1,721,228 research outputs found
Advances in the identification and analysis of allele-specific expression
Full text linkAllele-specific expression (ASE) is essential for normal development and many cellular processes but, if impaired, can result in disease. ASE is a feature of organisms with genomes consisting of more than one set of homologous chromosomes. The higher the number of chromosome sets (ploidy) per cell, the higher the potential complexity of ASE. Humans, for instance, are diploid (except germ cells, which are haploid), resulting in multiple possible expression states in time and space for each set of alleles. ASE is invoked and modulated by both genetic and epigenetic changes, affecting the underlying DNA sequence or chromatin of each allele, respectively. Although numerous methods have been developed to assay ASE, they usually require RNA to be available and are dependent upon genetic polymorphisms (such as single nucleotide polymorphisms (SNPs)) to differentiate between allelic transcripts. The rapid convergence to second-generation sequencing as the method of choice to examine genomic, epigenomic and transcriptomic data enables an integrated and more general approach to define and predict ASE, independent of SNPs. This 'Omni-Seq' approach has the potential to advance our understanding of the biology and pathophysiology of ASE-mediated processes by elucidating subtle combinatorial effects, leading to the accurate delineation of sub-phenotypes with consequential benefit for improved insight into disease etiology
The epigenomic interface between genome and environment in common complex diseases
No full textThe epigenome plays the pivotal role as interface between genome and environment. True genome-wide assessments of epigenetic marks, such as DNA methylation (methylomes) or chromatin modifications (chromatinomes), are now possible, either through high-throughput arrays or increasingly by second-generation DNA sequencing methods. The ability to collect these data at this level of resolution enables us to begin to be able to propose detailed questions, and interrogate this information, with regards to changes that occur due to development, lineage and tissue-specificity, and significantly those caused by environmental influence, such as ageing, stress, diet, hormones or toxins. Common complex traits are under variable levels of genetic influence and additionally epigenetic effect. The detection of pathological epigenetic alterations will reveal additional insights into their aetiology and how possible environmental modulation of this mechanism may occur. Due to the reversibility of these marks, the potential for sequence-specific targeted therapeutics exists. This review surveys recent epigenomic advances and their current and prospective application to the study of common disease
Two new species and synopsis of Chusquea subg. Platonia (Poaceae: Bambusoideae: Chusqueinae) in Bolivia and a new record for Peru
No full textGuerreiro, Carolina, Olivera, J. José Alegría, Rúgolo De Agrasar, Ma. E., Beck, Stephan G., Vega, Andrea S. (2014): Two new species and synopsis of Chusquea subg. Platonia (Poaceae: Bambusoideae: Chusqueinae) in Bolivia and a new record for Peru. Phytotaxa 183 (4): 224-238, DOI: 10.11646/phytotaxa.183.4.2, URL: http://dx.doi.org/10.11646/phytotaxa.183.4.
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
Human-specific CpG 'beacons' identify human-specific prefrontal cortex H3K4me3 chromatin peaks.
Full text linkBackground: Targeted recruitment of chromatin-modifying enzymes to clusters of CpG dinucleotides contributes toward the formation of accessible chromatin. By interprimate comparison we previously identified the set of nonpolymorphic human-specific CpGs (CpG 'beacons') and revealed that these loci were enriched for human disease traits. Due to their human-specific CpG density change, extreme CpG 'beacon' clusters (≥20 CpG beacons/kb) were predicted to identify permissive chromatin peaks within the human genome. Aim: We set out to explore these sequence-defined regions for evidence of an active chromatin signature. Results: Using available comparative primate epigenomic data from neurons of the prefrontal cortex, we show that these CpG 'beacon' clusters are indeed enriched for being human-specific H3K4me3 peaks (χ(2): p < 2.2 × 10(-16)) and thus predictive of permissive chromatin states. These sequence regions had a higher predictive value than previous selective analyses. We also show that both human-specific H3K4me3 and CpG 'beacon' clusters are increased within current and ancestral telomeric regions, supporting an association with recombination, which is higher towards the distal ends of chromosomes. Conclusion: Therefore, CpG-focused comparative sequence analysis can precisely pinpoint chromatin structures that contribute to the human-specific phenotype and further supports an integrated approach in genomic and epigenomic studies
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
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
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