Universal Code Research Articles

Prediction of strength and deformability of an interlocked blocky rock mass using UDEC

The accurate prediction of strength and deformability characteristics of rock mass is a challenging issue. In practice, properties of a rock mass are often estimated from available empirical relationships based on the uniaxial compressive strength (UCS). However, UCS does not always give a good indication of in situ rock mass strength and deformability. The aim of this paper is to present a methodology to predict the strength and deformability of a jointed rock mass using UDEC (universal distinct element code). In the study, the rock mass is modelled as an assemblage of deformable blocks that can yield as an intact material and/or slide along predefined joints within the rock mass. A range of numerical simulations of uniaxial and triaxial tests was conducted on rock mass samples in order to predict the equivalent mechanical properties for the rock mass under different loading directions. Finally, results are compared with the deformability parameters obtained by analytical methods.

What Froze the Genetic Code?

The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.

GitHub, Technical Debt, Code Formatting, and More

This issue's column reports on papers from the 19th International Conference on Model Driven Engineering Languages and Systems, the 2016 ACM SIGPLAN International Conference on Software Language Engineering, the 12th International ACM SIGSOFT Conference on the Quality of Software Architectures, and the 13th Working IEEE/IFIP Conference on Software Architecture. Topics discussed include GitHub and open source, technical debt in model-driven engineering, a universal code formatter, assuring architectural quality, and continuous architecting.

Slope topography-induced spatial variation correlation with observed building damages in Corso during the May 21, 2003, M w 6.8, Boumerdes earthquake (Algeria)

During the May 21, 2003 M w 6.8 Boumerdes earthquake, in the “Cite des 102 Logements” built on a hilltop, in Corso, heavy damages were observed: near the crest, a four-story RC building collapsed while others experienced severe structural damage and far from the crest, slight damage was observed. In the present paper, we perform a 2D slope topography seismic analysis and investigate its effects on the response at the plateau as well as the correlation with the observed damage distribution. A site-specific seismic scenario is used involving seismological, geological, and geotechnical data. 2D finite element numerical seismic study of the idealized Corso site subjected to vertical SV wave propagation is carried out by the universal code FLUSH. The results highlighted the main factors that explain the causes of block collapse, located 8-26 m far from the crest. These are as follows: (i) a significant spatial variation of ground response along the plateau due to the topographic effect, (ii) this spatial variation presents high loss of coherence, (iii) the seismic ground responses (PGA and response spectra) reach their maxima, and (iv) the fundamental frequency of the collapsed blocks coincides with the frequency content of the topographic component. For distances far from the crest where slight damages were observed, the topographic contribution is found negligible. On the basis of these results, it is important to take into account the topographic effect and the induced spatial variability in the seismic design of structures sited near the crest of slope.

Universal Weak Variable-Length Source Coding on Countably Infinite Alphabets

Motivated from the fact that universal source coding on countably infinite alphabets is not feasible, this work introduces the notion of almost lossless source coding. Analog to the weak variable-length source coding problem studied by Han (IEEE TIT, 2000, 46, 1217-1226), almost lossless source coding aims at relaxing the lossless block-wise assumption to allow an average per-letter distortion that vanishes asymptotically as the block-length tends to infinity. In this setup, we show on one hand that Shannon entropy characterizes the minimum achievable rate (similarly to the case of finite alphabet sources) while on the other that almost lossless universal source coding becomes feasible for the family of finite-entropy stationary memoryless sources with infinite alphabets. Furthermore, we study a stronger notion of almost lossless universality that demands uniform convergence of the average per-letter distortion to zero, where we establish a necessary and sufficient condition for the so-called family of envelope distributions to achieve it. Remarkably, this condition is the same necessary and sufficient condition needed for the existence of a strongly minimax (lossless) universal source code for the family of envelope distributions. Finally, we show that an almost lossless coding scheme offers faster rate of convergence for the (minimax) redundancy compared to the well-known information radius developed for the lossless case at the expense of tolerating a non-zero distortion that vanishes to zero as the block-length grows. This shows that even when lossless universality is feasible, an almost lossless scheme can offer different regimes on the rates of convergence of the (worst case) redundancy versus the (worst case) distortion.

Coding of Class I and II Aminoacyl-tRNA Synthetases.

The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels-protozymes and Urzymes-associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric-middle base-pairing frequencies in sense/antisense alignments-that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically-active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins.

Explicit reinforcement models for fully-grouted rebar rock bolts

This paper investigates the explicit use of rock reinforcement in a discontinuous stress analysis model. A series of numerical experiments was undertaken to evaluate the performance of local and global reinforcement models implemented in universal distinct element code (UDEC). This was made possible by calibrating the reinforcement models to the laboratory behavior of a fully-grouted rebar bolt tested under pure pull and pure shear loading conditions. The model calibration focuses on matching different loading stages of the force–displacement curve including the initial elastic response, the hardening behavior and the bolt rupture. The paper concludes with a discussion on the suitability of the different reinforcement models in UDEC including their advantages and limitations. Finally, it addresses the choice of input parameters required for a realistic simulation of fully-grouted rebar bolts.

Perspectives of cytomeres use in biology and medicine.

The law of the information structuregenesis is formulated: the information transforms into interaction, interaction into connection (link), and link into a new element. There is a dependence: the more signal is structured, the more informational potential it has. At a cell-like level greatest remote informogenesis have the fragments of the cytoplasm of cells surrounded by a cell-like membrane, i.e. cytomers. These are produced by many cells and migrate in all environments of an organism. The cytomers play an important role in immunological responses, inflammation, and tumor transformation. They are the predecessors of viruses, together with which they fulfill the role of universal informational code and provide informational integration between different levels of biosphere’s life organization into the united system.The new intercellular, intertissue and interorganic regeneration mechanism by the cytomers flow from regions of high functional load to regions with minimal functional load is described. The cytomers serve as an extracellular reserve to fulfill the needs of the cytoplasm regeneration of the cells. New pathogenetic algorithms of diseases development are based on a blockage of extravascular transport ways due to local informational (citomeric, trophical, immune etc.) deficit. A "pathogenic field" is formed because of extravasal transport ways blockage. This field limits the adaptive morphogenesis due to impossibility of structuring and proper arrangement of the informational streams.

A Universal Code for mRNA Stability?

Precise elimination of maternal mRNAs plays a critical role during the maternal-to-zygotic transition (MZT) to promote developmental processing. Two new studies demonstrate that, in eukaryotes, codon-mediated decay is a conserved mechanism to shape maternal mRNA stability by affecting deadenylation rate in a translation-dependent manner. These studies add to a growing body of literature suggesting that translational elongation rates are a major determinant of mRNA stability.

Optimum model extent for numerical simulation of tunnel inflow in fractured rock

The objective of this study is the introduction of an optimum model extent in discontinuous rock masses for tunnel inflow assessment using numerical models. Tunnel groundwater inflow is an important problem in tunneling, and numerical simulation is widely used for estimating the amount of tunnel inflow. An adequate size of the model domain is of very high importance when using such models. On the one hand, if the tunnel boundary is too close to the outer model boundary, the simulated inflow rate into the tunnel is significantly overestimated (which will be shown in the present study). On the other hand, if the model domain is very large, models may become “unhandy”, and simulations become very expensive with respect to computer memory and CPU. In this technical note, an approach is presented that derives an optimum model extent for numerical simulation of tunnel inflow in fractured rock. The approach uses the two-dimensional universal distinct element code (UDEC). The impact of different model parameters, such as tunnel radius, groundwater level, joint spacing, joint dip/dip direction and joint aperture on the optimum model extent has been evaluated. Based on the results, an optimum model extent chart is presented that allows modelers a quick determination of the optimum model extent as a function of the most significant parameters, which are the tunnel depth under the groundwater level, tunnel radius and joint spacing.

‘Männer wie Du und Ich’: Gay Magazines from the National to the Transnational

Print media has played a key role in the formation of queer culture since 1945. The popularity of gay print magazines in the German context was based to a great extent on their visual character and composition. After 1969 pornographic aesthetics played a key role in the production of meaning of German gay magazines and the forms of identification that they offered their readers. The history of gay magazines allows us to read the tensions between the national, the international and the transnational. In the context of German gay magazines, structural characteristics of porn were translated into a set of signs that came to signify ‘German’. While German gay magazines also related to an international code of representing gay masculinity, thanks to innovations in media technology since the 1980s, they had an alternative aesthetic to offer, which, in contrast to a more universal erotic code stemming from the gay US porn industry, functioned as ‘German’. This juxtaposition between international and German codes structures the field of gay publications in West Germany and remained a factor in publications in the reunified Germany into the 2000s. During the 2000s this paradigm partly dissolved in favour of a more universal gay aesthetics, which can no longer be positioned along the lines of national and international and therefore might be named ‘transnational.’

Comparative study of the radiative Energy Loss and RCSDA of electron within ranges (0.01 ≤ E ≤ 10 )MeV in (_15^31)P , (_19^39)K and (_20^40)Ca

(CSDA) ranges for electrons in the elements Calcium , Potassium and Phosphor in terms of energy (0.01 - 10) MeV have been studied by using two empirical formula of Berger-Seltzer and Tabata et al respectively . These two parameters depend upon the atomic number (Z) of the absorber and incident electron energy E. It has been found that these formulae gives better agreement with the available data of Estar universal code. In this paper ,we present the results of Radiative Energy Loss and continuous slowing down approximation

Using a Fluid–Solid Coupled Numerical Simulation to Determine a Suitable Size for Barrier Pillars When Mining Shallow Coal Seams Beneath an Unconsolidated, Confined Aquifer

Barrier pillars are an effective and fundamental measure to prevent water inrush when mining shallow coal seams under an unconsolidated, confined aquifer. Based on the complex geological and hydrogeological conditions in the southern area of the Qidong coal mine, the no. 61 coal seam there was selected for a research demonstration. A fluid–solid coupled numerical simulation was carried out using the universal distinct element code. The hydraulic pressures and seepage rates in overlying strata were analyzed for two mining cases, near the aquifer and near the fault. The results showed that the degree of interconnection between the bed-separated and vertical fractures, and increases in hydraulic pressures and seepage rates in overlying strata were key factors in predicting potential water inrush when mining shallow coal seams under an unconsolidated, confined aquifer. Combining the numerical simulation results with China’s coal mining requirements, the no. 61 coal seam can be mined up to 90 m beneath the unconsolidated, confined aquifer, which limits mining to an altitude of −509.36 m. The width of the barrier pillar should be 30.7 m near the fault.

Effects of Passive and Structural Stream Restoration Approaches on Transient Storage and Nitrate Uptake

Understanding nitrogen dynamics in headwater streams is important for ascertaining how they influence downstream nutrient loads and identifying strategies for reducing loading through stream restoration. We compare nitrate uptake associated with two restoration approaches in headwater streams, Sheep Creek and Nunn Creek, of northern Colorado, USA. Segments of Sheep Creek were exclosed (fenced off) from open rangeland cattle grazing in the 1950s, allowing riparian corridors of these segments to naturally revegetate (passive approach), while other segments have been continually grazed. In 2003, restoration structures including cross vanes, J‐hook vanes, rootwads, log vanes, and bank riprap (structural approach) were installed along portions of Nunn Creek for trout habitat enhancement and local bank stabilization. We performed detailed physical characterizations and multiple nutrient injections of Br⁻ and NO₃ ⁻ to estimate transient storage and nitrate uptake in four reaches along Sheep Creek (two reaches exclosed from grazing and two grazed reaches) and two reaches along Nunn Creek (one with restoration structures and one without structures). Parameters of transient storage and nitrate uptake were estimated with the one‐dimensional transport with inflow and storage model run through universal inverse modelling code for optimization. Responses of transient storage and nitrate uptake to restoration techniques depended upon the type and extent of restoration implemented, as well the context and physical setting of each study reach. For example, in the higher‐gradient pair of Sheep Creek reaches, the restored reach showed greater nitrate uptake, while in the lower‐gradient pair of reaches, the non‐restored reach had greater uptake. At Nunn Creek, the reach with instream wood but without restoration structures exhibited more transient storage and nitrate uptake when compared with the reach with extensive J‐hook vane structures. Copyright © 2016 John Wiley & Sons, Ltd.

Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code

The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes. We find that when horizontal transfer of genetic elements is incorporated in this more realistic model of code-sequence coevolution in a finite population, it can increase the likelihood of emergence of a more optimal code eventually leading to its universality through fixation in the population. The establishment of such an optimal code depends on the probability of HGT events. Only when the probability of HGT events is above a critical threshold, we find that the ten amino acid code having a structure that is most consistent with the standard genetic code (SGC) often gets fixed in the population with the highest probability. We examine how the threshold is determined by factors like the population size, length of the sequences and selection coefficient. Our simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

Genetic Code Expansion by Degeneracy Reprogramming of Arginyl Codons.

The genetic code in most organisms codes for 20 proteinogenic amino acids or translation stop. In order to encode more than 20 amino acids in the coding system, one of stop codons is usually reprogrammed to encode a non-proteinogenic amino acid. Although this approach works, usually only one amino acid is added to the amino acid repertoire. In this study, we incorporated non-proteinogenic amino acids into a protein by using a sense codon. As all the codons are allocated in the universal genetic code, we destroyed all the tRNA(Arg) in a cell-free protein synthesis system by using a tRNA(Arg) -specific tRNase, colicin D. Then by supplementing the system with tRNACCU , the translation system was partially restored. Through this creative destruction, reprogrammable codons were successfully created in the system to encode modified lysines along with the 20 proteinogenic amino acids.

From the Common Ancestor to the First Cells: The Code Theory

The phylogenetic trees reconstructed from molecular data have led to the discovery that all living creatures belong to three primary kingdoms, or domains, because there are three types of cells in nature. The primary kingdoms are referred to as Archaea, Bacteria, and Eukaya, and their first representatives were the first modern cells that appeared on Earth. All known cells, on the other hand, contain a virtually universal genetic code, and this implies that the code evolved in a population of primitive systems that preceded the first modern cells and is collectively known as the common ancestor of all life. This gives us the problem of understanding how the descendants of the common ancestor gave origin to the first modern cells. In this article it is argued that the appearance of the genetic code allowed the ancestral systems to translate genes into specific proteins, but their behavior was still ambiguous because they were unable to produce specific responses to the signals from the environment. To that purpose they needed to evolve signal processing codes, and here it is proposed that the development of these codes was a crucial step in the evolution of the first modern cells.

Exploring transparency: a new framework for responsible business management

Purpose – The purpose of this paper is to critically review the relevant literature on transparency, provide a comprehensive definition of transparency, and present a new framework for facilitating the adoption of transparency as an ethical cornerstone and pragmatic strategy for organizational responsible business management. Design/methodology/approach – A systematic literature review – a methodology adopted from medical sciences to eliminate research bias – was conducted. In doing so, the definitions, antecedents, and consequences of transparency are accessed and synthesized. Findings – Based upon this process transparency is defined as the extent to which a stakeholder perceives an organization provides learning opportunities about itself. A conceptual framework emerged from the data. It describes when transparency is especially important, what organizations can do to be more transparent, and the potential benefits of transparency. Practical implications – The transparency framework can be used as a guide for organizations attempting to change their behavior, image, and performance by adopting transparency as a value in their organization. In addition, the framework can be used to create and adopt a universal (i.e. industry-wide or even societal-wide) code of conduct. Furthermore, this review, definition, and framework provide a template for academics to advance transparency theory, and empirically test the construct’s application. Originality/value – As a new research field, transparency has lacked a concise definition as well as a conceptual framework. This is the first comprehensive summary of transparency. In addition, this study contributes to the methodology of evaluating construct definitions to advance empirical research.

African Communitarian Bioethics and the Question of Paternalism

Bioethics is a field of study and professional practice, variously conceptualized fashionably as: multidisciplinarity, interdisciplinarity, transdisciplinarity, pluriperspectivity and integrativity. Despite being a professional practice that bioethicists engage with everyday, bioethics in Africa is still poorly characterized both methodologically and pedagogically as its discourse is still narrowly focused and its worldviews are increasingly alienated and marginalized from mainstream. Core bioethical values and principles from Africa are among the most under-theorized, underresearched, under-valued and under-discussed aspect in mainstream bioethics and professional practice. This is the case with communitarian bioethics whose philosophical foundations and normative underpinnings, moral theories and principles are still largely unexplored, and the solid pillars not yet firmly implanted as scepticism characterize its future. But dominant mainstream bioethical values are portrayed as the only valid universal ideal and Western bioethicists still struggle to ‘remake’ or ‘recreate’ the discipline according to their cultural and ethical traditions’. Confronted with this crisis of negation of identity, self affirmation and the quest for authenticity, this work is a radical critique of the foreign oppressive systems and structures of power that serve to define African existence in certain erroneous beliefs, paradigm and the consequent alienation of its worldview. It critically examines how mainstream bioethical values become a universal code of knowledge, intelligence, superiority, orderliness, purity and how it functions as a master sign. How

Political Myth and Political Glory: Shaping Media Reality

Today we cannot but notice the sequence of the considerable changes in the present-day social and cultural order through the obvious process of its invasion by certain semiotic constructs, possibly described as political myths, and nearly all of them closely connected with the issue of past/present/future glory. This glory could be lost (e.g., the col-lapse of the USSR), or gained anew (e.g., the joining of Crimea in 2014). The concepts of glory and victory in Russian political discourse are bound up with each other so closely that it is difficult to divide them. Besides, glory and victory are being gradually possessed by the establishment. At the same time, political myths are the means and the aim of this process. Myth comes forward as a universal code, and moreover, as a universal social-cultural matrix which contains patterns of ethics that are to be installed into the society. Besides, myth is a structure based upon the category of shap-ing the reality in which people may believe, not the category of belief. In the sphere of the media, myth broadcasts itself mainly through memes, using them both as instruments and as a certain communication channel. The structure of a meme is semiotic, while there is still a communicative difference between a meme and a myth. The idea of political glory is closely connected with the sphere of myth and with the concepts of time and space. This kind of integration makes up what Bakhtin called a “chronotope.” Three main myths of historical glory in present-day political discourse can be distinguished: the myth of Byzantium and the so-called “The Fifth Empire,” the myth of the “Polite People,” and the myth of “Panfilov’s Twenty-Eight.”