travail montre que le succès du mouvement entre 1960 et 1964-65 ne se fait pas malgré une forte polémique, mais qu'au contraire, nombre de longs métrages intègrent la controverse en leur sein, interrogeant, sur un plan symbolique, l'abolition du filtre entre le film et son spectateur. Si les films qui s'inscrivent dans la mouvance du « cinéma vérité » octroient une large place à la confrontation, c'est parce que la « vérité » est pensée comme un processus dialectique, qui émerge dans une dynamique d'échanges (entre les réalisateurs de cette mouvance, entre les protagonistes, entre le film et son public). Les querelles internes ou publiques qui rythment ces quelques années font partie du dispositif « cinéma-vérité » et justifient de faire l'histoire de ce mouvement cinématographique par le biais des discours qu'il a suscité au sein de la cinéphilie française.

Le cinéma-vérité, films et controverses

Peut-on se réclamer du « cinéma » tout en prétendant rendre compte d'une « vérité »? Quelles sont les limites éthiques du dévoilement d'un individu face à une caméra ? Un cinéaste peut-il être pleinement « auteur » d'une oeuvre construite à partir de fragments de réel? Voilà quelques-unes des questions posées au début des années soixante par la sortie des films qui se revendiquent ou sont associés au « cinéma-vérité ». Proposée en 1960 par Edgar Morin, cette notion controversée sert durant quelques années de bannière à un mouvement cinématographique supposé renouveler les rapports entre film et réalité par une approche plus directe, un dispositif d'interactions avec les protagonistes, ou une démarche autoréflexive qui interroge en son sein le projet du film. Chronique d'un été de Jean Rouch et Edgar Morin, Les Inconnus de la terre et Regard sur la folie de Mario Ruspoli, les travaux de Richard Leacock pour la Drew Associates, Le Chemin de la mauvaise route de Jean Herman, Hitler, connais pas de Bertrand Blier, La Punition de Jean Rouch ou encore Le Joli Mai de Pierre Lhomme et Chris Marker : tous ces « films-vérité » renouvellent les débats et construisent de nouveaux clivages dans la cinéphilie française. Sans chercher à se positionner sur le contenu des polémiques, le présent ouvrage retrace pour la première fois l'histoire du mouvement « cinéma-vérité » en s'intéressant aux films (contexte de production, tournages, innovations techniques) et aux discours (articles, débats, tables rondes) qui les ont précédés, accompagnés et traversés. Grâce à de nombreuses sources inédites, Cinéma-vérité, films et controverses met au jour un phénomène d'une importance méconnue dans l'histoire du cinéma en France.

Nombres 11-12 et la question d'une rédaction deutéronomique dans le Pentateuque

(Résumé de l'ouvrage) The volume is presented to Professor C.H.W. Brekelmans in celebration of his 75th birthday. The editors were of the opinion that there could be no better way to honour Chris Brekelmans than with a collection of articles treating the "Deuteronomic" traditions found in the Book of Deuteronomy as well as in the so-called Tertrateuch, and Deuteronomistic History. In the past years, a renewed impetus has been given to the development of Deuteronomic Studies. The present Festschrift aims at contributing to the current debate which has a special interest in methodological questions regarding the identification and characterization of "Deuteronomistic" texts in the aforementioned complexes of Old Testament writings. The volume is divided into four sections. The first section offers a collection of articles which focus on the Book of Deuteronomy itself. The second section contains contributions dealing with Deuteronomic History. The third section is devoted to the relationship between the Deuteronomic - in the largest sense of the word - traditions and the Tetrateuch. The fourth and final section presents a collection of articles on a number of important issues, each of which offers its own direct or indirect contribution to the study of the Deuteronomi(sti)c literature and its relationship to the remaining texts of the Old Testament.

An integrated encyclopedia of DNA elements in the human genome.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.