scholarly journals Similarity Comparison of Multiple Coronavirus Sequences from 2D to 1D Linearizing Transformation

2020 ◽  
Author(s):  
Feng Deng ◽  
Jeffrey Zheng
Keyword(s):  
Density Matrix ◽  
Similarity Comparison ◽  
Rna Sequences ◽  
The Core ◽  
Scientific Exploration ◽  
Index Of Entropy

Abstract Many studies on COVID-19 have been carried out, and it is interesting to apply methods and models to process the whole sequence of RNA. Similarity comparison of SARS-CoV-2 genomes plays a key role in naturally tracing its origin in scientific exploration, and further explorations are required. In this paper, an innovative of transformation from a 2D density matrix to 1D measuring vector is proposed based on the A5 module of the MAS for visualization. The core transformation projects whole RNA sequences of multiple coronaviruses in 2D matrices and then forms 1D measuring vectors on variant maps. The relationships of SARSCoV-2 genomes are compared by their similarity properties and genomic index of entropy quantities applied to classify relevant results into groups.

scholarly journals Similarity Comparison of Multiple Coronavirus Sequences from 2D to 1D Linearizing Transformation

2021 ◽  
Author(s):  
Feng Deng ◽  
Jeffrey Zheng
Keyword(s):  
Density Matrix ◽  
Similarity Comparison ◽  
Rna Sequences ◽  
The Core ◽  
Scientific Exploration ◽  
Index Of Entropy

Abstract Many studies on COVID-19 have been carried out, and it is interesting to apply methods and models to process the whole sequence of RNA. Similarity comparison of SARS-CoV-2 genomes plays a key role in naturally tracing its ori-gin in scientific exploration, and further explorations are required. In this paper, an innovative of transformation from a 2D density matrix to 1D measuring vector is proposed based on the A5 module of the MAS for visualization. The core transformation projects whole RNA sequences of multiple coronaviruses in 2D matrices and then forms 1D measuring vectors on variant maps. The relationships of SARS-CoV-2 genomes are compared by their similarity properties and genomic index of entropy quantities applied to classify relevant results into groups.

scholarly journals Functional Group Decomposition of Multiple Coronaviruses on Variant Maps

2021 ◽  
Author(s):  
Liuyun Du ◽  
Jeffrey Zheng
Keyword(s):  
Density Matrix ◽  
Measurement Method ◽  
Functional Group ◽  
Discrete Mathematics ◽  
Coordinate Systems ◽  
Rna Sequences ◽  
Statistical Measures ◽  
Visual Results

Abstract Different coronaviruses can be identified as three categories: common coronaviruses, fatal coronaviruses, and domestic coronaviruses. It is convenient to generate various visual results for their RNA sequences on variant maps. In this paper, a functional group measurement method is proposed to combine discrete mathematics and computational technologies on the A2 module of the MAS. Various samples are processed by this scheme and interesting results can be observed. The projections of the segmented groups on each coronavirus compared with the projective effects on different coronaviruses in 2D maps of coordinate systems are shown by statistical measures on the density matrix with similarity and dissimilarity properties for further exploration.

scholarly journals Functional Group Decomposition of Multiple Coronaviruses on Variant Maps

2020 ◽  
Author(s):  
Liuyun Du ◽  
Jeffrey Zheng
Keyword(s):  
Density Matrix ◽  
Measurement Method ◽  
Functional Group ◽  
Discrete Mathematics ◽  
Coordinate Systems ◽  
Rna Sequences ◽  
Statistical Measures ◽  
Visual Results

Abstract Different coronaviruses can be identified as three categories: common coronaviruses, fatal coronaviruses, and domestic coronaviruses. It is convenient to generate various visual results for their RNA sequences on variant maps. In this paper, a functional group measurement method is proposed to combine discrete mathematics and computational technologies on the A2 module of the MAS. Various samples are processed by this scheme and interesting results can be observed. The projections of the segmented groups on each coronavirus compared with the projective effects on different coronaviruses in 2D maps of coordinate systems are shown by statistical measures on the density matrix with similarity and dissimilarity properties for further exploration.

High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1993-2002 ◽  
Author(s):  
Elisabeth R M Tillier ◽  
Richard A Collins
Keyword(s):  
Base Pair ◽  
Large Subunit ◽  
Small Subunit ◽  
High Ratio ◽  
Small Subunit Rrna ◽  
Rna Sequences ◽  
Instantaneous Rate ◽  
The Core ◽  
Rrna Sequences ◽  
Simultaneous Substitution

Abstract We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-U→G-C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, αd, vs. rates of substitution of individual bases, αs in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of αd/αs, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of αd/αs in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of αd/αs. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.

scholarly journals Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix.

1985 ◽  
Vol 5 (6) ◽  
pp. 1287-1294 ◽  
Author(s):  
R I Bolla ◽  
D C Braaten ◽  
Y Shiomi ◽  
M B Hebert ◽  
D Schlessinger
Keyword(s):  
Nuclear Dna ◽  
Micrococcal Nuclease ◽  
Rna Sequences ◽  
S1 Nuclease ◽  
The Core ◽  
Rdna Sequences ◽  
L Cell ◽  
Cytoplasmic Rna ◽  
Rrna Species ◽  
Tight Association

Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-like, and 5S RNA sequences. It also lacked sequences coding for cytoplasmic rRNA species, since it did not hybridize to the 18S to 28S portion of rDNA in Northern blot analyses and none of it was protected by hybridization to a 100-fold excess of total cytoplasmic RNA in S1 nuclease assays. However, the core nucleolar DNA did hybridize to nontranscribed and external transcribed spacer rDNA sequences. We infer that specific portions of rDNA are protected from DNase action by a tight association with nucleolar structural proteins.

Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix

1985 ◽  
Vol 5 (6) ◽  
pp. 1287-1294 ◽  
Author(s):  
R I Bolla ◽  
D C Braaten ◽  
Y Shiomi ◽  
M B Hebert ◽  
D Schlessinger
Keyword(s):  
Nuclear Dna ◽  
Micrococcal Nuclease ◽  
Rna Sequences ◽  
S1 Nuclease ◽  
The Core ◽  
Rdna Sequences ◽  
L Cell ◽  
Cytoplasmic Rna ◽  
Rrna Species ◽  
Tight Association

Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-like, and 5S RNA sequences. It also lacked sequences coding for cytoplasmic rRNA species, since it did not hybridize to the 18S to 28S portion of rDNA in Northern blot analyses and none of it was protected by hybridization to a 100-fold excess of total cytoplasmic RNA in S1 nuclease assays. However, the core nucleolar DNA did hybridize to nontranscribed and external transcribed spacer rDNA sequences. We infer that specific portions of rDNA are protected from DNase action by a tight association with nucleolar structural proteins.

What face familiarity feelings say about the lateralization of specific entities within the core system

2019 ◽  
Vol 42 ◽  
Author(s):  
Guido Gainotti
Keyword(s):  
Temporal Lobe ◽  
Memory System ◽  
Core System ◽  
The Core ◽  
Memory Traces ◽  
Specific Memory ◽  
Target Article ◽  
Temporal Structures ◽  
The Right

Abstract The target article carefully describes the memory system, centered on the temporal lobe that builds specific memory traces. It does not, however, mention the laterality effects that exist within this system. This commentary briefly surveys evidence showing that clear asymmetries exist within the temporal lobe structures subserving the core system and that the right temporal structures mainly underpin face familiarity feelings.

A scanning electron microscopic study on dissolving process of cholesterol gallstones by chenodeoxycholic acid (CDCA)

1978 ◽  
Vol 36 (2) ◽  
pp. 522-523
Author(s):  
T. Kanetaka ◽  
M. Cho ◽  
S. Kawamura ◽  
T. Sado ◽  
K. Hara
Keyword(s):  
Electron Microscope ◽  
Chenodeoxycholic Acid ◽  
Outer Surface ◽  
Electron Microscopic ◽  
Cholesterol Gallstones ◽  
The Core ◽  
Scanning Electron Microscopic Study ◽  
Scanning Electron Microscopic ◽  
Acceleration Voltage ◽  
Scanning Electron

The authors have investigated the dissolution process of human cholesterol gallstones using a scanning electron microscope(SEM). This study was carried out by comparing control gallstones incubated in beagle bile with gallstones obtained from patients who were treated with chenodeoxycholic acid(CDCA).The cholesterol gallstones for this study were obtained from 14 patients. Three control patients were treated without CDCA and eleven patients were treated with CDCA 300-600 mg/day for periods ranging from four to twenty five months. It was confirmed through chemical analysis that these gallstones contained more than 80% cholesterol in both the outer surface and the core.The specimen were obtained from the outer surface and the core of the gallstones. Each specimen was attached to alminum sheet and coated with carbon to 100Å thickness. The SEM observation was made by Hitachi S-550 with 20 kV acceleration voltage and with 60-20, 000X magnification.

The Structure and Development of Microbodies in the Fat Body and other Tissues of an Insect (Calpodes Ethlius)

1970 ◽  
Vol 28 ◽  
pp. 148-149
Author(s):  
M. Locke ◽  
J. T. McMahon
Keyword(s):  
Electron Microscopy ◽  
Liquid Crystals ◽  
Fat Body ◽  
Competitive Inhibitor ◽  
Dense Core ◽  
Urate Oxidase ◽  
Blood Proteins ◽  
Free Base ◽  
The Core ◽  
The Matrix

The fat body of insects has always been compared functionally to the liver of vertebrates. Both synthesize and store glycogen and lipid and are concerned with the formation of blood proteins. The comparison becomes even more apt with the discovery of microbodies and the localization of urate oxidase and catalase in insect fat body.The microbodies are oval to spherical bodies about 1μ across with a depression and dense core on one side. The core is made of coiled tubules together with dense material close to the depressed membrane. The tubules may appear loose or densely packed but always intertwined like liquid crystals, never straight as in solid crystals (Fig. 1). When fat body is reacted with diaminobenzidine free base and H2O2 at pH 9.0 to determine the distribution of catalase, electron microscopy shows the enzyme in the matrix of the microbodies (Fig. 2). The reaction is abolished by 3-amino-1, 2, 4-triazole, a competitive inhibitor of catalase. The fat body is the only tissue which consistantly reacts positively for urate oxidase. The reaction product is sharply localized in granules of about the same size and distribution as the microbodies. The reaction is inhibited by 2, 6, 8-trichloropurine, a competitive inhibitor of urate oxidase.

Exsolution and inversion in pigeonite from the Whin Sill, Northern England

1978 ◽  
Vol 36 (1) ◽  
pp. 474-475
Author(s):  
P.P.K. Smith
Keyword(s):  
High Temperature ◽  
Low Temperature ◽  
Homogeneous Nucleation ◽  
Silicate Mineral ◽  
Antiphase Boundaries ◽  
Two Phase ◽  
Primitive Form ◽  
The Core ◽  
Nucleation Mechanisms ◽  
And Inversion

Grains of pigeonite, a calcium-poor silicate mineral of the pyroxene group, from the Whin Sill dolerite have been ion-thinned and examined by TEM. The pigeonite is strongly zoned chemically from the composition Wo8En64FS28 in the core to Wo13En34FS53 at the rim. Two phase transformations have occurred during the cooling of this pigeonite:- exsolution of augite, a more calcic pyroxene, and inversion of the pigeonite from the high- temperature C face-centred form to the low-temperature primitive form, with the formation of antiphase boundaries (APB's). Different sequences of these exsolution and inversion reactions, together with different nucleation mechanisms of the augite, have created three distinct microstructures depending on the position in the grain.In the core of the grains small platelets of augite about 0.02μm thick have farmed parallel to the (001) plane (Fig. 1). These are thought to have exsolved by homogeneous nucleation. Subsequently the inversion of the pigeonite has led to the creation of APB's.

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