1,721,075 research outputs found
Focus on In Silico Aptamer Synthesis New Food for Thought
Full text linkThe use of aptamers (short single strands of DNA or RNA) in therapy, diagnosis and early detection of illness is a challenging field of research.
Aptamers are artificially produced, tailored to best fit a specific target, and are a competitive alternative to antibodies. The in vivo procedures to
synthetize aptamers are in continuous development, enlarging the scenario of the possible targets and improving the effectiveness of the products.
However, as of today, these methods are still quite time consuming and expensive to allow mass production. On the other side, guessing the 3D
structure of macromolecules is the task of several computational procedures, which have, over time, refined their predictive power and that can be
used to look for the complexes with the highest stability. In the near future, hopefully, the joint use of in vitro and in silico techniques will accelerate
and ameliorate the selection procedure. At the moment nor the in vitro neither the insilico procedures are flawless
A validation strategy for in silico generated aptamers
Full text linkThe selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A
novel strategy is proposed to validate the reliability of the 3D structures of a group of anti- Angiopoietin-2
aptamers, produced in silico by using free software. In a previous literature these aptamers were processed both
in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS
experiment. Computational expectations and experimental outcomes did not agree.
The procedure here proposed consists of three steps: a. the production of a large set of conformations for each
candidate aptamer; b. the rigid docking upon the receptor; c. the topological and electrical characterization of
the products. Steps a. and b. allow a global binding score of the ligand-receptor complexes based on the dis-
tribution of the "effective affinity", i.e. the sum of the conformational and the docking energies. Step c. employs a
complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the
ligand-receptor complexes. Finally, the results are discussed and compared with the literature on the same
aptamers. The computational predictions are in good agreement with the known experimental measurements
In-silico studies of Macromolecules as Sensors
No full textPhotosensitive proteins are extremely interesting, since they can regulate many functional processes in living cells, through the change of their structure in response to light absorption. This activation produces processes such as photosynthesis and phototaxis, or biomass, which can be used as renewable form of energy. Moreover, optogenetics and superresolution fluorescence microscopy approaches have triggered the generation of genetically modified photosensitive proteins. Due to these implications, the characterization of photosensitive proteins and their functioning is of crucial importance in real life. This review aims to collect the fundamental theoretical issues and the prominent advances in dealing with photosensitive proteins, with particular attention to the modeling of the behavior and organization of these molecules in the realm of Proteotronics. Together with the most interesting results, we recall some computational tools developed to achieve these results. The overview is completed by some open questions that emerge in this field of research
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
- …
