scholarly journals An Alignment-Independent Approach for the Study of Viral Sequence Diversity at Any Given Rank of Taxonomy Lineage

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 853
Author(s):  
Li Chuin Chong ◽  
Wei Lun Lim ◽  
Kenneth Hon Kim Ban ◽  
Asif M. Khan
Keyword(s):  
Sequence Diversity ◽  
Viral Diversity ◽  
Pathogenic Microorganisms ◽  
Viral Sequence ◽  
Minimal Set ◽  
Viral Origin ◽  
Input Dataset ◽  
Approaches To Study ◽  
Complete Set ◽  
The Given

The study of viral diversity is imperative in understanding sequence change and its implications for intervention strategies. The widely used alignment-dependent approaches to study viral diversity are limited in their utility as sequence dissimilarity increases, particularly when expanded to the genus or higher ranks of viral species lineage. Herein, we present an alignment-independent algorithm, implemented as a tool, UNIQmin, to determine the effective viral sequence diversity at any rank of the viral taxonomy lineage. This is done by performing an exhaustive search to generate the minimal set of sequences for a given viral non-redundant sequence dataset. The minimal set is comprised of the smallest possible number of unique sequences required to capture the diversity inherent in the complete set of overlapping k-mers encoded by all the unique sequences in the given dataset. Such dataset compression is possible through the removal of unique sequences, whose entire repertoire of overlapping k-mers can be represented by other sequences, thus rendering them redundant to the collective pool of sequence diversity. A significant reduction, namely ~44%, ~45%, and ~53%, was observed for all reported unique sequences of species Dengue virus, genus Flavivirus, and family Flaviviridae, respectively, while still capturing the entire repertoire of nonamer (9-mer) viral peptidome diversity present in the initial input dataset. The algorithm is scalable for big data as it was applied to ~2.2 million non-redundant sequences of all reported viruses. UNIQmin is open source and publicly available on GitHub. The concept of a minimal set is generic and, thus, potentially applicable to other pathogenic microorganisms of non-viral origin, such as bacteria.

scholarly journals Hygienic assessment of minimal set of provisions which constitute consumersbasket for main social-demographic groupsof the Tomsk region population

2007 ◽  
Vol 6 (2) ◽  
pp. 122-128
Author(s):  
L. P. Volkotroub ◽  
Ye. A. Novatnay ◽  
N. I. Laskeyeva
Keyword(s):  
Minimum Cost ◽  
Living Wage ◽  
Minimal Set ◽  
Population Groups ◽  
Chemical Substances ◽  
Demographic Group ◽  
Mineral Substances ◽  
Tomsk Region ◽  
Social Demographic ◽  
The Given

Hygienic assessment of five minimum sets of provisions which constitute consumers basket (mean model of nourishment of mean-statistical inhabitant of the Tomsk region of definite social-demographic group) was performed. Number of chemical substances (proteins, fats, carbohydrates, vitamins, mineral substances) which constitute provisions structure was calculated. Hygienic assessment was performed by comparing the calculations obtained with the norms of physiologic needs in provisions and energy for several population groups. The given model can be used for calculation of living wage as the model which provides healthy nourishment , meets physiologic needs of the organism in nourishing substances and energy at minimum cost of the provisions.

GEORGE KAISER’S WRITING IN THE RECEPTION OF YURI KLEN

2019 ◽  
pp. 201-206
Author(s):  
Nataliia Lazirko
Keyword(s):  
World View ◽  
Scientific Work ◽  
Literary Critic ◽  
Structural Formulas ◽  
History Of ◽  
Approaches To Study ◽  
General Action ◽  
Georg Kaiser ◽  
Original Interpretation ◽  
The Given

The given article deals with Klen’s research of the German dramatist George Kaiser. The main parameters of artistic universe of this author are presented in the article. There are also outlined the methodological strategies of research the German dramatist’s creativity by Yuri Klen – a well-known Ukrainian literary critic. Georg Kaiser is one of the brightest representatives of theatrical and literary expressionism. His plays are the unique phenomenon in the 20th century drama. His expressionism appeared to be the special one and the global and scope of plots allowed scientists to call G. Kaiser a «new myth creator». Among world scientists, who comprehended the features of author manner of this sign artist for history of world drama, a main place belongs to the Ukrainian literary critic – Yuri Klen. In his scientific work there is the article «George Kaiser», which an author compositionally divides into seven parts. Its pre-condition is an original metaphorical lineation (vivid registration of which is adopted from astronomy), structural-semiotics assertion that every writer creation has a basic idea or favourite main image, that can be found in many writings of the author. However, in the Ukrainian literary critic’s opinion, it is not impossible to say it on the first sight about George of Kaiser because every work of this author has a new incarnate idea, new and unexpected development of a plot, new and original interpretation of that problem which has been solved in his previous works. In the article “George Kaiser” by Yuri Klen the biographic approach can be highlighted while analyzing creative works of the German dramatist. The Ukrainian literary critic also outlines the secrets of psychology of the German artist creation in expressionism manner. Expressionism drama is always drama of ideas; therefore acting persons of this drama are not individuals, but types which helps writer to lead the general action of the characters. Yuri Klen asserts transformation of images in dramas by George of Kaiser, their original reduction up to separate characters and allegories: his characters lost the outlines of people and become symbols of idea, super individual creatures, typical samples, and logic of acting can be sacrificed for the sake of the higher logic – logic of composition and dramatic construction. Few times a researcher accents on closeness an artistic world view of the German dramatist to cubism: characters mainly don’t have the names, but appear on the stage under the names: a «father», «multimillionaire», «black», «yellow» – they are structural formulas. Summarizing these the structural-semiotics searches, Yuri Klen marks once again that in George Kayiser’s works can be found: 1) central idea of man renewing which is peculiar for all his creative work; 2) leading motive of escape-chasing and 3) element of contingency which manages events, that is a case-shove which suddenly gives dynamic of action and sets fire before a man as a distant lighthouse – dream about renewal. It is also possible to assert that researches of expressionism by some authors whose creation correlates with expressionism views demonstrates complete maturity of Yuri Klen to be a serious literary critic armed by the newest methodological approaches to study literature as theoretician and practician of literature studies.

Phase and signal velocities of eigenwaves in a binary dissipative plasma

1974 ◽  
Vol 11 (2) ◽  
pp. 269-298 ◽  
Author(s):  
M. Kranyš ◽  
J. Teichmann
Keyword(s):  
Electromagnetic Wave ◽  
Bulk Viscosity ◽  
Present Theory ◽  
Speed Of Light ◽  
Longitudinal Diffusion ◽  
Front Speed ◽  
Phase Velocities ◽  
Special Cases ◽  
Complete Set ◽  
The Given

The signal and phase velocities of the possible waves (eigenwaves) in a dissipative binary plasma have been studied on the basis of the linearized thirteenmoment theory. The complete set of eigenmodes for the given system is formed using approximations in the range of frequencies high compared with typical collision or plasma frequencies. There are twenty non-trivial propagation modes. Four of them are modes with signal-front speed c associated with the induced electromagnetic wave. Eight modes belong to each of the gas constituents, among them two longitudinal diffusion modes (±WI), four transverse viscosity modespolarized respectively along two transverse axes ±W⊥ in the direction x1 and ±W⊥ in the direction x2) and two longitudinal thermal modes (±WII). The signalfront speed of all eigenwaves is lower than the speed of light, so that the system is hyperbolic. The ultra-relativistic plasma is also briefly discussed. In this case, all the mixture constituents will have the same set of signal-front speeds as a single gas, irrespective of the bulk viscosity. Comparison is made of the present theory and results with other theories (for some special cases).

scholarly journals Continual evolution through coupled fast and slow feedbacks

2019 ◽  
Author(s):  
Meike T. Wortel ◽  
Han Peters ◽  
Juan A. Bonachela ◽  
Nils Chr. Stenseth
Keyword(s):  
Negative Feedback ◽  
Evolutionary Dynamics ◽  
Functional Form ◽  
Biotic Interactions ◽  
Theoretical Framework ◽  
Red Queen Hypothesis ◽  
Red Queen ◽  
Minimal Set ◽  
The Given ◽  
The Red Queen

AbstractThe Red Queen Hypothesis, which suggests that continual evolution can result from solely biotic interactions, has been studied in macroevolutionary and microevolutionary contexts. While microevolutionary studies have described examples in which evolution does not cease, understanding which general conditions lead to continual evolution or to stasis remains a major challenge. In many cases, it is unclear which experimental features or model assumptions are necessary for the observed continual evolution to emerge, and whether the described behavior is robust to variations in the given setup. Here, we aim to find the minimal set of conditions under which continual evolution occurs. To this end, we present a theoretical framework that does not assume any specific functional form and, therefore, can be applied to a wide variety of systems. Our framework is also general enough to cast predictions about both monomorphic and polymorphic populations. We show that the combination of a fast positive and a slow negative feedback causes continual evolution to emerge even from the evolution of one single evolving trait, provided that the ecological timescale is sufficiently separated from the timescales of mutation and the negative feedback. Our approach and results thus contribute to a deeper understanding of the evolutionary dynamics resulting from biotic interactions.

scholarly journals Dynamics of Influenza A (H5N1) virus protein sequence diversity

PeerJ ◽  
2020 ◽  
Vol 7 ◽  
pp. e7954
Author(s):  
Hadia Syahirah Abd Raman ◽  
Swan Tan ◽  
Joseph Thomas August ◽  
Asif M. Khan
Keyword(s):  
Immune System ◽  
Influenza A ◽  
H5n1 Virus ◽  
Vaccine Design ◽  
Sequence Diversity ◽  
Influenza Viruses ◽  
Viral Fitness ◽  
Viral Population ◽  
Viral Diversity ◽  
Peak Incidence

Background Influenza A (H5N1) virus is a global concern with potential as a pandemic threat. High sequence variability of influenza A viruses is a major challenge for effective vaccine design. A continuing goal towards this is a greater understanding of influenza A (H5N1) proteome sequence diversity in the context of the immune system (antigenic diversity), the dynamics of mutation, and effective strategies to overcome the diversity for vaccine design. Methods Herein, we report a comprehensive study of the dynamics of H5N1 mutations by analysis of the aligned overlapping nonamer positions (1–9, 2–10, etc.) of more than 13,000 protein sequences of avian and human influenza A (H5N1) viruses, reported over at least 50 years. Entropy calculations were performed on 9,408 overlapping nonamer position of the proteome to study the diversity in the context of immune system. The nonamers represent the predominant length of the binding cores for peptides recognized by the cellular immune system. To further dissect the sequence diversity, each overlapping nonamer position was quantitatively analyzed for four patterns of sequence diversity motifs: index, major, minor and unique. Results Almost all of the aligned overlapping nonamer positions of each viral proteome exhibited variants (major, minor, and unique) to the predominant index sequence. Each variant motif displayed a characteristic pattern of incidence change in relation to increased total variants. The major variant exhibited a restrictive pyramidal incidence pattern, with peak incidence at 50% total variants. Post this peak incidence, the minor variants became the predominant motif for majority of the positions. Unique variants, each sequence observed only once, were present at nearly all of the nonamer positions. The diversity motifs (index and variants) demonstrated complex inter-relationships, with motif switching being a common phenomenon. Additionally, 25 highly conserved sequences were identified to be shared across viruses of both hosts, with half conserved to several other influenza A subtypes. Discussion The presence of distinct sequences (nonatypes) at nearly all nonamer positions represents a large repertoire of reported viral variants in the proteome, which influence the variability dynamics of the viral population. This work elucidated and provided important insights on the components that make up the viral diversity, delineating inherent patterns in the organization of sequence changes that function in the viral fitness-selection. Additionally, it provides a catalogue of all the mutational changes involved in the dynamics of H5N1 viral diversity for both avian and human host populations. This work provides data relevant for the design of prophylactics and therapeutics that overcome the diversity of the virus, and can aid in the surveillance of existing and future strains of influenza viruses.

scholarly journals Application of Thermal Engineering in Building Stock, Sophisticated Thermotechnical Systems Integrated in Buildings, and Pathogenic Microorganisms

2020 ◽  
Author(s):  
Mile Šiljak ◽  
Keyword(s):  
Residential Buildings ◽  
Target Function ◽  
Residential Building ◽  
Theory And Practice ◽  
Thermal Engineering ◽  
Causal Connection ◽  
Pathogenic Microorganisms ◽  
Building Stock ◽  
The Subject ◽  
The Given

Planned and/or unplanned developments in the setting, which are directly or indirectly in connection to a certain profession or are of multidisciplinary character, have impact on initiation and steering of the course and direction of research campaigns of “vigilant” professional analysts and/or researchers of a profession, i.e. professions. It was the occurrence of the “vicious infection - SARS CoV 2” at the territory of Planet Earth which also initiated the subject professional research in the area of applied thermal engineering within two partial units which may be in interaction with the infection, i.e. which may also be in causal connection: “applied thermal engineering in building stock (only business and residential buildings)”- “sophisticated thermotechnical system integrated in a business or residential building”- “pathogenic microorganisms”. When general, professional and/or scientific public was faced with occurrence of plentitude of information, misinformation, interpretations, misconceptions, and/or ambiguities in the “black box of SARS CoV 2 pandemic”, the subject research was initiated in an analytical and principled manner with application of methods of analysis based on the “logic of rational action” in the given area. The aspects of the approach are adapted to the subject of the research, imperatively and consecutively imposed by the need for analysis and evaluation of causality between the given partial units and pathogenic microorganisms. In relation to the accepted partial units in the stage of utilization of the existing business or residential building for the dedicated purpose, the findings point that, inter alia, if such buildings were constructed as a result of conscientious, competent, responsible, and highly professional work of multidisciplinary builders and if they comprise adequate integrated sophisticated thermotechnical systems which have systematic, functional, and operating capability and which achieve satisfactory target function of the system, they do not “generate” pathogenic microorganisms, do not participate in their transfer, do not intensify their pathogenic properties and activity, do not contribute to occurrence of pandemics, do not jeopardize human health, and do not cause their mortality, etc. but are basically also not intended to “destroy” pathogenic microorganisms reaching the system from the outside and/or treated limited closed spaced within the building frequented by people off their working activities and/or pursuing their working activities, individually or in groups. Depending on the type of the current sophisticated thermotechnical system in the building, if necessary, it is possible to perform interventions aimed at reconstruction so as to “immunize” the system in a manner which may be recognized and designed by professional, competent, experienced, and dedicated thermal engineers. It needs to be noted that the subject exploration is conducted for deontological reasons, with the aim to promote theory and practice in the given.

INTEGRABLE SYSTEMS DETERMINED BY DIFFERENTIAL FORMS FOR MOVING FRAMES ON IMMERSED SUBMANIFOLDS

2008 ◽  
Vol 05 (07) ◽  
pp. 1041-1049 ◽  
Author(s):  
PAUL BRACKEN
Keyword(s):  
Euclidean Space ◽  
Differential Equations ◽  
Nonlinear Equations ◽  
Integrable Systems ◽  
Differential Forms ◽  
Lax Pair ◽  
Dimensional Manifold ◽  
Moving Frames ◽  
Complete Set ◽  
The Given

It is shown how a system of differential forms can reproduce the complete set of differential equations generated by an SO(m) matrix Lax pair. By selecting the elements in the given matrices appropriately, examples of integrable nonlinear equations can be produced. The SO(3) case is discussed in detail, then extended to an m - 1 dimensional manifold immersed in Euclidean space.

scholarly journals The conceptual model of agroecological properties of land. Methods

2020 ◽  
Vol 50 (5) ◽  
pp. 77-86
Author(s):  
V. K. Kalichkin ◽  
R. A. Koryakin ◽  
K. Yu. Maksimovich ◽  
R. R. Galimov
Keyword(s):  
Conceptual Model ◽  
Domain Knowledge ◽  
Farming Systems ◽  
Adaptive Landscape ◽  
Intelligent Information Systems ◽  
Logical Language ◽  
Input Dataset ◽  
Mathematical Formulas ◽  
Intelligent Information ◽  
The Given

To solve the problem of automating the agroecological land estimation (natural resource potential) and creating intelligent information systems for their further programming, the necessary stage is the conceptualization of the domain knowledge (DK), or conceptual modelling. In this work, the conceptual model of DK “Agroecological properties of land”, developed on the basis of the abstract logical language UML and proposed in the previous part of the series of articles by the authors, is supplemented by the type of abstract objects “method”. The methods in UML reflect the types of relationships between data of various nature and are designed to distinguish the ways with which it is possible to fill in the missing data and information when solving practical problems in the framework of designing and building adaptive landscape farming systems. UML methods are considered for one of DK abstract classes – class “Relief”. In this class, 31 groups of input datasets and 23 groups of output datasets are suggested. All 54 datasets are based on the "method – attribute" connection that operate within this class or by abstract relationships between classes previously built into the conceptual model. This means that a class method as an abstract object defines a set of dependencies between data associated with the given class attributes, as input dataset, and data associated with the given or related class attributes, as output dataset. The elements of such set of dependencies can be deterministic or stochastic algorithms, statistical and other data processing methods, data analysis and artificial intelligence methods, as well as specific mathematical formulas. The technology of building a knowledge base by UML methods of class “Relief” is shown, containing 713 groups of UML methods classified by seven types, and also examples of UML methods of three different types are given.

scholarly journals A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Norman Goodacre ◽  
Aisha Aljanahi ◽  
Subhiksha Nandakumar ◽  
Mike Mikailov ◽  
Arifa S. Khan
Keyword(s):  
High Throughput ◽  
Selection Criteria ◽  
High Throughput Sequencing ◽  
Bioinformatics Analysis ◽  
Virus Detection ◽  
Sequence Diversity ◽  
Endogenous Retroviruses ◽  
Viral Sequence ◽  
Novel Virus ◽  
Viral Sequences

ABSTRACTDetection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank.IMPORTANCETo facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection.

scholarly journals Viral sequence diversity: challenges for AIDS vaccine designs

2008 ◽  
Vol 7 (9) ◽  
pp. 1405-1417 ◽  
Author(s):  
Sean P McBurney ◽  
Ted M Ross
Keyword(s):  
Sequence Diversity ◽  
Viral Sequence ◽  
Aids Vaccine
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