scholarly journals Six Fractal Codes of Biological Life:perspectives in Exobiology, Cancers Basic Research and Artificial Intelligence Biomimetism Decisions Making

2018 ◽  
Author(s):  
Jean Claude Perez
Keyword(s):  
Local Stability ◽  
Binary Code ◽  
Basic Research ◽  
Atomic Mass ◽  
Amino Acid Sequences ◽  
Binary Codes ◽  
Fractal Nature ◽  
Whole Genomes ◽  
Nested Codes ◽  
Numerical Formula

The discovery of a simple numerical formula for the projection of all the atomic mass of life-sustaining CONHSP bioatoms leads to the emergence of a set of Nested CODES unifying all the biological, genetic and genomic components by unifying them from bioatoms up to 'to whole genomes. In particular, we demonstrate the existence of a digital meta-code common to the three languages ​​of biology that are RNA, DNA and amino acid sequences. Through this meta-code, genomic and proteomic images appear almost analogous and correlated. The analysis of the textures of these images then reveals a binary code as well as an undulatory code whose analysis on the human genome makes it possible to predict the alternating bands constituting the cariotypes of the chromosomes. The application of these codes to perspectives in astrobiology, in Cancers basic research and the emergence of binary codes and regions of local stability (voting process), whose fractal nature we demonstrate, is illustrated.

scholarly journals SIX FRACTAL CODES OF LIFE FROM BIOATOMS ATOMIC MASS TO CHROMOSOMES NUMERICAL STANDING WAVES: THREE BREAKTHOUGHS IN ASTROBIOLOGY, CANCERS AND ARTIFICIAL INTELLIGENCE

2021 ◽  
Vol 9 (9) ◽  
pp. 133-191
Author(s):  
Jean Claude Perez ◽  
Luc Montagnier
Keyword(s):  
Local Stability ◽  
Binary Code ◽  
Standing Waves ◽  
Atomic Mass ◽  
Amino Acid Sequences ◽  
Fractal Nature ◽  
Living Things ◽  
Whole Genomes ◽  
Nested Codes ◽  
Numerical Formula

The discovery of a simple numerical formula for the projection of all the atomic mass of life-sustaining CONHSP bioatoms leads to the emergence of a set of Nested CODES unifying all the biological, genetic and genomic components by unifying them from bioatoms up to 'to whole genomes. In particular, we demonstrate the existence of a digital meta-code common to the three languages ​​of biology that are RNA, DNA and amino acid sequences. Through this meta-code, genomic and proteomic images appear almost analogous and correlated. The analysis of the textures of these images then reveals a binary code as well as an undulatory code whose analysis on the human genome makes it possible to predict the alternating bands constituting the cariotypes of the chromosomes. The application of these codes to perspectives in astrobiology and the emergence of binary codes and regions of local stability (voting process), whose fractal nature we demonstrate, is illustrated. The fundamental discovery described here will undoubtedly one day constitute a new biomathematic approach to the emergence of living things.

scholarly journals New Bounds on the Minimum Average Distance of Binary Codes

2010 ◽  
Vol 2 (3) ◽  
pp. 489
Author(s):  
M. Basu ◽  
S. Bagchi
Keyword(s):  
Lower Bounds ◽  
Binary Code ◽  
Hamming Distance ◽  
Average Distance ◽  
Upper And Lower Bounds ◽  
Binary Codes ◽  
Large N

The minimum average Hamming distance of binary codes of length n and cardinality M is denoted by b(n,M). All the known lower bounds b(n,M) are useful when M is at least of size about 2n-1/n . In this paper, for large n, we improve upper and lower bounds for b(n,M). Keywords: Binary code; Hamming distance; Minimum average Hamming distance. © 2010 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. DOI: 10.3329/jsr.v2i3.2708                  J. Sci. Res. 2 (3), 489-493 (2010) 

scholarly journals Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution

2019 ◽  
Vol 69 (1) ◽  
pp. 38-60 ◽  
Author(s):  
Rémi Allio ◽  
Céline Scornavacca ◽  
Benoit Nabholz ◽  
Anne-Laure Clamens ◽  
Felix AH Sperling ◽  
...  
Keyword(s):  
Missing Data ◽  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Amino Acid Sequences ◽  
Molecular Dating ◽  
Whole Genome ◽  
Gene Trees ◽  
Data Set ◽  
Whole Genomes ◽  
Bayesian Mixture Models

Abstract Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.

Data Hiding for Text and Binary Files

2013 ◽  
pp. 351-371
Author(s):  
Hioki Hirohisa
Keyword(s):  
Data Hiding ◽  
Binary Code ◽  
Binary Codes ◽  
Secret Information ◽  
Textual Data ◽  
Executable File

This chapter presents an overview of text-based and binary-based data hiding methods. Text methods, through which secret information is embedded into innocent-looking textual data, are mostly used for steganography. Binary methods are applied to program binary codes: executables and libraries. In binary methods, information is embedded into a binary code so that its functionality is preserved. Data hiding methods for binary codes have been studied intensively to perform watermarking for protecting software from piracy acts. A message can also be embedded into a binary code in a steganographic manner. Another method is also introduced, which is proposed for enhancing the performance of an executable file.

scholarly journals Unique and Universal Proteins in Human Genome

2020 ◽  
Vol 16 (11) ◽  
pp. 45
Author(s):  
Essam Al-Daoud ◽  
Ghadeer Albesani
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Human Genome ◽  
Reference Genome ◽  
Amino Acid Sequences ◽  
The Other ◽  
Entire Genome ◽  
Whole Genomes ◽  
The Common ◽  
Similar Amino Acid

<span>One of the major troubles with a comparative analysis between human and other species is that only similar amino acid sequences are selected for analysis. To find the connection among the species and find out the unique, the common and the universal proteins, the entire genome of 40 species are compared with the human genome which is utilized as reference genome. More than 11 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 330 unique proteins in human genome and have insignificant hits in all tested genomes, the number of universal proteins in human genome and conserved in all tested species is 82, and there are 180 proteins common in vertebrates genomes, but have insignificant hits in the other tested species. In contrary to the previous studies which use selected set of the genes and do not consider the whole genomes, this study proves that the similarity between human and chimpanzee is only 94.8.</span>

scholarly journals Online Hashing with Efficient Updating of Binary Codes

2020 ◽  
Vol 34 (07) ◽  
pp. 12354-12361
Author(s):  
Zhenyu Weng ◽  
Yuesheng Zhu
Keyword(s):  
Image Retrieval ◽  
Binary Code ◽  
Hash Functions ◽  
Image Databases ◽  
Streaming Data ◽  
Binary Codes ◽  
Retrieval Process ◽  
Retrieval Accuracy ◽  
Projection Functions

Online hashing methods are efficient in learning the hash functions from the streaming data. However, when the hash functions change, the binary codes for the database have to be recomputed to guarantee the retrieval accuracy. Recomputing the binary codes by accumulating the whole database brings a timeliness challenge to the online retrieval process. In this paper, we propose a novel online hashing framework to update the binary codes efficiently without accumulating the whole database. In our framework, the hash functions are fixed and the projection functions are introduced to learn online from the streaming data. Therefore, inefficient updating of the binary codes by accumulating the whole database can be transformed to efficient updating of the binary codes by projecting the binary codes into another binary space. The queries and the binary code database are projected asymmetrically to further improve the retrieval accuracy. The experiments on two multi-label image databases demonstrate the effectiveness and the efficiency of our method for multi-label image retrieval.

scholarly journals Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Yundan Liu ◽  
Kaiyang Zheng ◽  
Baohong Liu ◽  
Yantao Liang ◽  
Siyuan You ◽  
...  
Keyword(s):  
Algal Blooms ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Hydrocarbon Biodegradation ◽  
Associated Bacteria ◽  
Viral Genomes ◽  
Transmission Electron ◽  
Whole Genomes

Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from −20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.

scholarly journals Data Hiding for Text and Binary Files

2014 ◽  
pp. 1495-1514
Author(s):  
Hioki Hirohisa
Keyword(s):  
Data Hiding ◽  
Binary Code ◽  
Binary Codes ◽  
Secret Information ◽  
Textual Data ◽  
Executable File

This chapter presents an overview of text-based and binary-based data hiding methods. Text methods, through which secret information is embedded into innocent-looking textual data, are mostly used for steganography. Binary methods are applied to program binary codes: executables and libraries. In binary methods, information is embedded into a binary code so that its functionality is preserved. Data hiding methods for binary codes have been studied intensively to perform watermarking for protecting software from piracy acts. A message can also be embedded into a binary code in a steganographic manner. Another method is also introduced, which is proposed for enhancing the performance of an executable file.

scholarly journals On a Class of Constant Weight Codes

10.37236/1228 ◽  
1996 ◽  
Vol 3 (1) ◽  
Author(s):  
Mihai Caragiu
Keyword(s):  
Prime Power ◽  
Binary Code ◽  
Hamming Distance ◽  
Character Sums ◽  
Bch Codes ◽  
Binary Codes ◽  
Quadratic Character ◽  
Constant Weight Codes ◽  
Constant Weight ◽  
Non Linear

For any odd prime power $q$ we first construct a certain non-linear binary code $C(q,2)$ having $(q^2-q)/2$ codewords of length $q$ and weight $(q-1)/2$ each, for which the Hamming distance between any two distinct codewords is in the range $[q/2-3\sqrt q/2,\ q/2+3\sqrt q/2]$ that is, 'almost constant'. Moreover, we prove that $C(q,2)$ is distance-invariant. Several variations and improvements on this theme are then pursued. Thus, we produce other classes of binary codes $C(q,n)$, $n\geq 3$, of length $q$ that have 'almost constant' weights and distances, and which, for fixed $n$ and big $q$, have asymptotically $q^n/n$ codewords. Then we prove the possibility of extending our codes by adding the complements of their codewords. Also, by using results on Artin $L-$series, it is shown that the distribution ofthe $0$'s and $1$'s in the codewords we constructed is quasi-random. Our construction uses character sums associated with the quadratic character $\chi$ of $F_{q^n}$ in which the range of summation is $F_q$. Relations with the duals of the double error correcting BCH codes and the duals of the Melas codes are also discussed.

scholarly journals Three novel canine papillomaviruses support taxonomic clade formation

2009 ◽  
Vol 90 (11) ◽  
pp. 2615-2621 ◽  
Author(s):  
Christian E. Lange ◽  
Kurt Tobler ◽  
Mathias Ackermann ◽  
Lucia Panakova ◽  
Keith L. Thoday ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Human Papillomaviruses ◽  
Sequence Alignments ◽  
Conserved Sequence ◽  
Whole Genomes ◽  
Sequence Elements ◽  
Sequence Similarities

More than 100 human papillomaviruses (HPVs) have been identified and had their whole genomes sequenced. Most of these HPVs can be classified into three distinct genera, the alpha-, beta- and gamma-papillomaviruses (PVs). Of note, only one or a small number of PVs have been identified for each individual animal species. However, four canine PVs (CPVs) (COPV, CPV2, CPV3 and CPV4) have been described and their entire genomic sequences have been published. Based on their sequence similarities, they belong to three distinct clades. In the present study, circular viral DNA was amplified from three dogs showing signs of pigmented plaques, endophytic papilloma or in situ squamous cell carcinoma. Analysis of the DNA sequences suggested that these are three novel viruses (CPV5, CPV6 and CPV7) whose genomes comprise all the conserved sequence elements of known PVs. The genomes of these seven CPVs were compared in order properly classify them. Interestingly, phylogenetic analyses, as well as pairwise sequence alignments of the putative amino acid sequences, revealed that CPV5 grouped well with CPV3 and CPV4, whereas CPV7 grouped with CPV2 but neither group fitted with other classified PVs. However, CPV6 grouped with COPV, a lambda-PV. Based on this evidence, allocation of CPVs into three distinct clades could therefore be supported. Thus, similar to HPVs, it might be that the known and currently unknown CPVs are related and form just a few clades or genera.

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