The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any further change. Others see it as a consequence of primordial biochemical pathways and their evolution. Here we examine a scenario in which evolution drives the emergence of a genetic code by selecting for an amino-acid map that minimizes the impact of errors. We treat the stochastic mapping of codons to amino-acids as a noisy information channel with a natural fitness measure. Organisms compete by the fitness of their codes and, as a result, a genetic code emerges at a supercritical transition in the noisy channel, when the mapping of codons to amino-acids becomes nonrandom. At the phase transition, a small expansion is valid and the emergent code is governed by smooth modes of the Laplacian of errors. These modes are in turn governed by the topology of the error-graph, in which codons are connected if they are likely to be confused. This topology sets an upper bound - which is related to the classical map-coloring problem - on the number of possible
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.
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
Rankings of scholarly journals based on citation data are often met with skepticism by the scientific community. Part of the skepticism is due to disparity between the common perception of journals' prestige and their ranking based on citation counts. A more serious concern is the inappropriate use of journal rankings to evaluate the scientific influence of authors. This paper focuses on analysis of the table of cross-citations among a selection of Statistics journals. Data are collected from the Web of Science database published by Thomson Reuters. Our results suggest that modelling the exchange of citations between journals is useful to highlight the most prestigious journals, but also that journal citation data are characterized by considerable heterogeneity, which needs to be properly summarized. Inferential conclusions require care in order to avoid potential over-interpretation of insignificant differences between journal ratings. Comparison with published ratings of institutions from the UK's Research Assessment Exercise shows strong correlation at aggregate level between assessed research quality and journal citation `export scores' within the discipline of Statistics.
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
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
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
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.
A previous study of symmetric collisions of massive nuclei has shown that current models of multi-nucleon transfer (MNT) reactions do not adequately describe the transfer product yields. To gain further insight into this problem, we have measured the yields of MNT products in the interaction of 977 (E/A = 4.79 MeV) and 1143 MeV (E/A = 5.60 MeV) $^{204}$Hg with $^{208}$Pb. We find that the yield of multi-nucleon transfer products are similar in these two reactions and are substantially lower than those observed in the reaction of 1257 MeV (E/A = 6.16 MeV) $^{204}$Hg + $^{198}$Pt. We compare our measurements with the predictions of the GRAZING-F, di-nuclear systems (DNS) and improved quantum molecular dynamics (ImQMD) models. For the observed isotopes of the elements Au, Hg, Tl, Pb and Bi, the measured values of the MNT cross sections are orders of magnitude larger than the predicted values. Furthermore, the various models predict the formation of nuclides near the N=126 shell, which are not observed.
Phosphorus (P) is considered to be one of the key elements for life, making it an important element to look for in the abundance analysis of spectra of stellar systems. Yet, there exists only a handful of spectroscopic studies to estimate the P abundances and investigate its trend across a range of metallicities. We have observed full HK band spectra at a spectral resolving power of R=45,000 with IGRINS instrument. Abundances are determined using SME in combination with 1D MARCS stellar atmosphere models. The investigated sample of stars have reliable stellar parameters estimated using optical FIES spectra (GILD; Jönsson et al. in prep.). In order to determine the P abundances from the 16482.92 Angstrom P line, we take special care of the CO($ν=7-4$) blend. We determine the C, N, O abundances from atomic carbon and a range of non-blended molecular lines (CO, CN, OH) which are aplenty in the H band region of K giant stars, assuring an appropriate modelling of the blending CO($ν=7-4$) line. We present [P/Fe] vs [Fe/H] trend for 38 K giant stars in the metallicity range of -1.2 dex $<$ [Fe/H] $<$ 0.4 dex. We find that our trend matches well with the compiled literature sample of
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.
Dyads of journals related by citations can agglomerate into specialties through the mechanism of triadic closure. Using the Journal Citation Reports 2011, 2012, and 2013, we analyze triad formation as indicators of integration (specialty growth) and disintegration (restructuring). The strongest integration is found among the large journals that report on studies in different scientific specialties, such as PLoS ONE, Nature Communications, Nature, and Science. This tendency towards large-scale integration has not yet stabilized. Using the Islands algorithm, we also distinguish 51 local maxima of integration. We zoom into the cited articles that carry the integration for: (i) a new development within high-energy physics and (ii) an emerging interface between the journals Applied Mathematical Modeling and the International Journal of Advanced Manufacturing Technology. In the first case, integration is brought about by a specific communication reaching across specialty boundaries, whereas in the second, the dyad of journals indicates an emerging interface between specialties. These results suggest that integration picks up substantive developments at the specialty level. An advantage o
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
Integration of data from genome-wide single nucleotide polymorphism (SNP) association studies of different traits should allow researchers to disentangle the genetics of potentially related traits within individually associated regions. Formal statistical colocalisation testing of individual regions, which requires selection of a set of SNPs summarizing the association in a region. We show that the SNP selection method greatly affects type 1 error rates, with published studies having used methods expected to result in substantially inflated type 1 error rates. We show that either avoiding variable selection and instead testing the most informative principal components or integrating over variable selection using Bayesian model averaging can lead to correct control of type 1 error rates. Application to data from Graves' disease and Hashimoto's thyroiditis reveals a common genetic signature across seven regions shared between the diseases, and indicates that in five of six regions associated with Graves' disease and not Hashimoto's thyroiditis, this more likely reflects genuine absence of association with the latter rather than lack of power. Our examination, by simulation, of the pe
Eccentric planets may spend a significant portion of their orbits at large distances from their host stars, where low temperatures can cause atmospheric CO2 to condense out onto the surface, similar to the polar ice caps on Mars. The radiative effects on the climates of these planets throughout their orbits would depend on the wavelength-dependent albedo of surface CO2 ice that may accumulate at or near apoastron and vary according to the spectral energy distribution of the host star. To explore these possible effects, we incorporated a CO2 ice-albedo parameterization into a one-dimensional energy balance climate model. With the inclusion of this parameterization, our simulations demonstrated that F-dwarf planets require 29% more orbit-averaged flux to thaw out of global water ice cover compared with simulations that solely use a traditional pure water ice-albedo parameterization. When no eccentricity is assumed, and host stars are varied, F-dwarf planets with higher bond albedos relative to their M-dwarf planet counterparts require 30% more orbit-averaged flux to exit a water snowball state. Additionally, the intense heat experienced at periastron aids eccentric planets in exiting
The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state of the art for computational prediction of genetic variant impact, particularly those relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. Overall, results show that while current methods are imperfect, they have major utility for research and clinical applications. Missense variant interpretation methods are able to estimate biochemical effects with increasing accuracy. Performance is particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Assessment of methods for regulatory variants and complex trait disease risk is less definitive, and indicates performance potentially suitable for auxiliary use in the clinic. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
While an integration by parts formula for the bilinear form of the hypersingular boundary integral operator for the transient heat equation in three spatial dimensions is available in the literature, a proof of this formula seems to be missing. Moreover, the available formula contains an integral term including the time derivative of the fundamental solution of the heat equation, whose interpretation is difficult at second glance. To fill these gaps we provide a rigorous proof of a general version of the integration by parts formula and an alternative representation of the mentioned integral term, which is valid for a certain class of functions including the typical tensor-product discretization spaces.
We present the results of processing the effects of the powerful Gamma Ray Burst GRB221009A captured by the charged particle detectors (electrostatic analyzers and solid-state detectors) onboard spacecraft at different points in the heliosphere on October 9, 2022. To follow the GRB221009A propagation through the heliosphere we used the electron and proton flux measurements from solar missions Solar Orbiter and STEREO-A; Earth magnetosphere and the solar wind missions THEMIS and Wind; meteorological satellites POES15, POES19, MetOp3; and MAVEN - a NASA mission orbiting Mars. GRB221009A had a structure of four bursts: less intense Pulse 1 - the triggering impulse - was detected by gamma-ray observatories at 131659 UT (near the Earth); the most intense Pulses 2 and 3 were detected on board all the spacecraft from the list, and Pulse 4 detected in more than 500 s after Pulse 1. Due to their different scientific objectives, the spacecraft, which data was used in this study, were separated by more than 1 AU (Solar Orbiter and MAVEN). This enabled tracking GRB221009A as it was propagating across the heliosphere. STEREO-A was the first to register Pulse 2 and 3 of the GRB, almost 100 secon
Proposed as blanket structural materials for fusion power reactors, reduced activation ferritic/martensitic (RAFM) steel undergoes volume expanding and contracting in a cyclic mode under service environment. Particularly, being subjected to significant fluxes of fusion neutrons RAFM steel suffers considerable local volume variations in the radiation damage involved regions. It is necessary to study the structure properties of the alloying elements in contraction and expansion states. In this paper we studied local substitution structures of thirteen alloying elements Al, Co, Cr, Cu, Mn, Mo, Nb, Ni, Si, Ta, Ti, V, and W in bcc Fe and calculated their substitutional energies in the volume variation range from -1.0% to 1.0%. From the structure relaxation results of the first five neighbor shells around the substitutional atom we find the relaxation in each neighbor shell keeps approximately uniform within the volume variation from -1.0% to 1.0% except those of Mn and the relaxation of the fifth neighbor shell is stronger than that of the third and forth, indicating that the lattice distortion due to the substitution atom is easier to spread in <111> direction than in other direc
In this paper, we investigate conformal Killing's vectors (CKVs) admitted by some plane symmetric spacetimes. Ten conformal Killing's equations and their general forms of CKVs are derived along with their conformal factor. The existence of conformal Killing's symmetry imposes restrictions on the metric functions. The conditions imposing restrictions on these metric functions are obtained as a set of integrability conditions. Considering the cases of time-like and inheriting CKVs, we obtain spacetimes admitting plane conformal symmetry. Integrability conditions are solved completely for some known non-conformally flat and conformally flat classes of plane symmetric spacetimes. A special vacuum plane symmetric spacetime is obtained, and it is shown that for such a metric CKVs are just the homothetic vectors (HVs). Among all the examples considered, there exists only one case with a six dimensional algebra of special CKVs admitting one proper CKV. In all other examples of non-conformally flat metrics, no proper CKV is found and CKVs are either HVs or Killing's vectors (KVs). In each of the three cases of conformally flat metrics, a fifteen dimensional algebra of CKVs is obtained of wh