Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Which diagrams and when? Health workers' choice and usage of different diagram types for service improvement

Diagrammatic representations, such as process mapping and care pathways, have been often used for service evaluation and improvement in healthcare. While a broad range of diagrammatic representations exist, their application in healthcare has been very limited. There is a lack of understanding about how and which diagrams could be usable and useful to health workers. In this study, ten mental health workers were asked to discuss positive and negative issues around their service delivery using one or two diagrams of their choice out of seven different diagrams representing their service: care pathway diagram; organisation diagram; communication diagram; service blueprint; patient state transition diagram; free form diagram; geographic map. Their interactions with diagrams were video-taped for analysis. The patient state transition diagram was the most popular choice in spite of relatively low previous familiarity. The overall findings provided insight into a better use of diagrams in healthcare. © 2012 Springer-Verlag.

Rapid entropy-based detection and properties measurement of concrete spalling with machine vision for post-earthquake safety assessments

The current procedures in post-earthquake safety and structural assessment are performed manually by a skilled triage team of structural engineers/certified inspectors. These procedures, and particularly the physical measurement of the damage properties, are time-consuming and qualitative in nature. This paper proposes a novel method that automatically detects spalled regions on the surface of reinforced concrete columns and measures their properties in image data. Spalling has been accepted as an important indicator of significant damage to structural elements during an earthquake. According to this method, the region of spalling is first isolated by way of a local entropy-based thresholding algorithm. Following this, the exposure of longitudinal reinforcement (depth of spalling into the column) and length of spalling along the column are measured using a novel global adaptive thresholding algorithm in conjunction with image processing methods in template matching and morphological operations. The method was tested on a database of damaged RC column images collected after the 2010 Haiti earthquake, and comparison of the results with manual measurements indicate the validity of the method.

Visualising a stochastic model of California Water Resources Using Sankey Diagrams

This paper describes a novel approach to the analysis of supply and demand of water in California. A stochastic model is developed to assess the future supply of and demand for water resources in California. The results are presented in the form of a Sankey diagram where present and stochastically-varying future fluxes of water in California and its sub-regions are traced from source to services by mapping the various transformations of water from when it is first made available for use, through its treatment, recycling and reuse, to its eventual loss in a variety of sinks. This helps to highlight the connections of water with energy and land resources, including the amount of energy used to pump and treat water, the amount of water used for energy production, and the land resources that create a water demand to produce crops for food. By mapping water in this way, policy-makers can more easily understand the competing uses of water, through the identification of the services it delivers (e.g. sanitation, food production, landscaping), the potential opportunities for improving themanagement of the resource and the connections with other resources which are often overlooked in a traditional sector-based management strategy. This paper focuses on a Sankey diagram for water, but the ultimate aim is the visualisation of linked resource futures through inter-connected Sankey diagrams for energy, land and water, tracking changes from the basic resources for all three, their transformations, and the final services they provide.

Obtaining bifurcation diagrams with a thermoacoustic network model

Linear techniques can predict whether the non-oscillating (steady) state of a thermoacoustic system is stable or unstable. With a sufficiently large impulse, however, a thermoacoustic system can reach a stable oscillating state even when the steady state is also stable. A nonlinear analysis is required to predict the existence of this oscillating state. Continuation methods are often used for this but they are computationally expensive. In this paper, an acoustic network code called LOTAN is used to obtain the steady and the oscillating solutions for a horizontal Rijke tube. The heat release is modelled as a nonlinear function of the mass flow rate. Several test cases from the literature are analysed in order to investigate the effect of various nonlinear terms in the flame model. The results agree well with the literature, showing that LOTAN can be used to map the steady and oscillating solutions as a function of the control parameters. Furthermore, the nature of the bifurcation between steady and oscillating states can be predicted directly from the nonlinear terms inside the flame model. Copyright © 2012 by ASME.

Predictive entropy search for efficient global optimization of black-box functions

We propose a novel information-theoretic approach for Bayesian optimization called Predictive Entropy Search (PES). At each iteration, PES selects the next evaluation point that maximizes the expected information gained with respect to the global maximum. PES codifies this intractable acquisition function in terms of the expected reduction in the differential entropy of the predictive distribution. This reformulation allows PES to obtain approximations that are both more accurate and efficient than other alternatives such as Entropy Search (ES). Furthermore, PES can easily perform a fully Bayesian treatment of the model hyperparameters while ES cannot. We evaluate PES in both synthetic and real-world applications, including optimization problems in machine learning, finance, biotechnology, and robotics. We show that the increased accuracy of PES leads to significant gains in optimization performance.

Phase diagrams for the MOVPE growth of ZnTe and ZnSeTe

The phase diagrams for the MOVPE growth of ZnTe and ZnSeTe have been proposed for the first time, based on the thermodynamic equilibrium established at the solid-vapor interface, The regions for the single condensed phase of ZnTe(s) and of ZnSeTe(s) have been investigated, respectively, Additionally, the growth conditions of appearance for the double condensed phase of ZnTe(s) + Zn(s or l) and ZnTe(s)+ Te(s or l) for the ZnTe system, of ZnSeTe(s) + Zn(s or l) and ZnSeTe(s)+ Te(s or l) for the ZnSeTe system are discussed.

Molecular dynamics simulation of entropy and surface tension for grain boundary of α-Fe

The grain boundary is an interface and the surface tension is one of its important thermodynamic properties. In this paper, the surface tension of the ∑9 grain boundary for α-Fe at various temperatures and pressures is calculated by means of Computer Molecular Dynamics (CMD). The results agree satisfactorily with the experimental data. It is shown that the contribution of entropy to surface tension of grain boundary can be ignored.