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BackgroundIn diploid organisms, phasing is the problem of assigning the heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation such as structural variants. However, current phasing tools typically only phase small variants, leaving larger structural variants unphased.MethodsWe developed HiPhase, a tool that jointly phases SNVs, indels, and structural variants. The main benefits of HiPhase are 1) dual mode allele assignment for detecting structural variants, 2) a novel application of the A*-algorithm to phasing, and 3) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions.ResultsIn our assessment, HiPhase produced an average phase block NG50 of 493 kb with 933 switchflip errors and fully phased 95.2% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, and structural variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation.Availabilityhttps://github.com/PacificBiosciences/HiPhase

Spinal muscular atrophy, a leading cause of early infant death, is caused by biallelic mutations of theSMN1gene. Sequence analysis ofSMN1is challenging due to high sequence similarity with its paralogSMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is impossible to identify silent carriers (2+0) with two copies ofSMN1on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-lengthSMN1andSMN2haplotypes, determines the gene copy numbers and calls phased variants using long-read PacBio HiFi data. TheSMN1andSMN2copy number calls by Paraphase are highly concordant with orthogonal methods (99.2% forSMN1and 100% forSMN2). We applied Paraphase to 438 samples across five ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified majorSMN1andSMN2haplogroups and characterized their co-segregation through pedigree-based analyses. We identified twoSMN1haplotypes that form a common two-copySMN1allele in African populations. Testing positive for these two haplotypes in an individual with two copies ofSMN1gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7-3.0%). Extending beyond simple copy number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.

Expansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 40 neurodegenerative diseases. However, repeat expansions have not been systematically examined in contexts beyond neurological disorders. In a specific form of cancer, termed microsatellite instability (MSI), mutations accumulate in short ( Citation Format: Graham S. Erwin, Gamze Gursoy, Rashid Al-Abri, Christian Hoerner, Egor Dolzhenko, Michael Eberle, Alice Fan, John Leppert, Mark Gerstein, Michael P. Snyder. A genome-wide atlas of recurrent repeat expansions in human cancer genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 55.

Digital technologies have profoundly changed our research practices, our editing and publication practices, and how we exchange information. The means have certainly changed, but these striking changes have also influenced the methods and meaning of writing, the concepts of writer and reader, and the methods of access, the tools and methods of distributing texts, images, sounds, etc. Literature has played a major role in the development of cultural domains; it still holds a prominent place, perhaps even more so today, as our current context is greatly associated to the predominance of the textual form. The explosion of data and the transformation of knowledge, both in terms of the quality of available information and the manner of representing it, have furthermore had a considerable impact on human and social sciences research.This special issue, which brings texts together from presentations made at the 2015 Digital Humanities colloquium at Concordia University, offers an overview of current trends in theory and practice observed in the digital humanities domain in French, more specifically in the sphere of production and distribution of knowledge in the human and social sciences. ResumeLes technologies numeriques ont profondement modifie nos pratiques de recherche, d’edition, de publication et d’echanges d’informations. Les supports ont certes change, mais les bouleversements ont aussi touche les modalites et le sens de l’ecriture, les concepts d’auteur et de lecteur, les modalites d’acces, les supports et les modes de diffusion de textes, d’images, de sons, etc. Si la litterature a toujours joue un role capital dans la formation des categories culturelles, elle s’approprie de maniere peut-etre encore plus marquee aujourd’hui, une place fondamentale, puisque le contexte actuel est largement associe a une predominance de la forme textuelle. L’explosion des donnees et la transformation des savoirs, tant au plan de la quantite d’information disponible que de la maniere de la representer, a en outre un impact considerable sur la recherche en sciences humaines et sociales.Ce dossier special, qui rassemble des textes decoulant de communications presentees lors du colloque Humanites numeriques 2015 a l’Universite Concordia, propose un apercu des tendances theoriques et pratiques observees actuellement dans le domaine des humanites numeriques en francais, plus precisement dans la sphere de production et de diffusion du savoir dans les sciences humaines et sociales. Mots cles: Humanites numeriques; outils de recherche; tendances theoriques et pratiques; edition electronique; pedagogie numerique; visualisation

Cet article se veut exploratoire en deux temps : une piste de réflexion sur l’impact du numérique sur les sciences humaines, et une lecture de l’essai « Le nénuphar et l’araignée » de Claire Legendre, publié le 4 février 2015 chez Les Allusifs. Notre hypothèse est qu’il est nécessaire de jeter les bases d’une théorie et d’une pensée du numérique, comme de poursuivre et de favoriser l’implémentation de nouveaux outils de recherche conçus par et pour les humanités, en lien direct avec les questions d’édition, de diffusion, d’encodage, de fouille, de curation, ou encore de visualisation et de représentation des données textuelles, sonores et visuelles. Cet article propose ainsi une première piste d’exploration de l’usage de ces nouvelles possibilités pour la littérature québécoise., This article is both a reflexion on the impact of digital culture on social sciences and humanities, and a theoretical reading of Claire Legendre’s essay « Le nénuphar et l’araignée », published on 4 February 2015 by Les Allusifs. Our hypothesis is that it is important to think simultaneously about the theoretical aspect of digital culture along with the pragmatic implementation of new research tools developed for and by social sciences and humanities researchers. The latter are tied directly to a new generation of critical editions with new possibilities of data mining or representing an array of data, be it sound, visual, or text based. This article thus offers a preliminary case study for exploring these new possibilities within Quebec literature.

Parallelement a l’histoire du developpement d’Internet et du web, une autre histoire est fondamentale pour comprendre les enjeux de l’edition numerique : celle des humanites numeriques. Il y a encore quelques decennies, on pouvait penser que les ordinateurs et les technologies numeriques etaient destines uniquement aux sciences dures, les sciences exactes dont le calcul et les mathematiques sont les principaux outils. Cette idee est manifestement fausse aujourd’hui : le numerique habite l’ens...

In his biography of Leigh Hunt, Anthony Holden asserts, “Alongside Wordsworth, who largely eschewed literary London, Hunt’s was the longest nineteenth-century literary life, with the widest circle of acquaintance and as large a claim as any to the shaping of literary opinion” (2). In my earlier monograph, Leigh Hunt and the London Literary Scene, I illustrated the kinds of change that Hunt’s reputation went through over a 30-year timespan. That study attempted to elaborate the problematic of his position within the London literary and political scene between the years 1805 and 1828, the contributions he made to British literature and journalism, and his public standing at the end of the romantic period. Since Hunt’s life is obviously too complex to be rendered fully in any single study, the idea was not to attempt an exhaustive history, but rather to present a starting point for further inquiry into Hunt’s career as a writer and public figure under the reign of Queen Victoria.

A qualidade na educação tem diferentes definições, que dependem do ponto de vista sob qual é analisado. A gestão da qualidade na educação busca a melhoria dos processos, independente da definição aplicável. O objetivo deste artigo é analisar os benefícios da implementação de um sistema de gestão da qualidade na educação com base no ciclo PDCA. O artigo foi escrito com base em um levantamento bibliográfico. A metodologia PDCA tem quatro etapas: planejar, executar, controlar e estabelecer ações que possam corrigir os rumos e encaminhar para um novo ciclo. Ao planejar, estabelecer objetivos e metas, construir métricas, acompanhar indicadores, analisar resultados e propor planos de ações preventivas ou corretivas, estão sendo identificadas as necessidades de interferência e oportunidades de melhoria na educação. O presente estudo identificou alguns casos onde a aplicação da metodologia PDCA em processos educacionais comprova os estudos teóricos que reforçam a importância da implementação de gestão da qualidade na educação.

We analyze the errors of optical 3D area sensors in measuring geometric parameters, taking planarity as our example. If the planarity of the surface is comparable to the repeat accuracy, the measured planarity is in general unduly poor and the object appears less planar. This error manifests itself to the observer as an apparently systematic offset. This error arises from the interplay of typical properties of optical sensors with standardized methods of interpretation. The standardized interpretation methods for planarity require the use of the maximum departures of the measured heights from the fitted (reference) plane. Optical area sensors can yield very large values for this maximum deviation, even when the standard deviation is small, because these sensors measure up to a million points at a time. The probability of a large maximum error is much lower when the measurement is done on a few points, as it usually is with mechanical sensors. As a consequence, the qualification of optical 3D area sensors calls for a correction with respect to mechanical sensors. In this article, we use methods of extreme-value statistics to determine the errors that occur. Once the error is known, the measured results can be corrected and incorporated into known and standardized methods of interpretation.

0 0 1 149 823 Universite de Montreal 6 1 971 14.0 Normal 0 21 false false false EN-US JA X-NONE This article discusses the relationship between digital humanities and disciplinary boundaries in the last decade, primarily in the context of the national project Synergies . It offers first an overview of Synergies as a concrete example of the way technological change impacts the very notion of disciplines by trying to create a platform that was interdisciplinary by nature, then discusses the creation of a new Digital Humanities centre in Quebec— Le Centre de recherche interuniversitaire sur les humanites numeriques – and the ways it was conceived as encompassing a range of disciplinary approach.

Le constat duquel part notre idée de colloque est très simple : tout le monde s’accorde à dire que la réflexion sur le numérique est une priorité, mais l’on est encore loin d’avoir une définition précise des méthodes pour développer cette dernière, des œuvres et des auteurs à considérer comme référents dans ce domaine et d’un langage qui puisse être partagé par la communauté des chercheurs et compris par le grand public. L’analyse du monde numérique doit donc être en premier lieu une réflexion sur la culture numérique et non seulement sur les outils. Pareillement, avec le changement des supports, des modalités de publication, des mécanismes de visibilité, d’accessibilité et de circulation des contenus, c’est l’ensemble de notre rapport au savoir qui se trouve remis en question. Il est nécessaire de mettre en place une recherche qui puisse avoir une fonction structurante dans le développement d’une théorie et d’une pensée du numérique mais aussi dans l’implémentation de nouveaux outils de recherche et de visualisation conçus pour les humanités. Le numérique touche désormais l’ensemble de notre vie. Nous vivons dans une société numérique et dans une culture numérique. Les transformations qui ont engendré ce monde numérique se sont produites très rapidement et n’ont pas laissé le temps de développer une réflexion structurée capable de les comprendre. Il est impératif de créer au plus vite des repères théoriques permettant de situer notre culture numérique par rapport à notre vision du monde et aux catégories conceptuelles qui ont structuré nos valeurs, nos traditions et notre imaginaire.

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies., Wellcome Trust (London, England) (Core Award 090532/Z/09/Z), Wellcome Trust (London, England) (Senior Investigator Award 095552/Z/11/Z ), Wellcome Trust (London, England) (WT095908), Wellcome Trust (London, England) (WT109497), Wellcome Trust (London, England) (WT098051), Wellcome Trust (London, England) (WT086084/Z/08/Z), Wellcome Trust (London, England) (WT100956/Z/13/Z ), Wellcome Trust (London, England) (WT097307), Wellcome Trust (London, England) (WT0855322/Z/08/Z ), Wellcome Trust (London, England) (WT090770/Z/09/Z ), Wellcome Trust (London, England) (Major Overseas program in Vietnam grant 089276/Z.09/Z), Medical Research Council (Great Britain) (grant G0801823), Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I02593X/1), Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I021213/1), Zhongguo ke xue ji shu qing bao yan jiu suo. Office of 863 Programme of China (2012AA02A201), National Basic Research Program of China (2011CB809201), National Basic Research Program of China (2011CB809202), National Basic Research Program of China (2011CB809203), National Natural Science Foundation of China (31161130357), Shenzhen Municipal Government of China (grant ZYC201105170397A), Canadian Institutes of Health Research (grant 136855), Quebec Ministry of Economic Development, Innovation, and Exports (PSR-SIIRI-195), Germany. Bundesministerium für Bildung und Forschung (0315428A), Germany. Bundesministerium für Bildung und Forschung (01GS08201), Germany. Bundesministerium für Bildung und Forschung (BMBF-EPITREAT grant 0316190A), Deutsche Forschungsgemeinschaft (Emmy Noether Grant KO4037/1-1), Beatriu de Pinos Program (2006 BP-A 10144), Beatriu de Pinos Program (2009 BP-B 00274), Spanish National Institute for Health (grant PRB2 IPT13/0001-ISCIII-SGEFI/FEDER), Japan Society for the Promotion of Science (fellowship number PE13075), Marie Curie Actions Career Integration (grant 303772), Fonds National Suisse del la Recherche, SNSF, Scientifique (31003A_130342), National Center for Biotechnology Information (U.S.) (U54HG3067), National Center for Biotechnology Information (U.S.) (U54HG3273), National Center for Biotechnology Information (U.S.) (U01HG5211), National Center for Biotechnology Information (U.S.) (U54HG3079), National Center for Biotechnology Information (U.S.) (R01HG2898), National Center for Biotechnology Information (U.S.) (R01HG2385), National Center for Biotechnology Information (U.S.) (RC2HG5552), National Center for Biotechnology Information (U.S.) (U01HG6513), National Center for Biotechnology Information (U.S.) (U01HG5214), National Center for Biotechnology Information (U.S.) (U01HG5715), National Center for Biotechnology Information (U.S.) (U01HG5718), National Center for Biotechnology Information (U.S.) (U01HG5728), National Center for Biotechnology Information (U.S.) (U41HG7635), National Center for Biotechnology Information (U.S.) (U41HG7497), National Center for Biotechnology Information (U.S.) (R01HG4960), National Center for Biotechnology Information (U.S.) (R01HG5701), National Center for Biotechnology Information (U.S.) (R01HG5214), National Center for Biotechnology Information (U.S.) (R01HG6855), National Center for Biotechnology Information (U.S.) (R01HG7068), National Center for Biotechnology Information (U.S.) (R01HG7644), National Center for Biotechnology Information (U.S.) (DP2OD6514), National Center for Biotechnology Information (U.S.) (DP5OD9154), National Center for Biotechnology Information (U.S.) (R01CA166661), National Center for Biotechnology Information (U.S.) (R01CA172652), National Center for Biotechnology Information (U.S.) (P01GM99568), National Center for Biotechnology Information (U.S.) (R01GM59290), National Center for Biotechnology Information (U.S.) (R01GM104390), National Center for Biotechnology Information (U.S.) (T32GM7790), National Center for Biotechnology Information (U.S.) (R01HL87699), National Center for Biotechnology Information (U.S.) (R01HL104608), National Center for Biotechnology Information (U.S.) (T32HL94284), National Center for Biotechnology Information (U.S.) (HHSN268201100040C), National Center for Biotechnology Information (U.S.) (HHSN272201000025C), Lundbeck Foundation (grant R170-2014-1039, Simons Foundation (SFARI award SF51), National Science Foundation (U.S.) (Research Fellowship DGE-1147470)

The thirteenth annual meeting of the North American Society for the Study of Romanticism took place August 13–16, 2005 in Montreal, Canada, sponsored by Université de Montréal. The conference was held in conjunction with the seventh biennial meeting of the International Gothic Association (August 11–14) and was the first major collaborative effort between NASSR and IGA. The theme for both conferences was “Deviance and Defiance,” to underscore the fact that in recent years the interrelation of Gothic and Romantic studies has emerged as a central topic of scholarly study.

This essay proposes to read one more time the issue of homosexuality in Mary Shelley's first novel, "Frankenstein". In order to offer a new angle on the homosexual component of Victor Frankenstein's relationship with his creature when next teaching this most canonical Romantic novel, this essay considers Shelley's work alongside four film adaptations : James Whale's 1931 "Frankenstein", Whale's 1935 "The bride of Frankenstein", Richard O'Brien's 1975 "The rocky horror picture show", and Kenneth Branagh's 1994 "Mary Shelley's Frankenstein". [...]

In his well-known analysis of the evolution of sexuality in society in "Making sexual history", Jeffrey Weeks comments that, following a series of major challenges throughout the twentieth century (ranging from Freud's work to the challenges of feminism and queer politics), "sexuality becomes a source of meaning, of social and political placing, and of individual sense of self". [...]

Compte rendu de la presentation de la piece « Count Basil » de Joanna Baillie montee par la compagnie Horizon Theatre lors du Congres 2004 de la North American society for the study of romanticism (NASSR).