2.5D cascaded context-based network for liver and tumor segmentation from CT images

The existing 2D/3D strategies still have limitations in human liver and tumor segmentation efficiency. Therefore, this paper proposes a 2.5D network combing cascaded context module (CCM) and Ladder Atrous Spatial Pyramid Pooling (L-ASPP), named CCLNet, for automatic liver and tumor segmentation from CT. First, we utilize the 2.5D mode to improve the training efficiency; Second, we employ the ResNet-34 as the encoder to enhance the segmentation accuracy. Third, the L-ASPP module is used to enlarge the receptive field. Finally, the CCM captures more local and global feature information. We experimented on the LiTS17 and 3DIRCADb datasets. Experimental results prove that the method skillfully balances accuracy and cost, thus having good prospects in liver and liver segmentation in clinical assistance

S-diclofenac Protects against Doxorubicin-Induced Cardiomyopathy in Mice via Ameliorating Cardiac Gap Junction Remodeling

Hydrogen sulfide (H2S), as a novel gaseous mediator, plays important roles in mammalian cardiovascular tissues. In the present study, we investigated the cardioprotective effect of S-diclofenac (2-[(2,6-dichlorophenyl)amino] benzeneacetic acid 4-(3H-1,2,dithiol-3-thione-5-yl)phenyl ester), a novel H2S-releasing derivative of diclofenac, in a murine model of doxorubicin-induced cardiomyopathy. After a single dose injection of doxorubicin (15 mg/kg, i.p.), male C57BL/6J mice were given daily treatment of S-diclofenac (25 and 50 µmol/kg, i.p.), diclofenac (25 and 50 µmol/kg, i.p.), NaHS (50 µmol/kg, i.p.), or same volume of vehicle. The cardioprotective effect of S-diclofenac was observed after 14 days. It showed that S-diclofenac, but not diclofenac, dose-dependently inhibited the doxorubicin-induced downregulation of cardiac gap junction proteins (connexin 43 and connexin 45) and thus reversed the remodeling of gap junctions in hearts. It also dose-dependently suppressed doxorubicin-induced activation of JNK in hearts. Furthermore, S-diclofenac produced a dose-dependent anti-inflammatory and anti-oxidative effect in this model. As a result, S-diclofenac significantly attenuated doxorubicin-related cardiac injury and cardiac dysfunction, and improved the survival rate of mice with doxorubicin-induced cardiomyopathy. These effects of S-diclofenac were mimicked in large part by NaHS. Therefore, we propose that H2S released from S-diclofenac in vivo contributes to the protective effect in doxorubicin-induced cardiomyopathy. These data also provide evidence for a critical role of H2S in the pathogenesis of doxorubicin-induced cardiomyopathy

Multiple targets related to mitochondrial function unveiled by metabolomics and proteomics profiles of hearts from atrial fibrillation patients

Background: The prominent mitochondrial metabolic changes of the atrium reportedly have significant impact on electrical signals and structural remodeling which play important roles in the occurrence and development of atrial fibrillation (AF). However, the mechanism is not completely known.Objective: This study was aimed to explore the mitochondrial metabolism reprogrammed in AF patients by integrating metabolomics as well as proteomics of human atrium tissues.Methods and Results: Left atrial tissue samples were harvested from 10 non-valvular AF patients and 10 matched samples from healthy donors for transplantation. In metabolomics analysis, 113 metabolites were upregulated and 10 metabolites were downregulated in AF, where multiple pathways related to mitochondrial energy metabolism were enriched. Correlation analysis between the differentially expressed proteins and metabolites identified several hub proteins related to mitochondrial function including Glycerol-3-phosphate dehydrogenase 2 (GPD2), Synemin (SYNM), Plectin (PLEC), with MCC score of 27, 17, 16, respectively, which have the most interactions with the dysregulated metabolites and ranked at the top in network string interactions scored by MCC method. All 330 differentially expressed proteins including 225 upregulated and 105 downregulated molecules were revealed and analyzed, which identified the downregulation of GPD2 (p = 0.02 and FC = 0.77), PLEC (p < 0.001 and FC = 0.71) and SYNM (p = 0.04 and FC = 0.76) in AF patients. Gene Set Variation Analysis (GSEA) showed mitochondrial metabolism-associated pathways including oxidative phosphorylation (NES: −1.73) and ATP biosynthetic process (NES: −2.29), were dramatically diversified in human AF. In GSVA, the expression levels of GPD2, PLEC, and SYNM were demonstrated to be associated with multiple metabolic pathways related to mitochondrial function (e.g., lipid metabolism and AMP activated protein kinase signaling) and cardiac structural and electrical remodeling (e.g., contractile fiber, ion homeostasis), which were proven vital in the development and maintenance of AF.Conclusion: In all, this study provides new insights into understanding the mechanisms of AF progression, especially the reprogramming mitochondrial metabolism, and identifies several genes related to mitochondrial function as novel targets for AF, which may be involved in the occurrence and development of AF

Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning

IntroductionA better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period.MethodsA total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period.ResultsIn the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01).DiscussionAltogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys

Automatic construction of statistical shape models using deformable simplex meshes with vector field convolution energy

Abstract Background In the active shape model framework, principal component analysis (PCA) based statistical shape models (SSMs) are widely employed to incorporate high-level a priori shape knowledge of the structure to be segmented to achieve robustness. A crucial component of building SSMs is to establish shape correspondence between all training shapes, which is a very challenging task, especially in three dimensions. Methods We propose a novel mesh-to-volume registration based shape correspondence establishment method to improve the accuracy and reduce the computational cost. Specifically, we present a greedy algorithm based deformable simplex mesh that uses vector field convolution as the external energy. Furthermore, we develop an automatic shape initialization method by using a Gaussian mixture model based registration algorithm, to derive an initial shape that has high overlap with the object of interest, such that the deformable models can then evolve more locally. We apply the proposed deformable surface model to the application of femur statistical shape model construction to illustrate its accuracy and efficiency. Results Extensive experiments on ten femur CT scans show that the quality of the constructed femur shape models via the proposed method is much better than that of the classical spherical harmonics (SPHARM) method. Moreover, the proposed method achieves much higher computational efficiency than the SPHARM method. Conclusions The experimental results suggest that our method can be employed for effective statistical shape model construction

Origin, Evolution, and Research Development of Donkeys

Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population

Vector Field Convolution-Based B-Spline Deformation Model for 3D Segmentation of Cartilage in MRI

In this paper, a novel 3D vector field convolution (VFC)-based B-spline deformation model is proposed for accurate and robust cartilage segmentation. Firstly, the anisotropic diffusion method is utilized for noise reduction, and the Sinc interpolation method is employed for resampling. Then, to extract the rough cartilage, features derived from Hessian matrix are chosen to enhance the cartilage, followed by binarizing the images via an optimal thresholding method. Finally, the proposed VFC-based B-spline deformation model is used to refine the rough segmentation. In the experiments, the proposed method was evaluated and demonstrated on 46 magnetic resonance images (MRI) (including 20 hip joints and 26 knee joints), and the results were compared with three state-of-the-art cartilage segmentation methods. Both qualitative and quantitative segmentation results indicate that the proposed method can be deployed for accurate and robust cartilage segmentation. Furthermore, from the segmentation results, patient-specific 3D models of the patient’s anatomy can be derived, which then can be utilized in a wide range of clinical applications, such as 3D visualization for surgical planning and guidance

Comparative Transcriptome Analysis of Slow-Twitch and Fast-Twitch Muscles in Dezhou Donkeys

The skeletal muscle fiber profile is closely related to livestock meat quality. However, the molecular mechanisms determining muscle fiber types in donkeys are not completely understood. In this study, we selected the psoas major muscle (PM; mainly composed of oxidative-type muscle fibers) and biceps femoris muscle (BF; mainly composed of glycolytic-type muscle fibers) and systematically compared their mRNA and microRNA transcriptomes via RNA-seq. We identified a total of 2881 differentially expressed genes (DEGs) and 21 known differentially expressed miRNAs (DEmiRs). Furthermore, functional enrichment analysis showed that the DEGs were mainly involved in energy metabolism and actin cytoskeleton regulation. The glycolysis/gluconeogenesis pathway (including up-regulated genes such as PKM, LDHA, PGK1 and ALDOA) was more highly enriched in BF, whereas the oxidative phosphorylation pathway and cardiac muscle contraction (including down-regulated genes such as LDHB, ATP2A2, myosin-7 (MYH7), TNNC1, TPM3 and TNNI1) was more enriched in PM. Additionally, we identified several candidate miRNA–mRNA pairs that might regulate muscle fiber types using the integrated miRNA–mRNA analysis. Combined with the results of protein–protein interaction (PPI) analysis, some interesting DEGs (including ACTN3, TNNT3, TPM2, TNNC2, PKM, TNNC1 and TNNI1) might be potential candidate target genes involved in the miRNA-mediated regulation of the myofibril composition. This study is the first to indicate that DEmiRs, especially eca-miR-193a-5p and eca-miR-370, and potential candidate target genes that are mainly involved in actin binding (e.g., ACTN3, TNNT3 and TNNC1) and the glycolysis/gluconeogenesis pathways (e.g., PKM) might coregulate the myofibril composition in donkeys. This study may provide useful information for improving meat quality traits in Dezhou donkeys