1,721,032 research outputs found
Minimal Dark Matter bound states at future colliders
No full textThe hypothesis that Dark Matter is one electroweak multiplet leads to predictive candidates with multi-TeV masses that can form electroweak bound states. Bound states with the same quantum numbers as electroweak vectors are found to be especially interesting, as they can be produced resonantly with large cross sections at lepton colliders. Such bound states exist e.g. if DM is an automatically stable fermionic weak 5-plet with mass M ≈ 14 TeV such that the DM abundance is reproduced thermally. In this model, a muon collider could resolve three such bound states. Production rates are so large that details of DM spectroscopy can be probed with larger statistics: we compute the characteristic pattern of single and multiple γ lines
Towards de novo RNA 3D Structure Prediction
Full text linkRNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which aim at the prediction of the three-dimensional (3D) native fold from the sole knowledge of the sequence. In a recent paper, we have introduced a scoring function for RNA structure prediction. Here, we analyze in detail the performance of the method, we underline strengths and shortcomings, and we discuss the results with respect to state-of-the-art techniques. These observations provide a starting point for improving current methodologies, thus paving the way to the advances of more accurate approaches for RNA 3D structure prediction
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
Stellar limits on scalars from electron-nucleus bremsstrahlung
Full text linkWe revisit stellar energy-loss bounds on the Yukawa couplings g B,L of baryophilic and leptophilic scalars φ. The white-dwarf luminosity function yields g B ≲ 7 × 10-13 and g L ≲ 4 × 10-16, based on bremsstrahlung from 12C and 16O collisions with electrons. In models with a Higgs portal, this also implies a bound on the scalar-Higgs mixing angle sinθ ≲ 2 × 10-10. Our new bounds apply for mφ ≲ 1 keV and are among the most restrictive ones, whereas for mφ ≲ 0.5 eV, long-range force measurements dominate. Besides a detailed calculation of the bremsstrahlung rate for degenerate and semi-relativistic electrons, we prove with a simple argument that non-relativistic bremsstrahlung by the heavy partner is suppressed relative to that by the light one by their squared-mass ratio. This large reduction was overlooked in previous much stronger bounds on g B. In an appendix, we provide fitting formulas (few percent precision) for the bremsstrahlung emission of baryophilic and leptophilic scalars as well as axions for white-dwarf conditions, i.e., degenerate, semi-relativistic electrons and ion-ion correlations in the “liquid” phase
A Nucleobase-Centric Coarse-Grained Model for Structure Prediction of RNA Fragments
No full textThe structural characterization of RNA usually poses additional challenges when compared to other biomolecular systems. For example, there is a relatively scarce amount of structural data available, which demands the development of three-dimensional structure prediction tools. In addition, full-resolution simulations can be a hard task not only because of the complexity of the interactions involved, but also due to the limitations of the current force fields. At this point, coarse-grained simulations are a good candidate to fill the gaps in this growing research field. The use of these techniques has rapidly increased in the past decades in the study of biological systems on which the experiments require an additional interpretation or where an atomistic computational approach results difficult or unfeasible. Nevertheless, the development of coarse-grained models involves the understanding of the main structural features of the original system, which can represent a challenge by itself.
In this work, we present a knowledge-base coarse-grained model for RNA structure prediction, representing each nucleotide by a single anisotropic particle. The mapping and the main interactions are designed to reproduce the geometrical distribution of the closest pairs of nucleotides, extracted from a set of ribosomal structures. The model is inspired in the ESCORE function [1], a knowledge-based scoring function that has been shown to perform better compared to fully atomistic techniques in identifying native-like structures from a set of decoys. Its minimalistic nature and successful application on a broad range of structures straightforwardly suggest a representation for a coarse-grained approach. We show the preliminary results of our simulations and discuss the role of pair interactions in the prediction of RNA structures.
[1] S. Bottaro, F. Di Palma and G. Bussi, “The Role of Nucleobase Interactions in RNA Structure and Dynamics”, Nucleic Acids Res., accepted
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
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
Full text linkIntroduction: Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts.
Methods
In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts.
Results
Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies.
Discussion and Conclusions
Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations
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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