1,723,659 research outputs found
Combining 3D-RISM calculation with hydropathic character for water selection: an application in docking with flexible explicit water
Full text linkDocking and virtual screening with explicit water has become a hot topic within the docking community in the past decade. It was suggested that the bridging water molecules, existed between the ligand and the receptor, are important contributors to binding free energy. Multiple methods are since developed, either through direct evaluation or scoring of crystal waters, or predictions for water positions when crystal waters are in absence. However, the likelihood of introducing human bias increases during the process of water selection. Moreover, wrong choices about water molecules will result in fault screening, giving ineffective candidates. Therefore, in our work, we have combined a well-established water-predicting method, 3D-RISM, and a relatively simple and efficient water selection criteria by evaluating hydropathic characteristic of water molecules. This flow of work has allowed automatic selection of water molecules between protein-ligand or protein-protein interface. We have observed optimistic results in predicting crystal water positions within the binding pocket using several benchmark systems. We will further combine these steps with flexible water docking, included in the PLANTS docking package, to improve virtual screening with explicit waters both in efficiency and accuracy
Combining 3D-RISM with hydrophatic characteristic water evaluation: first step preparation for further PLANTS virtual screening with flexible explicit water molecules
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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
Mid-Cretaceous oceanic red beds in the Umbria–Marche Basin, central Italy: Constraints on paleoceanography and paleoclimate
Full text linkDetailed studies of the mid-Cretaceous sedimentary strata in the Umbria–Marche Basin in Italy revealed that aside from severalwell-known organic-rich bblack shaleQ horizons that record OAEs, several varicolored, mainly reddish horizons indicate oxicconditions at the ocean bottom. Eight such horizons have been identified in Aptian–Cenomanian sequences in the Umbria–MarcheBasin. The dysoxic/oxic beds alternate regularly but not cyclically and seem to be the result of non-random processes. Theiroccurrence is not a completely random process. The duration of deposition of these oceanic red beds (ORBs) varies from ~ 0.13 my(ORB4) recorded in the Ticinella primula zone, to ~4.54 my for ORB1, which spans the Globigerinelloides ferreolensis zone to theTicinella bejaouaensis zone in the Piobbico core.Mid-Cretaceous ORBs are not a local phenomenon because they occur in the Tethyan deposits in the Southern and AustrianAlps, the Carpathians, the Northern Caucasus, the central North Atlantic, in northeastern England and in the western Himalayas.They provide evidence for periodic changes in redox conditions at the ocean bottom. Such changes could have been caused bychanges in bioproductivity, basin geometry, sedimentation rates, paleocirculation and/or production of bottom waters with highercontent of dissolved oxygen in response to changes in paleoclimate. We suggest that the periodic inflow of colder, moreoxygenated bottom waters was the probable cause of ORBs development, either as a result of changes in the ocean bottomtopography, or as a result of brief cool climate periods. However, reliable proxies for changes in deep ocean circulation are stilllacking. If ORBs were the result of the paleoclimate and, therefore, indirectly caused by changes in CO2 in atmosphere, theydocument the increased sensitivity and instability of the mid-Cretaceous climate. Thus, changes in ocean dynamics were on a scaleof several hundred thousand years to several million years, which has not been considered by most theories of CO2 cycling, mid-Cretaceous greenhouse paleoclimate and paleocean dynamics
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
Technological entrepreneurship with Chinese characteristics: the Qrobot case
No full textThe chapter off er an overview of how technological entrepreneurship works in China using the case of Qrobot –a brand new product that interacts with Tencent’s QQ, China’s most used instant messaging service and the world’s largest community. More specifi cally, the brief life of Qrobot is used to illustrate how government policies, government research institutes, entrepreneurs, enterprises and investors worked together, from the development of the technology to its introduction to the market, describing what has been referred to as ‘technological entrepreneurship with Chinese characteristics’.
In doing so a comprehensive picture of the actors, roles and dynamics of Chinese technological entrepreneurship will be off ered, along with a discussion of the eff ects of such factors as government and its research institutions’ direct and indirect support, foreign companies, transnational
communities and the overall environment. In addition the diff erences and similarities with Western counterparts will be highlighted. Concerning the latter, conclusions will refl ect on whether there is really something like a ‘technological entrepreneurship with Chinese characteristics’ or if the differences underlined are just the temporary eff ects of China’s transitional state. In this regard the study of contingencies is suggested as a viable
research direction to answer this question, and some thoughts are given on how this kind of research should be crafted
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