PERSISTENCY AND PERMANENCY OF TWO STAGES SPLICING LANGUAGES VIA YUSOF-GOODE APPROACH: TWO INITIAL STRINGS AND TWO RULES

2015 ◽  
Vol 77 (1) ◽  
Author(s):  
Mohammad Hassan Mudaber ◽  
Yuhani Yusof ◽  
Mohd Sham Mohamad ◽  
Wen Li Lim
Keyword(s):  
Deoxyribonucleic Acid ◽  
Recombinant Dna ◽  
Restriction Enzymes ◽  
Real Situation ◽  
Second Stage ◽  
Context Factors ◽  
Dna Strands ◽  
Dna Strand ◽  
Two Stages ◽  
Dna Splicing

The notation of representing restriction enzymes in the form of double-triple in order to formulate Yusof-Goode (Y-G) splicing system was mathematically proposed by Yusof in 2012. The aim of introducing Y-G splicing system was to study the process of recombinant deoxyribonucleic acid or DNA strand in a translucent way. In real situation, when the recombination action occurs, the recombinant DNA strands which will arise often contain the patterns of the restriction enzymes. Persistency and permanency are two properties of splicing system, which show whether the recombinant DNA strands will be split by the existence of restrictions enzymes or not if the reaction goes to the second stage. In this research, the persistency and permanency of two stages splicing languages according to the number of cutting sites of initial strings as well as crossing sites and context factors of splicing rules are investigated. Therefore, a Y-G splicing system consisting of two initial strings (with two cutting sites) and two rules is used to present the above properties of two stages DNA splicing languages.

MODELLING OF TWO STAGES DNA SPLICING LANGUAGES ON DE BRUIJN GRAPH

2015 ◽  
Vol 78 (1) ◽  
Author(s):  
Mohammad Hassan Mudaber ◽  
Yuhani Yusof ◽  
Mohd Sham Mohamad ◽  
Aizi Nor Mazila Ramli ◽  
Wen Li Lim
Keyword(s):  
Dna Sequence ◽  
Restriction Enzymes ◽  
De Bruijn Graph ◽  
Dna Molecule ◽  
Interesting Topic ◽  
De Bruijn ◽  
Two Stages ◽  
Mathematical Graph ◽  
Dna Splicing

Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular.  Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible.  In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular.   This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model.

A Hybrid Atomistic Approach for the Mechanics of Deoxyribonucleic Acid Molecules

2013 ◽  
Vol 4 (4) ◽  
Author(s):  
S. Adhikari ◽  
E. I. Saavedra Flores ◽  
F. Scarpa ◽  
R. Chowdhury ◽  
M. I. Friswell
Keyword(s):  
Mechanical Properties ◽  
Deoxyribonucleic Acid ◽  
Vibration Mode ◽  
Complex Geometry ◽  
Lumped Parameter Model ◽  
Mode Shapes ◽  
Lumped Parameter ◽  
Dna Strands ◽  
Dna Strand ◽  
Equivalent Continuum

The paper proposes a new modeling approach for the prediction and analysis of the mechanical properties in deoxyribonucleic acid (DNA) molecules based on a hybrid atomistic-finite element continuum representation. The model takes into account of the complex geometry of the DNA strands, a structural mechanics representation of the atomic bonds existing in the molecules and the mass distribution of the atoms by using a lumped parameter model. A 13-base-pair DNA model is used to illustrate the proposed approach. The properties of the equivalent bond elements used to represent the DNA model have been derived. The natural frequencies, vibration mode shapes, and equivalent continuum mechanical properties of the DNA strand are obtained. The results from our model compare well with a high-fidelity molecular mechanics simulation and existing MD and experimental data from open literature.

FPGA Based Data Hiding Methods using DNA Cryptography Techniques

2016 ◽  
Vol 5 (3) ◽  
pp. 141
Author(s):  
B. Murali Krishna ◽  
CH. Surendra ◽  
K. Mani Varma ◽  
K. Mani Kanta ◽  
S.K. Shabbeer ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Specific Reference ◽  
Insertion Technique ◽  
Second Stage ◽  
Dna Cryptography ◽  
Single Strategy ◽  
Security Algorithm ◽  
Two Stages

<p>To convey the information safely DNA grouping mechanisms are used. There are many methods used by DNA sequences. The proposed method is of both encryption and information concealing utilizing a few properties of Deoxyribonucleic Acid (DNA) groupings. This technique is highlighted that DNA groupings have many more intriguing properties which are used for concealing the information. There are three strategies in this encryption strategy: the Insertion Technique, the Complimentary Pair Technique and the Substitution Strategy .For every single strategy, a specific reference DNA grouping P is chosen and then the taken sequence is changed over with the mystery message M and is consolidated, so that P0 is acquired. P0 is then sent to the collector and the beneficiary can recognize and separate the message M covered up in P. This technique is proposed to utilize INSERTION Strategy. Subsequently, the proposed plan comprises for the most part of two stages. In the principal stage, the mystery information is encoded utilizing a DNA Sequence. In the second stage the encoded information is steganographically covered up into some reference DNA grouping utilizing an insertion strategy. The effectiveness of this security algorithm is seen with many merits and limitations. A, C, G, and T are the 4 nucleotides which are taken for this project.</p>

Altered Fine Structure of B Lymphocytes Correlated with Defective Terminal Differentiation

1973 ◽  
Vol 31 ◽  
pp. 386-387
Author(s):  
Dale E. Bockman ◽  
L. Y. Frank Wu ◽  
Alexander R. Lawton ◽  
Max D. Cooper
Keyword(s):  
Immune Deficiency ◽  
B Lymphocytes ◽  
Plasma Cells ◽  
Present Report ◽  
Specific Antigen ◽  
Terminal Differentiation ◽  
Second Stage ◽  
Two Stages ◽  
Deficiency Diseases ◽  
Cell Line Generation

B-lymphocytes normally synthesize small amounts of immunoglobulin, some of which is incorporated into the cell membrane where it serves as receptor of antigen. These cells, on contact with specific antigen, proliferate and differentiate to plasma cells which synthesize and secrete large quantities of immunoglobulin. The two stages of differentiation of this cell line (generation of B-lymphocytes and antigen-driven maturation to plasma cells) are clearly separable during ontogeny and in some immune deficiency diseases. The present report describes morphologic aberrations of B-lymphocytes in two diseases in which second stage differentiation is defective.

Distributed Entropy Energy-Efficient Clustering algorithm for cluster head selection (DEEEC)

2020 ◽  
Vol 39 (6) ◽  
pp. 8139-8147
Author(s):  
Ranganathan Arun ◽  
Rangaswamy Balamurugan
Keyword(s):  
Energy Efficient ◽  
Clustering Algorithm ◽  
Cluster Head ◽  
Residual Energy ◽  
Energy Utilization ◽  
Sensor Nodes ◽  
Second Stage ◽  
Energy Efficient Clustering ◽  
Two Stages ◽  
Ch Selection

In Wireless Sensor Networks (WSN) the energy of Sensor nodes is not certainly sufficient. In order to optimize the endurance of WSN, it is essential to minimize the utilization of energy. Head of group or Cluster Head (CH) is an eminent method to develop the endurance of WSN that aggregates the WSN with higher energy. CH for intra-cluster and inter-cluster communication becomes dependent. For complete, in WSN, the Energy level of CH extends its life of cluster. While evolving cluster algorithms, the complicated job is to identify the energy utilization amount of heterogeneous WSNs. Based on Chaotic Firefly Algorithm CH (CFACH) selection, the formulated work is named “Novel Distributed Entropy Energy-Efficient Clustering Algorithm”, in short, DEEEC for HWSNs. The formulated DEEEC Algorithm, which is a CH, has two main stages. In the first stage, the identification of temporary CHs along with its entropy value is found using the correlative measure of residual and original energy. Along with this, in the clustering algorithm, the rotating epoch and its entropy value must be predicted automatically by its sensor nodes. In the second stage, if any member in the cluster having larger residual energy, shall modify the temporary CHs in the direction of the deciding set. The target of the nodes with large energy has the probability to be CHs which is determined by the above two stages meant for CH selection. The MATLAB is required to simulate the DEEEC Algorithm. The simulated results of the formulated DEEEC Algorithm produce good results with respect to the energy and increased lifetime when it is correlated with the current traditional clustering protocols being used in the Heterogeneous WSNs.

Analisis Kebutuhan Petunjuk Praktikum Berbasis Keterampilan Proses Sains untuk Mencapai Kemampuan Merancang Eksperimen

2019 ◽  
Vol 2 (2) ◽  
Author(s):  
Fitriah Khoirunnisa ◽  
Friska Septiani Silitonga ◽  
Veri Firmansyah
Keyword(s):  
Core Competence ◽  
Process Skills ◽  
Learning Materials ◽  
Science Process Skills ◽  
Second Stage ◽  
The Core ◽  
The Core Competence ◽  
Two Stages ◽  
Practical Instruction ◽  
Design Experiments

Penelitian ini bertujuan menganalisis kebutuhan petunjuk praktikum berbasis Keterampilan Proses Sains (KPS) untuk mencapai kemampuan merancang eksperimen pada materi kalor reaksi kalorimetri. Penelitian dilakukan terhadap peserta didik kelas XI SMA Negeri 2 Kota Tanjungpinang. Variabel penelitian mencakup analisis kebutuhan bahan ajar dan analisis kesesuaian Kompetensi Inti (KI) dan Kompetensi Dasar (KD). Jenis penelitian yang dilakukan adalah penelitian deskriptif kualitatif. Tahapan pertama dalam penelitian ini adalah menganalisis kebutuhan bahan ajar dengan cara membandingkan dua petunjuk praktikum yang selama ini telah digunakan di sekolah tersebut, ditinjau dari aspek struktur format penulisan, aspek kreativitas, dan aspek keterampilan proses sains yang terdapat dalam petunjuk praktikum. Sehingga didapatkan kesimpulan bahwa petunjuk praktikum yang selama ini digunakan tidak memberikan kesempatan kepada peserta didiknya untuk merancang eksperimen yang telah ditentukan. Tahapan kedua yaitu menganalisis kesesuaian kompetensi inti dan kompetensi dasar, yang bertujuan untuk menentukan indikator pencapaian kompetensi (IPK) yang akan menjadi acuan dalam mengembangkan petunjuk praktikum berbasis keterampilan proses sains. Dari kedua tahapan yang telah dilakukan maka dapat disimpulkan bahwa peserta didik memerlukan petunjuk praktikum yang mampu mengonstruksi pikiran dan mengaktifkan kinerja mereka, sehingga pendekatan Keterampilan Proses Sains menjadi pilihan dalam mengembangkan petunjuk praktikum yang sesuai dengan karakteristik kurikulum 2013.   This research aims to analyze the needs of Science Process Skills based Practical Instruction to achieve the ability to design experiments on the calor of reaction. This research was done to the students of class XI SMA Negeri 2 Tanjungpinang City. Research Variable includes the analysis of the needs of the learning materials and analysis of the suitability of the Core Competence (KI) and Basic Competence (KD). The type of research conducted is descriptive qualitative research. The first stages in this research is to analyze the needs of learning materials by comparing two practical instructions that had been implementing in the school, from the aspects of the structure of writing format, creativity, and science process skills embedded in practical instructions. The conclusion of this research that current practical instructions does not give an opportunity to the participants to design determined experiments. The second stage, namely analyzing the suitability of core competence and basic competence, which aims to determine the indicators of achievement of the competencies (GPA) which will be a reference in developing process skills-based teaching instructions science. Of the two stages that has been done then it can be concluded that learners need practical instructions to construct  thinking and and their performance, so the Science Process Skills approach is an option in developing practical instruction suitable for the characteristics of the curriculum of 2013.

ESTIMATING GAS AND ROCK OUTBURST RISK ON THE BASIS OF KNOWLEDGE AND EXPERIENCE – THE EXPERT SYSTEM BASED ON FUZZY LOGIC

2014 ◽  
Vol 59 (1) ◽  
pp. 41-52 ◽  
Author(s):  
Norbert Skoczylas
Keyword(s):  
Fuzzy Logic ◽  
Expert System ◽  
Mining Industry ◽  
Automatic Assessment ◽  
Science Field ◽  
Second Stage ◽  
Two Stages ◽  
Outburst Hazard

Abstract The Author endeavored to consult some of the Polish experts who deal with assessing and preventing outburst hazards as to their knowledge and experience. On the basis of this knowledge, an expert system, based on fuzzy logic, was created. The system allows automatic assessment of outburst hazard. The work was completed in two stages. The first stage involved researching relevant sources and rules concerning outburst hazard, and, subsequently, determining a number of parameters measured or observed in the mining industry that are potentially connected with the outburst phenomenon and can be useful when estimating outburst hazard. Then, the Author contacted selected experts who are actively involved in preventing outburst hazard, both in the industry and science field. The experts were anonymously surveyed, which made it possible to select the parameters which are the most essential in assessing outburst hazard. The second stage involved gaining knowledge from the experts by means of a questionnaire-interview. Subjective opinions on estimating outburst hazard on the basis of the parameters selected during the first stage were then systematized using the structures typical of the expert system based on fuzzy logic.

Integrated assessment and mapping of the environmental situation in the Russian Federation regions

2017 ◽  
Vol 924 (6) ◽  
pp. 6-16
Author(s):  
V.S. Tikunov ◽  
O.Yu. Chereshnia
Keyword(s):  
Russian Federation ◽  
Pollution Index ◽  
Pollution Level ◽  
Anthropogenic Pressure ◽  
Environmental Capacity ◽  
Environmental Friendliness ◽  
Second Stage ◽  
Environmental Situation ◽  
The Russian Federation ◽  
Two Stages

The article presents a methodology for a comprehensive assessment of the environmental situation in Russian Federation regions based on the pollution index and the index of the ecological tension. The evaluation was carried out in two stages. At the first stage, the degree of pollution of the atmosphere, hydrosphere and lithosphere of the regions was estimated on the basis of the emission of pollutants into the atmosphere, departing from stationary sources, the formation of solid domestic wastes (SDW) and the discharge of contaminated wastewater. Based on these three indicators, a pollution index was constructed that estimates aggregate pollution level. In the second stage, the authors made the estimation of loads generated by atmospheric emissions, solid waste and waste water discharged into the territory of each region, per capita and in relation to the environmental capacity of the economy. This allows us to take into account the area of pollution, anthropogenic pressure and environmental responsibility of the population, as well as the environmental friendliness of production. On the basis of relative indicators, the index of ecological tension was created.

scholarly journals 3′ → 5′ Exonucleases of DNA Polymerases ϵ and δ Correct Base Analog Induced DNA Replication Errors on Opposite DNA Strands in Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 717-726 ◽  
Author(s):  
Polina V Shcherbakova ◽  
Youri I Pavlov
Keyword(s):  
Dna Replication ◽  
Dna Polymerases ◽  
Replication Errors ◽  
Dna Strands ◽  
Base Analog ◽  
Chromosome Iii ◽  
Dna Strand ◽  
Dna Replication Errors ◽  
Yeast Mutants ◽  
Lagging Strand

Abstract The base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC → AT and AT → GC transitions that are enhanced in DNA polymerase ϵ and δ 3′ → 5′ exonuclease-deficient yeast mutants, pol2-4 and pol3-01, respectively. We have constructed a set of isogenic strains to determine whether the DNA polymerases δ and ϵ contribute equally to proofreading of replication errors provoked by HAP during leading and lagging strand DNA synthesis. Site-specific GC → AT and AT → GC transitions in a Pol→, pol2-4 or pol3-01 genetic background were scored as reversions of ura3 missense alleles. At each site, reversion was increased in only one proofreading-deficient mutant, either pol2-4 or pol3-01, depending on the DNA strand in which HAP incorporation presumably occurred. Measurement of the HAP-induced reversion frequency of the ura3 alleles placed into chromosome III near to the defined active replication origin ARS306 in two orientations indicated that DNA polymerases ϵ and δ correct HAP-induced DNA replication errors on opposite DNA strands.

scholarly journals The Psychology behind Knowledge Hiding in an Organization

2021 ◽  
Vol 11 (2) ◽  
pp. 57
Author(s):  
Roksana Binte Rezwan ◽  
Yoshi Takahashi
Keyword(s):  
Knowledge Management ◽  
Literature Review ◽  
Systematic Literature Review ◽  
Personal Goals ◽  
Psychological Process ◽  
Personal Goal ◽  
Second Stage ◽  
Management Literature ◽  
Two Stages ◽  
Knowledge Hiding

This study aimed to understand the psychological process behind employees’ knowledge hiding (KH) behaviors in organizations. KH is an intentional act of concealing knowledge when it is requested by a colleague and can lead to counterproductive consequences for the organization. Therefore, this study synthesized previous studies (n = 88) on KH through a systematic literature review. We used the cognitive–motivational–relational (CMR) theory of emotion to create a framework for the studies’ findings. Based on the framework, the psychological process behind KH has two stages—personal goal generation and the knowledge-request event appraisal process, each of which contains its own CMR process. In the first stage, an individual’s internal and external attributes related to the organization shape their personal goals. In the second stage, an individual appraises the features of a knowledge-request event in terms of both their personal goal and the internal and external attributes that created the goal. If the knowledge request is appraised as harmful for the personal goal, emotion arises and leads to the manifestation of KH. This study contributes to the knowledge management literature as, to our knowledge, it is the first to propose a CMR theory-based framework to understand the overall psychological process behind KH.

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