The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to translate information written in one class of molecules into another molecular "language" . The present paper examines the emergence and evolution of molecular codes in terms of rate-distortion theory and reviews recent results of this approach. We discuss how the biological problem of maximizing the fitness of an organism by optimizing its molecular coding machinery is equivalent to the communication engineering problem of designing an optimal information channel. The fitness of a molecular code takes into account the interplay between the quality of the channel and the cost of resources which the organism needs to invest in its construction and maintenance. We analyze the dynamics of a population of organisms that compete according to the fitness of their codes. The model suggests a generic mechanism for the emergence of molecular codes as a phase transition in an information channel. This mechanism is put into biological context and demonstrated
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.
Safety has become the central value around which dominant AI governance efforts are being shaped. Recently, this culminated in the publication of the International AI Safety Report, written by 96 experts of which 30 nominated by the Organisation for Economic Co-operation and Development (OECD), the European Union (EU), and the United Nations (UN). The report focuses on the safety risks of general-purpose AI and available technical mitigation approaches. In this response, informed by a system safety perspective, I refl ect on the key conclusions of the report, identifying fundamental issues in the currently dominant technical framing of AI safety and how this frustrates meaningful discourse and policy efforts to address safety comprehensively. The system safety discipline has dealt with the safety risks of software-based systems for many decades, and understands safety risks in AI systems as sociotechnical and requiring consideration of technical and non-technical factors and their interactions. The International AI Safety report does identify the need for system safety approaches. Lessons, concepts and methods from system safety indeed provide an important blueprint for overcoming
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
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
In this work, we expand the idea of Samuelson[3] and Shepp[2,5,6] for stock optimization using the Bachelier model [4] as our models for the stock price at the money (X[stock price]= K[strike price]) for the American call and put options [1]. At the money (X= K) for American options, the expected payoff of both the call and put options is zero. Shepp investigated several stochastic optimization problems using martingale and stopping time theories [2,5,6]. One of the problems he investigated was how to optimize the stock price using both the Black-Scholes (multiplicative) and the Bachelier (additive) models [7,6] for the American option above the strike price K (exercise price) to a stopping point. In order to explore the non-relativistic quantum effect on the expected payoff for both the call and put options at the money, we assumed the stock price to undergo a stochastic process governed by the Bachelier (additive) model [4]. Further, using Ito calculus and martingale theory, we obtained a differential equation for the expected payoff for both the call and put options in terms of delta and gamma. We also obtained the solution to the non-relativistic Schroedinger equation as the ex
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
We have developed a (freeware) routine for "referenced publication years spectroscopy" (RPYS) and apply this method to the historiography of "iMetrics," that is, the junction of the journals Scientometrics, Informetrics, and the relevant subset of JASIST (approx. 20%) that shapes the intellectual space for the development of information metrics (bibliometrics, scientometrics, informetrics, and webometrics). The application to information metrics (our own field of research) provides us with the opportunity to validate this methodology, and to add a reflection about using citations for the historical reconstruction. The results show that the field is rooted in individual contributions of the 1920s-1950s (e.g., Alfred J. Lotka), and was then shaped intellectually in the early 1960s by a confluence of the history of science (Derek de Solla Price), documentation (e.g., Michael M. Kessler's "bibliographic coupling"), and "citation indexing" (Eugene Garfield). Institutional development at the interfaces between science studies and information science has been reinforced by the new journal Informetrics since 2007. In a concluding reflection, we return to the question of how the historiogra
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.
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.
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
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.
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
Binomial tree methods (BTM) and explicit difference schemes (EDS) for the variational inequality model of American options with time dependent coefficients are studied. When volatility is time dependent, it is not reasonable to assume that the dynamics of the underlying asset's price forms a binomial tree if a partition of time interval with equal parts is used. A time interval partition method that allows binomial tree dynamics of the underlying asset's price is provided. Conditions under which the prices of American option by BTM and EDS have the monotonic property on time variable are found. Using convergence of EDS for variational inequality model of American options to viscosity solution the decreasing property of the price of American put options and increasing property of the optimal exercise boundary on time variable are proved. First, put options are considered. Then the linear homogeneity and call-put symmetry of the price functions in the BTM and the EDS for the variational inequality model of American options with time dependent coefficients are studied and using them call options are studied.
Biological systems possess negative entropy. In them, one form of order produces another, more organized form of order. We propose a formal scheme to calculate robustness of an entire biological system by quantifying the negative entropy present in it. Our Methodology is based upon a computational implementation of two-person non-cooperative finite zero-sum game between positive (physico-chemical) and negative (biological) entropy, present in the system(TCA cycle, for this work). Biochemical analogue of Nash equilibrium, proposed here, could measure the robustness in TCA cycle in exact numeric terms, whereas the mixed strategy game between these entropies could quantitate the progression of stages of biological adaptation. Synchronization profile amongst macromolecular concentrations (even under environmental perturbations) is found to account for negative entropy and biological robustness. Emergence of synchronization profile was investigated with dynamically varying metabolite concentrations. Obtained results were verified with that from the deterministic simulation methods. Categorical plans to apply this algorithm in Cancer studies and anti-viral therapies are proposed alongsid
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
We report on the gamma-ray activity of the blazar Mrk 501 during the first 480 days of Fermi operation. We find that the average LAT gamma-ray spectrum of Mrk 501 can be well described by a single power-law function with a photon index of 1.78 +/- 0.03. While we observe relatively mild flux variations with the Fermi-LAT (within less than a factor of 2), we detect remarkable spectral variability where the hardest observed spectral index within the LAT energy range is 1.52 +/- 0.14, and the softest one is 2.51 +/- 0.20. These unexpected spectral changes do not correlate with the measured flux variations above 0.3GeV. In this paper, we also present the first results from the 4.5-month-long multifrequency campaign (2009 March 15 - August 1) on Mrk 501, which included the VLBA, Swift, RXTE, MAGIC and VERITAS, the F-GAMMA, GASP-WEBT, and other collaborations and instruments which provided excellent temporal and energy coverage of the source throughout the entire campaign. The average spectral energy distribution of Mrk 501 is well described by the standard one-zone synchrotron self-Compton model. In the framework of this model, we find that the dominant emission region is characterized b
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
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
This paper develops a Geometric Analysis-based Route Safety Assessment (GARSA) framework to enhance the safety of marine vehicles navigating in restricted waters. Utilizing line and point geometric elements to define waterway boundaries, the framework enables the construction of a dynamic width characterization function to quantify spatial safety within complex restricted navigation spaces. An iterative method is developed to calculate the dynamic width characterization function, enabling an abstracted spatial property representation of waterways. Based on this, a navigational safety index that accounts for the overall route safety as well as the spatial constraints of local segments is created, enabling the selection of the safest waterway to pass through. Case studies in Hamburg Port and hypothetical waterways show that GARSA identifies spatial safety differences among routes. For example, GARSA assigned safety assessment values of 0.6 and 135 to two intra-port transit routes of 7,258 m and 7,845 m, respectively, with the higher value indicating a safer route. Overall, GARSA provides a quantitative basis for safety-oriented route decision-making of marine vehicles in restricted w