Search Results (13)

Deoxyribonucleic Acid (DNA) computing has demonstrated great potential in data encryption due to its capability of parallel computation, minimal storage requirement, and unbreakable cryptography. Focusing on high-dimensional image data for encryption with DNA computing, we propose a novel hash encoding-based DNA computing algorithm, which consists of a DNA hash encoding module and content-aware encrypting module. Inspired by the significant properties of the hash function, we build a quantity of hash mappings from image pixels to DNA computing bases, properly integrating the advantages of the hash function and DNA computing to boost performance. Considering the correlation relationship of pixels and patches for modeling, a content-aware encrypting module is proposed to reorganize the image data structure, resisting the crack with non-linear and high dimensional complexity originating from the correlation relationship. The experimental results suggest that the proposed method performs better than most comparative methods in key space, histogram analysis, pixel correlation, information entropy, and sensitivity measurements. Full article

Freshwater invasive alien species (IAS) are non-native organisms that were intentionally or unintentionally released into local water bodies and later harmed the invaded habitat by disrupting the ecological processes. Over the last few years, environmental deoxyribonucleic acid (eDNA) analyses have been used in many studies to detect IAS, with positive results. However, with the help of geographic information systems (GIS), efforts to detect the presence of IAS can be made faster and more efficiently. In this paper, we review the background of IAS in Southeast Asia and management efforts undertaken involving the input of known habitat-specific geographical parameters into GIS mapping. Via this strategy, it is possible to identify and distinguish areas that fit IAS habitat features from those that do not. eDNA analysis can later be applied to confirm the presence of IAS in detected areas, enabling further studies and actions. The presence of IAS in certain areas can be used as an indicator to assess the environmental integrity of native waterways. This combined method is likely the first approach to be applied to the detection of freshwater IAS in local water bodies. Apart from saving energy and resources, embedding GIS and eDNA into the study of IAS not only benefits the ecosystem but also assists locals and authorities in managing and taking necessary enforcement actions to curb further spread. Full article

Due to the rapid growth in the global volume of data, deoxyribonucleic acid (DNA) data storage has emerged. Error correction in DNA data storage is a key part of this storage technology. In this paper, an improved marker code scheme is proposed to correct insertion, deletion, and substitution errors in deoxyribonucleic acid (DNA) data storage. To correct synchronization (i.e., insertion and deletion) errors, a novel base-symbol-based synchronization algorithm is proposed and used. In the improved scheme, the marker bits are encoded as the information part of the LDPC code, and then mapped into marker bases to correct the synchronization errors. Thus marker bits not only assist in regaining synchronization, but also play a role in LDPC decoding to improve decoding performance. An improved low-complexity normalized min-sum (INMS) algorithm is proposed to correct residual substitution errors after regaining synchronization. The simulation results demonstrate that the improved scheme provides a substantial performance improvement over the concatenated marker code scheme and concatenated watermark code scheme. At the same time, the complexity of the INMS algorithm was reduced, while its bit error rate (BER) performance was approximate to that of the belief propagation (BP) algorithm. Full article

Smart City (SC) is a booming model of urban development with great potential, armed to be one of the urban development’s most powerful developing weapons. However, the development of SC is far from satisfactory. Therefore, finding new paths for SC becomes imperative. Transit Oriented Development (TOD), which often focuses on the core areas of SC, is believed to be a substantial contributor to the development of SC. Nonetheless, the relationship between SC and TOD and the effects of TOD in promoting SC are rarely studied. In this study, we proposed a conceptual framework of Smart TOD (S-TOD), which could highlight TOD 5.0 but more than that. S-TOD is an integration of SC and TOD, utilizing the deconstructive method and the abductive method. We first defined S-TOD, which integrates SC and TOD as the twin sources. Then, we employed the concept of Deoxyribonucleic Acid (DNA) to construct S-TOD in a cross-boundary path as the connection between DNA and its twin subchains can perfectly reflect the inner relationship between S-TOD and its twin sources, SC and TOD. Finally, we built up the structure of S-TOD with three layers, i.e., the cloud layer, the tactile layer, and the land zones layer. The purpose of this paper is to enhance the practical value of SC, from a perspective that has been neglected, that is, the combination with TOD, provide a new perspective for the research and practice of the integration of SC and TOD, and effectively facilitate the advantages of SC and global sustainable development. Full article

Early diagnosis of drug susceptibility for tuberculosis (TB) patients could guide the timely initiation of effective treatment. We evaluated a novel multiplex xMAP TIER (Tuberculosis-Isoniazid-Ethambutol-Rifampicin) assay based on the Luminex xMAP system to detect first-line anti-tuberculous drug resistance. Deoxyribonucleic acid samples from 353 Mycobacterium tuberculosis clinical isolates were amplified by multiplex polymerase chain reaction, followed by hybridization and analysis through the xMAP system. Compared with the broth microdilution method, the sensitivity and specificity of the xMAP TIER assay for detecting resistance was 94.9% (95%CI, 90.0–99.8%) and 98.9% (95%CI, 97.7–100.0%) for rifampicin; 89.1% (95%CI, 83.9–94.3%) and 100.0% (95%CI, 100.0–100.0%) for isoniazid; 82.1% (95% CI, 68.0–96.3%) and 99.7% (95% CI, 99.0–100.0%) for ethambutol. With DNA sequencing as the reference standard, the sensitivity and specificity of xMAP TIER for detecting resistance were 95.0% (95% CI, 90.2–99.8%) and 99.6% (95% CI, 98.9–100.0%) for rifampicin; 96.9% (95% CI, 93.8–99.9%) and 100.0% (95% CI, 100.0–100.0%) for isoniazid; 86.1% (95% CI, 74.8–97.4%) and 100.0% (95% CI, 100.0–100.0%) for ethambutol. The results achieved showed that the xMAP TIER assay had good performance for detecting first-line anti-tuberculosis drug resistance, and it has the potential to diagnose drug-resistant tuberculosis more accurately due to the addition of more optimal design primers and probes on open architecture xMAP system. Full article

The need for information security has become urgent due to the constantly changing nature of the Internet and wireless communications, as well as the daily generation of enormous volumes of multimedia. In this paper, a 3-stage image cryptosystem is developed and proposed. A tan variation of the logistic map is utilized to carry out deoxyribonucleic acid (DNA) encoding in the first stage. For the second encryption stage, the numerical solution of the Lorenz differential equations and a linear descent algorithm are jointly employed to build a robust S-box. The logistic map in its original form is utilized in the third stage. Diffusion is guaranteed through the first and third encryption stages, while confusion is guaranteed through the application of the S-box in the second encryption stage. Carrying out both confusion- and diffusion-inducing stages results in encrypted images that are completely asymmetric to their original (plain) counterparts. An extensive numerical analysis is carried out and discussed, showcasing the robustness and efficacy of the proposed algorithm in terms of resistance to visual, statistical, entropy, differential, known plaint text and brute-force attacks. Average values for the computed metrics are: Information entropy of $7.99$, MSE of 9704, PSNR of $8.3$ dB, MAE of $80.8$, NPCR of $99.6$ and UACI of 33. The proposed algorithm is shown to exhibit low computational complexity, encrypting images at an average rate of $1.015$ Mbps. Moreover, it possesses a large key space of $2^{372}$, and is demonstratd to successfully pass all the tests of the NIST SP 800 suite. In order to demonstrate the superior performance of the proposed algorithm, a comparison with competing image encryption schemes from the literature is also provided. Full article

Tracer technologies based on naturally occurring substances or intentionally introduced compounds have a broad spectrum of applications in hydrogeological research and subsurface resource management. DNA (deoxyribonucleic acid)-based tracers, with unlimited unique variations and exceptional specificity, could potentially map the complex intricacies of subsurface flow networks in greater detail than traditional tracer methods. Here, we review recent advances in DNA-based tracer research involving modern culture-independent (i.e., molecular) measurement techniques for subsurface/flowpath characterization purposes. The two broad categories of DNA-based tracers, i.e., synthetic and naturally occurring, are further classified into four specific types: “naked DNA”, “encapsulated DNA”, “barcoding microbial communities”, and “indicator microbial communities”. We summarize and compare the basic methodological workflows for each type of DNA-based tracer and provide an overview of research developments in the past two decades, covering both laboratory/field-scale experiments and data interpretation methods. Finally, we highlight remaining questions and challenges for each type of DNA-based tracer in terms of practicality. Future research directions are also identified, including the application of emerging DNA tracer methods to a wider range of geological formations. Fundamental characteristics of these novel tracers need to be better understood, and their applicability under a broader range of engineering scenarios requires further validation. Full article

Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures. Full article

With the advancement of technology worldwide, security is essential for online information and data. This research work proposes a novel image encryption method based on combined chaotic maps, Halton sequence, five-dimension (5D) Hyper-Chaotic System and Deoxyribonucleic Acid (DNA) encoding. Halton sequence is a known low-discrepancy sequence having uniform distribution in space for application in numerical methods. In the proposed work, we derived a new chaotic map (HaLT map) by combining chaotic maps and Halton sequence to scramble images for cryptography applications. First level scrambling was done by using the HaLT map along with a modified quantization unit. In addition, the scrambled image underwent inter- and intra-bit scrambling for enhanced security. Hash values of the original and scrambled image were used for initial conditions to generate a 5D hyper-chaotic map. Since a 5D chaotic map has complex dynamic behavior, it could be used to generate random sequences for image diffusion. Further, DNA level permutation and pixel diffusion was applied. Seven DNA operators, i.e., ADD, SUB, MUL, XOR, XNOR, Right-Shift and Left-Shift, were used for pixel diffusion. The simulation results showed that the proposed image encryption method was fast and provided better encryption compared to ‘state of the art’ techniques. Furthermore, it resisted various attacks. Full article

A hybrid domain image encryption algorithm is developed by integrating with improved Henon map, integer wavelet transform (IWT), bit-plane decomposition, and deoxyribonucleic acid (DNA) sequence operations. First, we improve the classical two-dimensional Henon map. The improved Henon map is called 2D-ICHM, and its chaotic performance is analyzed. Compared with some existing chaotic maps, 2D-ICHM has larger parameter space, continuous chaotic range, and more complex dynamic behavior. Second, an image encryption structure based on diffusion–scrambling–diffusion and spatial domain–frequency domain–spatial domain is proposed, which we call the double sandwich structure. In the encryption process, the diffusion and scrambling operations are performed in the spatial and frequency domains, respectively. In addition, initial values and system parameters of the 2D-ICHM are obtained by the secure hash algorithm-512 (SHA-512) hash value of the plain image and the given parameters. Consequently, the proposed algorithm is highly sensitive to plain images. Finally, simulation experiments and security analysis show that the proposed algorithm has a high level of security and strong robustness to various cryptanalytic attacks. Full article

The parasite species of genus Plasmodium causes Malaria, which remains a major global health problem due to parasite resistance to available Antimalarial drugs and increasing treatment costs. Consequently, computational prediction of new Antimalarial compounds with novel targets in the proteome of Plasmodium sp. is a very important goal for the pharmaceutical industry. We can expect that the success of the pre-clinical assay depends on the conditions of assay per se, the chemical structure of the drug, the structure of the target protein to be targeted, as well as on factors governing the expression of this protein in the proteome such as genes (Deoxyribonucleic acid, DNA) sequence and/or chromosomes structure. However, there are no reports of computational models that consider all these factors simultaneously. Some of the difficulties for this kind of analysis are the dispersion of data in different datasets, the high heterogeneity of data, etc. In this work, we analyzed three databases ChEMBL (Chemical database of the European Molecular Biology Laboratory), UniProt (Universal Protein Resource), and NCBI-GDV (National Center for Biotechnology Information—Genome Data Viewer) to achieve this goal. The ChEMBL dataset contains outcomes for 17,758 unique assays of potential Antimalarial compounds including numeric descriptors (variables) for the structure of compounds as well as a huge amount of information about the conditions of assays. The NCBI-GDV and UniProt datasets include the sequence of genes, proteins, and their functions. In addition, we also created two partitions (c_assayj = c_aj and c_dataj = cd_j) of categorical variables from theChEMBL dataset. These partitions contain variables that encode information about experimental conditions of preclinical assays (c_aj) or about the nature and quality of data (c_dj). These categorical variables include information about 22 parameters of biological activity (c_a0), 28 target proteins (c_a1), and 9 organisms of assay (c_a2), etc. We also created another partition of (c_protj = c_pj) including categorical variables with biological information about the target proteins, genes, and chromosomes. These variables cover32 genes (c_p0), 10 chromosomes (c_p1), gene orientation (c_p2), and 31 protein functions (c_p3). We used a Perturbation-Theory Machine Learning Information Fusion (IFPTML) algorithm to map all this information (from three databases) into and train a predictive model. Shannon’s entropy measure Sh_k (numerical variables) was used to quantify the information about the structure of drugs, protein sequences, gene sequences, and chromosomes in the same information scale. Perturbation Theory Operators (PTOs) with the form of Moving Average (MA) operators have been used to quantify perturbations (deviations) in the structural variables with respect to their expected values for different subsets (partitions) of categorical variables. We obtained three IFPTML models using General Discriminant Analysis (GDA), Classification Tree with Univariate Splits (CTUS), and Classification Tree with Linear Combinations (CTLC). The IFPTML-CTLC presented the better performance with Sensitivity Sn(%) = 83.6/85.1, and Specificity Sp(%) = 89.8/89.7 for training/validation sets, respectively. This model could become a useful tool for the optimization of preclinical assays of new Antimalarial compounds vs. different proteins in the proteome of Plasmodium. Full article

Multimedia encryption innovation is one of the primary ways of securely and privately guaranteeing the security of media transmission. There are many advantages when utilizing the attributes of chaos, for example, arbitrariness, consistency, ergodicity, and initial condition affectability, for any covert multimedia transmission. Additionally, many more benefits can be introduced with the exceptional space compliance, unique information, and processing capability of real mitochondrial deoxyribonucleic acid (mtDNA). In this article, color image encryption employs a confusion process based on a hybrid chaotic map, first to split each channel of color images into n-clusters; then to create global shuffling over the whole image; and finally, to apply intrapixel shuffling in each cluster, which results in very disordered pixels in the encrypted image. Then, it utilizes the rationale of human mitochondrial genome mtDNA to diffuse the previously confused pixel values. Hypothetical examination and trial results demonstrate that the anticipated scheme exhibits outstanding encryption, as well as successfully opposes chosen/known plain text, statistical, and differential attacks. Full article

Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA) intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA) including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human. Full article