MSTracer: A Machine Learning Software Tool for Peptide Feature Detection from Liquid Chromatography-Mass Spectrometry Data.

Liquid chromatography with tandem mass spectrometry (MS/MS) has been widely used in proteomics. Although a typical experiment includes both MS and MS/MS scans, existing bioinformatics research has focused far more on MS/MS data than on MS data. In MS data, each peptide produces a few trails of signal peaks, which are collectively called a peptide feature. Here, we introduce MSTracer, a new software tool for detecting peptide features from MS data. The software incorporates two scoring functions based on machine learning: one for detecting the peptide features and the other for assigning a quality score to each detected feature. The software was compared with several existing tools and demonstrated significantly better performance.

Effects of cold plasma treatment on cherry quality during storage.

Cherry samples were treated with cold plasma under different voltages (40, 60, 80 kV) and different treatment durations (60, 80, 100, 140 s), then stored in a refrigerator at 0 ℃. Data on the decay rate, respiration rate, and physiological properties of the cherries and their correlational relationships after different treatments of cold plasma were collected under the conditions of ambient temperature and dry air. The decay rate, respiration rate, total soluble solids, total phenol, flavonoids, anthocyanin, VC, titratable acidity, firmness, and a* value were investigated at regular intervals to analyze the quality of the cherries under different treatment conditions. Additionally, the total colony number was estimated at the end of storage. The results indicated that cold plasma treatment under moderate conditions was effective for prolonging cherry storage, inactivating microorganisms, decreasing the decay rate, and inhibiting respiration with either no compromise on the cherry quality or only a slightly noticeable influence. A significant positive correlation was found between the decay rate and respiration rate, as well as between the VC content and titratable acidity. Antioxidant contents and firmness were found to be negatively correlated with the a* value. In conclusion, this study demonstrated that cold plasma has potential applications in the storage and preservation of cherries.

MagWorm: A Biomimetic Magnet Embedded Worm-Like Soft Robot.

Emerging worm-like soft robots with various soft materials and different actuation mechanism have been frequently discussed. It is very challenging for soft robots in realizing a fast and untethered crawling. In this article, a biomimetic magnet embedded worm-like robot (shorted as "MagWorm") in the size of centimeter level is designed and investigated. The actuation of the MagWorm is achieved by housing permanent magnetic patches in its soft body, which interact with an external moving drive-magnet system. A dynamic model is established, coupling the discrete elastic rod model with magnetic actuation. The driving mechanism is then numerically studied. Quantitative comparisons between the numerical solution and experiment results show reasonable agreement. It is shown that the MagWorm can deform part of its body into a "Ω" shape and generate biomimetic crawling locomotion. The crawling speed of the robot is studied experimentally with different sizes. Some potential applications are also proposed and demonstrated. The MagWorm represents compact and low-cost solutions that use permanent magnets for remote actuation of soft robot and can be continuously operated during long procedures.

The Correlation Between Heart Failure and Gut Microbiome Metabolites.

Heart failure (HF) is a global public health problem, with morbidity and mortality increasing year by year. The gut microbiome actively affects the physiological and pathological activities of the human body in a variety of ways. More and more studies have suggested a strong correlation between HF and gut microbiome metabolites. Our review summarizes the specific alteration of these metabolites and their connection to the progression of HF, aiming at considering new approaches toward regulating the gut microbiome and using its metabolic pathways to treat HF, potentially decreasing the morbidity and mortality of HF as well as improving prognosis.

[The expression of heat shock protein 70 (HSP70) in the cells of rat liver and cardiac muscle in different heat exposure stages].

OBJECTIVE: To show the changes of heat shock protein 70(HSP70) expression at cellular level in different heat exposure stages and the significance of HSP70 expression in heat exposure organism. METHOD: The heat exposure model was established in rats with artificial hot climatic chamber[34 +/- 1) degree C, RH 60%]. SD rats were randomly divided into control groups(C) and heat exposure groups(A), and into subgroups including 2, 7, 14, 28 d stages from each one of the groups. The immuno-histochemistry was used to detect HSP70 expression in rat liver and cardiac muscle, and photography analytic software was used to analyze HSP70 expression in liver and cardiac cells. RESULTS: The expression intensity of HSP70 in heat exposure groups(gray values of liver were 137.0 +/- 5.1, 137.0 +/- 5.2, 137.8 +/- 7.1, 139.2 +/- 5.2 respectively; of cardiac muscle 156.1 +/- 4.4, 155.1 +/- 6.2, 155.4 +/- 4.5, 156.2 +/- 5.1 respectively) was stronger than that in control groups(P < 0.01 or P < 0.05) during all stages of the heat exposure; There was no significant difference in expression intensity of HSP70 among various stages of heat exposure; after 2 d of heat exposure, HSP70 expression in cell nuclei of the liver and cardiac muscle cells was stronger than that in cytoplasm in heat exposure group; HSP70 expression in Kupffer's cells of liver was also stronger than that of control(P < 0.05), but not on 7, 14 and 28 d; the activities of alanine aminotransferase(ALT), aspartate aminotransferase(AST), creatine kinase(CK) and hydroxybutyrate dehydrogenase(HBD) showed an increase on 2 d and 28 d of heat exposure. CONCLUSION: The vital organs would be damaged on 2 d of heat exposure. High expression of HSP70 at this stage may be a marker of cell damage; Increased HSP70 expression on 7-14 d of heat exposure may play an important role in adaptation to heat, while long term(28 d) heat exposure, the protection of HSP70 from tissue damage may not be enough.

[Effect of NF-kappa B pathway on apoptosis of hepatic carcinoma cell line-7721 induced by TNF-alpha].

BACKGROUND & OBJECTIVE: It was proved that nuclear factor-kappa B play an important role in the activation of immune cell, anti-virus, various stress reaction, and regulation of apoptosis, etc. The objective of this study was to investigate the effect of NF-kappa B signal-transduction pathway on apoptosis of hepatic carcinoma cell line-7721 induced by TNF-alpha. METHODS: The activation of TNF-alpha on NF-kappa B conduction pathway was determined with ELISA and immunohistochemistry. Then the activation of TNF-alpha was blocked with TPCK. Flow cytometry was used to detect apoptosis. RESULTS: 1. TNF-alpha could activate the NF-kappa B conduction pathway. 2. TPCK could inhibit the activation of NF-kappa B induced by TNF-alpha. 3. Inactivation of NF-kappa B by TPCK could enhance apoptosis induced by TNF-alpha. CONCLUSION: NF-kappa B conduction pathway of 7721 cell takes part in anti-apoptosis and plays an important role in the tolerance on cytotoxicity of TNF-alpha of 7721 cell. Inhibition of NF-kappa B conduction pathway may has potential value in tumor treatment.