Attention Mechanisms in Medical Image Segmentation: A Survey

Medical image segmentation plays an important role in computer-aided diagnosis. Attention mechanisms that distinguish important parts from irrelevant parts have been widely used in medical image segmentation tasks. This paper systematically reviews the basic principles of attention mechanisms and their applications in medical image segmentation. First, we review the basic concepts of attention mechanism and formulation. Second, we surveyed over 300 articles related to medical image segmentation, and divided them into two groups based on their attention mechanisms, non-Transformer attention and Transformer attention. In each group, we deeply analyze the attention mechanisms from three aspects based on the current literature work, i.e., the principle of the mechanism (what to use), implementation methods (how to use), and application tasks (where to use). We also thoroughly analyzed the advantages and limitations of their applications to different tasks. Finally, we summarize the current state of research and shortcomings in the field, and discuss the potential challenges in the future, including task specificity, robustness, standard evaluation, etc. We hope that this review can showcase the overall research context of traditional and Transformer attention methods, provide a clear reference for subsequent research, and inspire more advanced attention research, not only in medical image segmentation, but also in other image analysis scenarios.Comment: Submitted to Medical Image Analysis, survey paper, 34 pages, over 300 reference

Comparison of the gut microbiota and untargeted gut tissue metabolome of Chinese mitten crabs (Eriocheir sinensis) with different shell colors

IntroductionThe Chinese mitten crab (Eriocheir sinensis) is a highly valued freshwater crustacean in China. While the natural shell color of E. sinensis is greenish brown (GH), we found a variety with a brownish-orange shell color (RH). Although RH is more expensive, it exhibits a lower molting frequency and growth rate compared with GH, which significantly reduces its yield and hinders large-scale farming. The growth and development of animals are closely related to their gut microbiota and gut tissue metabolic profiles.MethodsIn this study, we compared the gut microbiome communities and metabolic profiles of juvenile RH and GH crabs using 16S rRNA gene sequencing and liquid chromatography–mass spectrometry (LC–MS), respectively.ResultsOur findings indicated that the intestinal microbial composition and metabolic characteristics of E. sinensis differed significantly between RH and GH. At the operational taxonomic unit (OTU) level, the α-diversity of the gut microbiota did not differ significantly between RH and GH, while the β-diversity of the RH gut microbiota was higher than that of the GH gut microbiota. At the species level, the richness of unclassified_c_Alphaproteobacteria was significantly higher in the GH group, while the RH group had a significantly higher richness of three low-abundance species, Flavobacteria bacterium BAL38, Paraburkholderia ferrariae, and uncultured_bacterium_g__Legionella. In the current study, 598 gut tissue metabolites were identified, and 159 metabolites were significantly different between GH and RH. The metabolite profile of RH was characteristic of a low level of most amino acids and lipid metabolites and a high level of several pigments compared with that of GH. These metabolites were enriched in 102 KEGG pathways. Four pathways, including (1) Central carbon metabolism in cancer, (2) protein digestion and absorption, (3) alanine, aspartate and glutamate metabolism, and (4) aminoacyl-tRNA biosynthesis, were significantly enriched. The correlation analysis between metabolites and microbiotas indicated that most key differential metabolites were positively correlated with the abundance of Shewanella_sp_MR-7.DiscussionThis research provided a greater understanding of the physiological conditions of E. sinensis varieties with different shell colors by comparing the gut microbiota and gut tissue metabolome

HO-1 Is Essential for Tetrahydroxystilbene Glucoside Mediated Mitochondrial Biogenesis and Anti-Inflammation Process in LPS-Treated RAW264.7 Macrophages

2,3,5,4′-Tetrahydroxystilbene-2-O-β-D-glucoside (TSG), an important monomer extracted from Polygonum multiflorum, can prevent a number of inflammation associated chronic diseases. However, the mechanism involved in TSG inducing anti-inflammatory role remains unclear. As an inducible antioxidant enzyme, Heme oxygenase-1 (HO-1), is crucial for protecting the mammalian cells against adverse stimuli. Here, we found that the TSG treatment strongly induces the expression of HO-1 in an NRF2-depended manner. Meanwhile, TSG increased the mitochondrial mass through upregulation of the mitochondrial biogenesis activators (PGC-1α, NRF1, and TFAM) as well as the mitochondrial complex IV. Furthermore, TSG attenuated Lipopolysaccharide (LPS) mediated RAW264.7 cells activation and secretion of proinflammatory cytokines, including interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). Zinc Protoporphyrin (ZnPP), a selective inhibitor of HO-1 activity, was able to attenuate TSG mediated mitochondrial biogenesis and anti-inflammatory process. Finally, we observed that LPS induced obvious mtDNA depletion and ATP deficiency, which indicated a severe damage of mitochondria. TSG restored the LPS induced mitochondrial dysfunction via activation of the mitochondrial biogenesis. ZnPP treatment markedly reversed the inhibitory effects of TSG on mitochondrial damage and oxidative stress in LPS stimulated macrophages. Taken together, these findings suggest that TSG enhances mitochondrial biogenesis and function mainly via activation the HO-1. TSG can be developed as a potential drug for treatment of inflammatory diseases

Production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from excess activated sludge as a promising substitute of pure culture

通讯作者地址: Wang, YPThis study aimed to investigate the feasibility and technology to harvest poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) by mixed culture. Copolymer PHBHHx, usually fermented by pure strains, was reported to be synthesized from activated sludge for the first time. Sodium laurate was used as the sole carbon substrate for sludge acclimation and PHBHHx accumulation. Batch experiments were designed to look into the impact of the carbon, nitrogen, phosphorus and oxygen supply on PHBHHx production. The results showed that the acclimated excess sludge was able to produce PHBHHx, and the maximum output (505.6 mg/L PHBHHx containing 6.34 mol% HHx) was achieved with conditions of the continuous aeration, nitrogen and phosphorus limitation, and adequate carbon source implemented by pulse feeding 0.5 g/L sodium laurate every 4 h. Moreover, composition and structure of the PHBHHx from sludge were found similar to that from pure culture, according to literature, FTIR and NMR spectra. Finally, high-throughput sequencing technique characterized that phylum Chlorobi and genus Leadbetterella should be critical groups for PHBHHx synthesis in the sludge community.National Basic Research Program of China 2013CB733505 National Natural Science Foundation of China 21206143 41271260 Program for New Century Excellent Talents in University NCET-12-0326 Development and Reform Commission of Fujian Province, China 2011-159

Plant-mediated fabrication and surface enhanced raman property of flower-like Au@Pd nanoparticles

The flower-like nanostructures of an Au core and Pd petals with the average size of 47.8 nm were fabricated through the successive reduction of HAuCl4 and Na2PdCl4 at room temperature. During the synthesis, Cacumen Platycladi leaf extract served as weak reductant and capping agent. Characterization techniques such as Energy-dispersive X-ray spectroscopy, UV-Vis spectroscopy, and X-ray diffraction characterizations were employed to confirm that the as-synthesized nanoparticles have the structure of core-shell. The obtained core-shell nanoflowers exhibited good surface enhanced Raman spectroscopic activity with Rhodamine 6G. ? 2014 by the authors

Theoretical calculations and analysis for n + 6

R-matrix theory is an important methodology for applications on light, medium and heavy mass nuclides nuclear reaction in the resonance energy range. Full R-matrix formalism contains the diagonal elements of the energy levels matrix and it is a rigorous theory. Because of different assumptions and approximations, many kinds of R-matrix derived methods are obtained. The new R-matrix code FDRR is presented and includes 4 kinds of R-matrix applications. It can be used for calculating integral cross sections and angular distributions of 2-bodies reactions. The cross sections and angular distributions of n+ 6Li reaction are calculated and analyzed by FDRR code. The results are in good agreement with experimental data below 20 MeV

Biogenic flower-shaped Au-Pd nanoparticles: Synthesis, SERS detection and catalysis towards benzyl alcohol oxidation

～40 nm flower-shaped Au-Pd bimetallic nanoparticles were prepared in a facile and eco-friendly way based on the simultaneous bioreduction of HAuCl 4 and Na2PdCl4 with ascorbic acid and Cacumen Platycladi leaf extract at room temperature. Characterization techniques, such as transmission electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray diffraction, were employed to confirm that the as-synthesized nanoparticles were alloys. The obtained flower-shaped Au-Pd alloy nanoparticles exhibited an excellent surface enhanced Raman spectroscopic activity with rhodamine 6G and efficient catalytic ability for the oxidation of benzyl alcohol to benzaldehyde. ? 2014 The Royal Society of Chemistry