A denoised multi-omics integration framework for cancer subtype classification and survival prediction.

The availability of high-throughput sequencing data creates opportunities to comprehensively understand human diseases as well as challenges to train machine learning models using such high dimensions of data. Here, we propose a denoised multi-omics integration framework, which contains a distribution-based feature denoising algorithm, Feature Selection with Distribution (FSD), for dimension reduction and a multi-omics integration framework, Attention Multi-Omics Integration (AttentionMOI) to predict cancer prognosis and identify cancer subtypes. We demonstrated that FSD improved model performance either using single omic data or multi-omics data in 15 The Cancer Genome Atlas Program (TCGA) cancers for survival prediction and kidney cancer subtype identification. And our integration framework AttentionMOI outperformed machine learning models and current multi-omics integration algorithms with high dimensions of features. Furthermore, FSD identified features that were associated to cancer prognosis and could be considered as biomarkers.

Loss of chromosome Y in primary tumors.

Certain cancer types afflict female and male patients disproportionately. The reasons include differences in male/female physiology, effect of sex hormones, risk behavior, environmental exposures, and genetics of the sex chromosomes X and Y. Loss of Y (LOY) is common in peripheral blood cells in aging men, and this phenomenon is associated with several diseases. However, the frequency and role of LOY in tumors is little understood. Here, we present a comprehensive catalog of LOY in >5,000 primary tumors from male patients in the TCGA. We show that LOY rates vary by tumor type and provide evidence for LOY being either a passenger or driver event depending on context. LOY in uveal melanoma specifically is associated with age and survival and is an independent predictor of poor outcome. LOY creates common dependencies on DDX3X and EIF1AX in male cell lines, suggesting that LOY generates unique vulnerabilities that could be therapeutically exploited.

White light emission and energy transfer of LaMgAl11 O19 :Eu3+ , Tb3+ phosphors.

White-light-tunable LaMgAl11 O19 :x%Tb3+ , y%Eu3+ series phosphors were prepared using the gel-combustion method. The structure and luminescence properties were studied, and the energy transfer of Eu3+ and Tb3+ in the LaMgAl11 O19 system was also discussed. The results showed that the LaMgAl11 O19 matrix exhibited strong emission in the blue-light region under the excitation of ultraviolet light, which resulted in conditions suitable for the preparation of white-light-tunable phosphors. The emission spectra of LaMgAl11 O19 :2%Tb3+ , y%Eu3+ (y = 2%-9%) series phosphors were obtained through optimization experiments. It could be seen from the CIE diagram that by adjusting the doping quantities of Eu3+ and Tb3+ in the LaMgAl11 O19 host, multicolor luminescence and white light emission in a single host could be achieved. By calculating the energy transfer efficiency and critical distance between Eu3+ and Tb3+ series phosphors, the mechanism of energy transfer between Tb3+ and Eu3+ was found to be the interaction between electric quadruples.

The network pharmacology study and molecular docking to investigate the potential mechanism of Acoritataninowii Rhizoma against Alzheimer's Disease.

Alzheimer's Disease is considered as an insidious neurodegenerative progressive disease but its pathogenesis has not been elucidated. Acoritataninowii Rhizoma exhibits anti-dementia effects as a traditional Chinese medicine (TCM), which is linked to its anti- Alzheimer's Disease mechanism. In this study, network pharmacology and molecular docking were used to examine the potential of Acoritataninowii Rhizoma for Alzheimer's Disease. In order to construct PPI networks and drug-component-target-disease networks, disease-related genes and proteins were gathered from the database. Gene ontology (GO), pathway enrichment (KEGG), and molecular docking were used to forecast the potential mechanism of Acoritataninowii Rhizoma on Alzheimer's disease. Therefore, 4 active ingredients and 81 target genes were screened from Acoritataninowii Rhizoma, 6765 specific target genes were screened from Alzheimer's Disease, and 61 drug-disease cross genes were validated. GO analysis showed that Acoritataninowii Rhizoma can regulate processes such as the protein serine/threonine kinase associated with MAPK. KeGG pathway analysis showed that the signaling pathways affected by Acoritataninowii Rhizoma were fluid shear stress and atherosclerosis, AGE-RAGE and other pathways. Molecular docking implied that the pharmacological influences of the bioactive constituents of Acoritataninowii Rhizoma (Cycloaartenol and kaempferol) on Alzheimer's Disease may related to ESR1 and AKT1, respectively. AKT1 and ESR1 may be the core target genes of the treatment for Alzheimer's disease. Kaempferol and Cycloartenol might be core bioactive constituents for treatment.

Weighted gene co-expression network analysis revealed the key pathways and hub genes of potassium regulating cotton root adaptation to salt stress.

Soil salinization is one of the main abiotic stresses affecting cotton yield and planting area. Potassium application has been proven to be an important strategy to reduce salt damage in agricultural production. However, the mechanism of potassium regulating the salt adaptability of cotton has not been fully elucidated. In the present research, the appropriate potassium application rate for alleviating salt damage of cotton based on different K+/Na+ ratios we screened, and a gene co-expression network based on weighted gene co-expression network analysis (WGCNA) using the transcriptome data sets treated with CK (0 mM NaCl), S (150 mM NaCl), and SK8 (150 mM NaCl + 9.38 mM K2SO4) was constructed. In this study, four key modules that are highly related to potassium regulation of cotton salt tolerance were identified, and the mitogen-activated protein kinase (MAPK) signaling pathway, tricarboxylic acid (TCA) cycle and glutathione metabolism pathway were identified as the key biological processes and metabolic pathways for potassium to improve cotton root salt adaptability. In addition, 21 hub genes and 120 key candidate genes were identified in this study, suggesting that they may play an important role in the enhancement of salt adaptability of cotton by potassium. The key modules, key biological pathways and hub genes discovered in this study will provide a new understanding of the molecular mechanism of potassium enhancing salinity adaptability in cotton, and lay a theoretical foundation for the improvement and innovation of high-quality cotton germplasm.

Potassium ameliorates cotton (Gossypium hirsutum L.) fiber length by regulating osmotic and K+ /Na+ homeostasis under salt stress.

Potassium (K) application can alleviate cotton salt stress, but the regulatory mechanisms affecting cotton fiber elongation and ion homeostasis are still unclear. A two-year field experiment was conducted to explore the effects of K on the osmolyte contents (soluble sugar, K+ content, and malate) and related enzyme activities during the fiber elongation of two cotton cultivars with contrasting salt sensitivity (CCRI-79; salt tolerant cultivar, and Simian 3; salt-sensitive cultivar). Three K application treatments (0, 150, and 300 kg K2 O ha-1 ) were applied at three soil salinity levels (low salinity, EC = 1.73 ± 0.05 dS m-1 ; medium salinity, EC = 6.32 ± 0.10 dS m-1 ; high salinity, EC = 10.84 ± 0.24 dS m-1 ). K application improved fiber length and alleviated salt stress by increasing the maximum velocity of fiber elongation (Vmax ). The increase rate of K on fiber length decreased with elevating salt stress, and the increase rate of K on Vmax of CCRI-79 was greater than that of Simian3. K application can increase the enzyme activities (phosphoenolpyruvate carboxylase, PEPC, E.C. 4.1.1.31; pyrophosphatase, PPase, E.C. 3.6.1.1; and plasma membrane H+ -ATPase, PM H+ -ATPase, E.C. 3.6.3.14) as well as the content of osmolytes associated with the enzymes mentioned above. K increased the osmolyte contents under salt stress, and the increase in the K+ content of the fibers was much higher than that of soluble sugar and malate. The results of this study indicated K fertilizer application rates regulate the metabolism of osmolytes in cotton fiber development under salt stress, K+ is more critical to fiber elongation.

A novel technology for preparing the placebos of vortioxetine hydrobromide tablets using LCD 3D printing.

This study aimed to describe the use of liquid crystal display (LCD) three-dimensional (3D) printing technology to prepare moulds for vortioxetine hydrobromide (VOR) tablet placebos and provide an economical, convenient, and flexible method for the small-batch preparation of special-shaped, scored, and coated placebo tablets. First, LCD 3D printing was used to generate different placebo moulds of VOR tablets based on VOR tablet digital models subtracted from the digital models of cuboid moulds by Boolean operation to optimise the structures of moulds. The better placebo mould had a parting surface located at the 7/10 height of the packing cavities and the positioning columns and slots were three pairs, and the efflux space had slender efflux channels combined with wide efflux tanks. Next, the placebo mould was corrected by the dimensional compensation method due to the shrinkage rates of the packing cavities (2.42%) and placebo prescription (1.12%) and the thickness of the film coating (25.08 µm). The placebo prescription was 8% hydroxypropyl methylcellulose (SH K15M) hydroalcoholic gel, and its mass ratio to lactose was 0.8:2. The placebos were coated with 13% gastric-soluble film coating solution for 30 min and polished with the 30% PEG 4000 solution. The National Bureau of Standards value between the VOR tablets and their placebos was 1.22 ± 0.10 (less than1.5). Finally, the mass of the placebos was similar to that of the VOR tablets. Their dimensional differences were less than 0.1 mm. Their mass, colour, odour, shape, and texture were all similar, which were assessed by manual evaluation. In conclusion, the preparations of VOR tablet placebos can be applied in placebo-controlled trials, and LCD 3D printing has an extensive application value in preparing placebo tablets.

A Novel Preparation Method for Effervescent Tablets of Xianganfang Containing Fresh Juice using a Semi-Solid Extrusion 3D Printer with Three Cartridge Holders.

This study aimed to prepare effervescent tablets of traditional Chinese medicine Xianganfang with fresh juice using a semi-solid 3D printer with three cartridge holders to seperate acid and alkali source by drug paste through model design to avoid sticking impact and premature effervescence during the tableting in the conventional preparation process. The powder of Xianganfang including fresh juice of Phyllanthus emblica and licorice extract was obtained by vacuum freeze-drying with 50% mannitol as cryoprotectant. Then, the formulation of 3D-printed effervescent tablets was investigated. Further 5% HPMC hydroalcoholic gel was mixed with sodium bicarbonate and freeze-dried Xianganfang powder to prepare alkali source and drug paste respectively while 30% PVP ethanol solution was mixed with tartaric acid to prepare acid source paste; these three pastes had good printability. The pastes of drug, acid, and alkali were loaded into three syringe cartridges separately and numbered as "3," "5," and "7," according to cartridge holders of the 3D printer, and printed in the order of "537,353,735" for separating acid and alkali by drug to avoid premature effervescence. And the basic printing parameters were optimized. The tablets were evaluated by the appearance, tablet weight variation, hardness, disintegration time, friability, pH, and stability. The physicochemical properties all conformed to the Chinese Pharmacopoeia 2020 edition. The content of the active ingredient gallic acid was 0.769 ± 0.019 mg/g. This study provided a new method to prepare effervescent tablets of traditional Chinese medicine with fresh juice using 3D printing technology.

Assessment of the global circulation and endemicity of dengue.

Dengue is a significant public health issue, affecting hundreds of millions of people worldwide. As it is spreading from tropical and subtropical zones, some regions previously recognised as non-endemic are at risk of becoming endemic. However, the global circulation of dengue is not fully understood and quantitative measurements of endemicity levels are lacking, posing an obstacle in the precise control of dengue spread. In this study, a sequence-based pipeline was designed based on random sampling to study the transmission of dengue. The limited intercontinental transmission was identified, while regional circulation of dengue was quantified in terms of importation, local circulation and exportation. Additionally, hypo- and hyper-endemic regions were identified using a new metric, with the former characterised by low local circulation and increased importation, whereas the latter by high local circulation and reduced importation. In this study, the global circulation pattern of dengue was examined and a sequence-based endemicity measurement was proposed, which will be helpful for future surveillance and targeted control of dengue.

A network pharmacology study with molecular docking to investigate the possibility of licorice against posttraumatic stress disorder.

Post traumatic stress disorder (PTSD) is a mental health condition that has a debilitating effect on a person's quality of life and leads to a high socioeconomic burden. Licorice has been demonstrated to have neuroprotective and antidepressant-like effects, but little is known about its effects for the treatment of PTSD. The present study aimed to explore the potential of licorice for PTSD therapy using a network pharmacology approach with molecular docking studies. The compounds of licorice were obtained from databases with screening by absorption, distribution, metabolism and excretion (ADME) evaluation. Genes associated with compounds or PTSD were obtained from public databases, and the genes overlapping between licorice compounds and PTSD were compared by Venn diagram. A network of medicine-ingredients-targets-disease was constructed, visualized, and analyzed using cytoscape software. Protein-protein interactions, gene ontology, pathway enrichment and molecular docking were performed to evaluate the effect of licorice for the treatment of PTSD. 69 potential compounds were screened after ADME evaluation. A total of 81 compound-related genes and 566 PTSD-related genes were identified in the databases with 27 overlapping genes. Licorice compounds (e.g., medicarpin, 7-methoxy-2-methyl isoflavone, shinpterocarpin, formononetin, licochalcone a) and target proteins (e.g., ESR1, PTGS2, NOS2, and ADRB2) with high degree in the network were involved in G protein-coupled receptor signaling pathways at the postsynaptic/synaptic membrane. Moreover, neuroactive ligand-receptor interactions, calcium signaling, cholinergic synapse, serotonergic synapse and adrenergic signaling in cardiomyocytes may play important roles in the treatment of PTSD by licorice. This study provides molecular evidence of the beneficial effects of licorice for the treatment of PTSD.

Effect of Dihydropyridine Enrichment in the Microstructure of the Palisade Layer on the Stability of Fat Nano-emulsions.

Relationship between the stability of fat nano-emulsions and the incorporated drug at the molecular level are rarely known. Herein, fat nano-emulsions containing dihydropyridine drugs were prepared and the microstructure of their palisade layers were investigated.The prepared 1.0 mg/mL nimodipine nano-emulsion was found to contain 65.50% drug in the palisade layer. The increasing drug concentration led to a decrease-increase-decrease trend in centrifugal stability constant, particle size and proton nuclear magnetic resonance (1H NMR) signal intensity of the lecithin trimethyl ammonium group in the nimodipine and felodipine nano-emulsions. The 1H NMR spectra of test solutions including nano-emulsions suggest that increasing drugs penetrated into the palisade layer, resulting in the lecithin arrangement from loose to tight, and then from monolayer to bilayer. Nimodipine and felodipine nano-emulsions showed two valley values at concentrations of 0.15 and 0.75 mg/mL, and 0.30 and 0.90 mg/mL respectively, which indicated that the nano-emulsion has two more stable states corresponding to the tightly arranged mono- and bi-palisade layer. These two concentrations are positively correlated with lipophilicity of nimodipine and felodipine. Further, nimodipine liposomes were prepared to validate the effect of drugs on the arrangement of lecithin in the palisade layer. 1H NMR characterizations of the liposomes showed a similar profile to that of nano-emulsions. These results demonstrated that the increasing drug concentration could cause a rearrangement of lecithin in the palisade layer, thus affecting emulsion stability.

New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2.

The 2019 novel coronavirus (SARS-CoV-2) has spread rapidly worldwide and was declared a pandemic by the WHO in March 2020. The evolution of SARS-CoV-2, either in its natural reservoir or in the human population, is still unclear, but this knowledge is essential for effective prevention and control. We propose a new framework to systematically identify recombination events, excluding those due to noise and convergent evolution. We found that several recombination events occurred for SARS-CoV-2 before its transfer to humans, including a more recent recombination event in the receptor-binding domain. We also constructed a probabilistic mutation network to explore the diversity and evolution of SARS-CoV-2 after human infection. Clustering results show that the novel coronavirus has diverged into several clusters that cocirculate over time in various regions and that several mutations across the genome are fixed during transmission throughout the human population, including D614G in the S gene and two accompanied mutations in ORF1ab. Together, these findings suggest that SARS-CoV-2 experienced a complicated evolution process in the natural environment and point to its continuous adaptation to humans. The new framework proposed in this study can help our understanding of and response to other emerging pathogens.

Preparation and application of subdivided tablets using 3D printing for precise hospital dispensing.

This study aimed to use three-dimensional printing technology to provide patients with accurate, safe and convenient subdivided drugs and bring the transformation of subdivided drugs' fabrication in the hospital. The formulation, preparation process, model and printing parameters, relationship between dose and preset model for printing of spironolactone of 2 mg, 4 mg and hydrochlorothiazide of 5 mg subdivided tablets prepared by three-dimensional printers were investigated in the study. The three-dimensional printed material consists of commercial tablets powders and other excipients, including lactose, corn starch, microcrystalline cellulose, and so on. Mass variation, drug content and drug content uniformity of subdivided tablets obtained by three-dimensional printing were compared with the pharmacists splitting subdivided tablets. Besides, the results from fourier transform infrared spectroscopy, differential scanning calorimetry and X-ray powder diffraction confirmed that the preparation process of spironolactone of 2 mg, 4 mg and hydrochlorothiazide of 5 mg did not change the crystal structure of the active pharmaceutical ingredient. Furthermore, mass variation, drug content range and drug content uniformity of spironolactone of 2 mg, 4 mg and hydrochlorothiazide of 5 mg tablets split by pharmacists failed to comply with European Pharmacopoeia and Chinese Pharmacopoeia, while those of the three-dimensional printed subdivided tablets did. After the review of the ethics committee as a new technology for hospital dispensing, three-dimensional printed spironolactone subdivided tablets of 2 mg have been used in clinical inpatients and was accepted by pharmacists, nurses and patients. Compared with tablets subdivided split by pharmacists, three-dimensional printed spironolactone tablets of 2 mg were more accurate, safer and more customized, which indicated considerable potential in using three-dimensional printing technology as a new method for hospital dispensing.

Warpage optimization and influence factors analysis of 3D printing personalized JJY tablets.

To explore the feasibility of preparing traditional Chinese medicine using 3 D printing technology and reduce warpage commonly occurs in large-size tablets, we investigated the prescription, warpage optimization and influence factors of 3 D printing Jiuxiang Jianpi Yangwei (JJY) tablets. The procedures used conformed to the requirements of the 2015 edition of the Chinese Pharmacopeia. The results of the prescription screening showed that 75% ethanol and HPMC (9%) could be adhesives. Meanwhile, stevia (0.5%) and citric acid (0.5%) improved the taste of the 3 D printed JJY tablets. To ensure the quality and appearance of the printed tablets, the best parameters were as follows: drying at room temperature, 40% of the filling density, a 3 mm model height, two outer ring numbers and a printing speed of 15 mm/s. The optimized printed tablets had a smooth appearance, suitable hardness, with the weight uniformity in accordance with the Pharmacopeia. We also prepared personalized JJY cartoon tablets (which contained images of a big-headed pig and a small yellow duck) which were designed to increase the compliance of children when taking their medications. In conclusion, this study reported that 3 D printing technology has great potential for preparing traditional Chinese medicines, and it provided guidance for 3 D printing tablets without warpage.

Optimized preparation of vinpocetine micelles and in vivo evaluation of its pharmacokinetics in rats.

This study aimed to develop a novel monomethoxy poly(ethylene glycol)-b-poly(D, L-lactide) (mPEG5000-PLA10 000) micelle drug delivery system to improve vinpocetine's (VP) dissolution and sustain VP concentrations in plasma. Three micelle fabrication methods were examined to maximize VP loading, followed by structurally characterization and investigation in vitro release and in vivo pharmacokinetics in Sprague-Dawley rats. The thin-film hydration is the most appropriate method of the three methods because of its high loading content. The loaded micelles exhibited a sustained release behavior up to 48 h. Following intraperitoneal administration (9 mg/kg), VP loaded micelles provided significantly higher (335%) AUC (area under concentration-time) compared to VP injection. And also increased the mean residence time [MRT(0-t)] and elimination half-life (t1/2z). There were obviously two peaks at 2 h and 9 h in VP loaded micelles concentration-time profile. In summary, these data demonstrated that poly mPEG-PLA micelles can efficiently sustain VP concentrations in plasma for 36 h, thus apprehending polymeric micelles suitability as poor aqueous solubility drug carriers.