Genetically modified pigs:Emerging animal models for hereditary hearing loss

Hereditary hearing loss(HHL),a genetic disorder that impairs auditory function,significantly affects quality of life and incurs substantial economic losses for society.To investigate the underlying causes of HHL and evaluate therapeutic outcomes,appropriate animal models are necessary.Pigs have been extensively used as valuable large animal models in biomedical research.In this review,we highlight the advantages of pig models in terms of ear anatomy,inner ear morphology,and electrophysiological characteristics,as well as recent advancements in the development of distinct genetically modified porcine models of hearing loss.Additionally,we discuss the prospects,challenges,and recommendations regarding the use pig models in HHL research.Overall,this review provides insights and perspectives for future studies on HHL using porcine models.

Evaluation of volcanic reservoirs with the "QAPM mineral model" using a genetic algorithm

Gas-bearing volcanic reservoirs have been found in the deep Songliao Basin, China. Choosing proper interpretation parameters for log evaluation is difficult due to complicated mineral compositions and variable mineral contents. Based on the QAPF classification scheme given by IUGS, we propose a method to determine the mineral contents of volcanic rocks using log data and a genetic algorithm. According to the QAPF scheme, minerals in volcanic rocks are divided into five groups： Q（quartz）, A （Alkaline feldspar）, P （plagioclase）, M （mafic） and F （feldspathoid）. We propose a model called QAPM including porosity for the volumetric analysis of reservoirs. The log response equations for density, apparent neutron porosity, transit time, gamma ray and volume photoelectrical cross section index were first established with the mineral parameters obtained from the Schlumberger handbook of log mineral parameters. Then the volumes of the four minerals in the matrix were calculated using the genetic algorithm （GA）. The calculated porosity, based on the interpretation parameters, can be compared with core porosity, and the rock names given in the paper based on QAPF classification according to the four mineral contents are compatible with those from the chemical analysis of the core samples.

Dynamic finite element model updating using meta-model and genetic algorithm

Current dynamic finite element model updating methods are not efficient or restricted to the problem of local optima. To circumvent these, a novel updating method which integrates the meta-model and the genetic algorithm is proposed. Experimental design technique is used to determine the best sampling points for the estimation of polynomial coefficients given the order and the number of independent variables. Finite element analyses are performed to generate the sampling data. Regression analysis is then used to estimate the response surface model to approximate the functional relationship between response features and design parameters on the entire design space. In the fitness evaluation of the genetic algorithm, the response surface model is used to substitute the finite element model to output features with given design parameters for the computation of fitness for the individual. Finally, the global optima that corresponds to the updated design parameter is acquired after several generations of evolution. In the application example, finite element analysis and modal testing are performed on a real chassis model. The finite element model is updated using the proposed method. After updating, root-mean-square error of modal frequencies is smaller than 2%. Furthermore, prediction ability of the updated model is validated using the testing results of the modified structure. The root-mean-square error of the prediction errors is smaller than 2%.

Genetic Regression Model for Dam Safety Monitoring

Under-fitting problems usually occur in regression models for dam safety monitoring.To overcome the local convergence of the regression, a genetic algorithm (GA) was proposed using a real parameter coding, a ranking selection operator, an arithmetical crossover operator and a uniform mutation operator, and calculated the least-square error of the observed and computed values as its fitness function. The elitist strategy was used to improve the speed of the convergence. After that, the modified genetic algorithm was applied to reassess the coefficients of the regression model and a genetic regression model was set up. As an example, a slotted gravity dam in the Northeast of China was introduced. The computational results show that the genetic regression model can solve the under-fitting problems perfectly.

Analysis of Genetic Effects of Nuclear-Cytoplasmic Interaction on Quantitative Traits:Genetic Model for Diploid Plants

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction （NCI） as well as their genotype by environment （GE） interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction （AUP） method. Data on four quantitative traits （boll number, lint percentage, fiber length, and micronaire） in Upland cotton （Gossypium hirsutum L.） were analyzed as a worked example to show the effectiveness of the model.

Application of Genetic Algorithm to Solving Nonlinear Model of Aeroengines

Solving the nonlinear model of an aeroengine is converted to an optimization problem, and thus some optimization search methods can be used. An approach to solving the nonlinear model of an aeroengine by use of the genetic algorithm (GA) is developed. By comparison with N R algorithm, the accuracy of the values of initial guesses is not required for GA. Especially, the approach developed can be used when no priori knowledges of the values of initial guesses are availabe, and the convergence is improved significantly. GA properly combined with N R algorithm can increase the convergence speed.

Geochemical characteristics and genetic model of dolomite reservoirs in the eastern margin of the Pre-Caspian Basin

The widespread Carboniferous KT-I dolomite in the eastern margin of the Pre-Caspian Basin is an important hydrocarbon reservoir. The dolomite lithology is dominated by crystalline dolomite. The δ18O values range from -6.71‰ to 2.45‰, and average 0.063‰, obviously larger than -2.5‰, indicating low-temperature dolomite of evaporation origin. Stable strontium isotope ratios （87Sr/86Sr） range from 0.70829 to 0.70875 and average 0.708365, very consistent with 87Sr/86Sr ratios in Carboniferous seawater. Chemical analysis of Ca and Mg elements shows that the dolomite has 9.1 mole% excess Ca or even higher before stabilization. The degree of order of dolomite is medium–slightly poor, varying in a range of 0.336-0.504 and averaging 0.417. It suggests that the dolomite formed under near-surface conditions. There are two models for the origin of the Carboniferous KT-I dolomite reservoir. These are 1） the evaporation concentration – weathering crust model and 2） the shoal facies – seepage reflux model. The former is mainly developed in restricted platforms – evaporate platforms of restricted marine deposition environments with a representation of dolomite associated with gypsum and mudstone. The latter mainly formed in platform edge shoals and intra-platform shoals and is controlled by dolomitization due to high salinity sea water influx from adjacent restricted sea or evaporate platform.

WOMBAT—A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML)

WOMBAT is a software package for quantitative genetic analyses of continuous traits, fitting a linear, mixed model; estimates of covariance components and the resulting genetic parameters are obtained by restricted maximum likelihood. A wide range of models, comprising numerous traits, multiple fixed and random effects, selected genetic covariance structures, random regression models and reduced rank estimation are accommodated. WOMBAT employs up-to-date numerical and computational methods. Together with the use of efficient compilers, this generates fast executable programs, suitable for large scale analyses. Use of WOMBAT is illustrated for a bivariate analysis. The package consists of the executable program, available for LINUX and WINDOWS environments, manual and a set of worked example, and can be downloaded free of charge from http：//agbu. une.edu.au/-kmeyer/wombat.html

Genetic control of flowering time in woody plants： Roses as an emerging model

Genetic control of the timing of flowering in woody plants is complex and has yet to be adequately investigated due to their long life-cycle and difficulties in genetic modification.Studies in Populus,one of the best woody plant models,have revealed a highly conserved genetic network for flowering timing in annuals.However,traits like continuous flowering cannot be addressed with Populus.Roses and strawberries have relatively small,diploid genomes and feature enormous natural variation.With the development of new genetic populations and genomic tools,roses and strawberries have become good models for studying the molecular mechanisms underpinning the regulation of flowering in woody plants.Here,we review findings on the molecular and genetic factors controlling continuous flowering in roses and woodland strawberries.Natural variation at TFL1 orthologous genes in both roses and strawberries seems be the key plausible factor that regulates continuous flowering.However,recent efforts suggest that a two-recessive-loci model may explain the controlling of continuous flowering in roses.We propose that epigenetic factors,including non-coding RNAs or chromatin-related factors,might also play a role.Insights into the genetic control of flowering time variation in roses should benefit the development of new germplasm for woody crops and shed light on the molecular genetic bases for the production and maintenance of plant biodiversity.

A genetic algorithm based stochastic programming model for air quality management

This paper presents a model that can aid planners in defining the total allowable pollutant discharge in the planning region, accounting for the dynamic and stochastic character of meteorological conditions. This is accomplished by integrating Monte Carlo simulation and using genetic algorithm to solve the model. The model is demonstrated by using a realistic air urban scale SO 2 control problem in the Yuxi City of China. To evaluate effectiveness of the model, results of the approach are shown to compare with those of the linear deterministic procedures. This paper also provides a valuable insight into how air quality targets should be made when the air pollutant will not threat the residents' health. Finally, a discussion of the areas for further research are briefly delineated.

Genetic Types and Metallogenic Model for the Polymetallic Copper–Gold Deposits in the Tongling Ore District, Anhui Province, Eastern China

The Tongling ore district is one of the most economically important ore areas in the Middle–Lower Yangtze River Metallogenic Belt, eastern China. It contains hundreds of polymetallic copper–gold deposits and occurrences. Those deposits are mainly clustered(from west to east) within the Tongguanshan, Shizishan, Xinqiao, Fenghuangshan, and Shatanjiao orefields. Until recently, the majority of these deposits were thought to be skarn-or porphyry–skarn-type deposits; however there have been recent discoveries of numerous vein-type Au, Ag, and Pb-Zn deposits that do not fall into either of these categories. This indicates that there is some uncertainty over this classification. Here, we present the results of several systematic geological studies of representative deposits in the Tongling ore district. From investigation of the ore-controlling structures, lithology of the host rock, mineral assemblages, and the characteristics of the mineralization and alteration within these deposits, three genetic types of deposits(skarn-, porphyry-, and vein-type deposits) have been identified. The spatial and temporal relationships between the orebodies and Yanshanian intrusions combined with the sources of the ore-forming fluids and metals, as well as the geodynamic setting of this ore district, indicate that all three deposit types are genetically related each other and constitute a magmatic–hydrothermal system. This study outlines a model that relates the polymetallic copper–gold porphyry-, skarn-, and vein-type deposits within the Tongling ore district. This model provides a theoretical basis to guide exploration for deep-seated and concealed porphyry-type Cu(–Mo, –Au) deposits as well as shallow vein-type Au, Ag, and Pb–Zn deposits in this area and elsewhere.

Application of numerical modeling and genetic programming to estimate rock mass modulus of deformation

Estimation of the rock mass modulus of deformation(Em)is one of the most important design parameters in designing many structures in and on rock.This parameter can be obtained by in situ tests,empirical relations between deformation modulus and rock mass classifcation,and estimating from laboratory tests results.In this paper,a back analysis calculation is performed to present an equation for estimation of the rock mass modulus of deformation using genetic programming(GP)and numerical modeling.A database of 40,960 datasets,including vertical stress(rz),horizontal to vertical stresses ratio(k),Poisson’s ratio(m),radius of circular tunnel(r)and wall displacement of circular tunnel on the horizontal diameter(d)for input parameters and modulus of deformation for output,was established.The selected parameters are easy to determine and rock mass modulus of deformation can be obtained from instrumentation data of any size circular galleries.The resulting RMSE of 0.86 and correlation coeffcient of97%of the proposed equation demonstrated the capability of the computer program(CP)generated by GP.

Genetic Model for Fresh-keeping Character in Sweet Corn

This study was conducted to investigate the genetic regularity of indexes related to freshness keeping and its molecular basis by acquiring 6 generations （P1, P2, F1, B1, B2 and F2） of an inbred line T3 with long freshness period × an inbred line T15 with short freshness period in sweet corn. The genetic analysis of the indexes was performed by major gene＋polygene mixed genetic model combined with the genetic analysis combining six generations.The results showed that the decreasing rate of the postharvest sugar content in the T3 was controlled by two pairs of additive-dominante-epistatic major genes＋additive-dominant polygenes; each segregating generation was affected by its major genes, the heritability of major genes and polygene in the B1 generation was 74.63% and 17.67%, respectively; the heritability of major gene and potygene in the B2 was 91.98% and 0,00%, respectively; and the heritability of major gene and polygene inthe F2 was 82.67%, and 12.93%, respectively.

Linear-in-Parameter Models Based on Parsimonious Genetic Programming Algorithm and Its Application to Aero-Engine Start Modeling

A novel Parsimonious Genetic Programming （PGP） algorithm together with a novel aero-engine optimum data-driven dynamic start process model based on PGP is proposed. In application of this method, first, the traditional Genetic Programming（GP） is used to generate the nonlinear input-output models that are represented in a binary tree structure; then, the Orthogonal Least Squares algorithm （OLS） is used to estimate the contribution of the branches of the tree （refer to basic function term that cannot be decomposed anymore according to special rule） to the accuracy of the model, which contributes to eliminate complex redundant subtrees and enhance GP＇s convergence speed; and finally, a simple, reliable and exact linear-in-parameter nonlinear model via GP evolution is obtained. The real aero-engine start process test data simulation and the comparisons with Support Vector Machines （SVM） validate that the proposed method can generate more applicable, interpretable models and achieve comparable, even superior results to SVM.

Combined Novel Gate Level Model and Critical Primary Input Sharing for Genetic Algorithm Based Maximum Power Supply Noise Estimation

A gate level maximum power supply noise （PSN） model is defined that captures both IR drop and di/dt noise effects. Experimental results show that this model improves PSN estimation by 5.3% on average and reduces computation time by 10.7% compared with previous methods. Furthermore,a primary input critical factor model that captures the extent of primary inputs＇ PSN contribution is formulated. Based on these models,a novel niche genetic algorithm is proposed to estimate PSN more effectively. Compared with general genetic algorithms, this novel method can achieve up to 19.0% improvement on PSN estimation with a much higher convergence speed.

Forward and backward models for fault diagnosis based on parallel genetic algorithms

In this paper, a mathematical model consisting of forward and backward models is built on parallel genetic algorithms (PGAs) for fault diagnosis in a transmission power system. A new method to reduce the scale of fault sections is developed in the forward model and the message passing interface (MPI) approach is chosen to parallel the genetic algorithms by global sin-gle-population master-slave method (GPGAs). The proposed approach is applied to a sample system consisting of 28 sections, 84 protective relays and 40 circuit breakers. Simulation results show that the new model based on GPGAs can achieve very fast computation in online applications of large-scale power systems.

Preset model of bending force for 6-high reversing cold rolling mill based on genetic algorithm

The hydraulic roll-bending device was studied, which was widely used in modem cold rolling mills to regulate the strip flatness. The loaded roll gap crown mathematic model and the strip crown mathematic model of the reversing cold rolling process were established, and the deformation model of roll stack system of the 6-high 1 250 mm high crown （HC） reversing cold rolling mill was built by slit beam method. The simulation results show that, the quadratic component of strip crown decreases nearly linearly with the increase of the work roll bending force, when the shifting value of intermediate roll is determined by the rolling process. From the first pass to the fifth pass of reversing rolling process, the crown controllability of bending force is gradually weakened. Base on analyzing the relationship among the main factors associated with roll-bending force in reversing multi-pass rolling, such as strip width and rolling force, a preset mathematic model of bending force is developed by genetic algorithm. The simulation data demonstrate that the relative deviation of flatness criterions in each rolling pass is improved significantly and the mean relative deviation of all five passes is decreased from 25.1% to 1.7%. The model can keep good shape in multi-pass reversing cold rolling process with the high prediction accuracy and can be used to guide the production process.

Genetic Analysis of Stripe Disease Resistance in Rice Restorer Line C224 Using Major Gene plus Polygene Mixed Effect Model

The inheritance of stripe disease resistance in a rice restorer line C224 was analyzed using the mixed effect model of major gene plus polygene for quantitative traits.In addition,the resistance was investigated in seven crosses of C224 with maintainer lines.The results showed that the stripe resistance of C224 was controlled by two major genes with additive-dominance-epistasis effects plus polygenes with additive-dominance effects （E-1 model）.These two genes had additive effects of-12.47% and-24.75%,respectively,showing negative dominance effects.There were significant epistasis and interaction effects between the two major genes.The heritability of the two major genes was 92.12%,while that of polygenes was 2.74%,indicating that the stripe resistance had dominant major gene effect.Of the seven crosses,five displayed high or medium resistance to the stripe disease.

Use of genetic algorithm in new approach to modeling of flood routing

The hydrological models and simpli?ed methods of Saint-venant equations are used extensively in hydrological modeling, in particular for the simulation of the ?ood routing. These models require speci?c and extensive data that usually makes the study of ?ood propagation an arduous practice. We present in this work a new model, based on a transfer function, this function is a function of parametric probability density, having a physical meaning with respect to the propagation of a hydrological signal. The inversion of the model is carried out by an optimization technique called Genetic Algorithm. It consists of evolving a population of parameters based primarily on genetic recombination operators and natural selection to?nd the minimum of an objective function that measures the distance between observed and simulated data. The precision of the simulations of the proposed model is compared with the response of the Hayami model and the applicability of the model is tested on a real case, the N'Fis basin river, located in the High Atlas Occidental, which presents elements that appear favorable to the study of the propagation. The results obtained are very satisfactory and the simulation of the proposed model is very close to the response of the Hayami model.

RECONFIGURABLE PRODUCTION LINE MODELING AND SCHEDULING USING PETRI NETS AND GENETIC ALGORITHM

In response to the production capacity and functionality variations, a genetic algorithm （GA） embedded with deterministic timed Petri nets（DTPN） for reconfigurable production line（RPL） is proposed to solve its scheduling problem. The basic DTPN modules are presented to model the corresponding variable structures in RPL, and then the scheduling model of the whole RPL is constructed. And in the scheduling algorithm, firing sequences of the Petri nets model are used as chromosomes, thus the selection, crossover, and mutation operator do not deal with the elements in the problem space, but the elements of Petri nets model. Accordingly, all the algorithms for GA operations embedded with Petri nets model are proposed. Moreover, the new weighted single-objective optimization based on reconfiguration cost and E/T is used. The results of a DC motor RPL scheduling suggest that the presented DTPN-GA scheduling algorithm has a significant impact on RPL scheduling, and provide obvious improvements over the conventional scheduling method in practice that meets duedate, minimizes reconfiguration cost, and enhances cost effectivity.