Left Ventricle: Fully Automated Segmentation Based on Spatiotemporal Continuity and Myocardium Information in Cine Cardiac Magnetic Resonance Imaging (LV-FAST)

CMR quantification of LV chamber volumes typically and manually defines the basal-most LV, which adds processing time and user-dependence. This study developed an LV segmentation method that is fully automated based on the spatiotemporal continuity of the LV (LV-FAST). An iteratively decreasing threshold region growing approach was used first from the midventricle to the apex, until the LV area and shape discontinued, and then from midventricle to the base, until less than 50% of the myocardium circumference was observable. Region growth was constrained by LV spatiotemporal continuity to improve robustness of apical and basal segmentations. The LV-FAST method was compared with manual tracing on cardiac cine MRI data of 45 consecutive patients. Of the 45 patients, LV-FAST and manual selection identified the same apical slices at both ED and ES and the same basal slices at both ED and ES in 38, 38, 38, and 41 cases, respectively, and their measurements agreed within −1.6 ± 8.7 mL, −1.4 ± 7.8 mL, and 1.0 ± 5.8% for EDV, ESV, and EF, respectively. LV-FAST allowed LV volume-time course quantitatively measured within 3 seconds on a standard desktop computer, which is fast and accurate for processing the cine volumetric cardiac MRI data, and enables LV filling course quantification over the cardiac cycle

Mechanism of crocin I on ANIT-induced intrahepatic cholestasis by combined metabolomics and transcriptomics

Background: Intrahepatic cholestasis (IC) is a disorder of bile production, secretion, and excretion with various causes. Crocin I (CR) is effective in the treatment of IC, but its underlying mechanisms need to be further explored. We aimed to reveal the therapeutic mechanism of crocin I for IC by combining an integrated strategy of metabolomics and transcriptomics.Methods: The hepatoprotective effect of CR against cholestasis liver injury induced by α-naphthylisothiocyanate (ANIT) was evaluated in rats. The serum biochemical indices, including alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bile acid (TBA), total bilirubin (TBIL), direct bilirubin (DBIL), tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6), and interleukin 1β (IL-1β), as well as the liver oxidative stress indexes and the pathological characteristics of the liver were analyzed. In addition, we also performed a serum metabolomics study using UPLC-Q Exactive HF-X technology to investigate the effect of CR on the serum of rats with ANIT-induced IC and screened potential biomarkers. The enrichment analysis of differential expressed genes (DEGs) was performed by transcriptomics. Finally, the regulatory targets of CR on potential biomarkers were obtained by combined analysis, and the relevant key targets were verified by western blotting.Results: CR improved serum and liver homogenate indexes and alleviated liver histological injury. Compared with ANIT group, the CR group had 76 differential metabolites, and 10 metabolic pathways were enriched. There were 473 DEGs significantly changed after CR treatment, most of which were enriched in the retinol metabolism, calcium signaling pathway, PPAR signaling pathway, circadian rhythm, chemokine signaling pathway, arachidonic acid metabolism, bile secretion, primary bile acid biosynthesis, and other pathways. By constructing the “compound-reaction-enzyme-gene” interaction network, three potential key-target regulation biomarkers were obtained, including 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), ATP-binding cassette transporter G5 (ABCG5), and sulfotransferase2A1(SULT2A1), which were further verified by western blotting. Compared with the ANIT group, the CR group significantly increased the expression of ABCG5 and SULT2A1, and the expression of HMGCR significantly decreased.Conclusion: Combined metabolomic and transcriptomic analyses show that CR has a therapeutic effect on IC through regulation of the biosynthesis of bile acids and bilirubin in the bile secretion pathway and regulation of the expression of HMGCR, ABCG5, and SULT2A1

Direct Phasing of Protein Crystals with Non-Crystallographic Symmetry

An iterative projection algorithm proposed previously for direct phasing of high-solvent-content protein crystals is extended to include non-crystallographic symmetry (NCS) averaging. For proper NCS, when the NCS axis is positioned, the molecular envelope can be automatically rebuilt. For improper NCS, when the NCS axis and the translation vector are known, the molecular envelope can also be automatically reconstructed. Some structures with a solvent content of around 50% could be directly solved using this ab initio phasing method. Trial calculations are described to illustrate the methodology. Real diffraction data are used and the calculated phases are good for automatic model building. The refinement of approximate NCS parameters is discussed

Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography

For direct phasing of protein crystals, a method based on the hybrid-input-output (HIO) algorithm has been proposed and tested on a variety of structures. So far, however, the diffraction data have been limited to high-resolution ones, i.e., higher than 2 Å. In principle, the methodology can be applied to data of lower resolutions, which might be particularly useful for phasing membrane protein crystals. For resolutions higher than 3.5 Å, it seems the atomic structure is solvable. For data of lower resolutions, information of the secondary structures and the protein boundary can still be obtained. Examples are given to support the conclusions. Real experimental data are used. Two aspects of the observed data have been discussed: removal of the measured low-resolution reflections and involvement of the unmeasured high-resolution reflections. The ab initio phasing employs histogram matching for density modification. A question arises whether the reference histogram used should match the resolution of the diffraction data or not. It seems that there is an optimal histogram which is good to use for data at various resolutions

Calibration Strategy of the JUNO-TAO Experiment

The Taishan Antineutrino Observatory (JUNO-TAO, or TAO) is a satellite detector for the Jiangmen Underground Neutrino Observatory (JUNO). Located near the Taishan reactor, TAO independently measures the reactor's antineutrino energy spectrum with unprecedented energy resolution. To achieve this goal, energy response must be well calibrated. Using the Automated Calibration Unit (ACU) and the Cable Loop System (CLS) of TAO, multiple radioactive sources are deployed to various positions in the detector to perform a precise calibration of energy response. The non-linear energy response can be controlled within 0.6% with different energy points of these radioactive sources. It can be further improved by using $^{12}\rm B$ decay signals produced by cosmic muons. Through the energy non-uniformity calibration, residual non-uniformity is less than 0.2%. The energy resolution degradation and energy bias caused by the residual non-uniformity can be controlled within 0.05% and 0.3%, respectively. In addition, the stability of other detector parameters, such as the gain of each silicon photo-multiplier, can be monitored with a special ultraviolet LED calibration system