1,720,978 research outputs found
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties
No full textWe present a coarse-grain protein model PaLaCe (Pasi–Lavery–Ceres)
that has been developed principally to allow fast computational studies
of protein mechanics and to clarify the links between mechanics and
function. PaLaCe uses a two-tier protein representation with one to
three pseudoatoms representing each amino acid for the main nonbonded
interactions, combined with atomic-scale peptide groups and some side
chain atoms to allow the explicit representation of backbone hydrogen
bonds and to simplify the treatment of bonded interactions. The PaLaCe
force field is composed of physics-based terms, parametrized using
Boltzmann inversion of conformational probability distributions derived
from a protein structure data set, and iteratively refined to reproduce
the experimental distributions.
PaLaCe has been implemented in the MMTK simulation package and can
be used for energy minimization, normal mode calculations, and molecular
or stochastic dynamics. We present simulations with PaLaCe that test
its ability to maintain stable structures for folded proteins, reproduce
their dynamic fluctuations, and correctly model large-scale, force-induced
conformational changes
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties
No full textWe present a coarse-grain protein model PaLaCe (Pasi–Lavery–Ceres)
that has been developed principally to allow fast computational studies
of protein mechanics and to clarify the links between mechanics and
function. PaLaCe uses a two-tier protein representation with one to
three pseudoatoms representing each amino acid for the main nonbonded
interactions, combined with atomic-scale peptide groups and some side
chain atoms to allow the explicit representation of backbone hydrogen
bonds and to simplify the treatment of bonded interactions. The PaLaCe
force field is composed of physics-based terms, parametrized using
Boltzmann inversion of conformational probability distributions derived
from a protein structure data set, and iteratively refined to reproduce
the experimental distributions.
PaLaCe has been implemented in the MMTK simulation package and can
be used for energy minimization, normal mode calculations, and molecular
or stochastic dynamics. We present simulations with PaLaCe that test
its ability to maintain stable structures for folded proteins, reproduce
their dynamic fluctuations, and correctly model large-scale, force-induced
conformational changes
sj-docx-1-wso-10.1177_17474930221085443 – Supplemental material for Long-term anxiety in spontaneous intracerebral hemorrhage survivors
No full textSupplemental material, sj-docx-1-wso-10.1177_17474930221085443 for Long-term anxiety in spontaneous intracerebral hemorrhage survivors by Giuseppe Scopelliti, Barbara Casolla, Grégoire Boulouis, Grégory Kuchcinski, Solène Moulin, Didier Leys, Hilde Hénon, Charlotte Cordonnier and Marco Pasi in International Journal of Stroke</p
sj-pdf-2-wso-10.1177_17474930211059636 - Supplemental material for Early-onset delirium after spontaneous intracerebral hemorrhage
No full textSupplemental material, sj-pdf-2-wso-10.1177_17474930211059636 for Early-onset delirium after spontaneous intracerebral hemorrhage by Federico Marrama, Maéva Kyheng, Marco Pasi, Matthieu Pierre Rutgers, Solène Moulin, Marina Diomedi, Didier Leys, Charlotte Cordonnier, Hilde Hénon and Barbara Casolla in International Journal of Stroke</p
sj-pdf-1-wso-10.1177_17474930211059636 - Supplemental material for Early-onset delirium after spontaneous intracerebral hemorrhage
No full textSupplemental material, sj-pdf-1-wso-10.1177_17474930211059636 for Early-onset delirium after spontaneous intracerebral hemorrhage by Federico Marrama, Maéva Kyheng, Marco Pasi, Matthieu Pierre Rutgers, Solène Moulin, Marina Diomedi, Didier Leys, Charlotte Cordonnier, Hilde Hénon and Barbara Casolla in International Journal of Stroke</p
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
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