MeInfoText: associated gene methylation and cancer information from text mining

<p>Abstract</p> <p>Background</p> <p>DNA methylation is an important epigenetic modification of the genome. Abnormal DNA methylation may result in silencing of tumor suppressor genes and is common in a variety of human cancer cells. As more epigenetics research is published electronically, it is desirable to extract relevant information from biological literature. To facilitate epigenetics research, we have developed a database called MeInfoText to provide gene methylation information from text mining.</p> <p>Description</p> <p>MeInfoText presents comprehensive association information about gene methylation and cancer, the profile of gene methylation among human cancer types and the gene methylation profile of a specific cancer type, based on association mining from large amounts of literature. In addition, MeInfoText offers integrated protein-protein interaction and biological pathway information collected from the Internet. MeInfoText also provides pathway cluster information regarding to a set of genes which may contribute the development of cancer due to aberrant methylation. The extracted evidence with highlighted keywords and the gene names identified from each methylation-related abstract is also retrieved. The database is now available at <url>http://mit.lifescience.ntu.edu.tw/</url>.</p> <p>Conclusion</p> <p>MeInfoText is a unique database that provides comprehensive gene methylation and cancer association information. It will complement existing DNA methylation information and will be useful in epigenetics research and the prevention of cancer.</p

The Effects Between Numerical Tabulations And Graphs Of Financial Information On The Judgment Of Investors

Due to developments in information markets and advancements in information technology, and with the rapidity of information flow on the Internet, it is vital to increase the level of information transparency. Disclosure methods of financial information have presently become an important topic of discussion. By using numerical tables, non-distorted graphs or distorted graphs of financial information, this research discusses whether financial information display types indeed influence investors’ judgments and decisions. We investigate and analyze the use of graph disclosure in Taiwan and use experiment design methods to test the effect of investors’ judgment by comparing different display types of financial information. Our results find graphs are used to display comparative than numerical financial information, showing how this can influence investors’ awareness and judgments and use of graphs can be used to manipulate impressions (impression management)

Methanol plug assisted sweeping-micellar electrokinetic chromatography for the determination of dopamine in urine by violet light emitting diode-induced fluorescence detection

Abstract The use and limitations of a methanol plug assisted sweeping-micellar electrokinetic chromatography (sweeping-MEKC) method is described. Using naphthalene-2,3-dicarboxaldehyde (NDA)-labeled dopamine as a model compound, this new method was also used in the determination of dopamine in actual urine samples. An inexpensive violet light emitting diode (LED) was used for the light source, because this is suitable for fluorescence excitation. The number of theoretical plates of the analyte was determined to be ∼1 × 10 5 and ∼2 × 10 5 by means of MEKC and sweeping-MEKC and this was improved to ∼1 × 10 6 when the methanol plug assisted mode was applied. In addition, the detection limit of NDA-labeled dopamine was determined to be 9.1 × 10 −7 and 1.2 × 10 −8 M by means of MEKC and sweeping-MEKC and this was improved to 4.7 × 10 −9 M when the methanol plug assisted sweeping-MEKC mode was applied

Membrane repair against H. pylori promotes cancer cell proliferation

Membrane repair is a universal response against physical and biological insults and enables cell survival. Helicobacter pylori is one of the most common human pathogens and the first formally recognized bacterial carcinogen associated with gastric cancer. However, little is known about host membrane repair in the context of H. pylori infection. Here we show that H. pylori disrupts the host plasma membrane and induces Ca2+ influx, which triggers the translocation of annexin family members A1 and A4 to the plasma membrane. This in turn activates a membrane repair response through the recruitment of lysosomal membranes and the induction of downstream signaling transduction pathways that promote cell survival and proliferation. Based on our data, we propose a new model by which H. pylori infection activates annexin A1 and A4 for membrane repair and how annexin A4 over-expression induced signaling promotes cell proliferation. Continual activation of this membrane repair response signaling cascade may cause abnormal cellular states leading to carcinogenesis. This study links H. pylori infection to membrane repair, providing insight into potential mechanisms of carcinogenesis resulting from membrane damage

An Extended Analytic Solution of Combined Refraction and Diffraction of Long Waves Propagating over Circular Island

An analytic solution of long waves scattering by a cylindrical island mounted on a permeable circular shoal was obtained by solving the linear long wave equation (LWE). The solution is in terms of the Bessel function expressed by complex variables. The present solution is suitable for arbitrary bottom configurations described by a power function with two independent parameters. For the case of the paraboloidal shoal, there exists a singular point (α=2) which can be removed using Frobenius series, where α is a real constant. The present solution is reduced to Yu and Zhang’s (2003) solution for impermeable circular shoal. The numerical results show some special features of the combined effect of wave refraction and diffraction caused by a porous circular island. The effect of key parameters of the island dimension, the shoal slope, and permeability on wave scattering was discussed based on the analytic solution

Coregulation of transcription factors and microRNAs in human transcriptional regulatory network

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level. Recent studies have suggested that miRNAs and transcription factors are primary metazoan gene regulators; however, the crosstalk between them still remains unclear.</p> <p>Methods</p> <p>We proposed a novel model utilizing functional annotation information to identify significant coregulation between transcriptional and post-transcriptional layers. Based on this model, function-enriched coregulation relationships were discovered and combined into different kinds of functional coregulation networks.</p> <p>Results</p> <p>We found that miRNAs may engage in a wider diversity of biological processes by coordinating with transcription factors, and this kind of cross-layer coregulation may have higher specificity than intra-layer coregulation. In addition, the coregulation networks reveal several types of network motifs, including feed-forward loops and massive upstream crosstalk. Finally, the expression patterns of these coregulation pairs in normal and tumour tissues were analyzed. Different coregulation types show unique expression correlation trends. More importantly, the disruption of coregulation may be associated with cancers.</p> <p>Conclusion</p> <p>Our findings elucidate the combinatorial and cooperative properties of transcription factors and miRNAs regulation, and we proposes that the coordinated regulation may play an important role in many biological processes.</p

Integrative network analysis reveals active microRNAs and their functions in gastric cancer

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are a class of endogenous, small and highly conserved noncoding RNAs that control gene expression either by degradation of target mRNAs or by inhibition of protein translation. They play important roles in cancer progression. A single miRNA can provoke a chain reaction and further affect protein interaction network (PIN). Therefore, we developed a novel integrative approach to identify the functional roles and the regulated PIN of oncomirs.</p> <p>Results</p> <p>We integrated the expression profiles of miRNA and mRNA with the human PIN to reveal miRNA-regulated PIN in specific biological conditions. The potential functions of miRNAs were determined by functional enrichment analysis and the activities of miRNA-regulated PINs were evaluated by the co-expression of protein-protein interactions (PPIs). The function of a specific miRNA, miR-148a, was further examined by clinical data analysis and cell-based experiments. We uncovered several miRNA-regulated networks which were enriched with functions related to cancer progression. One miRNA, miR-148a, was identified and its function is to decrease tumor proliferation and metastasis through its regulated PIN. Furthermore, we found that miR-148a could reduce the invasiveness, migratory and adhesive activities of gastric tumor cells. Most importantly, elevated miR-148a level in gastric cancer tissues was strongly correlated with distant metastasis, organ and peritoneal invasion and reduced survival rate.</p> <p>Conclusions</p> <p>This study provides a novel method to identify active oncomirs and their potential functions in gastric cancer progression. The present data suggest that miR-148a could be a potential prognostic biomarker of gastric cancer and function as a tumor suppressor through repressing the activity of its regulated PIN.</p