Artifact Restoration in Histology Images with Diffusion Probabilistic Models

Histological whole slide images (WSIs) can be usually compromised by artifacts, such as tissue folding and bubbles, which will increase the examination difficulty for both pathologists and Computer-Aided Diagnosis (CAD) systems. Existing approaches to restoring artifact images are confined to Generative Adversarial Networks (GANs), where the restoration process is formulated as an image-to-image transfer. Those methods are prone to suffer from mode collapse and unexpected mistransfer in the stain style, leading to unsatisfied and unrealistic restored images. Innovatively, we make the first attempt at a denoising diffusion probabilistic model for histological artifact restoration, namely ArtiFusion.Specifically, ArtiFusion formulates the artifact region restoration as a gradual denoising process, and its training relies solely on artifact-free images to simplify the training complexity.Furthermore, to capture local-global correlations in the regional artifact restoration, a novel Swin-Transformer denoising architecture is designed, along with a time token scheme. Our extensive evaluations demonstrate the effectiveness of ArtiFusion as a pre-processing method for histology analysis, which can successfully preserve the tissue structures and stain style in artifact-free regions during the restoration. Code is available at https://github.com/zhenqi-he/ArtiFusion.Comment: Accepted by MICCAI202

Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes

Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter violaceus PCC 7421 was isolated from calcareous rock and lacks thylakoid membranes. The types and amounts of desaturases of this strain are distinct to those of other cyanobacteria, reflecting the earliest divergence of it from the cyanobacterial line. Three thermophilic unicellular strains, Thermosynechococcus elongatus BP-1 and two Synechococcus Yellowstone species, lack highly unsaturated fatty acids in lipids and contain only one Δ9 desaturase in contrast with mesophilic strains, which is probably due to their thermic habitats. Thus, the amounts and types of fatty acid desaturases are various among different cyanobacterial species, which may result from the adaption to environments in evolution

課題解決型グループワークにおける「深まり」について -「深まり」を可能にするものとは-

departmental bulletin pape

SAM-Med3D

Although the Segment Anything Model (SAM) has demonstrated impressive performance in 2D natural image segmentation, its application to 3D volumetric medical images reveals significant shortcomings, namely suboptimal performance and unstable prediction, necessitating an excessive number of prompt points to attain the desired outcomes. These issues can hardly be addressed by fine-tuning SAM on medical data because the original 2D structure of SAM neglects 3D spatial information. In this paper, we introduce SAM-Med3D, the most comprehensive study to modify SAM for 3D medical images. Our approach is characterized by its comprehensiveness in two primary aspects: firstly, by comprehensively reformulating SAM to a thorough 3D architecture trained on a comprehensively processed large-scale volumetric medical dataset; and secondly, by providing a comprehensive evaluation of its performance. Specifically, we train SAM-Med3D with over 131K 3D masks and 247 categories. Our SAM-Med3D excels at capturing 3D spatial information, exhibiting competitive performance with significantly fewer prompt points than the top-performing fine-tuned SAM in the medical domain. We then evaluate its capabilities across 15 datasets and analyze it from multiple perspectives, including anatomical structures, modalities, targets, and generalization abilities. Our approach, compared with SAM, showcases pronouncedly enhanced efficiency and broad segmentation capabilities for 3D volumetric medical images. Our code is released at https://github.com/uni-medical/SAM-Med3D

α-Glucosidase Inhibitors From the Coral-Associated Fungus Aspergillus terreus

Nine novel butenolide derivatives, including four pairs of enantiomers, named (±)-asperteretones A–D (1a/1b–4a/4b), and a racemate, named asperteretone E (5), were isolated and identified from the coral-associated fungus Aspergillus terreus. All the structures were established based on extensive spectroscopic analyses, including HRESIMS and NMR data. The chiral chromatography analyses allowed the separation of (±)-asperteretones A–D, whose absolute configurations were further confirmed by experimental and calculated electronic circular dichroism (ECD) analysis. Structurally, compounds 2–5 represented the first examples of prenylated γ-butenolides bearing 2-phenyl-3-benzyl-4H-furan-1-one motifs, and their crucial biogenetically related metabolite, compound 1, was uniquely defined by an unexpected cleavage of oxygen bridge between C-1 and C-4. Importantly, (±)-asperteretal D and (4S)-4-decarboxylflavipesolide C were revised to (±)-asperteretones B (2a/2b) and D (4), respectively. Additionally, compounds 1a/1b–4a/4b and 5 were evaluated for the α-glucosidase inhibitory activity, and all these compounds exhibited potent inhibitory potency against α-glucosidase, with IC50 values ranging from 15.7 ± 1.1 to 53.1 ± 1.4 μM, which was much lower than that of the positive control acarbose (IC50 = 154.7 ± 8.1 μM), endowing them as promising leading molecules for the discovery of new α-glucosidase inhibitors for type-2 diabetes mellitus treatment

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

δ-Tocotrienol, Isolated from Rice Bran, Exerts an Anti-Inflammatory Effect via MAPKs and PPARs Signaling Pathways in Lipopolysaccharide-Stimulated Macrophages

&delta;-Tocotrienol, an important component of vitamin E, has been reported to possess some physiological functions, such as anticancer and anti-inflammation, however their molecular mechanisms are not clear. In this study, &delta;-tocotrienol was isolated and purified from rice bran. The anti-inflammatory effect and mechanism of &delta;-tocotrienol against lipopolysaccharides (LPS) activated pro-inflammatory mediator expressions in RAW264.7 cells were investigated. Results showed that &delta;-tocotrienol significantly inhibited LPS-stimulated nitric oxide (NO) and proinflammatory cytokine (TNF-&alpha;, IFN-&gamma;, IL-1&beta; and IL-6) production and blocked the phosphorylation of c-Jun N-terminal kinase (JNK) and extracellular regulated protein kinases 1/2 (ERK1/2). &delta;-Tocotrienol repressed the transcriptional activations and translocations of nuclear factor-kappa B (NF-&kappa;B) and activator protein-1 (AP-1), which were closely related with downregulated cytokine expressions. Meanwhile, &delta;-tocotrienol also affected the PPAR signal pathway and exerted an anti-inflammatory effect. Taken together, our data showed that &delta;-tocotrienol inhibited inflammation via mitogen-activated protein kinase (MAPK) and peroxisome proliferator-activated receptor (PPAR) signalings in LPS-stimulated macrophages

Depositional Paleo-Environments of Lower Cambrian Qiongzhusi Formation in the Western Middle Yangtze Block and Its Controlling Effect on the Organic Matter Enrichment

No systematic comparative study has been conducted on the factors controlling organic matter enrichment in the different depositional environments of the Lower Cambrian Qiongzhusi Formation in the western Middle Yangtze Block, leading to a large discrepancy in our understanding. Based on organic geochemical and elemental analyses of core, outcrop, rock, and mineral samples from the slope, deep-water shelf, and shallow-water shelf, in this study, comparative analysis of the organic matter content, sedimentological characteristics, and depositional paleoenvironments of the Lower Cambrian Qiongzhusi Formation in the western Middle Yangtze Block was conducted, and the main controlling factors and models of the organic matter enrichment were investigated. The results revealed that the organic matter enrichment in the Qiongzhusi Formation was jointly controlled by redox conditions, water restriction, upwelling currents, terrigenous inputs, and paleo-productivity, but the main factors controlling the enrichment during the different periods were significantly different. (1) During the deposition of the Qiong 1 Member, the extensional rifting was strong, and the sea level was always high. The low degree of terrigenous dilution and anoxic conditions favored organic matter preservation. In this period, the upwelling currents were the main factor controlling organic matter enrichment. The paleo-productivity decreased as the intensity of the upwelling currents gradually weakened from the slope to the shelf, leading to a decrease in the total organic carbon (TOC) content and thereby a gradual decrease in the biogenic silica content of the shale. (2) During the deposition of the Qiong 2 Member, the extensional rifting weakened, and the sea level continued to drop. The upwelling currents, terrigenous input, and redox conditions were all important factors controlling the organic matter enrichment in the region. From the slope to the shelves, the conditions favorable for organic matter enrichment gradually worsened, and the TOC content gradually decreased, with the lithofacies gradually transitioning from biogenic siliceous shale to clayey shale or clayey-calcareous shale. (3) During the deposition of the Qiong 3 Member, the Yangzi Platform underwent a filling and leveling-up process, and the redox conditions played a major role in controlling the organic matter enrichment. The entire region was dominated by an oxygen-rich environment, and the conditions were no longer favorable for organic matter preservation, leading to a low average TOC content. Overall, the spatial variability of the TOC content was closely associated with changes in the depositional paleoenvironment caused by sea-level changes