Pattern Based Matrix Insertion Deletion System for Efficient Bio Molecular Computing System

2019 ◽  
Vol 16 (2) ◽  
pp. 507-511
Author(s):  
C. Kotteeswaran ◽  
V. Khanaa ◽  
A. Rajesh
Keyword(s):  
Gene Sequence ◽  
Computing System ◽  
Molecular Computing ◽  
Gene Sequences ◽  
Molecular Sequence ◽  
Insertion And Deletion ◽  
Matrix Operations ◽  
The Matrix ◽  
Molecular Patterns ◽  
Single Sequence

The problem of bio molecular computing has been well studied and there are number of approaches discussed for the detection of false gene sequences. However, they suffer to achieve higher performance in the detection of false sequences. To improve the performance of detection of fake molecular patterns, an pattern based approach is discussed in this paper. As of the biomolecular strings a set of patterns, the method first identifies the list of sequences available and based on the set of patterns being maintained, the method identifies the list of patterns present in the gene sequence. Based on the sequences, the method identifies the incomplete and fake sequences and performs insertion and deletion using matrix operations. The method maintains number of patterns for the matrix insertion and deletion operation. For each pattern available, the method compute the bio molecular sequence weight. Finally a single sequence has been selected and based on the selected pattern, the method performs insertion and deletion operation. The proposed method produces efficient results on the detection as well as correction.

scholarly journals DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1797
Author(s):  
Shaoxia Xu ◽  
Yuan Liu ◽  
Shihua Zhou ◽  
Qiang Zhang ◽  
Nikola K. Kasabov
Keyword(s):  
Numerical Computation ◽  
Dna Computing ◽  
Computing System ◽  
Matrix Operation ◽  
Computing Systems ◽  
Multiplication Operation ◽  
Matrix Operations ◽  
The Matrix ◽  
Speed And Accuracy ◽  
Binding Substrate

Numerical computation is a focus of DNA computing, and matrix operations are among the most basic and frequently used operations in numerical computation. As an important computing tool, matrix operations are often used to deal with intensive computing tasks. During calculation, the speed and accuracy of matrix operations directly affect the performance of the entire computing system. Therefore, it is important to find a way to perform matrix calculations that can ensure the speed of calculations and improve the accuracy. This paper proposes a DNA matrix operation method based on the mechanism of the DNAzyme binding to auxiliary strands to cleave the substrate. In this mechanism, the DNAzyme binding substrate requires the connection of two auxiliary strands. Without any of the two auxiliary strands, the DNAzyme does not cleave the substrate. Based on this mechanism, the multiplication operation of two matrices is realized; the two types of auxiliary strands are used as elements of the two matrices, to participate in the operation, and then are combined with the DNAzyme to cut the substrate and output the result of the matrix operation. This research provides a new method of matrix operations and provides ideas for more complex computing systems.

scholarly journals Identification of lactobacilli by pheS and rpoA gene sequence analyses

2007 ◽  
Vol 57 (12) ◽  
pp. 2777-2789 ◽  
Author(s):  
Sabri M. Naser ◽  
Peter Dawyndt ◽  
Bart Hoste ◽  
Dirk Gevers ◽  
Katrien Vandemeulebroecke ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Alpha Subunit ◽  
Identification System ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Intraspecies Variation ◽  
Reliable Identification ◽  
Genomic Markers ◽  
Identification Of Species ◽  
Rpoa Gene

The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.

scholarly journals A note on the eigenvalue free intervals of some classes of signed threshold graphs

2019 ◽  
Vol 7 (1) ◽  
pp. 218-225
Author(s):  
Milica Anđelić ◽  
Tamara Koledin ◽  
Zoran Stanić
Keyword(s):  
Tridiagonal Matrix ◽  
Constant Sign ◽  
Equitable Partition ◽  
Elementary Matrix ◽  
Matrix Operations ◽  
Threshold Graphs ◽  
The Matrix ◽  
Threshold Graph

Abstract We consider a particular class of signed threshold graphs and their eigenvalues. If Ġ is such a threshold graph and Q(Ġ ) is a quotient matrix that arises from the equitable partition of Ġ , then we use a sequence of elementary matrix operations to prove that the matrix Q(Ġ ) – xI (x ∈ ℝ) is row equivalent to a tridiagonal matrix whose determinant is, under certain conditions, of the constant sign. In this way we determine certain intervals in which Ġ has no eigenvalues.

Application of Fuzzy Petri Nets in Hydraulic Pump Fault Diagnosis

2014 ◽  
Vol 1008-1009 ◽  
pp. 1176-1179
Author(s):  
Hai Dong ◽  
Heng Bao Xin
Keyword(s):  
Fault Diagnosis ◽  
Petri Nets ◽  
Hydraulic Pump ◽  
Modeling And Analysis ◽  
Matrix Operations ◽  
Knowledge Reasoning ◽  
Fuzzy Production Rules ◽  
The Matrix ◽  
Fuzzy Petri Nets ◽  
Definition Of

In this paper, an approach of fuzzy Petri nets (FPN) is proposed to simulate the fault spreading and diagnosis of hydraulic pump. First, the fuzzy production rules and the definition of FPN were briefly introduced. Then, its knowledge reasoning process and the matrix operations based on an algorithm were conducted, which makes full use of its parallel reasoning ability and makes it simpler and easier to implement. Finally, a case of hydraulic pump fault diagnosis with FPN was presented in detail, for illustrating the interest of the proposed modeling and analysis algorithm.

scholarly journals Generating a Cancellable Fingerprint using Matrices Operations and Its Fingerprint Processing Requirements

2018 ◽  
Vol 14 (6) ◽  
pp. 1 ◽  
Author(s):  
Riki Mukhaiyar
Keyword(s):  
Region Of Interest ◽  
Original Form ◽  
Biometric Data ◽  
Matrix Operations ◽  
The Matrix ◽  
Robust Image ◽  
Reciprocal Matrix ◽  
Processing Steps ◽  
Fingerprint Feature

Cancellable fingerprint uses transformed or intentionally distorted biometric data instead of the original biometric data for identifying person. When a set of biometric data is found to be compromised, they can be discarded, and a new set of biometric data can be regenerated. This initial principal is identical with a non-invertible concept in matrices operations. In matrix domain, a matrix cannot be transformed into its original form if it meets several requirements such as non-square form matrix, consist of one zero row/column, and no row as multiple of another row. These conditions can be acquired by implementing three matrix operations using Kronecker Product (KP) operation, Elementary Row Operation (ERO), and Inverse Matrix (INV) operation. KP is useful to produce a non-square form matrix, to enlarge the size of matrix, to distinguish and disguise the element of matrix by multiplying each of elements of the matrix with a particular matrix. ERO can be defined as multiplication and addition force to matrix rows. INV is utilized to transform one matrix to another one with a different element or form as a reciprocal matrix of the original. These three matrix operations should be implemented together in generating the cancellable feature to robust image. So, if once three conditions are met by imposter, it is impossible to find the original image of the fingerprint. The initial aim of these operations is to camouflage the original look of the fingerprint feature into an abstract-look to deceive an un-authorized personal using the fingerprint irresponsibly. In this research, several fingerprint processing steps such as fingerprint pre-processing, core-point identification, region of interest, minutiae extration, etc; are determined to improve the quality of the cancellable feature. Three different databases i.e. FVC2002, FVC2004, and BRC are utilized in this work.

scholarly journals Effect of Environmental Conditions on the Yield of Peel and Composition of Essential Oils from Citrus Cultivated in Bahia (Brazil) and Corsica (France)

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1256
Author(s):  
François Luro ◽  
Claudia Garcia Neves ◽  
Gilles Costantino ◽  
Abelmon da Silva Gesteira ◽  
Mathieu Paoli ◽  
...  
Keyword(s):  
Essential Oils ◽  
Environmental Conditions ◽  
Cultural Practices ◽  
Citrus Fruit ◽  
Water Distillation ◽  
Single Sequence Repeat ◽  
Insertion And Deletion ◽  
Fruit Pericarp ◽  
Single Sequence ◽  
Different Climates

The cosmetic and fragrance industry largely exploits citrus essential oils (EOs) because of their aromatic properties. EO compositions are complex and differ between fruit pericarp (PEO) and leaf (LEO). Citrus fruit grow in many countries under very different climates. Seventeen citrus cultivars were selected and their similarities between the two collections were verified by SSR (Single Sequence Repeat) and InDel (Insertion and Deletion) markers to assess the effects of the environment and cultivation practices on the EO yield and composition. LEOs and PEOs were extracted by water distillation and analyzed by GC-MS. PEO yields were generally higher in Corsica than in Bahia, especially in the citron family. PEOs in this family were richer in limonene in Bahia than in Corsica while, conversely, neral, geranial and derivatives were present in a higher proportion in Corsican varieties. A few minor components were site-specific, such as nookaton, a pummelo-specific compound that was not present in grapefruit cultivated in Bahia. If climate change over the last 20 years has not affected the PEO composition in Corsica, the contrasted environmental conditions and cultural practices between Bahia and Corsica could possibly explain the EO variations.

Performance Analysis of the PISO-Based CFD Simulation

2014 ◽  
Vol 607 ◽  
pp. 872-876 ◽  
Author(s):  
Xiao Guang Ren
Keyword(s):  
Performance Optimization ◽  
Execution Time ◽  
Cfd Simulation ◽  
Fluid Flows ◽  
Total Execution Time ◽  
Simulation Performance ◽  
Simulation Efficiency ◽  
Matrix Operations ◽  
The Matrix ◽  
Computational Fluid Dynamics Cfd

Computational Fluid Dynamics (CFD) is widely applied for the simulation of fluid flows, and the performance of the simulation process is critical for the simulation efficiency. In this paper, we analyze the performance of CFD simulation application with profiling technology, which gets the portions of the main parts’ execution time. Through the experiment, we find that the PISO algorithm has a significant impact on the CFD simulation performance, which account for more than 90% of the total execution time. The matrix operations are also account for more than 60% of the total execution time, which provides opportunity for performance optimization.

Bone Marrow and Peripheral Blood Dendritic Cells From Patients With Multiple Myeloma Are Phenotypically and Functionally Normal Despite the Detection of Kaposi’s Sarcoma Herpesvirus Gene Sequences

Blood ◽  
1999 ◽  
Vol 93 (5) ◽  
pp. 1487-1495 ◽  
Author(s):  
Noopur Raje ◽  
Jianlin Gong ◽  
Dharminder Chauhan ◽  
Gerrard Teoh ◽  
David Avigan ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Dendritic Cells ◽  
Gene Sequence ◽  
Patient Specific ◽  
Normal Donor ◽  
Cyclin D ◽  
Gene Sequences ◽  
Hla Dr ◽  
Viral Cyclin ◽  
Kshv Gene

Multiple myeloma (MM) cells express idiotypic proteins and other tumor-associated antigens which make them ideal targets for novel immunotherapeutic approaches. However, recent reports show the presence of Kaposi’s sarcoma herpesvirus (KSHV) gene sequences in bone marrow dendritic cells (BMDCs) in MM, raising concerns regarding their antigen-presenting cell (APC) function. In the present study, we sought to identify the ideal source of DCs from MM patients for use in vaccination approaches. We compared the relative frequency, phenotype, and function of BMDCs or peripheral blood dendritic cells (PBDCs) from MM patients versus normal donors. DCs were derived by culture of mononuclear cells in the presence of granulocyte-macrophage colony-stimulating factor and interleukin-4. The yield as well as the pattern and intensity of Ag (HLA-DR, CD40, CD54, CD80, and CD86) expression were equivalent on DCs from BM or PB of MM patients versus normal donors. Comparison of PBDCs versus BMDCs showed higher surface expression of HLA-DR (P = .01), CD86 (P = .0003), and CD14 (P = .04) on PBDCs. APC function, assessed using an allogeneic mixed lymphocyte reaction (MLR), demonstrated equivalent T-cell proliferation triggered by MM versus normal DCs. Moreover, no differences in APC function were noted in BMDCs compared with PBDCs. Polymerase chain reaction (PCR) analysis of genomic DNA from both MM patient and normal donor DCs for the 233-bp KSHV gene sequence (KS330233) was negative, but nested PCR to yield a final product of 186 bp internal to KS330233 was positive in 16 of 18 (88.8%) MM BMDCs, 3 of 8 (37.5%) normal BMDCs, 1 of 5 (20%) MM PBDCs, and 2 of 6 (33.3%) normal donor PBDCs. Sequencing of 4 MM patient PCR products showed 96% to 98% homology to the published KSHV gene sequence, with patient specific mutations ruling out PCR artifacts or contamination. In addition, KHSV-specific viral cyclin D (open reading frame [ORF] 72) was amplified in 2 of 5 MM BMDCs, with sequencing of the ORF 72 amplicon revealing 91% and 92% homology to the KSHV viral cyclin D sequence. These sequences again demonstrated patient specific mutations, ruling out contamination. Therefore, our studies show that PB appears to be the preferred source of DCs for use in vaccination strategies due to the ready accessibility and phenotypic profile of PBDCs, as well as the comparable APC function and lower detection rate of KSHV gene sequences compared with BMDCs. Whether active KSHV infection is present and important in the pathophysiology of MM remains unclear; however, our study shows that MMDCs remain functional despite the detection of KSHV gene sequences.

A Trust Evaluation of Networks Utilizing Matrix Operations Based on t-norms and t-conorms

2012 ◽  
Vol 16 (1) ◽  
pp. 154-161
Author(s):  
Masaya Nohmi ◽  
◽  
Aoi Honda ◽  
Yoshiaki Okazaki
Keyword(s):  
Trust Evaluation ◽  
Matrix Operations ◽  
Fuzzy Graphs ◽  
Algebraic Properties ◽  
The Matrix ◽  
Membership Value

A new scheme for numerical trust evaluation of networks is proposed. Matrix operations based on t-norms and t-conorms are used for the evaluation. The algebraic properties of the matrix operations are studied. Fuzzy graphs, in which nodes are linked with some membership value, are proposed, using the matrices as adjacent matrices. Furthermore, the fuzzinesses of the trustability distribution are calculated.

scholarly journals Evolution and origins of tobamoviruses

1999 ◽  
Vol 354 (1383) ◽  
pp. 593-602 ◽  
Author(s):  
Adrian Gibbs
Keyword(s):  
Mosaic Virus ◽  
Host Species ◽  
Phylogenetic Relationships ◽  
Gene Sequence ◽  
Hepatitis Virus ◽  
Infected Plant ◽  
Gene Sequences ◽  
Protein Motifs

More than a dozen tobamoviruses are known. In nature, each species probably survives by moving between several closely related host species. Each infected plant contains a population of variants, but in most host populations the tobamovirus population is stable. The phylogenetic relationships of tobamovirus species broadly correlate with those of their angiosperm hosts. The simplest explanation for this correlation is that they have coevolved with the angiosperms, and hence, like them, are about 120–140 million years old. Gene sequence differences between species also indicate that the tobamoviruses are an ancient genus. Their gene sequences, and the protein motifs they encode, link them to tobraviruses, hordeiviruses and soil–borne wheat mosaic virus, more distantly to the tricornaviruses, and even to hepatitis virus E and other furoviruses, rubiviruses and alphaviruses. Their progenitors may have been associated with charophycean algae, and perhaps also plasmodiophoromycete fungi.

Sign in / Sign up

Export Citation Format

Share Document