This paper proposes a compression algorithm based on K-means clustering for high-through DNA sequence (DNAC-K). In DNAC-K, we create cluster of sequences based on K-means clustering method at first, then iterate clusters according to the edit distances of subsequences, and finally, adopt Huffman coding to encode the result of clustering result. Experimental results on several sequencing data sets demonstrate better performance of DNAC-K than many of the current high-throughput DNA sequence compression algorithms.
Specific to the difficulty of optimization on complex multimodal problems, this paper proposes a spring oscillator model used for particle swarm optimizer algorithm (SOMPSO). In SOMPSO, the particles that trapped in the local optima in some dimensions and certain individual extreme points whose corresponding dimensions' positions are the farthest from them, will constitute the vibrators and the equilibrium points of several spring oscillator models (SOM) respectively. Velocities and positions of particles will be updated dynamically referred to the physical principle of SOM. This SOM enlarges the search space of particles to increase the diversity of the swarm. The experiment results show that, SOMPSO algorithm has good performance when compared with other four variants of the particle swarm optimizer (PSO) on the optimization of the multimodal composition functions.
In order to improve the blind equalizer performance of QAM signals, the dual-mode algorithm combining Modified Constant Modulus Algorithm (MCMA) and Decision Directed (DD) rule is improved in three aspects-- improving the error function of MCMA, updating equalizer's weight coefficients with variable step size, and setting reset rule of dual-mode algorithm with short-time mean error energy. A series of experiments are carried out under different QAM modulation signals, different channels and different SNR to verify the effectiveness of the improved algorithm. The simulation results show that the improved algorithm has less residual inter-symbol interference for high-order QAM signals, and its performance improvements will increase with the rise of QAM order.
Abstract In this paper, waste wood (sawdust) was modified with layered double hydroxides (LDHs) to improve its adsorption capacity for Pb(II). The LDHs grew easily and evenly on the sawdust in situ through a hydrothermal method. Then, the functional groups and favorable crystal structures of sawdust/LDHs composites were demonstrated by FTIR and XRD. The results showed that the adsorption capacity of sawdust/LDHs composites for Pb(II) increased by 83.61% compared to sawdust, and the optimum conditions for adsorption were at pH 6 for 180 min with an adsorbent dosage of 3 g/L. Moreover, the behavior of Pb(II) adsorption preferably followed pseudo‐second‐order, Langmuir and Freundlich models, with all the R 2 values exceeding 0.97. It was indicated that Pb(II) adsorption occurred on the monolayer and heterogeneous surfaces through chemical bonding and electrostatic interaction. Due to their low cost and high adsorption capacity, the plant‐based composites have great potential in the treatment of lead‐containing wastewater.
Alginate hydrogels are a class of biomaterials that can be used as local release depots for therapeutic agents. A particular drug that can take advantage of alginate hydrogel for controlled release is hydrocortisone acetate. Hydrocortisone acetate is a widely used anti-inflammatory agent, but is limited in application due to poor solubility and lack of controlled delivery. To overcome this limitation, a mechanically responsive β-cyclodextrin-conjugated alginate (Alg-β-CD) hydrogel was synthesized and characterized for enhanced aqueous solubility and controlled release of hydrocortisone acetate. We demonstrated that mono-6-deoxy-6-ethylenediamine-β-cyclodextrin and hydrocortisone acetate formed a 1:1 inclusion complex, thus resulting in marked increase in hydrocortisone acetate solubility, while causing no significant inhibition to the growth of cultured mouse fibroblasts (L929). More importantly, the release of hydrocortisone acetate from the hydrogel system was increasingly sensitive to mechanical compression, and the mechanical responsiveness of hydrocortisone acetate release increased dramatically as the concentration of mono-6-deoxy-6-ethylenediamine-β-cyclodextrin increased from 0% to 46%, whereas the swelling rate and stiffness of the hydrogel decreased as the concentration of mono-6-deoxy-6-ethylenediamine-β-cyclodextrin increased. The mechanical responsiveness of hydrocortisone acetate release was attributable to conformational distortion of mono-6-deoxy-6-ethylenediamine-β-cyclodextrin moieties and deformation of the polymer network. Moreover, we demonstrated that the hydrogel continuously released and accumulated hydrocortisone acetate in the medium when compressed for up to 72 h, which led to increasing suppression of nitric oxide production in the lipopolysaccharide-stimulated mouse macrophages (RAW264.7), indicating desirable anti-inflammatory effect at the cell level. Hence, this hydrogel system may provide a useful platform for drug delivery, such as hydrocortisone acetate release to wound site, by intentionally generated mechanical force.
Carboxymethyl sago pulp (CMSP) with a degree of substitution 0.8 was synthesised from sago waste and cross-linked with chitosan to form a hydrogel by electron beam (EB) irradiation. Diclofenac sodium was loaded into 40% CMSP/3% chitosan solution mixture and irradiated at 25 kGy. The hydrogel exhibited pH and temperature-sensitive swelling behaviour. Fourier-transform infrared spectroscopy, field emission scanning electron microscope, X-ray diffraction, differential scanning calorimetry, and thermogravimetric analysis were performed to characterise its properties. Drug entrapment efficiency of diclofenac sodium-loaded hydrogel was 65.4 ± 0.2%. The release of diclofenac sodium from CMSP/chitosan hydrogel disc was low in an acidic environment (pH 1.2) and there was slow and sustained release in colonic pH (pH 6.8) over 32 h in a first-order manner. Based on the results of the disk diffusion test, the hydrogel exhibited antimicrobial activity against the tested microorganisms. Among tested formulations, 40% CMSP/3% chitosan hydrogel was shown to be the potential drug carrier for sustained drug delivery.
In this paper, we present a new reference-free and lossless approach to compress next-generation sequencing (NGS) data in FASTQ format, splitting the input FASTQ data into three parts of metadata, short reads and quality scores, and eliminating their redundancy independently according to their own characteristics. Experiments were conducted on five real-world NGS data. The results show that the proposed algorithm has better compression gain as compared to the previous state of the art compression algorithms.
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