Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital and probably appeared during biogenesis four billion years ago. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and protein molecules, drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: tRNAs, aaRS, mRNAs, and ribosomes. When assembled in the right order, the translation machine created biosynthetic polypeptides, a process that transferred information from mRNAs to proteins. This was the beginning of the prebiotic information age. The molecular attraction between tRNA and amino acids led to different stages of the translation machines and the genetic code. tRNA is an ancient molecule that designed and built mRNA for storing the information of its cognate amino acid. Each mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional. The origin of the genetic code is enigmatic; herein we propose an evolutionary explanation: the demand for a wide range of specific enzymes in the peptide/RNA world was the main selective pressure for the origin of information-directed protein synthesis. We review three main concepts on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the adaptive theory. These three theories are compatible with our coevolution model of the translation machines and the genetic code. We suggest biosynthetic pathways as the origin of the specific translation machines which provided the framework for the origin of the genetic code. During translation, the genetic code developed in three stages coincident with the refinement of the translation machines: GNC code developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to understand the prebiotic information system better, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software called CATI (Codon-Amino Acid-Translator-Imitator) to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the translation might have worked in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. Using AnyLogic software we were able to simulate and visualize the entire evolution of the translation machines and the genetic code. The results indicate that the emergence of the information age from the peptide/RNA world was a watershed event in the origin of life about four billion years ago.

A new approach is presented to defining the amount of information, in which information is understood as the data about a finite set as a whole, whereas the average length of an integrative code of elements serves as a measure of information. We obtain a formula for the syntropy of reflection, that is, the information that two intersecting finite sets reflect about each other. The specificities of reflection of discrete systems through the combination of their parts are considered, and it is shown that the additive syntropy and entropy of reflection are measures of structural order and chaos. Three information laws have been established: the law of conservation of the sum of chaos and order; information law of reflection; the law of conservation and transformation of information. An assessment of the structural organization and the level of development of discrete systems is presented. It is shown that various measures of information are structural characteristics of integrative codes of elements of discrete systems. The conclusion is made that, from the informational-genetic positions, the synergetic theory of information is primary in relation to the Hartley-Shannon information theory. In the appendix we consider the asymmetry of the mutual reflection of finite sets and the proportionality of arbitrary quantities.

The Late Heavy Bombardment Period (4.1 to 3.8 billion years ago) of heightened impact cratering activity on young Earth is likely the driving force for the origin of life. During the Eoarchean, asteroids such as carbonaceous chondrites delivered the building blocks of life and water to early Earth. Asteroid collisions created innumerable hydrothermal crater lakes in the Eoarchean crust which inadvertently became the perfect cradle for prebiotic chemistry. These hydrothermal crater lakes were filled with cosmic water and the building blocks of life. forming a thick prebiotic soup. The unique combination of exogenous delivery of extraterrestrial building blocks of life, and the endogenous biosynthesis in hydrothermal impact crater lakes very likely gave rise to life. A new symbiotic model for the origin of life within the hydrothermal crater lakes is here proposed. In this scenario, life arose around four billion years ago through five hierarchical stages of increasing molecular complexity: cosmic, geologic, chemical, information, and biological. During the prebiotic synthesis, membranes first appeared in the hydrothermal crater lakes, followed by the simultaneous origin of RNA and protein molecules, creating the RNA/protein world. These proteins were noncoded protein enzymes that facilitated chemical reactions. RNA molecules formed in the hydrothermal crater basin by polymerization of the nucleotides on the montmorillonite mineral substrate. Similarly, the initial synthesis of abiotic protein enzymes was mediated by the condensation of amino acids on pyrite surfaces. The regular wet-dry cycles within the crater lakes assisted further concentration, condensation, and polymerization of the RNAs and proteins. Lipid membranes randomly encapsulated amino acids, RNA, and protein molecules from the prebiotic soup to initiate a molecular symbiosis inside the protocells, this led to the hierarchical emergence of several cell components. As the role of protein enzymes became essential for catalytic process in the RNA/protein world, Darwinian selection from noncoded to coded protein synthesis led to translation systems and the genetic code, heralding the information stage. In this stage, the biochemical pathways suggest the successive emergence of translation machineries such as tRNAs, aaRS, mRNAs, and of ribosomes for protein synthesis. The molecular attraction between tRNA and amino acid led to the emergence of translation machinery and the genetic code. tRNA is an ancient molecule that created mRNA for the purpose of storing amino acid information like a digital strip. Each mRNA strand became the storage device for genetic information that encoded the amino acid sequences in triplet nucleotides. As information became available in the digital languages of the codon within mRNA, biosynthesis became less random and more organized and directional. The original translation machinery was simpler before the emergence of the ribosome than that of today. We review three main concepts on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and adaptive theory. We believe that these three theories are not mutually exclusive, but are compatible with our coevolution model of translations machines and the genetic code. We suggest biosynthetic pathways as the origin of the translation machine that provided the framework for the origin of the genetic code. During translation, the genetic code developed in three stages coincident with the refinement of the translation machinery: GNC code with four codons and four amino acids during interactions of pre-tRNA/pre-aaRS /pre-mRNA, SNS code consisting of 16 codons and 10 amino acids appeared during the tRNA/aaRS/mRNA interaction, and finally the universal genetic code evolved with the emergence of the tRNA/aaRS/mRNA/ribosome machine. The universal code consists of 64 codons and 20 amino acids, with a redundancy that minimizes errors in translation. To address the question of the origin of the biological information system in the RNA/protein world, we converted letter codons into numerical codons in the Universal Genetic Code Table. We developed a software called CATI (Codon-Amino Acid-Translator-Imitator) to translate randomly chosen numerical codons into corresponding amino acids and vice versa, gaining insight into how translation might have worked in the RNA/protein world. We simulated the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. We used AnyLogic software to simulate and visualize the evolution of the translation machines and the genetic code. We conclude that the emergence of the information age from the RNA/protein world was a watershed event in the origin of life about four billion years ago.

In the coded pulse scanning light detection and ranging (LIDAR) system, the number of laser pulses used at a given measurement point changes depending on the modulation and the method of spreading used in optical code-division multiple access (OCDMA). The number of laser pulses determines the pulse width, output power, and duration of the pulse transmission of a measurement point. These parameters determine the maximum measurement distance of the laser and the number of measurement points that can be employed per second. In this paper, we evaluate the performance and characteristics of combinations of modulation and spreading technology that can be used for OCDMA, and study optimal combinations according to varying operating environments.

Context: Code smells are associated with poor design and programming style that often degrades code quality and hampers code comprehensibility and maintainability. Goal: Identify reports from the literature that provide evidence of the influence of code smells on the occurrence of software bugs. Method: We conducted a Systematic Literature Review (SLR) to reach the~stated goal. Results: The SLR includes selected studies from July 2007 to September 2017 which analyzed the source code for open source and proprietary projects, as well, as several code smells and anti-patterns. The results of this SLR show that 24 code smells are more influential in the occurrence of bugs according to 16 studies. In contrast, three studies reported that at least 6 code smells are less influential in such occurrences. Evidence from the selected studies also point out tools, techniques and procedures applied to analyze the influence. Conclusion: To the best of our knowledge, this is the first SLR to target this goal. This study provides an up-to-date and structured understanding of the influence of code smells on the occurrence of software bugs based on findings systematically collected from a list of relevant references in the latest decade.

Information molecules of DNA and RNA should obey principles of quantum mechanics where unitary operators in form of unitary matrices have key meanings. Unitary matrices are the basis of calculations in quantum computers. This article presents some author's results, which show that matrix forms of the representation of structured systems of molecular-genetic alphabets can be considered as sets of sparse unitary matrices related with phenomenologic features of the degeneracy of the genetic code. These sparse unitary matrices have orthogonal systems of functions in their rows and columns. A complementarity exists among some unitary genetic matrices in relation each other. Decompositions of numeric genetic matrices into sets of sparse unitary matrices are connected with the logical operation of modulo-2 addition used in quantum computers as well. Tensor (or Kronecker) families of unitary genetic matrices with their fractal-like properties are also considered. The described results are discussed in the frame of development of quantum-information approaches for modeling genetic systems.

A new optical steganography scheme is proposed that transmits a stealth optical code-division multiple-access (OCDMA) signal through a public binary phase-shift keying (BPSK) channel. Polarization beam splitters and arrayed waveguide gratings are used to implement a spectral-polarization coding (SPC) system with an incoherent optical source. We employ a Walsh–Hadamard code as the signature code of the user who wants to transmit stealth information using the system. A free space optical link applied to this system maintains the polarization states of light during propagation. The secret data is extracted using correlation detection and balanced subtraction in the OCDMA decoder of the intended receiver, and the other signal from the public channel is reduced by the OCDMA decoder. At the demodulator of the public channel, BPSK demodulation eliminates the stealth signal so that the public channel is not affected by the stealth signal. The two signals cannot interfere with each other. The results of this study show that our proposed optical steganography system is highly secure. The stealth signal can be favorably hidden in the public channel when the average source power of the stealth signal, public noise, and public signal are −5, −3, and 0 dBm, respectively.

Software-based ultrasound imaging systems provide high flexibility that allows easy and fast adoption of newly developed algorithms. However, the extremely high data rate required for data transfer from sensors (e.g., transducers) to the ultrasound imaging systems is a major bottleneck in the software-based architecture, especially in the context of real-time imaging. To overcome this limitation, in this paper, we present a Binary cLuster (BL) code, which yields an improved compression ratio compared to the exponential Golomb code. Owing to the real-time encoding/decoding features without overheads, the universal code is a good solution to reduce the data transfer rate for software-based ultrasound imaging. The performance of the proposed method was evaluated using in vitro and in vivo data sets. It was demonstrated that the BL-beta code has a good stable lossless compression performance of 20 ~ 30% while requiring no auxiliary memory or storage.

Akt1 is a proto-oncogene that is over active in most cancers. Akt1 activation requires phosphorylation at Thr308; phosphorylation at Ser473 further enhances catalytic activity. Akt1 activity is also regulated via interactions between the kinase domain and the N-terminal auto-inhibitory pleckstrin homology (PH) domain. As it was previously difficult to produce Akt1 in site-specifically phosphorylated forms, the contribution of each activating phosphorylation site to auto-inhibition was unknown. Using a combination of genetic code expansion and in vivo enzymatic phosphorylation, we produced Akt1 variants containing programmed phosphorylation to probe the interplay between Akt1 phosphorylation status and the auto-inhibitory function of the PH domain. Deletion of the PH domain increased the enzyme activity for all three phosphorylated Akt1 variants. For the doubly phosphorylated enzyme, deletion of the PH domain relieved auto-inhibition by 295-fold. We next found that phosphorylation at Ser473 provided resistance to chemical inhibition by Akti-1/2 inhibitor VIII. The Akti-1/2 inhibitor was most effective against pAkt1T308 and showed 4-fold decreased potency with Akt1 variants phosphorylated at Ser473. The data highlight the need to design more potent Akt1 inhibitors that are effective against the doubly phosphorylated and most pathogenic form of Akt1.

Due to the complexity, high-risk, and conservative character of construction companies, advanced digital technologies do not become widely adopted in the short term, while vendors make determined efforts to overcome this and disseminate their technologies. This paper presents the methods of an investigation addressing the extremely complex issues related to the current practices of digital technology adoption in construction. It discusses how construction companies follow a specific logical process linked to need, project objectives, characteristics of the adopting organization, and the characteristics of the new technology to be adopted. The study aims to demonstrate a novel method of data collection and analysis including data and methodological triangulation techniques including the use of NVivo and AHP to explore how companies make the decision to uptake a new technology (e.g. advanced crane, tunnel boring machine or drones) by focusing on customer and vendor activities, their interactions, contributing factors, and people involved in the process. The major original contribution of this paper is to develop an innovative methodological Cube for investigating the Construction Technology Adoption Process (CTAP) covering technology adoption, acceptance, diffusion and implementation concepts. CTAP is a framework that delineates the phases of the process that customer organizations use when deciding to adopt a new digital technology and the parallel vendor activities. The significance of these contributions is that they enable vendors to understand how to match their strategies with customer expectations in each phase of the CTAP. It also provides a benchmark for new construction companies to use the current best practice of decision making. Future research is warranted to more clearly delineate any differences with developing nations or related industries such as mining and property management.

Passive plasma spectroscopy is a well-established non-intrusive diagnostic technique. Depending on the emitter and its environment which determine the dominant interactions and effects governing emission line shapes, passive spectroscopy allows the determination of electron densities, emitter and perturber temperatures as well as other quantities like abundances. However, using spectroscopy needs appropriate line shape codes retaining all the physical effects governing the emission line profiles. This requires for line shape code developers to continuously correct or improve them to increase their accuracy when applied for diagnostics. This is exactly the aim expected from code-code and code-data comparisons. In this context, the He I 492 nm emitted in a helium corona discharge at room temperature represents an ideal case since its profile results from several broadening mechanisms: Stark, Doppler, resonance and van der Waals. The importance of each broadening mechanism depends on the plasma parameters. Here the profiles of the He I 492 nm in a helium plasma computed by various codes are compared for a selected set of plasma parameters. In addition, preliminary results related to plasma parameter determination using experimental spectra from a helium corona discharge at low pressure 1- 2 bars, are presented.

Many spectroscopic diagnostics are routinely used as a technique to infer the plasma parameters from line emission spectra but their accuracy depends on the numerical model or code used for the fitting process. However, the validation of a line shape code requires some steps : comparison of the line shape code with other similar codes for some academic (simple) cases and then more complex ones, comparison of the fitting parameters obtained from the best fit of the experimental spectra with those obtained with other diagnostic techniques and/or comparison of the fitting parameters obtained by different codes to fit the same experimental data. Here we compare the profiles of the hydrogen Balmer β line in a helium plasma computed by six codes for a selected set of plasma parameters and we report on the plasma parameters inferred by each of them from the fitting to a number of experimental spectra measured in a helium corona discharge where the pressure was in the range 1- 5 bar.

All life on Earth uses three integrated molecular systems in which genetic information contained in DNA base sequences is transmitted to ribosomes by RNA and a genetic code, then translated into the amino acid sequences of structural and catalytic proteins. Therefore, the most important point for understanding the origin of life is to determine how such systems could emerge from random processes on the early Earth. In this review, two alternatives are compared: the RNA world hypothesis and the [GADV]-protein world hypothesis. [GADV] refers to four amino acids, Gly [G], Ala [A], Asp [D] and Val [V] that are conserved in the amino acid sequences of many common proteins. Here I will argue that the origins of the three primary processes required for life to begin can be better explained by the GADV hypothesis than the RNA world hypothesis. The GADV hypothesis also incorporates a conversion process by which random polymers can evolve into proteins with ordered sequences.

The aim of this work was to determine if the development of low-cost or no-cost finite element analysis (FEA) software has advanced to the point where it can be used in place of trusted commercial FEA packages for linear static structural analyses using isotropic material models. Nonlinear structural analysis will be covered in a separate paper. Several suitable packages were identified, these underwent a process of systematic elimination when they were unable to meet the minimum imposed qualitative criteria. Three packages were chosen to be subjected to performance benchmarking, namely: Code_Aster/Salome Meca; Mecway and Z88 Aurora. SimScale, a browser-based analysis package was included as well because it met all the baseline criteria and has the potential to offer a completely cloud-based approach to computer aided engineering, potentially reshaping the way an engineering business views its operational capabilities. This paper presents the test cases and simulation results for packages that fall under the linear static structural analysis type.

Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code. The subsequent 49 years of code studies have elucidated notable features of the standard code, such as high robustness to errors, but failed to develop a compelling explanation for codon assignments. In particular, stereochemical affinity between amino acids and the cognate codons or anticodons does not seem to account for the origin and evolution of the code. Here I expand Crick’s hypothesis on RNA-only translation system by presenting evidence that this early translation already attained high fidelity that allowed protein evolution. I outline an experimentally testable scenario for the evolution of the code that combines a distinct version of the stereochemical hypothesis, in which amino acids are recognized via unique sites in the tertiary structure of proto-tRNAs, rather than by anticodons, expansion of the code via proto-tRNA duplication and the frozen accident.

The proposal that the genetic code was formed on the basis of protein synthesis directed by tRNA dimers is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes – structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process – anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are able to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don’t accumulate to saturation, which would trigger inhibition.

As argued by ‘Declaration of Concrete Environment (2010)’ of Korea and ‘Declaration of Asian Concrete Environment (2011)’ of six Asian countries, concrete as a single material has lately shown extremely large impact on environmental issues such as climate change. Assessment of environmental impact from concrete material and production has considerable importance. Concrete is a major material used in the construction industry that emits a large amount of substances with environmental impacts during its life cycle. Accordingly, technologies for the reduction in and assessment of the environmental impact of concrete from the perspective of Life Cycle Assessment must be developed. At present, the studies in relation to greenhouse gas emission from concrete are being carried out globally as a countermeasure against climate change. In this study, a sustainable concrete mix design algorithm was designed using correlation analyses, and its carbon emission and cost reduction performances were assessed. Using correlation analyses, the concrete strength, w/b and s/a ratios, and CO₂ emissions were identified as major variables of concrete mix design that influenced other variables. Also, this study aims to evaluate the CO₂ emission reduction performance of the algorithm-deduced sustainable concrete mix design, and therefore, the CO₂ emissions of the sustainable concrete mix design are compared with those of the actual concrete mix design applied to the construction of the office building A in South Korea.