1,721,050 research outputs found
Systematic benchmarking of statistical methods to assess differential expression of circular RNAs
Full text linkCircular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data's statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs' performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments
Amplificatori dimensionali per l'utilizzo della microscopia a forza atomica in campo diagnostico
No full textI recenti sviluppi delle ricerche mirate all’immobilizzazione selettiva di biomolecole quali DNA, oligonucleotidi e proteine hanno aperto la strada ad un possibile utilizzo della microscopia a forza atomica come nuova tecnica di indagine diagnostica. La strategia generale prevede l’immobilizzazione su un supporto solido di una molecola complementare alla biomolecola di interesse, che possa legare quest’ultima in modo specifico e ne renda così possibile la successiva rilevazione tramite microscopia a forza atomica. Il limite inferiore di rilevabilità a fini diagnostici non risiede tanto nella concentrazione dell’analita (in quanto la microscopia a forza atomica è teoricamente in grado di rilevare la singola biomolecola immobilizzata sulla superficie del supporto) quanto piuttosto nelle dimensioni molecolari dell’analita stesso: essendo le minime dimensioni determinabili dipendenti dalla rugosità matriciale della superficie, l’utilizzo di un amplificatore di rugosità specifica, cioè di un “amplificatore dimensionale” della specifica biomolecola d’interesse, contribuisce ad abbassare la minima dimensione molecolare rilevabile a fini diagnostici dalla microscopia a forza atomica. Scopo del lavoro è stato quello di individuare un set di possibili amplificatori dimensionali di natura inorganica, superficialmente modificabili mediante l’inserimento di opportuni bio-gruppi funzionali tali da renderli atti ad un accoppiamento specifico con l’analita di interesse, e di mettere a punto un sistema modello per la titolazione quantitativa delle biomolecole oggetto di indagini diagnostiche.
Metodi
Il sistema modello preso in considerazione è centrato su un DNA virale quale biomolecola di interesse, per il quale sono state disegnate come molecole partner alcune sequenze complementari costituite da oligonucleotidi di 2030 basi. Come supporti solidi sono stati scelti vetrini silanizzati. Come amplificatori dimensionali sono state utilizzate nanosfere di lattice, di dimensioni 20-40-80 e 200 nm, funzionalizzate superficialmente con gruppi -COOH, sfruttati per il successivo accoppiamento delle nanosfere alle opportune molecole partner. Tutte le molecole partner usate contenevano un linker amminico utilizzato per la loro immobilizzazione chimica tramite carbodiimmidi ai gruppi –COOH presenti sia sulla superficie del supporto sia sulla superficie degli amplificatori dimensionali. Ogni stadio della procedura sperimentale è stato esaminato mediante microscopio a forza atomica, operando in tapping mode in soluzioni tamponate a pH 7.
Risultati
Le nanosfere della dimensione di 80nm sono risultate il miglior compromesso per il loro utilizzo come amplificatori dimensionali. La modulazione delle condizioni di forza ionica, pH e sonicazione per le procedure di lavaggio successive alla immobilizzazione su supporto solido hanno permesso di ridurre al minimo il binding aspecifico e di ottenere una riproduci bile curva di calibrazione per soluzioni contenenti complessi biomolecola-nanosfera in concentrazioni nel range 10-15 – 10-12M.
Conclusioni
Sono state ottenute superfici piatte chimicamente modificate per l’immobilizzazione specifica di complessi oligonucleotide-DNA-oligonucleotide, accoppiati a nanosfere funzionalizzate quali amplificatori dimensionali per la loro determinazione tramite microscopia a forza atomica in soluzione. È stata realizzata una modulazione quantitativa del binding specifico di complessi modello, utilizzabile per la titolazione quantitativa di varie biomolecole di interesse diagnostic
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
Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection
Full text linkMicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome some of its limitations by carefully integrating into the analysis the paired expression profiles of miRNAs and mRNAs. In this work, we show how the choice of a proper probe annotation for microarray platforms is an essential requirement to achieve good sensitivity in the identification of miRNA-mRNA interactions. We compare the results obtained from the analysis of the same expression profiles using both gene and transcript based custom CDFs that we have developed for a number of different annotations (ENSEMBL, RefSeq, AceView). In all cases, transcript-based annotations clearly improve the effectiveness of data integration and thus provide a more reliable confirmation of computationally predicted miRNA-mRNA interaction
Bioinformatic Analysis of Circular RNA Expression
No full textCircular RNAs (circRNAs) are stable RNA molecules generated by backsplicing that play regulatory functions through interaction with other RNA and proteins, as well as by encoding peptides. Dysregulation of circRNA expression can drive cancer development and progression with different mechanisms. CircRNAs are currently regarded as extremely attractive molecules in cancer research for the identification of new and possibly targetable disease regulatory networks and for the development of biomarkers for cancer diagnosis, prognosis definition, and monitoring. Using specific experimental and computational protocols, circRNAs can be identified through RNA-seq by spotting the reads spanning backsplice junctions, which are specific to circular molecules. In this chapter, we report a state-of-the-art computational protocol for a genome-wide analysis of circRNAs from RNA-seq data, which considers circRNA detection, quantification, and differential expression testing. Finally, we indicate how to determine circular transcript sequences and the resources for an in silico functional characterization of circRNAs
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