Complete Complementary Sequence Research Articles

Unimodular Complete Complementary Sequence with Optimal Trade-off between Auto- and Cross-ambiguity Functions for MIMO Radars

Unimodular Complete Complementary Sequence with Optimal Trade-off between Auto- and Cross-ambiguity Functions for MIMO Radars

Bacterial drug-resistance and viability phenotyping upon disinfectant exposure revealed by single-nucleotide resolved-allele specific isothermal RNA amplification

Disinfectant abuse poses a risk of bacterial evolution against stresses, especially during the coronavirus disease 2019 (COVID-19) pandemic. However, bacterial phenotypes, such as drug resistance and viability, are hard to access quickly. Here, we reported an allele specific isothermal RNA amplification (termed AlleRNA) assay, using an isothermal RNA amplification technique, i.e., nucleic acid sequence-based amplification (NASBA), integrated the amplification refractory mutation system (ARMS), involving the use of sequence-specific primers to allow the amplification of the targets with complete complementary sequences. AlleRNA assay enables rapid and simultaneous detection of the single nucleotide polymorphism (SNP) (a detection limit, a LOD of 0.5 % SNP) and the viability (a LOD of 80 CFU) of the quinolone resistant Salmonella enterica. With the use of AlleRNA assay, we found that the quinolone resistant S. enterica exhibited higher survival ability during exposure toquaternary ammonium salt, 75 % ethanol and peracetic acid, which might be attributed to the upregulation of stress response-associated genescompared with the susceptible counterparts. Additionally, the AlleRNA assay indicated the potential risk in a high-frequency occurrence of viable but nonculturable (VBNC) quinolone resistant S. enterica induced by disinfectants due to the depression of ATP biosynthesis. The excessive usage of disinfectants during the COVID-19 pandemic should be carefully evaluated due to the latent threat to ecological and human health.

An Interference-Reducing Precoding for SCMA Multicast Design Based on Complementary Sequences

In a multi-group multicast sparse code multiple access (SCMA) system, one base station multicasts common messages to multiple multicast groups via different code books. To accommodate more user terminals (UTs), traditional multicast systems have multiple transmitters, each of which works in one-to-many mode. In this way, each UT is subject to inter-transmitter interference. Considering the high degrees of freedom for transmitting and receiving, it is difficult to separate the desired signal from interference signals. Therefore, an interference-reducing precoding scheme is required to ensure the reliability of SCMA multicast communication system. For the SCMA multicast system design, we present three necessary conditions that the interference-reducing matrix should satisfy. Then, the precoding matrix satisfying the three necessary conditions simultaneously is designed by utilizing the complementary sequences (CS) and complete complementary sequences (CCS). In this context, we consider two scenarios with different transmission modes (single-cell and multiple-cell) and different precoding schemes (based on CS and CCS). Simulation results show that proposed transmission schemes can significantly reduce the bit error rate of multicast groups while ensuring the communication throughput, and behave a superior performance over other alternatives. Moreover, theoretical and simulation results also prove that the proposed precoding vectors have perfect average power radiation and omnidirectional coverage performance.

Induced heat shock protein 70 confers biological tolerance in UV-B stress–adapted Myzus persicae (Hemiptera)

As an environmental stress factor, ultraviolet-B (UV-B) radiation directly affects insect growth, development, and reproduction. Heat shock protein 70s kDa (Hsp70s) plays an important role in the environmental adaptation of insects. To determine the role of MpHsp70s in the UV-B tolerance of Myzus persicae (Sulzer), we identified the complete complementary DNA sequences of seven MpHsp70s. They were found to be ubiquitously expressed during different developmental stages and were highly expressed in second-instar nymphs and wingless adults. The expression levels of the MpHsp70s were significantly upregulated when exposed to different durations of UV-B stress. Nanocarrier-mediated dsMpHsp70 suppressed the expression of the MpHsp70s and reduced the body length, weight, survival rate, and fecundity of M. persicae under UV-B exposure. When the combinational RNAi approach was adopted, the effects on the survival rate and fecundity were greater under UV-B stress, except for MpHsc70-4. These results suggest that MpHsp70s are essential for the resistance of M. persicae to UV-B stress.

Design of Complete Complementary Sequences for Ambiguity Functions Optimization With a PAR Constraint

Complete complementary sequence (CCS) design has become an important topic in recent years due to its theoretically ideal zero sidelobe performance. However, the main obstacle for the widespread use of the CCS is its sensitivity to the Doppler shift. In this letter, a method for constructing the CCS with the desired matrix-valued ambiguity functions under a peak-to-average-power ratio (PAR) and an energy constraint is proposed. A gradient-based nonlinear iterative algorithm is used to solve the constrained sequence design problem. Numerical results are presented to show that, compared with the state-of-the-art methods, the proposed method can produce CCS with better correlation properties and the Doppler tolerance. Finally, indoor experiments are conducted to verify the superior performance of the designed CCS, and a peak sidelobe level under −45 dB is realized on the hardware system.

Research on PDMA communication system based on complete complementary sequence

Pattern division multiple access (PDMA) is a new non-orthogonal multiple access (NOMA) technology. It is proposed to meet the challenge of 5G large-scale connectivity and high-frequency spectral efficiency. Compared with traditional orthogonal multiple access (OMA), PDMA can support more users through the allocation of non-orthogonal resources. Due to perfect aperiodic correlation, complete complementary sequence (CCS) greatly improves the spectrum efficiency of the system. It has been widely used in wireless communication and radar sensing, and it still has research value in 5G. In order to apply the advantages of CCS to NOMA communication system, this paper proposes a system model of CCS spread spectrum coding based on PDMA. CCS is used as spread spectrum code to improve the performance of PDMA communication system. At the same time, on the basis of spread spectrum technology, this paper analyzes the average power allocation algorithm and water-filling power allocation algorithm, and a dynamic power allocation algorithm based on the transmission rate and practical application is proposed. The simulation results show that the system model can effectively improve the performance of the system.

Designing Constant Modulus Complete Complementary Sequence With High Doppler Tolerance for Simultaneous Polarimetric Radar

A pair of waveforms with good auto- and crosscorrelation properties is required in simultaneous polarimetric radar. Complete complementary sequence (CCS) has ideal range sidelobes along the zero Doppler axis, which is desirable in polarimetric radar. However, CCS is not widely used due to its sensitivity to the Doppler shift. In this letter, a L-BFGS (Limited Memory Broyden Flecher Goldfarb and Shanno) iterative method of constructing CCS with high Doppler tolerance is proposed, by which the range sidelobes can be suppressed in certain Doppler shifts. Numerical results are shown to demonstrate that the sidelobe peak of the designed CCS is about 30 dB lower than that of the CCS designed by the state-of-the-art GPTM (Generalized Prouhet-Thue-Morse) method in a certain Doppler shift interval.

Joint measure matrix and channel estimation for millimeter-wave massive MIMO with hybrid precoding

Millimeter-wave (mmWave) massive multiple-input multiple-output (MIMO) with hybrid precoding is a promising technology for future 5G wireless communications. Channel estimation for the millimeter-wave (mmWave) MIMO systems with hybrid precoding can be performed by estimating the path directions of the channel and corresponding path gains. This paper considers joint measure matrix and channel estimation for a massive MIMO system. By exploiting the sparsity of a massive MIMO system, a channel estimation scheme based on a Toeplitz-structured measure matrix and complete complementary sequence (CC-S) is proposed. Moreover, analytic studies show that the measurement matrix based on CC-S yields either optimal performance or feasibility in practice than an independent identically distributed Gaussian matrix. The performance of the scheme is shown with numerical examples.

Electrochemical Determination of the p53 Tumor Suppressor Gene Using a Gold Nanoparticle-Graphene Nanocomposite Modified Glassy Carbon Electrode

ABSTRACTA novel sensitive and simple electrochemical DNA sensor is reported for the determination of p53 tumor suppressor gene. A gold nanoparticle/graphene nanocomposite-modified glassy carbon electrode was prepared and methylene blue was used as the hybridization redox indicator. Scanning electron microscopic and electrochemical characterization demonstrated that the gold nanoparticles and graphene were present on the electrode. The resulting sensor provided suitable electrochemical response to the p53 tumor suppressor gene with a linear dynamic range from 0.1 to 1000 nM. The limit of detection was 0.012 nM. The sensor was able to differentiate a complete complementary DNA sequence, single-base mismatched DNA sequence, and a three-base mismatched DNA sequence. The precision of the device was satisfactory, with a relative standard deviation of 4.1% for 11 measurements. The combination of gold nanoparticles and a graphene nanocomposite provided enhanced capabilities for the determination of DNA for clinical applications.

Perfect orthogonal waveform scheme used for high-resolution multiple-input multiple-output synthetic aperture radar system

We investigate multiple-input multiple-output (MIMO) synthetic aperture radar (SAR) scheme with an ultra-low side-lobe ratio performance for using complete complementary sequences (CCS) waveform. It is shown that the CCS can be applied in a MIMO SAR system to obtain high resolution in range direction. In addition, the azimuth channel scheme with the multiple subsequences of CCS is also considered. First, we introduce the concept of CCS and establish the transmitter model based on CCS in MIMO SAR system. Then, we propose the corresponding imaging algorithm for employing the CCS to accurately focus the raw data of the MIMO SAR system and derive the range cell migration correction. Considering the signal complexity, we make use of the CCS pairs to analyze the MIMO SAR imaging algorithm. Finally, simulation results demonstrate the validity and feasibility of the proposed MIMO SAR scheme and the potential advantage of CCS.

Graphene oxide–gold nanoparticles hybrids-based surface plasmon resonance for sensitive detection of microRNA

In this study, a simple and sensitive surface plasmon resonance (SPR) biosensor for miRNA detection was developed using graphene oxide–gold nanoparticles (GO–AuNPs) hybrids as signal amplification element. Taking advantage of the GO–AuNPs hybrids and their enhanced performance in SPR biosensors, the detection of miRNA was carried out in only two steps. Firstly, the thiolated capture DNA probe with a short complete complementary sequence was immobilized on the Au film surface to recognize the part sequence of target miRNA. Subsequently, the assistant DNA-linked GO–AuNPs hybrids were employed to bind the other section of the target. It was found that the developed SPR biosensor was able to achieve a detection limit as low as 1fM. Moreover, the method showed excellent ability to discriminate differences among miRNA-200 family members. Notably, human miRNA from cancer cells could also be detected, and the results were in excellent agreement with the ones obtained using qRT-PCR. On the basis of these findings, we believe that this method has great potential for quantitative detection of miRNA in biomedical research and early clinical diagnostics.

Superior fluorescent probe for detection of potassium ion

Here, a simple, and highly sensitive fluorescent assay is designed to monitor K+. The versatile, robust biosensing strategy is based on the specific recognition utility of label-free aptamers with their targets and PicoGreen dye as the signal probe. The aptamers undergo a conformational change to a secondary structure such as G-quadruplex in the presence of targets. In addition to a conformational change with its targets, the remaining single-stranded DNA (ssDNA) aptamer form a duplex structure with its complete complementary sequence. Conformational changes of aptamers as well as fluorescence amplification produce clear signal-off in the presence of targets. Fluorescent assay employing this mechanism for the detection of K+ is highly sensitive, and selective. The detection limit of the K+ assay is determined to be 2.37pM. The sensing strategy is low-cost and simple in its operation without requirement for complex labeling of probe DNA or sophisticated synthesis of the fluorescent compound. Also, the method has less structural requirement of complexes of aptamers with their targets, thus rending its wilder applications for various targets.

Novel design of Doppler resilient complete complementary sequence for MIMO radar

Complete complementary sequence (CCS) has ideal correlation performance along the zero Doppler axis. However, its correlation property is extremely sensitive to the Doppler shift. In this letter, by employing a sequential quadratic programming (SQP) optimization method, a novel design of the Doppler resilient CCS is presented for multiple-input multiple-output (MIMO) radar. Compared to the existing methods, this design can reduce the range sidelobes associated with a matrix-valued ambiguity function without restrictions on the waveform number, the pulse number and the waveform length. In addition, the superior orthogonality of CCS can also be achieved. Several numerical examples are provided to demonstrate the effectiveness of this design.

Construction of Several Classes of Binary and Quaternary Complete Sequences and Sequence Pairs

In this paper, several constructions of binary and quaternary complete sequences and sequence pairs are presented. Based on singed shift sequence and interleaving technique, several binary and quaternary complete sequences and sequence pairs are generated by employing binary complete sequence, binary complete complementary sequence mate and binary complete sequence pair as the initial sequence. By means of interleaving iteration, more complete sequences and sequence pairs with novel parameters can be obtained.

Electrochemical DNA Sensor for Determination of p53 Tumor Suppressor Gene Incorporating Gold Nanoparticles Modification

Abstract A novel electrochemical DNA (E-DNA) sensor was designed with incorporating gold nanoparticles on a gold electrode for the determination of p53 tumor suppressor gene. A modified gold nanoparticles (GNPs) was prepared by modifying the GNPs prepared by the in situ potentiostatic deposition method on the gold electrode surface. The surface topography of the gold electrode and GNPs/Au were characterized by field emission scanning electron microscope. The E-DNA sensor was prepared through the self-assembly of a 5′-end thiolated probe DNA onto the surface of GNPs/Au followed by the hybridization of complementary sequence DNA. Cyclic voltammetry and electrochemical impedance spectroscopy were used to investigate each immobilization and hybridization step. By using methylene blue (MB) as an indicator for electrochemical hybridization detection, p53 tumor suppressor gene was quantitatively detected by differential pulse voltammetry (DPV) with the reduction peak current of MB. The increase in electrochemical signal upon hybridization was due to that MB had a higher affinity for dsDNA rather than ssDNA. Under the optimal conditions, the reduction peak current of MB was linearly related to the concentration of p53 tumor suppressor gene from 1.0 to 1000 nM with a detection limit of 0.8 nM ( S/N = 3). The relative standard deviation obtained was 3.8%. The E-DNA sensor could differentiate the complete complementary DNA sequence, single-base mismatch DNA sequence and three-base mismatched DNA sequence, indicating a good selectivity.

Streptavidin-enhanced surface plasmon resonance biosensor for highly sensitive and specific detection of microRNA

We are presenting a method for sensitive and specific detection of microRNA (miRNA) using surface plasmon resonance. A thiolated capture DNA probe with a short complete complementary sequence was immobilized on the gold surface of the sensor to recognize the part sequence of target miRNA, and then an oligonucleotide probe linked to streptavidin was employed to bind the another section of the target. The use of the streptavidin-oligonucleotide complex caused a ~5-fold increase in signal, improved the detection sensitivity by a factor of ~24, and lowered the detection limit to 1.7 fmol of miR-122. This specificity allowed a single mismatch in the target miRNA to be discriminated. The whole assay takes 30 min, and the surface of the sensor can be regenerated at least 30 times without loss in performance. The method was successfully applied to the determination of miRNA spiked into human total RNA samples.

COMPLETE COMPLEMENTARY SEQUENCE CODING WAVEFORM BASED AZIMUTH MULTI-CHANNEL SPACE-BORNE SAR WITH ULTRA-LOW RANGE SIDELOBE RATIO PERFORMANCE

Sidelobes of strong targets substantially impact image quality of synthetic aperture radar (SAR) using linear frequency modulation (LFM) waveform, especially in urban areas. A novel space-borne azimuth multi-channel SAR scheme with ultra-low range sidelobe-ratio (RSLR) performance was proposed, employing complete complementary sequence (CC-S) coding waveform. The CC-S waveform was utilized to acquire ultra-low RSLR performance in range direction. Azimuth multi-channel scheme was introduced, to compensate reduction of efiective PRF due to employing CC-S, and to mitigate azimuth resolution lost resulted from strong azimuth weighting, in order to implement low side-lobe performance in both range and azimuth direction. The method for pre-processing the CC- S based multi-channel SAR data was proposed, which would both compensate receiving time difierence of sub-sequences and reconstruct azimuth spectrum of multi-channel SAR data. Furthermore, the corresponding image formation algorithm for accurately focusing raw data of the SAR system was also proposed. Computer simulation results were presented, which demonstrated the validity of the proposed SAR scheme and image formation algorithm.

DNA Electrochemical Biosensor Based on Au Nanoparticles Self-Assembled Au Electrode

A novel electrochemical DNA biosensor system based on Au nanoparticles (AuNPs) modified Au electrode and anthraquinone-2,6-disulfonic acid (AQDS) as hybridization indicator was presented in this paper. AuNPs with different particle sizes were prepared from gold chloride by reduction, and self-assembled on Au electrode (AuNPs/Au electrode) by cysteamine as linker. Then, 5’ end –SH modified DNA (HS-DNA) as nucleotide probes were self-assembled onto the surface of AuNPs modified Au electrode (HS-DNA/AuNPs/Au electrode), and the HS-DNA/AuNPs/Au electrode could detect target DNA (completely complementary with HS-DNA). Because AuNPs were on Au electrode, the surface of Au electrode was increased. Therefore, this would result in the increase of electrochemical signal and increase the sensitivity of biosensor. If a completely complementary single stranded DNA (ssDNA) as target existed in the detection system, the cathodic peak current (△Ip) of AuNPs modified Au electrode was increased about 3 times than the HS-DNA/AuNPs/Au electrode because of the hybridization between HS-DNA and complementary DNA target and the formation of double stranded DNA (dsDNA), and if the target was a mismatching base-pair with HS-DNA, the electrochemical signal of electrode would have no obviously change. These results showed that this DNA biosensor system based on AuNPs self-assembled Au electrode had an excellent sensitivity with a complete complementary DNA sequence.

Electrochemical DNA Hybridization Assay: Enzyme‐Labeled Detection of Mutation in p53 Gene

AbstractThis paper discusses a new electrochemical DNA hybridization sensing approach based on the detection of a linked enzyme label. In this method we employ enzyme that is attached to a tethered ssDNA oligomer on the surface and the target analyte is a complementary ssDNA oligomer that does not require any pre‐treatment. The advantage of using of enzyme label is in its amplification of the registration of the hybridization event due to the catalytic reaction facilitated in the process. One particular novelty is associated with the use of enzymes that directly communicate with the electrode surface thus allowing for minimizing the need of additional reagents in the assay. The electrochemical assay was demonstrated when using mixed self‐assembled monolayers from thiolated oligonucleotide and 6‐mercapto 1‐hexanol on gold surfaces. Horseradish peroxidase (HRP) is attached to the surface tethered oligonucleotide using streptavidin‐biotin chemistry, and the enzyme successfully established direct electron transfer (DET) with the electrode or mediated electron transfer (MET) using a mediator. Hybridization results in increasing the angle of contact between electrode and DNA and also the stiffness of the ds DNA, which results in displacing the enzyme away from the electrode surface, and thereby reducing the occurrence of direct electron transfer between the enzyme and the electrode. The cyclic voltammetry showed a clear distinction in response between the complete complementary sequence and the two‐base mismatch sequence. Ellipsometric measurements show that the thickness of the thiol modified oligonucleotide on gold surfaces changes before and after hybridization for the complementary sequence, where as a minimal change in thickness was observed for the noncomplementary sequence. The model target analyte in this study was TP53 gene where a specific mutation is a marker for a list of cancers. Mutations of the TP53 gene have been demonstrated in tumors of the colon, breast, lung, ovary, bladder, and many other organs. Analysis of p53 mutations may provide useful information for the diagnosis, prognosis and therapy of cancer.

A NOVEL STRATEGY FOR TOPSIDE IONOSPHERE SOUNDER BASED ON SPACEBORNE MIMO RADAR WITH FDCD

A novel strategy for topside ionosphere sounder based on spaceborne Multiple-Input Multiple-Output (MIMO) radar is proposed, which takes advantage of frequency division and code division (FDCD) as a substitution for swept-frequency regime employed by the current ionosphere explorers, e.g., TOPside Automated Sounder (TOPAS). The azimuth resolution can be improved by 153times compared with TOPAS by means of frequency division, producing two-dimensional electron density images. The signal-to-noise ratio (SNR) can be enhanced and complete orthogonality among channels at difierent frequencies can be achieved by code division, which uses Complete Complementary Sequence (CC- S) as phase coding waveform. The simulation results show that root mean square (RMS) of normalized electron density measurements error of novel ionosphere sounder is as low as 1.7%.