scholarly journals Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of Flaviviridae.

2021 ◽  
Author(s):  
Connor G G Bamford ◽  
William Marciel Souza ◽  
Rhys Parry ◽  
Robert J Gifford
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Domain Knowledge ◽  
Global Scale ◽  
Biological Properties ◽  
Animal Evolution ◽  
Novel Approach ◽  
Animal Phyla ◽  
Genomic Studies ◽  
Positive Strand Rna

The flaviviruses (family Flaviviridae) are a group of positive-strand RNA viruses, many of which pose serious risks to human health on a global scale. Here, we calibrate the timeline of flavivirus evolution using flavivirus-derived DNA sequences identified in animal genomes. We demonstrate that the family is at least 100 million years old and show that this timing can be integrated with dates inferred from co-phylogenetic analysis and paleontological records to produce a cohesive overview of flavivirus evolution in which the main subgroups originate early in animal evolution and broadly co-diverge with animal phyla. In addition, we show that the arthropod-borne 'classical' flaviviruses first evolved from tick-specific viruses, and only later adapted to become insect-borne. Our findings demonstrate that the biological properties of flaviviruses have been acquired over many millions of years of evolution, implying that broad-scale comparative analysis can reveal fundamental insights into flavivirus biology. We implement a novel approach to computational genomic studies of viruses that can support these efforts by enabling more efficient utilization of evolution-related domain knowledge in virus research.

Impact of Globalisation on Pandemics: A comparative study on SARS and Covid-19 (Preprint)

2020 ◽  
Author(s):  
Johann Johann And Devika
Keyword(s):  
Comparative Analysis ◽  
Comparative Study ◽  
Descriptive Analysis ◽  
Qualitative Comparative Analysis ◽  
Global Scale ◽  
Global Level ◽  
Economic Stability ◽  
The Past ◽  
The World ◽  
Close Relationship

BACKGROUND Since November 2019, Covid - 19 has spread across the globe costing people their lives and countries their economic stability. The world has become more interconnected over the past few decades owing to globalisation and such pandemics as the Covid -19 are cons of that. This paper attempts to gain deeper understanding into the correlation between globalisation and pandemics. It is a descriptive analysis on how one of the factors that was responsible for the spread of this virus on a global scale is globalisation. OBJECTIVE - To understand the close relationship that globalisation and pandemics share. - To understand the scale of the spread of viruses on a global scale though a comparison between SARS and Covid -19. - To understand the sale of globalisation present during SARS and Covid - 19. METHODS A descriptive qualitative comparative analysis was used throughout this research. RESULTS Globalisation does play a significant role in the spread of pandemics on a global level. CONCLUSIONS - SARS and Covid - 19 were varied in terms of severity and spread. - The scale of globalisation was different during the time of SARS and Covid - 19. - Globalisation can be the reason for the faster spread in Pandemics.

Using the Concept of “Social Distancing” in Advertising Designs: A Comparative Analysis

2021 ◽  
Author(s):  
Begüm Aylin Önder
Keyword(s):  
Corporate Social Responsibility ◽  
Comparative Analysis ◽  
Social Responsibility ◽  
Social Benefit ◽  
Global Scale ◽  
Social Distancing ◽  
Corona Virus ◽  
New Type ◽  
Corporate Social ◽  
The Impact

Corporate social responsibility is one of the activities that goes beyond philanthropy, based on volunteerism in line with the responsibilities of enterprises towards society. This concept, which offers businesses the opportunity to look after and develop their brand image in the eyes of society, has become a necessity, not a choice, especially in today's world. In order to meet social expectations, the effectiveness of static and dynamic advertising messages implemented in all social benefit-based studies for human development such as environment, health and education is very important in terms of ensuring audience communication. In the second half of 2019, people were confined to homes and life came to a standstill all over the world in order to reduce and prevent the impact of the pandemic within the scope of the “New Type Corona Virus” (COVID-19) measures, which are from the sars-cov-2 coronavirus family, which is spreading rapidly globally starting from Wohan, Hubei Province, China. As a basic protection module for humanity against corona virus, it has incorporated the concept of social distancing into their lives in order to reduce the contact of staying at home and increasing hygiene, except in mandatory situations. During this extraordinary period, many brands on a global scale have included the concept of “social distance” in their advertising messages with the awareness of corporate social responsibility and have started to inform and educate the community about this issue by emphasizing the importance of the process. Within the scope of this research, advertising designs prepared by brands acting with corporate social responsibility awareness through the concept of social distancing during the Pandemic period were discussed and how the meaning structures behind the messages were created and transmitted. The research is limited to 3 (three) advertising designs determined by the 'judicial sampling' method (selective method). In the sample of the study, advertising narratives of brands in different sectors were explained in general framework and similar and different aspects of messages were uncovered by performing comparative analysis between messages in line with the findings obtained from the narratives. In this context, it was determined that the contrasts of “pessimism and optimism, hope and despair, happiness and unhappiness, death and life, strong and powerless, youth and old age, unity/togetherness and separation, struggle and defeat, nature and culture” were constructed as the main discourse.

scholarly journals Mapping single-cell atlases throughout Metazoa unravels cell type evolution

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alexander J Tarashansky ◽  
Jacob M Musser ◽  
Margarita Khariton ◽  
Pengyang Li ◽  
Detlev Arendt ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Cell Types ◽  
The Self ◽  
Cell Type ◽  
Germ Layers ◽  
Animal Evolution ◽  
Self Assembling ◽  
Animal Phyla ◽  
Cell Data

Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.

scholarly journals Kritikan Orientalis Terhadap Keaslian Bahasa al-Quran: Analisis Terhadap Teori Perkataan Asing dalam al-Quran

2019 ◽  
Vol 15 (2) ◽  
pp. 93-108
Author(s):  
Ahmad Sanusi Azmi
Keyword(s):  
Comparative Analysis ◽  
Formative Period ◽  
Foreign Word ◽  
Novel Approach ◽  
Linguistic Aspect

Criticism on the originality of the Arabic words in the Quran had its inception at the formative period of Islam. The ambigious and mysterious verses in the Quran stimulate Qurasyh to cast their doubt on the etymologycal aspect of Quranic language. To date, the phenomenon continued to persist when part of its content were not recognised by the scholar of Quranic studies. Modern researchers have invented novel approach to explore this issue and their findings confirm the existence of loanword in the Quran. They believed that these foreign words acquired by Muhammad through his communication with various kinds of individuals. Thus, this study aims to explore the orientalist views on the linguistic aspect of the quran, and examine their findings with Muslim scholar’s standpoint using comparative analysis. The present study is qualitative in nature in which the researcher employed textual and comparative analysis on selected words and verses in the Quran. The study in its finding propose that the orientalist views on the issue of loandwords or foreign word of Quranic language is a standpoint that stem from plausibilities and possibilities.

scholarly journals Temporal Dominance of B.1.1.7 over B.1.354 SARS-CoV-2 Variant: A Hypothesis Based on Areas of Variant Co-Circulation

2021 ◽  
Author(s):  
Evangelia Georgia Kostaki ◽  
Ioulia Tseti ◽  
Sotirios Tsiodras ◽  
George N. Pavlakis ◽  
Petros P. Sfikakis ◽  
...  
Keyword(s):  
South Africa ◽  
Monoclonal Antibodies ◽  
Comparative Analysis ◽  
Biological Properties ◽  
Community Transmission ◽  
Temporal Dominance ◽  
Over Time

Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple monoclonal antibodies (mAbs), as well as convalescent and vaccination sera. To test this hypothesis, we examined the proportion of VOC over time across different geographic areas where the two VOC, B.1.1.7 and B.1.351, co-circulate. Our comparative analysis was based on the number of SARS-CoV-2 sequences on GISAID database. We report that B.1.1.7 dominates over B.1.351 in geographic areas where both variants co-circulate and the B.1.1.7 was the first variant introduced in the population. The only areas where B.1.351 was detected at higher proportion were South Africa and Mayotte in Africa, where this strain was associated with increased community transmission before the detection of B.1.1.7. The dominance of B.1.1.7 over B.1.351 could be important since B.1.351 was more resistant to certain mAbs, as well as heterologous convalescent and vaccination sera, thus suggesting that it may be transmitted more effectively in people with pre-existing immunity to other VOC. This scenario would lessen the effectiveness of vaccine and urge the need to update them with new strains.

scholarly journals A systematic comparison of eight new plastome sequences from Ipomoea L

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6563
Author(s):  
Jianying Sun ◽  
Xiaofeng Dong ◽  
Qinghe Cao ◽  
Tao Xu ◽  
Mingku Zhu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Next Generation Sequencing ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Next Generation ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Generation Sequencing

Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

COMPARING VIRUS CLASSIFICATION USING GENOMIC MATERIALS ACCORDING TO DIFFERENT TAXONOMIC LEVELS

2013 ◽  
Vol 11 (06) ◽  
pp. 1343003 ◽  
Author(s):  
JING-DOO WANG
Keyword(s):  
Molecular Biology ◽  
Dna Sequences ◽  
Protein Sequences ◽  
Experimental Results ◽  
Virus Classification ◽  
Taxonomic Level ◽  
Biological Classification ◽  
Novel Approach

In this paper, three genomic materials — DNA sequences, protein sequences, and regions (domains) are used to compare methods of virus classification. Virus classes (categories) are divided by various taxonomic level of virus into three datasets for 6 order, 42 family, and 33 genera. To increase the robustness and comparability of experimental results of virus classification, the classes are selected that contain at least 10 instances, and meanwhile each instance contains at least one region name. Experimental results show that the approach using region names achieved the best accuracies — reaching 99.9%, 97.3%, and 99.0% for 6 orders, 42 families, and 33 genera, respectively. This paper not only involves exhaustive experiments that compare virus classifications using different genomic materials, but also proposes a novel approach to biological classification based on molecular biology instead of traditional morphology.

European Court of Human Rights and the Bulgarian Judicial System

2021 ◽  
Vol 23 (6) ◽  
pp. 535-544
Author(s):  
Aleksandur Kirkov ◽  
◽  
Ana Andonova ◽  
Keyword(s):  
Human Rights ◽  
Comparative Analysis ◽  
Essential Feature ◽  
Methodological Approach ◽  
Scientific Work ◽  
Global Scale ◽  
Judicial System ◽  
European Convention ◽  
National Courts ◽  
European Court

Bulgaria ratified the European Convention for the Protection of Human Rights and Fundamental Freedoms in 1992, as such this European act has become part of our domestic legislation. Explaining in detail the differences and similarities between the European Court of Human Rights in Strasbourg and the Bulgarian judicial system, we will actually see how much they are similar. This is the purpose of the present study - comparative analysis in all aspects: territorial jurisdiction, legal jurisdiction, including procedurally legitimate persons to file complaints, procedural issues, stages of the process, court decisions and appeals. The first and most important task of the study is to get acquainted in detail with our European rights, as well as their judicial protection. On the other hand, the knowledge of the European judicial mechanisms leads to the expansion of our national horizons in a supranational perspective, to opportunities for professional realization outside the borders of the country, on a European and global scale. The research method used in the present scientific work is the comparative analysis. The methodology we refer to in preparing the analysis is based on a predetermined methodological approach and structure in conducting the analysis. The methodological approach itself includes a general overview of the legal framework, regulating the administration of justice in national courts and at European level. An essential feature of the approach used is to compare the two established legal systems, at home and in Strasbourg, at all levels, to explore links and interdependencies possible differences. Expected results: acquainting the Bulgarians with their European rights, as in case of violation of these rights, learning about the mechanisms for their protection in court. Conclusions and summaries: Bulgaria is part of the common European framework. As such, its citizens are Bulgarians, but also Europeans. Namely, as Europeans, they have rights that are guaranteed to them by Europe and that should be respected in Bulgaria. Failure to respect these European rights creates conflicts that should be resolved by both national courts and the European Court of Human Rights.

Modelling Thousands of Fractures Using Analytic Elements

2021 ◽  
Author(s):  
Erik Toller ◽  
Otto Strack
Keyword(s):  
Exact Solution ◽  
Plane Strain ◽  
Numerical Models ◽  
Element Model ◽  
Global Scale ◽  
Hydraulic Fractures ◽  
Infinite Domain ◽  
Novel Approach ◽  
Analytic Elements ◽  
Kolosov Functions

<p>Understanding and modelling hydraulic fractures and fracture networks have a fundamental role in mapping the mechanical behaviour of rocks. A problem arises in the discontinuous behaviour of the fractures and how to accurately and efficiently model this. We present a novel approach for modelling many cracks randomly using analytic elements placed under plane strain conditions in an elastic medium. The analytic elements allow us to model the assembly computationally efficiently and up to machine precision. The crack element is the first step in the development of a model suitable for investigating the effect of fissures on tunnels in rock. The model can be used to validate numerical models and more.The solution for a single hydraulic pressurized crack in an infinite domain in plane strain was initially developed by Griffith (1921). We demonstrate that it is possible, by using series expansions in terms of complex variables, based on the Muskhelisvili-Kolosov functions, to generalize this solution to the case of an assembly of non-intersecting pressurized cracks. The solution consists of infinite series for each element Strack & Toller (2020). The expressions for the displacements and stress tensor components approach the exact solution, as the number of terms in the series approaches infinity.We present the case where two cracks approach each other orthogonally to less than 1/2000th of the cracks length. We show the effect of increasing the number of terms in the expansion and how this influences the precision, demonstrating that the result approaches the exact solution. We also present a case with 10,000 cracks; the coefficients are determined using an iterative solver. By using analytic elements, we can both present the corresponding stress and deformations field for the global scale and for small scales in the close proximity of individual cracks.ReferencesGriffith, A. A. (1921). The phenomena of rupture and flow in solids. Philosophical Transactions of the Royal Society of London. Series A, Containing Papers of a Mathematical or Physical Character, 221(582-593):163–198.Strack, O. D. L. and Toller, E. A. L. (2020). An analytic element model for highly fractured elastic media, manuscript submitted for publication in International Journal for Numerical and Analytical Methods in Geomechanics.</p>

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