1,721,007 research outputs found
Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models
Full text linkCircular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.Alexander von Humboldt-Stiftung https://doi.org/10.13039/100005156Max Plank Societ
The ionic states of iodobenzene studied by photoionization and ab initio configuration interaction and DFT computations
Full text linkNew valence electron photoelectron spectra of iodobenzene obtained using synchrotron radiation have been recorded. Ionization energies (IEs) determined using multi-configuration SCF calculation (MCSCF) procedures confirmed the adiabatic IE order as: X2B1 < A2A2 < B2B2 < C2B1. Although it is convenient to retain C2v labelling, there is an evidence that minor distortion to CS symmetry occurs at the MCSCF level for the C state. The fifth ionization process shown to be D2A1 exhibits dissociation to C6H5+ + I both in the experimental and theoretical studies. The calculated Franck- Condon vibrational spectral envelopes, including hot band contributions, for the first four ionic states reproduce the observed peak positions and intensities with reasonable accuracy. In order to simulate the observed spectra, different bandwidths are required for different states. The increase in the required bandwidths for the A2A2 and B2B2 states is attributed to internal conversion to lower-lying states. The presence of relatively high intensity sequence bands leads to asymmetry of each of the X2B1 state bands
A Unique Synchrotron-Radiation Flow Linear Dichroism Spectroscopy Facility for the Study of Oriented Macromolecules
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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
Interpretation of the vacuum ultraviolet photoabsorption spectrum of iodobenzene by ab initio computations
Full text linkIdentification of many Rydberg states in iodobenzene, especially from the first and fourth ionization energies (IE1 and IE4, X2B1 and C2B1), has become possible using a new ultraviolet (UV) and vacuum-ultraviolet (VUV) absorption spectrum, in the region 29000-87000 cm−1 (3.60-10.79 eV), measured at room temperature with synchrotron radiation. A few Rydberg states based on IE2 (A2A2) were found, but those based on IE3 (B2B2) are undetectable. The almost complete absence of observable Rydberg states relating to IE2 and IE3 (A2A2 and B2B2, respectively) is attributed to them being coupled to the near-continuum, high-energy region of Rydberg series converging on IE1. Theoretical studies of the UV and VUV spectra used both time-dependent density functional (TDDFT) and multi-reference multi-root doubles and singles-configuration interaction methods. The theoretical adiabatic excitation energies, and their corresponding vibrational profiles, gave a satisfactory interpretation of the experimental results. The calculations indicate that the UV onset contains both 11B1 and 11B2 states with very low oscillator strength, while the 21B1 state was found to lie under the lowest ππ∗ 11A1 state. All three of these 1B1 and 1B2 states are excitations into low-lying σ∗ orbitals. The strongest VUV band near 7 eV contains two very strong ππ∗ valence states, together with other weak contributors. The lowest Rydberg 4b16s state (31B1) is very evident as a sharp multiplet near 6 eV; its position and vibrational structure are well reproduced by the TDDFT results
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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