Kled: an ultra-fast and sensitive structural variant detection tool for long-read sequencing data.

Structural Variants (SVs) are a crucial type of genetic variant that can significantly impact phenotypes. Therefore, the identification of SVs is an essential part of modern genomic analysis. In this article, we present kled, an ultra-fast and sensitive SV caller for long-read sequencing data given the specially designed approach with a novel signature-merging algorithm, custom refinement strategies and a high-performance program structure. The evaluation results demonstrate that kled can achieve optimal SV calling compared to several state-of-the-art methods on simulated and real long-read data for different platforms and sequencing depths. Furthermore, kled excels at rapid SV calling and can efficiently utilize multiple Central Processing Unit (CPU) cores while maintaining low memory usage. The source code for kled can be obtained from https://github.com/CoREse/kled.

A study on the application of radiomics based on cardiac MR non-enhanced cine sequence in the early diagnosis of hypertensive heart disease.

BACKGROUND: The prevalence of hypertensive heart disease (HHD) is high and there is currently no easy way to detect early HHD. Explore the application of radiomics using cardiac magnetic resonance (CMR) non-enhanced cine sequences in diagnosing HHD and latent cardiac changes caused by hypertension. METHODS: 132 patients who underwent CMR scanning were divided into groups: HHD (42), hypertension with normal cardiac structure and function (HWN) group (46), and normal control (NOR) group (44). Myocardial regions of the end-diastolic (ED) and end-systolic (ES) phases of the CMR short-axis cine sequence images were segmented into regions of interest (ROI). Three feature subsets (ED, ES, and ED combined with ES) were established after radiomic least absolute shrinkage and selection operator feature selection. Nine radiomic models were built using random forest (RF), support vector machine (SVM), and naive Bayes. Model performance was analyzed using receiver operating characteristic curves, and metrics like accuracy, area under the curve (AUC), precision, recall, and specificity. RESULTS: The feature subsets included first-order, shape, and texture features. SVM of ED combined with ES achieved the highest accuracy (0.833), with a macro-average AUC of 0.941. AUCs for HHD, HWN, and NOR identification were 0.967, 0.876, and 0.963, respectively. Precisions were 0.972, 0.740, and 0.826; recalls were 0.833, 0.804, and 0.863, respectively; and specificities were 0.989, 0.863, and 0.909, respectively. CONCLUSIONS: Radiomics technology using CMR non-enhanced cine sequences can detect early cardiac changes due to hypertension. It holds promise for future use in screening for latent cardiac damage in early HHD.

Lemon essential oil nanoemulsions: Potential natural inhibitors against Escherichia coli.

Lemon essential oil (LEO) is a common natural antibacterial substance, and encapsulating LEO into nanoemulsions (NEs) can improve their stability and broaden its application. Our study aimed to investigate the bacterial inhibitory effect of LEO-NEs against Escherichia coli (E. coli). Results showed that the minimum inhibitory concentration (MIC) of LEO-NEs was 6.25 mg/mL, and the time-kill curve showed that E. coli were significantly killed by LEO-NEs after 5 h of treatment at 1MIC. Flow-cytometry analysis showed that LEO-NEs adversely affected the cell-membrane depolarisation, cell-membrane integrity, and efflux pump function of E. coli. Confocal laser scanning microscopy demonstrated that 8MIC of LEO-NEs induced changes in the cell-membrane permeability and cell-wall integrity of E. coli. Proteomic results suggested that the mode of action LEO-NEs against E. coli was to enhance bacterial chemotaxis and significantly inhibit ribosomal assembly. They may also affect butyric acid, ascorbic acid and aldehyde metabolism, and sulphur-relay system pathways. In conclusion, LEO-NEs had potential application as a natural antibacterial agent for the control of E. coli in the food industry.

Untargeted Metabolomic Analyses and Antilipidemic Effects of Citrus Physiological Premature Fruit Drop.

Increasingly globally prevalent obesity and related metabolic disorders have underscored the demand for safe and natural therapeutic approaches, given the limitations of weight loss drugs and surgeries. This study compared the phytochemical composition and antioxidant activity of five different varieties of citrus physiological premature fruit drop (CPFD). Untargeted metabolomics was employed to identify variations in metabolites among different CPFDs, and their antilipidemic effects in vitro were assessed. The results showed that Citrus aurantium L. 'Daidai' physiological premature fruit drop (DDPD) and Citrus aurantium 'Changshan-huyou' physiological premature fruit drop (HYPD) exhibited higher levels of phytochemicals and stronger antioxidant activity. There were 97 differential metabolites identified in DDPD and HYPD, including phenylpropanoids, flavonoids, alkaloids, organic acids, terpenes, and lipids. Additionally, DDPD and HYPD demonstrated potential antilipidemic effects against oleic acid (OA)-induced steatosis in HepG2 hepatocytes and 3T3-L1 adipocytes. In conclusion, our findings reveal the outstanding antioxidant activity and antilipidemic effects of CPFD, indicating its potential use as a natural antioxidant and health supplement and promoting the high-value utilization of this resource.

Se-Elemental Concentration Gradient Regulation for Efficient Sb2(S,Se)3 Solar Cells with High Open-Circuit Voltages.

Antimony selenosulfide (Sb2(S,Se)3), featuring large absorption coefficient, excellent crystal structure stability, benign non-toxic characteristic, outstanding humidity and ultraviolet tolerability, has recently attracted enormous attention and research interest regarding its photoelectric conversion properties. However, the open-circuit voltage (Voc) for Sb2(S,Se)3-based photovoltaic devices is relatively low, especially for the device with a high power conversion efficiency (η). Herein, an innovative Se-elemental concentration gradient regulation strategy has been exploited to produce high-quality Sb2(S,Se)3 films on TiO2/CdS substrates through a thioacetamide(TA)-synergistic dual-sulfur source hydrothermal-processed method. The Se-elemental gradient distribution produces a favorable energy band structure, which suppresses the energy level barriers for hole transport and enhances the driving force for electron transport in Sb2(S,Se)3 film. This facilitates efficient charge transport/separation of photogenerated carriers and boosts significantly the Voc of Sb2(S,Se)3 photovoltaic devices. The champion TA-Sb2(S,Se)3 planar heterojunction (PHJ) solar cell displays an considerable η of 9.28% accompanied by an exciting Voc rising to 0.70 V that is currently the highest among Sb2(S,Se)3-based solar cells with efficiencies exceeding 9.0%. This research is anticipated to contribute to the preparation of high-quality Sb2(S,Se)3 thin film and the achievement of efficient inorganic Sb2(S,Se)3 PHJ photovoltaic device.

Transport and retention of sinking microplastics in a well-mixed estuary.

Estuaries have been shown to be potential hotspots of microplastic accumulation, but the hydrodynamic conditions and particle properties that control this process need further investigation. We have designed a series of numerical particle-tracking experiments to examine the sensitivity of retention in estuaries to particle size, particle density and varying tides and freshwater flow. At the end of the simulation, over 90 % of sinking particles are retained in the estuary, and the retention rate is further increased by high river runoff. In contrast, increased river discharge increases the number of marginally-buoyant (i.e. density close to estuarine water) particles that escape the estuary. Larger particle size tends to limit the downstream transport of sinking particles but can facilitate the transport of marginally-buoyant particles. Tidal asymmetry, vertical turbulent mixing and the vertical structure of the subtidal circulation are proposed as the underlying mechanisms controlling the fate of particles.

Effect of Sprouted Buckwheat on Glycemic Index and Quality of Reconstituted Rice.

This study utilized sprouted buckwheat as the main component and aimed to optimize its combination with other grains to produce reconstituted rice with enhanced taste and a reduced glycemic index (GI). The optimal blend comprised wheat flour, sprouted buckwheat flour, black rice flour, and purple potato flour in a ratio of 34.5:28.8:26.7:10.0. Based on this blend, the reconstituted rice processed through extrusion puffing exhibited a purple-black hue; meanwhile, the instant reconstituted rice, produced through further microwave puffing, displayed a reddish-brown color. both imparted a rich cereal flavor. The starch in both types of rice exhibited a V-shaped structure with lower relative crystallinity. Compared to commercial rice, the reconstituted rice and instant reconstituted rice contained higher levels of flavonoids, polyphenols, and other flavor compounds, along with 1.63-fold and 1.75-fold more proteins, respectively. The GI values of the reconstituted rice and the instant reconstituted rice were 68.86 and 69.47, respectively; thus, they are medium-GI foods that can alleviate the increase in blood glucose levels.

Classifying breast cancer using multi-view graph neural network based on multi-omics data.

Introduction: As the evaluation indices, cancer grading and subtyping have diverse clinical, pathological, and molecular characteristics with prognostic and therapeutic implications. Although researchers have begun to study cancer differentiation and subtype prediction, most of relevant methods are based on traditional machine learning and rely on single omics data. It is necessary to explore a deep learning algorithm that integrates multi-omics data to achieve classification prediction of cancer differentiation and subtypes. Methods: This paper proposes a multi-omics data fusion algorithm based on a multi-view graph neural network (MVGNN) for predicting cancer differentiation and subtype classification. The model framework consists of a graph convolutional network (GCN) module for learning features from different omics data and an attention module for integrating multi-omics data. Three different types of omics data are used. For each type of omics data, feature selection is performed using methods such as the chi-square test and minimum redundancy maximum relevance (mRMR). Weighted patient similarity networks are constructed based on the selected omics features, and GCN is trained using omics features and corresponding similarity networks. Finally, an attention module integrates different types of omics features and performs the final cancer classification prediction. Results: To validate the cancer classification predictive performance of the MVGNN model, we conducted experimental comparisons with traditional machine learning models and currently popular methods based on integrating multi-omics data using 5-fold cross-validation. Additionally, we performed comparative experiments on cancer differentiation and its subtypes based on single omics data, two omics data, and three omics data. Discussion: This paper proposed the MVGNN model and it performed well in cancer classification prediction based on multiple omics data.

Redox-sensitive self-assembling polymer micelles based on oleanolic modified hydroxyethyl starch: Synthesis, characterisation, and oleanolic release.

Our study aimed at developing polymer micelles that possess redox sensitivity and excellent controlled release properties. 3,3'-dithiodipropionic acid (DTDPA, Abbreviation in synthetic polymers: SS) was introduced as ROS (Reactive oxygen species)response bond and connecting arm to couple hydroxyethyl starch (HES) with oleanolic acid (OA), resulting in the synthesis of four distinct grafting ratios of HES-SS-OA. FTIR (Fourier Transform infrared spectroscopy) and 1H NMR (1H Nuclear magnetic resonance spectra) were used to verify the triumphant combination of HES-SS-OA. Polymer micelles were found to encapsulate OA in an amorphous form, as indicated by the results of XRD (X-ray diffraction) and DSC (Differential scanning calorimetry). When the OA grafting rate on HES increased from 7.72 % to 11.75 %, the particle size decreased from 297.79 nm to 201.39 nm as the polymer micelles became compact due to enhanced hydrophobicity. In addition, the zeta potential changed from -16.42 mv to -25.78 mv, the PDI (polydispersity index) decreased from 0.3649 to 0.2435, and the critical micelle concentration (CMC) decreased from 0.0955 mg/mL to 0.0123 mg/mL. Results of erythrocyte hemolysis, cytotoxicity and cellular uptake illustrated that HES-SS-OA had excellent biocompatibility and minimal cytotoxicity for AML-12 cells. Disulfide bond breakage of HES-SS-OA in the presence of H2O2 and GSH confirmed the redox sensitivity of the HES-SS-OA micelles and their excellent controlled release properties for OA. These findings suggest that HES-SS-OA can be potentially used in the future as a healthcare drug and medicine for the prevention or adjuvant treatment of inflammation.

Consistency label-activated region generating network for weakly supervised medical image segmentation.

The current methods of auto-segmenting medical images are limited due to insufficient and ambiguous pathonmorphological labeling. In clinical practice, rough classification labels (such as disease or normal) are more commonly used than precise segmentation masks. However, there is still much to be explored regarding utilizing these weak clinical labels to accurately determine the lesion mask and guide medical image segmentation. In this paper, we proposed a weakly supervised medical image segmentation model to directly generate the lesion mask through a class activation map (CAM) guided cycle-consistency label-activated region transferring network. Cycle-consistency enforces that the mappings between the two domains should be reversible, which ensures that the original image can be reconstructed from the translated image. We developed a complementary branches fusion module to address the issue of blurry boundaries in CAM-guided segmentation. The complementary branch preserves the original semantic information of the non-lesion region and perfectly fuses the transferred feature of the lesion region with a complementary mask-constrained fake image generation process to clear the boundary of the lesion and non-lesion regions. This module allows the class transformation to focus solely on the label-activated region, resulting in more explicit segmentation. This model can accurately identify different region of medical images at the pixel-level while preserving the overall semantic structure semantion. It organizes disease labels and corresponding regions during image synthesis. Our method utilizes a joint discrimination strategy that significantly enhances the precision of the produced lesion mask. Extensive experiments of the proposed method on BraTs, ISIC and COVID-19 datasets demonstrate superior performance over existing state-of-the-art methods. The code and datasets are available at: https://github.com/mlcb-jlu/MedImgSeg.

Cyanidin-3-O-Glucoside Alleviates Alcoholic Liver Injury via Modulating Gut Microbiota and Metabolites in Mice.

Alcoholic liver disease (ALD) is primarily caused by long-term excessive alcohol consumption. Cyanidin-3-O-glucoside (C3G) is a widely occurring natural anthocyanin with multiple biological activities. This study aims to investigate the effects of C3G isolated from black rice on ALD and explore the potential mechanism. C57BL/6J mice (male) were fed with standard diet (CON) and Lieber-DeCarli liquid-fed (Eth) or supplemented with a 100 mg/kg/d C3G Diet (Eth-C3G), respectively. Our results showed that C3G could effectively ameliorate the pathological structure and liver function, and also inhibited the accumulation of liver lipids. C3G supplementation could partially alleviate the injury of intestinal barrier in the alcohol-induced mice. C3G supplementation could increase the abundance of Norank_f_Muribaculaceae, meanwhile, the abundances of Bacteroides, Blautia, Collinsella, Escherichia-Shigella, Enterococcus, Prevotella, [Ruminococcus]_gnavus_group, Methylobacterium-Methylorubrum, Romboutsia, Streptococcus, Bilophila, were decreased. Spearman's correlation analysis showed that 12 distinct genera were correlated with blood lipid levels. Non-targeted metabolic analyses of cecal contents showed that C3G supplementation could affect the composition of intestinal metabolites, particularly bile acids. In conclusion, C3G can attenuate alcohol-induced liver injury by modulating the gut microbiota and metabolites, suggesting its potential as a functional food ingredient against alcoholic liver disease.

Physicochemical and antioxidant properties of pectin fractions extracted from lemon (Citrus Eureka) peels.

Pectin, a natural polysaccharide, holds versatile applications in food and pharmaceuticals. However, there is a need for further exploration into extracting novel functional fractions and characterizing them thoroughly. In this study, a sequential extraction approach was used to obtain three distinct lemon pectin (LP) fractions from lemon peels (Citrus Eureka): LP extracted with sodium acetate (LP-SA), LP extracted with ethylenediaminetetraacetic acid (LP-EDTA), and LP extracted with sodium carbonate and sodium borohydride (LP-SS). Comprehensive analysis revealed low methyl-esterification in all fractions. LP-SA and LP-SS displayed characteristics of rhamnogalacturonan-I type pectin, while LP-EDTA mainly consisted of homogalacturonan pectin. Notably, LP-SA formed self-aggregated particles with rough surfaces, LP-EDTA showed interlocking linear structures with smooth planes, and LP-SS exhibited branch chain structures with smooth surfaces. Bioactivity analysis indicated that LP-SA had significant apparent viscosity and ABTS radical scavenging activity, while both LP-EDTA and LP-SS showed excellent thermal stability according to thermogravimetric analysis (TGA). Furthermore, LP-SS exhibited remarkable gel-forming ability and significant hydroxyl free radicals scavenging activity. In conclusion, this study presents a novel method for extracting various lemon pectin fractions with unique structural and bioactive properties, contributing insights for advanced applications in the food and pharmaceutical sectors.

Reduced EO771-induced tumour growth and increased overall-survival of mice ablated for immune cell-specific catalytic subunit Cß2 of protein kinase A.

Ablation of the immune-specific catalytic subunit Cß2 of protein kinase A is associated with a proinflammatory phenotype and increased sensitivity to autoimmunity in mice. Here we show that tumour growth of the adenocarcinoma cell line EO771 in the breast and in the lung after injection into the mammary fat pad and tail vein, respectively, was significantly reduced in mice ablated for Cß2 compared to wild-type mice. In both cases, the breast and lung tumours showed increased infiltration of immune cells in the mice lacking Cß2 compared to wild-type mice. Despite this, it appeared that solid tissue- versus intravenously injected EO771 cells evoked different immune responses. This was reflected by significantly increased levels of splenic proinflammatory immune cells and circulating cytokines in Cß2 ablated mice carrying breast- but not the lung tumours. Moreover, Cß2 ablated mice injected with EO771 cells showed increased overall survival compared to wild-type mice. Taken together, our results suggest for a role for immune cell-specific Cß2 in protecting against tumour growth induced by EO771 cells in mice that is reflected in improved overall survival.

Preliminary investigation of TIM-3 ligand galectin-9 inducing apoptosis of NK/T cell lymphoma cells / 中国肿瘤生物治疗杂志

@# Objective: To identify the expression pattern of TIM-3 in natural killer/T-cell lymphoma (NK/TCL) cell lines, and to investigate the effect and mechanism of its ligand galectin-9 (GAL-9) inducing apoptosis of NK/TCL cell lines. Methods: Expression of TIM-3 in NK cell of peripheral blood from healthy donors and NK/TCL cell lines (SNK-1、SNK-6、SNT-8) was detected by Western blotting. After being treated with rhGAL-9 at various concentrations for 24h, the cell proliferation ability was analyzed with CCK-8 assay. Apoptosis ratio of the cells was determined by flow cytometry. Expressions of caspase-3, PARP and their cleavages were detected by Western blotting; moreover, phosphorylation levels of proteins in MAPK signaling pathway were also detected by Western blotting. Results: The expression of TIM-3 in SNK-1, SNK-6 and SNT-8 cell lines was significantly higher than that of NK cells from healthy donors (P<0.05). CCK-8 result showed that rhGAL-9 obviously inhibited the proliferation of NK/TCL cell lines in a concentration dependent manner. Flow cytometry showed that rhGAL-9 induced the apoptosis of NK/TCLcells; and Western blotting proved that the expression of cleaved caspase-3, cleaved-PARP, and p-JNK in MAPK signaling pathway were significantly elevated. Conclusion: TIM-3 was over-expressed in NK/TCL cell lines, and its ligand galectin-9 induced cell apoptosis probably through the activation of JNK kinase pathways.