Technological Substitutions in the Computer Industry

The logistic substitution model is used to study substitutions of different microcomputer models and technologies at the low end of the computer range in Digital Equipment Corporation.

Модели осложненных предложений с сопоставительными оборотами в хакасском языке

Introduction. This article, based on the material of the Khakass language, describes models of complicated sentences with comparative constructions. Notably, many issues related to the description of complicated sentences in Khakass have not received proper coverage yet, which determines the relevance of this study. The article aims to identify and analyze the structural-semantic types, as well as ways of expressing complicated sentences with comparative constructions in the Khakass language. The research is based on a solid sample of examples from the texts of fiction of various genres, folklore, and journalistic texts, as well as recordings of oral speech. Results. The research shows that there are three types of complicated sentences in Khakass, including a comparative model based on the equality of compared features, a comparative-gradation model, and a substitution model. Each model is described in terms of its basic semantics and ways of formalizing the relationship between dependent and main parts, with specific examples illustrating their use. Each model varies in semantic and structural terms. The comparative model of equal features and the comparative-gradation model have two variants, the substitution model has five. In a comparative model based on equality of features, equal relations between two given events are expressed, while the comparison-gradation model compares the degree of significance of given events, with the action in the main part becoming significant. The substitution model may be of two types: substitutive per se and substitutive-preferential. In substitutive models proper, the actions of the main part do not meet the speaker’s expectation, while in the other model, preference is given to the main event.

HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models

Diverse phylogenetic methods require a substitution model of evolution that should mimic, as accurately as possible, the real substitution process. At the protein level, empirical substitution models have traditionally been based on a large number of different proteins from particular taxonomic levels. However, these models assume that all of the proteins of a taxonomic level evolve under the same substitution patterns. We believe that this assumption is highly unrealistic and should be relaxed by considering protein-specific substitution models that account for protein-specific selection processes. In order to test this hypothesis, we inferred and evaluated four new empirical substitution models for the protease and integrase of HIV and other viruses. We found that these models more accurately fit, compared with any of the currently available empirical substitution models, the evolutionary process of these proteins. We conclude that evolutionary inferences from protein sequences are more accurate if they are based on protein-specific substitution models rather than taxonomic-specific (generalist) substitution models. We also present four new empirical substitution models of protein evolution that could be useful for phylogenetic inferences of viral protease and integrase.

Forecasting Energy Needs with Logistics

The logistic function is used to forecast energy consumed worldwide and oil production in the U.S. The logistic substitution model is used to describe the energy mix since 1965 presenting a picture significantly different from the one covering the previous 100 years. In the new picture coal gently gains on oil and hydroelectric gains on natural gas even if it is three times smaller. Finally, renewables—wind, geothermal, solar, biomass, and waste—grow exclusively on the expense of nuclear, and are poised to overtake it by the late 2030s. By mid-21st century, coal, oil, and natural gas still remain the main players of comparable size. Hydroelectric has almost doubled in size. The only significant substitution is that of renewables having replaced nuclear albeit remaining at less than a ¼ the size of the other three energy sources. U.S. oil produced by fracking is forecasted to cease by mid-21st century, while oil produced by traditional methods should continue on its slowly declining trend. US oil production is likely to represent less than 1% of the oil consumed worldwide by mid-21st century.

Forecasting the Mix of World Energy Needs by mid-21st Century

The logistic function is used to forecast energy consumed worldwide. The logistic substitution model is used to describe the energy mix since 1965 presenting a picture significantly different from the one covering the previous 100 years. In the new picture the share of heavy pollutants, i.e. coal plus oil, keeps declining systematically in favor of natural gas and renewables (wind, geothermal, solar, biomass, and waste), the share of which grows rapidly. The shares of these three energy sources are poised to reach around 30% each by mid-21st century. Nuclear and hydroelectric energy, both with rather stable shares, are responsible for the remaining 10%, which goes mostly to hydroelectric; Zooming into the composition of renewables we find that today’s dominant wind power is about to begin losing share to solar energy, which will overtake wind after 2024 and account for more than 90% of all renewables by mid-21st century, by which time geothermal, biomass, and other sources of energy will have dropped to insignificant levels. Forecasts in exajoules are given for all energy sources up to 2050.

SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels

Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. Results GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. Conclusions The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.

Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (?). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ?=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.

83Replacing sedentary time with moderate-to-vigorous physical activity is associated with decreased serum SPARC in men

Background Secreted protein acidic and rich in cysteine (SPARC) may play a role in the prevention of colon cancer through exercise, while SPARC is considered as a promoter of insulin resistance. The purpose of the present study was to clarify the effects of replacing sedentary time with either light-intensity PA (LPA) or moderate- to vigorous-intensity PA (MVPA) on serum SPARC in a general population. Methods The study subjects were 4000 men and 6040 women (40 to 69 years) who participated in baseline surveys of a population-based cohort study. Sedentary time, LPA, and MVPA were objectively measured by an accelerometer. The serum SPARC concentration was measured by an enzyme-linked immunosorbent assay. Using an isotemporal substitution model, cross-sectional associations of replacing sedentary time with either LPA or MVPA on serum SPARC levels were analyzed according to sex. Adjustment was made for potential confounding factors. Results In men, replacing 60 min of sedentary time with 60 min of MVPA was associated with 23 ng/mL (confidence interval -43, -2) lower serum SPARC levels even after adjusting for confounders, including the BMI (P = 0.028), while no such association was observed for LPA. Furthermore, no such significant replacement effects were observed in women. Conclusions The current study showed that replacing sedentary time with MVPA results in reduced serum SPARC concentrations in men. Key messages Effect of habitual PA to decrease circulating SPARC is PA intensity-specific.