1,720,957 research outputs found
Large scale analysis of protein stability in OMIM disease related human protein variants
Full text linkModern genomic techniques allow to associate several Mendelian human diseases to single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears to assume a particular relevance in annotating whether a single residue substitution can or cannot be associated to a given disease. Thermodynamic properties of human proteins and of their disease related variants are lacking. In the present work, we take advantage of the available three dimensional structure of human proteins for predicting the role of disease related variations on the perturbation of protein stability
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
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
A large-scale investigation on the Enhancer-Promoter interaction mediated by transcription factors
Full text linkContesto
Il differenziamento dei tessuti durante lo sviluppo embrionale dei mammiferi richiede una complessa regolazione dell'espressione genica che può essere modulata da enhancer distali. Geni coinvolti nello sviluppo sono fiancheggiati da sequenze altamente conservate che potrebbero essere enhancer distali di tali geni. Uno dei possibili meccanismi per la regolazione della trascrizione è la formazione di un'ansa tra enhancer e promotore mediata da fattori di trascrizione specifici.
Metodologie/Risultati
Per studiare l'interazione enhancer-promotore abbiamo generato un set di 1011 Coppie Enhancer-Promotore (CEP) accoppiando 702 enhancer, coinvolti nello sviluppo e validati sperimentalmente, ai 621 promotori più prossimi. Su enhancer e promotori accoppiati sono stati predetti Siti di Legame dei Fattori di Trascrizione (SLFT) specifici per l'organismo umano. Utilizzando metodi statistici, partendo da un set di 2837 Coppie di Fattori di Trascrizione (CFT), sono state filtrate 364 CFT significative, composte da 196 Fattori di Trascrizione (FT). Queste sono state successivamente validate consultando diverse fonti di informazione disponibili e abbiamo osservato che il 98% dei FT significativi sono presenti nell'interattoma umano. L'analisi delle loro interazioni indica che il 96% delle CFT sono separate da due o meno proteine intermedie. Il 99% delle CFT sono composte da FT espressi in tessuti comuni. Dallo stesso set di CEP e SLFT sono stati identificati 48 bicluster significativi composti da 22 FT e 222 CEP e osservato che il 92% di questi FT sono condivisi con le CFT. I bicluster contenevano da 2 a 6 FT e dopo una comparazione con le CFT ipotizziamo che i bicluster potrebbero evidenziare meccanismi di regolazione più fini.
Conclusioni
L'analisi computazionale integra informazioni provenienti da diverse risorse sperimentali, supporta la nozione che l'accoppiamento/raggruppamento di FT è alla base di interazioni a lungo raggio biologicamente rilevanti di enhancer dello sviluppo e contribuisce alla caratterizzazione dei meccanismi di regolazione genica dello sviluppo dei mammiferi.Background
Development of mammalian tissues rely on complex regulations of tissue specific gene expression, possibly due to distant-acting transcriptional enhancers. Flanking regions of important developmental genes contain highly conserved sequences, supporting the notion that these regions are distal enhancers of their flanking genes. One possible mechanism of gene transcription regulation is the “enhancer-promoter” looping, mediated by sequence-specific transcription factors.
Methodology/Principal Findings
In order to investigate mechanisms of enhancer-promoter interaction, we generated 1011 Enhancer-Promoter Pairs (EPP) by coupling 702 in vivo validated developmental enhancers and their nearest 621 promoters. We predicted human-specific Transcription Factors Binding Sites (TFBSs) to the paired enhancers and promoters. From an initial set of 2837 Transcription Factor Pairs (TFPs) and by adopting a statistical approach, we filtered 364 significant TFPs, comprising 196 transcription factors (TFs). We then validated our finding by extracting information from presently available databases and found that 98% of significant TFs are part of the human interactome. The analysis of their interaction network indicates that 96% of the interacting pairs are from zero to two proteins apart. Moreover, 99% of TFPs are composed by TFs expressed in the same tissues.
From the same sets of EPPs and TFBSs we also identified 48 significant biclusters composed by 22 TFs and 222 EPPs and found that 92% of these TFs are shared with the TFPs. Biclusters contained from 2 to 6 TFs and after a comparison with TFPs we speculate that biclusters could point out mechanisms of a finer regulation.
Conclusions
Our computational analysis, integrating information from different experimental resources, supports the notion that transcription factor pairing/grouping is at the basis of biologically relevant long-distance interactions of developmental enhancers and add to the characterization of complex gene regulation mechanisms in mammal development
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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