Contrastive Diffusion Model with Auxiliary Guidance for Coarse-to-Fine PET Reconstruction

To obtain high-quality positron emission tomography (PET) scans while reducing radiation exposure to the human body, various approaches have been proposed to reconstruct standard-dose PET (SPET) images from low-dose PET (LPET) images. One widely adopted technique is the generative adversarial networks (GANs), yet recently, diffusion probabilistic models (DPMs) have emerged as a compelling alternative due to their improved sample quality and higher log-likelihood scores compared to GANs. Despite this, DPMs suffer from two major drawbacks in real clinical settings, i.e., the computationally expensive sampling process and the insufficient preservation of correspondence between the conditioning LPET image and the reconstructed PET (RPET) image. To address the above limitations, this paper presents a coarse-to-fine PET reconstruction framework that consists of a coarse prediction module (CPM) and an iterative refinement module (IRM). The CPM generates a coarse PET image via a deterministic process, and the IRM samples the residual iteratively. By delegating most of the computational overhead to the CPM, the overall sampling speed of our method can be significantly improved. Furthermore, two additional strategies, i.e., an auxiliary guidance strategy and a contrastive diffusion strategy, are proposed and integrated into the reconstruction process, which can enhance the correspondence between the LPET image and the RPET image, further improving clinical reliability. Extensive experiments on two human brain PET datasets demonstrate that our method outperforms the state-of-the-art PET reconstruction methods. The source code is available at \url{https://github.com/Show-han/PET-Reconstruction}.Comment: Accepted and presented in MICCAI 2023. To be published in Proceeding

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

Altitudinal Heterogeneity of UV Adaptation in Phytophthora infestans Is Associated with the Spatial Distribution of a DNA Repair Gene

Climate change is considered a major threat to society and nature. UV irradiation is the most important environmental genotoxic agent. Thus, how elevated UV irradiation may influence human health and ecosystems has generated wide concern in the scientific community, as well as with policy makers and the public in general. In this study, we investigated patterns and mechanisms of UV adaptation in natural ecosystems by studying a gene-specific variation in the potato late blight pathogen, Phytophthora infestans. We compared the sequence characteristics of radiation sensitive 23 (RAD23), a gene involved in the nucleotide excision repair (NER) pathway and UV tolerance, in P. infestans isolates sampled from various altitudes. We found that lower genetic variation in the RAD23 gene was caused by natural selection. The hypothesis that UV irradiation drives this selection was supported by strong correlations between the genomic characteristics and altitudinal origin (historic UV irradiation) of the RAD23 sequences with UV tolerance of the P. infestans isolates. These results indicate that the RAD23 gene plays an important role in the adaptation of P. infestans to UV stress. We also found that different climatic factors could work synergistically to determine the evolutionary adaptation of species, making the influence of climate change on ecological functions and resilience more difficult to predict. Future attention should aim at understanding the collective impact generated by simultaneous change in several climate factors on species adaptation and ecological sustainability, using state of the art technologies such as experimental evolution, genome-wide scanning, and proteomics

Comparative Effects of Er-Xian Decoction, Epimedium

Er-Xian Decoction (EXD), Epimedium herbs (herbs of Epimedium brevicornum Maxim, EBH), and icariin (ICA) have been proven to have estrogen-like and antiosteoporotic activity and are used for the treatment of osteoporosis, menopausal syndrome, and age-associated diseases. The present study found that EXD, EBH, and ICA treatments, emulating estrogen, significantly contributed to bone density and architecture in OVX rats and that EXD is similar to estrogen and exerts a concomitant effect on bone formation and bone resorption at the tissue level, while EBH and ICA produced bone-protective effects mainly by inhibiting bone resorption. Nevertheless, EXD, EBH, and ICA treatments manifested a fewer adverse effects on the uterus, mammary gland, and vagina compared to estrogen administrations. Among the EXD, EBH, and ICA, EXD was found to have superior efficacy and safety profile

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Background Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. Findings Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. Conclusions Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species

Microbial diversity and community composition of fecal microbiota in dual-purpose and egg type ducks

IntroductionDucks are important agricultural animals, which can be divided into egg and dual-purpose type ducks according to economic use. The gut microbiota of ducks plays an important role in their metabolism, immune regulation, and health maintenance.MethodsHere, we use 16S rDNA V4 hypervariable amplicon sequencing to investigate the compositions and community structures of fecal microbiota between egg (five breeds, 96 individuals) and dual-purpose type ducks (four breeds, 73 individuals) that were reared under the same conditions.ResultsThe alpha diversity of fecal microflora in egg type ducks was significantly higher than that in dual-type ducks. In contrast, there is no significant difference in the fecal microbial community richness between the two groups. MetaStat analysis showed that the abundance of Peptostreptococcaceae, Streptococcaceae, Lactobacillus, Romboutsia, and Campylobacter were significantly different between the two groups. The biomarkers associated with the egg and dual-purpose type ducks were identified using LEfSe analysis and IndVal index. Function prediction of the gut microbiota indicated significant differences between the two groups. The functions of environmental information processing, carbohydrate metabolism, lipid metabolism, xenobiotic biodegradation and metabolism, and metabolism of terpenoids and polyketides were more abundant in egg type ducks. Conversely, the genetic information processing, nucleotide metabolism, biosynthesis of amino acids and secondary metabolites, glycan biosynthesis and metabolism, fatty acid elongation, and insulin resistance were significantly enriched in dual-purpose type ducks.DiscussionThis study explored the structure and diversity of the gut microbiota of ducks from different economic-use groups, and provides a reference for improving duck performance by using related probiotics in production