1,720,955 research outputs found
Molecular simulations of monomeric sarcosine oxidase
Get PDFMonomeric sarcosine oxidase (MSOX) is a flavoenzyme that catalyzes the oxidation of sarcosine to form formaldehyde, glycine and hydrogen peroxide. MSOX also reduces molecular oxygen. There is no channel detected by experiment that transports oxygen from the protein surface to the buried active site for oxygen reduction. The main purpose of this work is to determine the oxygen transport channels in MSOX using molecular simulations. Here we used two methods: Molecular Dynamics (MD) and Single-sweep free energy reconstruction. Our results show that there exist two different pathways to the oxygen activation site: the so called si-side and re-side entry pathways. Between these two, the si-side entry pathway is more thermodynamically favorable. This highlights the efficiency of MSOX because the substrate and O2 access the catalytic center via two distinct pathways.M.S., Chemical and Biological Engineering -- Drexel University, 201
Recommended from our members
Molecular Dynamics Simulations of Microtubule-associated protein 1A/1B-light chain 3 (LC3) and its membrane associated form(LC3-II)
Get PDFAutophagy is the process by which cells eliminate its unwanted or dysfunctional components. A major step in autophagy is the formation of autophagosome, the double membrane that engulfs the unwanted cellular components. Dysregulation of autophagy affects neurodegenerative disorders, infectious diseases, cancer, and aging. In yeast, Atg8 protein is considered to play a crucial role in autophagosome maturation. Studies have shown that yeast lacking Atg8 protein form extremely small autophagosomes. Similarly, mammalian cells lacking Atg8 homologues produced “open” autophagosomes. Microtubule-associated protein (MAP) light chain3 (LC3), a human homologue of Atg8 protein is considered to play a major role in autophagosome maturation. However the exact mechanism by which Atg8/LC3 affects the autophagosome maturation is not completely known. A possible mechanism evolving from various studies is the following: Upon binding to the autophagosome, Atg8 family undergoes a conformational transition, which allows it to associate with another membrane-bound Atg8 in a trans-fashion. The proposed goals of this research include testing this hypothesis, identifying the stable conformations of LC3 and LC3-II (membrane bound LC3) and getting insights into the molecular mechanism by which LC3 influence autophagosome maturation. To accomplish this, we are performing Hamiltonian replica exchange molecular dynamics (HREMD) simulations on LC3 and on LC3-II. The most stable conformations of LC3, and LC3-II are identified via clustering analysis. As autophagy modulation is considered as a potential therapeutic target for various diseases, understanding the molecular mechanisms of different stages of autophagy is very important
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Get PDFWe 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
- …
