Computational prediction, experiment design and statistical validations of non-coding regulatory RNA

Non-coding regulatory RNAs (ncRNAs) regulate a host of gene functions in prokaryotes, e.g., transcription and translation regulations, RNA processing and modification, and mRNA stability. Some ncRNAs have been identified experimentally, but many are yet to be found. ncRNAs can be classified as either cis- or trans-acting. cis-ncRNAs perfectly complement their target genes and are usually encoded on the anti-sense strands of the targets. On the contrary, trans-ncRNAs regulate their target genes through short and often imperfect base-pairings with the targets, and are usually encoded elsewhere on the genome. A whole-genome thermodynamic analysis can be performed to identify all imperfect but stable base-pairings between all annotated genes and some genomic regions encoding ncRNAs from the same species. However, the sizes of these base-paring regions are short and variable, and their melting temperatures vary greatly between perfectly and imperfectly matched targets. It is difficult to predict trans-acting ncRNAs solely based on the thermodynamic analysis. Therefore, we also have to consider known ncRNA structures to improve our predictions. We find that Hfq-binding ncRNAs, which require Hfq protein to function, share three common structural properties. We predict these special ncRNAs in E. coli and Agrobacterium tumefaciens according to a systematic, novel 5-step approach based on thermodynamic analyses as well as known structural properties of this class of ncRNAs. Whole genome tiling microarrays are chosen to validate our predictions. We describe how the microarrays have been designed, created, and validated for E. coli MG1655 and Agrobacterium tumefaciens C58. We match our new ncRNA prediction results with known ncRNAs, calculate correlation coefficient values between each ncRNA candidate and their predicted targets measure by the whole-genome tiling microarrays, and confirm the results with 3 other ncRNA identification software tools. We also perform a gene ontology network analysis to reveal the associations of ncRNA candidates and their predicted targets. Our novel 5-step prediction method is generally applicable to other prokaryote species and may help advance ncRNA research in prokaryotes

The Bank Capital Regulation (BCR) Model

International audienceThe motivation of this article is to induce the bank capital management solution for banks and regulation bodies on commercial banks. The goal of the paper is intended to mitigate the risk of a banking area and also provide the right incentive for banks to support the real economy

The casualty transportation of Ebola outbreak in Liberia: A simulation study

In this paper, we have solved the unique problem of casualty transportation problem under Ebola by developing dynamic policies for vehicle routing in order to provide practical decision support. The objective of the proposed model is to minimize the total transmission risk. We describe the problem with real- constraints and parameters based on the empirical data of the 2014 Ebola outbreak in Liberia. The casualty transportation problem is a variant of Dynamic Pick-up and Delivery Problems (DPDP), in which a vehicle is dispatched to demand location in real time and it then transports the demands to the aimed area (destination). DPDP integrates various sources of dynamic events as well as real-world aspects. All decision made in dynamic vehicle routing problems are taken in real-time. In same light, the casualty transportation problem is solved in real-time under infectious disease environment. Particularly in case of Ebola, the prompt burial or cremation of deceased Ebola victims would is critical in reducing the transmission of the virus thus casualty transportation problem should be considered mandatory to stop transmission. To solve the casualty transportation problem, our approach involves developing adequate policies for vehicle routing construction under Ebola situation, to evaluate those policies performance through simulations, and to recommend the best policy resulted from experimental results that can reduce the total transmission risk a lot

Thermodynamically optimal whole-genome tiling microarray design and validation

Additional file 2. Assembled genome sequences for E. coli MG1655 and Agrobacterium tumefaciens C58. Two FASTA files containing the assembled genomic sequences are provided in this compressed ZIP archive

Effect Of Liability Of Foreignness And Family Ownership On Cross-Listing Location Choice

Firms incur liability of foreignness (LOF) when they expand their businesses to foreign countries. This study examines the applicability of LOF in the context of financing in a foreign capital market. Using an alternative-specific conditional logit model, we investigate the cross-listing decisions of firms from 28 countries that select among eight target destinations from 1994 to 2008. These firms target capital markets with lower LOF, which is measured by institutional, economic, geographic, and cultural distance. Such preference is particularly stronger for firms with higher levels of family ownership, suggesting family owners’ tendency to be averse to risk is also manifested in financing context

bank capital regulation model

The motivation of this article is to induce the bank capital management solution for banks and regulation bodies on commercial bank. The goal of the paper is intended to mitigate the risk of banking area and also provide the right incentive for banks to support the real economy

CO2 Conversion to Chemicals and Fuel for Carbon Utilization

Recent direction dealing with climate change has changed more to focus on carbon utilization rather than the direct carbon capture and storage. Conceptually converting CO2 to sellable chemicals or fuels should be more benign to environment by substituting the fossil raw materials like oil, natural gas, or coal. Instead of converting CO2 fully to valuable chemicals or fuels, it is much easier to employ a portion of CO2 with existing raw materials in many natural gas conversion processes. Dimethyl ether (DME) and gas-to-liquids (GTL) are most prominent processes that can be modified to accommodate CO2 as a reacting raw material. There are already several successful technology developments in using CO2-rich natural gas for DME and liquid fuels, although they are not yet fully reached the commercialized level. This chapter highlights recent developments in utilizing CO2-containing natural gas and landfill gas to yield valuable chemicals and fuels like diesel or DME

Chronological Description about Financial Crisis and Gap between Academic and Professional Approach

This essay aims to describe the financial crisis in the chronological way and explain the gap between academic and professional approach

Economics of Regulation: Credit Rationing and Excess Liquidity

: In examining the global imbalance by the excess liquidity level, the argument is whether commercial banks want to hold excess reserves for the precautionary aim or expect to get better return through risky decision. By pictorial representations, risk preference in the Machina’s triangle (1982, 1987) encapsulates motivation to hold excess liquidity. This paper introduces an endogenous liquidity model for the financial sector where the imbalance argument comes from credit rationing extended from outside liquidity (Holmstrom and Tirole, 2011). We also conduct a stylistic analysis of excess liquidity in Jordan and Lebanon from 1993 to 2015. As such, the proposed model exemplifies the combination of credit, liquidity and regulation

Chronological Description about Financial Crisis and Gap between Academic and Professional Approach

This essay aims to describe the financial crisis in the chronological way and explain the gap between academic and professional approach