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We compare the network of aggregated journal-journal citation relations provided by the Journal Citation Reports (JCR) 2012 of the Science and Social Science Citation Indexes (SCI and SSCI) with similar data based on Scopus 2012. First, global maps were developed for the two sets separately; sets of documents can then be compared using overlays to both maps. Using fuzzy-string matching and ISSN numbers, we were able to match 10,524 journal names between the two sets; that is, 96.4% of the 10,936 journals contained in JCR or 51.2% of the 20,554 journals covered by Scopus. Network analysis was then pursued on the set of journals shared between the two databases and the two sets of unique journals. Citations among the shared journals are more comprehensively covered in JCR than Scopus, so the network in JCR is denser and more connected than in Scopus. The ranking of shared journals in terms of indegree (that is, numbers of citing journals) or total citations is similar in both databases overall (Spearman's \r{ho} > 0.97), but some individual journals rank very differently. Journals that are unique to Scopus seem to be less important--they are citing shared journals rather than bein

This study examines the social media uptake of scientific journals on two different platforms - X and WeChat - by comparing the adoption of X among journals indexed in the Science Citation Index-Expanded (SCIE) with the adoption of WeChat among journals indexed in the Chinese Science Citation Database (CSCD). The findings reveal substantial differences in platform adoption and user engagement, shaped by local contexts. While only 22.7% of SCIE journals maintain an X account, 84.4% of CSCD journals have a WeChat official account. Journals in Life Sciences & Biomedicine lead in uptake on both platforms, whereas those in Technology and Physical Sciences show high WeChat uptake but comparatively lower presence on X. User engagement on both platforms is dominated by low-effort interactions rather than more conversational behaviors. Correlation analyses indicate weak-to-moderate relationships between bibliometric indicators and social media metrics, confirming that online engagement reflects a distinct dimension of journal impact, whether on an international or a local platform. These findings underscore the need for broader social media metric frameworks that incorporate locally dom

Using the Scopus dataset (1996-2007) a grand matrix of aggregated journal-journal citations was constructed. This matrix can be compared in terms of the network structures with the matrix contained in the Journal Citation Reports (JCR) of the Institute of Scientific Information (ISI). Since the Scopus database contains a larger number of journals and covers also the humanities, one would expect richer maps. However, the matrix is in this case sparser than in the case of the ISI data. This is due to (i) the larger number of journals covered by Scopus and (ii) the historical record of citations older than ten years contained in the ISI database. When the data is highly structured, as in the case of large journals, the maps are comparable, although one may have to vary a threshold (because of the differences in densities). In the case of interdisciplinary journals and journals in the social sciences and humanities, the new database does not add a lot to what is possible with the ISI databases.

Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for the visualization of massive molecular systems and molecular dynamics trajectories. VTX includes multiple interactive camera and user interaction features, notably free-fly navigation and a fully modular graphical user interface designed for increased usability. It allows the production of high-resolution images for presentations and posters with custom background. VTX design is focused on performance and usability for research, teaching and educative purposes. Availability and implementation: VTX is open source and free for non commercial use. Builds for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. The source code is available at https://github.com/VTX-Molecular-Visualization . Supplementary Information: A video displaying free-fly navigation in a whole-cell model is available

A number of journal classification systems have been developed in bibliometrics since the launch of the Citation Indices by the Institute of Scientific Information (ISI) in the 1960s. These systems are used to normalize citation counts with respect to field-specific citation patterns. The best known system is the so-called "Web-of-Science Subject Categories" (WCs). In other systems papers are classified by algorithmic solutions. Using the Journal Citation Reports 2014 of the Science Citation Index and the Social Science Citation Index (n of journals = 11,149), we examine options for developing a new system based on journal classifications into subject categories using aggregated journal-journal citation data. Combining routines in VOSviewer and Pajek, a tree-like classification is developed. At each level one can generate a map of science for all the journals subsumed under a category. Nine major fields are distinguished at the top level. Further decomposition of the social sciences is pursued for the sake of example with a focus on journals in information science (LIS) and science studies (STS). The new classification system improves on alternative options by avoiding the problem

A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model epigenetic evolution.

Using three years of the Journal Citation Reports (2011, 2012, and 2013), indicators of transitions in 2012 (between 2011 and 2013) are studied using methodologies based on entropy statistics. Changes can be indicated at the level of journals using the margin totals of entropy production along the row or column vectors, but also at the level of links among journals by importing the transition matrices into network analysis and visualization programs (and using community-finding algorithms). Seventy-four journals are flagged in terms of discontinuous changes in their citations; but 3,114 journals are involved in "hot" links. Most of these links are embedded in a main component; 78 clusters (containing 172 journals) are flagged as potential "hot spots" emerging at the network level. An additional finding is that PLoS ONE introduced a new communication dynamics into the database. The limitations of the methodology are elaborated using an example. The results of the study indicate where developments in the citation dynamics can be considered as significantly unexpected. This can be used as heuristic information; but what a "hot spot" in terms of the entropy statistics of aggregated cit

Using "Analyze Results" at the Web of Science, one can directly generate overlays onto global journal maps of science. The maps are based on the 10,000+ journals contained in the Journal Citation Reports (JCR) of the Science and Social Science Citation Indices (2011). The disciplinary diversity of the retrieval is measured in terms of Rao-Stirling's "quadratic entropy." Since this indicator of interdisciplinarity is normalized between zero and one, the interdisciplinarity can be compared among document sets and across years, cited or citing. The colors used for the overlays are based on Blondel et al.'s (2008) community-finding algorithms operating on the relations journals included in JCRs. The results can be exported from VOSViewer with different options such as proportional labels, heat maps, or cluster density maps. The maps can also be web-started and/or animated (e.g., using PowerPoint). The "citing" dimension of the aggregated journal-journal citation matrix was found to provide a more comprehensive description than the matrix based on the cited archive. The relations between local and global maps and their different functions in studying the sciences in terms of journal lit

Using Scopus data, we construct a global map of science based on aggregated journal-journal citations from 1996-2012 (N of journals = 20,554). This base map enables users to overlay downloads from Scopus interactively. Using a single year (e.g., 2012), results can be compared with mappings based on the Journal Citation Reports at the Web-of-Science (N = 10,936). The Scopus maps are more detailed at both the local and global levels because of their greater coverage, including, for example, the arts and humanities. The base maps can be interactively overlaid with journal distributions in sets downloaded from Scopus, for example, for the purpose of portfolio analysis. Rao-Stirling diversity can be used as a measure of interdisciplinarity in the sets under study. Maps at the global and the local level, however, can be very different because of the different levels of aggregation involved. Two journals, for example, can both belong to the humanities in the global map, but participate in different specialty structures locally. The base map and interactive tools are available online (with instructions) at http://www.leydesdorff.net/scopus_ovl.

Numerous biological functions-such as enzymatic catalysis, the immune response system, and the DNA-protein regulatory network-rely on the ability of molecules to specifically recognize target molecules within a large pool of similar competitors in a noisy biochemical environment. Using the basic framework of signal detection theory, we treat the molecular recognition process as a signal detection problem and examine its overall performance. Thus, we evaluate the optimal properties of a molecular recognizer in the presence of competition and noise. Our analysis reveals that the optimal design undergoes a "phase transition" as the structural properties of the molecules and interaction energies between them vary. In one phase, the recognizer should be complementary in structure to its target (like a lock and a key), while in the other, conformational changes upon binding, which often accompany molecular recognition, enhance recognition quality. Using this framework, the abundance of conformational changes may be explained as a result of increasing the fitness of the recognizer. Furthermore, this analysis may be used in future design of artificial signal processing devices based on bio

While large vision-language models can generate motion graphics animations from text prompts, they regularly fail to include all spatio-temporal properties described in the prompt. We introduce MoVer, a motion verification DSL based on first-order logic that can check spatio-temporal properties of a motion graphics animation. We identify a general set of such properties that people commonly use to describe animations (e.g., the direction and timing of motions, the relative positioning of objects, etc.). We implement these properties as predicates in MoVer and provide an execution engine that can apply a MoVer program to any input SVG-based motion graphics animation. We then demonstrate how MoVer can be used in an LLM-based synthesis and verification pipeline for iteratively refining motion graphics animations. Given a text prompt, our pipeline synthesizes a motion graphics animation and a corresponding MoVer program. Executing the verification program on the animation yields a report of the predicates that failed and the report can be automatically fed back to LLM to iteratively correct the animation. To evaluate our pipeline, we build a synthetic dataset of 5600 text prompts paire

Publication patterns of 79 forest scientists awarded major international forestry prizes during 1990-2010 were compared with the journal classification and ranking promoted as part of the 'Excellence in Research for Australia' (ERA) by the Australian Research Council. The data revealed that these scientists exhibited an elite publication performance during the decade before and two decades following their first major award. An analysis of their 1703 articles in 431 journals revealed substantial differences between the journal choices of these elite scientists and the ERA classification and ranking of journals. Implications from these findings are that additional cross-classifications should be added for many journals, and there should be an adjustment to the ranking of several journals relevant to the ERA Field of Research classified as 0705 Forestry Sciences.

We report here how the hydration of complex surfaces can be efficiently studied thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophylite clay. After presenting the most recent advances, we show that the strength of this implicit method is that (i) it is in quantitative or semi-quantitative agreement with reference all-atoms simulations (molecular dynamics here) for both the solvation structure and energetics, and that (ii) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect, in that it locally overestimates the polarization of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry a systematic study of the electrostatic and van der Waals components of the surface-solvant interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend upon the electrostatics. We conclude on the consequences of such findings in future force-field development.

We introduce a novel methodology for mapping academic institutions based on their journal publication profiles. We believe that journals in which researchers from academic institutions publish their works can be considered as useful identifiers for representing the relationships between these institutions and establishing comparisons. However, when academic journals are used for research output representation, distinctions must be introduced between them, based on their value as institution descriptors. This leads us to the use of journal weights attached to the institution identifiers. Since a journal in which researchers from a large proportion of institutions published their papers may be a bad indicator of similarity between two academic institutions, it seems reasonable to weight it in accordance with how frequently researchers from different institutions published their papers in this journal. Cluster analysis can then be applied to group the academic institutions, and dendrograms can be provided to illustrate groups of institutions following agglomerative hierarchical clustering. In order to test this methodology, we use a sample of Spanish universities as a case study. We f

Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction potential model for water. In various studies, the models have been evaluated based on their ability to reproduce different properties of water. This work focuses on the atomic-scale structure in the liquid phase of water. Forty-four classical water potential models are compared to identify those that can accurately describe the structure in alignment with experimental results. In addition to some older models that are still popular today, new or re-parametrized classical models using effective pair-additive potentials that have appeared in recent years are examined. Molecular dynamics simulations were performed over a wide range of temperatures and the resulting trajectories were used to calculate the partial radial distribution functions. The total scattering structure factors were compared with data from neutron and X-ray diffraction experiments. Our analysis indicates that models with more than four interaction sites, as well as flexible or polariza

Vision Transformers, ViTs, have emerged as a powerful alternative to convolutional neural networks, CNNs, in a variety of image-based tasks. While CNNs have previously been evaluated for their ability to perform graphical perception tasks, which are essential for interpreting visualizations, the perceptual capabilities of ViTs remain largely unexplored. In this work, we investigate the performance of ViTs in elementary visual judgment tasks inspired by the foundational studies of Cleveland and McGill, which quantified the accuracy of human perception across different visual encodings. Inspired by their study, we benchmark ViTs against CNNs and human participants in a series of controlled graphical perception tasks. Our results reveal that, although ViTs demonstrate strong performance in general vision tasks, their alignment with human-like graphical perception in the visualization domain is limited. This study highlights key perceptual gaps and points to important considerations for the application of ViTs in visualization systems and graphical perceptual modeling.

Predatory journals are Open Access journals of highly questionable scientific quality. Such journals pretend to use peer review for quality assurance, and spam academics with requests for submissions, in order to collect author payments. In recent years predatory journals have received a lot of negative media. While much has been said about the harm that such journals cause to academic publishing in general, an overlooked aspect is how much articles in such journals are actually read and in particular cited, that is if they have any significant impact on the research in their fields. Other studies have already demonstrated that only some of the articles in predatory journals contain faulty and directly harmful results, while a lot of the articles present mediocre and poorly reported studies. We studied citation statistics over a five-year period in Google Scholar for 250 random articles published in such journals in 2014, and found an average of 2,6 citations per article and that 60 % of the articles had no citations at all. For comparison a random sample of articles published in the approximately 25,000 peer reviewed journals included in the Scopus index had an average of 18,1 cit

The catalog section of the Cologne Database for Molecular Spectroscopy, CDMS, contains mostly rotational transition frequencies, with auxiliary information, of molecules observable in space. The frequency lists are generated mostly from critically evaluated laboratory data employing established Hamiltonian models. The CDMS has been online publicly for more than 12 years, e.g., via the short-cut http://www.cdms.de. Initially constructed as ascii tables, its inclusion into a database environment within the Virtual Atomic and Molecular Data Centre (VAMDC, http://www.vamdc.eu) has begun in June 2008. A test version of the new CDMS is about to be released. The CDMS activities have been part of the extensive laboratory spectroscopic investigations in Cologne. Moreover, these activities have also benefit from collaborations with other laboratory spectroscopy groups as well as with astronomers. We will provide some basic information on the CDMS and its participation in the VAMDC project. In addition, some recent detections of molecules as well as spectroscopic studies will be discussed to evaluate the spectroscopic data needs of Herschel, SOFIA, and ALMA in particular in terms of light hyd

We aim to characterize the U-band variability of young brown dwarfs in the Taurus Molecular Cloud and discuss its origin. We used the XMM-Newton Extended Survey of the Taurus Molecular Cloud, where a sample of 11 young bona fide brown dwarfs (spectral type later than M6) were observed simultaneously in X-rays with XMM-Newton and in the U-band with the XMM-Newton Optical/UV Monitor (OM). We obtained upper limits to the U-band emission of 10 brown dwarfs (U>19.6-20.6 mag), whereas 2MASSJ04141188+2811535 was detected in the U-band. Remarkably, the magnitude of this brown dwarf increased regularly from U~19.5 mag at the beginning of the observation, peaked 6h later at U~18.4 mag, and then decreased to U~18.65 mag in the next 2h. The first OM U-band measurement is consistent with the quiescent level observed about one year later thanks to ground follow-up observations. This brown dwarf was not detected in X-rays by XMM-Newton during the OM observation. We discuss the possible sources of U-band variability for this young brown dwarf, namely a magnetic flare, non-steady accretion onto the substellar surface, and rotational modulation of a hot spot. We conclude that this event is relate