1,721,303 research outputs found
Universal annotation of the human genome through integration of over a thousand epigenomic datasets
Full text linkAbstract
Background: Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative ‘stacked modeling’ approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges.
Results: Using a version of ChromHMM enhanced for large-scale applications, we apply the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, with the learned model denoted as the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we use in characterizing each state. Compared to per-cell-type annotations, the full-stack annotations directly differentiate constitutive from cell type specific activity and is more predictive of locations of external genomic annotations.
Conclusions: The full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing per-cell-type annotations for studying the non-coding human genome
Letter calling for urgent help - From the family of Dr Cu Huy Ha Vu
No full text[ndlr] Publiée sur le site Bauxite Viet Nam, nous reproduisons ici la lettre de Nguyen Thi Duong Ha, l'épouse de l'avocat Cu Huy Ha Vu : un appel au secours pour son époux dont la santé s'est dégradée après 9 jours de grève de la faim. Hanoi, 4 June 2013 LETTER CALLING FOR URGENT HELP From the family of Dr Cu Huy Ha Vu To the attention of: - The Vietnamese people inside the country and overseas; - The Party and Nation Leaders with conscience; - The patriotic Personalities, Intellectuals, rel..
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Recommended from our members
Vietnam ::the party vs. legal activist Cu Hay Ha Vu.
No full text"On November 5, 2010, Ho Chi Minh City police arrested Dr. Cu Huy Ha Vu, a prominent legal activist and scion of an influential political family. The arrest marked the end of a 17-month struggle between Dr. Vu and some of the most powerful political figures in the country, including Prime Minister Nguyen Tan Dung. Five months later, on April 4, 2011, the Hanoi People's Court sentenced Dr. Vu to seven years in prison on the charge of conducting propaganda against the government under article 88 of Vietnam's penal code. Critics, however, charge that Dr. Vu was imprisoned simply for exercising his right to peaceful expression. In June 2009, Dr. Vu filed a lawsuit against the prime minister for authorizing Chinese bauxite mining in Vietnam's Central Highlands, followed by a second lawsuit in October 2010 against the prime minister for prohibiting class action petitions. Dr. Vu publicly denounced high-ranking leaders for corruption and illegal activities. In June 2010, he accused Lt. Gen. Vu Hai Trieu of the Ministry of Public Security of ordering cyber-attacks against approximately 300 websites opposed by the Vietnamese government. Three months later, he alleged that Le Thanh Hai, Ho Chi Minh City Communist Party general secretary, forcibly confiscated land from the relatives of "martyred" soldiers killed during the French-Vietnam War. In the months following Dr. Vu's arrest, many sectors of Vietnamese society joined in a remarkable outpouring of support for him. Independent bloggers demanded his release in online petitions. Democratic advocacy groups, such as Bloc 8406, and local religious communities issued public statements of solidarity. Catholic parishes in Hanoi and Nam Dinh conducted candlelight vigils attended by thousands of people to pray for Dr. Vu's exoneration. Statements, appeals, and legal motions issued by his wife, the lawyer Nguyen Thi Duong Ha, and his extended family have drawn a remarkable level of public attention to the violation of Dr. Vu's rights. The Party vs. Legal Activist Cu Huy Ha Vu illuminates Dr. Vu's background, depicts his past and present activities, and exposes the Vietnamese government's campaign to silence and suppress one of its most high-profile critics. It also sheds light upon the growing capacity and resourcefulness of Vietnamese lawyers, activists, bloggers, and ordinary citizens to struggle for civil rights, due process, and freedom of speech."--P. [4] of cover
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
