Efficient Mining of Partial Periodic Patterns in Time Series Database

Partial periodicity search, i.e., search for partial periodic patterns in time-series databases, is an interesting data mining problem. Previous studies on periodicity search mainly consider finding full periodic patterns, where every point in time contributes (precisely or approximately) to the periodicity. However, partial periodicity is very common in practice since it is more likely that only some of the time episodes may exhibit periodic patterns

Morphological and phylogenetic analyses reveal two new Penicillium species isolated from the ancient Great Wall loess in Beijing, China

IntroductionPenicillium species exhibit a broad distribution in nature and play a crucial role in human and ecological environments.MethodsTwo Penicillium species isolated from the ancient Great Wall loess in the Mentougou District of Beijing, China, were identified and described as new species, namely, Penicillium acidogenicum and P. floccosum, based on morphological characteristics and phylogenetic analyses of multiple genes including ITS, BenA, CaM, and RPB2 genes.ResultsPhylogenetic analyses showed that both novel species formed a distinctive lineage and that they were most closely related to P. chrzaszczii and P. osmophilum, respectively.DiscussionPenicillium acidogenicum is characterized by biverticillate conidiophores that produce globose conidia and is distinguished from similar species by its capacity to grow on CYA at 30°C. Penicillium floccosum is typically recognized by its restricted growth and floccose colony texture. The description of these two new species provided additional knowledge and new insights into the ecology and distribution of Penicillium

Classification and differential metabolite discovery of liver diseases based on plasma metabolic profiling and support vector machines

Discovery of differential metabolites is the focus of metabonomics study. It has very important applications in pathogenesis and disease classification. The aim of this work is to identify differential metabolites for classifying the patients with hepatocellular carcinoma, cirrhosis and hepatitis based on metabolic profiling data analyzed by gas chromatography-time of flight mass spectrometry. A two-stage feature selection algorithm, F-SVM, combining F-score in analysis of variance and support vector machine (SVM), was applied in discovering discriminative metabolites for three different types of liver diseases. The results show that the accuracy rate of the double cross-validation was 73.68 +/- 2.98%. 22 important differential metabolites selected by F-SVM were identified and related pathophysiological process of liver diseases was set forth. We conclude that F-SVM is quite feasible to be applied in the selection of biologically relevant features in metabonomics

Knockdown of Matrix Metallopeptidase 9 Inhibits Metastasis of Oral Squamous Cell Carcinoma Cells in a Zebrafish Xenograft Model

Destruction of extracellular matrix (ECM) is one of the basic steps of tumor invasion and metastasis. Matrix metalloproteinase (MMP) 9, a kind of zinc-ion-dependent endopeptidase, can degrade almost all protein components in the ECM, destroy the histological barrier of tumor cell invasion, and play a key role in tumor invasion and metastasis. The role of MMP-9 in tumor invasion and metastasis has attracted increasing attention and is considered the main proteolytic enzyme in this process. Although the overexpression of MMP-9 was detected in Oral squamous cell carcinoma (OSCC) tissues, further basic studies in vivo and in vitro are needed to investigate the role of MMP-9 in OSCCs and provide scientific validation. In this research, we developed a novel OSCC zebrafish xenograft model to study the role of the MMP-9 gene in oral carcinogenesis. Firstly, the MMP-9/shRNA lentiviral clone and control virus were constructed and transfected into OSCC cells. Then, the decreasing expression of MMP-9 was verified by RT-PCR and immunocytochemistry. Cell proliferation was detected by MTT assay. Colony formation was evaluated by colony formation assay. Cell invasion was evaluated using transwell invasion assay in vitro. In addition, OSCC cells with MMP-9/shRNA knockdown and control vector were injected into zebrafish and an OSCC tumor model in zebrafish was established to evaluate invasion and metastasis in vivo. Knockdown of MMP-9 gene by shRNA could inhibit OSCC cell growth and clone formation and markedly suppress cell invasion in vitro. And the knockdown of the MMP-9 gene could also significantly decrease the metastatic distance and number of metastatic tumor cells or lesions in vivo and suppress the metastasis rate in xenografted zebrafish. Taken together, these evidences indicated that the knockdown of MMP-9 might suppress OSCC cell invasion and metastasis in vivo and in vitro. The MMP-9 gene may be a promising therapeutic target for OSCCs in the future

Analysis of Urinary Metabolic Signatures of Early Hepatocellular Carcinoma Recurrence after Surgical Removal Using Gas Chromatography-Mass Spectrometry

The objective of present study was to offer insights into the metabolic responses of hepatocellular carcinoma (HCC) to surgical resection and the metabolic signatures latent in early HCC recurrence (one year after operation). Urinary metabolic profiling employing gas chromatography time-of-flight mass spectrometry (GC-TOF MS) was utilized to investigate the complex physiopathologic regulations in HCC after operational intervention. It was revealed that an intricate series of metabolic regulations including energy metabolism, amino acid metabolism, nucleoside metabolism, tricarboxylic acid (TCA) cycle, gut floral metabolism, etc., principally leading to the direction of biomass synthesis, could be observed after tumor surgical removal. Moreover, metabolic differences between recurrent and nonrecurrent patients had emerged 7 days after initial operation. The metabolic signatures of HCC recurrence principally comprised notable up-regulations of lactate excretion, succinate production, purine and pyrimidine nucleosides turnover, glycine, serine and threonine metabolism, aromatic amino acid turnover, cysteine and methionine metabolism, and glyoxylate metabolism, similar to metabolic behaviors of HCC burden. Sixteen metabolites were found to be significantly increased in the recurrent patients compared with those in nonrecurrent patients and healthy controls. Five metabolites (ethanolamine, lactic acid, acotinic acid, phenylalanine and ribose) were further defined; they were favorable to the prediction of early recurrence

Noralashinol A, a new norlignan from stem barks of <i>Syringa pinnatifolia</i>

<p>One new norlignan, namely noralashinol A (<b>1</b>), one known analogue (<b>2</b>), together with seven known lignans (<b>3</b>–<b>9</b>) were isolated from the stem barks of <i>Syringa pinnatifolia</i>. Their structures were elucidated extensively by spectroscopic methods, including mass spectrometry and 1D and 2D NMR spectroscopies. Compound <b>8</b> significantly inhibited NO production in LPS-induced BV-2 murine microglia cells with its IC₅₀ value of 20.7 μM, compared to a positive control quercetin with its IC₅₀ value of 15.3 μM.</p