Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates

BACKGROUND: A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process. RESULTS: Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T), while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template. CONCLUSION: Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding

Browning of Pig White Preadipocytes by Co-Overexpressing Pig PGC-1α and Mice UCP1

Background/Aims: Brown adipose tissue (BAT) is critical for mammals’ survival in the cold environment. BAT-dependent non-shivering thermogenesis is attributed to uncoupling protein 1 (UCP1)’s disengagement of oxidative phosphorylation from ATP synthesis and dissipates energy as heat. Thus individuals with a substantial amount of BAT are better equipped during cold stress and less likely to become obese. Recently, our laboratory has shown pig adipocytes have no UCP1 protein. The inability of newborn piglets to generate heat contributed to its high death rate. Repairing the genetic defect of UCP1 in pig adipocytes has implications in defending against cold for piglets and developing an alternative treatment for human obesity. Methods: Q-PCR, western blotting (WB) and oxygen consumption measurement were used to enable functional UCP1 protein in preadipocytes. Immunoprecipitation (IP), chromatin immunoprecipitation (CHIP), and dual-luciferase reporter assay system were used to clarify the thermogenesis mechanism of functional UCP1. Results: Only co-overexpressing mice UCP1 and pig PGC-1α increased not only the mitochondrial number but also the uncoupled respiration rate in the transfected pig adipocytes. The functional mice UCP1 increased the pig PGC-1α activity through the AMPK-SIRT1 pathway. The active form PGC-1α interacted with transcription factors Lhx8, Zic1, ERRα, and PPARα to regulate the expression of mitochondrial energy metabolism and adipocytes browning-related genes. Conclusion: Our data suggest a model in which pig PGC-1α and mice UCP1 work collaboratively to restore uncoupling respiration in pig preadipocytes. These results have great implications for piglet survival and developing an alternative treatment for human obesity in the future

A 0.35 THz Extended Interaction Oscillator based on Overmoded and Bi-Periodic Structure

An improved topology of Extended interaction oscillators (EIO) is presented with enhanced efficiency at 0.35 THz. A bi-periodic ladder-type structure is used for optimizing the performance of the TM 31−2π mode operation, based on bi-periodic interaction gaps composed of staggered short and long slots. The bi-periodic interaction mechanism permits to operate the circuit with a standing-wave field between the π and 2π modes, thus providing the potential to combine the advantages of both π and 2π modes in terms of both coupling and output performance. The resulting transverse TM 31 operating mechanism exhibits a good agreement with the bi-periodic structure in terms of coupling performance, with the short slot length positively correlated with the value of effective characteristic impedance M2R/Q . The circuit demonstrates attractive coupling and output characteristics by optimization of M2R/Q and Qe . A state-of-the-art value M2R/Q of 59.69 Ω and a moderate Qe of 2523.52 are achieved for a proposed eight-period ladder-type EIO. An RF power of 540 W is obtained with a 42.5 kV, 0.6 A sheet beam, with 2.1% electronic efficiency at 0.35 THz

theoreticalanalysisofeffectsofboundarylayerbleedonscramjetthrust

The effects of boundary layer bleed on the scramjet thrust are studied in the present paper. A theoretical model is developed to evaluate the thrust increment and influencing factors. The thrust increment resulting from the bleed is dominated by the rise in total pressure recovery and bleed mass flow rate. The bleed mass flow rate exerts stronger impact on the engine thrust than the total pressure. According to current bleed design, it is a severe challenge for the engine to enhance its total pressure to maintain the original thrust when there is no bleeding. Furthermore, the initial total pressure recovery, fuel mass addition, combustion efficiency and area ratio of engine exit to entrance can affect the contributions of the bleeding to the thrust increment. The scramjet needs a higher rise in total pressure recovery to counteract the negative effect of bleed mass loss at higher initial total pressure recovery or larger area ratio of engine exit/entrance. More heat release results in a little lower demand on the rise in total pressure recovery for maintaining the scramjet thrust. These results will aid in understanding the fundamental mechanism of bleeding on engine thrust

Effect of driver roll rotational speed on hot ring rolling of AZ31 magnesium alloy

Based on the ABAQUS/Explicit code, A 3D elastic–plastic and coupled thermo-mechanical FE model of radial ring rolling of AZ31 Magnesium alloy has been proposed to analyze the influence of rotational speed of driver roll to study the inhomogeneity distribution of strain and temperature, fishtail coefficient, rolling force parameters. The results show that: (1) when the rotational speed of driver roll n increases, the strain distribution of the rolled ring becomes less homogeneous, and the temperature distribution more homogeneous yet, and leading to an optimal n value; (2) the fishtail coefficient firstly decreases, then increases with the increase of n; (3) the rolling force, contact area and rolling moment gradually descend with the increase of n

Influence of built environment and user experience on the waterfront vitality of historical urban areas: A case study of the Qinhuai River in Nanjing, China

Urban waterfronts are important gateways that reflect a city's image and characteristics. Evaluating waterfront vitality and its influencing factors is critical for guiding urban waterfront planning and redevelopment. Hourly human movement data, provided by the Baidu Heatmap, were used to explore the weekday and weekend urban vitality spatial distribution characteristics of the waterfronts of the Qinhuai River in Nanjing. Global (ordinary least squares) and local (multiscale geographically weighted regression) models revealed the influence of physical–environmental characteristics (objective) and spatial experience evaluation factors (subjective) on urban vitality. (1) The Qinhuai River waterfront urban vitality agglomeration characteristics were similar between weekdays and weekends, and the core vitality areas were distributed in the dense tourism, commercial, and residential areas along the river. (2) The evaluation of catering experience had the strongest positive correlation with vitality, whereas the waterfront distance had the strongest negative correlation. (3) The influence of each factor on waterfront vitality in the study area exhibited considerable spatial differences, with attenuation trends observed from the east-to-west river sections. This study shows the urban vitality distribution characteristics of the Qinhuai River waterfront spaces. Exploring the influence of physical–environmental and spatial evaluation factors on the vitality distribution can provide a scientific basis and reference for urban waterfront planning and redevelopment focusing on cultivating vitality

Site Selection Models in Natural Disaster Shelters: A Review

Constructing natural disaster shelters is important for disaster emergency management, and site selection models provide a feasible technique and method. This paper presents site selection models for natural disaster shelters. A synthesis of the types, objectives, constraints, methods of solutions, targeted disasters and applications of different site selection models for natural disaster shelters is investigated. Shelter location models can be classified as single-objective models, multiobjective models and hierarchical models, according to the objective and hierarchy type. Minimizing the evacuation distance or time, shelter construction cost or number, and the total risk are the general objectives of the models. Intelligent optimization algorithms are widely used to solve the models, instead of the Geographic Information System (GIS) method, due to the complexity of the problem. The results indicate that the following should be the main focuses of future works: How to set a model that can be applied for determining the shelter locations of multiple disasters; how to consider the uncertainty in the models; how to improve the existing algorithms or models to solve large-scale location-allocation problems; and how to develop a new resource-saving model that is consistent with the concept of sustainable development, as advocated by shelter planners and policy makers, which can be applied in real situations. This study allows those undertaking shelter location research to situate their work within the context of shelter planning

Numerical study of periodic flame flashback in a cavity-based scramjet combustor

The periodic flame flashback phenomenon in an ethylene-fueled cavity-based scramjet combustor was numerically investigated by a three-dimensional unsteady Reynolds-averaged Navier-Stokes solver with two-step kinetics. The air inflow stagnation temperature is 1225 K, and its Mach number is 2.6. Spectral analyses revealed the combustion oscillations with flame flashbacks maintained in the separated scramjet mode with the establishment/vanishment of flow separation near the fuel injector, differing from previous studies of flame flashbacks connected to the ramjet/scramjet mode transitions. A mechanism with four evolution stages was proposed to elucidate the flow-flame interaction. In stage I, a rapid flame flashback upstream and shock-train extension were caused by the high-temperature induced auto-ignition tendency of well-mixed unburned gas in the near-sidewall low-speed region. In stage II, the combustion-induced back pressure and shock train gradually achieved an aerodynamic balance. The combustion flow barely changed in stage III. Meanwhile, a simplified model suggested that the gradual temperature rises occurring upstream of the cavity and away from the sidewall were caused by spanwise heat conduction. The higher temperatures would cause upstream flame propagation with enhanced heat release due to auto-ignition. However, the enhanced heat release occurred mostly in the subsonic flow, resulting in pressure decreases according to one-dimensional flow equations. A smaller near-sidewall separation was produced by the lower back-pressures, which prompted the rapid flame recession downstream in stage IV. Moreover, a simplified flame-spreading model was proposed to illuminate the flame propagation nature. The comparison of flame speeds with theoretical estimations indicated that the current flame was in the regime of turbulent flame propagation, rather than the C-J detonation or deflagration speculated in previous studies

Spatial Distribution Estimates of the Urban Population Using DSM and DEM Data in China

Spatial distribution and population density are important parameters in studies on urban development, resource allocation, emergency management, and risk analysis. High-resolution height data can be used to estimate the total or spatial pattern of the urban population for small study areas, e.g., the downtown area of a city or a community. However, there has been no case of population estimation for large areas. This paper tries to estimate the urban population of prefectural cities in China using building height data. Building height in urban population settlement (Mdiffs) was first extracted using the digital surface model (DSM), digital elevation model (DEM), and land use data. Then, the relationships between the census-based urban population density (CPD) and the Mdiffs density (MDD) for different regions were regressed. Using these results, the urban population for prefectural cities of China was finally estimated. The results showed that a good linear correlation was found between Mdiffs and the census data in each type of region, as all the adjusted R2 values were above 0.9 and all the models passed the significance test (95% confidence level). The ratio of the estimated population to the census population (PER) was between 0.7 and 1.3 for 76% of the cities in China. This is the first attempt to estimate the urban population using building height data for prefectural cities in China. This method produced reasonable results and can be effectively used for spatial distribution estimates of the urban population in large scale areas

Emergency shelters location-allocation problem concerning uncertainty and limited resources: a multi-objective optimization with a case study in the Central area of Beijing, China

The special planning for shelters is an integral part of overall city planning and is a key issue in solving the urban security problem. During the planning of earthquake emergency shelters, it is usually necessary to prioritize the designated shelters to avoid wasting resources. However, in previous research initiatives, special attention has been given to the general location-allocation model without prior consideration of the designated shelters. This article presents a multi-objective supplemental location-allocation optimization model for earthquake emergency shelters that addresses the concerns related to the designated shelters. This model is believed to remain more consistent with the knowledge of shelter planners and policy makers by incorporating the uncertainties of the temporal dynamics of population distribution and the spatially heterogeneous distribution of evacuees under various earthquake damage scenarios by using the elliptical attenuation model for seismic intensity into the location-allocation problem. A case study of the central area of Beijing, China is presented. A modified particle swarm optimization algorithm is applied to solve the supplemental location-allocation model and the general location-allocation model, and the solutions obtained from the two models are then compared. The results show that the solutions of the supplemental location-allocation model significantly minimized the shelter area by prioritizing the designated shelters. By contrast, without prior consideration of the designated shelters, the shelter areas significantly increased, which slightly decreased the evacuation distance in the general location-allocation model. The policy makers could select solutions from the obtained minimal-area scheme using the supplemental location-allocation model that ensures acceptable evacuation distances and minimal budgets by prioritizing the designated shelters during the phased planning of shelters in Beijing