Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach with Enhanced Error Resilience and Biological Constraint Optimization

In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme for DNA image storage, designated as DJSCC-DNA. This paradigm distinguishes itself from conventional DNA storage techniques through three key modifications: 1) it employs advanced deep learning methodologies, employing convolutional neural networks for DNA encoding and decoding processes; 2) it seamlessly integrates DNA polymerase chain reaction (PCR) amplification into the network architecture, thereby augmenting data recovery precision; and 3) it restructures the loss function by targeting biological constraints for optimization. The performance of the proposed model is demonstrated via numerical results from specific channel testing, suggesting that it surpasses conventional deep learning methodologies in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Additionally, the model effectively ensures positive constraints on both homopolymer run-length and GC content

A Tutorial on Coding Methods for DNA-based Molecular Communications and Storage

Exponential increase of data has motivated advances of data storage technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage provides a much higher data density and superior durability, compared with state-of-the-art media. In this paper, we provide a tutorial on DNA storage and its role in molecular communications. Firstly, we introduce fundamentals of DNA-based molecular communications and storage (MCS), discussing the basic process of performing DNA storage in MCS. Furthermore, we provide tutorials on how conventional coding schemes that are used in wireless communications can be applied to DNA-based MCS, along with numerical results. Finally, promising research directions on DNA-based data storage in molecular communications are introduced and discussed in this paper

Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach With Enhanced Error Resilience and Biological Constraint Optimization

In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme for DNA image storage, designated as DJSCC-DNA. This paradigm distinguishes itself from conventional DNA storage techniques through three key modifications: 1) it employs advanced deep learning methodologies, employing convolutional neural networks for DNA encoding and decoding processes; 2) it seamlessly integrates DNA polymerase chain reaction (PCR) amplification into the network architecture, thereby augmenting data recovery precision; and 3) it restructures the loss function by targeting biological constraints for optimization. The performance of the proposed model is demonstrated via numerical results from specific channel testing, suggesting that it surpasses conventional deep learning methodologies in terms of peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Additionally, the model effectively ensures positive constraints on both homopolymer run-length and GC content

Dmbg-Net: Dilated multiresidual boundary guidance network for COVID-19 infection segmentation

Accurate segmentation of infected regions in lung computed tomography (CT) images is essential for the detection and diagnosis of coronavirus disease 2019 (COVID-19). However, lung lesion segmentation has some challenges, such as obscure boundaries, low contrast and scattered infection areas. In this paper, the dilated multiresidual boundary guidance network (Dmbg-Net) is proposed for COVID-19 infection segmentation in CT images of the lungs. This method focuses on semantic relationship modelling and boundary detail guidance. First, to effectively minimize the loss of significant features, a dilated residual block is substituted for a convolutional operation, and dilated convolutions are employed to expand the receptive field of the convolution kernel. Second, an edge-attention guidance preservation block is designed to incorporate boundary guidance of low-level features into feature integration, which is conducive to extracting the boundaries of the region of interest. Third, the various depths of features are used to generate the final prediction, and the utilization of a progressive multi-scale supervision strategy facilitates enhanced representations and highly accurate saliency maps. The proposed method is used to analyze COVID-19 datasets, and the experimental results reveal that the proposed method has a Dice similarity coefficient of 85.6% and a sensitivity of 84.2%. Extensive experimental results and ablation studies have shown the effectiveness of Dmbg-Net. Therefore, the proposed method has a potential application in the detection, labeling and segmentation of other lesion areas

Critical role of interleukin (IL)-17 in inflammatory and immune disorders: An updated review of the evidence focusing in controversies

Interleukin 17 (IL-17) is a proinflammatory cytokine that has been the focus of intensive research because of its crucial role in the pathogenesis of different diseases across many medical specialties. In this context, the present review in which a panel of 13 experts in immunology, dermatology, rheumatology, neurology, hematology, infectious diseases, hepatology, cardiology, ophthalmology and oncology have been involved, puts in common the mechanisms through which IL-17 is considered a molecular target for the development of novel biological therapies in these different fields. A comprehensive review of the literature and analysis of the most outstanding evidence have provided the basis for discussing the most relevant data related to IL-17A blocking agents for the treatment of different disorders, such as psoriasis, psoriatic arthritis, rheumatoid arthritis, ankylosing spondylitis, cardiovascular disorders, non alcoholic fatty liver disease, multiple sclerosis, inflammatory bowel disease, uveitis, hematological and solid cancer. Current controversies are presented giving an opening line for future research.This work was supported by Novartis Pharmaceuticals Spain

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe