PELMI: Realize robust DNA image storage under general errors via parity encoding and local mean iteration.

DNA molecules as storage media are characterized by high encoding density and low energy consumption, making DNA storage a highly promising storage method. However, DNA storage has shortcomings, especially when storing multimedia data, wherein image reconstruction fails when address errors occur, resulting in complete data loss. Therefore, we propose a parity encoding and local mean iteration (PELMI) scheme to achieve robust DNA storage of images. The proposed parity encoding scheme satisfies the common biochemical constraints of DNA sequences and the undesired motif content. It addresses varying pixel weights at different positions for binary data, thus optimizing the utilization of Reed-Solomon error correction. Then, through lost and erroneous sequences, data supplementation and local mean iteration are employed to enhance the robustness. The encoding results show that the undesired motif content is reduced by 23%-50% compared with the representative schemes, which improves the sequence stability. PELMI achieves image reconstruction under general errors (insertion, deletion, substitution) and enhances the DNA sequences quality. Especially under 1% error, compared with other advanced encoding schemes, the peak signal-to-noise ratio and the multiscale structure similarity address metric were increased by 10%-13% and 46.8%-122%, respectively, and the mean squared error decreased by 113%-127%. This demonstrates that the reconstructed images had better clarity, fidelity, and similarity in structure, texture, and detail. In summary, PELMI ensures robustness and stability of image storage in DNA and achieves relatively high-quality image reconstruction under general errors.

DNA-QLC: an efficient and reliable image encoding scheme for DNA storage.

BACKGROUND: DNA storage has the advantages of large capacity, long-term stability, and low power consumption relative to other storage mediums, making it a promising new storage medium for multimedia information such as images. However, DNA storage has a low coding density and weak error correction ability. RESULTS: To achieve more efficient DNA storage image reconstruction, we propose DNA-QLC (QRes-VAE and Levenshtein code (LC)), which uses the quantized ResNet VAE (QRes-VAE) model and LC for image compression and DNA sequence error correction, thus improving both the coding density and error correction ability. Experimental results show that the DNA-QLC encoding method can not only obtain DNA sequences that meet the combinatorial constraints, but also have a net information density that is 2.4 times higher than DNA Fountain. Furthermore, at a higher error rate (2%), DNA-QLC achieved image reconstruction with an SSIM value of 0.917. CONCLUSIONS: The results indicate that the DNA-QLC encoding scheme guarantees the efficiency and reliability of the DNA storage system and improves the application potential of DNA storage for multimedia information such as images.

EPO promotes the progression of rheumatoid arthritis by inducing desialylation via increasing the expression of neuraminidase 3.

OBJECTIVE: Erythropoietin (EPO) known as an erythrocyte-stimulating factor is increased in patients with rheumatoid arthritis (RA). Nevertheless, the function of EPO in the process of RA and relative mechanism needs to be further clarified. METHODS: The level of EPO in serum and synovial fluid from patients with RA and healthy controls was determined by . Collagen-induced arthritis (CIA) mice were constructed to confirm the role of EPO on RA pathogenesis. Differentially expressed genes (DEGs) of EPO-treated fibroblast-like synoviocyte (FLS) were screened by transcriptome sequencing. The transcription factor of neuraminidase 3 (NEU3) of DEGs was verified by double luciferase reporting experiment, DNA pulldown, electrophoretic mobility shift assay and chromatin immunoprecipitation-quantitative PCR (qPCR) assay. RESULTS: The overexpression of EPO was confirmed in patients with RA, which was positively associated with Disease Activity Score 28-joint count. Additionally, EPO intervention could significantly aggravate the joint destruction in CIA models. The upregulation of NEU3 was screened and verified by transcriptome sequencing and qPCR in EPO-treated FLS, and signal transducer and activator of transcription 5 was screened and verified to be the specific transcription factor of NEU3. EPO upregulates NEU3 expression via activating the Janus kinase 2 (JAK2)-STAT5 signalling pathway through its receptor EPOR, thereby to promote the desialylation through enhancing the migration and invasion ability of FLS, which is verified by JAK2 inhibitor and NEU3 inhibitor. CONCLUSION: EPO, as a proinflammatory factor, accelerates the process of RA through transcriptional upregulation of the expression of NEU3 by JAK2/STAT5 pathway.

Storing Images in DNA via base128 Encoding.

Current DNA storage schemes lack flexibility and consistency in processing highly redundant and correlated image data, resulting in low sequence stability and image reconstruction rates. Therefore, according to the characteristics of image storage, this paper proposes storing images in DNA via base128 encoding (DNA-base128). In the data writing stage, data segmentation and probability statistics are carried out, and then, the data block frequency and constraint encoding set are associated with achieving encoding. When the image needs to be recovered, DNA-base128 completes internal error correction by threshold setting and drift comparison. Compared with representative work, the DNA-base128 encoding results show that the undesired motifs were reduced by 71.2-90.7% and that the local guanine-cytosine content variance was reduced by 3 times, indicating that DNA-base128 can store images more stably. In addition, the structural similarity index (SSIM) and multiscale structural similarity (MS-SSIM) of image reconstruction using DNA-base128 were improved by 19-102 and 6.6-20.3%, respectively. In summary, DNA-base128 provides image encoding with internal error correction and provides a potential solution for DNA image storage. The data and code are available at the GitHub repository: https://github.com/123456wk/DNA_base128.

A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme.

Living organisms can produce corresponding functions by responding to external and internal stimuli, and this irritability plays a pivotal role in nature. Inspired by such natural temporal responses, the development and design of nanodevices with the ability to process time-related information could facilitate the development of molecular information processing systems. Here, we proposed a DNA finite-state machine that can dynamically respond to sequential stimuli signals. To build this state machine, a programmable allosteric strategy of DNAzyme was developed. This strategy performs the programmable control of DNAzyme conformation using a reconfigurable DNA hairpin. Based on this strategy, we first implemented a finite-state machine with two states. Through the modular design of the strategy, we further realized the finite-state machine with five states. The DNA finite-state machine endows molecular information systems with the ability of reversible logic control and order detection, which can be extended to more complex DNA computing and nanomachines to promote the development of dynamic nanotechnology.

Active Self-Assembly of Ladder-Shaped DNA Carrier for Drug Delivery.

With the advent of nanotechnology, DNA molecules have been transformed from solely genetic information carriers to multifunctional materials, showing a tremendous potential for drug delivery and disease diagnosis. In drug delivery systems, DNA is used as a building material to construct drug carriers through a variety of DNA self-assembly methods, which can integrate multiple functions to complete in vivo and in situ tasks. In this study, ladder-shaped drug carriers are developed for drug delivery on the basis of a DNA nanoladder. We first demonstrate the overall structure of the nanoladder, in which a nick is added into each rung of the nanoladder to endow the nanoladder with the ability to incorporate a drug loading site. The structure is designed to counteract the decrement of stability caused by the nick and investigated in different conditions to gain insight into the properties of the nicked DNA nanoladders. As a proof of concept, we fix the biotin in every other nick as a loading site and assemble the protein (streptavidin) on the loading site to demonstrate the feasibility of the drug-carrying function. The protein can be fixed stably and can be extended to different biological and chemical drugs by altering the drug loading site. We believe this design approach will be a novel addition to the toolbox of DNA nanotechnology, and it will be useful for versatile applications such as in bioimaging, biosensing, and targeted therapy.

Synthesis of Fibrous Phosphorus Micropillar Arrays with Pyro-Phototronic Effects.

The bottom-up preparation of two-dimensional material micro-nano structures at scale facilitates the realisation of integrated applications in optoelectronic devices. Fibrous Phosphorus (FP), an allotrope of black phosphorus (BP), is one of the most promising candidate materials in the field of optoelectronics with its unique crystal structure and properties.[1] However, to date, there are no bottom-up micro-nano structure preparation methods for crystalline phosphorus allotropes.[1c, 2] Herein, we present the bottom-up preparation of fibrous phosphorus micropillar (FP-MP) arrays via a low-pressure gas-phase transport (LP-CVT) method that controls the directional phase transition from amorphous red phosphorus (ARP) to FP. In addition, self-powered photodetectors (PD) of FP-MP arrays with pyro-phototronic effects achieved detection beyond the band gap limit. Our results provide a new approach for bottom-up preparation of other crystalline allotropes of phosphorus.

High-speed graphene/InGaN heterojunction photodetectors for potential application in visible light communication.

Due to the wavelength-selective absorption characteristic of indium gallium nitride (InGaN) ternary alloy, the InGaN-based photodetectors (PDs) show great potential as high signal-to-noise ratio (SNR) receivers in the visible light communication (VLC) system. However, the application of InGaN-based PDs with simple structure in the VLC system is limited by slow speed. Integration of graphene (Gr) with InGaN is an effective strategy for overcoming the limitation. Herein, we report on a high responsivity and fast response PDs based on Gr/InGaN heterojunctions. It finds that the three-layer Gr (T-Gr) can effectively improve the InGaN-based PDs photoelectric properties. The T-Gr/InGaN PDs show a high responsivity of 1.39 A/W@-3 V and a short rise/fall time of 60/200 µs, which are attributed to the combination of the high-quality InGaN epitaxial films and finite density of states of three-layer graphene. The fast response with high responsivity endows the T-Gr/InGaN PDs with great potential for selective detection of the VLC system.

Highly Efficient InGaN Nanorods Photoelectrode by Constructing Z-scheme Charge Transfer System for Unbiased Water Splitting.

Unbiased photoelectrochemical water splitting for the promising InGaN nanorods photoelectrode is highly desirable, but it is practically hindered by the serious recombination of charge carrier in bulk and surface of InGaN nanorods. Herein, an unbiased Z-scheme InGaN nanorods/Cu2 O nanoparticles heterostructured system with boosted interfacial charge transfer is constructed for the first time. The introduced Cu2 O nanoparticles pose double-sided effect on photoelectrochemical (PEC) performance of InGaN nanorods, which enables a robust hybrid structure and induces weakened light absorption capability simultaneously. As a result, the optimized InGaN/Cu2 O-1.5C photoelectrode with the uniform morphology exhibits an enhanced photocurrent density of ≈170 µA cm-2 at 0 V versus Pt, with 8.5-fold enhancement compared with pure InGaN nanorods. Comprehensive investigations into experimental results and theoretical calculations reveal that the electrons accumulation and holes depletion of Cu2 O facilitate to form a typical Z-scheme band alignment, thus providing a large photovoltage to drive unbiased water splitting and enhancing the stability of Cu2 O. This work provides a novel and facile strategy to achieve InGaN nanorods and other catalyst-based PEC water splitting without external bias, and to relieve the bottlenecks of charge transfer dynamics at the electrode bulk and electrode/electrolyte interface by constructing Z-scheme heterostructure.

An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO.

The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant constraints to avoid nonspecific hybridization reactions, such as the No-runlength constraint, GC-content, and the Hamming distance. In this work, a new nonlinear control parameter strategy and a random opposition-based learning strategy were used to improve the Harris hawks optimization algorithm (for the improved algorithm NOL-HHO) in order to prevent it from falling into local optima. Experimental testing was performed on 23 widely used benchmark functions, and the proposed algorithm was used to obtain better coding lower bounds for DNA storage. The results show that our algorithm can better maintain a smooth transition between exploration and exploitation and has stronger global exploration capabilities as compared with other algorithms. At the same time, the improvement of the lower bound directly affects the storage capacity and code rate, which promotes the further development of DNA storage technology.

Modeling of leachate recirculation using combined drainage blanket-horizontal trench systems in bioreactor landfills.

Leachate recirculation in municipal solid waste (MSW) landfills operated as bioreactors offers significant economic and environmental benefits. Combined drainage blanket (DB)-horizontal trench (HT) systems can be an alternative to single conventional recirculation approaches and can have competitive advantages. The key objectives of this study are to investigate combined drainage blanket -horizontal trench systems, to analyze the effects of applying two recirculation systems on the leachate migration in landfills, and to estimate some key design parameters (e.g., the steady-state flow rate, the influence width, and the cumulative leachate volume). It was determined that an effective recirculation model should consist of a moderate horizontal trench injection pressure head and supplementary leachate recirculated through drainage blanket, with an objective of increasing the horizontal unsaturated hydraulic conductivity and thereby allowing more leachate to flow from the horizontal trench system in a horizontal direction. In addition, design charts for engineering application were established using a dimensionless variable formulation.

Three-dimensional modelling of leachate recirculation using vertical wells in bioreactor landfills.

Bioreactor landfills use leachate recirculation to enhance the biodegradation of municipal solid waste and accelerate landfill stabilisation, which can provide significant environmental and economic benefits. Vertical wells are operated as a major method for leachate recirculation systems. The objectives of this article are to analyse the leachate migration in bioreactor landfills using vertical wells and to offer theoretical basis for the design of leachate recirculation systems. A three-dimensional numerical model was built using FLAC-3D, and this model can consider the saturated and unsaturated flow of leachate within anisotropic waste to reflect the actual conditions. First, main influence factors of leachate migration were analysed, including the vertical well height, hydraulic conductivity, and anisotropic coefficient, in a single-well recirculation system. Then, the effects of different configurations of a group-well system were studied and the optimal well spacing was obtained. Some key design parameters (e.g. the recirculation flow rate, volume of impact zone, radius of impact zone and time to reach steady state) were also evaluated. The results show that the hydraulic conductivity has a great impact on the optimal height of vertical wells and uniform configuration is the best option in terms of both volume of impact zone and time to reach steady state.

Efficacy and safety of traditional Chinese manual therapy (Tuina) in patients with non-specific chronic low back pain: a study protocol for a randomised controlled trial.

INTRODUCTION: Non-pharmacological interventions play a crucial role in the management of non-specific chronic low back pain (NSCLBP). One prime example is Tuina, a traditional Chinese manual therapy that incorporates pressing, kneading and rubbing techniques to alleviate physical discomfort and enhance overall well-being. It serves as a widely used technique in China and other East Asian countries. However, the effectiveness and safety of Tuina for managing NSCLBP have not been substantiated through rigorous clinical research. We sought to carry out a randomised controlled trial with an open-label design, blinded assessors and parallel arms to assess the effectiveness and safety of Tuina as a treatment for NSCLBP. The trial aims to provide high-quality evidence regarding the efficacy and safety of Tuina in improving outcomes for patients with NSCLBP. METHODS AND ANALYSIS: A total of 150 patients aged 18-60 years with NSCLBP will be recruited. Participants will be randomly assigned to one of the two groups. Both groups will receive standard health education. In addition, the treatment group will receive Tuina therapy, while the control group will participate in core stability exercises. Each group will undergo a total of 18 interventions over 6 weeks, with the interventions administered three times per week. The primary outcome measure is the patient's pain intensity, assessed using the Numerical Rating Scale, at week 6 following randomisation. Secondary outcomes encompass disability (measured by the Roland-Morris Disability Questionnaire), quality of life (assessed using the EuroQoL-5 dimensions questionnaire), adverse emotions (evaluated with the Pain Catastrophizing Scale, Tampa Scale of Kinesiophobia and Depression Anxiety Stress Scale), biomechanical outcomes, socioeconomic indicators (medication use, healthcare utilisation and absenteeism), patient satisfaction, treatment adherence and other relevant factors.The statistical analysis will follow the intention-to-treat principle. Two-way repeated measures analysis of variance will be used to compare the clinical data across different time points within both groups. ETHICS AND DISSEMINATION: The study protocol has received approval from the Ethics Committee of Shuguang Hospital, Shanghai University of Traditional Chinese Medicine (2023-1366-133-01). All study participants will be required to give written informed consent. The findings of the study will be submitted to a peer-reviewed journal for publication and presented at scientific conferences. Additionally, the participants will receive copies of the results. TRIAL REGISTRATION NUMBER: ChiCTR2300076257.

Efficient data reconstruction: The bottleneck of large-scale application of DNA storage.

Over the past decade, the rapid development of DNA synthesis and sequencing technologies has enabled preliminary use of DNA molecules for digital data storage, overcoming the capacity and persistence bottlenecks of silicon-based storage media. DNA storage has now been fully accomplished in the laboratory through existing biotechnology, which again demonstrates the viability of carbon-based storage media. However, the high cost and latency of data reconstruction pose challenges that hinder the practical implementation of DNA storage beyond the laboratory. In this article, we review existing advanced DNA storage methods, analyze the characteristics and performance of biotechnological approaches at various stages of data writing and reading, and discuss potential factors influencing DNA storage from the perspective of data reconstruction.

GCNSA: DNA storage encoding with a graph convolutional network and self-attention.

DNA Encoding, as a key step in DNA storage, plays an important role in reading and writing accuracy and the storage error rate. However, currently, the encoding efficiency is not high enough and the encoding speed is not fast enough, which limits the performance of DNA storage systems. In this work, a DNA storage encoding system with a graph convolutional network and self-attention (GCNSA) is proposed. The experimental results show that DNA storage code constructed by GCNSA increases by 14.4% on average under the basic constraints, and by 5%-40% under other constraints. The increase of DNA storage codes effectively improves the storage density of 0.7-2.2% in the DNA storage system. The GCNSA predicted more DNA storage codes in less time while ensuring the quality of codes, which lays a foundation for higher read and write efficiency in DNA storage.

DUHI: Dynamically updated hash index clustering method for DNA storage.

The exponential growth of global data leads to the problem of insufficient data storage capacity. DNA storage can be an ideal storage method due to its high storage density and long storage time. However, the DNA storage process is subject to unavoidable errors that can lead to increased cluster redundancy during data reading, which in turn affects the accuracy of the data reads. This paper proposes a dynamically updated hash index (DUHI) clustering method for DNA storage, which clusters sequences by constructing a dynamic core index set and using hash lookup. The proposed clustering method is analyzed in terms of overall reliability evaluation and visualization evaluation. The results show that the DUHI clustering method can reduce the redundancy of more than 10% of the sequences within the cluster and increase the reconstruction rate of the sequences to more than 99%. Therefore, our method solves the high redundancy problem after DNA sequence clustering, improves the accuracy of data reading, and promotes the development of DNA storage.

DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage.

DNA is a high-density, long-term stable, and scalable storage medium that can meet the increased demands on storage media resulting from the exponential growth of data. The existing DNA storage encoding schemes tend to achieve high-density storage but do not fully consider the local and global stability of DNA sequences and the read and write accuracy of the stored information. To address these problems, this article presents a graph-based De Bruijn Trim Rotation Graph (DBTRG) encoding scheme. Through XOR between the proposed dynamic binary sequence and the original binary sequence, k-mers can be divided into the De Bruijn Trim graph, and the stored information can be compressed according to the overlapping relationship. The simulated experimental results show that DBTRG ensures base balance and diversity, reduces the likelihood of undesired motifs, and improves the stability of DNA storage and data recovery. Furthermore, the maintenance of an encoding rate of 1.92 while storing 510 KB images and the introduction of novel approaches and concepts for DNA storage encoding methods are achieved.

High Net Information Density DNA Data Storage by the MOPE Encoding Algorithm.

DNA has recently been recognized as an attractive storage medium due to its high reliability, capacity, and durability. However, encoding algorithms that simply map binary data to DNA sequences have the disadvantages of low net information density and high synthesis cost. Therefore, this paper proposes an efficient, feasible, and highly robust encoding algorithm called MOPE (Modified Barnacles Mating Optimizer and Payload Encoding). The Modified Barnacles Mating Optimizer (MBMO) algorithm is used to construct the non-payload coding set, and the Payload Encoding (PE) algorithm is used to encode the payload. The results show that the lower bound of the non-payload coding set constructed by the MBMO algorithm is 3%-18% higher than the optimal result of previous work, and theoretical analysis shows that the designed PE algorithm has a net information density of 1.90 bits/nt, which is close to the ideal information capacity of 2 bits per nucleotide. The proposed MOPE encoding algorithm with high net information density and satisfying constraints can not only effectively reduce the cost of DNA synthesis and sequencing but also reduce the occurrence of errors during DNA storage.

RBS: A Rotational Coding Based on Blocking Strategy for DNA Storage.

The data volume of global information has grown exponentially in recent years, but the development of silicon-based memory has entered a bottleneck period. Deoxyribonucleic acid (DNA) storage is drawing attention owing to its advantages of high storage density, long storage time, and easy maintenance. However, the base utilization and information density of existing DNA storage methods are insufficient. Therefore, this study proposes a rotational coding based on blocking strategy (RBS) for encoding digital information such as text and images in DNA data storage. This strategy satisfies multiple constraints and produces low error rates in synthesis and sequencing. To illustrate the superiority of the proposed strategy, it was compared and analyzed with existing strategies in terms of entropy value change, free energy size, and Hamming distance. The experimental results show that the proposed strategy has higher information storage density and better coding quality in DNA storage, so it will improve the efficiency, practicality, and stability of DNA storage.

Biomolecule-Driven Two-Factor Authentication Strategy for Access Control of Molecular Devices.

The rise of DNA nanotechnology is promoting the development of molecular security devices and marking an essential change in information security technology, to one that can resist the threats resulting from the increase in computing power, brute force attempts, and quantum computing. However, developing a secure and reliable access control strategy to guarantee the confidentiality of molecular security devices is still a challenge. Here, a biomolecule-driven two-factor authentication strategy for access control of molecular devices is developed. Importantly, the two-factor is realized by applying the specificity and nicking properties of the nicking enzyme and the programmable design of the DNA sequence, endowing it with the characteristic of a one-time password. To demonstrate the feasibility of this strategy, an access control module is designed and integrated to further construct a role-based molecular access control device. By constructing a command library composed of three commands (Ca, Cb, Ca and Cb), the authorized access of three roles in the molecular device is realized, in which the command Ca corresponds to the authorization of role A, Cb corresponds to the authorization of role B, and Ca and Cb corresponds to the authorization of role C. In this way, when users access the device, they not only need the correct factor but also need to apply for role authorization in advance to obtain secret information. This strategy provides a highly robust method for the research on access control of molecular devices and lays the foundation for research on the next generation of information security.