Evolution Of Code Research Articles

The impact of building energy codes evolution on the residential thermal demand

The building stock decarbonization by 2050 requires the implementation of an energy transition strategy. Building energy codes must be considered to minimize the energy consumption of the residential sector. This paper aims to evaluate the evolution of the building energy codes of Spain based on energy simulation. A quantitative assessment of the residential thermal demand according to the new energy efficiency requirements introduced in national regulations over the years was performed. Heating, cooling, and domestic hot water demands were assessed for 60 cases modeled in DesignBuilder, combining different building geometric typologies, energy codes, and climate zones. Heating presented the largest contribution to the total energy demand reaching up to 75%. The codes’ evolution led to a significant reduction in heating and a slighter decrease in cooling. The results showed an average energy demand improvement of 50% from the first regulatory release to the latest one.

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness.

Body hair is a defining mammalian characteristic, but several mammals, such as whales, naked mole-rats, and humans, have notably less hair. To find the genetic basis of reduced hair quantity, we used our evolutionary-rates-based method, RERconverge, to identify coding and noncoding sequences that evolve at significantly different rates in so-called hairless mammals compared to hairy mammals. Using RERconverge, we performed a genome-wide scan over 62 mammal species using 19,149 genes and 343,598 conserved noncoding regions. In addition to detecting known and potential novel hair-related genes, we also discovered hundreds of putative hair-related regulatory elements. Computational investigation revealed that genes and their associated noncoding regions show different evolutionary patterns and influence different aspects of hair growth and development. Many genes under accelerated evolution are associated with the structure of the hair shaft itself, while evolutionary rate shifts in noncoding regions also included the dermal papilla and matrix regions of the hair follicle that contribute to hair growth and cycling. Genes that were top ranked for coding sequence acceleration included known hair and skin genes KRT2, KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary rate shifts in nearby noncoding regions. Conversely, accelerated noncoding regions are most strongly enriched near regulatory hair-related genes and microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show rate shifts in their protein-coding sequences. Such dichotomy highlights the interplay between the evolution of protein sequence and regulatory sequence to contribute to the emergence of a convergent phenotype.

Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro

The ribosome is a macromolecular machine that catalyzes the sequence-defined polymerization of L-α-amino acids into polypeptides. The catalysis of peptide bond formation between amino acid substrates is based on entropy trapping, wherein the adjacency of transfer RNA (tRNA)-coupled acyl bonds in the P-site and the α-amino groups in the A-site aligns the substrates for coupling. The plasticity of this catalytic mechanism has been observed in both remnants of the evolution of the genetic code and modern efforts to reprogram the genetic code (e.g., ribosomal incorporation of non-canonical amino acids, ribosomal ester formation). However, the limits of ribosome-mediated polymerization are underexplored. Here, rather than peptide bonds, we demonstrate ribosome-mediated polymerization of pyridazinone bonds via a cyclocondensation reaction between activated γ-keto and α-hydrazino ester monomers. In addition, we demonstrate the ribosome-catalyzed synthesis of peptide-hybrid oligomers composed of multiple sequence-defined alternating pyridazinone linkages. Our results highlight the plasticity of the ribosome’s ancient bond-formation mechanism, expand the range of non-canonical polymeric backbones that can be synthesized by the ribosome, and open the door to new applications in synthetic biology.

30 Years of Video Coding Evolution - What Can We Learn from it in Terms of QoE?

From the beginnings of ITU-T H.261 to H.265 (HEVC), each new video coding standard has aimed at halving the bitrate at the same perceptual quality by redundancy and irrelevancy reduction. Each improvement has been explained by comparably small changes in the video coding toolset. This contribution aims at starting the Quality of Experience (QoE) analysis of the accumulated improvements over the last thirty years. Based on an overview of the changes in the coding tools, we analyze the changes in the quantized residual information. Visual comparison and statistical measures are performed and some interpretations are provided towards explaining how irrelevancy reduction may have led to such a huge reduction in bitrate. The interpretation of the results in terms of QoE paves the way towards an understanding of the coding tools in terms of visual quality. It may help in understanding how the irrelevancy reduction has been improved over the decades. Understanding how the differences of the residuals relate to known or yet unknown properties of the human visual system, may enable a closer collaboration between perception research and video compression research.

One-off events? An empirical study of hackathon code creation and reuse

ContextHackathons have become popular events for teams to collaborate on projects and develop software prototypes. Most existing research focuses on activities during an event with limited attention to the evolution of the hackathon code.ObjectiveWe aim to understand the evolution of code used in and created during hackathon events, with a particular focus on the code blobs, specifically, how frequently hackathon teams reuse pre-existing code, how much new code they develop, if that code gets reused afterwards, and what factors affect reuse.MethodWe collected information about 22,183 hackathon projects from Devpost and obtained related code blobs, authors, project characteristics, original author, code creation time, language, and size information from World of Code. We tracked the reuse of code blobs by identifying all commits containing blobs created during hackathons and identifying all projects that contain those commits. We also conducted a series of surveys in order to gain a deeper understanding of hackathon code evolution that we sent out to hackathon participants whose code was reused, whose code was not reused, and developers who reused some hackathon code.Result9.14% of the code blobs in hackathon repositories and 8% of the lines of code (LOC) are created during hackathons and around a third of the hackathon code gets reused in other projects by both blob count and LOC. The number of associated technologies and the number of participants in hackathons increase reuse probability.ConclusionThe results of our study demonstrates hackathons are not always “one-off” events as the common knowledge dictates and it can serve as a starting point for further studies in this area.

On the Seismic Behavior of Masonry Infilled Frame Structures

Infilled frames are usually modelled in the context of global building analysis using simplified procedures without considering the aspects resulting from the interaction between the panel and the frame. Other aspects, such as adequate design of the floor beams and the beam-columns’ joints, and control of potential sliding shear failure of the columns, that significantly affect the structural response, are also typically not accounted for. In the present work it is intended to look over the literature to evaluate the state of the art regarding the lessons learn from recent earthquakes, the evolution of the structural codes considering the infill masonry panels, and how this influences the evolution of the numerical models and the experimental works to overcome the existent gaps.

On the Evolutionary History of the Twenty Encoded Amino Acids.

α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.

Evolution of Seismic Reliability of Code-Conforming Italian Buildings

ABSTRACT It is well known that the seismic structural reliability is not explicitly controlled in design carried out according to seismic contemporary building codes; that is, those enforcing a simplified version of performance-based design. This is even more true for structures designed with obsolete seismic codes or without any seismic provisions at all, which constitute most of the building stock in countries such as Italy. Between 2019 and 2021, a large research project, RINTC – Rischio Implicito delle Norme Tecniche per le Costruzioni (i.e. implicit risk of existing buildings designed according to the Italian codes), has addressed, in a coherent manner, the inherent seismic structural reliability of existing Italian structures built according to evolving codes, which have now been superseded by multi-limit-state-based provisions. To this aim, five structural typologies of residential and industrial buildings have been considered, that is, reinforced concrete, pre-cast reinforced concrete, base-isolated reinforced concrete, masonry, and steel structures. The building design accounts for the evolution of codes within the last century or more. Structures are supposedly located at five sites in the country, representative of different seismic hazard, both currently and at the time of design. Nonlinear state-of-the-art three-dimensional numerical models for the considered structures have been analyzed via multi-stripe nonlinear dynamic analysis, the results of which, in turn, have been used to evaluate the annual failure rate as a measure of seismic reliability with respect to two performance levels defined within the project and named global collapse and usability-preventing damage. These rates, finally, allowed to appreciate the variation of seismic safety with the evolution of codes and to compare with that implied by current design. The results of the study allowed to conclude that the evolution of seismic codes clearly tends to enhance the seismic reliability with the largest average improvement attributable to the enforcement of the current code.

Large-Scale Open-Jet Testing: A new frontier in structural wind Engineering

This study aims to meet the widely reported challenges associated with building aerodynamics by testing large-scale models in flows that exhibit complete turbulence (low- and high-frequency spectral content) at high Reynolds numbers. We tested 1:5 and 1:10 scale models of the Silsoe cube at multiple locations in the Louisiana State University (LSU) open-jet facility. The paper investigates the velocity-related parameters and the statistical quantities of roof pressures to yield a suitable scale and testing location in the facility. Moreover, we compare measured surface pressures with those from Tokyo Polytechnic University’s (TPU) wind tunnel and the Silsoe full-scale data to validate the results. We attempt to generate both small- and large-scale turbulence by employing the concept of flow without boundaries. The paper reveals the open-jet facility’s promising capabilities to produce mean and peak pressures on buildings, which accurately conform with the full-scale counterparts. The results suggest that the open-jet facility can generate realistic wind loads on low-rise buildings, a fundamental step towards reconciling current design guidelines for the evolution of code and standard provisions.

The evolution of Indonesian seismic and concrete building codes: From the past to the present

The factors primarily affecting the seismic vulnerability of existing concrete buildings are the seismic base shear strength which is regulated in the seismic loading codes and the seismic detailing which is regulated through the concrete design codes since both of them are specified and legally enforceable as the minimum standard. This study provides a comprehensive summary of the evolution of the seismic loading and detailing codes for reinforced concrete buildings in Indonesia from 1970 to the present. It specifically focuses on substantial changes in various Indonesian seismic loading and concrete codes for buildings due to the increase in the seismic demand for both strength and ductility. Moreover, lessons learned obtained from the recent two considerable earthquakes, Palu and Lombok earthquakes 2018, were also presented. The main aim is to construct the universal framework of seismic resistance of existing concrete buildings in Indonesia designed through prior versions of Indonesian codes in line with preparing the first Indonesian National Standard (SNI) for seismic evaluation and rehabilitation. The base shear of the low, medium, and high-rise buildings designed using different versions of Indonesian seismic design codes were also compared comprehensively to indicate their significant changes on buildings and identify the possibility of strength deficiency of existing buildings in several big cities in Indonesia which represent most of the seismic zones.

Trinucleotide [formula omitted]-circular codes II: Biology

A code X is (⩾k)-circular if every concatenation of words from X that admits, when read on a circle, more than one partition into words from X, must contain at least k+1 words. In other words, the reading frame retrieval is guaranteed for any concatenation of up to k words from X. A code that is (⩾k)-circular for all integers k is said to be circular. Any code is (⩾0)-circular and it turns out that a code of trinucleotides is circular as soon as it is (⩾4)-circular. A code is k-circular if it is (⩾k)-circular and not (⩾k+1)-circular. The theoretical aspects of trinucleotide k-circular codes have been developed in a companion article (Michel et al., 2022).Trinucleotide circular codes always retrieve the reading frame, leaving no ambiguous sequences. On the contrary, trinucleotide k-circular codes, for k∈{0,1,2,3} all have ambiguous sequences, for which the reading frame cannot always be retrieved. However, such a trinucleotide k-circular code is still able to retrieve the reading frame for a number of sequences, thereby exhibiting a partial circularity property. We describe this combinatorial property for each class of trinucleotide k-circular codes with k∈{0,1,2,3}. The circularity, i.e. the reading frame retrieval, is an ordinary property in genes. In order to consider the different cases of ambiguous sequences, we derive a new and general formula to measure the reading frame loss, whatever the trinucleotide k-circular code. This formula allows us to study the evolution of any trinucleotide k-circular code of (maximal) cardinality 20 to the genetic code, based on the reading frame retrieval property. We apply this approach to analyse the evolution of the trinucleotide circular code X observed in genes to the genetic code.The (⩾1)-circular codes of maximal size 20 necessarily have the same number of each nucleotide, specifically 15=3⋅20/4. This balanceness property can also be achieved by trinucleotide codes of cardinality 4,8,12 and 16. We call such trinucleotide codes balanced. We develop a general mathematical method to compute the number of balanced trinucleotide codes of each size, which also applies to self-complementary trinucleotide codes. We establish and quantify a relation between this balanceness property and the self-complementarity property.The combinatorial hierarchy of trinucleotide k-circular codes is updated with the growth function results. The numbers of amino acids coded by the trinucleotide k-circular codes are given for the cases maximal, minimal, self-complementary k-, (k,k,k)- and self-complementary (k,k,k)-circular.

Unbiased simplified seismic fragility estimation of non-ductile infilled RC structures

Infilled reinforced concrete (RC) buildings represent a prevalent taxonomy class in the Mediterranean region. Many were constructed before proper seismic provisions and detailing were enforced meaning they typically possess non-ductile failure mechanisms. Therefore, their simple but adequate seismic fragility estimation remains a challenge for the research community and practitioners. Moreover, their performance quantification can typically require characterisation via detailed numerical models that capture salient behaviour features, which involves extensive non-linear dynamic analyses with large computational burden. In this regard, an unbiased seismic fragility estimation methodology for the simplified assessment of infilled RC frame structures is described for both collapsing and non-collapsing scenarios. Its development is using extensive cloud analyses carried out with a large set of oscillators representative of the infilled RC frame's structural behaviour to permit the well-established pushover-based methods to be adopted in practice. The result is a novel set of empirical relationships relating the seismic behaviour of these typologies to their pushover curve parameters to allow practitioners to perform an accurate risk assessment and verification in an expedited manner. The choice of average spectral acceleration as the intensity measure used to characterise the fragility parameters for these relationships is shown to present notable advantages in reducing bias compared with other existing approaches. The results are validated via comparison with a detailed hazard-consistent assessment of case studies from a database of three-dimensional archetype building models. These were also developed here to capture the temporal evolution of building codes and architectural features of the building class in Italy.

From matter to form: the evolution of the genetic code as semio-poiesis

Abstract We address issues of description of the origin and evolution of the genetic code from a semiotics standpoint. Developing the concept of codepoiesis introduced by Barbieri, a new idea of semio-poiesis is proposed. Semio-poiesis, a recursive auto-referential processing of semiotic system, becomes a form of organization of the bio-world when and while notions of meaning and aiming are introduced into it. The description of the genetic code as a semiotic system (grammar and vocabulary) allows us to apply the method of internal reconstruction to it: on the basis of heterogeneity and irregularity of the current state, to explicate possible previous states and various ways of forming mechanisms of coding and textualization. The revealed patterns are consistent with hypotheses about the origin and evolution of the genetic code.

RefactoringMiner 2.0

Refactoring detection is crucial for a variety of applications and tasks: (i) empirical studies about code evolution, (ii) tools for library API migration, (iii) code reviews and change comprehension. However, recent research has questioned the accuracy of the state-of-the-art refactoring mining tools, which poses threats to the reliability of the detected refactorings. Moreover, the majority of refactoring mining tools depend on code similarity thresholds. Finding universal threshold values that can work well for all projects, regardless of their architectural style, application domain, and development practices is extremely challenging. Therefore, in a previous work [N. Tsantalis, M. Mansouri, L. M. Eshkevari, D. Mazinanian, and D. Dig, Accurate and efficient refactoring detection in commit history, in 40th International Conference on Software Engineering, 2018, pp. 483–494], we introduced the first refactoring mining tool that does not require any code similarity thresholds to operate. In this work, we extend our tool to support low-level refactorings that take place within the body of methods. To evaluate our tool, we created one of the most accurate, complete, and representative refactoring oracles to date, including 7,226 true instances for 40 different refactoring types detected by one (minimum) up to six (maximum) different tools, and validated by one up to four refactoring experts. Our evaluation showed that our approach achieves the highest average precision (99.6 percent) and recall (94 percent) among all competitive tools, and on median is 2.6 times faster than the second faster competitive tool.

Bias-free estimation of information content in temporally sparse neuronal activity.

Applying information theoretic measures to neuronal activity data enables the quantification of neuronal encoding quality. However, when the sample size is limited, a naïve estimation of the information content typically contains a systematic overestimation (upward bias), which may lead to misinterpretation of coding characteristics. This bias is exacerbated in Ca2+ imaging because of the temporal sparsity of elevated Ca2+ signals. Here, we introduce methods to correct for the bias in the naïve estimation of information content from limited sample sizes and temporally sparse neuronal activity. We demonstrate the higher accuracy of our methods over previous ones, when applied to Ca2+ imaging data recorded from the mouse hippocampus and primary visual cortex, as well as to simulated data with matching tuning properties and firing statistics. Our bias-correction methods allowed an accurate estimation of the information place cells carry about the animal’s position (spatial information) and uncovered the spatial resolution of hippocampal coding. Furthermore, using our methods, we found that cells with higher peak firing rates carry higher spatial information per spike and exposed differences between distinct hippocampal subfields in the long-term evolution of the spatial code. These results could be masked by the bias when applying the commonly used naïve calculation of information content. Thus, a bias-free estimation of information content can uncover otherwise overlooked properties of the neural code.

"Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code.

The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.

Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling.

The role of aminoacyl-tRNA synthetases (aaRS) in the emergence and evolution of genetic coding poses challenging questions concerning their provenance. We seek evidence about their ancestry from curated structure-based multiple sequence alignments of a structurally invariant “scaffold” shared by all 10 canonical Class I aaRS. Three uncorrelated phylogenetic metrics—mutation frequency, its uniformity, and row-by-row cladistic congruence—imply that the Class I scaffold is a mosaic assembled from successive genetic sources. Metrics for different modules vary in accordance with their presumed functionality. Sequences derived from the ATP– and amino acid– binding sites exhibit specific two-way coupling to those derived from Connecting Peptide 1, a third module whose metrics suggest later acquisition. The data help validate: (i) experimental fragmentations of the canonical Class I structure into three partitions that retain catalytic activities in proportion to their length; and (ii) evidence that the ancestral Class I aaRS gene also encoded a Class II ancestor in frame on the opposite strand. A 46-residue Class I “protozyme” roots the Class I tree prior to the adaptive radiation of the Rossmann dinucleotide binding fold that refined substrate discrimination. Such rooting implies near simultaneous emergence of genetic coding and the origin of the proteome, resolving a conundrum posed by previous inferences that Class I aaRS evolved after the genetic code had been implemented in an RNA world. Further, pinpointing discontinuous enhancements of aaRS fidelity establishes a timeline for the growth of coding from a binary amino acid alphabet.

Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems.

Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.

RNP-world: The ultimate essence of life is a ribonucleoprotein process.

The fundamental essence of life is based on process of interaction between nucleic acids and proteins. In a prebiotic world, amino acids, peptides, ions, and other metabolites acted in protobiotic routes at the same time on which RNAs performed catalysis and self-replication. Nevertheless, it was only when nucleic acids and peptides started to interact together in an organized process that life emerged. First, the ignition was sparked with the formation of a Peptidyl Transferase Center (PTC), possibly by concatenation of proto-tRNAs. This molecule that would become the catalytic site of ribosomes started a process of self-organization that gave origin to a protoorganism named FUCA, a ribonucleic ribosomal-like apparatus capable to polymerize amino acids. In that sense, we review hypotheses about the origin and early evolution of the genetic code. Next, populations of open biological systems named progenotes were capable of accumulating and exchanging genetic material, producing the first genomes. Progenotes then evolved in two paths: some presented their own ribosomes and others used available ribosomes in the medium to translate their encoded information. At some point, two different types of organisms emerged from populations of progenotes: the ribosome-encoding organisms (cells) and the capsid-encoding organisms (viruses).

Multi-Level Visualization of Aggregated Information About Source Code Evolution Across Multiple Versions

Multi-Level Visualization of Aggregated Information About Source Code Evolution Across Multiple Versions