Simultaneous clustering of multiview biomedical data using manifold optimization.

MOTIVATION: Multiview clustering has attracted much attention in recent years. Several models and algorithms have been proposed for finding the clusters. However, these methods are developed either to find the consistent/common clusters across different views, or to identify the differential clusters among different views. In reality, both consistent and differential clusters may exist in multiview datasets. Thus, development of simultaneous clustering methods such that both the consistent and the differential clusters can be identified is of great importance. RESULTS: In this paper, we proposed one method for simultaneous clustering of multiview data based on manifold optimization. The binary optimization model for finding the clusters is relaxed to a real value optimization problem on the Stiefel manifold, which is solved by the line-search algorithm on manifold. We applied the proposed method to both simulation data and four real datasets from TCGA. Both studies show that when the underlying clusters are consistent, our method performs competitive to the state-of-the-art algorithms. When there are differential clusters, our method performs much better. In the real data study, we performed experiments on cancer stratification and differential cluster (module) identification across multiple cancer subtypes. For the patients of different subtypes, both consistent clusters and differential clusters are identified at the same time. The proposed method identifies more clusters that are enriched by gene ontology and KEGG pathways. The differential clusters could be used to explain the different mechanisms for the cancer development in the patients of different subtypes. AVAILABILITY AND IMPLEMENTATION: Codes can be downloaded from: http://homepage.fudan.edu.cn/sqzhang/files/2018/12/MVCMOcode.zip. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[Protective Effects of Ginkgolide N Against Glutamate-Induced Injury in PC12 Cells].

OBJECTIVE: To study the protective effects of ginkgolide N against glutamte-induced injury in PC12 cells and its mechanisms. METHODS: The injury model was established by treating PC12 cells with glutamate, and PC12 cells were treated with different concentrations of ginkgolide N with ginkgolide B as control. The cells activity was analyzed by MTT assay. The apoptosis of PC12 cells were examined by acridine orange( AO) staining, the reactive oxygen species and mitochondrial membrane potential of PC12 cells were examined by flow cytometry. Western blot method was used to examine the expression of Cleaved Caspase-3 protein. RESULTS: Ginkgolides N of 2-8 µgmol/L inhibited PC12 cells apoptosis and ROS accumulation induced by glutamate,stabilized membrane potential of damaged PC12, and reduced the expression of Cleaved Caspase-3 protein. CONCLUSION: Ginkgolide N has a protective effect on PC12 cells injury induced by glutamate, and the mechanism may be associated with reducing ROS generation, stabilizing membrane potential and inhibiting the expression of Cleaved Caspase-3 protein.

[Research on survey analysis and development strategies of traditional Chinese preparations in Guangdong Province hospitals].

OBJECTIVE: To provide reference for the government to formulate policies and medical institution to formulate development plan, the present situation of medical institutions of traditional Chinese preparation and some countermeasures for developing the research of traditional Chinese preparation in Guangdong province were studied. METHODS: Combined with development situation of traditional Chinese preparation of medical institutions in Guangdong province in recent years, the development countermeasure of traditional Chinese preparation was discussed. RESULTS: In order to promote the development of traditional Chinese preparation of medical institutions, suggestions and countermeasures for the government and related departments were proposed. CONCLUSION: Government departments should formulate policies to support the development of traditional Chinese preparation, the medical institutions should make scientific development planning, strengthen the construction of hardware and software and develop special traditional Chinese preparation to promote the healthy development of traditional Chinese preparation.

A Self-Consistent-Field Iteration for Orthogonal Canonical Correlation Analysis.

We propose an efficient algorithm for solving orthogonal canonical correlation analysis (OCCA) in the form of trace-fractional structure and orthogonal linear projections. Even though orthogonality has been widely used and proved to be a useful criterion for visualization, pattern recognition and feature extraction, existing methods for solving OCCA problem are either numerically unstable by relying on a deflation scheme, or less efficient by directly using generic optimization methods. In this paper, we propose an alternating numerical scheme whose core is the sub-maximization problem in the trace-fractional form with an orthogonality constraint. A customized self-consistent-field (SCF) iteration for this sub-maximization problem is devised. It is proved that the SCF iteration is globally convergent to a KKT point and that the alternating numerical scheme always converges. We further formulate a new trace-fractional maximization problem for orthogonal multiset CCA and propose an efficient algorithm with an either Jacobi-style or Gauss-Seidel-style updating scheme based on the SCF iteration. Extensive experiments are conducted to evaluate the proposed algorithms against existing methods, including real-world applications of multi-label classification and multi-view feature extraction. Experimental results show that our methods not only perform competitively to or better than the existing methods but also are more efficient.

Chemical constituents from Eupatorium chinense.

Two new monoterpenoid glycosides, α-(E)-acaridiol 8-O-ß-d-glucopyranoside (1) and α-(E)-acaridiol 9-O-ß-d-glucopyranoside (2), as well as a new thiophen, 2-acetyl-3-hydroxy-5-(prop-1-ynyl)thiophen 3-O-ß-d-glucopyranoside (3), were isolated from the roots of Eupatorium chinense. Their structures were determined on the basis of extensive spectroscopic and chemical analyses.

[Determination of geniposide, crocin and crocetin in different processing products of fructus gardeniae by HPLC-ELSD].

OBJECTIVE: To develop a HPLC- ELSD method for determination the contents of geniposide, crocin and crocetin in different processing products of Fructus Gardeniae. METHODS: The separation was performed in the HyperClone ODS C18 column (250 mm x 4. 6 mm, 5 microm) with linear gradient elution using methanol-water and 0.05% phosphoric acid in water, the flowing rate was 0.8 mL/min, the column temperature was 30 degrees C, and the ELSD parameter was as follow: 70 degrees C as atomization temperature and 2.0 L/min as the gas flowing rate. RESULTS: The contents of geniposide and crocin in raw, yellowish, carbocoal and scorched Fructus Gardeniae decreased with the deepening of processing degree. However, the content of crocetin in carbocoal and scorched Fructus Gardeniae increased comparing with the raw one. CONCLUSION: This is a simple and credible quality control method, and can be used for the quality control and comprehensive evaluation for different processed products of Fructus Gardeniae.

[Study on flavonoiels and phenolic acids from the herb of Lygodium japonicum].

OBJECTIVE: To study the chemical constituents of the herb of Lygodium japonicum. METHODS: The constituents isolated by column chromatography and their structrues were elucidated through spectroscopic analysis. RESULTS: The compounds were identified as 3,4-dihydroxyl benzoic acid 4-O-beta-D-(4'-O-methyl) glucopyranoside (I), protocatechuic acid (II), acacetin 7-O-(6'-O-a-L-rhamnopyranosyl)-beta-sophoroside (III), 6,8-di-glucosylapigenin (vinenin) (IV), tricin-7-O-beta-D-glucopyranoside (V), 2-anilino-1,4-naphthoquinone (VI). CONCLUSION: All these compounds are obtained from Lygodiaeae for the first time.

[Chemical constituents from root barks of Periploca sepium].

OBJECTIVE: To investigate the chemical constituents of the root barks of Periploca sepium. METHOD: Column chromatographic techniques were used to isolate the chemical constituents. NMR and MS methods were employed for their structural elucidation. RESULT: Eight compounds were isolated and identified as isovanillin (1), vanillin (2), 4-methoxysalicylic acid (3), (24R)-9, 19-cycloart-25-ene-3beta, 24-diol (4), (24S)-9, 19-cycloart-25-ene-3beta, 24-diol (5), cycloeucalenol (6), beta-amyrin acetate (7) and alpha-amyrin (8). CONCLUSION: Compounds 1-6 were isolated from this plant for the first time.

[Studies on the chemical constituents in herb of Lygodium japonicum].

OBJECTIVE: To study the chemical constituents of Lygodium japonicum. METHOD: Column chromatographic techniques were used for isolation and purification of chemical constituents of this plant and their structures were identified by spectroscopic analysis. RESULT: Eight compounds were isolated and identified as tilianin (I), kaempferol-7-O-alpha-L-rhamnopyranoside (II), kaempferol (III), p-coumaric acid (IV), hexadecanoic acid 2, 3-dihydroxy-propyl ester (V), daucosterol (VI), beta-sitosterol (VII, and 1-hentriacontanol (VIII) respectively. CONCLUSION: Compounds I, II, V, VI, VII, VIII were isolated from L. japonicum for the first time, compounds I, II, V were isolated from genus Lygodium for the first time.

New cycloartane glycosides from the aerial part of Thalictrum fortunei.

Four new cycloartane glycosides, 3-O-ß-D-xylopyranosyl-(1 → 6)-ß-D-glucopyranosyl-(1 → 4)-ß-D-fucopyranosyl (22S,24Z)-cycloart-24-en-3ß,22,26-triol 26-O-(6-O-acetyl)-ß-D-glucopyranoside (1), 3-O-α-L-arabinopyranosyl-(1 → 6)-ß-D-glucopyranosyl-(1 → 4)-ß-D-fucopyranosyl (22S,24Z)-cycloart-24-en-3ß,22,26-triol 26-O-(6-O-acetyl)-ß-D-glucopyranoside (2), 3-O-ß-D-glucopyranosyl (24S)-cycloartane-3ß,16ß,24,25,30-pentaol 25-O-ß-D-glucopyranosyl-(1 → 6)-ß-D-glucopyranoside (3) and 3-O-ß-D-glucopyranosyl (24S)-cycloartane-3ß,16ß,24,25,30-pentaol 25-O-ß-D-glucopyranosyl-(1 → 4)-ß-D-glucopyranoside (4), were isolated from the aerial parts of Thalictrum fortunei. Their structures were established on the basis of extensive NMR and HR-ESI-MS analyses, along with acid hydrolysis.

Four new cycloartane glycosides from Thalictrum fortunei.

Four new cycloartane glycosides were isolated from the aerial parts of Thalictrum fortunei (Ranunculaceae). The chemical structures of these new glycosides were elucidated as 3-O-beta-D-glucopyranosyl-(1-->4)-beta-D-fucopyranosyl (22S,24Z)-cycloart-24-en-3beta,22,26-triol 26-O-beta-D-glucopyranoside, 3-O-beta-D-glucopyranosyl-(1-->4)-beta-D-fucopyranosyl (22S,24Z)-cycloart-24-en-3beta,22,26-triol 26-O-beta-D-quinovopyranosyl-(1-->6)-beta-D-glucopyranoside, 3-O-beta-D-glucopyranosyl-(1-->4)-beta-D-fucopyranosyl (22S,24Z)-cycloart-24-en-3beta,22,26-triol 26-O-beta-D-xylopyranosyl-(1-->6)-beta-D-glucopyranoside, and 3-O-beta-D-glucopyranosyl-(1-->4)-beta-D-fucopyranosyl (22S,24Z)-cycloart-24-en-3beta,22,26-triol 26-O-alpha-L-arabinopyranosyl-(1-->6)-beta-D-glucopyranoside by extensive NMR methods, HR-ESI-MS, and hydrolysis. This is the first report of (22S,24Z)-3beta,22,26-trihydroxycycloartan-24-ene (thelictogenin A, 5) being glycosylated at C-26.