1,720,968 research outputs found
MD simulation trajectory for Heterogenous lipid bilayer with 150mM CaCl2 concentration
No full textEquilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 73 Ca2+, 110 Cl2- , 18915 water (TIP3P) molecules
MD simulation trajectory for Heterogenous lipid bilayer with 150mM NaCl concentration
No full textEquilibrated symmetric heterogenous lipid bilayer simulation ran with Gromacs 2020.4, Force field= Charmm36m, 300ns, T=300K, composed of 152 POPC, 96 POPE, 20 POPS, 80 CHOL, 36 PSM, and 16 GM1 molecules, 92 Na+, 56 Cl- , 19348 water (TIP3P) molecules
Essays on the interplay between glycosaminoglycans and amyloid-β peptides
No full textIntrinsically disordered proteins (IDPs), which represent ~40% of the human proteome, play crucial roles in a variety of biological pathways and biomolecular assemblies. Monomeric IDPs such as amyloid-β (Aβ), can aggregate into insoluble, relatively inert, rigid structures called fibrils, but also much more toxic, soluble struc- tures of intermediate size and varying shapes, which are called oligomers. The toxic aggregates of Aβ peptide are implicated in the pathogenesis of Alzheimer’s disease (AD). In this thesis, we use in-silico approaches to model Aβ under different physiological and pathological conditions to unravel their effects on the structures and kinetics of the amyloid oligomers. We first highlight the ramifications of molecular mechanics parameters on the structural heterogeneity of Aβ and the aggregation process of various Aβ fragments. Next, we demonstrate how Aβ fragments aggregate in the presence of glycosaminoglycans. To this end, the conformational dynamics of different glycosaminoglycans was first elucidated to understand their behavior in the absence Aβ fragments. The conclusions from these investigations enabled us to identify force fields which predict Aβ structures and dynamics in agreement with experimental observations. From transition networks applied to the aggregation data we deduced the structural transitions during the early and intermediate stages of oligomer formation. Furthermore, we elucidated the intermolecular interactions between Aβ and glycosaminoglycans that transpire towards enhancing, stabilizing, or inhibition of Aβ aggregation behavior
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
The Effects of Different Glycosaminoglycans on the Structure and Aggregation of the Amyloid-β (16–22) Peptide
No full textAggregates of the amyloid-β (Aβ) peptide are implicated as a causative substance in Alzheimer’s disease. Molecular dynamics simulations provide valuable contributions for elucidating the conformational transitions of monomeric and aggregated forms of Aβ be it in solution or in the presence of other molecules. Here, we study the effects of four different glycosaminoglycans (GAGs), three sulfated ones and a nonsulfated one, on the aggregation of Aβ16–22. From experiments, it has been suggested that GAGs, which belong to the main components of the brain’s extracellular space, favor amyloid fibril formation. Our simulation results reveal that the binding of Aβ16–22 to the GAGs is driven by electrostatic attraction between the negative GAG charges and the positively charged K16 of Aβ16–22. While these interactions have only minor effects on the GAG and Aβ16–22 conformations at the 1 Aβ16–22/1 GAG ratio, at the 2:2 stoichiometry the aggregation of Aβ16–22 is considerably changed. In solution, the aggregation of Aβ16–22 is strongly influenced by K16–E22 attraction, leading to antiparallel β-sheets. In the presence of GAGs, on the other hand, the interaction of K16 with the GAGs increases the importance of the hydrophobic interactions during Aβ16–22 aggregation, which in turn yields parallel alignments. A templating and ordering effect of the GAGs on the Aβ16–22 aggregates is observed. In summary, this study provides new insight at the atomic level on GAG–amyloid interactions, strengthening the view that sulfation of the GAGs plays a major role in this context
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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