Evolutionary tree-based quasi identifier and federated gradient privacy preservations over big healthcare data

<span>Big data has remodeled the way organizations supervise, examine and leverage data in any industry. To safeguard sensitive data from public contraventions, several countries investigated this issue and carried out privacy protection mechanism. With the aid of quasi-identifiers privacy is not said to be preserved to a greater extent. This paper proposes a method called evolutionary tree-based quasi-identifier and federated gradient (ETQI-FD) for privacy preservations over big healthcare data. The first step involved in the ETQI-FD is learning quasi-identifiers. Learning quasi-identifiers by employing information loss function separately for categorical and numerical attributes accomplishes both the largest dissimilarities and partition without a comprehensive exploration between tuples of features or attributes. Next with the learnt quasi-identifiers, privacy preservation of data item is made by applying federated gradient arbitrary privacy preservation learning model. This model attains optimal balance between privacy and accuracy. In the federated gradient privacy preservation learning model, we evaluate the determinant of each attribute to the outputs. Then injecting Adaptive Lorentz noise to data attributes our ETQI-FD significantly minimizes the influence of noise on the final results and therefore contributing to privacy and accuracy. An experimental evaluation of ETQI-FD method achieves better accuracy and privacy than the existing methods.</span>

Four Types of ST11 Novel Mutations From Increasing Carbapenem-Resistant Klebsiella pneumoniae in Guangdong, 2016–2020

Objectives: This study aimed to explore changes in carbapenem-resistant Klebsiella pneumoniae (CR-KP) isolates collected in Guangdong over the period of 2016–2020.Methods: Antibacterial susceptibility was quantified through VITEK 2 compact and K-B method. Carbapenemase phenotypes and genotypes were characterized by modified carbapenem inactivation method (mCIM), EDTA-carbapenem inactivation method (eCIM), and polymerase chain reaction (PCR). Molecular characteristics and evolutionary trends were analyzed by multilocus sequence typing and evolutionary tree.Results: Isolates (2,847) of K. pneumoniae were separated in 2016–2020, and the separate rate of CR-KP increased from 5.65 to 9.90% (p = 0.009). The top 3 wards were intensive care unit (ICU) (21.92%), neonatal wards (13.70%), and respiratory wards (12.33%). In 146 CR-KP strains, serine carbapenemase was the main phenotype, and KPC was the main genotype, and 57 contained two resistant genes, and 1 contained three resistant genes. Two polygenic strains were first found: IMP + GES and KPC + NDM + VIM, but all the phenotypes were metalloenzyme, which indicated that metalloenzyme was usually the first choice for CR-KP resistance. In addition, all the ST54 of metalloenzyme type contained IMP, and all the ST45, ST37, and ST76 contained OXA. ST11 was the most prevalent (42.47%); ST11 and its mutants proved the predominant sequence type making up 51.1% of the carbapenemase-producing isolates. A novel type of ST11 mutation, the rpoB was mutated from sequence 1 to sequence 146, was in an independent separate branch on the evolutionary tree and was resistant to all antibacterial agents. The other three mutants, rpoB 1–15, infB 3–148, and infB 3–80, are also resistant to all antibacteria. Of note, all the four mutants produced serine carbapenemase and contained KPC, and indicated that the prevalent strain in China, ST11, has serious consequences and potential outbreaks.Conclusion: The infection rate of CR-KP has increased, and ICU and neonatal wards have become the key infection areas. Producing serine enzyme, the KPC genotype, and ST11 are the predominant CR-KP. Polygenic strains and ST11 mutation made clinical treatment difficult and may become a potential threat.

mSphere of Influence: How I Learned to Love Bacteria and their Tangled Evolutionary Tree

Tera Levin works in the fields of evolution, microbiology, and genetics, studying how adaptation shapes the molecular interactions between eukaryotic hosts and bacterial pathogens. In this mSphere of Influence article, she reflects on how the paper “Population genomics of early events in the ecological differentiation of bacteria” by Shapiro et al. (B.

Use of the Codon Table to Quantify the Evolutionary Role of Random Mutations

The various biases affecting RNA mutations during evolution is the subject of intense research, leaving the extent of the role of random mutations undefined. To remedy this lacuna, using the codon table, the number of codons representing each amino acid was correlated with the amino acid frequencies in different branches of the evolutionary tree. The correlations were seen to increase as evolution progressed. Furthermore, the number of RNA mutations that resulted in a given amino acid mutation were found to be correlated with several widely used amino acid similarity tables (used in sequence alignments). These correlations were seen to increase when the observed codon usage was factored in.

2. The evolution of amphibians

‘The evolution of amphibians’ traces the evolutionary origin of living amphibians: anurans, urodeles, and caecilians. The comparison of the DNA sequence of their genes shows that the living amphibians taken together are a monophyletic group. This means that they all go back to a single common ancestor that had already separated from the common ancestor of the amniotes in the evolutionary tree. However, molecular evidence is little help in discovering which of the ancient tetrapod groups are related to the modern groups. Moreover, the earliest fossils of the three modern groups do not occur until far later, tens of millions years later, than any plausible relatives amongst the Carboniferous and Permian tetrapods.

Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7

The SARS-CoV-2 variant of concern B.1.1.7 has quickly spread. To identify its crucial mutations, we explored the B.1.1.7 associated mutations on an evolutionary tree by the Coronavirus GenBrowser and VENAS. We found that a non-coding deletion g.a28271-, at upstream of the nucleocapsid (N) gene, has triggered the high transmissibility of B.1.1.7. The deletion changes the core Kozak site of the N gene and may reduce the expression of N protein and increase that of ORF9b. The expression of ORF9b is also regulated by another mutation (g.gat28280cta) that mutates the core Kozak sites of the ORF9b gene. If both mutations back-mutate, the B.1.1.7 variant loses its high transmissibility. Moreover, the deletion may interact with ORF1a:p.SGF3675-, S:p.P681H, and S:p.T716I to increase the viral transmissibility. Overall, these results demonstrate the importance of the non-coding deletion and provide evolutionary insight into the crucial mutations of B.1.1.7.

ZAERA-POLO’S ARCHITECTURAL COMPASS AS A RESEARCH TOOL FOR MODERN CONCEPTS OF ARCHITECTURAL ENVIRONMENT DESIGN

The article examines the trends in modern architecture, outlined in the studies of architectural critic Alejandro Zaera-Polo and his team. The tool they’ve created was named ‘Interactive Map of Modern Architecture’. Charles Jencks’s ‘Evolutionary Tree’ (diagram of 20th-century architecture) had a significant influence on this tool. The functionality of Zaera-Polo’s map has been examined for five years by the author of this article while tutoring future architects at the Department of Architectural Environment Design at Lviv Polytechnic National University. These examinations allowed us to formulate a number of proposals to improve both - the structure of this map and the methodology of its creation.

Understanding Molecular Clocks and Time Trees

This chapter examines molecular clocks and time trees. Although laden with numerous process assumptions that may or may not be true (or knowable), the idea is appealingly straightforward: if amino acid substitutions in proteins occurred at a relatively steady pace that were more or less constant both over time and along each of the branches of a diverging evolutionary tree, then the number of substitutions would be directly related to the time since the taxa in question diverged from one another. However, evidence does not support a universal molecular clock. Evidence might or might not support “local” clocklike evolution among closely related taxa over relatively short time spans. Although absolute minimum ages for clades may be inferred from fossils, from biogeographical patterns, or extrapolated from secondary calibrations, such age estimates are subject to potentially significant error due to vagaries of geological dating as well as ambiguities of fossil identity. The test of a time tree hypothesis is to discover new fossil evidence that corroborates or falsifies it.

Natural Cybernetics of Time, or about the Half of any Whole

Norbert Wiener’s idea of “cybernetics” is linked to temporality as in a physical as in a philosophical sense. “Time orders” can be the slogan of that natural cybernetics of time: time orders by itself in its “screen” in virtue of being a well-ordering valid until the present moment and dividing any totality into two parts: the well-ordered of the past and the yet unordered of the future therefore sharing the common boundary of the present between them when the ordering is taking place by choices. Thus, the quantity of information defined by units of choices, whether bits or qubits, describes that process of ordering happening in the present moment. The totality (which can be considered also as a particular or “regional” totality) turns out to be divided into two parts: the internality of the past and the externality of the future by the course of time, but identifiable to each other in virtue of scientific transcendentalism (e.g. mathematical, physical, and historical transcendentalism). A properly mathematical approach to the “totality and time” is introduced by the abstract concept of “evolutionary tree” (i.e. regardless of the specific nature of that to which refers: such as biological evolution, Feynman trajectories, social and historical development, etc.), Then, the other half of the future can be represented as a deformed mirror image of the evolutionary tree taken place already in the past: therefore the past and future part are seen to be unifiable as a mirrorly doubled evolutionary tree and thus representable as generalized Feynman trajectories. The formalism of the separable complex Hilbert space (respectively, the qubit Hilbert space) applied and further elaborated in quantum mechanics in order to uniform temporal and reversible, discrete and continuous processes is relevant. Then, the past and future parts of evolutionary tree would constitute a wave function (or even only a single qubit once the concept of actual infinity be involved to real processes). Each of both parts of it, i.e. either the future evolutionary tree or its deformed mirror image, would represented a “half of the whole”. The two halves can be considered as the two disjunctive states of any bit as two fundamentally inseparable (in virtue of quantum correlation) “halves” of any qubit. A few important corollaries exemplify that natural cybernetics of time.

Luigi Luca Cavalli-Sforza. 25 January 1922—31 August 2018

Though it was as a bacteriologist that Luca Cavalli-Sforza first flourished scientifically, it was the subject of human population genetics that he dominated for the second half of the twentieth century. He pioneered both genetical demography and the construction of the genetical evolutionary tree of man, initially from gene-frequency data and ultimately from tracing the paths of descent of individual DNA sequences. He was among the first to apply the new computers to the problems he encountered, using his self-taught knowledge of mathematics and statistics. He conducted expeditions to the Pygmies of the African rainforest and studied the spread of agriculture in Europe, demonstrating the similarity between its wave of advance and the contours of population gene frequency. He noted the correspondence between the descent tree of languages and the human evolutionary tree. Cavalli headed university departments in Pavia and then Stanford, surrounding himself with young colleagues and driving forward research with vigorous discussion and unceasing enthusiasm. His knowledge was spread across medicine and genetics, anthropology and linguistics, archaeology and history, and he expressed himself fluently in speech and writing in Italian, English and French. A true Renaissance man. His published work in human population genetics and cultural evolution over more than 50 years constituted ‘one long argument’, as Darwin said of The origin of species . The villages of the Parma valley were his Galapagos Islands, and random genetic drift his adjunct to natural selection for the case of man. His demonstration of the importance of drift in recent human evolution informed the model for constructing evolutionary trees from gene-frequency data. On this one long argument he wrote and lectured ceaselessly, not only for other scientists but also for a wider audience, always mindful of a responsibility to promote an understanding of man's biology and evolutionary history for society's benefit. In so doing he brought an informed and rational approach to the problem of human diversity and the problems of human diversity.