Feature Selection in Classification of Eye Movements Using Electrooculography for Activity Recognition

PubMed Central

Mala, S.; Latha, K.

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition. PMID:25574185

Feature selection in classification of eye movements using electrooculography for activity recognition.

PubMed

Mala, S; Latha, K

2014-01-01

Activity recognition is needed in different requisition, for example, reconnaissance system, patient monitoring, and human-computer interfaces. Feature selection plays an important role in activity recognition, data mining, and machine learning. In selecting subset of features, an efficient evolutionary algorithm Differential Evolution (DE), a very efficient optimizer, is used for finding informative features from eye movements using electrooculography (EOG). Many researchers use EOG signals in human-computer interactions with various computational intelligence methods to analyze eye movements. The proposed system involves analysis of EOG signals using clearness based features, minimum redundancy maximum relevance features, and Differential Evolution based features. This work concentrates more on the feature selection algorithm based on DE in order to improve the classification for faultless activity recognition.

Stochastic Evolution Equations Driven by Fractional Noises

DTIC Science & Technology

2016-11-28

rate of convergence to zero or the error and the limit in distribution of the error fluctuations. We have studied time discrete numerical schemes...error fluctuations. We have studied time discrete numerical schemes based on Taylor expansions for rough differential equations and for stochastic...variations of the time discrete Taylor schemes for rough differential equations and for stochastic differential equations driven by fractional Brownian

Differential evolution-based multi-objective optimization for the definition of a health indicator for fault diagnostics and prognostics

NASA Astrophysics Data System (ADS)

Baraldi, P.; Bonfanti, G.; Zio, E.

2018-03-01

The identification of the current degradation state of an industrial component and the prediction of its future evolution is a fundamental step for the development of condition-based and predictive maintenance approaches. The objective of the present work is to propose a general method for extracting a health indicator to measure the amount of component degradation from a set of signals measured during operation. The proposed method is based on the combined use of feature extraction techniques, such as Empirical Mode Decomposition and Auto-Associative Kernel Regression, and a multi-objective Binary Differential Evolution (BDE) algorithm for selecting the subset of features optimal for the definition of the health indicator. The objectives of the optimization are desired characteristics of the health indicator, such as monotonicity, trendability and prognosability. A case study is considered, concerning the prediction of the remaining useful life of turbofan engines. The obtained results confirm that the method is capable of extracting health indicators suitable for accurate prognostics.

Cloud computing task scheduling strategy based on differential evolution and ant colony optimization

NASA Astrophysics Data System (ADS)

Ge, Junwei; Cai, Yu; Fang, Yiqiu

2018-05-01

This paper proposes a task scheduling strategy DEACO based on the combination of Differential Evolution (DE) and Ant Colony Optimization (ACO), aiming at the single problem of optimization objective in cloud computing task scheduling, this paper combines the shortest task completion time, cost and load balancing. DEACO uses the solution of the DE to initialize the initial pheromone of ACO, reduces the time of collecting the pheromone in ACO in the early, and improves the pheromone updating rule through the load factor. The proposed algorithm is simulated on cloudsim, and compared with the min-min and ACO. The experimental results show that DEACO is more superior in terms of time, cost, and load.

[Feature extraction for breast cancer data based on geometric algebra theory and feature selection using differential evolution].

PubMed

Li, Jing; Hong, Wenxue

2014-12-01

The feature extraction and feature selection are the important issues in pattern recognition. Based on the geometric algebra representation of vector, a new feature extraction method using blade coefficient of geometric algebra was proposed in this study. At the same time, an improved differential evolution (DE) feature selection method was proposed to solve the elevated high dimension issue. The simple linear discriminant analysis was used as the classifier. The result of the 10-fold cross-validation (10 CV) classification of public breast cancer biomedical dataset was more than 96% and proved superior to that of the original features and traditional feature extraction method.

An Enhanced Differential Evolution Algorithm Based on Multiple Mutation Strategies.

PubMed

Xiang, Wan-li; Meng, Xue-lei; An, Mei-qing; Li, Yin-zhen; Gao, Ming-xia

2015-01-01

Differential evolution algorithm is a simple yet efficient metaheuristic for global optimization over continuous spaces. However, there is a shortcoming of premature convergence in standard DE, especially in DE/best/1/bin. In order to take advantage of direction guidance information of the best individual of DE/best/1/bin and avoid getting into local trap, based on multiple mutation strategies, an enhanced differential evolution algorithm, named EDE, is proposed in this paper. In the EDE algorithm, an initialization technique, opposition-based learning initialization for improving the initial solution quality, and a new combined mutation strategy composed of DE/current/1/bin together with DE/pbest/bin/1 for the sake of accelerating standard DE and preventing DE from clustering around the global best individual, as well as a perturbation scheme for further avoiding premature convergence, are integrated. In addition, we also introduce two linear time-varying functions, which are used to decide which solution search equation is chosen at the phases of mutation and perturbation, respectively. Experimental results tested on twenty-five benchmark functions show that EDE is far better than the standard DE. In further comparisons, EDE is compared with other five state-of-the-art approaches and related results show that EDE is still superior to or at least equal to these methods on most of benchmark functions.

Multiple Active Contours Guided by Differential Evolution for Medical Image Segmentation

PubMed Central

Cruz-Aceves, I.; Avina-Cervantes, J. G.; Lopez-Hernandez, J. M.; Rostro-Gonzalez, H.; Garcia-Capulin, C. H.; Torres-Cisneros, M.; Guzman-Cabrera, R.

2013-01-01

This paper presents a new image segmentation method based on multiple active contours guided by differential evolution, called MACDE. The segmentation method uses differential evolution over a polar coordinate system to increase the exploration and exploitation capabilities regarding the classical active contour model. To evaluate the performance of the proposed method, a set of synthetic images with complex objects, Gaussian noise, and deep concavities is introduced. Subsequently, MACDE is applied on datasets of sequential computed tomography and magnetic resonance images which contain the human heart and the human left ventricle, respectively. Finally, to obtain a quantitative and qualitative evaluation of the medical image segmentations compared to regions outlined by experts, a set of distance and similarity metrics has been adopted. According to the experimental results, MACDE outperforms the classical active contour model and the interactive Tseng method in terms of efficiency and robustness for obtaining the optimal control points and attains a high accuracy segmentation. PMID:23983809

Enhanced differential evolution to combine optical mouse sensor with image structural patches for robust endoscopic navigation.

PubMed

Luo, Xiongbiao; Jayarathne, Uditha L; McLeod, A Jonathan; Mori, Kensaku

2014-01-01

Endoscopic navigation generally integrates different modalities of sensory information in order to continuously locate an endoscope relative to suspicious tissues in the body during interventions. Current electromagnetic tracking techniques for endoscopic navigation have limited accuracy due to tissue deformation and magnetic field distortion. To avoid these limitations and improve the endoscopic localization accuracy, this paper proposes a new endoscopic navigation framework that uses an optical mouse sensor to measure the endoscope movements along its viewing direction. We then enhance the differential evolution algorithm by modifying its mutation operation. Based on the enhanced differential evolution method, these movement measurements and image structural patches in endoscopic videos are fused to accurately determine the endoscope position. An evaluation on a dynamic phantom demonstrated that our method provides a more accurate navigation framework. Compared to state-of-the-art methods, it improved the navigation accuracy from 2.4 to 1.6 mm and reduced the processing time from 2.8 to 0.9 seconds.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift.

PubMed

Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

2014-11-01

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. © 2014 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift

PubMed Central

Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

2014-01-01

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. PMID:25244680

Wavelength Selection Method Based on Differential Evolution for Precise Quantitative Analysis Using Terahertz Time-Domain Spectroscopy.

PubMed

Li, Zhi; Chen, Weidong; Lian, Feiyu; Ge, Hongyi; Guan, Aihong

2017-12-01

Quantitative analysis of component mixtures is an important application of terahertz time-domain spectroscopy (THz-TDS) and has attracted broad interest in recent research. Although the accuracy of quantitative analysis using THz-TDS is affected by a host of factors, wavelength selection from the sample's THz absorption spectrum is the most crucial component. The raw spectrum consists of signals from the sample and scattering and other random disturbances that can critically influence the quantitative accuracy. For precise quantitative analysis using THz-TDS, the signal from the sample needs to be retained while the scattering and other noise sources are eliminated. In this paper, a novel wavelength selection method based on differential evolution (DE) is investigated. By performing quantitative experiments on a series of binary amino acid mixtures using THz-TDS, we demonstrate the efficacy of the DE-based wavelength selection method, which yields an error rate below 5%.

Efficient hybrid evolutionary algorithm for optimization of a strip coiling process

NASA Astrophysics Data System (ADS)

Pholdee, Nantiwat; Park, Won-Woong; Kim, Dong-Kyu; Im, Yong-Taek; Bureerat, Sujin; Kwon, Hyuck-Cheol; Chun, Myung-Sik

2015-04-01

This article proposes an efficient metaheuristic based on hybridization of teaching-learning-based optimization and differential evolution for optimization to improve the flatness of a strip during a strip coiling process. Differential evolution operators were integrated into the teaching-learning-based optimization with a Latin hypercube sampling technique for generation of an initial population. The objective function was introduced to reduce axial inhomogeneity of the stress distribution and the maximum compressive stress calculated by Love's elastic solution within the thin strip, which may cause an irregular surface profile of the strip during the strip coiling process. The hybrid optimizer and several well-established evolutionary algorithms (EAs) were used to solve the optimization problem. The comparative studies show that the proposed hybrid algorithm outperformed other EAs in terms of convergence rate and consistency. It was found that the proposed hybrid approach was powerful for process optimization, especially with a large-scale design problem.

Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation

PubMed Central

Wu, Chia-Chou; Lin, Che

2015-01-01

The induction of stem cells toward a desired differentiation direction is required for the advancement of stem cell-based therapies. Despite successful demonstrations of the control of differentiation direction, the effective use of stem cell-based therapies suffers from a lack of systematic knowledge regarding the mechanisms underlying directed differentiation. Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. A proposed relevance score identified the essential components in the directed differentiation. Inspection of well-known proteins and functional modules in the directed differentiation showed the plausibility of the proposed relevance score, with the higher scores of several proteins and function modules indicating their essential roles in the directed differentiation. During the differentiation process, the proteins and functional modules with higher relevance scores also became more specific to the neuronal identity. Ultimately, the essential components revealed by the relevance scores may play a role in controlling the direction of differentiation. In addition, these components may serve as a starting point for understanding the systematic mechanisms of directed differentiation and for increasing the efficiency of stem cell-based therapies. PMID:25977693

Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes

PubMed Central

Matias Rodrigues, João F.; Rankin, Daniel J.; Rossetti, Valentina; Wagner, Andreas; Bagheri, Homayoun C.

2012-01-01

Multicellular differentiated organisms are composed of cells that begin by developing from a single pluripotent germ cell. In many organisms, a proportion of cells differentiate into specialized somatic cells. Whether these cells lose their pluripotency or are able to reverse their differentiated state has important consequences. Reversibly differentiated cells can potentially regenerate parts of an organism and allow reproduction through fragmentation. In many organisms, however, somatic differentiation is terminal, thereby restricting the developmental paths to reproduction. The reason why terminal differentiation is a common developmental strategy remains unexplored. To understand the conditions that affect the evolution of terminal versus reversible differentiation, we developed a computational model inspired by differentiating cyanobacteria. We simulated the evolution of a population of two cell types –nitrogen fixing or photosynthetic– that exchange resources. The traits that control differentiation rates between cell types are allowed to evolve in the model. Although the topology of cell interactions and differentiation costs play a role in the evolution of terminal and reversible differentiation, the most important factor is the difference in division rates between cell types. Faster dividing cells always evolve to become the germ line. Our results explain why most multicellular differentiated cyanobacteria have terminally differentiated cells, while some have reversibly differentiated cells. We further observed that symbioses involving two cooperating lineages can evolve under conditions where aggregate size, connectivity, and differentiation costs are high. This may explain why plants engage in symbiotic interactions with diazotrophic bacteria. PMID:22511858

Adaptive grid based multi-objective Cauchy differential evolution for stochastic dynamic economic emission dispatch with wind power uncertainty

PubMed Central

Lei, Xiaohui; Wang, Chao; Yue, Dong; Xie, Xiangpeng

2017-01-01

Since wind power is integrated into the thermal power operation system, dynamic economic emission dispatch (DEED) has become a new challenge due to its uncertain characteristics. This paper proposes an adaptive grid based multi-objective Cauchy differential evolution (AGB-MOCDE) for solving stochastic DEED with wind power uncertainty. To properly deal with wind power uncertainty, some scenarios are generated to simulate those possible situations by dividing the uncertainty domain into different intervals, the probability of each interval can be calculated using the cumulative distribution function, and a stochastic DEED model can be formulated under different scenarios. For enhancing the optimization efficiency, Cauchy mutation operation is utilized to improve differential evolution by adjusting the population diversity during the population evolution process, and an adaptive grid is constructed for retaining diversity distribution of Pareto front. With consideration of large number of generated scenarios, the reduction mechanism is carried out to decrease the scenarios number with covariance relationships, which can greatly decrease the computational complexity. Moreover, the constraint-handling technique is also utilized to deal with the system load balance while considering transmission loss among thermal units and wind farms, all the constraint limits can be satisfied under the permitted accuracy. After the proposed method is simulated on three test systems, the obtained results reveal that in comparison with other alternatives, the proposed AGB-MOCDE can optimize the DEED problem while handling all constraint limits, and the optimal scheme of stochastic DEED can decrease the conservation of interval optimization, which can provide a more valuable optimal scheme for real-world applications. PMID:28961262

Evidence of correlated evolution and adaptive differentiation of stem and leaf functional traits in the herbaceous genus, Helianthus.

PubMed

Pilote, Alex J; Donovan, Lisa A

2016-12-01

Patterns of plant stem traits are expected to align with a "fast-slow" plant economic spectrum across taxa. Although broad patterns support such tradeoffs in field studies, tests of hypothesized correlated trait evolution and adaptive differentiation are more robust when taxa relatedness and environment are taken into consideration. Here we test for correlated evolution of stem and leaf traits and their adaptive differentiation across environments in the herbaceous genus, Helianthus. Stem and leaf traits of 14 species of Helianthus (28 populations) were assessed in a common garden greenhouse study. Phylogenetically independent contrasts were used to test for evidence of correlated evolution of stem hydraulic and biomechanical properties, correlated evolution of stem and leaf traits, and adaptive differentiation associated with source habitat environments. Among stem traits, there was evidence for correlated evolution of some hydraulic and biomechanical properties, supporting an expected tradeoff between stem theoretical hydraulic efficiency and resistance to bending stress. Population differentiation for suites of stem and leaf traits was found to be consistent with a "fast-slow" resource-use axis for traits related to water transport and use. Associations of population traits with source habitat characteristics supported repeated evolution of a resource-acquisitive "drought-escape" strategy in arid environments. This study provides evidence of correlated evolution of stem and leaf traits consistent with the fast-slow spectrum of trait combinations related to water transport and use along the stem-to-leaf pathway. Correlations of traits with source habitat characteristics further indicate that the correlated evolution is associated, at least in part, with adaptive differentiation of Helianthus populations among native habitats differing in climate. © 2016 Botanical Society of America.

Time Evolution of Modeled Reynolds Stresses in Planar Homogeneous Flows

NASA Technical Reports Server (NTRS)

Jongen, T.; Gatski, T. B.

1997-01-01

The analytic expression of the time evolution of the Reynolds stress anisotropy tensor in all planar homogeneous flows is obtained by exact integration of the modeled differential Reynolds stress equations. The procedure is based on results of tensor representation theory, is applicable for general pressure-strain correlation tensors, and can account for any additional turbulence anisotropy effects included in the closure. An explicit solution of the resulting system of scalar ordinary differential equations is obtained for the case of a linear pressure-strain correlation tensor. The properties of this solution are discussed, and the dynamic behavior of the Reynolds stresses is studied, including limit cycles and sensitivity to initial anisotropies.

A Self Adaptive Differential Evolution Algorithm for Global Optimization

NASA Astrophysics Data System (ADS)

Kumar, Pravesh; Pant, Millie

This paper presents a new Differential Evolution algorithm based on hybridization of adaptive control parameters and trigonometric mutation. First we propose a self adaptive DE named ADE where choice of control parameter F and Cr is not fixed at some constant value but is taken iteratively. The proposed algorithm is further modified by applying trigonometric mutation in it and the corresponding algorithm is named as ATDE. The performance of ATDE is evaluated on the set of 8 benchmark functions and the results are compared with the classical DE algorithm in terms of average fitness function value, number of function evaluations, convergence time and success rate. The numerical result shows the competence of the proposed algorithm.

Concepts in solid tumor evolution.

PubMed

Sidow, Arend; Spies, Noah

2015-04-01

Evolutionary mechanisms in cancer progression give tumors their individuality. Cancer evolution is different from organismal evolution, however, and we discuss where concepts from evolutionary genetics are useful or limited in facilitating an understanding of cancer. Based on these concepts we construct and apply the simplest plausible model of tumor growth and progression. Simulations using this simple model illustrate the importance of stochastic events early in tumorigenesis, highlight the dominance of exponential growth over linear growth and differentiation, and explain the clonal substructure of tumors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conspecific Crop-Weed Introgression Influences Evolution of Weedy Rice (Oryza sativa f. spontanea) across a Geographical Range

PubMed Central

Xia, Han-Bing; Wang, Wei; Xia, Hui; Zhao, Wei; Lu, Bao-Rong

2011-01-01

Background Introgression plays an important role in evolution of plant species via its influences on genetic diversity and differentiation. Outcrossing determines the level of introgression but little is known about the relationships of outcrossing rates, genetic diversity, and differentiation particularly in a weedy taxon that coexists with its conspecific crop. Methodology/Principal Findings Eleven weedy rice (Oryza sativa f. spontanea) populations from China were analyzed using microsatellite (SSR) fingerprints to study outcrossing rate and its relationship with genetic variability and differentiation. To estimate outcrossing, six highly polymorphic SSR loci were used to analyze >5500 progeny from 216 weedy rice families, applying a mixed mating model; to estimate genetic diversity and differentiation, 22 SSR loci were analyzed based on 301 weedy individuals. Additionally, four weed-crop shared SSR loci were used to estimate the influence of introgression from rice cultivars on weedy rice differentiation. Outcrossing rates varied significantly (0.4∼11.7%) among weedy rice populations showing relatively high overall Nei's genetic diversity (0.635). The observed heterozygosity was significantly correlated with outcrossing rates among populations (r2 = 0.783; P<0.001) although no obvious correlation between outcrossing rates and genetic diversity parameters was observed. Allelic introgression from rice cultivars to their coexisting weedy rice was detected. Weedy rice populations demonstrated considerable genetic differentiation that was correlated with their spatial distribution (r2 = 0.734; P<0.001), and possibly also influenced by the introgression from rice cultivars. Conclusions/Significance Outcrossing rates can significantly affect heterozygosity of populations, which may shape the evolutionary potential of weedy rice. Introgression from the conspecific crop rice can influence the genetic differentiation and possibly evolution of its coexisting weedy rice populations. PMID:21249201

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles.

PubMed

van Gestel, Jordi; Nowak, Martin A

2016-02-01

Most bacteria live in colonies, where they often express different cell types. The ecological significance of these cell types and their evolutionary origin are often unknown. Here, we study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a 'sticky' cell type that is required for surface attachment, but is costly to express. The sticky cells not only facilitate their own attachment, but also that of non-sticky cells. Using individual-based simulations, we show that surface colonization rapidly evolves and in most cases leads to phenotypic heterogeneity, in which sticky and non-sticky cells occur side by side on the surface. In the presence of regulation, cell differentiation leads to a remarkable set of bacterial life cycles, in which cells alternate between living in the liquid and living on the surface. The dominant life stage is formed by the surface-attached colony that shows many complex features: colonies reproduce via fission and by producing migratory propagules; cells inside the colony divide labour; and colonies can produce filaments to facilitate expansion. Overall, our model illustrates how the evolution of an adhesive cell type goes hand in hand with the evolution of complex bacterial life cycles.

A Differential Evolution-Based Routing Algorithm for Environmental Monitoring Wireless Sensor Networks

PubMed Central

Li, Xiaofang; Xu, Lizhong; Wang, Huibin; Song, Jie; Yang, Simon X.

2010-01-01

The traditional Low Energy Adaptive Cluster Hierarchy (LEACH) routing protocol is a clustering-based protocol. The uneven selection of cluster heads results in premature death of cluster heads and premature blind nodes inside the clusters, thus reducing the overall lifetime of the network. With a full consideration of information on energy and distance distribution of neighboring nodes inside the clusters, this paper proposes a new routing algorithm based on differential evolution (DE) to improve the LEACH routing protocol. To meet the requirements of monitoring applications in outdoor environments such as the meteorological, hydrological and wetland ecological environments, the proposed algorithm uses the simple and fast search features of DE to optimize the multi-objective selection of cluster heads and prevent blind nodes for improved energy efficiency and system stability. Simulation results show that the proposed new LEACH routing algorithm has better performance, effectively extends the working lifetime of the system, and improves the quality of the wireless sensor networks. PMID:22219670

Optimization of the p-xylene oxidation process by a multi-objective differential evolution algorithm with adaptive parameters co-derived with the population-based incremental learning algorithm

NASA Astrophysics Data System (ADS)

Guo, Zhan; Yan, Xuefeng

2018-04-01

Different operating conditions of p-xylene oxidation have different influences on the product, purified terephthalic acid. It is necessary to obtain the optimal combination of reaction conditions to ensure the quality of the products, cut down on consumption and increase revenues. A multi-objective differential evolution (MODE) algorithm co-evolved with the population-based incremental learning (PBIL) algorithm, called PBMODE, is proposed. The PBMODE algorithm was designed as a co-evolutionary system. Each individual has its own parameter individual, which is co-evolved by PBIL. PBIL uses statistical analysis to build a model based on the corresponding symbiotic individuals of the superior original individuals during the main evolutionary process. The results of simulations and statistical analysis indicate that the overall performance of the PBMODE algorithm is better than that of the compared algorithms and it can be used to optimize the operating conditions of the p-xylene oxidation process effectively and efficiently.

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Battery parameterisation based on differential evolution via a boundary evolution strategy

NASA Astrophysics Data System (ADS)

Yang, Guangya

2014-01-01

Attention has been given to the battery modelling in the electric engineering field following the current development of renewable energy and electrification of transportation. The establishment of the equivalent circuit model of the battery requires data preparation and parameterisation. Besides, as the equivalent circuit model is an abstract map of the battery electric characteristics, the determination of the possible ranges of parameters can be a challenging task. In this paper, an efficient yet easy to implement method is proposed to parameterise the equivalent circuit model of batteries utilising the advances of evolutionary algorithms (EAs). Differential evolution (DE) is selected and modified to parameterise an equivalent circuit model of lithium-ion batteries. A boundary evolution strategy (BES) is developed and incorporated into the DE to update the parameter boundaries during the parameterisation. The method can parameterise the model without extensive data preparation. In addition, the approach can also estimate the initial SOC and the available capacity. The efficiency of the approach is verified through two battery packs, one is an 8-cell battery module and one from an electrical vehicle.

Analysis of high-order SNP barcodes in mitochondrial D-loop for chronic dialysis susceptibility.

PubMed

Yang, Cheng-Hong; Lin, Yu-Da; Chuang, Li-Yeh; Chang, Hsueh-Wei

2016-10-01

Positively identifying disease-associated single nucleotide polymorphism (SNP) markers in genome-wide studies entails the complex association analysis of a huge number of SNPs. Such large numbers of SNP barcode (SNP/genotype combinations) continue to pose serious computational challenges, especially for high-dimensional data. We propose a novel exploiting SNP barcode method based on differential evolution, termed IDE (improved differential evolution). IDE uses a "top combination strategy" to improve the ability of differential evolution to explore high-order SNP barcodes in high-dimensional data. We simulate disease data and use real chronic dialysis data to test four global optimization algorithms. In 48 simulated disease models, we show that IDE outperforms existing global optimization algorithms in terms of exploring ability and power to detect the specific SNP/genotype combinations with a maximum difference between cases and controls. In real data, we show that IDE can be used to evaluate the relative effects of each individual SNP on disease susceptibility. IDE generated significant SNP barcode with less computational complexity than the other algorithms, making IDE ideally suited for analysis of high-order SNP barcodes. Copyright © 2016 Elsevier Inc. All rights reserved.

The fine-scale genetic structure and evolution of the Japanese population.

PubMed

Takeuchi, Fumihiko; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua; Teo, Yik-Ying; Kato, Norihiro

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups-Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

Progressive Recombination Suppression and Differentiation in Recently Evolved Neo-sex Chromosomes

PubMed Central

Natri, Heini M.; Shikano, Takahito; Merilä, Juha

2013-01-01

Recombination suppression leads to the structural and functional differentiation of sex chromosomes and is thus a crucial step in the process of sex chromosome evolution. Despite extensive theoretical work, the exact processes and mechanisms of recombination suppression and differentiation are not well understood. In threespine sticklebacks (Gasterosteus aculeatus), a different sex chromosome system has recently evolved by a fusion between the Y chromosome and an autosome in the Japan Sea lineage, which diverged from the ancestor of other lineages approximately 2 Ma. We investigated the evolutionary dynamics and differentiation processes of sex chromosomes based on comparative analyses of these divergent lineages using 63 microsatellite loci. Both chromosome-wide differentiation patterns and phylogenetic inferences with X and Y alleles indicated that the ancestral sex chromosomes were extensively differentiated before the divergence of these lineages. In contrast, genetic differentiation appeared to have proceeded only in a small region of the neo-sex chromosomes. The recombination maps constructed for the Japan Sea lineage indicated that recombination has been suppressed or reduced over a large region spanning the ancestral and neo-sex chromosomes. Chromosomal regions exhibiting genetic differentiation and suppressed or reduced recombination were detected continuously and sequentially in the neo-sex chromosomes, suggesting that differentiation has gradually spread from the fusion point following the extension of recombination suppression. Our study illustrates an ongoing process of sex chromosome differentiation, providing empirical support for the theoretical model postulating that recombination suppression and differentiation proceed in a gradual manner in the very early stage of sex chromosome evolution. PMID:23436913

The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

NASA Astrophysics Data System (ADS)

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-08-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

Differential Cloud Particles Evolution Algorithm Based on Data-Driven Mechanism for Applications of ANN

PubMed Central

2017-01-01

Computational scientists have designed many useful algorithms by exploring a biological process or imitating natural evolution. These algorithms can be used to solve engineering optimization problems. Inspired by the change of matter state, we proposed a novel optimization algorithm called differential cloud particles evolution algorithm based on data-driven mechanism (CPDD). In the proposed algorithm, the optimization process is divided into two stages, namely, fluid stage and solid stage. The algorithm carries out the strategy of integrating global exploration with local exploitation in fluid stage. Furthermore, local exploitation is carried out mainly in solid stage. The quality of the solution and the efficiency of the search are influenced greatly by the control parameters. Therefore, the data-driven mechanism is designed for obtaining better control parameters to ensure good performance on numerical benchmark problems. In order to verify the effectiveness of CPDD, numerical experiments are carried out on all the CEC2014 contest benchmark functions. Finally, two application problems of artificial neural network are examined. The experimental results show that CPDD is competitive with respect to other eight state-of-the-art intelligent optimization algorithms. PMID:28761438

Global biogeography and evolution of Cuvierina pteropods.

PubMed

Burridge, Alice K; Goetze, Erica; Raes, Niels; Huisman, Jef; Peijnenburg, Katja T C A

2015-03-12

Shelled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic variation in pteropods belonging to the genus Cuvierina in relation to their biogeographic distribution across the world's oceans. We aimed to assess species boundaries and to reconstruct their evolutionary history. We distinguished six morphotypes based on geometric morphometric analyses of shells from 926 museum and 113 fresh specimens. These morphotypes have distinct geographic distributions across the Atlantic, Pacific and Indian oceans, and belong to three major genetic clades based on COI and 28S DNA sequence data. Using a fossil-calibrated phylogeny, we estimated that these clades separated in the Late Oligocene and Early to Middle Miocene. We found evidence for ecological differentiation among all morphotypes based on ecological niche modelling with sea surface temperature, salinity and phytoplankton biomass as primary determinants. Across all analyses, we found highly congruent patterns of differentiation suggesting species level divergences between morphotypes. However, we also found distinct morphotypes (e.g. in the Atlantic Ocean) that were ecologically, but not genetically differentiated. Given the distinct ecological and phenotypic specializations found among both described and undescribed Cuvierina taxa, they may not respond equally to future ocean changes and may not be equally sensitive to ocean acidification. Our findings support the view that ecological differentiation may be an important driving force in the speciation of zooplankton.

Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution.

PubMed

Tang, Min; Zhao, Rui; van de Velde, Helgi; Tross, Jennifer G; Mitsiades, Constantine; Viselli, Suzanne; Neuwirth, Rachel; Esseltine, Dixie-Lee; Anderson, Kenneth; Ghobrial, Irene M; San Miguel, Jesús F; Richardson, Paul G; Tomasson, Michael H; Michor, Franziska

2016-08-15

Since the pioneering work of Salmon and Durie, quantitative measures of tumor burden in multiple myeloma have been used to make clinical predictions and model tumor growth. However, such quantitative analyses have not yet been performed on large datasets from trials using modern chemotherapy regimens. We analyzed a large set of tumor response data from three randomized controlled trials of bortezomib-based chemotherapy regimens (total sample size n = 1,469 patients) to establish and validate a novel mathematical model of multiple myeloma cell dynamics. Treatment dynamics in newly diagnosed patients were most consistent with a model postulating two tumor cell subpopulations, "progenitor cells" and "differentiated cells." Differential treatment responses were observed with significant tumoricidal effects on differentiated cells and less clear effects on progenitor cells. We validated this model using a second trial of newly diagnosed patients and a third trial of refractory patients. When applying our model to data of relapsed patients, we found that a hybrid model incorporating both a differentiation hierarchy and clonal evolution best explains the response patterns. The clinical data, together with mathematical modeling, suggest that bortezomib-based therapy exerts a selection pressure on myeloma cells that can shape the disease phenotype, thereby generating further inter-patient variability. This model may be a useful tool for improving our understanding of disease biology and the response to chemotherapy regimens. Clin Cancer Res; 22(16); 4206-14. ©2016 AACR. ©2016 American Association for Cancer Research.

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles

PubMed Central

van Gestel, Jordi; Nowak, Martin A.

2016-01-01

Most bacteria live in colonies, where they often express different cell types. The ecological significance of these cell types and their evolutionary origin are often unknown. Here, we study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a ‘sticky’ cell type that is required for surface attachment, but is costly to express. The sticky cells not only facilitate their own attachment, but also that of non-sticky cells. Using individual-based simulations, we show that surface colonization rapidly evolves and in most cases leads to phenotypic heterogeneity, in which sticky and non-sticky cells occur side by side on the surface. In the presence of regulation, cell differentiation leads to a remarkable set of bacterial life cycles, in which cells alternate between living in the liquid and living on the surface. The dominant life stage is formed by the surface-attached colony that shows many complex features: colonies reproduce via fission and by producing migratory propagules; cells inside the colony divide labour; and colonies can produce filaments to facilitate expansion. Overall, our model illustrates how the evolution of an adhesive cell type goes hand in hand with the evolution of complex bacterial life cycles. PMID:26894881

Bell-polynomial approach and Wronskian determinant solutions for three sets of differential-difference nonlinear evolution equations with symbolic computation

NASA Astrophysics Data System (ADS)

Qin, Bo; Tian, Bo; Wang, Yu-Feng; Shen, Yu-Jia; Wang, Ming

2017-10-01

Under investigation in this paper are the Belov-Chaltikian (BC), Leznov and Blaszak-Marciniak (BM) lattice equations, which are associated with the conformal field theory, UToda(m_1,m_2) system and r-matrix, respectively. With symbolic computation, the Bell-polynomial approach is developed to directly bilinearize those three sets of differential-difference nonlinear evolution equations (NLEEs). This Bell-polynomial approach does not rely on any dependent variable transformation, which constitutes the key step and main difficulty of the Hirota bilinear method, and thus has the advantage in the bilinearization of the differential-difference NLEEs. Based on the bilinear forms obtained, the N-soliton solutions are constructed in terms of the N × N Wronskian determinant. Graphic illustrations demonstrate that those solutions, more general than the existing results, permit some new properties, such as the solitonic propagation and interactions for the BC lattice equations, and the nonnegative dark solitons for the BM lattice equations.

Study of the fractional order proportional integral controller for the permanent magnet synchronous motor based on the differential evolution algorithm.

PubMed

Zheng, Weijia; Pi, Youguo

2016-07-01

A tuning method of the fractional order proportional integral speed controller for a permanent magnet synchronous motor is proposed in this paper. Taking the combination of the integral of time and absolute error and the phase margin as the optimization index, the robustness specification as the constraint condition, the differential evolution algorithm is applied to search the optimal controller parameters. The dynamic response performance and robustness of the obtained optimal controller are verified by motor speed-tracking experiments on the motor speed control platform. Experimental results show that the proposed tuning method can enable the obtained control system to achieve both the optimal dynamic response performance and the robustness to gain variations. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Differential Evolution Based IDWNN Controller for Fault Ride-Through of Grid-Connected Doubly Fed Induction Wind Generators

PubMed Central

Manonmani, N.; Subbiah, V.; Sivakumar, L.

2015-01-01

The key objective of wind turbine development is to ensure that output power is continuously increased. It is authenticated that wind turbines (WTs) supply the necessary reactive power to the grid at the time of fault and after fault to aid the flowing grid voltage. At this juncture, this paper introduces a novel heuristic based controller module employing differential evolution and neural network architecture to improve the low-voltage ride-through rate of grid-connected wind turbines, which are connected along with doubly fed induction generators (DFIGs). The traditional crowbar-based systems were basically applied to secure the rotor-side converter during the occurrence of grid faults. This traditional controller is found not to satisfy the desired requirement, since DFIG during the connection of crowbar acts like a squirrel cage module and absorbs the reactive power from the grid. This limitation is taken care of in this paper by introducing heuristic controllers that remove the usage of crowbar and ensure that wind turbines supply necessary reactive power to the grid during faults. The controller is designed in this paper to enhance the DFIG converter during the grid fault and this controller takes care of the ride-through fault without employing any other hardware modules. The paper introduces a double wavelet neural network controller which is appropriately tuned employing differential evolution. To validate the proposed controller module, a case study of wind farm with 1.5 MW wind turbines connected to a 25 kV distribution system exporting power to a 120 kV grid through a 30 km 25 kV feeder is carried out by simulation. PMID:26516636

Differential Evolution Based IDWNN Controller for Fault Ride-Through of Grid-Connected Doubly Fed Induction Wind Generators.

PubMed

Manonmani, N; Subbiah, V; Sivakumar, L

2015-01-01

The key objective of wind turbine development is to ensure that output power is continuously increased. It is authenticated that wind turbines (WTs) supply the necessary reactive power to the grid at the time of fault and after fault to aid the flowing grid voltage. At this juncture, this paper introduces a novel heuristic based controller module employing differential evolution and neural network architecture to improve the low-voltage ride-through rate of grid-connected wind turbines, which are connected along with doubly fed induction generators (DFIGs). The traditional crowbar-based systems were basically applied to secure the rotor-side converter during the occurrence of grid faults. This traditional controller is found not to satisfy the desired requirement, since DFIG during the connection of crowbar acts like a squirrel cage module and absorbs the reactive power from the grid. This limitation is taken care of in this paper by introducing heuristic controllers that remove the usage of crowbar and ensure that wind turbines supply necessary reactive power to the grid during faults. The controller is designed in this paper to enhance the DFIG converter during the grid fault and this controller takes care of the ride-through fault without employing any other hardware modules. The paper introduces a double wavelet neural network controller which is appropriately tuned employing differential evolution. To validate the proposed controller module, a case study of wind farm with 1.5 MW wind turbines connected to a 25 kV distribution system exporting power to a 120 kV grid through a 30 km 25 kV feeder is carried out by simulation.

Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas.

PubMed

Sri, Tanu; Mayee, Pratiksha; Singh, Anandita

2015-09-01

Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (∼14-20 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKC(C)) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification.

The evolution of duplicate gene expression in mammalian organs

PubMed Central

Guschanski, Katerina; Warnefors, Maria; Kaessmann, Henrik

2017-01-01

Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis- and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates. PMID:28743766

A Differential Evolution Based Approach to Estimate the Shape and Size of Complex Shaped Anomalies Using EIT Measurements

NASA Astrophysics Data System (ADS)

Rashid, Ahmar; Khambampati, Anil Kumar; Kim, Bong Seok; Liu, Dong; Kim, Sin; Kim, Kyung Youn

EIT image reconstruction is an ill-posed problem, the spatial resolution of the estimated conductivity distribution is usually poor and the external voltage measurements are subject to variable noise. Therefore, EIT conductivity estimation cannot be used in the raw form to correctly estimate the shape and size of complex shaped regional anomalies. An efficient algorithm employing a shape based estimation scheme is needed. The performance of traditional inverse algorithms, such as the Newton Raphson method, used for this purpose is below par and depends upon the initial guess and the gradient of the cost functional. This paper presents the application of differential evolution (DE) algorithm to estimate complex shaped region boundaries, expressed as coefficients of truncated Fourier series, using EIT. DE is a simple yet powerful population-based, heuristic algorithm with the desired features to solve global optimization problems under realistic conditions. The performance of the algorithm has been tested through numerical simulations, comparing its results with that of the traditional modified Newton Raphson (mNR) method.

A Novel Hybrid Firefly Algorithm for Global Optimization.

PubMed

Zhang, Lina; Liu, Liqiang; Yang, Xin-She; Dai, Yuntao

Global optimization is challenging to solve due to its nonlinearity and multimodality. Traditional algorithms such as the gradient-based methods often struggle to deal with such problems and one of the current trends is to use metaheuristic algorithms. In this paper, a novel hybrid population-based global optimization algorithm, called hybrid firefly algorithm (HFA), is proposed by combining the advantages of both the firefly algorithm (FA) and differential evolution (DE). FA and DE are executed in parallel to promote information sharing among the population and thus enhance searching efficiency. In order to evaluate the performance and efficiency of the proposed algorithm, a diverse set of selected benchmark functions are employed and these functions fall into two groups: unimodal and multimodal. The experimental results show better performance of the proposed algorithm compared to the original version of the firefly algorithm (FA), differential evolution (DE) and particle swarm optimization (PSO) in the sense of avoiding local minima and increasing the convergence rate.

A Novel Hybrid Firefly Algorithm for Global Optimization

PubMed Central

Zhang, Lina; Liu, Liqiang; Yang, Xin-She; Dai, Yuntao

2016-01-01

Global optimization is challenging to solve due to its nonlinearity and multimodality. Traditional algorithms such as the gradient-based methods often struggle to deal with such problems and one of the current trends is to use metaheuristic algorithms. In this paper, a novel hybrid population-based global optimization algorithm, called hybrid firefly algorithm (HFA), is proposed by combining the advantages of both the firefly algorithm (FA) and differential evolution (DE). FA and DE are executed in parallel to promote information sharing among the population and thus enhance searching efficiency. In order to evaluate the performance and efficiency of the proposed algorithm, a diverse set of selected benchmark functions are employed and these functions fall into two groups: unimodal and multimodal. The experimental results show better performance of the proposed algorithm compared to the original version of the firefly algorithm (FA), differential evolution (DE) and particle swarm optimization (PSO) in the sense of avoiding local minima and increasing the convergence rate. PMID:27685869

The fine-scale genetic structure and evolution of the Japanese population

PubMed Central

Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics. PMID:29091727

Appraisal of jump distributions in ensemble-based sampling algorithms

NASA Astrophysics Data System (ADS)

Dejanic, Sanda; Scheidegger, Andreas; Rieckermann, Jörg; Albert, Carlo

2017-04-01

Sampling Bayesian posteriors of model parameters is often required for making model-based probabilistic predictions. For complex environmental models, standard Monte Carlo Markov Chain (MCMC) methods are often infeasible because they require too many sequential model runs. Therefore, we focused on ensemble methods that use many Markov chains in parallel, since they can be run on modern cluster architectures. Little is known about how to choose the best performing sampler, for a given application. A poor choice can lead to an inappropriate representation of posterior knowledge. We assessed two different jump moves, the stretch and the differential evolution move, underlying, respectively, the software packages EMCEE and DREAM, which are popular in different scientific communities. For the assessment, we used analytical posteriors with features as they often occur in real posteriors, namely high dimensionality, strong non-linear correlations or multimodality. For posteriors with non-linear features, standard convergence diagnostics based on sample means can be insufficient. Therefore, we resorted to an entropy-based convergence measure. We assessed the samplers by means of their convergence speed, robustness and effective sample sizes. For posteriors with strongly non-linear features, we found that the stretch move outperforms the differential evolution move, w.r.t. all three aspects.

Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient.

PubMed

Kooyers, Nicholas J; James, Brooke; Blackman, Benjamin K

2017-05-01

Closely related species may evolve to coexist stably in sympatry through niche differentiation driven by in situ competition, a process termed character displacement. Alternatively, past evolution in allopatry may have already sufficiently reduced niche overlap to permit establishment in sympatry, a process called ecological sorting. The relative importance of each process to niche differentiation is contentious even though they are not mutually exclusive and are both mediated via multivariate trait evolution. We explore how competition has impacted niche differentiation in two monkeyflowers, Mimulus alsinoides and M. guttatus, which often co-occur. Through field observations, common gardens, and competition experiments, we demonstrate that M. alsinoides is restricted to marginal habitats in sympatry and that the impacts of character displacement on niche differentiation are complex. Competition with M. guttatus alters selection gradients and has favored taller M. alsinoides with earlier seasonal flowering at low elevation and floral shape divergence at high elevation. However, no trait exhibits the pattern typically associated with character displacement, higher divergence between species in sympatry than allopatry. Thus, although character displacement was unlikely the process driving initial divergence along niche axes necessary for coexistence, we conclude that competition in sympatry has likely driven trait evolution along additional niche axes. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. These approaches are implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Optimization of seasonal ARIMA models using differential evolution - simulated annealing (DESA) algorithm in forecasting dengue cases in Baguio City

NASA Astrophysics Data System (ADS)

Addawe, Rizavel C.; Addawe, Joel M.; Magadia, Joselito C.

2016-10-01

Accurate forecasting of dengue cases would significantly improve epidemic prevention and control capabilities. This paper attempts to provide useful models in forecasting dengue epidemic specific to the young and adult population of Baguio City. To capture the seasonal variations in dengue incidence, this paper develops a robust modeling approach to identify and estimate seasonal autoregressive integrated moving average (SARIMA) models in the presence of additive outliers. Since the least squares estimators are not robust in the presence of outliers, we suggest a robust estimation based on winsorized and reweighted least squares estimators. A hybrid algorithm, Differential Evolution - Simulated Annealing (DESA), is used to identify and estimate the parameters of the optimal SARIMA model. The method is applied to the monthly reported dengue cases in Baguio City, Philippines.

Constraining the evolution of the Hubble Parameter using cosmic chronometers

NASA Astrophysics Data System (ADS)

Dickinson, Hugh

2017-08-01

Substantial investment is being made in space- and ground-based missions with the goal of revealing the nature of the observed cosmic acceleration. This is one of the most important unsolved problems in cosmology today.We propose here to constrain the evolution of the Hubble parameter [H(z)] between 1.3 < z < 2, using the cosmic chronometer method, based on differential age measurements for passively evolving galaxies. Existing WFC3-IR G102 and G141 grisms data obtained by the WISP, 3D-HST+AGHAST, FIGS, and CLEAR surveys will yield a sample of 140 suitable standard clocks, expanding existing samples by a factor of five. These additional data will enable us to improve existing constraints on the evolution of H at high redshift, and insodoing to better understand the fundamental nature of dark energy.

Wrinkling pattern evolution of cylindrical biological tissues with differential growth.

PubMed

Jia, Fei; Li, Bo; Cao, Yan-Ping; Xie, Wei-Hua; Feng, Xi-Qiao

2015-01-01

Three-dimensional surface wrinkling of soft cylindrical tissues induced by differential growth is explored. Differential volumetric growth can cause their morphological stability, leading to the formation of hexagonal and labyrinth wrinkles. During postbuckling, multiple bifurcations and morphological transitions may occur as a consequence of continuous growth in the surface layer. The physical mechanisms underpinning the morphological evolution are examined from the viewpoint of energy. Surface curvature is found to play a regulatory role in the pattern evolution. This study may not only help understand the morphogenesis of soft biological tissues, but also inspire novel routes for creating desired surface patterns of soft materials.

Automatic Clustering Using FSDE-Forced Strategy Differential Evolution

NASA Astrophysics Data System (ADS)

Yasid, A.

2018-01-01

Clustering analysis is important in datamining for unsupervised data, cause no adequate prior knowledge. One of the important tasks is defining the number of clusters without user involvement that is known as automatic clustering. This study intends on acquiring cluster number automatically utilizing forced strategy differential evolution (AC-FSDE). Two mutation parameters, namely: constant parameter and variable parameter are employed to boost differential evolution performance. Four well-known benchmark datasets were used to evaluate the algorithm. Moreover, the result is compared with other state of the art automatic clustering methods. The experiment results evidence that AC-FSDE is better or competitive with other existing automatic clustering algorithm.

Directed evolution of bacteriorhodopsin for applications in bioelectronics

PubMed Central

Wagner, Nicole L.; Greco, Jordan A.; Ranaghan, Matthew J.; Birge, Robert R.

2013-01-01

In nature, biological systems gradually evolve through complex, algorithmic processes involving mutation and differential selection. Evolution has optimized biological macromolecules for a variety of functions to provide a comparative advantage. However, nature does not optimize molecules for use in human-made devices, as it would gain no survival advantage in such cooperation. Recent advancements in genetic engineering, most notably directed evolution, have allowed for the stepwise manipulation of the properties of living organisms, promoting the expansion of protein-based devices in nanotechnology. In this review, we highlight the use of directed evolution to optimize photoactive proteins, with an emphasis on bacteriorhodopsin (BR), for device applications. BR, a highly stable light-activated proton pump, has shown great promise in three-dimensional optical memories, real-time holographic processors and artificial retinas. PMID:23676894

Global Ionospheric Perturbations Monitored by the Worldwide GPS Network

NASA Technical Reports Server (NTRS)

Ho, C. M.; Mannucci, A. T.; Lindqwister, U. J.; Pi, X. Q.

1996-01-01

Based on the delays of these (Global Positioning System-GPS)signals, we have generated high resolution global ionospheric TEC (Total Electronic Changes) maps at 15-minute intervals. Using a differential method comparing storm time maps with quiet time maps, we find that the ionopshere during this time storm has increased significantly (the percentage change relative to quiet times is greater than 150 percent) ...These preliminary results (those mentioned above plus other in the paper)indicate that the differential maping method, which is based on GPS network measurements appears to be a useful tool for studying the global pattern and evolution process of the entire ionospheric perturbation.

Differential transferability of EST-SSR primers developed from diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Th. elongatum

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid T...

Evolution of tuf genes: ancient duplication, differential loss and gene conversion.

PubMed

Lathe, W C; Bork, P

2001-08-03

The tuf gene of eubacteria, encoding the EF-tu elongation factor, was duplicated early in the evolution of the taxon. Phylogenetic and genomic location analysis of 20 complete eubacterial genomes suggests that this ancient duplication has been differentially lost and maintained in eubacteria.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

PubMed

Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Critical spaces for quasilinear parabolic evolution equations and applications

NASA Astrophysics Data System (ADS)

Prüss, Jan; Simonett, Gieri; Wilke, Mathias

2018-02-01

We present a comprehensive theory of critical spaces for the broad class of quasilinear parabolic evolution equations. The approach is based on maximal Lp-regularity in time-weighted function spaces. It is shown that our notion of critical spaces coincides with the concept of scaling invariant spaces in case that the underlying partial differential equation enjoys a scaling invariance. Applications to the vorticity equations for the Navier-Stokes problem, convection-diffusion equations, the Nernst-Planck-Poisson equations in electro-chemistry, chemotaxis equations, the MHD equations, and some other well-known parabolic equations are given.

Effect of deformation path on microstructure, microhardness and texture evolution of interstitial free steel fabricated by differential speed rolling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamad, Kotiba; Chung, Bong Kwon; Ko, Young Gun, E-mail: younggun@ynu.ac.kr

2014-08-15

This paper reports the effect of the deformation path on the microstructure, microhardness, and texture evolution of interstitial free (IF) steel processed by differential speed rolling (DSR) method. For this purpose, total height reductions of 50% and 75% were imposed on the samples by a series of differential speed rolling operations with various height reductions per pass (deformation levels) ranging from 10 to 50% under a fixed roll speed ratio of 1:4 for the upper and lower rolls, respectively. Microstructural observations using transmission electron microscopy and electron backscattered diffraction measurements showed that the samples rolled at deformation level of 50%more » had the finest mean grain size (∼ 0.5 μm) compared to the other counterparts; also the samples rolled at deformation level of 50% showed a more uniform microstructure. Based on the microhardness measurements along the thickness direction of the deformed samples, gradual evolution of the microhardness value and its homogeneity was observed with the increase of the deformation level per pass. Texture analysis showed that, as the deformation level per pass increased, the fraction of alpha fiber and gamma fiber in the deformed samples increased. The textures obtained by the differential speed rolling process under the lubricated condition would be equivalent to those obtained by the conventional rolling. - Highlights: • Effect of DSR deformation path on microstructure of IF steel is significant. • IF steel rolled at deformation level of 50% has the ultrafine grains of ∼ 0.5 μm. • Rolling texture components are pronounced with increasing deformation level.« less

Utilization of the Discrete Differential Evolution for Optimization in Multidimensional Point Clouds.

PubMed

Uher, Vojtěch; Gajdoš, Petr; Radecký, Michal; Snášel, Václav

2016-01-01

The Differential Evolution (DE) is a widely used bioinspired optimization algorithm developed by Storn and Price. It is popular for its simplicity and robustness. This algorithm was primarily designed for real-valued problems and continuous functions, but several modified versions optimizing both integer and discrete-valued problems have been developed. The discrete-coded DE has been mostly used for combinatorial problems in a set of enumerative variants. However, the DE has a great potential in the spatial data analysis and pattern recognition. This paper formulates the problem as a search of a combination of distinct vertices which meet the specified conditions. It proposes a novel approach called the Multidimensional Discrete Differential Evolution (MDDE) applying the principle of the discrete-coded DE in discrete point clouds (PCs). The paper examines the local searching abilities of the MDDE and its convergence to the global optimum in the PCs. The multidimensional discrete vertices cannot be simply ordered to get a convenient course of the discrete data, which is crucial for good convergence of a population. A novel mutation operator utilizing linear ordering of spatial data based on the space filling curves is introduced. The algorithm is tested on several spatial datasets and optimization problems. The experiments show that the MDDE is an efficient and fast method for discrete optimizations in the multidimensional point clouds.

Utilization of the Discrete Differential Evolution for Optimization in Multidimensional Point Clouds

PubMed Central

Radecký, Michal; Snášel, Václav

2016-01-01

The Differential Evolution (DE) is a widely used bioinspired optimization algorithm developed by Storn and Price. It is popular for its simplicity and robustness. This algorithm was primarily designed for real-valued problems and continuous functions, but several modified versions optimizing both integer and discrete-valued problems have been developed. The discrete-coded DE has been mostly used for combinatorial problems in a set of enumerative variants. However, the DE has a great potential in the spatial data analysis and pattern recognition. This paper formulates the problem as a search of a combination of distinct vertices which meet the specified conditions. It proposes a novel approach called the Multidimensional Discrete Differential Evolution (MDDE) applying the principle of the discrete-coded DE in discrete point clouds (PCs). The paper examines the local searching abilities of the MDDE and its convergence to the global optimum in the PCs. The multidimensional discrete vertices cannot be simply ordered to get a convenient course of the discrete data, which is crucial for good convergence of a population. A novel mutation operator utilizing linear ordering of spatial data based on the space filling curves is introduced. The algorithm is tested on several spatial datasets and optimization problems. The experiments show that the MDDE is an efficient and fast method for discrete optimizations in the multidimensional point clouds. PMID:27974884

A POPULATION MEMETICS APPROACH TO CULTURAL EVOLUTION IN CHAFFINCH SONG: DIFFERENTIATION AMONG POPULATIONS.

PubMed

Lynch, Alejandro; Baker, Allan J

1994-04-01

We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, and Canaries) and neighboring continental regions (Morocco and Iberia) by employing a population-memetic approach. To quantify differentiation, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The levels of cultural differentiation are higher among the Canaries populations than among the Azorean ones, even though the islands are on average closer to each other geographically. This is likely the result of reduced levels of migration, lower population sizes, and bottlenecks (possibly during the colonization of these populations) in the Canaries; all these factors produce a smaller effective population size and therefore accentuate the effects of differentiation by random drift. Significant levels of among-population differentiation in the Azores, in spite of substantial levels of migration, attest to the differentiating effects of high mutation rates of memes, which allow the accumulation of new mutants in different populations before migration can disperse them throughout the entire region. © 1994 The Society for the Study of Evolution.

Differential pleiotropy and HOX functional organization.

PubMed

Sivanantharajah, Lovesha; Percival-Smith, Anthony

2015-02-01

Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrated model of multiple kernel learning and differential evolution for EUR/USD trading.

PubMed

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits.

Modeling evolution of the mind and cultures: emotional Sapir-Whorf hypothesis

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid I.

2009-05-01

Evolution of cultures is ultimately determined by mechanisms of the human mind. The paper discusses the mechanisms of evolution of language from primordial undifferentiated animal cries to contemporary conceptual contents. In parallel with differentiation of conceptual contents, the conceptual contents were differentiated from emotional contents of languages. The paper suggests the neural brain mechanisms involved in these processes. Experimental evidence and theoretical arguments are discussed, including mathematical approaches to cognition and language: modeling fields theory, the knowledge instinct, and the dual model connecting language and cognition. Mathematical results are related to cognitive science, linguistics, and psychology. The paper gives an initial mathematical formulation and mean-field equations for the hierarchical dynamics of both the human mind and culture. In the mind heterarchy operation of the knowledge instinct manifests through mechanisms of differentiation and synthesis. The emotional contents of language are related to language grammar. The conclusion is an emotional version of Sapir-Whorf hypothesis. Cultural advantages of "conceptual" pragmatic cultures, in which emotionality of language is diminished and differentiation overtakes synthesis resulting in fast evolution at the price of self doubts and internal crises are compared to those of traditional cultures where differentiation lags behind synthesis, resulting in cultural stability at the price of stagnation. Multi-language, multi-ethnic society might combine the benefits of stability and fast differentiation. Unsolved problems and future theoretical and experimental directions are discussed.

Niche evolution and adaptive radiation: Testing the order of trait divergence

USGS Publications Warehouse

Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

2006-01-01

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in many adaptive radiations. ?? 2006 by the Ecological Society of America.

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been provEn effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. Several approaches that have proven effective for other evolutionary algorithms are modified and implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for standard test optimization problems and for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Aerodynamic optimization of supersonic compressor cascade using differential evolution on GPU

NASA Astrophysics Data System (ADS)

Aissa, Mohamed Hasanine; Verstraete, Tom; Vuik, Cornelis

2016-06-01

Differential Evolution (DE) is a powerful stochastic optimization method. Compared to gradient-based algorithms, DE is able to avoid local minima but requires at the same time more function evaluations. In turbomachinery applications, function evaluations are performed with time-consuming CFD simulation, which results in a long, non affordable, design cycle. Modern High Performance Computing systems, especially Graphic Processing Units (GPUs), are able to alleviate this inconvenience by accelerating the design evaluation itself. In this work we present a validated CFD Solver running on GPUs, able to accelerate the design evaluation and thus the entire design process. An achieved speedup of 20x to 30x enabled the DE algorithm to run on a high-end computer instead of a costly large cluster. The GPU-enhanced DE was used to optimize the aerodynamics of a supersonic compressor cascade, achieving an aerodynamic loss minimization of 20%.

Habitat use affects morphological diversification in dragon lizards

PubMed Central

COLLAR, D C; SCHULTE, J A; O’MEARA, B C; LOSOS, J B

2010-01-01

Habitat use may lead to variation in diversity among evolutionary lineages because habitats differ in the variety of ways they allow for species to make a living. Here, we show that structural habitats contribute to differential diversification of limb and body form in dragon lizards (Agamidae). Based on phylogenetic analysis and ancestral state reconstructions for 90 species, we find that multiple lineages have independently adopted each of four habitat use types: rock-dwelling, terrestriality, semi-arboreality and arboreality. Given these reconstructions, we fit models of evolution to species’ morphological trait values and find that rock-dwelling and arboreality limit diversification relative to terrestriality and semi-arboreality. Models preferred by Akaike information criterion infer slower rates of size and shape evolution in lineages inferred to occupy rocks and trees, and model-averaged rate estimates are slowest for these habitat types. These results suggest that ground-dwelling facilitates ecomorphological differentiation and that use of trees or rocks impedes diversification. PMID:20345808

Modeling eutrophic lakes: From mass balance laws to ordinary differential equations

NASA Astrophysics Data System (ADS)

Marasco, Addolorata; Ferrara, Luciano; Romano, Antonio

Starting from integral balance laws, a model based on nonlinear ordinary differential equations (ODEs) describing the evolution of Phosphorus cycle in a lake is proposed. After showing that the usual homogeneous model is not compatible with the mixture theory, we prove that an ODEs model still holds but for the mean values of the state variables provided that the nonhomogeneous involved fields satisfy suitable conditions. In this model the trophic state of a lake is described by the mean densities of Phosphorus in water and sediments, and phytoplankton biomass. All the quantities appearing in the model can be experimentally evaluated. To propose restoration programs, the evolution of these state variables toward stable steady state conditions is analyzed. Moreover, the local stability analysis is performed with respect to all the model parameters. Some numerical simulations and a real application to lake Varese conclude the paper.

A Generalized National Planning Approach for Admission Capacity in Higher Education: A Nonlinear Integer Goal Programming Model with a Novel Differential Evolution Algorithm

PubMed Central

El-Qulity, Said Ali; Mohamed, Ali Wagdy

2016-01-01

This paper proposes a nonlinear integer goal programming model (NIGPM) for solving the general problem of admission capacity planning in a country as a whole. The work aims to satisfy most of the required key objectives of a country related to the enrollment problem for higher education. The system general outlines are developed along with the solution methodology for application to the time horizon in a given plan. The up-to-date data for Saudi Arabia is used as a case study and a novel evolutionary algorithm based on modified differential evolution (DE) algorithm is used to solve the complexity of the NIGPM generated for different goal priorities. The experimental results presented in this paper show their effectiveness in solving the admission capacity for higher education in terms of final solution quality and robustness. PMID:26819583

A Generalized National Planning Approach for Admission Capacity in Higher Education: A Nonlinear Integer Goal Programming Model with a Novel Differential Evolution Algorithm.

PubMed

El-Qulity, Said Ali; Mohamed, Ali Wagdy

2016-01-01

This paper proposes a nonlinear integer goal programming model (NIGPM) for solving the general problem of admission capacity planning in a country as a whole. The work aims to satisfy most of the required key objectives of a country related to the enrollment problem for higher education. The system general outlines are developed along with the solution methodology for application to the time horizon in a given plan. The up-to-date data for Saudi Arabia is used as a case study and a novel evolutionary algorithm based on modified differential evolution (DE) algorithm is used to solve the complexity of the NIGPM generated for different goal priorities. The experimental results presented in this paper show their effectiveness in solving the admission capacity for higher education in terms of final solution quality and robustness.

A Novel Discrete Differential Evolution Algorithm for the Vehicle Routing Problem in B2C E-Commerce

NASA Astrophysics Data System (ADS)

Xia, Chao; Sheng, Ying; Jiang, Zhong-Zhong; Tan, Chunqiao; Huang, Min; He, Yuanjian

2015-12-01

In this paper, a novel discrete differential evolution (DDE) algorithm is proposed to solve the vehicle routing problems (VRP) in B2C e-commerce, in which VRP is modeled by the incomplete graph based on the actual urban road system. First, a variant of classical VRP is described and a mathematical programming model for the variant is given. Second, the DDE is presented, where individuals are represented as the sequential encoding scheme, and a novel reparation operator is employed to repair the infeasible solutions. Furthermore, a FLOYD operator for dealing with the shortest route is embedded in the proposed DDE. Finally, an extensive computational study is carried out in comparison with the predatory search algorithm and genetic algorithm, and the results show that the proposed DDE is an effective algorithm for VRP in B2C e-commerce.

Aerodynamic optimization of supersonic compressor cascade using differential evolution on GPU

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aissa, Mohamed Hasanine; Verstraete, Tom; Vuik, Cornelis

Differential Evolution (DE) is a powerful stochastic optimization method. Compared to gradient-based algorithms, DE is able to avoid local minima but requires at the same time more function evaluations. In turbomachinery applications, function evaluations are performed with time-consuming CFD simulation, which results in a long, non affordable, design cycle. Modern High Performance Computing systems, especially Graphic Processing Units (GPUs), are able to alleviate this inconvenience by accelerating the design evaluation itself. In this work we present a validated CFD Solver running on GPUs, able to accelerate the design evaluation and thus the entire design process. An achieved speedup of 20xmore » to 30x enabled the DE algorithm to run on a high-end computer instead of a costly large cluster. The GPU-enhanced DE was used to optimize the aerodynamics of a supersonic compressor cascade, achieving an aerodynamic loss minimization of 20%.« less

Two-Swim Operators in the Modified Bacterial Foraging Algorithm for the Optimal Synthesis of Four-Bar Mechanisms

PubMed Central

Hernández-Ocaña, Betania; Pozos-Parra, Ma. Del Pilar; Mezura-Montes, Efrén; Portilla-Flores, Edgar Alfredo; Vega-Alvarado, Eduardo; Calva-Yáñez, Maria Bárbara

2016-01-01

This paper presents two-swim operators to be added to the chemotaxis process of the modified bacterial foraging optimization algorithm to solve three instances of the synthesis of four-bar planar mechanisms. One swim favors exploration while the second one promotes fine movements in the neighborhood of each bacterium. The combined effect of the new operators looks to increase the production of better solutions during the search. As a consequence, the ability of the algorithm to escape from local optimum solutions is enhanced. The algorithm is tested through four experiments and its results are compared against two BFOA-based algorithms and also against a differential evolution algorithm designed for mechanical design problems. The overall results indicate that the proposed algorithm outperforms other BFOA-based approaches and finds highly competitive mechanisms, with a single set of parameter values and with less evaluations in the first synthesis problem, with respect to those mechanisms obtained by the differential evolution algorithm, which needed a parameter fine-tuning process for each optimization problem. PMID:27057156

Two-Swim Operators in the Modified Bacterial Foraging Algorithm for the Optimal Synthesis of Four-Bar Mechanisms.

PubMed

Hernández-Ocaña, Betania; Pozos-Parra, Ma Del Pilar; Mezura-Montes, Efrén; Portilla-Flores, Edgar Alfredo; Vega-Alvarado, Eduardo; Calva-Yáñez, Maria Bárbara

2016-01-01

This paper presents two-swim operators to be added to the chemotaxis process of the modified bacterial foraging optimization algorithm to solve three instances of the synthesis of four-bar planar mechanisms. One swim favors exploration while the second one promotes fine movements in the neighborhood of each bacterium. The combined effect of the new operators looks to increase the production of better solutions during the search. As a consequence, the ability of the algorithm to escape from local optimum solutions is enhanced. The algorithm is tested through four experiments and its results are compared against two BFOA-based algorithms and also against a differential evolution algorithm designed for mechanical design problems. The overall results indicate that the proposed algorithm outperforms other BFOA-based approaches and finds highly competitive mechanisms, with a single set of parameter values and with less evaluations in the first synthesis problem, with respect to those mechanisms obtained by the differential evolution algorithm, which needed a parameter fine-tuning process for each optimization problem.

A discrete artificial bee colony algorithm incorporating differential evolution for the flow-shop scheduling problem with blocking

NASA Astrophysics Data System (ADS)

Han, Yu-Yan; Gong, Dunwei; Sun, Xiaoyan

2015-07-01

A flow-shop scheduling problem with blocking has important applications in a variety of industrial systems but is underrepresented in the research literature. In this study, a novel discrete artificial bee colony (ABC) algorithm is presented to solve the above scheduling problem with a makespan criterion by incorporating the ABC with differential evolution (DE). The proposed algorithm (DE-ABC) contains three key operators. One is related to the employed bee operator (i.e. adopting mutation and crossover operators of discrete DE to generate solutions with good quality); the second is concerned with the onlooker bee operator, which modifies the selected solutions using insert or swap operators based on the self-adaptive strategy; and the last is for the local search, that is, the insert-neighbourhood-based local search with a small probability is adopted to improve the algorithm's capability in exploitation. The performance of the proposed DE-ABC algorithm is empirically evaluated by applying it to well-known benchmark problems. The experimental results show that the proposed algorithm is superior to the compared algorithms in minimizing the makespan criterion.

A physically based connection between fractional calculus and fractal geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butera, Salvatore, E-mail: sg.butera@gmail.com; Di Paola, Mario, E-mail: mario.dipaola@unipa.it

2014-11-15

We show a relation between fractional calculus and fractals, based only on physical and geometrical considerations. The link has been found in the physical origins of the power-laws, ruling the evolution of many natural phenomena, whose long memory and hereditary properties are mathematically modelled by differential operators of non integer order. Dealing with the relevant example of a viscous fluid seeping through a fractal shaped porous medium, we show that, once a physical phenomenon or process takes place on an underlying fractal geometry, then a power-law naturally comes up in ruling its evolution, whose order is related to the anomalousmore » dimension of such geometry, as well as to the model used to describe the physics involved. By linearizing the non linear dependence of the response of the system at hand to a proper forcing action then, exploiting the Boltzmann superposition principle, a fractional differential equation is found, describing the dynamics of the system itself. The order of such equation is again related to the anomalous dimension of the underlying geometry.« less

Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution

PubMed Central

Patterson, Larissa B.; Bain, Emily J.; Parichy, David M.

2014-01-01

Fishes have diverse pigment patterns, yet mechanisms of pattern evolution remain poorly understood. In zebrafish, Danio rerio, pigment-cell autonomous interactions generate dark stripes of melanophores that alternate with light interstripes of xanthophores and iridophores. Here, we identify mechanisms underlying the evolution of a uniform pattern in D. albolineatus in which all three pigment cell classes are intermingled. We show that in this species xanthophores differentiate precociously over a wider area, and that cis regulatory evolution has increased expression of xanthogenic Colony Stimulating Factor-1 (Csf1). Expressing Csf1 similarly in D. rerio has cascading effects, driving the intermingling of all three pigment cell classes and resulting in the loss of stripes, as in D. albolineatus. Our results identify novel mechanisms of pattern development and illustrate how pattern diversity can be generated when a core network of pigment-cell autonomous interactions is coupled with changes in pigment cell differentiation. PMID:25374113

Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua.

PubMed

Manousaki, Tereza; Hull, Pincelli M; Kusche, Henrik; Machado-Schiaffino, Gonzalo; Franchini, Paolo; Harrod, Chris; Elmer, Kathryn R; Meyer, Axel

2013-02-01

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)-from two Great Lakes and two crater lakes in Nicaragua-to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ(13)C and δ(15)N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

Differential evolution enhanced with multiobjective sorting-based mutation operators.

PubMed

Wang, Jiahai; Liao, Jianjun; Zhou, Ying; Cai, Yiqiao

2014-12-01

Differential evolution (DE) is a simple and powerful population-based evolutionary algorithm. The salient feature of DE lies in its mutation mechanism. Generally, the parents in the mutation operator of DE are randomly selected from the population. Hence, all vectors are equally likely to be selected as parents without selective pressure at all. Additionally, the diversity information is always ignored. In order to fully exploit the fitness and diversity information of the population, this paper presents a DE framework with multiobjective sorting-based mutation operator. In the proposed mutation operator, individuals in the current population are firstly sorted according to their fitness and diversity contribution by nondominated sorting. Then parents in the mutation operators are proportionally selected according to their rankings based on fitness and diversity, thus, the promising individuals with better fitness and diversity have more opportunity to be selected as parents. Since fitness and diversity information is simultaneously considered for parent selection, a good balance between exploration and exploitation can be achieved. The proposed operator is applied to original DE algorithms, as well as several advanced DE variants. Experimental results on 48 benchmark functions and 12 real-world application problems show that the proposed operator is an effective approach to enhance the performance of most DE algorithms studied.

Differential evolution algorithm based photonic structure design: numerical and experimental verification of subwavelength λ/5 focusing of light.

PubMed

Bor, E; Turduev, M; Kurt, H

2016-08-01

Photonic structure designs based on optimization algorithms provide superior properties compared to those using intuition-based approaches. In the present study, we numerically and experimentally demonstrate subwavelength focusing of light using wavelength scale absorption-free dielectric scattering objects embedded in an air background. An optimization algorithm based on differential evolution integrated into the finite-difference time-domain method was applied to determine the locations of each circular dielectric object with a constant radius and refractive index. The multiobjective cost function defined inside the algorithm ensures strong focusing of light with low intensity side lobes. The temporal and spectral responses of the designed compact photonic structure provided a beam spot size in air with a full width at half maximum value of 0.19λ, where λ is the wavelength of light. The experiments were carried out in the microwave region to verify numerical findings, and very good agreement between the two approaches was found. The subwavelength light focusing is associated with a strong interference effect due to nonuniformly arranged scatterers and an irregular index gradient. Improving the focusing capability of optical elements by surpassing the diffraction limit of light is of paramount importance in optical imaging, lithography, data storage, and strong light-matter interaction.

Differential evolution algorithm based photonic structure design: numerical and experimental verification of subwavelength λ/5 focusing of light

PubMed Central

Bor, E.; Turduev, M.; Kurt, H.

2016-01-01

Photonic structure designs based on optimization algorithms provide superior properties compared to those using intuition-based approaches. In the present study, we numerically and experimentally demonstrate subwavelength focusing of light using wavelength scale absorption-free dielectric scattering objects embedded in an air background. An optimization algorithm based on differential evolution integrated into the finite-difference time-domain method was applied to determine the locations of each circular dielectric object with a constant radius and refractive index. The multiobjective cost function defined inside the algorithm ensures strong focusing of light with low intensity side lobes. The temporal and spectral responses of the designed compact photonic structure provided a beam spot size in air with a full width at half maximum value of 0.19λ, where λ is the wavelength of light. The experiments were carried out in the microwave region to verify numerical findings, and very good agreement between the two approaches was found. The subwavelength light focusing is associated with a strong interference effect due to nonuniformly arranged scatterers and an irregular index gradient. Improving the focusing capability of optical elements by surpassing the diffraction limit of light is of paramount importance in optical imaging, lithography, data storage, and strong light-matter interaction. PMID:27477060

Oxidative Stress, Redox Regulation and Diseases of Cellular Differentiation

PubMed Central

Ye, Zhi-Wei; Zhang, Jie; Townsend, Danyelle M.; Tew, Kenneth D.

2015-01-01

Background Within cells, there is a narrow concentration threshold that governs whether reactive oxygen species (ROS) induce toxicity or act as second messengers. Scope of review We discuss current understanding of how ROS arise, facilitate cell signaling, cause toxicities and disease related to abnormal cell differentiation and those (primarily) sulfur based pathways that provide nucleophilicity to offset these effects. Primary conclusions Cellular redox homeostasis mediates a plethora of cellular pathways that determine life and death events. For example, ROS intersect with GSH based enzyme pathways to influence cell differentiation, a process integral to normal hematopoiesis, but also affecting a number of diverse cell differentiation related human diseases. Recent attempts to manage such pathologies have focused on intervening in some of these pathways, with the consequence that differentiation therapy targeting redox homeostasis has provided a platform for drug discovery and development. General Significance The balance between electrophilic oxidative stress and protective biomolecular nucleophiles predisposes the evolution of modern life forms. Imbalances of the two can produce aberrant redox homeostasis with resultant pathologies. Understanding the pathways involved provides opportunities to consider interventional strategies. PMID:25445706

Neuronal Populations in the Basolateral Nuclei of the Amygdala Are Differentially Increased in Humans Compared With Apes: A Stereological Study

PubMed Central

Barger, Nicole; Stefanacci, Lisa; Schumann, Cynthia M.; Sherwood, Chet C.; Annese, Jacopo; Allman, John M.; Buckwalter, Joseph A.; Hof, Patrick R.; Semendeferi, Katerina

2016-01-01

In human and nonhuman primates, the amygdala is known to play critical roles in emotional and social behavior. Anatomically, individual amygdaloid nuclei are connected with many neural systems that are either differentially expanded or conserved over the course of primate evolution. To address amygdala evolution in humans and our closest living relatives, the apes, we used design-based stereological methods to obtain neuron counts for the amygdala and each of four major amygdaloid nuclei (the lateral, basal, accessory basal, and central nuclei) in humans, all great ape species, lesser apes, and one monkey species. Our goal was to determine whether there were significant differences in the number or percent of neurons distributed to individual nuclei among species. Additionally, regression analyses were performed on independent contrast data to determine whether any individual species deviated from allometric trends. There were two major findings. In humans, the lateral nucleus contained the highest number of neurons in the amygdala, whereas in apes the basal nucleus contained the highest number of neurons. Additionally, the human lateral nucleus contained 59% more neurons than predicted by allometric regressions on nonhuman primate data. Based on the largest sample ever analyzed in a comparative study of the hominoid amygdala, our findings suggest that an emphasis on the lateral nucleus is the main characteristic of amygdala specialization over the course of human evolution. PMID:22473387

From stochastic processes to numerical methods: A new scheme for solving reaction subdiffusion fractional partial differential equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Angstmann, C.N.; Donnelly, I.C.; Henry, B.I., E-mail: B.Henry@unsw.edu.au

We have introduced a new explicit numerical method, based on a discrete stochastic process, for solving a class of fractional partial differential equations that model reaction subdiffusion. The scheme is derived from the master equations for the evolution of the probability density of a sum of discrete time random walks. We show that the diffusion limit of the master equations recovers the fractional partial differential equation of interest. This limiting procedure guarantees the consistency of the numerical scheme. The positivity of the solution and stability results are simply obtained, provided that the underlying process is well posed. We also showmore » that the method can be applied to standard reaction–diffusion equations. This work highlights the broader applicability of using discrete stochastic processes to provide numerical schemes for partial differential equations, including fractional partial differential equations.« less

Karyological characterization of the endemic Iberian rock lizard, Iberolacerta monticola (Squamata, Lacertidae): insights into sex chromosome evolution.

PubMed

Rojo, V; Giovannotti, M; Naveira, H; Nisi Cerioni, P; González-Tizón, A M; Caputo Barucchi, V; Galán, P; Olmo, E; Martínez-Lage, A

2014-01-01

Rock lizards of the genus Iberolacerta constitute a promising model to examine the process of sex chromosome evolution, as these closely related taxa exhibit remarkable diversity in the degree of sex chromosome differentiation with no clear phylogenetic segregation, ranging from cryptic to highly heteromorphic ZW chromosomes and even multiple chromosome systems (Z1Z1Z2Z2/Z1Z2W). To gain a deeper insight into the patterns of karyotype and sex chromosome evolution, we performed a cytogenetic analysis based on conventional staining, banding techniques and fluorescence in situ hybridization in the species I. monticola, for which previous cytogenetic investigations did not detect differentiated sex chromosomes. The karyotype is composed of 2n = 36 acrocentric chromosomes. NORs and the major ribosomal genes were located in the subtelomeric region of chromosome pair 6. Hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes and interstitially in 5 chromosome pairs. C-banding showed constitutive heterochromatin at the centromeres of all chromosomes, as well as clear pericentromeric and light telomeric C-bands in several chromosome pairs. These results highlight some chromosomal markers which can be useful to identify species-specific diagnostic characters, although they may not accurately reflect the phylogenetic relationships among the taxa. In addition, C-banding revealed the presence of a heteromorphic ZW sex chromosome pair, where W is smaller than Z and almost completely heterochromatic. This finding sheds light on sex chromosome evolution in the genus Iberolacerta and suggests that further comparative cytogenetic analyses are needed to understand the processes underlying the origin, differentiation and plasticity of sex chromosome systems in lacertid lizards. © 2013 S. Karger AG, Basel.

The early thermal evolution of Mars

NASA Astrophysics Data System (ADS)

Bhatia, G. K.; Sahijpal, S.

2016-01-01

Hf-W isotopic systematics of Martian meteorites have provided evidence for the early accretion and rapid core formation of Mars. We present the results of numerical simulations performed to study the early thermal evolution and planetary scale differentiation of Mars. The simulations are confined to the initial 50 Myr (Ma) of the formation of solar system. The accretion energy produced during the growth of Mars and the decay energy due to the short-lived radio-nuclides 26Al, 60Fe, and the long-lived nuclides, 40K, 235U, 238U, and 232Th are incorporated as the heat sources for the thermal evolution of Mars. During the core-mantle differentiation of Mars, the molten metallic blobs were numerically moved using Stoke's law toward the center with descent velocity that depends on the local acceleration due to gravity. Apart from the accretion and the radioactive heat energies, the gravitational energy produced during the differentiation of Mars and the associated heat transfer is also parametrically incorporated in the present work to make an assessment of its contribution to the early thermal evolution of Mars. We conclude that the accretion energy alone cannot produce widespread melting and differentiation of Mars even with an efficient consumption of the accretion energy. This makes 26Al the prime source for the heating and planetary scale differentiation of Mars. We demonstrate a rapid accretion and core-mantle differentiation of Mars within the initial ~1.5 Myr. This is consistent with the chronological records of Martian meteorites.

Simulating Chemical Kinetics Without Differential Equations: A Quantitative Theory Based on Chemical Pathways.

PubMed

Bai, Shirong; Skodje, Rex T

2017-08-17

A new approach is presented for simulating the time-evolution of chemically reactive systems. This method provides an alternative to conventional modeling of mass-action kinetics that involves solving differential equations for the species concentrations. The method presented here avoids the need to solve the rate equations by switching to a representation based on chemical pathways. In the Sum Over Histories Representation (or SOHR) method, any time-dependent kinetic observable, such as concentration, is written as a linear combination of probabilities for chemical pathways leading to a desired outcome. In this work, an iterative method is introduced that allows the time-dependent pathway probabilities to be generated from a knowledge of the elementary rate coefficients, thus avoiding the pitfalls involved in solving the differential equations of kinetics. The method is successfully applied to the model Lotka-Volterra system and to a realistic H 2 combustion model.

Nonexistence of global solutions of abstract wave equations with high energies.

PubMed

Esquivel-Avila, Jorge A

2017-01-01

We consider an undamped second order in time evolution equation. For any positive value of the initial energy, we give sufficient conditions to conclude nonexistence of global solutions. The analysis is based on a differential inequality. The success of our result is based in a detailed analysis which is different from the ones commonly used to prove blow-up. Several examples are given improving known results in the literature.

Keck Deep Fields. II. The Ultraviolet Galaxy Luminosity Function at z ~ 4, 3, and 2

NASA Astrophysics Data System (ADS)

Sawicki, Marcin; Thompson, David

2006-05-01

We use very deep UnGRI multifield imaging obtained at the Keck telescope to study the evolution of the rest-frame 1700 Å galaxy luminosity function as the universe doubles its age from z~4 to ~2. We use exactly the same filters and color-color selection as those used by the Steidel team but probe significantly fainter limits, well below L*. The depth of our imaging allows us to constrain the faint end of the luminosity function, reaching M1700~-18.5 at z~3 (equivalent to ~1 Msolar yr-1), accounting for both N1/2 uncertainty in the number of galaxies and cosmic variance. We carefully examine many potential sources of systematic bias in our LF measurements before drawing the following conclusions. We find that the luminosity function of Lyman break galaxies evolves with time and that this evolution is differential with luminosity. The result is best constrained between the epochs at z~4 and ~3, where we find that the number density of sub-L* galaxies increases with time by at least a factor of 2.3 (11 σ statistical confidence); while the faint end of the LF evolves, the bright end appears to remain virtually unchanged, indicating that there may be differential, luminosity-dependent evolution (98.5% statistical probability). Potential systematic biases restrict our ability to draw strong conclusions about continued evolution of the luminosity function to lower redshifts, z~2.2 and ~1.7, but, nevertheless, it appears certain that the number density of z~2.2 galaxies at all luminosities we studied, -22>M1700>-18, is at least as high as that of their counterparts at z~3. While it is not yet clear what mechanism underlies the observed evolution, the fact that this evolution is differential with luminosity opens up new avenues of improving our understanding of how galaxies form and evolve at high redshift. Based on data obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and NASA and was made possible by the generous financial support of the W. M. Keck Foundation.

Lunar initial Nd-143/Nd-144 - Differential evolution of the lunar crust and mantle

NASA Technical Reports Server (NTRS)

Lugmair, G. W.; Marti, K.

1978-01-01

The Sm-Nd evolution of Apollo 15 green glass is discussed. The ICE age (intercept with chondritic evolution) of 3.8 + or - 0.4 eons overlaps the range of reported (Ar-39)-(Ar-40) ages and implies a distinct source region for green glass, characterized by very low and unfractionated REE abundances. Evidence is presented that LINd (lunar initial Nd) is compatible with a 'chondritic'-type Nd isotopic evolution as observed in the Juvinas meteorite. This normalization is used to study the Sm-Nd system of various lunar rock types. The results obtained from a limited number of rocks clearly indicate differential Sm-Nd evolution for the lunar crust and mantle. High-Ti basalts returned by the Apollo 11 and 17 missions were derived from distinct source regions. The Nd-143 evolution in KREEP requires a source region which is clearly distinct from any mantle reservoir.

Genome rearrangement shapes Prochlorococcus ecological adaptation.

PubMed

Yan, Wei; Wei, Shuzhen; Wang, Qiong; Xiao, Xilin; Zeng, Qinglu; Jiao, Nianzhi; Zhang, Rui

2018-06-18

Prochlorococcus is the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles. Prochlorococcus can be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructed Prochlorococcus evolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role in Prochlorococcus evolution. We also found that the Prochlorococcus clades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations. Importance Prochlorococcus , the most abundant and smallest known free-living photosynthetic microorganism, play a key role in marine ecosystems and biogeochemical cycles. The Prochlorococcus genome evolution is a fundamental question related to how Prochlorococcus clades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted the Prochlorococcus genome evolution from the perspective of genome structure, and associated the genome rearrangement with the Prochlorococcus clade differentiation and subsequent ecological adaptation. Copyright © 2018 Yan et al.

Tissue Specificity and Dynamics of Sex-Biased Gene Expression in a Common Frog Population with Differentiated, Yet Homomorphic, Sex Chromosomes.

PubMed

Ma, Wen-Juan; Veltsos, Paris; Toups, Melissa A; Rodrigues, Nicolas; Sermier, Roberto; Jeffries, Daniel L; Perrin, Nicolas

2018-06-12

Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage- or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.

Non-linear hydrodynamical evolution of rotating relativistic stars: numerical methods and code tests

NASA Astrophysics Data System (ADS)

Font, José A.; Stergioulas, Nikolaos; Kokkotas, Kostas D.

2000-04-01

We present numerical hydrodynamical evolutions of rapidly rotating relativistic stars, using an axisymmetric, non-linear relativistic hydrodynamics code. We use four different high-resolution shock-capturing (HRSC) finite-difference schemes (based on approximate Riemann solvers) and compare their accuracy in preserving uniformly rotating stationary initial configurations in long-term evolutions. Among these four schemes, we find that the third-order piecewise parabolic method scheme is superior in maintaining the initial rotation law in long-term evolutions, especially near the surface of the star. It is further shown that HRSC schemes are suitable for the evolution of perturbed neutron stars and for the accurate identification (via Fourier transforms) of normal modes of oscillation. This is demonstrated for radial and quadrupolar pulsations in the non-rotating limit, where we find good agreement with frequencies obtained with a linear perturbation code. The code can be used for studying small-amplitude or non-linear pulsations of differentially rotating neutron stars, while our present results serve as testbed computations for three-dimensional general-relativistic evolution codes.

CMOS analogue amplifier circuits optimisation using hybrid backtracking search algorithm with differential evolution

NASA Astrophysics Data System (ADS)

Mallick, S.; Kar, R.; Mandal, D.; Ghoshal, S. P.

2016-07-01

This paper proposes a novel hybrid optimisation algorithm which combines the recently proposed evolutionary algorithm Backtracking Search Algorithm (BSA) with another widely accepted evolutionary algorithm, namely, Differential Evolution (DE). The proposed algorithm called BSA-DE is employed for the optimal designs of two commonly used analogue circuits, namely Complementary Metal Oxide Semiconductor (CMOS) differential amplifier circuit with current mirror load and CMOS two-stage operational amplifier (op-amp) circuit. BSA has a simple structure that is effective, fast and capable of solving multimodal problems. DE is a stochastic, population-based heuristic approach, having the capability to solve global optimisation problems. In this paper, the transistors' sizes are optimised using the proposed BSA-DE to minimise the areas occupied by the circuits and to improve the performances of the circuits. The simulation results justify the superiority of BSA-DE in global convergence properties and fine tuning ability, and prove it to be a promising candidate for the optimal design of the analogue CMOS amplifier circuits. The simulation results obtained for both the amplifier circuits prove the effectiveness of the proposed BSA-DE-based approach over DE, harmony search (HS), artificial bee colony (ABC) and PSO in terms of convergence speed, design specifications and design parameters of the optimal design of the analogue CMOS amplifier circuits. It is shown that BSA-DE-based design technique for each amplifier circuit yields the least MOS transistor area, and each designed circuit is shown to have the best performance parameters such as gain, power dissipation, etc., as compared with those of other recently reported literature.

Integrated Model of Multiple Kernel Learning and Differential Evolution for EUR/USD Trading

PubMed Central

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits. PMID:25097891

Single-bubble sonoluminescence in sulfuric acid and water: bubble dynamics, stability, and continuous spectra.

PubMed

Puente, Gabriela F; García-Martínez, Pablo; Bonetto, Fabián J

2007-01-01

We present theoretical calculations of an argon bubble in a liquid solution of 85%wt sulfuric acid and 15%wt water in single-bubble sonoluminescence. We used a model without free parameters to be adjusted. We predict from first principles the region in parameter space for stable bubble evolution, the temporal evolution of the bubble radius, the maximum temperature, pressures, and the light spectra due to thermal emissions. We also used a partial differential equation based model (hydrocode) to compute the temperature and pressure evolutions at the center of the bubble during maximum compression. We found the behavior of this liquid mixture to be very different from water in several aspects. Most of the models in sonoluminescence were compared with water experimental results.

Effect of differential speed rolling on the texture evolution of Mg-4Zn-1Gd alloy

NASA Astrophysics Data System (ADS)

Shim, Myeong-Shik; Suh, Byeong-Chan; Kim, Jae H.; Kim, Nack J.

2015-05-01

The microstructural and texture evolution during differential speed rolling process of Mg 4Zn-1Gd (wt%) alloy have been investigated by means of electron backscatter diffraction observation and texture analysis. The angular distribution of basal poles are inclined about 10° from the normal direction towards the rolling direction and the maximum intensities of basal poles are decreased, compared to the conventional rolling process. Such an inclination of angular distribution of basal poles can be induced by the operation of shear stress along the rolling direction, as much as one quarter of tensile stress along the RD and one quarter of compressive stress along the ND. When the reduction ratios in differential speed rolling increase, there is no difference in texture evolution although there is a significant change in activated twinning systems. In addition, the engineering stresses after differential speed rolling are also similar to that after conventional rolling process, while ductility and stretch formability in the former are worse than those in the latter.

Mars Geological Province Designations for the Interpretation of GRS Data

NASA Technical Reports Server (NTRS)

Dohm, J. M.; Kerry, K.; Baker, V. R.; Boynton, W.; Maruyama, Shige; Anderson, R. C.

2005-01-01

Introduction: An overarching geologic theory, GEOMARS, coherently explains many otherwise anomalous aspects of the geological history of Mars. Premises for a theory of martian geologic evolution include: (1) Mars is a water-rich terrestrial planet, (2) terrestrial planets should evolve through progressive stages of dynamical history (accretion, differentiation, tectonism) and mantle convection (magma ocean, plate tectonism, stagnant lid), and (3) the early history of Earth affords an analogue to the evolution of Mars. The theory describes the following major stages of evolution for Mars (from oldest to youngest): Stage 1 - shortly after accretion, Mars differentiates to a liquid metallic core, a mantle boundary (MBL) of high-pressure silicate mineral phases, upper mantle, magma ocean, thin komatiic crust, and convecting steam atmosphere; Stage 2- Mars cools to condense its steam atmosphere and transform its mode of mantle convection to plate tectonism; subduction of waterrich oceanic crust initiates arc volcanism and transfers water, carbonates and sulfates to the mantle; Stage 3 - the core dynamo initiates, and the associated magnetosphere leads to conditions conducive to the development of near-surface life and photosynthetic production of oxygen; Stage 4 - accretion of thickened, continental crust and subduction of hydrated oceanic crust to the mantle boundary layer and lower mantle of Mars occurs; Stage 5 - the core dynamo stops during Noachian heavy bombardment while plate tectonism continues; Stage 6 - initiation of the Tharsis superplume (approx. between 4.0 and 3.8Ga) occurs, and Stage 7 - the superlume phase (stagnant-lid regime) of martian planetary evolution with episodic phases of volcanism and water outflows continues into the present. The GEOMARS Theory is testable through a multidisciplinary approach, including utilizing GRS-based information. Based on a synthesis of published geologic, paleohydrologic, topographic, geophysical, spectral, and elemental information, we have defined geologic provinces that represent significant windows into the geological evolution of Mars, unfolding the GEOMARS Theory and forming the basis for interpreting GRS data.

Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity

PubMed Central

2014-01-01

Background Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of ‘adaptive differentiation with minimal gene flow’ in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Results Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Conclusions Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments. PMID:24674227

Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity.

PubMed

Odendaal, Lizelle J; Jacobs, David S; Bishop, Jacqueline M

2014-03-27

Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of 'adaptive differentiation with minimal gene flow' in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments.

A novel composite adaptive flap controller design by a high-efficient modified differential evolution identification approach.

PubMed

Li, Nailu; Mu, Anle; Yang, Xiyun; Magar, Kaman T; Liu, Chao

2018-05-01

The optimal tuning of adaptive flap controller can improve adaptive flap control performance on uncertain operating environments, but the optimization process is usually time-consuming and it is difficult to design proper optimal tuning strategy for the flap control system (FCS). To solve this problem, a novel adaptive flap controller is designed based on a high-efficient differential evolution (DE) identification technique and composite adaptive internal model control (CAIMC) strategy. The optimal tuning can be easily obtained by DE identified inverse of the FCS via CAIMC structure. To achieve fast tuning, a high-efficient modified adaptive DE algorithm is proposed with new mutant operator and varying range adaptive mechanism for the FCS identification. A tradeoff between optimized adaptive flap control and low computation cost is successfully achieved by proposed controller. Simulation results show the robustness of proposed method and its superiority to conventional adaptive IMC (AIMC) flap controller and the CAIMC flap controllers using other DE algorithms on various uncertain operating conditions. The high computation efficiency of proposed controller is also verified based on the computation time on those operating cases. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies.

PubMed

Yang, Cheng-Hong; Chuang, Li-Yeh; Lin, Yu-Da

2017-08-01

Detecting epistatic interactions in genome-wide association studies (GWAS) is a computational challenge. Such huge numbers of single-nucleotide polymorphism (SNP) combinations limit the some of the powerful algorithms to be applied to detect the potential epistasis in large-scale SNP datasets. We propose a new algorithm which combines the differential evolution (DE) algorithm with a classification based multifactor-dimensionality reduction (CMDR), termed DECMDR. DECMDR uses the CMDR as a fitness measure to evaluate values of solutions in DE process for scanning the potential statistical epistasis in GWAS. The results indicated that DECMDR outperforms the existing algorithms in terms of detection success rate by the large simulation and real data obtained from the Wellcome Trust Case Control Consortium. For running time comparison, DECMDR can efficient to apply the CMDR to detect the significant association between cases and controls amongst all possible SNP combinations in GWAS. DECMDR is freely available at https://goo.gl/p9sLuJ . chuang@isu.edu.tw or e0955767257@yahoo.com.tw. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Neuronal populations in the basolateral nuclei of the amygdala are differentially increased in humans compared with apes: a stereological study.

PubMed

Barger, Nicole; Stefanacci, Lisa; Schumann, Cynthia M; Sherwood, Chet C; Annese, Jacopo; Allman, John M; Buckwalter, Joseph A; Hof, Patrick R; Semendeferi, Katerina

2012-09-01

In human and nonhuman primates, the amygdala is known to play critical roles in emotional and social behavior. Anatomically, individual amygdaloid nuclei are connected with many neural systems that are either differentially expanded or conserved over the course of primate evolution. To address amygdala evolution in humans and our closest living relatives, the apes, we used design-based stereological methods to obtain neuron counts for the amygdala and each of four major amygdaloid nuclei (the lateral, basal, accessory basal, and central nuclei) in humans, all great ape species, lesser apes, and one monkey species. Our goal was to determine whether there were significant differences in the number or percent of neurons distributed to individual nuclei among species. Additionally, regression analyses were performed on independent contrast data to determine whether any individual species deviated from allometric trends. There were two major findings. In humans, the lateral nucleus contained the highest number of neurons in the amygdala, whereas in apes the basal nucleus contained the highest number of neurons. Additionally, the human lateral nucleus contained 59% more neurons than predicted by allometric regressions on nonhuman primate data. Based on the largest sample ever analyzed in a comparative study of the hominoid amygdala, our findings suggest that an emphasis on the lateral nucleus is the main characteristic of amygdala specialization over the course of human evolution. Copyright © 2012 Wiley Periodicals, Inc.

Optimization of a mirror-based neutron source using differential evolution algorithm

NASA Astrophysics Data System (ADS)

Yurov, D. V.; Prikhodko, V. V.

2016-12-01

This study is dedicated to the assessment of capabilities of gas-dynamic trap (GDT) and gas-dynamic multiple-mirror trap (GDMT) as potential neutron sources for subcritical hybrids. In mathematical terms the problem of the study has been formulated as determining the global maximum of fusion gain (Q pl), the latter represented as a function of trap parameters. A differential evolution method has been applied to perform the search. Considered in all calculations has been a configuration of the neutron source with 20 m long distance between the mirrors and 100 MW heating power. It is important to mention that the numerical study has also taken into account a number of constraints on plasma characteristics so as to provide physical credibility of searched-for trap configurations. According to the results obtained the traps considered have demonstrated fusion gain up to 0.2, depending on the constraints applied. This enables them to be used either as neutron sources within subcritical reactors for minor actinides incineration or as material-testing facilities.

Adaptive array technique for differential-phase reflectometry in QUEST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Idei, H., E-mail: idei@triam.kyushu-u.ac.jp; Hanada, K.; Zushi, H.

2014-11-15

A Phased Array Antenna (PAA) was considered as launching and receiving antennae in reflectometry to attain good directivity in its applied microwave range. A well-focused beam was obtained in a launching antenna application, and differential-phase evolution was properly measured by using a metal reflector plate in the proof-of-principle experiment at low power test facilities. Differential-phase evolution was also evaluated by using the PAA in the Q-shu University Experiment with Steady State Spherical Tokamak (QUEST). A beam-forming technique was applied in receiving phased-array antenna measurements. In the QUEST device that should be considered as a large oversized cavity, standing wave effectmore » was significantly observed with perturbed phase evolution. A new approach using derivative of measured field on propagating wavenumber was proposed to eliminate the standing wave effect.« less

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes.

PubMed

Li, Shu-Fen; Zhang, Guo-Jun; Yuan, Jin-Hong; Deng, Chuan-Liang; Gao, Wu-Jun

2016-05-01

The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.

Evolution of plant conducting cells: perspectives from key regulators of vascular cell differentiation.

PubMed

Ohtani, Misato; Akiyoshi, Nobuhiro; Takenaka, Yuto; Sano, Ryosuke; Demura, Taku

2017-01-01

One crucial problem that plants faced during their evolution, particularly during the transition to growth on land, was how to transport water, nutrients, metabolites, and small signaling molecules within a large, multicellular body. As a solution to this problem, land plants developed specific tissues for conducting molecules, called water-conducting cells (WCCs) and food-conducting cells (FCCs). The well-developed WCCs and FCCs in extant plants are the tracheary elements and sieve elements, respectively, which are found in vascular plants. Recent molecular genetic studies revealed that transcriptional networks regulate the differentiation of tracheary and sieve elements, and that the networks governing WCC differentiation are largely conserved among land plant species. In this review, we discuss the molecular evolution of plant conducting cells. By focusing on the evolution of the key transcription factors that regulate vascular cell differentiation, the NAC transcription factor VASCULAR-RELATED NAC-DOMAIN for WCCs and the MYB-coiled-coil (CC)-type transcription factor ALTERED PHLOEM DEVELOPMENT for sieve elements, we describe how land plants evolved molecular systems to produce the specialized cells that function as WCCs and FCCs. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation

PubMed Central

Zektser, Yulia; Mahajan, Shivani; Bachtrog, Doris

2013-01-01

Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution. PMID:24015111

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

PubMed Central

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Optimal Control for Stochastic Delay Evolution Equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Qingxin, E-mail: mqx@hutc.zj.cn; Shen, Yang, E-mail: skyshen87@gmail.com

2016-08-15

In this paper, we investigate a class of infinite-dimensional optimal control problems, where the state equation is given by a stochastic delay evolution equation with random coefficients, and the corresponding adjoint equation is given by an anticipated backward stochastic evolution equation. We first prove the continuous dependence theorems for stochastic delay evolution equations and anticipated backward stochastic evolution equations, and show the existence and uniqueness of solutions to anticipated backward stochastic evolution equations. Then we establish necessary and sufficient conditions for optimality of the control problem in the form of Pontryagin’s maximum principles. To illustrate the theoretical results, we applymore » stochastic maximum principles to study two examples, an infinite-dimensional linear-quadratic control problem with delay and an optimal control of a Dirichlet problem for a stochastic partial differential equation with delay. Further applications of the two examples to a Cauchy problem for a controlled linear stochastic partial differential equation and an optimal harvesting problem are also considered.« less

Estimating selection through male fitness: three complementary methods illuminate the nature and causes of selection on flowering time

PubMed Central

Austen, Emily J.; Weis, Arthur E.

2016-01-01

Our understanding of selection through male fitness is limited by the resource demands and indirect nature of the best available genetic techniques. Applying complementary, independent approaches to this problem can help clarify evolution through male function. We applied three methods to estimate selection on flowering time through male fitness in experimental populations of the annual plant Brassica rapa: (i) an analysis of mating opportunity based on flower production schedules, (ii) genetic paternity analysis, and (iii) a novel approach based on principles of experimental evolution. Selection differentials estimated by the first method disagreed with those estimated by the other two, indicating that mating opportunity was not the principal driver of selection on flowering time. The genetic and experimental evolution methods exhibited striking agreement overall, but a slight discrepancy between the two suggested that negative environmental covariance between age at flowering and male fitness may have contributed to phenotypic selection. Together, the three methods enriched our understanding of selection on flowering time, from mating opportunity to phenotypic selection to evolutionary response. The novel experimental evolution method may provide a means of examining selection through male fitness when genetic paternity analysis is not possible. PMID:26911957

Decoupling of the Leading Order DGLAP Evolution Equation with Spin Dependent Structure Functions

NASA Astrophysics Data System (ADS)

Azadbakht, F. Teimoury; Boroun, G. R.

2018-02-01

We propose an analytical solution for DGLAP evolution equations with polarized splitting functions at the Leading Order (LO) approximation based on the Laplace transform method. It is shown that the DGLAP evolution equations can be decoupled completely into two second order differential equations which then are solved analytically by using the initial conditions δ FS(x,Q2)=F[partial δ FS0(x), δ FS0(x)] and {δ G}(x,Q2)=G[partial δ G0(x), δ G0(x)]. We used this method to obtain the polarized structure function of the proton as well as the polarized gluon distribution function inside the proton and compared the numerical results with experimental data of COMPASS, HERMES, and AAC'08 Collaborations. It was found that there is a good agreement between our predictions and the experiments.

Multiphysics of bone remodeling: A 2D mesoscale activation simulation.

PubMed

Spingarn, C; Wagner, D; Rémond, Y; George, D

2017-01-01

In this work, we present an evolutive trabecular model for bone remodeling based on a boundary detection algorithm accounting for both biology and applied mechanical forces, known to be an important factor in bone evolution. A finite element (FE) numerical model using the Abaqus/Standard® software was used with a UMAT subroutine to solve the governing coupled mechanical-biological non-linear differential equations of the bone evolution model. The simulations present cell activation on a simplified trabeculae configuration organization with trabecular thickness of 200µm. For this activation process, the results confirm that the trabeculae are mainly oriented in the active direction of the principal mechanical stresses and according to the principal applied mechanical load directions. The trabeculae surface activation is clearly identified and can provide understanding of the different bone cell activations in more complex geometries and load conditions.

Soliton evolution and radiation loss for the sine-Gordon equation.

PubMed

Smyth, N F; Worthy, A L

1999-08-01

An approximate method for describing the evolution of solitonlike initial conditions to solitons for the sine-Gordon equation is developed. This method is based on using a solitonlike pulse with variable parameters in an averaged Lagrangian for the sine-Gordon equation. This averaged Lagrangian is then used to determine ordinary differential equations governing the evolution of the pulse parameters. The pulse evolves to a steady soliton by shedding dispersive radiation. The effect of this radiation is determined by examining the linearized sine-Gordon equation and loss terms are added to the variational equations derived from the averaged Lagrangian by using the momentum and energy conservation equations for the sine-Gordon equation. Solutions of the resulting approximate equations, which include loss, are found to be in good agreement with full numerical solutions of the sine-Gordon equation.

Local Orientation and the Evolution of Foraging: Changes in Decision Making Can Eliminate Evolutionary Trade-offs

PubMed Central

van der Post, Daniel J.; Semmann, Dirk

2011-01-01

Information processing is a major aspect of the evolution of animal behavior. In foraging, responsiveness to local feeding opportunities can generate patterns of behavior which reflect or “recognize patterns” in the environment beyond the perception of individuals. Theory on the evolution of behavior generally neglects such opportunity-based adaptation. Using a spatial individual-based model we study the role of opportunity-based adaptation in the evolution of foraging, and how it depends on local decision making. We compare two model variants which differ in the individual decision making that can evolve (restricted and extended model), and study the evolution of simple foraging behavior in environments where food is distributed either uniformly or in patches. We find that opportunity-based adaptation and the pattern recognition it generates, plays an important role in foraging success, particularly in patchy environments where one of the main challenges is “staying in patches”. In the restricted model this is achieved by genetic adaptation of move and search behavior, in light of a trade-off on within- and between-patch behavior. In the extended model this trade-off does not arise because decision making capabilities allow for differentiated behavioral patterns. As a consequence, it becomes possible for properties of movement to be specialized for detection of patches with more food, a larger scale information processing not present in the restricted model. Our results show that changes in decision making abilities can alter what kinds of pattern recognition are possible, eliminate an evolutionary trade-off and change the adaptive landscape. PMID:21998571

Local orientation and the evolution of foraging: changes in decision making can eliminate evolutionary trade-offs.

PubMed

van der Post, Daniel J; Semmann, Dirk

2011-10-01

Information processing is a major aspect of the evolution of animal behavior. In foraging, responsiveness to local feeding opportunities can generate patterns of behavior which reflect or "recognize patterns" in the environment beyond the perception of individuals. Theory on the evolution of behavior generally neglects such opportunity-based adaptation. Using a spatial individual-based model we study the role of opportunity-based adaptation in the evolution of foraging, and how it depends on local decision making. We compare two model variants which differ in the individual decision making that can evolve (restricted and extended model), and study the evolution of simple foraging behavior in environments where food is distributed either uniformly or in patches. We find that opportunity-based adaptation and the pattern recognition it generates, plays an important role in foraging success, particularly in patchy environments where one of the main challenges is "staying in patches". In the restricted model this is achieved by genetic adaptation of move and search behavior, in light of a trade-off on within- and between-patch behavior. In the extended model this trade-off does not arise because decision making capabilities allow for differentiated behavioral patterns. As a consequence, it becomes possible for properties of movement to be specialized for detection of patches with more food, a larger scale information processing not present in the restricted model. Our results show that changes in decision making abilities can alter what kinds of pattern recognition are possible, eliminate an evolutionary trade-off and change the adaptive landscape.

Conical differentiability for evolution variational inequalities

NASA Astrophysics Data System (ADS)

Jarušek, Jiří; Krbec, Miroslav; Rao, Murali; Sokołowski, Jan

The conical differentiability of solutions to the parabolic variational inequality with respect to the right-hand side is proved in the paper. From one side the result is based on the Lipschitz continuity in H {1}/{2},1 (Q) of solutions to the variational inequality with respect to the right-hand side. On the other side, in view of the polyhedricity of the convex cone K={v∈ H;v |Σ c⩾0,v |Σ d=0}, we prove new results on sensitivity analysis of parabolic variational inequalities. Therefore, we have a positive answer to the question raised by Fulbert Mignot (J. Funct. Anal. 22 (1976) 25-32).

On the account of gravitational perturbations in computer simulation technology of meteoroid complex formation and evolution

NASA Astrophysics Data System (ADS)

Kulikova, N. V.; Chepurova, V. M.

2009-10-01

So far we investigated the nonperturbation dynamics of meteoroid complexes. The numerical integration of the differential equations of motion in the N-body problem by the Everhart algorithm (N=2-6) and introduction of the intermediate hyperbolic orbits build on the base of the generalized problem of two fixed centers permit to take into account some gravitational perturbations.

Vesta Evolution from Surface Mineralogy: Mafic and Ultramafic Mineral Distribution

NASA Technical Reports Server (NTRS)

DeSanctis, M. C.; Ammannito, E.; Palomba, E.; Longobardo, A.; Mittlefehldt, D. W.; McSween, H. Y; Marchi, S.; Capria, M. T.; Capaccioni, F.; Frigeri, A.;

Internal constitution and evolution of the moon.

NASA Technical Reports Server (NTRS)

Solomon, S. C.; Toksoz, M. N.

1973-01-01

The composition, structure and evolution of the moon's interior are narrowly constrained by a large assortment of physical and chemical data. Models of the thermal evolution of the moon that fit the chronology of igneous activity on the lunar surface, the stress history of the lunar lithosphere implied by the presence of mascons, and the surface concentrations of radioactive elements, involve extensive differentiation early in lunar history. This differentiation may be the result of rapid accretion and large-scale melting or of primary chemical layering during accretion; differences in present-day temperatures for these two possibilities are significant only in the inner 1000 km of the moon and may not be resolvable.

Guiding the osteogenic fate of mouse and human mesenchymal stem cells through feedback system control.

PubMed

Honda, Yoshitomo; Ding, Xianting; Mussano, Federico; Wiberg, Akira; Ho, Chih-Ming; Nishimura, Ichiro

2013-12-05

Stem cell-based disease modeling presents unique opportunities for mechanistic elucidation and therapeutic targeting. The stable induction of fate-specific differentiation is an essential prerequisite for stem cell-based strategy. Bone morphogenetic protein 2 (BMP-2) initiates receptor-regulated Smad phosphorylation, leading to the osteogenic differentiation of mesenchymal stromal/stem cells (MSC) in vitro; however, it requires supra-physiological concentrations, presenting a bottleneck problem for large-scale drug screening. Here, we report the use of a double-objective feedback system control (FSC) with a differential evolution (DE) algorithm to identify osteogenic cocktails of extrinsic factors. Cocktails containing significantly reduced doses of BMP-2 in combination with physiologically relevant doses of dexamethasone, ascorbic acid, beta-glycerophosphate, heparin, retinoic acid and vitamin D achieved accelerated in vitro mineralization of mouse and human MSC. These results provide insight into constructive approaches of FSC to determine the applicable functional and physiological environment for MSC in disease modeling, drug screening and tissue engineering.

Guiding the osteogenic fate of mouse and human mesenchymal stem cells through feedback system control

PubMed Central

Honda, Yoshitomo; Ding, Xianting; Mussano, Federico; Wiberg, Akira; Ho, Chih-ming; Nishimura, Ichiro

2013-01-01

Stem cell-based disease modeling presents unique opportunities for mechanistic elucidation and therapeutic targeting. The stable induction of fate-specific differentiation is an essential prerequisite for stem cell-based strategy. Bone morphogenetic protein 2 (BMP-2) initiates receptor-regulated Smad phosphorylation, leading to the osteogenic differentiation of mesenchymal stromal/stem cells (MSC) in vitro; however, it requires supra-physiological concentrations, presenting a bottleneck problem for large-scale drug screening. Here, we report the use of a double-objective feedback system control (FSC) with a differential evolution (DE) algorithm to identify osteogenic cocktails of extrinsic factors. Cocktails containing significantly reduced doses of BMP-2 in combination with physiologically relevant doses of dexamethasone, ascorbic acid, beta-glycerophosphate, heparin, retinoic acid and vitamin D achieved accelerated in vitro mineralization of mouse and human MSC. These results provide insight into constructive approaches of FSC to determine the applicable functional and physiological environment for MSC in disease modeling, drug screening and tissue engineering. PMID:24305548

Mantle convection and the distribution of geochemical reservoirs in the silicate shell of the Earth

NASA Astrophysics Data System (ADS)

Walzer, Uwe; Hendel, Roland

2010-05-01

We present a dynamic 3-D spherical-shell model of mantle convection and the evolution of the chemical reservoirs of the Earth`s silicate shell. Chemical differentiation, convection, stirring and thermal evolution constitute an inseparable dynamic system. Our model is based on the solution of the balance equations of mass, momentum, energy, angular momentum, and four sums of the number of atoms of the pairs 238U-206Pb, 235U-207Pb, 232Th-208Pb, and 40K-40Ar. Similar to the present model, the continental crust of the real Earth was not produced entirely at the start of the evolution but developed episodically in batches [1-7]. The details of the continental distribution of the model are largely stochastic, but the spectral properties are quite similar to the present real Earth. The calculated Figures reveal that the modeled present-day mantle has no chemical stratification but we find a marble-cake structure. If we compare the observational results of the present-day proportion of depleted MORB mantle with the model then we find a similar order of magnitude. The MORB source dominates under the lithosphere. In our model, there are nowhere pure unblended reservoirs in the mantle. It is, however, remarkable that, in spite of 4500 Ma of solid-state mantle convection, certain strong concentrations of distributed chemical reservoirs continue to persist in certain volumes, although without sharp abundance boundaries. We deal with the question of predictable and stochastic portions of the phenomena. Although the convective flow patterns and the chemical differentiation of oceanic plateaus are coupled, the evolution of time-dependent Rayleigh number, Rat , is relatively well predictable and the stochastic parts of the Rat(t)-curves are small. Regarding the juvenile growth rates of the total mass of the continents, predictions are possible only in the first epoch of the evolution. Later on, the distribution of the continental-growth episodes is increasingly stochastic. Independently of the varying individual runs, our model shows that the total mass of the present-day continents is not generated in a single process at the beginning of the thermal evolution of the Earth but in episodically distributed processes in the course of geological time. This is in accord with observation. Finally, we present results regarding the numerical method, implementation, scalability and performance. References [1] Condie, K. C., Episodie continental growth models: Afterthoughts and extensions, Tectonophysics, 322 (2000), 153-162. [2] Davidson, J. P. and Arculus, R. J., The significance of Phanerozoic arc magmatism in generating continental crust, in Evolution and Differentiation of the Continental Crust, edited by M. Brown and T. Rushmer (2006), 135-172, Cambridge Univ. Press, Cambridge, UK. [3] Hofmann, A. W., Sampling mantle heterogeneity through oceanic basalts: Isotopes and trace elements, in Treatise on Geochemistry, Vol. 2: The Mantle and the Core, edited by R. W. Carlson (2003), 61-101, Elsevier, Amsterdam. [4] Rollinson, H., Crustal generation in the Archean, in Evolution and Differentiation of the Continental Crust, edited by M. Brown and T. Rushmer (2006), 173-230, Cambridge Univ. Press, Cambridge, UK: [5] Taylor, S. R. and McLennan, S. M., Planetary Crusts. Their Composition, Origin and Evolution. (2009), 1-378, Cambridge Univ. Press, Cambridge, UK. [6] Walzer, U. and Hendel, R., Mantle convection and evolution with growing continents. J. Geophys. Res. 113 (2008), B09405, doi: 10.1029/2007JB005459 [7] http://www.igw.uni-jena.de/geodyn

Repeated evolution of soldier sub-castes suggests parasitism drives social complexity in stingless bees.

PubMed

Grüter, Christoph; Segers, Francisca H I D; Menezes, Cristiano; Vollet-Neto, Ayrton; Falcón, Tiago; von Zuben, Lucas; Bitondi, Márcia M G; Nascimento, Fabio S; Almeida, Eduardo A B

2017-02-23

The differentiation of workers into morphological castes represents an important evolutionary innovation that is thought to improve division of labor in insect societies. Given the potential benefits of task-related worker differentiation, it is puzzling that physical worker castes, such as soldiers, are extremely rare in social bees and absent in wasps. Following the recent discovery of soldiers in a stingless bee, we studied the occurrence of worker differentiation in 28 stingless bee species from Brazil and found that several species have specialized soldiers for colony defence. Our results reveal that worker differentiation evolved repeatedly during the last ~ 25 million years and coincided with the emergence of parasitic robber bees, a major threat to many stingless bee species. Furthermore, our data suggest that these robbers are a driving force behind the evolution of worker differentiation as targets of robber bees are four times more likely to have nest guards of increased size than non-targets. These findings reveal unexpected diversity in the social organization of stingless bees.Although common in ants and termites, worker differentiation into physical castes is rare in social bees and unknown in wasps. Here, Grüter and colleagues find a guard caste in ten species of stingless bees and show that the evolution of the guard caste is associated with parasitization by robber bees.

Evolution of sprint speed in African savannah herbivores in relation to predation.

PubMed

Bro-Jørgensen, Jakob

2013-11-01

Predator-prey arms races are widely speculated to underlie fast speed in terrestrial mammals. However, due to lack of empirical testing, both the specificity of any evolutionary coupling between particular predator and prey species, and the relevance of alternative food-based hypotheses of speed evolution, remain obscure. Here I examine the ecological links between the sprint speed of African savannah herbivores, their vulnerability to predators, and their diet. I show that sprint speed is strongly predicted by the vulnerability of prey to their main predators; however, the direction of the link depends on the hunting style of the predator. Speed increases with vulnerability to pursuit predators, whereas vulnerability to ambush predators is associated with particularly slow speed. These findings suggest that differential vulnerability to specific predators can indeed drive interspecific variation in speed within prey communities, but that predator hunting style influences the intensity and consistency with which selection on speed is coupled between particular species. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

The evolutionary theory of asymmetry by V. Geodakyan

NASA Astrophysics Data System (ADS)

Geodakyan, Sergey V.

2015-08-01

For more than 150 years, all biological theories, including those of C. Darwin and Mendel, were based on the idea of synchronous evolution. They fit for unitary monomodal systems (asexual, symmetrical) but do not work for binary (dioecious, asymmetrical) ones. Examples of such binary conjugated differentiations are two sexes, DNA-proteins, autosomes-sex chromosomes, right and left brain hemispheres, and hands. For their understanding, "asynchronous" theories are needed. Such theories were proposed by Russian theoretical biologist Vigen A. Geodakyan for sexual, brain and body, and chromosomal differentiations. All theories are interconnected and are based on the principle of conjugated subsystems. This article covers the basic tenets of the evolutionary theory of asymmetry and answers the following questions: What benefits does lateralization provide? What logic, what principle is it based on? Why do brain hemispheres control the opposite sides of the body? Why laterality is closely related to sex? What are the biological prerequisites of terrorism?

Development of time-domain differential Raman for transient thermal probing of materials

DOE PAGES

Xu, Shen; Wang, Tianyu; Hurley, David; ...

2015-01-01

A novel transient thermal characterization technology is developed based on the principles of transient optical heating and Raman probing: time-domain differential Raman. It employs a square-wave modulated laser of varying duty cycle to realize controlled heating and transient thermal probing. Very well defined extension of the heating time in each measurement changes the temperature evolution profile and the probed temperature field at μs resolution. Using this new technique, the transient thermal response of a tipless Si cantilever is investigated along the length direction. A physical model is developed to reconstruct the Raman spectrum considering the temperature evolution, while taking intomore » account the temperature dependence of the Raman emission. By fitting the variation of the normalized Raman peak intensity, wavenumber, and peak area against the heating time, the thermal diffusivity is determined as 9.17 × 10⁻⁵, 8.14 × 10⁻⁵, and 9.51 × 10⁻⁵ m²/s. These results agree well with the reference value of 8.66 × 10⁻⁵ m²/s considering the 10% fitting uncertainty. The time-domain differential Raman provides a novel way to introduce transient thermal excitation of materials, probe the thermal response, and measure the thermal diffusivity, all with high accuracy.« less

Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.

PubMed

Doolittle, W Ford; Inkpen, S Andrew

2018-04-17

Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution's principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider-as "units of selection" in their own right-the processes implemented by genes, cells, species, or communities. "It's the song not the singer" (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that "holobionts" (microbes and their animal or plant hosts) are aggregate "units of selection," claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.

Intrinsically Disordered Proteins and the Origins of Multicellular Organisms

NASA Astrophysics Data System (ADS)

Dunker, A. Keith

In simple multicellular organisms all of the cells are in direct contact with the surrounding milieu, whereas in complex multicellular organisms some cells are completely surrounded by other cells. Current phylogenetic trees indicate that complex multicellular organisms evolved independently from unicellular ancestors about 10 times, and only among the eukaryotes, including once for animals, twice each for green, red, and brown algae, and thrice for fungi. Given these multiple independent evolutionary lineages, we asked two questions: 1. Which molecular functions underpinned the evolution of multicellular organisms?; and, 2. Which of these molecular functions depend on intrinsically disordered proteins (IDPs)? Compared to unicellularity, multicellularity requires the advent of molecules for cellular adhesion, for cell-cell communication and for developmental programs. In addition, the developmental programs need to be regulated over space and time. Finally, each multicellular organism has cell-specific biochemistry and physiology. Thus, the evolution of complex multicellular organisms from unicellular ancestors required five new classes of functions. To answer the second question we used Key-words in Swiss Protein ranked for associations with predictions of protein structure or disorder. With a Z-score of 18.8 compared to random-function proteins, à differentiation was the biological process most strongly associated with IDPs. As expected from this result, large numbers of individual proteins associated with differentiation exhibit substantial regions of predicted disorder. For the animals for which there is the most readily available data all five of the underpinning molecular functions for multicellularity were found to depend critically on IDP-based mechanisms and other evidence supports these ideas. While the data are more sparse, IDPs seem to similarly underlie the five new classes of functions for plants and fungi as well, suggesting that IDPs were indeed crucial for the evolution of complex multicellular organisms. These new findings necessitate a rethinking of the gene regulatory network models currently used to explain cellular differentiation and the evolution of complex multicellular organisms.

Dynamic optimization of open-loop input signals for ramp-up current profiles in tokamak plasmas

NASA Astrophysics Data System (ADS)

Ren, Zhigang; Xu, Chao; Lin, Qun; Loxton, Ryan; Teo, Kok Lay

2016-03-01

Establishing a good current spatial profile in tokamak fusion reactors is crucial to effective steady-state operation. The evolution of the current spatial profile is related to the evolution of the poloidal magnetic flux, which can be modeled in the normalized cylindrical coordinates using a parabolic partial differential equation (PDE) called the magnetic diffusion equation. In this paper, we consider the dynamic optimization problem of attaining the best possible current spatial profile during the ramp-up phase of the tokamak. We first use the Galerkin method to obtain a finite-dimensional ordinary differential equation (ODE) model based on the original magnetic diffusion PDE. Then, we combine the control parameterization method with a novel time-scaling transformation to obtain an approximate optimal parameter selection problem, which can be solved using gradient-based optimization techniques such as sequential quadratic programming (SQP). This control parameterization approach involves approximating the tokamak input signals by piecewise-linear functions whose slopes and break-points are decision variables to be optimized. We show that the gradient of the objective function with respect to the decision variables can be computed by solving an auxiliary dynamic system governing the state sensitivity matrix. Finally, we conclude the paper with simulation results for an example problem based on experimental data from the DIII-D tokamak in San Diego, California.

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

PubMed

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

College students' use of science content during socioscientific issues negotiation: Impact of evolution understanding and acceptance

NASA Astrophysics Data System (ADS)

Fowler, Samantha R.

The purpose of this study was to explore the evolution science content used during college students' negotiation of biology-based socioscientific issues (SSI) and examine how it related to students' conceptual understanding and acceptance of biological evolution. Specific research questions were, (1a) what specific evolutionary science content do college students evoke during SSI negotiation, (1b) what is the depth of the evolutionary science content reflected in college students. SSI negotiation, and (2) what is the nature of the interaction between evolution understanding and evolution acceptance as they relate to depth of use of evolution content during SSI negotiation? The Socioscientific Issues Questionnaire (SSI-Q) was developed using inductive data analysis to examine science content use and to develop a rubric for measuring depth of evolutionary science content use during SSI negotiation. Sixty upper level undergraduate biology and non-biology majors completed the SSI-Q and also the Conceptual Inventory of Natural Selection (CINS: Anderson, Fisher, & Norman, 2002) to measure evolution understanding and the Measure of Acceptance of the Theory of Evolution (MATE: Rutledge & Warden, 1999) to measure evolution acceptance. A multiple regression analysis tested for interaction effects between the predictor variables, evolution understanding and evolution acceptance. Results indicate that college students primarily use science concepts related to evolution to negotiate biology-based SSI: variation in a population, inheritance of traits, differential success, and change through time. The hypothesis that the extent of one's acceptance of evolution is a mitigating factor in how evolution content is evoked during SSI negotiation was supported by the data. This was seen in that evolution was the predominant science content used by participants for each of the three SSI scenarios used in this study and used consistently throughout the three SSI scenarios. In addition to its potential to assess aspects of argumentation, a modification of the SSI-Q could be used for further study about students' misconceptions about evolution or scientific literacy, if it is defined as one's tendency to utilize science content during a decision-making process within an SSI context.

Stellar differential rotation and coronal time-scales

NASA Astrophysics Data System (ADS)

Gibb, G. P. S.; Jardine, M. M.; Mackay, D. H.

2014-10-01

We investigate the time-scales of evolution of stellar coronae in response to surface differential rotation and diffusion. To quantify this, we study both the formation time and lifetime of a magnetic flux rope in a decaying bipolar active region. We apply a magnetic flux transport model to prescribe the evolution of the stellar photospheric field, and use this to drive the evolution of the coronal magnetic field via a magnetofrictional technique. Increasing the differential rotation (i.e. decreasing the equator-pole lap time) decreases the flux rope formation time. We find that the formation time is dependent upon the lap time and the surface diffusion time-scale through the relation τ_Form ∝ √{τ_Lapτ_Diff}. In contrast, the lifetimes of flux ropes are proportional to the lap time (τLife∝τLap). With this, flux ropes on stars with a differential rotation of more than eight times the solar value have a lifetime of less than 2 d. As a consequence, we propose that features such as solar-like quiescent prominences may not be easily observable on such stars, as the lifetimes of the flux ropes which host the cool plasma are very short. We conclude that such high differential rotation stars may have very dynamical coronae.

Sexual and reproductive behaviour of Drosophila melanogaster from a microclimatically interslope differentiated population of "Evolution Canyon" (Mount Carmel, Israel).

PubMed

Iliadi, K; Iliadi, N; Rashkovetsky, E; Minkov, I; Nevo, E; Korol, A

2001-11-22

The strong microscale interslope environmental differences in "Evolution Canyon" provide an excellent natural model for sympatric speciation. Our previous studies revealed significant slope-specific differences for a fitness complex of Drosophila. This complex involved either adaptation traits (tolerance to high temperature, different viability and longevity pattern) or behavioural differentiation, manifested in habitat choice and non-random mating. This remarkable differentiation has evolved despite a very small interslope distance (a few hundred metres only). Our hypothesis is that strong interslope microclimatic contrast caused differential selection for fitness-related traits accompanied by behavioural differentiation and reinforced by some sexual isolation, which started incipient speciation. Here we describe the results of a systematic analysis of sexual behaviour in a non-choice situation and several reproductive parameters of D. melanogaster populations from the opposite slopes of "Evolution Canyon". The evidence indicates that: (i) mate choice derives from differences in mating propensity and discrimination; (ii) females from the milder north-facing slope discriminate strongly against males of the opposite slope; (iii) both sexes of the south-facing slope display distinct reproductive and behavioural patterns with females showing increased fecundity, shorter time before remating and relatively higher receptivity, and males showing higher mating propensity. These patterns represent adaptive life strategies contributing to higher fitness.

Europa's Crust and Ocean: Origin, Composition, and the Prospects for Life

USGS Publications Warehouse

Kargel, J.S.; Kaye, J.Z.; Head, J. W.; Marion, G.M.; Sassen, R.; Crowley, J.K.; Ballesteros, O.P.; Grant, S.A.; Hogenboom, D.L.

2000-01-01

We have considered a wide array of scenarios for Europa's chemical evolution in an attempt to explain the presence of ice and hydrated materials on its surface and to understand the physical and chemical nature of any ocean that may lie below. We postulate that, following formation of the jovian system, the europan evolutionary sequence has as its major links: (a) initial carbonaceous chondrite rock, (b) global primordial aqueous differentiation and formation of an impure primordial hydrous crust, (c) brine evolution and intracrustal differentiation, (d) degassing of Europa's mantle and gas venting, (e) hydrothermal processes, and (f) chemical surface alteration. Our models were developed in the context of constraints provided by Galileo imaging, near infrared reflectance spectroscopy, and gravity and magnetometer data. Low-temperature aqueous differentiation from a carbonaceous CI or CM chondrite precursor, without further chemical processing, would result in a crust/ocean enriched in magnesium sulfate and sodium sulfate, consistent with Galileo spectroscopy. Within the bounds of this simple model, a wide range of possible layered structures may result; the final state depends on the details of intracrustal differentiation. Devolatilization of the rocky mantle and hydrothermal brine reactions could have produced very different ocean/crust compositions, e.g., an ocean/crust of sodium carbonate or sulfuric acid, or a crust containing abundant clathrate hydrates. Realistic chemical-physical evolution scenarios differ greatly in detailed predictions, but they generally call for a highly impure and chemically layered crust. Some of these models could lead also to lateral chemical heterogeneities by diapiric upwellings and/or cryovolcanism. We describe some plausible geological consequences of the physical-chemical structures predicted from these scenarios. These predicted consequences and observed aspects of Europa's geology may serve as a basis for further analys is and discrimination among several alternative scenarios. Most chemical pathways could support viable ecosystems based on analogy with the metabolic and physiological versatility of terrestrial microorganisms. ?? 2000 Academic Press.

Sex Pheromone Evolution Is Associated with Differential Regulation of the Same Desaturase Gene in Two Genera of Leafroller Moths

PubMed Central

Albre, Jérôme; Liénard, Marjorie A.; Sirey, Tamara M.; Schmidt, Silvia; Tooman, Leah K.; Carraher, Colm; Greenwood, David R.; Löfstedt, Christer; Newcomb, Richard D.

2012-01-01

Chemical signals are prevalent in sexual communication systems. Mate recognition has been extensively studied within the Lepidoptera, where the production and recognition of species-specific sex pheromone signals are typically the defining character. While the specific blend of compounds that makes up the sex pheromones of many species has been characterized, the molecular mechanisms underpinning the evolution of pheromone-based mate recognition systems remain largely unknown. We have focused on two sets of sibling species within the leafroller moth genera Ctenopseustis and Planotortrix that have rapidly evolved the use of distinct sex pheromone blends. The compounds within these blends differ almost exclusively in the relative position of double bonds that are introduced by desaturase enzymes. Of the six desaturase orthologs isolated from all four species, functional analyses in yeast and gene expression in pheromone glands implicate three in pheromone biosynthesis, two Δ9-desaturases, and a Δ10-desaturase, while the remaining three desaturases include a Δ6-desaturase, a terminal desaturase, and a non-functional desaturase. Comparative quantitative real-time PCR reveals that the Δ10-desaturase is differentially expressed in the pheromone glands of the two sets of sibling species, consistent with differences in the pheromone blend in both species pairs. In the pheromone glands of species that utilize (Z)-8-tetradecenyl acetate as sex pheromone component (Ctenopseustis obliquana and Planotortrix octo), the expression levels of the Δ10-desaturase are significantly higher than in the pheromone glands of their respective sibling species (C. herana and P. excessana). Our results demonstrate that interspecific sex pheromone differences are associated with differential regulation of the same desaturase gene in two genera of moths. We suggest that differential gene regulation among members of a multigene family may be an important mechanism of molecular innovation in sex pheromone evolution and speciation. PMID:22291612

Partition-free approach to open quantum systems in harmonic environments: An exact stochastic Liouville equation

NASA Astrophysics Data System (ADS)

McCaul, G. M. G.; Lorenz, C. D.; Kantorovich, L.

2017-03-01

We present a partition-free approach to the evolution of density matrices for open quantum systems coupled to a harmonic environment. The influence functional formalism combined with a two-time Hubbard-Stratonovich transformation allows us to derive a set of exact differential equations for the reduced density matrix of an open system, termed the extended stochastic Liouville-von Neumann equation. Our approach generalizes previous work based on Caldeira-Leggett models and a partitioned initial density matrix. This provides a simple, yet exact, closed-form description for the evolution of open systems from equilibriated initial conditions. The applicability of this model and the potential for numerical implementations are also discussed.

Reduced mutation rate in exons due to differential mismatch repair

PubMed Central

Mularoni, Loris; Muiños, Ferran; Gonzalez-Perez, Abel; López-Bigas, Núria

2017-01-01

While recent studies have revealed higher than anticipated heterogeneity of mutation rate across genomic regions, mutations in exons and introns are assumed to be generated at the same rate. Here we find fewer somatic mutations in exons than expected based on their sequence content, and demonstrate that this is not due to purifying selection. Moreover, we show that it is caused by higher mismatch repair activity in exonic than in intronic regions. Our findings have important implications for our understanding of mutational and DNA repair processes, our knowledge of the evolution of eukaryotic genes, and practical ramifications for the study of the evolution of both tumors and species. PMID:29106418

Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae).

PubMed

McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

Multi-Objective Differential Evolution for Voltage Security Constrained Optimal Power Flow in Deregulated Power Systems

NASA Astrophysics Data System (ADS)

Roselyn, J. Preetha; Devaraj, D.; Dash, Subhransu Sekhar

2013-11-01

Voltage stability is an important issue in the planning and operation of deregulated power systems. The voltage stability problems is a most challenging one for the system operators in deregulated power systems because of the intense use of transmission line capabilities and poor regulation in market environment. This article addresses the congestion management problem avoiding offline transmission capacity limits related to voltage stability by considering Voltage Security Constrained Optimal Power Flow (VSCOPF) problem in deregulated environment. This article presents the application of Multi Objective Differential Evolution (MODE) algorithm to solve the VSCOPF problem in new competitive power systems. The maximum of L-index of the load buses is taken as the indicator of voltage stability and is incorporated in the Optimal Power Flow (OPF) problem. The proposed method in hybrid power market which also gives solutions to voltage stability problems by considering the generation rescheduling cost and load shedding cost which relieves the congestion problem in deregulated environment. The buses for load shedding are selected based on the minimum eigen value of Jacobian with respect to the load shed. In the proposed approach, real power settings of generators in base case and contingency cases, generator bus voltage magnitudes, real and reactive power demands of selected load buses using sensitivity analysis are taken as the control variables and are represented as the combination of floating point numbers and integers. DE/randSF/1/bin strategy scheme of differential evolution with self-tuned parameter which employs binomial crossover and difference vector based mutation is used for the VSCOPF problem. A fuzzy based mechanism is employed to get the best compromise solution from the pareto front to aid the decision maker. The proposed VSCOPF planning model is implemented on IEEE 30-bus system, IEEE 57 bus practical system and IEEE 118 bus system. The pareto optimal front obtained from MODE is compared with reference pareto front and the best compromise solution for all the cases are obtained from fuzzy decision making strategy. The performance measures of proposed MODE in two test systems are calculated using suitable performance metrices. The simulation results show that the proposed approach provides considerable improvement in the congestion management by generation rescheduling and load shedding while enhancing the voltage stability in deregulated power system.

Orbital-differentiated coherence-incoherence crossover identified by photoemission spectroscopy in LiFeAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miao, H.; Yin, Z. P.; Wu, S. F.

In the iron-based superconductors (FeSCs), orbital differentiation is an important phenomenon, whereby correlations stronger on the d xy orbital than on the d xz/d yz orbital yield quasi-particles with d xy orbital character having larger mass renormalization and abnormal temperature evolution. However, the physical origin of this orbital di erentiation is debated between the Hund's coupling induced unbinding of spin and orbital degrees of freedom and the Hubbard interaction instigated orbital selective Mott transition. Here we use angle-resolved photoemission spectroscopy to identify an orbital-dependent correlation-induced quasi-particle (QP) anomaly in LiFeAs. Lastly, the excellent agreement between our photoemission measurements and first-principlesmore » many-body theory calculations shows that the orbital-differentiated QP lifetime anomalies in LiFeAs are controlled by the Hund's coupling.« less

Orbital-differentiated coherence-incoherence crossover identified by photoemission spectroscopy in LiFeAs

DOE PAGES

Miao, H.; Yin, Z. P.; Wu, S. F.; ...

2016-11-14

In the iron-based superconductors (FeSCs), orbital differentiation is an important phenomenon, whereby correlations stronger on the d xy orbital than on the d xz/d yz orbital yield quasi-particles with d xy orbital character having larger mass renormalization and abnormal temperature evolution. However, the physical origin of this orbital di erentiation is debated between the Hund's coupling induced unbinding of spin and orbital degrees of freedom and the Hubbard interaction instigated orbital selective Mott transition. Here we use angle-resolved photoemission spectroscopy to identify an orbital-dependent correlation-induced quasi-particle (QP) anomaly in LiFeAs. Lastly, the excellent agreement between our photoemission measurements and first-principlesmore » many-body theory calculations shows that the orbital-differentiated QP lifetime anomalies in LiFeAs are controlled by the Hund's coupling.« less

Kullback-Leibler Divergence-Based Differential Evolution Markov Chain Filter for Global Localization of Mobile Robots.

PubMed

Martín, Fernando; Moreno, Luis; Garrido, Santiago; Blanco, Dolores

2015-09-16

One of the most important skills desired for a mobile robot is the ability to obtain its own location even in challenging environments. The information provided by the sensing system is used here to solve the global localization problem. In our previous work, we designed different algorithms founded on evolutionary strategies in order to solve the aforementioned task. The latest developments are presented in this paper. The engine of the localization module is a combination of the Markov chain Monte Carlo sampling technique and the Differential Evolution method, which results in a particle filter based on the minimization of a fitness function. The robot's pose is estimated from a set of possible locations weighted by a cost value. The measurements of the perceptive sensors are used together with the predicted ones in a known map to define a cost function to optimize. Although most localization methods rely on quadratic fitness functions, the sensed information is processed asymmetrically in this filter. The Kullback-Leibler divergence is the basis of a cost function that makes it possible to deal with different types of occlusions. The algorithm performance has been checked in a real map. The results are excellent in environments with dynamic and unmodeled obstacles, a fact that causes occlusions in the sensing area.

Day-Ahead PM2.5 Concentration Forecasting Using WT-VMD Based Decomposition Method and Back Propagation Neural Network Improved by Differential Evolution

PubMed Central

Wang, Deyun; Liu, Yanling; Luo, Hongyuan; Yue, Chenqiang; Cheng, Sheng

2017-01-01

Accurate PM2.5 concentration forecasting is crucial for protecting public health and atmospheric environment. However, the intermittent and unstable nature of PM2.5 concentration series makes its forecasting become a very difficult task. In order to improve the forecast accuracy of PM2.5 concentration, this paper proposes a hybrid model based on wavelet transform (WT), variational mode decomposition (VMD) and back propagation (BP) neural network optimized by differential evolution (DE) algorithm. Firstly, WT is employed to disassemble the PM2.5 concentration series into a number of subsets with different frequencies. Secondly, VMD is applied to decompose each subset into a set of variational modes (VMs). Thirdly, DE-BP model is utilized to forecast all the VMs. Fourthly, the forecast value of each subset is obtained through aggregating the forecast results of all the VMs obtained from VMD decomposition of this subset. Finally, the final forecast series of PM2.5 concentration is obtained by adding up the forecast values of all subsets. Two PM2.5 concentration series collected from Wuhan and Tianjin, respectively, located in China are used to test the effectiveness of the proposed model. The results demonstrate that the proposed model outperforms all the other considered models in this paper. PMID:28704955

Kullback-Leibler Divergence-Based Differential Evolution Markov Chain Filter for Global Localization of Mobile Robots

PubMed Central

Martín, Fernando; Moreno, Luis; Garrido, Santiago; Blanco, Dolores

2015-01-01

One of the most important skills desired for a mobile robot is the ability to obtain its own location even in challenging environments. The information provided by the sensing system is used here to solve the global localization problem. In our previous work, we designed different algorithms founded on evolutionary strategies in order to solve the aforementioned task. The latest developments are presented in this paper. The engine of the localization module is a combination of the Markov chain Monte Carlo sampling technique and the Differential Evolution method, which results in a particle filter based on the minimization of a fitness function. The robot’s pose is estimated from a set of possible locations weighted by a cost value. The measurements of the perceptive sensors are used together with the predicted ones in a known map to define a cost function to optimize. Although most localization methods rely on quadratic fitness functions, the sensed information is processed asymmetrically in this filter. The Kullback-Leibler divergence is the basis of a cost function that makes it possible to deal with different types of occlusions. The algorithm performance has been checked in a real map. The results are excellent in environments with dynamic and unmodeled obstacles, a fact that causes occlusions in the sensing area. PMID:26389914

Lie symmetries for systems of evolution equations

NASA Astrophysics Data System (ADS)

Paliathanasis, Andronikos; Tsamparlis, Michael

2018-01-01

The Lie symmetries for a class of systems of evolution equations are studied. The evolution equations are defined in a bimetric space with two Riemannian metrics corresponding to the space of the independent and dependent variables of the differential equations. The exact relation of the Lie symmetries with the collineations of the bimetric space is determined.

Evolution families of conformal mappings with fixed points and the Löwner-Kufarev equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goryainov, V V

2015-01-31

The paper is concerned with evolution families of conformal mappings of the unit disc to itself that fix an interior point and a boundary point. Conditions are obtained for the evolution families to be differentiable, and an existence and uniqueness theorem for an evolution equation is proved. A convergence theorem is established which describes the topology of locally uniform convergence of evolution families in terms of infinitesimal generating functions. The main result in this paper is the embedding theorem which shows that any conformal mapping of the unit disc to itself with two fixed points can be embedded into a differentiable evolution familymore » of such mappings. This result extends the range of the parametric method in the theory of univalent functions. In this way the problem of the mutual change of the derivative at an interior point and the angular derivative at a fixed point on the boundary is solved for a class of mappings of the unit disc to itself. In particular, the rotation theorem is established for this class of mappings. Bibliography: 27 titles.« less

A new medical image segmentation model based on fractional order differentiation and level set

NASA Astrophysics Data System (ADS)

Chen, Bo; Huang, Shan; Xie, Feifei; Li, Lihong; Chen, Wensheng; Liang, Zhengrong

2018-03-01

Segmenting medical images is still a challenging task for both traditional local and global methods because the image intensity inhomogeneous. In this paper, two contributions are made: (i) on the one hand, a new hybrid model is proposed for medical image segmentation, which is built based on fractional order differentiation, level set description and curve evolution; and (ii) on the other hand, three popular definitions of Fourier-domain, Grünwald-Letnikov (G-L) and Riemann-Liouville (R-L) fractional order differentiation are investigated and compared through experimental results. Because of the merits of enhancing high frequency features of images and preserving low frequency features of images in a nonlinear manner by the fractional order differentiation definitions, one fractional order differentiation definition is used in our hybrid model to perform segmentation of inhomogeneous images. The proposed hybrid model also integrates fractional order differentiation, fractional order gradient magnitude and difference image information. The widely-used dice similarity coefficient metric is employed to evaluate quantitatively the segmentation results. Firstly, experimental results demonstrated that a slight difference exists among the three expressions of Fourier-domain, G-L, RL fractional order differentiation. This outcome supports our selection of one of the three definitions in our hybrid model. Secondly, further experiments were performed for comparison between our hybrid segmentation model and other existing segmentation models. A noticeable gain was seen by our hybrid model in segmenting intensity inhomogeneous images.

Novel approach to differentiate subclades of varicella-zoster virus genotypes E1 and E2 in Germany.

PubMed

Schmidt-Chanasit, Jonas; Olschläger, Stephan; Bialonski, Alexandra; Heinemann, Patrick; Bleymehl, Karoline; Gross, Gerd; Günther, Stephan; Ulrich, Rainer G; Doerr, Hans Wilhelm

2009-11-01

Varicella-zoster virus (VZV) is the causative agent of chicken pox (varicella) in children and reactivation of VZV in elderly or immunocompromised persons can cause shingles (zoster). A subclade differentiation of the most prevalent VZV genotypes E1 and E2 in Germany was not possible with the current genotyping methods in use, but is highly important to understand the VZV molecular evolution in more detail and especially to follow up the routes of infection. Therefore the objective of this study was to develop a simple PCR-based method for differentiation of E1 and E2 subclades. Viral DNA was isolated from vesicle fluid samples of six selected German zoster patients and used to amplify nine complete open reading frames (ORFs) of the VZV genome by different PCR assays. Phylogenetic analysis was performed by a Bayesian approach. Based on the analysis of a total of nine ORFs, a 7482 bp stretch consisting of ORFs 5, 37 and 62 contained informative sites for identification of novel subclades E1a, E2a and E2b for VZV genotypes E1 and E2. Specific single nucleotide polymorphisms (SNPs) were demonstrated for subclades E2a and E2b within the ORFs 5, 37 and 62, whereas a subclade E1a-specific SNP was found in ORF 56. The classification of E1 and E2 subclades may facilitate a more exact and in-depth monitoring of the molecular evolution of VZV in Germany in the future.

The transcriptional landscape of seasonal coat colour moult in the snowshoe hare.

PubMed

Ferreira, Mafalda S; Alves, Paulo C; Callahan, Colin M; Marques, João P; Mills, L Scott; Good, Jeffrey M; Melo-Ferreira, José

2017-08-01

Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. "White" pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional "intermediate" and "brown" pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits. © 2017 John Wiley & Sons Ltd.

Algebraic aspects of evolution partial differential equation arising in the study of constant elasticity of variance model from financial mathematics

NASA Astrophysics Data System (ADS)

Motsepa, Tanki; Aziz, Taha; Fatima, Aeeman; Khalique, Chaudry Masood

2018-03-01

The optimal investment-consumption problem under the constant elasticity of variance (CEV) model is investigated from the perspective of Lie group analysis. The Lie symmetry group of the evolution partial differential equation describing the CEV model is derived. The Lie point symmetries are then used to obtain an exact solution of the governing model satisfying a standard terminal condition. Finally, we construct conservation laws of the underlying equation using the general theorem on conservation laws.

Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution.

PubMed

Renaud, Sabrina; Dufour, Anne-Béatrice; Hardouin, Emilie A; Ledevin, Ronan; Auffray, Jean-Christophe

2015-01-01

Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1) the Principal Component Analysis (PCA), which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2) the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA) for more than two groups), which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3) the between-group PCA (bgPCA) which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing 'better' than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA) will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA), by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred.

A new design approach based on differential evolution algorithm for geometric optimization of magnetorheological brakes

NASA Astrophysics Data System (ADS)

Le-Duc, Thang; Ho-Huu, Vinh; Nguyen-Thoi, Trung; Nguyen-Quoc, Hung

2016-12-01

In recent years, various types of magnetorheological brakes (MRBs) have been proposed and optimized by different optimization algorithms that are integrated in commercial software such as ANSYS and Comsol Multiphysics. However, many of these optimization algorithms often possess some noteworthy shortcomings such as the trap of solutions at local extremes, or the limited number of design variables or the difficulty of dealing with discrete design variables. Thus, to overcome these limitations and develop an efficient computation tool for optimal design of the MRBs, an optimization procedure that combines differential evolution (DE), a gradient-free global optimization method with finite element analysis (FEA) is proposed in this paper. The proposed approach is then applied to the optimal design of MRBs with different configurations including conventional MRBs and MRBs with coils placed on the side housings. Moreover, to approach a real-life design, some necessary design variables of MRBs are considered as discrete variables in the optimization process. The obtained optimal design results are compared with those of available optimal designs in the literature. The results reveal that the proposed method outperforms some traditional approaches.

An improved parent-centric mutation with normalized neighborhoods for inducing niching behavior in differential evolution.

PubMed

Biswas, Subhodip; Kundu, Souvik; Das, Swagatam

2014-10-01

In real life, we often need to find multiple optimally sustainable solutions of an optimization problem. Evolutionary multimodal optimization algorithms can be very helpful in such cases. They detect and maintain multiple optimal solutions during the run by incorporating specialized niching operations in their actual framework. Differential evolution (DE) is a powerful evolutionary algorithm (EA) well-known for its ability and efficiency as a single peak global optimizer for continuous spaces. This article suggests a niching scheme integrated with DE for achieving a stable and efficient niching behavior by combining the newly proposed parent-centric mutation operator with synchronous crowding replacement rule. The proposed approach is designed by considering the difficulties associated with the problem dependent niching parameters (like niche radius) and does not make use of such control parameter. The mutation operator helps to maintain the population diversity at an optimum level by using well-defined local neighborhoods. Based on a comparative study involving 13 well-known state-of-the-art niching EAs tested on an extensive collection of benchmarks, we observe a consistent statistical superiority enjoyed by our proposed niching algorithm.

The evolution of menstruation: A new model for genetic assimilation

PubMed Central

Emera, D.; Romero, R.; Wagner, G.

2012-01-01

Why do humans menstruate while most mammals do not? Here, we present our answer to this long-debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone-induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal-fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non-menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. PMID:22057551

Investigating the differences of cirrus cloud properties in nucleation, growth and sublimation regions based on airborne water vapor lidar measurements

NASA Astrophysics Data System (ADS)

Urbanek, Benedikt; Groß, Silke; Wirth, Martin

2017-04-01

Cirrus clouds impose high uncertainties on weather and climate prediction, as knowledge on important processes is still incomplete. For instance it remains unclear how cloud optical, microphysical, and radiative properties change as the cirrus evolves. To gain better understanding of cirrus clouds, their optical and microphysical properties and their changes with cirrus cloud evolution the ML-CIRRUS campaign was conducted in March and April 2014. Measurements with a combined in-situ and remote sensing payload were performed with the German research aircraft HALO based in Oberpfaffenhofen. 16 research flights with altogether 88 flight hours were performed over the North-Atlantic, western and central Europe to probe different cirrus cloud regimes and cirrus clouds at different stages of evolution. One of the key remotes sensing instruments during ML-CIRRUS was the airborne differential absorption and high spectral lidar system WALES. It measures the 2-dimensional distribution of water vapor inside and outside of cirrus clouds as well as the optical properties of the clouds. Bases on these airborne lidar measurements a novel classification scheme to derive the stage of cirrus cloud evolution was developed. It identifies regions of ice nucleation, particle growth by deposition of water vapor, and ice sublimation. This method is used to investigate differences in the distribution and value of optical properties as well as in the distribution of water vapor and relative humidity depending on the stage of evolution of the cloud. We will present the lidar based classification scheme and its application on a wave driven cirrus cloud case, and we will show first results of the dependence of optical cloud properties and relative humidity distributions on the determined stage of evolution.

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell.

PubMed

Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

2016-03-01

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution in fluctuating environments: decomposing selection into additive components of the Robertson-Price equation.

PubMed

Engen, Steinar; Saether, Bernt-Erik

2014-03-01

We analyze the stochastic components of the Robertson-Price equation for the evolution of quantitative characters that enables decomposition of the selection differential into components due to demographic and environmental stochasticity. We show how these two types of stochasticity affect the evolution of multivariate quantitative characters by defining demographic and environmental variances as components of individual fitness. The exact covariance formula for selection is decomposed into three components, the deterministic mean value, as well as stochastic demographic and environmental components. We show that demographic and environmental stochasticity generate random genetic drift and fluctuating selection, respectively. This provides a common theoretical framework for linking ecological and evolutionary processes. Demographic stochasticity can cause random variation in selection differentials independent of fluctuating selection caused by environmental variation. We use this model of selection to illustrate that the effect on the expected selection differential of random variation in individual fitness is dependent on population size, and that the strength of fluctuating selection is affected by how environmental variation affects the covariance in Malthusian fitness between individuals with different phenotypes. Thus, our approach enables us to partition out the effects of fluctuating selection from the effects of selection due to random variation in individual fitness caused by demographic stochasticity. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

A 1-D evolutionary model for icy satellites, applied to Enceladus

NASA Astrophysics Data System (ADS)

Malamud, Uri; Prialnik, Dina

2016-04-01

We develop a long-term 1-D evolution model for icy satellites that couples multiple processes: water migration and differentiation, geochemical reactions and silicate phase transitions, compaction by self-gravity, and ablation. The model further considers the following energy sources and sinks: tidal heating, radiogenic heating, geochemical energy released by serpentinization or absorbed by mineral dehydration, gravitational energy and insolation, and heat transport by conduction, convection, and advection. We apply the model to Enceladus, by guessing the initial conditions that would render a structure compatible with present-day observations, assuming the initial structure to have been homogeneous. Assuming the satellite has been losing water continually along its evolution, we postulate that it was formed as a more massive, more icy and more porous satellite, and gradually transformed into its present day state due to sustained long-term tidal heating. We consider several initial compositions and evolution scenarios and follow the evolution for the age of the Solar System, testing the present day model results against the available observational constraints. Our model shows the present configuration to be differentiated into a pure icy mantle, several tens of km thick, overlying a rocky core, composed of dehydrated rock at the center and hydrated rock in the outer part. For Enceladus, it predicts a higher rock/ice mass ratio than previously assumed and a thinner ice mantle, compatible with recent estimates based on gravity field measurements. Although, obviously, the model cannot be used to explain local phenomena, it sheds light on the internal structure invoked in explanations of localized features and activities.

Implications of monotreme and marsupial chromosome evolution on sex determination and differentiation.

PubMed

Deakin, Janine E

2017-04-01

Studies of chromosomes from monotremes and marsupials endemic to Australasia have provided important insight into the evolution of their genomes as well as uncovering fundamental differences in their sex determination/differentiation pathways. Great advances have been made this century into solving the mystery of the complicated sex chromosome system in monotremes. Monotremes possess multiple different X and Y chromosomes and a candidate sex determining gene has been identified. Even greater advancements have been made for marsupials, with reconstruction of the ancestral karyotype enabling the evolutionary history of marsupial chromosomes to be determined. Furthermore, the study of sex chromosomes in intersex marsupials has afforded insight into differences in the sexual differentiation pathway between marsupials and eutherians, together with experiments showing the insensitivity of the mammary glands, pouch and scrotum to exogenous hormones, led to the hypothesis that there is a gene (or genes) on the X chromosome responsible for the development of either pouch or scrotum. This review highlights the major advancements made towards understanding chromosome evolution and how this has impacted on our understanding of sex determination and differentiation in these interesting mammals. Copyright © 2015 Elsevier Inc. All rights reserved.

Progress toward a general species concept.

PubMed

Hausdorf, Bernhard

2011-04-01

New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Maize diversity associated with social origin and environmental variation in Southern Mexico.

PubMed

Orozco-Ramírez, Q; Ross-Ibarra, J; Santacruz-Varela, A; Brush, S

2016-05-01

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale.

Maize diversity associated with social origin and environmental variation in Southern Mexico

PubMed Central

Orozco-Ramírez, Q; Ross-Ibarra, J; Santacruz-Varela, A; Brush, S

2016-01-01

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale. PMID:26905463

Constrained multi-objective optimization of storage ring lattices

NASA Astrophysics Data System (ADS)

Husain, Riyasat; Ghodke, A. D.

2018-03-01

The storage ring lattice optimization is a class of constrained multi-objective optimization problem, where in addition to low beam emittance, a large dynamic aperture for good injection efficiency and improved beam lifetime are also desirable. The convergence and computation times are of great concern for the optimization algorithms, as various objectives are to be optimized and a number of accelerator parameters to be varied over a large span with several constraints. In this paper, a study of storage ring lattice optimization using differential evolution is presented. The optimization results are compared with two most widely used optimization techniques in accelerators-genetic algorithm and particle swarm optimization. It is found that the differential evolution produces a better Pareto optimal front in reasonable computation time between two conflicting objectives-beam emittance and dispersion function in the straight section. The differential evolution was used, extensively, for the optimization of linear and nonlinear lattices of Indus-2 for exploring various operational modes within the magnet power supply capabilities.

Parameter optimization of differential evolution algorithm for automatic playlist generation problem

NASA Astrophysics Data System (ADS)

Alamag, Kaye Melina Natividad B.; Addawe, Joel M.

2017-11-01

With the digitalization of music, the number of collection of music increased largely and there is a need to create lists of music that filter the collection according to user preferences, thus giving rise to the Automatic Playlist Generation Problem (APGP). Previous attempts to solve this problem include the use of search and optimization algorithms. If a music database is very large, the algorithm to be used must be able to search the lists thoroughly taking into account the quality of the playlist given a set of user constraints. In this paper we perform an evolutionary meta-heuristic optimization algorithm, Differential Evolution (DE) using different combination of parameter values and select the best performing set when used to solve four standard test functions. Performance of the proposed algorithm is then compared with normal Genetic Algorithm (GA) and a hybrid GA with Tabu Search. Numerical simulations are carried out to show better results from Differential Evolution approach with the optimized parameter values.

Structure and Evolution of the Lunar Interior

NASA Technical Reports Server (NTRS)

Andrews-Hanna, J. C.; Weber, R. C.; Ishihara, Y.; Kamata, S.; Keane, J.; Kiefer, W. S.; Matsuyama, I.; Siegler, M.; Warren, P.

2017-01-01

Early in its evolution, the Moon underwent a magma ocean phase leading to its differentiation into a feldspathic crust, cumulate mantle, and iron core. However, far from the simplest view of a uniform plagioclase flotation crust, the present-day crust of the Moon varies greatly in thickness, composition, and physical properties. Recent significant improvements in both data and analysis techniques have yielded fundamental advances in our understanding of the structure and evolution of the lunar interior. The structure of the crust is revealed by gravity, topography, magnetics, seismic, radar, electromagnetic, and VNIR remote sensing data. The mantle structure of the Moon is revealed primarily by seismic and laser ranging data. Together, this data paints a picture of a Moon that is heterogeneous in all directions and across all scales, whose structure is a result of its unique formation, differentiation, and subsequent evolution. This brief review highlights a small number of recent advances in our understanding of lunar structure.

Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization.

PubMed

González-Romero, Rodrigo; Eirín-López, José M; Ausió, Juan

2015-01-01

High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance-most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Numerical simulations of electrohydrodynamic evolution of thin polymer films

NASA Astrophysics Data System (ADS)

Borglum, Joshua Christopher

Recently developed needleless electrospinning and electrolithography are two successful techniques that have been utilized extensively for low-cost, scalable, and continuous nano-fabrication. Rational understanding of the electrohydrodynamic principles underneath these nano-manufacturing methods is crucial to fabrication of continuous nanofibers and patterned thin films. This research project is to formulate robust, high-efficiency finite-difference Fourier spectral methods to simulate the electrohydrodynamic evolution of thin polymer films. Two thin-film models were considered and refined. The first was based on reduced lubrication theory; the second further took into account the effect of solvent drying and dewetting of the substrate. Fast Fourier Transform (FFT) based spectral method was integrated into the finite-difference algorithms for fast, accurately solving the governing nonlinear partial differential equations. The present methods have been used to examine the dependencies of the evolving surface features of the thin films upon the model parameters. The present study can be used for fast, controllable nanofabrication.

The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanus

PubMed Central

Bradic, Martina; Teotónio, Henrique; Borowsky, Richard L.

2013-01-01

Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment. PMID:23927992

Quasi-Newton methods for parameter estimation in functional differential equations

NASA Technical Reports Server (NTRS)

Brewer, Dennis W.

1988-01-01

A state-space approach to parameter estimation in linear functional differential equations is developed using the theory of linear evolution equations. A locally convergent quasi-Newton type algorithm is applied to distributed systems with particular emphasis on parameters that induce unbounded perturbations of the state. The algorithm is computationally implemented on several functional differential equations, including coefficient and delay estimation in linear delay-differential equations.

Dynamical and Mechanistic Reconstructive Approaches of T Lymphocyte Dynamics: Using Visual Modeling Languages to Bridge the Gap between Immunologists, Theoreticians, and Programmers

PubMed Central

Thomas-Vaslin, Véronique; Six, Adrien; Ganascia, Jean-Gabriel; Bersini, Hugues

2013-01-01

Dynamic modeling of lymphocyte behavior has primarily been based on populations based differential equations or on cellular agents moving in space and interacting each other. The final steps of this modeling effort are expressed in a code written in a programing language. On account of the complete lack of standardization of the different steps to proceed, we have to deplore poor communication and sharing between experimentalists, theoreticians and programmers. The adoption of diagrammatic visual computer language should however greatly help the immunologists to better communicate, to more easily identify the models similarities and facilitate the reuse and extension of existing software models. Since immunologists often conceptualize the dynamical evolution of immune systems in terms of “state-transitions” of biological objects, we promote the use of unified modeling language (UML) state-transition diagram. To demonstrate the feasibility of this approach, we present a UML refactoring of two published models on thymocyte differentiation. Originally built with different modeling strategies, a mathematical ordinary differential equation-based model and a cellular automata model, the two models are now in the same visual formalism and can be compared. PMID:24101919

MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect

PubMed Central

Collins, David H.; Mohorianu, Irina; Beckers, Matthew; Moulton, Vincent; Dalmay, Tamas; Bourke, Andrew F. G.

2017-01-01

In eusocial Hymenoptera (ants, bees and wasps), queen and worker adult castes typically arise via environmental influences. A fundamental challenge is to understand how a single genome can thereby produce alternative phenotypes. A powerful approach is to compare the molecular basis of caste determination and differentiation along the evolutionary trajectory between primitively and advanced eusocial species, which have, respectively, relatively undifferentiated and strongly differentiated adult castes. In the advanced eusocial honeybee, Apis mellifera, studies suggest that microRNAs (miRNAs) play an important role in the molecular basis of caste determination and differentiation. To investigate how miRNAs affect caste in eusocial evolution, we used deep sequencing and Northern blots to isolate caste-associated miRNAs in the primitively eusocial bumblebee Bombus terrestris. We found that the miRNAs Bte-miR-6001-5p and -3p are more highly expressed in queen- than in worker-destined late-instar larvae. These are the first caste-associated miRNAs from outside advanced eusocial Hymenoptera, so providing evidence for caste-associated miRNAs occurring relatively early in eusocial evolution. Moreover, we found little evidence that miRNAs previously shown to be associated with caste in A. mellifera were differentially expressed across caste pathways in B. terrestris, suggesting that, in eusocial evolution, the caste-associated role of individual miRNAs is not conserved. PMID:28361900

Thermal evolution of the earth

NASA Technical Reports Server (NTRS)

Spohn, T.

1984-01-01

The earth's heat budget and models of the earth's thermal evolution are discussed. Sources of the planetary heat are considered and modes of heat transport are addressed, including conduction, convection, and chemical convection. Thermal and convectional models of the earth are covered, and models of thermal evolution are discussed in detail, including changes in the core, the influence of layered mantle convection on the thermal evolution, and the effect of chemical differentiation on the continents.

Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

PubMed Central

McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801

Stability and bifurcation in a model for the dynamics of stem-like cells in leukemia under treatment

NASA Astrophysics Data System (ADS)

Rǎdulescu, I. R.; Cândea, D.; Halanay, A.

2012-11-01

A mathematical model for the dynamics of leukemic cells during treatment is introduced. Delay differential equations are used to model cells' evolution and are based on the Mackey-Glass approach, incorporating Goldie-Coldman law. Since resistance is propagated by cells that have the capacity of self-renewal, a population of stem-like cells is studied. Equilibrium points are calculated and their stability properties are investigated.

From Determinism and Probability to Chaos: Chaotic Evolution towards Philosophy and Methodology of Chaotic Optimization

PubMed Central

2015-01-01

We present and discuss philosophy and methodology of chaotic evolution that is theoretically supported by chaos theory. We introduce four chaotic systems, that is, logistic map, tent map, Gaussian map, and Hénon map, in a well-designed chaotic evolution algorithm framework to implement several chaotic evolution (CE) algorithms. By comparing our previous proposed CE algorithm with logistic map and two canonical differential evolution (DE) algorithms, we analyse and discuss optimization performance of CE algorithm. An investigation on the relationship between optimization capability of CE algorithm and distribution characteristic of chaotic system is conducted and analysed. From evaluation result, we find that distribution of chaotic system is an essential factor to influence optimization performance of CE algorithm. We propose a new interactive EC (IEC) algorithm, interactive chaotic evolution (ICE) that replaces fitness function with a real human in CE algorithm framework. There is a paired comparison-based mechanism behind CE search scheme in nature. A simulation experimental evaluation is conducted with a pseudo-IEC user to evaluate our proposed ICE algorithm. The evaluation result indicates that ICE algorithm can obtain a significant better performance than or the same performance as interactive DE. Some open topics on CE, ICE, fusion of these optimization techniques, algorithmic notation, and others are presented and discussed. PMID:25879067

Magnetic Flux Transport at the Solar Surface

NASA Astrophysics Data System (ADS)

Jiang, J.; Hathaway, D. H.; Cameron, R. H.; Solanki, S. K.; Gizon, L.; Upton, L.

2014-12-01

After emerging to the solar surface, the Sun's magnetic field displays a complex and intricate evolution. The evolution of the surface field is important for several reasons. One is that the surface field, and its dynamics, sets the boundary condition for the coronal and heliospheric magnetic fields. Another is that the surface evolution gives us insight into the dynamo process. In particular, it plays an essential role in the Babcock-Leighton model of the solar dynamo. Describing this evolution is the aim of the surface flux transport model. The model starts from the emergence of magnetic bipoles. Thereafter, the model is based on the induction equation and the fact that after emergence the magnetic field is observed to evolve as if it were purely radial. The induction equation then describes how the surface flows—differential rotation, meridional circulation, granular, supergranular flows, and active region inflows—determine the evolution of the field (now taken to be purely radial). In this paper, we review the modeling of the various processes that determine the evolution of the surface field. We restrict our attention to their role in the surface flux transport model. We also discuss the success of the model and some of the results that have been obtained using this model.

Convergent evolution as natural experiment: the tape of life reconsidered.

PubMed

Powell, Russell; Mariscal, Carlos

2015-12-06

Stephen Jay Gould argued that replaying the 'tape of life' would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution-the independent origination of similar biological forms and functions-which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the 'critique from convergent evolution' fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life.

From determinism and probability to chaos: chaotic evolution towards philosophy and methodology of chaotic optimization.

PubMed

Pei, Yan

2015-01-01

We present and discuss philosophy and methodology of chaotic evolution that is theoretically supported by chaos theory. We introduce four chaotic systems, that is, logistic map, tent map, Gaussian map, and Hénon map, in a well-designed chaotic evolution algorithm framework to implement several chaotic evolution (CE) algorithms. By comparing our previous proposed CE algorithm with logistic map and two canonical differential evolution (DE) algorithms, we analyse and discuss optimization performance of CE algorithm. An investigation on the relationship between optimization capability of CE algorithm and distribution characteristic of chaotic system is conducted and analysed. From evaluation result, we find that distribution of chaotic system is an essential factor to influence optimization performance of CE algorithm. We propose a new interactive EC (IEC) algorithm, interactive chaotic evolution (ICE) that replaces fitness function with a real human in CE algorithm framework. There is a paired comparison-based mechanism behind CE search scheme in nature. A simulation experimental evaluation is conducted with a pseudo-IEC user to evaluate our proposed ICE algorithm. The evaluation result indicates that ICE algorithm can obtain a significant better performance than or the same performance as interactive DE. Some open topics on CE, ICE, fusion of these optimization techniques, algorithmic notation, and others are presented and discussed.

Phylogenomics of the killer whale indicates ecotype divergence in sympatry.

PubMed

Moura, A E; Kenny, J G; Chaudhuri, R R; Hughes, M A; Reisinger, R R; de Bruyn, P J N; Dahlheim, M E; Hall, N; Hoelzel, A R

2015-01-01

For many highly mobile species, the marine environment presents few obvious barriers to gene flow. Even so, there is considerable diversity within and among species, referred to by some as the 'marine speciation paradox'. The recent and diverse radiation of delphinid cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive dispersion and yet many show fine-scale genetic differentiation among populations. Proposed mechanisms include the division and isolation of populations based on habitat dependence and resource specializations, and habitat release or changing dispersal corridors during glacial cycles. Here we use a phylogenomic approach to investigate the origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales show strong specialization on prey choice in populations of stable matrifocal social groups (ecotypes), associated with genetic and phenotypic differentiation. Our data suggest evolution in sympatry among populations of resource specialists.

Phylogenomics of the killer whale indicates ecotype divergence in sympatry

PubMed Central

Moura, A E; Kenny, J G; Chaudhuri, R R; Hughes, M A; Reisinger, R R; de Bruyn, P J N; Dahlheim, M E; Hall, N; Hoelzel, A R

2015-01-01

For many highly mobile species, the marine environment presents few obvious barriers to gene flow. Even so, there is considerable diversity within and among species, referred to by some as the ‘marine speciation paradox'. The recent and diverse radiation of delphinid cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive dispersion and yet many show fine-scale genetic differentiation among populations. Proposed mechanisms include the division and isolation of populations based on habitat dependence and resource specializations, and habitat release or changing dispersal corridors during glacial cycles. Here we use a phylogenomic approach to investigate the origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales show strong specialization on prey choice in populations of stable matrifocal social groups (ecotypes), associated with genetic and phenotypic differentiation. Our data suggest evolution in sympatry among populations of resource specialists. PMID:25052415

On the Cause of Solar Differential Rotations in the Solar Interior and Near the Solar Surface

NASA Astrophysics Data System (ADS)

Lyu, L.

2012-12-01

A theoretical model is proposed to explain the cause of solar differential rotations observed in the solar interior and near the solar surface. We propose that the latitudinal differential rotation in the solar convection zone is a manifestation of an easterly wind in the mid latitude. The speed of the easterly wind is controlled by the magnitude of the poleward temperature gradient in the lower part of the solar convection zone. The poleward temperature gradient depends on the orientation and strength of the magnetic fields at different latitudes in the solar convection zone. The north-south asymmetry in the wind speed can lead to north-south asymmetry in the evolution of the solar cycle. The easterly wind is known to be unstable for a west-to-east rotating star or planet. Based on the observed differential rotations in the solar convection zone, we can estimate the easterly wind speed at about 60-degree latitude and determine the azimuthal wave number of the unstable wave modes along the zonal flow. The lowest azimuthal wave number is about m=7~8. This result is consistent with the average width of the elephant-trunk coronal hole shown in the solar X-ray images. The nonlinear evolution of the unstable easterly wind can lead to transpolar migration of coronal holes and can change the poloidal magnetic field in a very efficient way. In the study of radial differential rotation near the solar surface, we propose that the radial differential rotation depends on the radial temperature gradient. The radial temperature gradient depends on the magnetic field structure above the solar surface. The non-uniform magnetic field distribution above the solar surface can lead to non-uniform radial convections and formation of magnetic flux rope at different spatial scales. The possible cause of continuous formation and eruption of prominences near an active region will also be discussed.

3D non-linear inversion of magnetic anomalies caused by prismatic bodies using differential evolution algorithm

NASA Astrophysics Data System (ADS)

Balkaya, Çağlayan; Ekinci, Yunus Levent; Göktürkler, Gökhan; Turan, Seçil

2017-01-01

3D non-linear inversion of total field magnetic anomalies caused by vertical-sided prismatic bodies has been achieved by differential evolution (DE), which is one of the population-based evolutionary algorithms. We have demonstrated the efficiency of the algorithm on both synthetic and field magnetic anomalies by estimating horizontal distances from the origin in both north and east directions, depths to the top and bottom of the bodies, inclination and declination angles of the magnetization, and intensity of magnetization of the causative bodies. In the synthetic anomaly case, we have considered both noise-free and noisy data sets due to two vertical-sided prismatic bodies in a non-magnetic medium. For the field case, airborne magnetic anomalies originated from intrusive granitoids at the eastern part of the Biga Peninsula (NW Turkey) which is composed of various kinds of sedimentary, metamorphic and igneous rocks, have been inverted and interpreted. Since the granitoids are the outcropped rocks in the field, the estimations for the top depths of two prisms representing the magnetic bodies were excluded during inversion studies. Estimated bottom depths are in good agreement with the ones obtained by a different approach based on 3D modelling of pseudogravity anomalies. Accuracy of the estimated parameters from both cases has been also investigated via probability density functions. Based on the tests in the present study, it can be concluded that DE is a useful tool for the parameter estimation of source bodies using magnetic anomalies.

Magma oceanography. I - Thermal evolution. [of lunar surface

NASA Technical Reports Server (NTRS)

Solomon, S. C.; Longhi, J.

1977-01-01

Fractional crystallization and flotation of cumulate plagioclase in a cooling 'magma ocean' provides the simplest explanation for early emplacement of a thick feldspar-rich lunar crust. The complementary mafic cumulates resulting from the differentiation of such a magma ocean have been identified as the ultimate source of mare basalt liquids on the basis or rare-earth abundance patterns and experimental petrology studies. A study is conducted concerning the thermal evolution of the early differentiation processes. A range of models of increasing sophistication are considered. The models developed contain the essence of the energetics and the time scale for magma ocean differentiation. Attention is given to constraints on a magma ocean, modeling procedures, single-component magma oceans, fractionating magma oceans, and evolving magma oceans.

Hybrid Topological Lie-Hamiltonian Learning in Evolving Energy Landscapes

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

In this Chapter, a novel bidirectional algorithm for hybrid (discrete + continuous-time) Lie-Hamiltonian evolution in adaptive energy landscape-manifold is designed and its topological representation is proposed. The algorithm is developed within a geometrically and topologically extended framework of Hopfield's neural nets and Haken's synergetics (it is currently designed in Mathematica, although with small changes it could be implemented in Symbolic C++ or any other computer algebra system). The adaptive energy manifold is determined by the Hamiltonian multivariate cost function H, based on the user-defined vehicle-fleet configuration matrix W, which represents the pseudo-Riemannian metric tensor of the energy manifold. Search for the global minimum of H is performed using random signal differential Hebbian adaptation. This stochastic gradient evolution is driven (or, pulled-down) by `gravitational forces' defined by the 2nd Lie derivatives of H. Topological changes of the fleet matrix W are observed during the evolution and its topological invariant is established. The evolution stops when the W-topology breaks down into several connectivity-components, followed by topology-breaking instability sequence (i.e., a series of phase transitions).

Vibration Sensor-Based Bearing Fault Diagnosis Using Ellipsoid-ARTMAP and Differential Evolution Algorithms

PubMed Central

Liu, Chang; Wang, Guofeng; Xie, Qinglu; Zhang, Yanchao

2014-01-01

Effective fault classification of rolling element bearings provides an important basis for ensuring safe operation of rotating machinery. In this paper, a novel vibration sensor-based fault diagnosis method using an Ellipsoid-ARTMAP network (EAM) and a differential evolution (DE) algorithm is proposed. The original features are firstly extracted from vibration signals based on wavelet packet decomposition. Then, a minimum-redundancy maximum-relevancy algorithm is introduced to select the most prominent features so as to decrease feature dimensions. Finally, a DE-based EAM (DE-EAM) classifier is constructed to realize the fault diagnosis. The major characteristic of EAM is that the sample distribution of each category is realized by using a hyper-ellipsoid node and smoothing operation algorithm. Therefore, it can depict the decision boundary of disperse samples accurately and effectively avoid over-fitting phenomena. To optimize EAM network parameters, the DE algorithm is presented and two objectives, including both classification accuracy and nodes number, are simultaneously introduced as the fitness functions. Meanwhile, an exponential criterion is proposed to realize final selection of the optimal parameters. To prove the effectiveness of the proposed method, the vibration signals of four types of rolling element bearings under different loads were collected. Moreover, to improve the robustness of the classifier evaluation, a two-fold cross validation scheme is adopted and the order of feature samples is randomly arranged ten times within each fold. The results show that DE-EAM classifier can recognize the fault categories of the rolling element bearings reliably and accurately. PMID:24936949

Gene duplication and the evolution of phenotypic diversity in insect societies.

PubMed

Chau, Linh M; Goodisman, Michael A D

2017-12-01

Gene duplication is an important evolutionary process thought to facilitate the evolution of phenotypic diversity. We investigated if gene duplication was associated with the evolution of phenotypic differences in a highly social insect, the honeybee Apis mellifera. We hypothesized that the genetic redundancy provided by gene duplication could promote the evolution of social and sexual phenotypes associated with advanced societies. We found a positive correlation between sociality and rate of gene duplications across the Apoidea, indicating that gene duplication may be associated with sociality. We also discovered that genes showing biased expression between A. mellifera alternative phenotypes tended to be found more frequently than expected among duplicated genes than singletons. Moreover, duplicated genes had higher levels of caste-, sex-, behavior-, and tissue-biased expression compared to singletons, as expected if gene duplication facilitated phenotypic differentiation. We also found that duplicated genes were maintained in the A. mellifera genome through the processes of conservation, neofunctionalization, and specialization, but not subfunctionalization. Overall, we conclude that gene duplication may have facilitated the evolution of social and sexual phenotypes, as well as tissue differentiation. Thus this study further supports the idea that gene duplication allows species to evolve an increased range of phenotypic diversity. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Mathematics in Physics Education: Scanning Historical Evolution of the Differential to Find a More Appropriate Model for Teaching Differential Calculus in Physics

ERIC Educational Resources Information Center

Martinez-Torregrosa, Joaquin; Lopez-Gay, Rafael; Gras-Marti, Albert

2006-01-01

Despite its frequent use, there is little understanding of the concept of differential among upper high school and undergraduate students of physics. As a first step to identify the origin of this situation and to revert it, we have done a historic and epistemological study aimed at clarifying the role and the meaning of the differential in…

Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

PubMed

Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

2012-10-01

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest.

PubMed

Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

2007-11-01

Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals.

The Nature of Culture: an eight-grade model for the evolution and expansion of cultural capacities in hominins and other animals.

PubMed

Haidle, Miriam Noël; Bolus, Michael; Collard, Mark; Conard, Nicholas; Garofoli, Duilio; Lombard, Marlize; Nowell, April; Tennie, Claudio; Whiten, Andrew

2015-07-20

Tracing the evolution of human culture through time is arguably one of the most controversial and complex scholarly endeavors, and a broad evolutionary analysis of how symbolic, linguistic, and cultural capacities emerged and developed in our species is lacking. Here we present a model that, in broad terms, aims to explain the evolution and portray the expansion of human cultural capacities (the EECC model), that can be used as a point of departure for further multidisciplinary discussion and more detailed investigation. The EECC model is designed to be flexible, and can be refined to accommodate future archaeological, paleoanthropological, genetic or evolutionary psychology/behavioral analyses and discoveries. Our proposed concept of cultural behavior differentiates between empirically traceable behavioral performances and behavioral capacities that are theoretical constructs. Based largely on archaeological data (the 'black box' that most directly opens up hominin cultural evolution), and on the extension of observable problem-solution distances, we identify eight grades of cultural capacity. Each of these grades is considered within evolutionary-biological and historical-social trajectories. Importantly, the model does not imply an inevitable progression, but focuses on expansion of cultural capacities based on the integration of earlier achievements. We conclude that there is not a single cultural capacity or a single set of abilities that enabled human culture; rather, several grades of cultural capacity in animals and hominins expanded during our evolution to shape who we are today.

Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism

PubMed Central

Campennì, Marco

2016-01-01

Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated “social relationships” and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions. PMID:26998412

Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism.

PubMed

Campennì, Marco; Schino, Gabriele

2016-01-01

Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated "social relationships" and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions.

Sex-dependent selection differentially shapes genetic variation on and off the guppy Y chromosome.

PubMed

Postma, Erik; Spyrou, Nicolle; Rollins, Lee Ann; Brooks, Robert C

2011-08-01

Because selection is often sex-dependent, alleles can have positive effects on fitness in one sex and negative effects in the other, resulting in intralocus sexual conflict. Evolutionary theory predicts that intralocus sexual conflict can drive the evolution of sex limitation, sex-linkage, and sex chromosome differentiation. However, evidence that sex-dependent selection results in sex-linkage is limited. Here, we formally partition the contribution of Y-linked and non-Y-linked quantitative genetic variation in coloration, tail, and body size of male guppies (Poecilia reticulata)-traits previously implicated as sexually antagonistic. We show that these traits are strongly genetically correlated, both on and off the Y chromosome, but that these correlations differ in sign and magnitude between both parts of the genome. As predicted, variation in attractiveness was found to be associated with the Y-linked, rather than with the non-Y-linked component of genetic variation in male ornamentation. These findings show how the evolution of Y-linkage may be able to resolve sexual conflict. More generally, they provide unique insight into how sex-specific selection has the potential to differentially shape the genetic architecture of fitness traits across different parts of the genome. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Differential Activity-Driven Instabilities in Biphasic Active Matter

NASA Astrophysics Data System (ADS)

Weber, Christoph A.; Rycroft, Chris H.; Mahadevan, L.

2018-06-01

Active stresses can cause instabilities in contractile gels and living tissues. Here we provide a generic hydrodynamic theory that treats these systems as a mixture of two phases of varying activity and different mechanical properties. We find that differential activity between the phases causes a uniform mixture to undergo a demixing instability. We follow the nonlinear evolution of the instability and characterize a phase diagram of the resulting patterns. Our study complements other instability mechanisms in mixtures driven by differential adhesion, differential diffusion, differential growth, and differential motion.

Poorly Differentiated Thyroid Carcinoma.

PubMed

Setia, Namrata; Barletta, Justine A

2014-12-01

Poorly differentiated thyroid carcinoma (PDTC) has been recognized for the past 30 years as an entity showing intermediate differentiation and clinical behavior between well-differentiated thyroid carcinomas (ie, papillary thyroid carcinoma and follicular thyroid carcinoma) and anaplastic thyroid carcinoma; however, there has been considerable controversy around the definition of PDTC. In this review, the evolution in the definition of PDTC, current diagnostic criteria, differential diagnoses, potentially helpful immunohistochemical studies, and molecular alterations are discussed with the aim of highlighting where the diagnosis of PDTC currently stands. Published by Elsevier Inc.

An implementation of differential evolution algorithm for inversion of geoelectrical data

NASA Astrophysics Data System (ADS)

Balkaya, Çağlayan

2013-11-01

Differential evolution (DE), a population-based evolutionary algorithm (EA) has been implemented to invert self-potential (SP) and vertical electrical sounding (VES) data sets. The algorithm uses three operators including mutation, crossover and selection similar to genetic algorithm (GA). Mutation is the most important operator for the success of DE. Three commonly used mutation strategies including DE/best/1 (strategy 1), DE/rand/1 (strategy 2) and DE/rand-to-best/1 (strategy 3) were applied together with a binomial type crossover. Evolution cycle of DE was realized without boundary constraints. For the test studies performed with SP data, in addition to both noise-free and noisy synthetic data sets two field data sets observed over the sulfide ore body in the Malachite mine (Colorado) and over the ore bodies in the Neem-Ka Thana cooper belt (India) were considered. VES test studies were carried out using synthetically produced resistivity data representing a three-layered earth model and a field data set example from Gökçeada (Turkey), which displays a seawater infiltration problem. Mutation strategies mentioned above were also extensively tested on both synthetic and field data sets in consideration. Of these, strategy 1 was found to be the most effective strategy for the parameter estimation by providing less computational cost together with a good accuracy. The solutions obtained by DE for the synthetic cases of SP were quite consistent with particle swarm optimization (PSO) which is a more widely used population-based optimization algorithm than DE in geophysics. Estimated parameters of SP and VES data were also compared with those obtained from Metropolis-Hastings (M-H) sampling algorithm based on simulated annealing (SA) without cooling to clarify uncertainties in the solutions. Comparison to the M-H algorithm shows that DE performs a fast approximate posterior sampling for the case of low-dimensional inverse geophysical problems.

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell

PubMed Central

Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A.; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

2016-01-01

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation. PMID:26601937

A 1-D evolutionary model for icy satellites, applied to Enceladus

NASA Astrophysics Data System (ADS)

Prialnik, Dina; Malamud, Uri

2015-11-01

A 1-D long-term evolution code for icy satellites is presented, which couples multiple processes: water migration, geochemical reactions, water and silicate phase transitions, crystallization, compaction by self-gravity, and ablation. The code takes into account various energy sources: tidal heating, radiogenic heating, geochemical energy released by serpentinization or absorbed by mineral dehydration, gravitational energy, and insolation. It includes heat transport by conduction, convection, and advection.The code is applied to Enceladus, by guessing the initial conditions that would render a structure compatible with present-day observations, and adopting a homogeneous initial structure. Assuming that the satellite has been losing water continually along its evolution, it follows that it was formed as a more massive, more ice-rich and more porous object, and gradually transformed into its present day state, due to sustained tidal heating. Several initial compositions and evolution scenarios are considered, and the evolution is simulated for the age of the Solar System. The results corresponding to the present configuration are confronted with the available observational constraints. The present configuration is shown to be differentiated into a pure icy mantle, several tens of km thick, overlying a rocky core, composed of dehydrated rock in the central part and hydrated rock in the outer part. Such a differentiated structure is obtained not only for Enceladus, but for other medium size ice-rich bodies as well.Predictions for Enceladus are a higher rock/ice mass ratio than previously assumed, and a thinner ice mantle, compatible with recent estimates based on gravity field measurements. Although, obviously, the 1-D model cannot be used to explain local phenomena, it sheds light on the internal structure invoked in explanations of localized features and activities.

A novel framework of tissue membrane systems for image fusion.

PubMed

Zhang, Zulin; Yi, Xinzhong; Peng, Hong

2014-01-01

This paper proposes a tissue membrane system-based framework to deal with the optimal image fusion problem. A spatial domain fusion algorithm is given, and a tissue membrane system of multiple cells is used as its computing framework. Based on the multicellular structure and inherent communication mechanism of the tissue membrane system, an improved velocity-position model is developed. The performance of the fusion framework is studied with comparison of several traditional fusion methods as well as genetic algorithm (GA)-based and differential evolution (DE)-based spatial domain fusion methods. Experimental results show that the proposed fusion framework is superior or comparable to the other methods and can be efficiently used for image fusion.

DE and NLP Based QPLS Algorithm

NASA Astrophysics Data System (ADS)

Yu, Xiaodong; Huang, Dexian; Wang, Xiong; Liu, Bo

As a novel evolutionary computing technique, Differential Evolution (DE) has been considered to be an effective optimization method for complex optimization problems, and achieved many successful applications in engineering. In this paper, a new algorithm of Quadratic Partial Least Squares (QPLS) based on Nonlinear Programming (NLP) is presented. And DE is used to solve the NLP so as to calculate the optimal input weights and the parameters of inner relationship. The simulation results based on the soft measurement of diesel oil solidifying point on a real crude distillation unit demonstrate that the superiority of the proposed algorithm to linear PLS and QPLS which is based on Sequential Quadratic Programming (SQP) in terms of fitting accuracy and computational costs.

Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis.

PubMed

Tashkova, Katerina; Korošec, Peter; Silc, Jurij; Todorovski, Ljupčo; Džeroski, Sašo

2011-10-11

We address the task of parameter estimation in models of the dynamics of biological systems based on ordinary differential equations (ODEs) from measured data, where the models are typically non-linear and have many parameters, the measurements are imperfect due to noise, and the studied system can often be only partially observed. A representative task is to estimate the parameters in a model of the dynamics of endocytosis, i.e., endosome maturation, reflected in a cut-out switch transition between the Rab5 and Rab7 domain protein concentrations, from experimental measurements of these concentrations. The general parameter estimation task and the specific instance considered here are challenging optimization problems, calling for the use of advanced meta-heuristic optimization methods, such as evolutionary or swarm-based methods. We apply three global-search meta-heuristic algorithms for numerical optimization, i.e., differential ant-stigmergy algorithm (DASA), particle-swarm optimization (PSO), and differential evolution (DE), as well as a local-search derivative-based algorithm 717 (A717) to the task of estimating parameters in ODEs. We evaluate their performance on the considered representative task along a number of metrics, including the quality of reconstructing the system output and the complete dynamics, as well as the speed of convergence, both on real-experimental data and on artificial pseudo-experimental data with varying amounts of noise. We compare the four optimization methods under a range of observation scenarios, where data of different completeness and accuracy of interpretation are given as input. Overall, the global meta-heuristic methods (DASA, PSO, and DE) clearly and significantly outperform the local derivative-based method (A717). Among the three meta-heuristics, differential evolution (DE) performs best in terms of the objective function, i.e., reconstructing the output, and in terms of convergence. These results hold for both real and artificial data, for all observability scenarios considered, and for all amounts of noise added to the artificial data. In sum, the meta-heuristic methods considered are suitable for estimating the parameters in the ODE model of the dynamics of endocytosis under a range of conditions: With the model and conditions being representative of parameter estimation tasks in ODE models of biochemical systems, our results clearly highlight the promise of bio-inspired meta-heuristic methods for parameter estimation in dynamic system models within system biology.

Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis

PubMed Central

2011-01-01

Background We address the task of parameter estimation in models of the dynamics of biological systems based on ordinary differential equations (ODEs) from measured data, where the models are typically non-linear and have many parameters, the measurements are imperfect due to noise, and the studied system can often be only partially observed. A representative task is to estimate the parameters in a model of the dynamics of endocytosis, i.e., endosome maturation, reflected in a cut-out switch transition between the Rab5 and Rab7 domain protein concentrations, from experimental measurements of these concentrations. The general parameter estimation task and the specific instance considered here are challenging optimization problems, calling for the use of advanced meta-heuristic optimization methods, such as evolutionary or swarm-based methods. Results We apply three global-search meta-heuristic algorithms for numerical optimization, i.e., differential ant-stigmergy algorithm (DASA), particle-swarm optimization (PSO), and differential evolution (DE), as well as a local-search derivative-based algorithm 717 (A717) to the task of estimating parameters in ODEs. We evaluate their performance on the considered representative task along a number of metrics, including the quality of reconstructing the system output and the complete dynamics, as well as the speed of convergence, both on real-experimental data and on artificial pseudo-experimental data with varying amounts of noise. We compare the four optimization methods under a range of observation scenarios, where data of different completeness and accuracy of interpretation are given as input. Conclusions Overall, the global meta-heuristic methods (DASA, PSO, and DE) clearly and significantly outperform the local derivative-based method (A717). Among the three meta-heuristics, differential evolution (DE) performs best in terms of the objective function, i.e., reconstructing the output, and in terms of convergence. These results hold for both real and artificial data, for all observability scenarios considered, and for all amounts of noise added to the artificial data. In sum, the meta-heuristic methods considered are suitable for estimating the parameters in the ODE model of the dynamics of endocytosis under a range of conditions: With the model and conditions being representative of parameter estimation tasks in ODE models of biochemical systems, our results clearly highlight the promise of bio-inspired meta-heuristic methods for parameter estimation in dynamic system models within system biology. PMID:21989196

The Cotesia sesamiae story: insight into host-range evolution in a Hymenoptera parasitoid and implication for its use in biological control programs.

PubMed

Kaiser, L; Dupas, S; Branca, A; Herniou, E A; Clarke, C W; Capdevielle Dulac, C; Obonyo, J; Benoist, R; Gauthier, J; Calatayud, P A; Silvain, J F; Le Ru, B P

2017-12-01

This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding. In the second part, we consider the larger ecosystem of wild Poales plant species hosting many Lepidoptera stem borer species that are potential hosts for C. sesamiae. The hypothesis of other host-adapted C. sesamiae populations was investigated based on a large sampling of stem borer larvae on various Poales across sub-Saharan Africa. The sampling provided information on the respective contribution of local hosts, biogeography and Wolbachia in the genetic structure of C. sesamiae populations. Molecular evolution analyses highlighted that several bracovirus genes were under positive selection, some of them being under different selection pressure in C. sesamiae populations adapted to different hosts. This suggests that C. sesamiae host races result from co-evolution acting at the local scale on different bracovirus genes. The third part considers the mechanisms driving specialization. C. sesamiae host races are more or less host-specialized. This character is crucial for efficient and environmentally-safe use of natural enemies for biological control of pests. One method to get an insight in the evolutionary stability of host-parasite associations is to characterize the phylogenetic relationships between the so-called host-races. Based on the construction of a phylogeny of C. sesamiae samples from various host- and plant species, we revealed three main lineages. Mechanisms of differentiation are discussed with regard to the geography and ecology of the samples. One of the lineage presented all the hallmarks of a distinct species, which has been morphologically described and is now studied in the perspective of being used as biological control agent against Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), a major maize pest in West Africa and Mediterranean countries (see Benoist et al. 2017). The fourth part reviews past and present use of C. sesamiae in biological control, and points out the interest of such molecular ecology studies to reconcile biodiversity and food security stakes in future biological control.

Potential for the evolution of heavy metal tolerance in Bryum argenteum, a moss. II. Generalized tolerances among diverse populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaw, A.J.; Albright, D.L.

Tolerance of copper, zinc, lead, and nickel were measured in two individuals from each of seven populations of Bryum argenteum. The populations represented a range of habitats including industrial sites subject to atmospheric metal deposition, metal-contaminated mine tailings, serpentine barrens, and urban areas. Nevertheless, there was no evidence of adaptive differentiation in tolerance to any of the metals. Populations did differ significantly in general growth vigor across all experimental treatments. These observations contrast with results from studies of angiosperms, in which the evolution of heavy-metal tolerance almost always involves ecotypic differentiation among populations, but fit an emerging picture of B.more » argenteum as a plastic, broadly tolerant species with surprisingly little genetic differentiation among populations.« less

The magma ocean concept and lunar evolution

NASA Technical Reports Server (NTRS)

Warren, P. H.

1985-01-01

The model of lunar evolution in which the anorthositic plagioclase-rich oldest crust of the moon is formed over a period of 300 Myr or less by crystallization as it floats on a global ocean of magma tens or hundreds of km thick is examined in a review of petrological and theoretical studies. Consideration is given to the classification of lunar rocks, the evidence for primordial deep global differentiation, constraints on the depth of the molten zone, the effects of pressure on mineral stability relationships, mainly-liquid vs mainly-magmifer ocean models, and the evidence for multiple ancient differentiation episodes. A synthesis of the model of primordial differentiation and its aftereffects is presented, and the generalization of the model to the earth and to Mars, Mercury, Venus, and the asteroids is discussed.

Chandrasekhar equations for infinite dimensional systems

NASA Technical Reports Server (NTRS)

Ito, K.; Powers, R.

1985-01-01

The existence of Chandrasekhar equations for linear time-invariant systems defined on Hilbert spaces is investigated. An important consequence is that the solution to the evolutional Riccati equation is strongly differentiable in time, and that a strong solution of the Riccati differential equation can be defined. A discussion of the linear-quadratic optimal-control problem for hereditary differential systems is also included.

Evolution of the human-specific microRNA miR-941

PubMed Central

Hu, Hai Yang; He, Liu; Fominykh, Kseniya; Yan, Zheng; Guo, Song; Zhang, Xiaoyu; Taylor, Martin S.; Tang, Lin; Li, Jie; Liu, Jianmei; Wang, Wen; Yu, Haijing; Khaitovich, Philipp

2012-01-01

MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding sites, presumably to escape regulation. We further show that miR-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage. PMID:23093182

Quasistatic elastoplasticity via Peridynamics: existence and localization

NASA Astrophysics Data System (ADS)

Kružík, Martin; Mora-Corral, Carlos; Stefanelli, Ulisse

2018-04-01

Peridynamics is a nonlocal continuum mechanical theory based on minimal regularity on the deformations. Its key trait is that of replacing local constitutive relations featuring spacial differential operators with integrals over differences of displacement fields over a suitable positive interaction range. The advantage of such perspective is that of directly including nonregular situations, in which discontinuities in the displacement field may occur. In the linearized elastic setting, the mechanical foundation of the theory and its mathematical amenability have been thoroughly analyzed in the last years. We present here the extension of Peridynamics to linearized elastoplasticity. This calls for considering the time evolution of elastic and plastic variables, as the effect of a combination of elastic energy storage and plastic energy dissipation mechanisms. The quasistatic evolution problem is variationally reformulated and solved by time discretization. In addition, by a rigorous evolutive Γ -convergence argument we prove that the nonlocal peridynamic model converges to classic local elastoplasticity as the interaction range goes to zero.

The Minimum-Mass Surface Density of the Solar Nebula using the Disk Evolution Equation

NASA Technical Reports Server (NTRS)

Davis, Sanford S.

2005-01-01

The Hayashi minimum-mass power law representation of the pre-solar nebula (Hayashi 1981, Prog. Theo. Phys.70,35) is revisited using analytic solutions of the disk evolution equation. A new cumulative-planetary-mass-model (an integrated form of the surface density) is shown to predict a smoother surface density compared with methods based on direct estimates of surface density from planetary data. First, a best-fit transcendental function is applied directly to the cumulative planetary mass data with the surface density obtained by direct differentiation. Next a solution to the time-dependent disk evolution equation is parametrically adapted to the planetary data. The latter model indicates a decay rate of r -1/2 in the inner disk followed by a rapid decay which results in a sharper outer boundary than predicted by the minimum mass model. The model is shown to be a good approximation to the finite-size early Solar Nebula and by extension to extra solar protoplanetary disks.

Evolution of High Mobility Group Nucleosome-Binding Proteins and Its Implications for Vertebrate Chromatin Specialization

PubMed Central

González-Romero, Rodrigo; Eirín-López, José M.; Ausió, Juan

2015-01-01

High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance—most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates. PMID:25281808

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

PubMed

Wong, Ieong; Liu, Wenjia; Ho, Chih-Ming; Ding, Xianting

2017-06-01

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of desired drug combinations with minimal experimental effort. This article proposes an adaptive population-sizing method for the DE algorithm. Our new method presents improvements in terms of efficiency and convergence over the original DE algorithm and constant stepwise population reduction-based DE algorithm, which would lead to a reduced number of cells and animals required to identify an optimal drug combination. The method continuously adjusts the reduction of the population size in accordance with the stage of the optimization process. Our adaptive scheme limits the population reduction to occur only at the exploitation stage. We believe that continuously adjusting for a more effective population size during the evolutionary process is the major reason for the significant improvement in the convergence speed of the DE algorithm. The performance of the method is evaluated through a set of unimodal and multimodal benchmark functions. In combining with self-adaptive schemes for mutation and crossover constants, this adaptive population reduction method can help shed light on the future direction of a completely parameter tune-free self-adaptive DE algorithm.

On convergence of differential evolution over a class of continuous functions with unique global optimum.

PubMed

Ghosh, Sayan; Das, Swagatam; Vasilakos, Athanasios V; Suresh, Kaushik

2012-02-01

Differential evolution (DE) is arguably one of the most powerful stochastic real-parameter optimization algorithms of current interest. Since its inception in the mid 1990s, DE has been finding many successful applications in real-world optimization problems from diverse domains of science and engineering. This paper takes a first significant step toward the convergence analysis of a canonical DE (DE/rand/1/bin) algorithm. It first deduces a time-recursive relationship for the probability density function (PDF) of the trial solutions, taking into consideration the DE-type mutation, crossover, and selection mechanisms. Then, by applying the concepts of Lyapunov stability theorems, it shows that as time approaches infinity, the PDF of the trial solutions concentrates narrowly around the global optimum of the objective function, assuming the shape of a Dirac delta distribution. Asymptotic convergence behavior of the population PDF is established by constructing a Lyapunov functional based on the PDF and showing that it monotonically decreases with time. The analysis is applicable to a class of continuous and real-valued objective functions that possesses a unique global optimum (but may have multiple local optima). Theoretical results have been substantiated with relevant computer simulations.

Multiple-try differential evolution adaptive Metropolis for efficient solution of highly parameterized models

NASA Astrophysics Data System (ADS)

Eric, L.; Vrugt, J. A.

2010-12-01

Spatially distributed hydrologic models potentially contain hundreds of parameters that need to be derived by calibration against a historical record of input-output data. The quality of this calibration strongly determines the predictive capability of the model and thus its usefulness for science-based decision making and forecasting. Unfortunately, high-dimensional optimization problems are typically difficult to solve. Here we present our recent developments to the Differential Evolution Adaptive Metropolis (DREAM) algorithm (Vrugt et al., 2009) to warrant efficient solution of high-dimensional parameter estimation problems. The algorithm samples from an archive of past states (Ter Braak and Vrugt, 2008), and uses multiple-try Metropolis sampling (Liu et al., 2000) to decrease the required burn-in time for each individual chain and increase efficiency of posterior sampling. This approach is hereafter referred to as MT-DREAM. We present results for 2 synthetic mathematical case studies, and 2 real-world examples involving from 10 to 240 parameters. Results for those cases show that our multiple-try sampler, MT-DREAM, can consistently find better solutions than other Bayesian MCMC methods. Moreover, MT-DREAM is admirably suited to be implemented and ran on a parallel machine and is therefore a powerful method for posterior inference.

Comparative Analysis of Particle Swarm and Differential Evolution via Tuning on Ultrasmall Titanium Oxide Nanoclusters

NASA Astrophysics Data System (ADS)

Inclan, Eric; Lassester, Jack; Geohegan, David; Yoon, Mina

Optimization algorithms (OA) coupled with numerical methods enable researchers to identify and study (meta) stable nanoclusters without the control restrictions of empirical methods. An algorithm's performance is governed by two factors: (1) its compatibility with an objective function, (2) the dimension of a design space, which increases with cluster size. Although researchers often tune an algorithm's user-defined parameters (UDP), tuning is not guaranteed to improve performance. In this research, Particle Swarm (PSO) and Differential Evolution (DE), are compared by tuning their UDP in a multi-objective optimization environment (MOE). Combined with a Kolmogorov Smirnov test for statistical significance, the MOE enables the study of the Pareto Front (PF), made of the UDP settings that trade-off between best performance in energy minimization (``effectiveness'') based on force-field potential energy, and best convergence rate (``efficiency''). By studying the PF, this research finds that UDP values frequently suggested in the literature do not provide best effectiveness for these methods. Additionally, monotonic convergence is found to significantly improve efficiency without sacrificing effectiveness for very small systems, suggesting better compatibility. Work is supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.

The evolution of menstruation: a new model for genetic assimilation: explaining molecular origins of maternal responses to fetal invasiveness.

PubMed

Emera, Deena; Romero, Roberto; Wagner, Günter

2012-01-01

Why do humans menstruate while most mammals do not? Here, we present our answer to this long-debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone-induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal-fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non-menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. Copyright © 2012 WILEY Periodicals, Inc.

Pliocene-Pleistocene ecological niche evolution shapes the phylogeography of a Mediterranean plant group.

PubMed

Benítez-Benítez, C; Escudero, M; Rodríguez-Sánchez, F; Martín-Bravo, S; Jiménez-Mejías, P

2018-04-01

Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean Basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here, we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean Basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation. We carried out a dated phylogenetic-phylogeographic study based on seven DNA regions (nDNA and ptDNA) and fingerprinting data (AFLPs), and modelled ecological niches and species distributions for the Pliocene, Pleistocene and present. Phylogenetic and divergence time analyses revealed that both species form a monophyletic lineage originated in the late Pliocene-early Pleistocene. We detected clear genetic differentiation between both species with distinct genetic clusters in disjunct areas, indicating the predominant role of geographic barriers limiting gene flow. We found a remarkable shift in the climatic requirements between Pliocene and extant populations, although the niche seems to have been relatively conserved since the Pleistocene split of both species. This study highlights how an integrative approach combining different data sources and analyses, including fossils, allows solid and robust inferences about the evolutionary history of a plant group since the Pliocene. © 2018 John Wiley & Sons Ltd.

Differential evolution of the UV luminosity function of Lyman break galaxies from z ~ 5 to 3

NASA Astrophysics Data System (ADS)

Iwata, I.; Ohta, K.; Tamura, N.; Akiyama, M.; Aoki, K.; Ando, M.; Kiuchi, G.; Sawicki, M.

2007-04-01

We report the ultraviolet luminosity function (UVLF) of Lyman break galaxies at z ~ 5 derived from a deep and wide survey using the prime focus camera of the 8.2 m Subaru telescope (Suprime-Cam). Target fields consist of two blank regions of the sky, namely, the region including the Hubble Deep Field-North and the J0053+1234 region, and the total effective surveyed area is 1290 arcmin2. Applications of carefully determined colour selection criteria in V - Ic and Ic - z' yield a detection of 853 z ~ 5 candidates with z'AB < 26.5 mag. The UVLF at z ~ 5 based on this sample shows no significant change in the number density of bright (L >~ L*z=3) LBGs from that at z ~ 3, while there is a significant decline in the LF's faint end with increasing look-back time. This result means that the evolution of the number densities is differential with UV luminosity: the number density of UV luminous objects remains almost constant from z ~ 5 to 3 (the cosmic age is about 1.2 to 2.1 Gyr) while the number density of fainter objects gradually increases with cosmic time. This trend becomes apparent thanks to the small uncertainties in number densities both in the bright and faint parts of LFs at different epochs that are made possible by the deep and wide surveys we use. We discuss the origins of this differential evolution of the UVLF along the cosmic time and suggest that our observational findings are consistent with the biased galaxy evolution scenario: a galaxy population hosted by massive dark haloes starts active star formation preferentially at early cosmic time, while less massive galaxies increase their number density later. We also calculated the UV luminosity density by integrating the UVLF and at z ~ 5 found it to be 38.8+6.7-4.1 per cent of that at z ~ 3 for the luminosity range L > 0.1L*z=3. By combining our results with those from the literature, we find that the cosmic UV luminosity density marks its peak at and then slowly declines towards higher redshift. Based on data collected at Subaru Telescope and partly obtained from the SMOKA science archive at Astronomical Data Analysis Center, which are operated by the National Astronomical Observatory of Japan. E-mail: iwata@oao.nao.ac.jp (II)

Universal and integrable nonlinear evolution systems of equations in 2+1 dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maccari, A.

1997-08-01

Integrable systems of nonlinear partial differential equations (PDEs) are obtained from integrable equations in 2+1 dimensions, by means of a reduction method of broad applicability based on Fourier expansion and spatio{endash}temporal rescalings, which is asymptotically exact in the limit of weak nonlinearity. The integrability by the spectral transform is explicitly demonstrated, because the corresponding Lax pairs have been derived, applying the same reduction method to the Lax pair of the initial equation. These systems of nonlinear PDEs are likely to be of applicative relevance and have a {open_quotes}universal{close_quotes} character, inasmuch as they may be derived from a very large classmore » of nonlinear evolution equations with a linear dispersive part. {copyright} {ital 1997 American Institute of Physics.}« less

Evolution of Constitution, Structure, and Morphology in FeCo-Based Multicomponent Alloys

NASA Astrophysics Data System (ADS)

Li, R.; Stoica, M.; Liu, G.; Eckert, J.

2010-07-01

Constituent phases, melting behaviors, and microstructure of multicomponent (Fe0.5Co0.5) x (Mo0.1C0.2B0.5Si0.2)100- x alloys ( x = 95, 90, 85, 80, and 70) produced by copper mold casting were evaluated by various analysis techniques, i.e., X-ray diffractometry, scanning electronic microscopy with energy dispersive X-ray spectrometry, and differential scanning calorimetry. Metastable Fe3C- and Cr23C6-type phases were identified in the chill-cast alloys. A schematic illustration was proposed to explain the evolution of constituent phases and microstructure for the alloys with x = 95, 90, and 85 during the solidification process, which could be applicable to controlling microstructural formation of other multicomponent alloys with similar microstructures by artificially adjusting the composition.

Thermal evolution of a partially differentiated H chondrite parent body

NASA Astrophysics Data System (ADS)

Abrahams, J. N. H.; Bryson, J. F. J.; Weiss, B. P.; Nimmo, F.

2016-12-01

It has traditionally been assumed that planetesimals either melted entirely or remained completely undifferentiated as they accreted. The unmelted textures and cooling histories of chondrites have been used to argue that these meteorites originated from bodies that never differentiated. However, paleomagnetic measurements indicate that some chondrites (e.g., the H chondrite Portales Valley and several CV chondrites) were magnetized by a core dynamo magnetic field, implying that their parent bodies were partially differentiated. It has been unclear, however, whether planetesimal histories consistent with dynamo production can also be consistent with the diversity of chondrite cooling rates and ages. To address this, we modeled the thermal evolution of the H chondrite parent body, considering a variety of accretion histories and parent body radii. We considered partial differentiation using two-stage accretion involving the initial formation and differentiation of a small body, followed by the later addition of low thermal conductivity chondritic material that remains mostly unmelted. We were able to reproduce the measured thermal evolution of multiple H chondrites for a range of parent body parameters, including initial radii from 70-150 km, chondritic layer thicknesses from 50 km to over 100 km, and second stage accretion times of 2.5-3 Myr after solar system formation. Our predicted rates of core cooling and crystallization are consistent with dynamo generation by compositional convection beginning 60-200 Myr after solar system formation and lasting for at least tens of millions of years. This is consistent with magnetic studies of Portales Valley [Bryson et al., this meeting]. In summary, we find that thermal models of partial differentiation are consistent the radiometric ages, magnetization, and cooling rates of a diversity H chondrites.

Trait-specific processes of convergence and conservatism shape ecomorphological evolution in ground-dwelling squirrels.

PubMed

McLean, Bryan S; Helgen, Kristofer M; Goodwin, H Thomas; Cook, Joseph A

2018-03-01

Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity. Using four ecologically relevant trait datasets (body size, cranial, mandibular, and molariform tooth shape), we compared and contrasted variation, covariation, and disparity patterns in a new phylogenetic framework. Strong correlations existed between body size and two skull traits (allometry) and among skull traits themselves (integration). Inferred evolutionary modes were also concordant across traits (Ornstein-Uhlenbeck with two adaptive regimes). However, despite these broad similarities, we found divergent dynamics on the macroevolutionary landscape, with phenotypic disparity being differentially shaped by convergence and conservatism. Such among-trait heterogeneity in process (but not always pattern) reiterates the mosaic nature of morphological evolution, and suggests ground squirrel evolution is poorly captured by single process descriptors. Our results also highlight how use of single traits can bias macroevolutionary inference, affirming the importance of broader trait-bases in understanding phenotypic evolutionary dynamics. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Differential Evolution algorithm applied to FSW model calibration

NASA Astrophysics Data System (ADS)

Idagawa, H. S.; Santos, T. F. A.; Ramirez, A. J.

2014-03-01

Friction Stir Welding (FSW) is a solid state welding process that can be modelled using a Computational Fluid Dynamics (CFD) approach. These models use adjustable parameters to control the heat transfer and the heat input to the weld. These parameters are used to calibrate the model and they are generally determined using the conventional trial and error approach. Since this method is not very efficient, we used the Differential Evolution (DE) algorithm to successfully determine these parameters. In order to improve the success rate and to reduce the computational cost of the method, this work studied different characteristics of the DE algorithm, such as the evolution strategy, the objective function, the mutation scaling factor and the crossover rate. The DE algorithm was tested using a friction stir weld performed on a UNS S32205 Duplex Stainless Steel.

AI-BL1.0: a program for automatic on-line beamline optimization using the evolutionary algorithm.

PubMed

Xi, Shibo; Borgna, Lucas Santiago; Zheng, Lirong; Du, Yonghua; Hu, Tiandou

2017-01-01

In this report, AI-BL1.0, an open-source Labview-based program for automatic on-line beamline optimization, is presented. The optimization algorithms used in the program are Genetic Algorithm and Differential Evolution. Efficiency was improved by use of a strategy known as Observer Mode for Evolutionary Algorithm. The program was constructed and validated at the XAFCA beamline of the Singapore Synchrotron Light Source and 1W1B beamline of the Beijing Synchrotron Radiation Facility.

Language and emotions: emotional Sapir-Whorf hypothesis.

PubMed

Perlovsky, Leonid

2009-01-01

An emotional version of Sapir-Whorf hypothesis suggests that differences in language emotionalities influence differences among cultures no less than conceptual differences. Conceptual contents of languages and cultures to significant extent are determined by words and their semantic differences; these could be borrowed among languages and exchanged among cultures. Emotional differences, as suggested in the paper, are related to grammar and mostly cannot be borrowed. The paper considers conceptual and emotional mechanisms of language along with their role in the mind and cultural evolution. Language evolution from primordial undifferentiated animal cries is discussed: while conceptual contents increase, emotional reduced. Neural mechanisms of these processes are suggested as well as their mathematical models: the knowledge instinct, the dual model connecting language and cognition, neural modeling fields. Mathematical results are related to cognitive science, linguistics, and psychology. Experimental evidence and theoretical arguments are discussed. Dynamics of the hierarchy-heterarchy of human minds and cultures is formulated using mean-field approach and approximate equations are obtained. The knowledge instinct operating in the mind heterarchy leads to mechanisms of differentiation and synthesis determining ontological development and cultural evolution. These mathematical models identify three types of cultures: "conceptual" pragmatic cultures in which emotionality of language is reduced and differentiation overtakes synthesis resulting in fast evolution at the price of uncertainty of values, self doubts, and internal crises; "traditional-emotional" cultures where differentiation lags behind synthesis, resulting in cultural stability at the price of stagnation; and "multi-cultural" societies combining fast cultural evolution and stability. Unsolved problems and future theoretical and experimental directions are discussed.

Modeling KBOs Charon, Orcus and Salacia by means of a new equation of state for porous icy bodies

NASA Astrophysics Data System (ADS)

Malamud, U.; Prialnik, D.

2015-10-01

We use a one-dimensional adaptive-grid thermal evolution code to model intermediate sized Kuiper belt objects Charon, Orcus and Salacia and compare their measured bulk densities with those resulting from evolutionary calculations at the end of 4.6 Gyr. Our model assumes an initial homogeneous composition of mixed ice and rock, and follows the multiphase flow of water through the porous rocky medium, consequent differentiation and aqueous chemical alterations in the rock. Heating sources include long-lived radionuclides, serpentinization reactions, release of gravitational potential energy due to compaction, and crystallization of amorphous ice. The density profile is calculated by assuming hydrostatic equilibrium to be maintained through changes in composition, pressure and temperature. To this purpose, we construct an equation of state suitable for porous icy bodies with radii of a few hundred km, based on the best available empirical studies of ice and rock compaction, and on comparisons with rock porosities in Earth analog and Solar System silicates. We show that the observed bulk densities can be reproduced by assuming the same set of initial and physical parameters, including the same rock/ice mass ratio for all three bodies. We conclude that the mass of the object uniquely determines the evolution of porosity, and thus explains the observed differences in bulk density. The final structure of all three objects is differentiated, with an inner rocky core, and outer ice-enriched mantle. The degree of differentiation, too, is determined by the object's mass.

Modeling Kuiper belt objects Charon, Orcus and Salacia by means of a new equation of state for porous icy bodies

NASA Astrophysics Data System (ADS)

Malamud, Uri; Prialnik, Dina

2015-01-01

We use a one-dimensional adaptive-grid thermal evolution code to model Kuiper belt objects Charon, Orcus and Salacia and compare their measured bulk densities with those resulting from evolutionary calculations at the end of 4.6 Gyr. Our model assumes an initial homogeneous composition of mixed ice and rock, and follows the multiphase flow of water through the porous rocky medium, consequent differentiation and aqueous chemical alterations in the rock. Heating sources include long-lived radionuclides, serpentinization reactions, release of gravitational potential energy due to compaction, and crystallization of amorphous ice. The density profile is calculated by assuming hydrostatic equilibrium to be maintained through changes in composition, pressure and temperature. To this purpose, we construct an equation of state suitable for porous icy bodies with radii of a few hundred km, based on the best available empirical studies of ice and rock compaction, and on comparisons with rock porosities in Earth analog and Solar System silicates. We show that the observed bulk densities can be reproduced by assuming the same set of initial and physical parameters, including the same rock/ice mass ratio for all three bodies. We conclude that the mass of the object uniquely determines the evolution of porosity, and thus explains the observed differences in bulk density. The final structure of all three objects is differentiated, with an inner rocky core, and outer ice-enriched mantle. The degree of differentiation, too, is determined by the object's mass.

Chandrasekhar equations for infinite dimensional systems

NASA Technical Reports Server (NTRS)

Ito, K.; Powers, R. K.

1985-01-01

Chandrasekhar equations are derived for linear time invariant systems defined on Hilbert spaces using a functional analytic technique. An important consequence of this is that the solution to the evolutional Riccati equation is strongly differentiable in time and one can define a strong solution of the Riccati differential equation. A detailed discussion on the linear quadratic optimal control problem for hereditary differential systems is also included.

Meteoritic and Asteroidal Constraints on the Identification and Collisional Evolution of Asteroid Families

NASA Technical Reports Server (NTRS)

Gaffey, Michael J.; Kelley, Michael S.; Hardersen, Paul S.

2002-01-01

Studies of meteorites and observations of asteroids can provide important constraints on the formation and evolution of asteroid families. The iron meteorites alone require the disruption of 85 differentiated asteroids, and the potential formation of 85 families. Additional information is contained in the original extended abstract.

Darwinism Defined: The Difference Between Fact and Theory.

ERIC Educational Resources Information Center

Gould, Stephen Jay

1987-01-01

Discusses various developments in both science and theology following the work of Charles Darwin on evolution. Differentiates between the facts regarding evolution and the theory of natural selection as a mechanism for evolutionary change. Warns that the differences between facts and theory have not been adequately emphasized by scientists. (TW)

Pb evolution in the Martian mantle

NASA Astrophysics Data System (ADS)

Bellucci, J. J.; Nemchin, A. A.; Whitehouse, M. J.; Snape, J. F.; Bland, P.; Benedix, G. K.; Roszjar, J.

2018-03-01

The initial Pb compositions of one enriched shergottite, one intermediate shergottite, two depleted shergottites, and Nakhla have been measured by Secondary Ion Mass Spectrometry (SIMS). These values, in addition to data from previous studies using an identical analytical method performed on three enriched shergottites, ALH 84001, and Chassigny, are used to construct a unified and internally consistent model for the differentiation history of the Martian mantle and crystallization ages for Martian meteorites. The differentiation history of the shergottites and Nakhla/Chassigny are fundamentally different, which is in agreement with short-lived radiogenic isotope systematics. The initial Pb compositions of Nakhla/Chassigny are best explained by the late addition of a Pb-enriched component with a primitive, non-radiogenic composition. In contrast, the Pb isotopic compositions of the shergottite group indicate a relatively simple evolutionary history of the Martian mantle that can be modeled based on recent results from the Sm-Nd system. The shergottites have been linked to a single mantle differentiation event at 4504 Ma. Thus, the shergottite Pb isotopic model here reflects a two-stage history 1) pre-silicate differentiation (4504 Ma) and 2) post-silicate differentiation to the age of eruption (as determined by concordant radiogenic isochron ages). The μ-values (238U/204Pb) obtained for these two different stages of Pb growth are μ1 of 1.8 and a range of μ2 from 1.4-4.7, respectively. The μ1-value of 1.8 is in broad agreement with enstatite and ordinary chondrites and that proposed for proto Earth, suggesting this is the initial μ-value for inner Solar System bodies. When plotted against other source radiogenic isotopic variables (Sri, γ187Os, ε143Nd, and ε176Hf), the second stage mantle evolution range in observed mantle μ-values display excellent linear correlations (r2 > 0.85) and represent a spectrum of Martian mantle mixing-end members (depleted, intermediate, enriched).

Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations in Lake Tanganyika.

PubMed

Koblmüller, Stephan; Salzburger, Walter; Obermüller, Beate; Eigner, Eva; Sturmbauer, Christian; Sefc, Kristina M

2011-06-01

The conditions of phenotypic and genetic population differentiation allow inferences about the evolution, preservation and loss of biological diversity. In Lake Tanganyika, water level fluctuations are assumed to have had a major impact on the evolution of stenotopic littoral species, though this hypothesis has not been specifically examined so far. The present study investigates whether subtly differentiated colour patterns of adjacent Tropheus moorii populations are maintained in isolation or in the face of continuous gene flow, and whether the presumed influence of water level fluctuations on lacustrine cichlids can be demonstrated in the small-scale population structure of the strictly stenotopic, littoral Tropheus. Distinct population differentiation was found even across short geographic distances and minor habitat barriers. Population splitting chronology and demographic histories comply with our expectation of old and rather stable populations on steeper sloping shore, and more recently established populations in a shallower region. Moreover, population expansions seem to coincide with lake level rises in the wake of Late Pleistocene megadroughts ~100 KYA. The imprint of hydrologic events on current population structure in the absence of ongoing gene flow suggests that phenotypic differentiation among proximate Tropheus populations evolves and persists in genetic isolation. Sporadic gene flow is effected by lake level fluctuations following climate changes and controlled by the persistence of habitat barriers during lake level changes. Since similar demographic patterns were previously reported for Lake Malawi cichlids, our data furthermore strengthen the hypothesis that major climatic events synchronized facets of cichlid evolution across the East African Great Lakes. © 2011 Blackwell Publishing Ltd.

Evolution-Based Functional Decomposition of Proteins

PubMed Central

Rivoire, Olivier; Reynolds, Kimberly A.; Ranganathan, Rama

2016-01-01

The essential biological properties of proteins—folding, biochemical activities, and the capacity to adapt—arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation. PMID:27254668

A multi-populations multi-strategies differential evolution algorithm for structural optimization of metal nanoclusters

NASA Astrophysics Data System (ADS)

Fan, Tian-E.; Shao, Gui-Fang; Ji, Qing-Shuang; Zheng, Ji-Wen; Liu, Tun-dong; Wen, Yu-Hua

2016-11-01

Theoretically, the determination of the structure of a cluster is to search the global minimum on its potential energy surface. The global minimization problem is often nondeterministic-polynomial-time (NP) hard and the number of local minima grows exponentially with the cluster size. In this article, a multi-populations multi-strategies differential evolution algorithm has been proposed to search the globally stable structure of Fe and Cr nanoclusters. The algorithm combines a multi-populations differential evolution with an elite pool scheme to keep the diversity of the solutions and avoid prematurely trapping into local optima. Moreover, multi-strategies such as growing method in initialization and three differential strategies in mutation are introduced to improve the convergence speed and lower the computational cost. The accuracy and effectiveness of our algorithm have been verified by comparing the results of Fe clusters with Cambridge Cluster Database. Meanwhile, the performance of our algorithm has been analyzed by comparing the convergence rate and energy evaluations with the classical DE algorithm. The multi-populations, multi-strategies mutation and growing method in initialization in our algorithm have been considered respectively. Furthermore, the structural growth pattern of Cr clusters has been predicted by this algorithm. The results show that the lowest-energy structure of Cr clusters contains many icosahedra, and the number of the icosahedral rings rises with increasing size.

On the evolution of developmental mechanisms: Divergent polarities in leaf growth as a case study.

PubMed

Gupta, Mainak Das; Nath, Utpal

2016-01-01

Most model plants used to study leaf growth share a common developmental mechanism, namely basipetal growth polarity, wherein the distal end differentiates first with progressively more proliferative cells toward the base. Therefore, this base-to-tip growth pattern has served as a paradigm to explain leaf growth and also formed the basis for several computational models. However, our recent report in The Plant Cell on the investigation of leaf growth in 75 eudicot species covering a wide range of eudicot families showed that leaves grow with divergent polarities in the proximo-distal axis or without any obvious polarity. This divergence in growth polarity is linked to the expression divergence of a conserved microRNA-transcription factor module. This study raises several questions on the evolutionary origin of leaf growth pattern, such as 'when and why in evolution did the divergent growth polarities arise?' and 'what were the molecular changes that led to this divergence?'. Here, we discuss a few of these questions in some detail.

Evaluation of an Agricultural Meteorological Disaster Based on Multiple Criterion Decision Making and Evolutionary Algorithm

PubMed Central

Yu, Xiaobing; Yu, Xianrui; Lu, Yiqun

2018-01-01

The evaluation of a meteorological disaster can be regarded as a multiple-criteria decision making problem because it involves many indexes. Firstly, a comprehensive indexing system for an agricultural meteorological disaster is proposed, which includes the disaster rate, the inundated rate, and the complete loss rate. Following this, the relative weights of the three criteria are acquired using a novel proposed evolutionary algorithm. The proposed algorithm consists of a differential evolution algorithm and an evolution strategy. Finally, a novel evaluation model, based on the proposed algorithm and the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS), is presented to estimate the agricultural meteorological disaster of 2008 in China. The geographic information system (GIS) technique is employed to depict the disaster. The experimental results demonstrated that the agricultural meteorological disaster of 2008 was very serious, especially in Hunan and Hubei provinces. Some useful suggestions are provided to relieve agriculture meteorological disasters. PMID:29597243

Testing the adaptive radiation hypothesis for the lemurs of Madagascar.

PubMed

Herrera, James P

2017-01-01

Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.

Consistent individual differences in human social learning strategies.

PubMed

Molleman, Lucas; van den Berg, Pieter; Weissing, Franz J

2014-04-04

Social learning has allowed humans to build up extensive cultural repertoires, enabling them to adapt to a wide variety of environmental and social conditions. However, it is unclear which social learning strategies people use, especially in social contexts where their payoffs depend on the behaviour of others. Here we show experimentally that individuals differ in their social learning strategies and that they tend to employ the same learning strategy irrespective of the interaction context. Payoff-based learners focus on their peers' success, while decision-based learners disregard payoffs and exclusively focus on their peers' past behaviour. These individual differences may be of considerable importance for cultural evolution. By means of a simple model, we demonstrate that groups harbouring individuals with different learning strategies may be faster in adopting technological innovations and can be more efficient through successful role differentiation. Our study highlights the importance of individual variation for human interactions and sheds new light on the dynamics of cultural evolution.

Testing the adaptive radiation hypothesis for the lemurs of Madagascar

PubMed Central

2017-01-01

Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an ‘early burst’ of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the ‘early burst’ signal of adaptive radiation may have been eroded by extinction. PMID:28280597

SPR imaging based electronic tongue via landscape images for complex mixture analysis.

PubMed

Genua, Maria; Garçon, Laurie-Amandine; Mounier, Violette; Wehry, Hillary; Buhot, Arnaud; Billon, Martial; Calemczuk, Roberto; Bonnaffé, David; Hou, Yanxia; Livache, Thierry

2014-12-01

Electronic noses/tongues (eN/eT) have emerged as promising alternatives for analysis of complex mixtures in the domain of food and beverage quality control. We have recently developed an electronic tongue by combining surface plasmon resonance imaging (SPRi) with an array of non-specific and cross-reactive receptors prepared by simply mixing two small molecules in varying and controlled proportions and allowing the mixtures to self-assemble on the SPRi prism surface. The obtained eT generated novel and unique 2D continuous evolution profiles (CEPs) and 3D continuous evolution landscapes (CELs) based on which the differentiation of complex mixtures such as red wine, beer and milk were successful. The preliminary experiments performed for monitoring the deterioration of UHT milk demonstrated its potential for quality control applications. Furthermore, the eT exhibited good repeatability and stability, capable of operating after a minimum storage period of 5 months. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling tree crown dynamics with 3D partial differential equations.

PubMed

Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

2014-01-01

We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth toward light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications.

Leaf anatomy of two reciprocally non-monophyletic mountain plants (Heliosperma spp.): does heritable adaptation to divergent growing sites accompany the onset of speciation?

PubMed

Bertel, Clara; Schönswetter, Peter; Frajman, Božo; Holzinger, Andreas; Neuner, Gilbert

2017-05-01

Evolution is driven by natural selection, favouring individuals adapted in phenotypic traits to the environmental conditions at their growing site. To shed light on ecological and (epi-) genetically based differentiation between Heliosperma pusillum and Heliosperma veselskyi, two reciprocally non-monophyletic, but morphologically and ecologically divergent species from the south-eastern Alps, we studied various leaf anatomical traits and investigated chloroplast ultrastructure in leaves of the two species grown either in their natural habitat or in a common garden. The alpine H. pusillum occurs in open, wet rock habitats, whereas its close relative H. veselskyi is restricted to dry, shady habitats below overhanging rocks in the montane belt. H. pusillum exhibited higher thickness of leaves and palisade layers as adjustments and/or adaptations to higher irradiance and a higher stomatal area index reflecting better water availability. Traits were adjusted plastically, but differed between species grown in a common garden, suggesting that the differentiation between the two species is not solely based on phenotypic plasticity but also has a genetic basis. Our study thus supports the hypothesis that differentiation between the highly interfertile species is likely driven by natural selection.

On a generalized Ablowitz-Kaup-Newell-Segur hierarchy in inhomogeneities of media: soliton solutions and wave propagation influenced from coefficient functions and scattering data

NASA Astrophysics Data System (ADS)

Zhang, Sheng; Hong, Siyu

2018-07-01

In this paper, a generalized Ablowitz-Kaup-Newell-Segur (AKNS) hierarchy in inhomogeneities of media described by variable coefficients is investigated, which includes some important nonlinear evolution equations as special cases, for example, the celebrated Korteweg-de Vries equation modeling waves on shallow water surfaces. To be specific, the known AKNS spectral problem and its time evolution equation are first generalized by embedding a finite number of differentiable and time-dependent functions. Starting from the generalized AKNS spectral problem and its generalized time evolution equation, a generalized AKNS hierarchy with variable coefficients is then derived. Furthermore, based on a systematic analysis on the time dependence of related scattering data of the generalized AKNS spectral problem, exact solutions of the generalized AKNS hierarchy are formulated through the inverse scattering transform method. In the case of reflectionless potentials, the obtained exact solutions are reduced to n-soliton solutions. It is graphically shown that the dynamical evolutions of such soliton solutions are influenced by not only the time-dependent coefficients but also the related scattering data in the process of propagations.

Differential effects of RNAi treatments on field populations of the western corn rootworm.

PubMed

Chu, Chia-Ching; Sun, Weilin; Spencer, Joseph L; Pittendrigh, Barry R; Seufferheld, Manfredo J

2014-03-01

RNA interference (RNAi) mediated crop protection against insect pests is a technology that is greatly anticipated by the academic and industrial pest control communities. Prior to commercialization, factors influencing the potential for evolution of insect resistance to RNAi should be evaluated. While mutations in genes encoding the RNAi machinery or the sequences targeted for interference may serve as a prominent mechanism of resistance evolution, differential effects of RNAi on target pests may also facilitate such evolution. However, to date, little is known about how variation of field insect populations could influence the effectiveness of RNAi treatments. To approach this question, we evaluated the effects of RNAi treatments on adults of three western corn rootworm (WCR; Diabrotica virgifera virgifera LeConte) populations exhibiting different levels of gut cysteine protease activity, tolerance of soybean herbivory, and immune gene expression; two populations were collected from crop rotation-resistant (RR) problem areas and one from a location where RR was not observed (wild type; WT). Our results demonstrated that RNAi targeting DvRS5 (a highly expressed cysteine protease gene) reduced gut cysteine protease activity in all three WCR populations. However, the proportion of the cysteine protease activity that was inhibited varied across populations. When WCR adults were treated with double-stranded RNA of an immune gene att1, different changes in survival among WT and RR populations on soybean diets occurred. Notably, for both genes, the sequences targeted for RNAi were the same across all populations examined. These findings indicate that the effectiveness of RNAi treatments could vary among field populations depending on their physiological and genetic backgrounds and that the consistency of an RNAi trait's effectiveness on phenotypically different populations should be considered or tested prior to wide deployment. Also, genes that are potentially subjected to differential selection in the field should be avoided for RNAi-based pest control. Published by Elsevier Inc.

Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies

PubMed Central

2014-01-01

Background Expansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). Although the genome sequencing of soybeans is complete, our knowledge about the pattern of expansion and evolutionary history of soybean expansin genes remains limited. Results A total of 75 expansin genes were identified in the soybean genome, and grouped into four subfamilies based on their phylogenetic relationships. Structural analysis revealed that the expansin genes are conserved in each subfamily, but are divergent among subfamilies. Furthermore, in soybean and Arabidopsis, the expansin gene family has been mainly expanded through tandem and segmental duplications; however, in rice, segmental duplication appears to be the dominant process that generates this superfamily. The transcriptome atlas revealed notable differential expression in either transcript abundance or expression patterns under normal growth conditions. This finding was consistent with the differential distribution of the cis-elements in the promoter region, and indicated wide functional divergence in this superfamily. Moreover, some critical amino acids that contribute to functional divergence and positive selection were detected. Finally, site model and branch-site model analysis of positive selection indicated that the soybean expansin gene superfamily is under strong positive selection, and that divergent selection constraints might have influenced the evolution of the four subfamilies. Conclusion This study demonstrated that the soybean expansin gene superfamily has expanded through tandem and segmental duplication. Differential expression indicated wide functional divergence in this superfamily. Furthermore, positive selection analysis revealed that divergent selection constraints might have influenced the evolution of the four subfamilies. In conclusion, the results of this study contribute novel detailed information about the molecular evolution of the expansin gene superfamily in soybean. PMID:24720629

Mesh-free based variational level set evolution for breast region segmentation and abnormality detection using mammograms.

PubMed

Kashyap, Kanchan L; Bajpai, Manish K; Khanna, Pritee; Giakos, George

2018-01-01

Automatic segmentation of abnormal region is a crucial task in computer-aided detection system using mammograms. In this work, an automatic abnormality detection algorithm using mammographic images is proposed. In the preprocessing step, partial differential equation-based variational level set method is used for breast region extraction. The evolution of the level set method is done by applying mesh-free-based radial basis function (RBF). The limitation of mesh-based approach is removed by using mesh-free-based RBF method. The evolution of variational level set function is also done by mesh-based finite difference method for comparison purpose. Unsharp masking and median filtering is used for mammogram enhancement. Suspicious abnormal regions are segmented by applying fuzzy c-means clustering. Texture features are extracted from the segmented suspicious regions by computing local binary pattern and dominated rotated local binary pattern (DRLBP). Finally, suspicious regions are classified as normal or abnormal regions by means of support vector machine with linear, multilayer perceptron, radial basis, and polynomial kernel function. The algorithm is validated on 322 sample mammograms of mammographic image analysis society (MIAS) and 500 mammograms from digital database for screening mammography (DDSM) datasets. Proficiency of the algorithm is quantified by using sensitivity, specificity, and accuracy. The highest sensitivity, specificity, and accuracy of 93.96%, 95.01%, and 94.48%, respectively, are obtained on MIAS dataset using DRLBP feature with RBF kernel function. Whereas, the highest 92.31% sensitivity, 98.45% specificity, and 96.21% accuracy are achieved on DDSM dataset using DRLBP feature with RBF kernel function. Copyright © 2017 John Wiley & Sons, Ltd.

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

PubMed Central

Boullu, Loïs; Morin, Valérie; Vallin, Elodie; Guillemin, Anissa; Papili Gao, Nan; Cosette, Jérémie; Arnaud, Ophélie; Kupiec, Jean-Jacques; Espinasse, Thibault

2016-01-01

In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging. We were able to show that the correlation network was a very dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a “simple” program that all cells execute identically but results from the dynamical behavior of the underlying molecular network. PMID:28027290

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.

PubMed

Richard, Angélique; Boullu, Loïs; Herbach, Ulysse; Bonnafoux, Arnaud; Morin, Valérie; Vallin, Elodie; Guillemin, Anissa; Papili Gao, Nan; Gunawan, Rudiyanto; Cosette, Jérémie; Arnaud, Ophélie; Kupiec, Jean-Jacques; Espinasse, Thibault; Gonin-Giraud, Sandrine; Gandrillon, Olivier

2016-12-01

In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging. We were able to show that the correlation network was a very dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a "simple" program that all cells execute identically but results from the dynamical behavior of the underlying molecular network.

Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria.

PubMed

Koch, Robin; Kupczok, Anne; Stucken, Karina; Ilhan, Judith; Hammerschmidt, Katrin; Dagan, Tal

2017-08-31

Filamentous cyanobacteria that differentiate multiple cell types are considered the peak of prokaryotic complexity and their evolution has been studied in the context of multicellularity origins. Species that form true-branching filaments exemplify the most complex cyanobacteria. However, the mechanisms underlying the true-branching morphology remain poorly understood despite of several investigations that focused on the identification of novel genes or pathways. An alternative route for the evolution of novel traits is based on existing phenotypic plasticity. According to that scenario - termed genetic assimilation - the fixation of a novel phenotype precedes the fixation of the genotype. Here we show that the evolution of transcriptional regulatory elements constitutes a major mechanism for the evolution of new traits. We found that supplementation with sucrose reconstitutes the ancestral branchless phenotype of two true-branching Fischerella species and compared the transcription start sites (TSSs) between the two phenotypic states. Our analysis uncovers several orthologous TSSs whose transcription level is correlated with the true-branching phenotype. These TSSs are found in genes that encode components of the septosome and elongasome (e.g., fraC and mreB). The concept of genetic assimilation supplies a tenable explanation for the evolution of novel traits but testing its feasibility is hindered by the inability to recreate and study the evolution of present-day traits. We present a novel approach to examine transcription data for the plasticity first route and provide evidence for its occurrence during the evolution of complex colony morphology in true-branching cyanobacteria. Our results reveal a route for evolution of the true-branching phenotype in cyanobacteria via modification of the transcription level of pre-existing genes. Our study supplies evidence for the 'plasticity-first' hypothesis and highlights the importance of transcriptional regulation in the evolution of novel traits.

Back to basics--how the evolution of the extracellular matrix underpinned vertebrate evolution.

PubMed

Huxley-Jones, Julie; Pinney, John W; Archer, John; Robertson, David L; Boot-Handford, Raymond P

2009-04-01

The extracellular matrix (ECM) is a complex substrate that is involved in and influences a spectrum of behaviours such as growth and differentiation and is the basis for the structure of tissues. Although a characteristic of all metazoans, the ECM has elaborated into a variety of tissues unique to vertebrates, such as bone, tendon and cartilage. Here we review recent advances in our understanding of the molecular evolution of the ECM. Furthermore, we demonstrate that ECM genes represent a pivotal family of proteins the evolution of which appears to have played an important role in the evolution of vertebrates.

NARMAX model identification of a palm oil biodiesel engine using multi-objective optimization differential evolution

NASA Astrophysics Data System (ADS)

Mansor, Zakwan; Zakaria, Mohd Zakimi; Nor, Azuwir Mohd; Saad, Mohd Sazli; Ahmad, Robiah; Jamaluddin, Hishamuddin

2017-09-01

This paper presents the black-box modelling of palm oil biodiesel engine (POB) using multi-objective optimization differential evolution (MOODE) algorithm. Two objective functions are considered in the algorithm for optimization; minimizing the number of term of a model structure and minimizing the mean square error between actual and predicted outputs. The mathematical model used in this study to represent the POB system is nonlinear auto-regressive moving average with exogenous input (NARMAX) model. Finally, model validity tests are applied in order to validate the possible models that was obtained from MOODE algorithm and lead to select an optimal model.

Adaptation and colonization history affect the evolution of clines in two introduced species.

PubMed

Keller, Stephen R; Sowell, Dexter R; Neiman, Maurine; Wolfe, Lorne M; Taylor, Douglas R

2009-08-01

Phenotypic and genetic clines have long been synonymous with adaptive evolution. However, other processes (for example, migration, range expansion, invasion) may generate clines in traits or loci across geographical and environmental gradients. It is therefore important to distinguish between clines that represent adaptive evolution and those that result from selectively neutral demographic or genetic processes. We tested for the differentiation of phenotypic traits along environmental gradients using two species in the genus Silene, whilst statistically controlling for colonization history and founder effects. We sampled seed families from across the native and introduced ranges, genotyped individuals and estimated phenotypic differentiation in replicated common gardens. The results suggest that post-glacial expansion of S. vulgaris and S. latifolia involved both neutral and adaptive genetic differentiation (clines) of life history traits along major axes of environmental variation in Europe and North America. Phenotypic clines generally persisted when tested against the neutral expectation, although some clines disappeared (and one cline emerged) when the effects of genetic ancestry were statistically removed. Colonization history, estimated using genetic markers, is a useful null model for tests of adaptive trait divergence, especially during range expansion and invasion when selection and gene flow may not have reached equilibrium.

Structure and tectonic evolution of the NE segment of the Polish-Ukrainian Carpathians during the Late Cenozoic: subsurface cross-sections and palinspastic models

NASA Astrophysics Data System (ADS)

Kuśmierek, Jan; Baran, Urszula

2016-08-01

The discrepant arrangement of the Carpathian nappes and syntectonic deposits of the Carpathian Foredeep reveals the oroclinal migration of the subduction direction of the platform margin during the Late Cenozoic. Formation of the nappes was induced by their detachment from disintegrated segments of the European Platform; the segments were shortened as a result of their vertical rotation in zones of compressional sutures. It finds expression in local occurrence of the backward vergence of folding against the generally forward vergence toward the Carpathian Foredeep. The precompressional configuration of sedimentation areas of particular nappes was reconstructed with application of the palinspastic method, on the basis of the hitherto undervalued model which emphasizes the influence of the subduction and differentiated morphology of the platform basement on the tectonic evolution of the fold and thrust belt. Superposition of the palaeogeographic representations and the present geometry of the orogen allows understanding of the impact of the magnitudes of tectonic displacements on the differentiation of the geological structure in the NE segment of the Carpathians. The differentiation has inspired different views of Polish and Ukrainian geologists on structural classification and evolution of the frontal thrusts.

Demography and the Evolution of Educational Inequality.

ERIC Educational Resources Information Center

Mare, Robert D.

The combined effects of differential fertility, differential mortality, and intergenerational educational mobility on the distribution of educational attainment in the United States were studied for women in the past half century. A simple model for the reproduction of educational hierarchies was used that takes these factors, plus age structure…

The origin and evolution of Basigin(BSG) gene: A comparative genomic and phylogenetic analysis.

PubMed

Zhu, Xinyan; Wang, Shenglan; Shao, Mingjie; Yan, Jie; Liu, Fei

2017-07-01

Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites. We then identified BSG homologs from genomic sequences and analyzed their phylogenetic relationships. We identified that BSG genes exist not only in the vertebrate metazoans but also in the invertebrate metazoans such as Amphioxus B. floridae, D. melanogaster, A. mellifera, S. japonicum, C. gigas, and T. patagoniensis. After sequence analysis, we confirmed that only vertebrate metazoans and Cephalochordate (amphioxus B. floridae) have the classic structure (a signal peptide, two Ig-like domains (IgC2 and IgI), a transmembrane region, and an intracellular domain). The invertebrate metazoans (excluding amphioxus B. floridae) lack the N-terminal signal peptides and IgC2 domain. We then generated a phylogenetic tree, genome organization comparison, and chromosomal disposition analysis based on the biological information obtained from the NCBI and Ensembl databases. Finally, we established the possible evolutionary scenario of the BSG gene, which showed the restricted exon rearrangement that has occurred during evolution, forming the present-day BSG gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

Convergent evolution of heat-inducibility during subfunctionalization of the Hsp70 gene family

PubMed Central

2013-01-01

Background Heat-shock proteins of the 70 kDa family (Hsp70s) are essential chaperones required for key cellular functions. In eukaryotes, four subfamilies can be distinguished according to their function and localisation in different cellular compartments: cytosol, endoplasmic reticulum, mitochondria and chloroplasts. Generally, multiple cytosol-type Hsp70s can be found in metazoans that show either constitutive expression and/or stress-inducibility, arguing for the evolution of different tasks and functions. Information about the hsp70 copy number and diversity in microbial eukaryotes is, however, scarce, and detailed knowledge about the differential gene expression in most protists is lacking. Therefore, we have characterised the Hsp70 gene family of Paramecium caudatum to gain insight into the evolution and differential heat stress response of the distinct family members in protists and to investigate the diversification of eukaryotic hsp70s focusing on the evolution of heat-inducibility. Results Eleven putative hsp70 genes could be detected in P. caudatum comprising homologs of three major Hsp70-subfamilies. Phylogenetic analyses revealed five evolutionarily distinct Hsp70-groups, each with a closer relationship to orthologous sequences of Paramecium tetraurelia than to another P. caudatum Hsp70-group. These highly diverse, paralogous groups resulted from duplications preceding Paramecium speciation, underwent divergent evolution and were subject to purifying selection. Heat-shock treatments were performed to test for differential expression patterns among the five Hsp70-groups as well as for a functional conservation within Paramecium. These treatments induced exceptionally high mRNA up-regulations in one cytosolic group with a low basal expression, indicative for the major heat inducible hsp70s. All other groups showed comparatively high basal expression levels and moderate heat-inducibility, signifying constitutively expressed genes. Comparative EST analyses for P. tetraurelia hsp70s unveiled a corresponding expression pattern, which supports a functionally conserved evolution of the Hsp70 gene family in Paramecium. Conclusions Our analyses suggest an independent evolution of the heat-inducible cytosol-type hsp70s in Paramecium and in its close relative Tetrahymena, as well as within higher eukaryotes. This result indicates convergent evolution during hsp70 subfunctionalization and implies that heat-inducibility evolved several times during the course of eukaryotic evolution. PMID:23433225

Sub-specialization in plastic surgery in Sub-saharan Africa: capacities, gaps and opportunities

PubMed Central

Ibrahim, Abdulrasheed

2014-01-01

The skill set of a plastic surgeon, which addresses a broad range of soft tissue conditions that are prevalent in sub-Saharan Africa, remains relevant in the unmet need for surgical care. Recently, there has being a major paradigm shift from discipline-based to disease-based care, resulting in an emerging component of patient-centered care; adequate access to subspecialty care in plastic and reconstructive surgery. Given the need for an evolution in sub-specialization, this article focuses on the benefits and future role of differentiation of plastic surgeons into sub-specialty training pathways in sub-Saharan Africa. PMID:25584125

Modeling and optimization of the multiobjective stochastic joint replenishment and delivery problem under supply chain environment.

PubMed

Wang, Lin; Qu, Hui; Liu, Shan; Dun, Cai-xia

2013-01-01

As a practical inventory and transportation problem, it is important to synthesize several objectives for the joint replenishment and delivery (JRD) decision. In this paper, a new multiobjective stochastic JRD (MSJRD) of the one-warehouse and n-retailer systems considering the balance of service level and total cost simultaneously is proposed. The goal of this problem is to decide the reasonable replenishment interval, safety stock factor, and traveling routing. Secondly, two approaches are designed to handle this complex multi-objective optimization problem. Linear programming (LP) approach converts the multi-objective to single objective, while a multi-objective evolution algorithm (MOEA) solves a multi-objective problem directly. Thirdly, three intelligent optimization algorithms, differential evolution algorithm (DE), hybrid DE (HDE), and genetic algorithm (GA), are utilized in LP-based and MOEA-based approaches. Results of the MSJRD with LP-based and MOEA-based approaches are compared by a contrastive numerical example. To analyses the nondominated solution of MOEA, a metric is also used to measure the distribution of the last generation solution. Results show that HDE outperforms DE and GA whenever LP or MOEA is adopted.

Modeling and Optimization of the Multiobjective Stochastic Joint Replenishment and Delivery Problem under Supply Chain Environment

PubMed Central

Dun, Cai-xia

2013-01-01

As a practical inventory and transportation problem, it is important to synthesize several objectives for the joint replenishment and delivery (JRD) decision. In this paper, a new multiobjective stochastic JRD (MSJRD) of the one-warehouse and n-retailer systems considering the balance of service level and total cost simultaneously is proposed. The goal of this problem is to decide the reasonable replenishment interval, safety stock factor, and traveling routing. Secondly, two approaches are designed to handle this complex multi-objective optimization problem. Linear programming (LP) approach converts the multi-objective to single objective, while a multi-objective evolution algorithm (MOEA) solves a multi-objective problem directly. Thirdly, three intelligent optimization algorithms, differential evolution algorithm (DE), hybrid DE (HDE), and genetic algorithm (GA), are utilized in LP-based and MOEA-based approaches. Results of the MSJRD with LP-based and MOEA-based approaches are compared by a contrastive numerical example. To analyses the nondominated solution of MOEA, a metric is also used to measure the distribution of the last generation solution. Results show that HDE outperforms DE and GA whenever LP or MOEA is adopted. PMID:24302880

On the origin, homologies and evolution of primate facial muscles, with a particular focus on hominoids and a suggested unifying nomenclature for the facial muscles of the Mammalia

PubMed Central

Diogo, R; Wood, B A; Aziz, M A; Burrows, A

2009-01-01

The mammalian facial muscles are a subgroup of hyoid muscles (i.e. muscles innervated by cranial nerve VII). They are usually attached to freely movable skin and are responsible for facial expressions. In this study we provide an account of the origin, homologies and evolution of the primate facial muscles, based on dissections of various primate and non-primate taxa and a review of the literature. We provide data not previously reported, including photographs showing in detail the facial muscles of primates such as gibbons and orangutans. We show that the facial muscles usually present in strepsirhines are basically the same muscles that are present in non-primate mammals such as tree-shrews. The exceptions are that strepsirhines often have a muscle that is usually not differentiated in tree-shrews, the depressor supercilii, and lack two muscles that are usually differentiated in these mammals, the zygomatico-orbicularis and sphincter colli superficialis. Monkeys such as macaques usually lack two muscles that are often present in strepsirhines, the sphincter colli profundus and mandibulo-auricularis, but have some muscles that are usually absent as distinct structures in non-anthropoid primates, e.g. the levator labii superioris alaeque nasi, levator labii superioris, nasalis, depressor septi nasi, depressor anguli oris and depressor labii inferioris. In turn, macaques typically lack a risorius, auricularis anterior and temporoparietalis, which are found in hominoids such as humans, but have muscles that are usually not differentiated in members of some hominoid taxa, e.g. the platysma cervicale (usually not differentiated in orangutans, panins and humans) and auricularis posterior (usually not differentiated in orangutans). Based on our observations, comparisons and review of the literature, we propose a unifying, coherent nomenclature for the facial muscles of the Mammalia as a whole and provide a list of more than 300 synonyms that have been used in the literature to designate the facial muscles of primates and other mammals. A main advantage of this nomenclature is that it combines, and thus creates a bridge between, those names used by human anatomists and the names often employed in the literature dealing with non-human primates and non-primate mammals. PMID:19531159

Integrable Seven-Point Discrete Equations and Second-Order Evolution Chains

NASA Astrophysics Data System (ADS)

Adler, V. E.

2018-04-01

We consider differential-difference equations defining continuous symmetries for discrete equations on a triangular lattice. We show that a certain combination of continuous flows can be represented as a secondorder scalar evolution chain. We illustrate the general construction with a set of examples including an analogue of the elliptic Yamilov chain.

On the effects of higher convection modes on the thermal evolution of small planetary bodies

NASA Technical Reports Server (NTRS)

Arkani-Hamed, J.

1979-01-01

The effects of higher modes of convection on the thermal evolution of a small planetary body is investigated. Three sets of models are designed to specify an initially cold and differentiated, an initially hot and differentiated, and an initially cold and undifferentiated Moon-type body. The strong temperature dependence of viscosity enhances the thickening of lithosphere so that a lithosphere of about 400 km thickness is developed within the first billion years of the evolution of a Moon-type body. The thermally isolating effect of such a lithosphere hampers the heat flux out of the body and increases the temperature of the interior, causing the solid-state convection to occur with high velocity so that even the lower modes of convection can maintain an adiabatic temperature gradient there. It is demonstrated that the effect of solid-state convection on the thermal evolution of the models may be adequately determined by a combination of convection modes up to the third or the fourth order harmonic. The inclusion of higher modes does not affect the results significantly.

Vertebrate-like regeneration in the invertebrate chordate amphioxus

PubMed Central

Somorjai, Ildikó M. L.; Garcia-Fernàndez, Jordi; Escrivà, Hector

2012-01-01

An important question in biology is why some animals are able to regenerate, whereas others are not. The basal chordate amphioxus is uniquely positioned to address the evolution of regeneration. We report here the high regeneration potential of the European amphioxus Branchiostoma lanceolatum. Adults regenerate both anterior and posterior structures, including neural tube, notochord, fin, and muscle. Development of a classifier based on tail regeneration profiles predicts the assignment of young and old adults to their own class with >94% accuracy. The process involves loss of differentiated characteristics, formation of an msx-expressing blastema, and neurogenesis. Moreover, regeneration is linked to the activation of satellite-like Pax3/7 progenitor cells, the extent of which declines with size and age. Our results provide a framework for understanding the evolution and diversity of regeneration mechanisms in vertebrates. PMID:22203957

The cultural evolution of emergent group-level traits.

PubMed

Smaldino, Paul E

2014-06-01

Many of the most important properties of human groups - including properties that may give one group an evolutionary advantage over another - are properly defined only at the level of group organization. Yet at present, most work on the evolution of culture has focused solely on the transmission of individual-level traits. I propose a conceptual extension of the theory of cultural evolution, particularly related to the evolutionary competition between cultural groups. The key concept in this extension is the emergent group-level trait. This type of trait is characterized by the structured organization of differentiated individuals and constitutes a unit of selection that is qualitatively different from selection on groups as defined by traditional multilevel selection (MLS) theory. As a corollary, I argue that the traditional focus on cooperation as the defining feature of human societies has missed an essential feature of cooperative groups. Traditional models of cooperation assume that interacting with one cooperator is equivalent to interacting with any other. However, human groups involve differential roles, meaning that receiving aid from one individual is often preferred to receiving aid from another. In this target article, I discuss the emergence and evolution of group-level traits and the implications for the theory of cultural evolution, including ramifications for the evolution of human cooperation, technology, and cultural institutions, and for the equivalency of multilevel selection and inclusive fitness approaches.

Nanoscale Morphology Evolution Under Ion Irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aziz, Michael J.

We showed that the half-century-old paradigm of morphological instability under irradiation due to the curvature-dependence of the sputter yield, can account neither for the phase diagram nor the amplification or decay rates that we measure in the simplest possible experimental system -- an elemental semiconductor with an amorphous surface under noble-gas ion irradiation; We showed that a model of pattern formation based on the impact-induced redistribution of atoms that do not get sputtered away explains our experimental observations; We developed a first-principles, parameter-free approach for predicting morphology evolution, starting with molecular dynamics simulations of single ion impacts, lasting picoseconds, andmore » upscaling through a rigorous crater-function formalism to develop a partial differential equation that predicts morphology evolution on time scales more than twelve orders of magnitude longer than can be covered by the molecular dynamics; We performed the first quantitative comparison of the contributions to morphological instability from sputter removal and from impact-induced redistribution of atoms that are removed, and showed that the former is negligible compared to the latter; We established a new paradigm for impact-induced morphology evolution based on crater functions that incorporate both redistribution and sputter effects; and We developed a model of nanopore closure by irradiation-induced stress and irradiationenhanced fluidity, for the near-surface irradiation regime in which nuclear stopping predominates, and showed that it explains many aspects of pore closure kinetics that we measure experimentally.« less

From crater functions to partial differential equations: a new approach to ion bombardment induced nonequilibrium pattern formation.

PubMed

Norris, Scott A; Brenner, Michael P; Aziz, Michael J

2009-06-03

We develop a methodology for deriving continuum partial differential equations for the evolution of large-scale surface morphology directly from molecular dynamics simulations of the craters formed from individual ion impacts. Our formalism relies on the separation between the length scale of ion impact and the characteristic scale of pattern formation, and expresses the surface evolution in terms of the moments of the crater function. We demonstrate that the formalism reproduces the classical Bradley-Harper results, as well as ballistic atomic drift, under the appropriate simplifying assumptions. Given an actual set of converged molecular dynamics moments and their derivatives with respect to the incidence angle, our approach can be applied directly to predict the presence and absence of surface morphological instabilities. This analysis represents the first work systematically connecting molecular dynamics simulations of ion bombardment to partial differential equations that govern topographic pattern-forming instabilities.

Color separation in forensic image processing using interactive differential evolution.

PubMed

Mushtaq, Harris; Rahnamayan, Shahryar; Siddiqi, Areeb

2015-01-01

Color separation is an image processing technique that has often been used in forensic applications to differentiate among variant colors and to remove unwanted image interference. This process can reveal important information such as covered text or fingerprints in forensic investigation procedures. However, several limitations prevent users from selecting the appropriate parameters pertaining to the desired and undesired colors. This study proposes the hybridization of an interactive differential evolution (IDE) and a color separation technique that no longer requires users to guess required control parameters. The IDE algorithm optimizes these parameters in an interactive manner by utilizing human visual judgment to uncover desired objects. A comprehensive experimental verification has been conducted on various sample test images, including heavily obscured texts, texts with subtle color variations, and fingerprint smudges. The advantage of IDE is apparent as it effectively optimizes the color separation parameters at a level indiscernible to the naked eyes. © 2014 American Academy of Forensic Sciences.

Presupernova Evolution of Differentially Rotating Massive Stars Including Magnetic Fields

NASA Astrophysics Data System (ADS)

Heger, A.; Woosley, S. E.; Spruit, H. C.

2005-06-01

As a massive star evolves through multiple stages of nuclear burning on its way to becoming a supernova, a complex, differentially rotating structure is set up. Angular momentum is transported by a variety of classic instabilities and also by magnetic torques from fields generated by the differential rotation. We present the first stellar evolution calculations to follow the evolution of rotating massive stars including, at least approximately, all these effects, magnetic and nonmagnetic, from the zero-age main sequence until the onset of iron-core collapse. The evolution and action of the magnetic fields is as described by Spruit in 2002, and a range of uncertain parameters is explored. In general, we find that magnetic torques decrease the final rotation rate of the collapsing iron core by about a factor of 30-50 when compared with the nonmagnetic counterparts. Angular momentum in that part of the presupernova star destined to become a neutron star is an increasing function of main-sequence mass. That is, pulsars derived from more massive stars rotate faster and rotation plays a more important role in the star's explosion. The final angular momentum of the core has been determined-to within a factor of 2-by the time the star ignites carbon burning. For the lighter stars studied, around 15 Msolar, we predict pulsar periods at birth near 15 ms, though a factor of 2 range is easily tolerated by the uncertainties. Several mechanisms for additional braking in a young neutron star, especially by fallback, are explored.

Species-Specific 5 mC and 5 hmC Genomic Landscapes Indicate Epigenetic Contribution to Human Brain Evolution

PubMed Central

Madrid, Andy; Chopra, Pankaj; Alisch, Reid S.

2018-01-01

Human evolution from non-human primates has seen substantial change in the central nervous system, with the molecular mechanisms underlying human brain evolution remaining largely unknown. Methylation of cytosine at the fifth carbon (5-methylcytosine; 5 mC) is an essential epigenetic mark linked to neurodevelopment, as well as neurological disease. The emergence of another modified form of cytosine (5-hydroxymethylcytosine; 5 hmC) that is enriched in the brain further substantiates a role for these epigenetic marks in neurodevelopment, yet little is known about the evolutionary importance of these marks in brain development. Here, human and monkey brain tissue were profiled, identifying 5,516 and 4,070 loci that were differentially methylated and hydroxymethylated, respectively, between the species. Annotation of these loci to the human genome revealed genes critical for the development of the nervous system and that are associated with intelligence and higher cognitive functioning, such as RELN and GNAS. Moreover, ontological analyses of these differentially methylated and hydroxymethylated genes revealed a significant enrichment of neuronal/immunological–related processes, including neurogenesis and axon development. Finally, the sequences flanking the differentially methylated/hydroxymethylated loci contained a significant enrichment of binding sites for neurodevelopmentally important transcription factors (e.g., OTX1 and PITX1), suggesting that DNA methylation may regulate gene expression by mediating transcription factor binding on these transcripts. Together, these data support dynamic species-specific epigenetic contributions in the evolution and development of the human brain from non-human primates. PMID:29491831

Hands of early primates.

PubMed

Boyer, Doug M; Yapuncich, Gabriel S; Chester, Stephen G B; Bloch, Jonathan I; Godinot, Marc

2013-12-01

Questions surrounding the origin and early evolution of primates continue to be the subject of debate. Though anatomy of the skull and inferred dietary shifts are often the focus, detailed studies of postcrania and inferred locomotor capabilities can also provide crucial data that advance understanding of transitions in early primate evolution. In particular, the hand skeleton includes characteristics thought to reflect foraging, locomotion, and posture. Here we review what is known about the early evolution of primate hands from a comparative perspective that incorporates data from the fossil record. Additionally, we provide new comparative data and documentation of skeletal morphology for Paleogene plesiadapiforms, notharctines, cercamoniines, adapines, and omomyiforms. Finally, we discuss implications of these data for understanding locomotor transitions during the origin and early evolutionary history of primates. Known plesiadapiform species cannot be differentiated from extant primates based on either intrinsic hand proportions or hand-to-body size proportions. Nonetheless, the presence of claws and a different metacarpophalangeal [corrected] joint form in plesiadapiforms indicate different grasping mechanics. Notharctines and cercamoniines have intrinsic hand proportions with extremely elongated proximal phalanges and digit rays relative to metacarpals, resembling tarsiers and galagos. But their hand-to-body size proportions are typical of many extant primates (unlike those of tarsiers, and possibly Teilhardina, which have extremely large hands). Non-adapine adapiforms and omomyids exhibit additional carpal features suggesting more limited dorsiflexion, greater ulnar deviation, and a more habitually divergent pollex than observed plesiadapiforms. Together, features differentiating adapiforms and omomyiforms from plesiadapiforms indicate increased reliance on vertical prehensile-clinging and grasp-leaping, possibly in combination with predatory behaviors in ancestral euprimates. Copyright © 2013 Wiley Periodicals, Inc.

The Fast Debris Evolution Model

NASA Astrophysics Data System (ADS)

Lewis, Hugh G.; Swinerd, Graham; Newland, Rebecca; Saunders, Arrun

The ‘Particles-in-a-box' (PIB) model introduced by Talent (1992) removed the need for computerintensive Monte Carlo simulation to predict the gross characteristics of an evolving debris environment. The PIB model was described using a differential equation that allows the stability of the low Earth orbit (LEO) environment to be tested by a straightforward analysis of the equation's coefficients. As part of an ongoing research effort to investigate more efficient approaches to evolutionary modelling and to develop a suite of educational tools, a new PIB model has been developed. The model, entitled Fast Debris Evolution (FaDE), employs a first-order differential equation to describe the rate at which new objects (˜ 10 cm) are added and removed from the environment. Whilst Talent (1992) based the collision theory for the PIB approach on collisions between gas particles and adopted specific values for the parameters of the model from a number of references, the form and coefficients of the FaDE model equations can be inferred from the outputs of future projections produced by high-fidelity models, such as the DAMAGE model. The FaDE model has been implemented as a client-side, web-based service using Javascript embedded within a HTML document. Due to the simple nature of the algorithm, FaDE can deliver the results of future projections immediately in a graphical format, with complete user-control over key simulation parameters. Historical and future projections for the ˜ 10 cm low Earth orbit (LEO) debris environment under a variety of different scenarios are possible, including business as usual, no future launches, post-mission disposal and remediation. A selection of results is presented with comparisons with predictions made using the DAMAGE environment model. The results demonstrate that the FaDE model is able to capture comparable time-series of collisions and number of objects as predicted by DAMAGE in several scenarios. Further, and perhaps more importantly, its speed and flexibility allows the user to explore and understand the evolution of the space debris environment.

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

PubMed

Inglin, Raffael C; Meile, Leo; Stevens, Marc J A

2018-04-24

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed by the environment and HGT.

Musical emotions: Functions, origins, evolution

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid

2010-03-01

Theories of music origins and the role of musical emotions in the mind are reviewed. Most existing theories contradict each other, and cannot explain mechanisms or roles of musical emotions in workings of the mind, nor evolutionary reasons for music origins. Music seems to be an enigma. Nevertheless, a synthesis of cognitive science and mathematical models of the mind has been proposed describing a fundamental role of music in the functioning and evolution of the mind, consciousness, and cultures. The review considers ancient theories of music as well as contemporary theories advanced by leading authors in this field. It addresses one hypothesis that promises to unify the field and proposes a theory of musical origin based on a fundamental role of music in cognition and evolution of consciousness and culture. We consider a split in the vocalizations of proto-humans into two types: one less emotional and more concretely-semantic, evolving into language, and the other preserving emotional connections along with semantic ambiguity, evolving into music. The proposed hypothesis departs from other theories in considering specific mechanisms of the mind-brain, which required the evolution of music parallel with the evolution of cultures and languages. Arguments are reviewed that the evolution of language toward becoming the semantically powerful tool of today required emancipation from emotional encumbrances. The opposite, no less powerful mechanisms required a compensatory evolution of music toward more differentiated and refined emotionality. The need for refined music in the process of cultural evolution is grounded in fundamental mechanisms of the mind. This is why today's human mind and cultures cannot exist without today's music. The reviewed hypothesis gives a basis for future analysis of why different evolutionary paths of languages were paralleled by different evolutionary paths of music. Approaches toward experimental verification of this hypothesis in psychological and neuroimaging research are reviewed.

Using some results about the Lie evolution of differential operators to obtain the Fokker-Planck equation for non-Hamiltonian dynamical systems of interest

NASA Astrophysics Data System (ADS)

Bianucci, Marco

2018-05-01

Finding the generalized Fokker-Planck Equation (FPE) for the reduced probability density function of a subpart of a given complex system is a classical issue of statistical mechanics. Zwanzig projection perturbation approach to this issue leads to the trouble of resumming a series of commutators of differential operators that we show to correspond to solving the Lie evolution of first order differential operators along the unperturbed Liouvillian of the dynamical system of interest. In this paper, we develop in a systematic way the procedure to formally solve this problem. In particular, here we show which the basic assumptions are, concerning the dynamical system of interest, necessary for the Lie evolution to be a group on the space of first order differential operators, and we obtain the coefficients of the so-evolved operators. It is thus demonstrated that if the Liouvillian of the system of interest is not a first order differential operator, in general, the FPE structure breaks down and the master equation contains all the power of the partial derivatives, up to infinity. Therefore, this work shed some light on the trouble of the ubiquitous emergence of both thermodynamics from microscopic systems and regular regression laws at macroscopic scales. However these results are very general and can be applied also in other contexts that are non-Hamiltonian as, for example, geophysical fluid dynamics, where important events, like El Niño, can be considered as large time scale phenomena emerging from the observation of few ocean degrees of freedom of a more complex system, including the interaction with the atmosphere.

Quantum theory of open systems based on stochastic differential equations of generalized Langevin (non-Wiener) type

NASA Astrophysics Data System (ADS)

Basharov, A. M.

2012-09-01

It is shown that the effective Hamiltonian representation, as it is formulated in author's papers, serves as a basis for distinguishing, in a broadband environment of an open quantum system, independent noise sources that determine, in terms of the stationary quantum Wiener and Poisson processes in the Markov approximation, the effective Hamiltonian and the equation for the evolution operator of the open system and its environment. General stochastic differential equations of generalized Langevin (non-Wiener) type for the evolution operator and the kinetic equation for the density matrix of an open system are obtained, which allow one to analyze the dynamics of a wide class of localized open systems in the Markov approximation. The main distinctive features of the dynamics of open quantum systems described in this way are the stabilization of excited states with respect to collective processes and an additional frequency shift of the spectrum of the open system. As an illustration of the general approach developed, the photon dynamics in a single-mode cavity without losses on the mirrors is considered, which contains identical intracavity atoms coupled to the external vacuum electromagnetic field. For some atomic densities, the photons of the cavity mode are "locked" inside the cavity, thus exhibiting a new phenomenon of radiation trapping and non-Wiener dynamics.

Hypermutable DNA chronicles the evolution of human colon cancer

PubMed Central

Naxerova, Kamila; Brachtel, Elena; Salk, Jesse J.; Seese, Aaron M.; Power, Karen; Abbasi, Bardia; Snuderl, Matija; Chiang, Sarah; Kasif, Simon; Jain, Rakesh K.

2014-01-01

Intratumor genetic heterogeneity reflects the evolutionary history of a cancer and is thought to influence treatment outcomes. Here we report that a simple PCR-based assay interrogating somatic variation in hypermutable polyguanine (poly-G) repeats can provide a rapid and reliable assessment of mitotic history and clonal architecture in human cancer. We use poly-G repeat genotyping to study the evolution of colon carcinoma. In a cohort of 22 patients, we detect poly-G variants in 91% of tumors. Patient age is positively correlated with somatic mutation frequency, suggesting that some poly-G variants accumulate before the onset of carcinogenesis during normal division in colonic stem cells. Poorly differentiated tumors have fewer mutations than well-differentiated tumors, possibly indicating a shorter mitotic history of the founder cell in these cancers. We generate poly-G mutation profiles of spatially separated samples from primary carcinomas and matched metastases to build well-supported phylogenetic trees that illuminate individual patients’ path of metastatic progression. Our results show varying degrees of intratumor heterogeneity among patients. Finally, we show that poly-G mutations can be found in other cancers than colon carcinoma. Our approach can generate reliable maps of intratumor heterogeneity in large numbers of patients with minimal time and cost expenditure. PMID:24753616

Smart pitch control strategy for wind generation system using doubly fed induction generator

NASA Astrophysics Data System (ADS)

Raza, Syed Ahmed

A smart pitch control strategy for a variable speed doubly fed wind generation system is presented in this thesis. A complete dynamic model of DFIG system is developed. The model consists of the generator, wind turbine, aerodynamic and the converter system. The strategy proposed includes the use of adaptive neural network to generate optimized controller gains for pitch control. This involves the generation of controller parameters of pitch controller making use of differential evolution intelligent technique. Training of the back propagation neural network has been carried out for the development of an adaptive neural network. This tunes the weights of the network according to the system states in a variable wind speed environment. Four cases have been taken to test the pitch controller which includes step and sinusoidal changes in wind speeds. The step change is composed of both step up and step down changes in wind speeds. The last case makes use of scaled wind data collected from the wind turbine installed at King Fahd University beach front. Simulation studies show that the differential evolution based adaptive neural network is capable of generating the appropriate control to deliver the maximum possible aerodynamic power available from wind to the generator in an efficient manner by minimizing the transients.

Modelling the evolution and diversity of cumulative culture

PubMed Central

Enquist, Magnus; Ghirlanda, Stefano; Eriksson, Kimmo

2011-01-01

Previous work on mathematical models of cultural evolution has mainly focused on the diffusion of simple cultural elements. However, a characteristic feature of human cultural evolution is the seemingly limitless appearance of new and increasingly complex cultural elements. Here, we develop a general modelling framework to study such cumulative processes, in which we assume that the appearance and disappearance of cultural elements are stochastic events that depend on the current state of culture. Five scenarios are explored: evolution of independent cultural elements, stepwise modification of elements, differentiation or combination of elements and systems of cultural elements. As one application of our framework, we study the evolution of cultural diversity (in time as well as between groups). PMID:21199845

MicroRNA (miR)-203 and miR-205 expression patterns identify subgroups of prognosis in cutaneous squamous cell carcinoma.

PubMed

Cañueto, J; Cardeñoso-Álvarez, E; García-Hernández, J L; Galindo-Villardón, P; Vicente-Galindo, P; Vicente-Villardón, J L; Alonso-López, D; De Las Rivas, J; Valero, J; Moyano-Sanz, E; Fernández-López, E; Mao, J H; Castellanos-Martín, A; Román-Curto, C; Pérez-Losada, J

2017-07-01

Cutaneous squamous cell carcinoma (CSCC) is the second most widespread cancer in humans and its incidence is rising. These tumours can evolve as diseases of poor prognosis, and therefore it is important to identify new markers to better predict its clinical evolution. We aimed to identify the expression pattern of microRNAs (miRNAs or miRs) at different stages of skin cancer progression in a panel of murine skin cancer cell lines. Owing to the increasing importance of miRNAs in the pathogenesis of cancer, we considered the possibility that miRNAs could help to define the prognosis of CSCC and aimed to evaluate the potential use of miR-203 and miR-205 as biomarkers of prognosis in human tumours. Seventy-nine human primary CSCCs were collected at the University Hospital of Salamanca in Spain. We identified differential miRNA expression patterns at different stages of CSCC progression in a well-established panel of murine skin cancer cell lines, and then selected miR-205 and miR-203 to evaluate their association with the clinical prognosis and evolution of human CSCC. miR-205 was expressed in tumours with pathological features recognized as indicators of poor prognosis such as desmoplasia, perineural invasion and infiltrative growth pattern. miR-205 was mainly expressed in undifferentiated areas and in the invasion front, and was associated with both local recurrence and the development of general clinical events of poor evolution. miR-205 expression was an independent variable selected to predict events of poor clinical evolution using the multinomial logistic regression model described in this study. In contrast, miR-203 was mainly expressed in tumours exhibiting the characteristics associated with a good prognosis, was mainly present in well-differentiated zones, and rarely expressed in the invasion front. Therefore, the expression and associations of miR-205 and miR-203 were mostly mutually exclusive. Finally, using a logistic biplot we identified three clusters of patients with differential prognosis based on miR-203 and miR-205 expression, and pathological tumour features. miR-205 and miR-203 tended to exhibit mutually exclusive expression patterns in human CSCC. This work highlights the utility of miR-205 and miR-203 as prognostic markers in CSCC. © 2016 British Association of Dermatologists.

Ecological extension of the theory of evolution by natural selection from a perspective of Western and Eastern holistic philosophy.

PubMed

Nakajima, Toshiyuki

2017-12-01

Evolution by natural selection requires the following conditions: (1) a particular selective environment; (2) variation of traits in the population; (3) differential survival/reproduction among the types of organisms; and (4) heritable traits. However, the traditional (standard) model does not clearly explain how and why these conditions are generated or determined. What generates a selective environment? What generates new types? How does a certain type replace, or coexist with, others? In this paper, based on the holistic philosophy of Western and Eastern traditions, I focus on the ecosystem as a higher-level system and generator of conditions that induce the evolution of component populations; I also aim to identify the ecosystem processes that generate those conditions. In particular, I employ what I call the scientific principle of dependent-arising (SDA), which is tailored for scientific use and is based on Buddhism principle called "pratītya-samutpāda" in Sanskrit. The SDA principle asserts that there exists a higher-level system, or entity, which includes a focal process of a system as a part within it; this determines or generates the conditions required for the focal process to work in a particular way. I conclude that the ecosystem generates (1) selective environments for component species through ecosystem dynamics; (2) new genetic types through lateral gene transfer, hybridization, and symbiogenesis among the component species of the ecosystem; (3) mechanistic processes of replacement of an old type with a new one. The results of this study indicate that the ecological extension of the theoretical model of adaptive evolution is required for better understanding of adaptive evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Caste load and the evolution of reproductive skew.

PubMed

Holman, Luke

2014-01-01

Reproductive skew theory seeks to explain how reproduction is divided among group members in animal societies. Existing theory is framed almost entirely in terms of selection, though nonadaptive processes must also play some role in the evolution of reproductive skew. Here I propose that a genetic correlation between helper fecundity and breeder fecundity may frequently constrain the evolution of reproductive skew. This constraint is part of a wider phenomenon that I term "caste load," which is defined as the decline in mean fitness caused by caste-specific selection pressures, that is, differential selection on breeding and nonbreeding individuals. I elaborate the caste load hypothesis using quantitative and population genetic arguments and individual-based simulations. Although selection can sometimes erode genetic correlations and resolve caste load, this may be constrained when mutations have similar pleiotropic effects on breeder and helper traits. I document evidence for caste load, identify putative genomic adaptations to it, and suggest future research directions. The models highlight the value of considering adaptation within the boundaries imposed by genetic architecture and incidentally reaffirm that monogamy promotes the evolutionary transition to eusociality.

Fighting Viral Infections and Virus-Driven Tumors with Cytotoxic CD4+ T Cells

PubMed Central

Muraro, Elena; Merlo, Anna; Martorelli, Debora; Cangemi, Michela; Dalla Santa, Silvia; Dolcetti, Riccardo; Rosato, Antonio

2017-01-01

CD4+ T cells have been and are still largely regarded as the orchestrators of immune responses, being able to differentiate into distinct T helper cell populations based on differentiation signals, transcription factor expression, cytokine secretion, and specific functions. Nonetheless, a growing body of evidence indicates that CD4+ T cells can also exert a direct effector activity, which depends on intrinsic cytotoxic properties acquired and carried out along with the evolution of several pathogenic infections. The relevant role of CD4+ T cell lytic features in the control of such infectious conditions also leads to their exploitation as a new immunotherapeutic approach. This review aims at summarizing currently available data about functional and therapeutic relevance of cytotoxic CD4+ T cells in the context of viral infections and virus-driven tumors. PMID:28289418

ProbFAST: Probabilistic functional analysis system tool.

PubMed

Silva, Israel T; Vêncio, Ricardo Z N; Oliveira, Thiago Y K; Molfetta, Greice A; Silva, Wilson A

2010-03-30

The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

ProbFAST: Probabilistic Functional Analysis System Tool

PubMed Central

2010-01-01

Background The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast. PMID:20353576

The Hartman-Grobman theorem for semilinear hyperbolic evolution equations

NASA Astrophysics Data System (ADS)

Hein, Marie-Luise; Prüss, Jan

2016-10-01

The famous Hartman-Grobman theorem for ordinary differential equations is extended to abstract semilinear hyperbolic evolution equations in Banach spaces by means of simple direct proof. It is also shown that the linearising map is Hölder continuous. Several applications to abstract and specific damped wave equations are given, to demonstrate the strength of our results.

Evolution of marginal populations of an invasive vine increases the likelihood of future spread

Treesearch

Francis F. Kilkenny; Laura F. Galloway

2015-01-01

The prediction of invasion patterns may require an understanding of intraspecific differentiation in invasive species and its interaction with climate change. We compare Japanese honeysuckle (Lonicera japonica) plants from the core (100-150 yr old) and northern margin (< 65 yr old) of their North American invaded range to determine whether evolution...

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions Following Polyploidy in the Ancestor of Soybean

USDA-ARS?s Scientific Manuscript database

The genomes of most flowering plants have undergone polyploidization at some point in their evolution. How such polyploidization events have impacted the subsequent evolution of genome structure is poorly understood. We sequenced two homoeologous regions in soybean (Glycine max), which underwent a...

Mesoproterozoic Archaeoellipsoides: akinetes of heterocystous cyanobacteria

NASA Technical Reports Server (NTRS)

Golubic, S.; Sergeev, V. N.; Knoll, A. H.

1995-01-01

The genus Archaeoellipsoides Horodyski & Donaldson comprises large (up to 135 micrometers long) ellipsoidal and rod-shaped microfossils commonly found in silicified peritidal carbonates of Mesoproterozoic age. Based on morphometric and sedimentary comparisons with the akinetes of modern bloom-forming Anabaena species, Archaeoellipsoides is interpreted as the fossilized remains of akinetes produced by planktic heterocystous cyanobacteria. These fossils set a minimum date for the evolution of derived cyanobacteria capable of marked cell differentiation, and they corroborate geochemical evidence indicating that atmospheric oxygen levels were well above 1% of present day levels 1,500 million years ago.

Hyperboloidal evolution of test fields in three spatial dimensions

NASA Astrophysics Data System (ADS)

Zenginoǧlu, Anıl; Kidder, Lawrence E.

2010-06-01

We present the numerical implementation of a clean solution to the outer boundary and radiation extraction problems within the 3+1 formalism for hyperbolic partial differential equations on a given background. Our approach is based on compactification at null infinity in hyperboloidal scri fixing coordinates. We report numerical tests for the particular example of a scalar wave equation on Minkowski and Schwarzschild backgrounds. We address issues related to the implementation of the hyperboloidal approach for the Einstein equations, such as nonlinear source functions, matching, and evaluation of formally singular terms at null infinity.

DNA sequence-based comparative studies between non-extremophile and extremophile organisms with implications in exobiology

NASA Astrophysics Data System (ADS)

Holden, Todd; Marchese, P.; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Sullivan, R.; Schneider, P.; Flamholz, A.; Lieberman, D.; Cheung, T.

2008-08-01

We have characterized function related DNA sequences of various organisms using informatics techniques, including fractal dimension calculation, nucleotide and multi-nucleotide statistics, and sequence fluctuation analysis. Our analysis shows trends which differentiate extremophile from non-extremophile organisms, which could be reproduced in extraterrestrial life. Among the systems studied are radiation repair genes, genes involved in thermal shocks, and genes involved in drug resistance. We also evaluate sequence level changes that have occurred during short term evolution (several thousand generations) under extreme conditions.

Testing the recovery of stellar rotation signals from Kepler light curves using a blind hare-and-hounds exercise

NASA Astrophysics Data System (ADS)

Aigrain, S.; Llama, J.; Ceillier, T.; Chagas, M. L. das; Davenport, J. R. A.; García, R. A.; Hay, K. L.; Lanza, A. F.; McQuillan, A.; Mazeh, T.; de Medeiros, J. R.; Nielsen, M. B.; Reinhold, T.

2015-07-01

We present the results of a blind exercise to test the recoverability of stellar rotation and differential rotation in Kepler light curves. The simulated light curves lasted 1000 d and included activity cycles, Sun-like butterfly patterns, differential rotation and spot evolution. The range of rotation periods, activity levels and spot lifetime were chosen to be representative of the Kepler data of solar-like stars. Of the 1000 simulated light curves, 770 were injected into actual quiescent Kepler light curves to simulate Kepler noise. The test also included five 1000-d segments of the Sun's total irradiance variations at different points in the Sun's activity cycle. Five teams took part in the blind exercise, plus two teams who participated after the content of the light curves had been released. The methods used included Lomb-Scargle periodograms and variants thereof, autocorrelation function and wavelet-based analyses, plus spot modelling to search for differential rotation. The results show that the `overall' period is well recovered for stars exhibiting low and moderate activity levels. Most teams reported values within 10 per cent of the true value in 70 per cent of the cases. There was, however, little correlation between the reported and simulated values of the differential rotation shear, suggesting that differential rotation studies based on full-disc light curves alone need to be treated with caution, at least for solar-type stars. The simulated light curves and associated parameters are available online for the community to test their own methods.

Thermal evolution of magma reservoirs in the shallow crust and incidence on magma differentiation: the St-Jean-du-Doigt layered intrusion (Brittany, France)

NASA Astrophysics Data System (ADS)

Barboni, M.; Bussy, F.; Ovtcharova, M.; Schoene, B.

2009-12-01

Understanding the emplacement and growth of intrusive bodies in terms of mechanism, duration, thermal evolution and rates are fundamental aspects of crustal evolution. Recent studies show that many plutons grow in several Ma by in situ accretion of discrete magma pulses, which constitute small-scale magmatic reservoirs. The residence time of magmas, and hence their capacities to interact and differentiate, are controlled by the local thermal environment. The latter is highly dependant on 1) the emplacement depth, 2) the magmas and country rock composition, 3) the country rock thermal conductivity, 4) the rate of magma injection and 5) the geometry of the intrusion. In shallow level plutons, where magmas solidify quickly, evidence for magma mixing and/or differentiation processes is considered by many authors to be inherited from deeper levels. We show however that in-situ differentiation and magma interactions occurred within basaltic and felsic sills at shallow depth (0.3 GPa) in the St-Jean-du-Doigt bimodal intrusion, France. Field evidence coupled to high precision zircon U-Pb dating document progressive thermal maturation within the incrementally built laccolith. Early m-thick mafic sills are homogeneous and fine-grained with planar contacts with neighbouring felsic sills; within a minimal 0.5 Ma time span, the system gets warmer, adjacent sills interact and mingle, and mafic sills are differentiating in the top 40 cm of the layer. Rheological and thermal modelling show that observed in-situ differentiation-accumulation processes may be achieved in less than 10 years at shallow depth, provided that (1) the differentiating sills are injected beneath consolidated, yet still warm basalt sills, which act as low conductive insulating screens, (2) the early mafic sills accreted under the roof of the laccolith as a 100m thick top layer within 0.5 My, and (3) subsequent and sustained magmatic activity occurred on a short time scale (years) at an injection rate of ca. 0.5m/y. Extraction of differentiated residual liquids might eventually take place and mix with newly injected magma as documented in active syn-emplacement shear-zones. These low-pressure differentiated liquids can potentially contribute to subaerial volcanic activity along the major shear-zones.

Performance Review of Harmony Search, Differential Evolution and Particle Swarm Optimization

NASA Astrophysics Data System (ADS)

Mohan Pandey, Hari

2017-08-01

Metaheuristic algorithms are effective in the design of an intelligent system. These algorithms are widely applied to solve complex optimization problems, including image processing, big data analytics, language processing, pattern recognition and others. This paper presents a performance comparison of three meta-heuristic algorithms, namely Harmony Search, Differential Evolution, and Particle Swarm Optimization. These algorithms are originated altogether from different fields of meta-heuristics yet share a common objective. The standard benchmark functions are used for the simulation. Statistical tests are conducted to derive a conclusion on the performance. The key motivation to conduct this research is to categorize the computational capabilities, which might be useful to the researchers.

An Evolution-Based Screen for Genetic Differentiation between Anopheles Sister Taxa Enriches for Detection of Functional Immune Factors

PubMed Central

Takashima, Eizo; Williams, Marni; Eiglmeier, Karin; Pain, Adrien; Guelbeogo, Wamdaogo M.; Gneme, Awa; Brito-Fravallo, Emma; Holm, Inge; Lavazec, Catherine; Sagnon, N’Fale; Baxter, Richard H.; Riehle, Michelle M.; Vernick, Kenneth D.

2015-01-01

Nucleotide variation patterns across species are shaped by the processes of natural selection, including exposure to environmental pathogens. We examined patterns of genetic variation in two sister species, Anopheles gambiae and Anopheles coluzzii, both efficient natural vectors of human malaria in West Africa. We used the differentiation signature displayed by a known coordinate selective sweep of immune genes APL1 and TEP1 in A. coluzzii to design a population genetic screen trained on the sweep, classified a panel of 26 potential immune genes for concordance with the signature, and functionally tested their immune phenotypes. The screen results were strongly predictive for genes with protective immune phenotypes: genes meeting the screen criteria were significantly more likely to display a functional phenotype against malaria infection than genes not meeting the criteria (p = 0.0005). Thus, an evolution-based screen can efficiently prioritize candidate genes for labor-intensive downstream functional testing, and safely allow the elimination of genes not meeting the screen criteria. The suite of immune genes with characteristics similar to the APL1-TEP1 selective sweep appears to be more widespread in the A. coluzzii genome than previously recognized. The immune gene differentiation may be a consequence of adaptation of A. coluzzii to new pathogens encountered in its niche expansion during the separation from A. gambiae, although the role, if any of natural selection by Plasmodium is unknown. Application of the screen allowed identification of new functional immune factors, and assignment of new functions to known factors. We describe biochemical binding interactions between immune proteins that underlie functional activity for malaria infection, which highlights the interplay between pathogen specificity and the structure of immune complexes. We also find that most malaria-protective immune factors display phenotypes for either human or rodent malaria, with broad specificity a rarity. PMID:26633695

The landscape of sex-differential transcriptome and its consequent selection in human adults.

PubMed

Gershoni, Moran; Pietrokovski, Shmuel

2017-02-07

The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes. This can impact human evolution by differential selection on mutations with dissimilar effects on the two sexes. We comprehensively mapped human sex-differential genetic architecture across 53 tissues. Analyzing available RNA-sequencing data from 544 adults revealed thousands of genes differentially expressed in the reproductive tracts and tissues common to both sexes. Sex-differential genes are related to various biological systems, and suggest new insights into the pathophysiology of diverse human diseases. We also identified a significant association between sex-specific gene transcription and reduced selection efficiency and accumulation of deleterious mutations, which might affect the prevalence of different traits and diseases. Interestingly, many of the sex-specific genes that also undergo reduced selection efficiency are essential for successful reproduction in men or women. This seeming paradox might partially explain the high incidence of human infertility. This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids.

PubMed

Meier, Joana Isabel; Marques, David Alexander; Wagner, Catherine Elise; Excoffier, Laurent; Seehausen, Ole

2018-06-01

The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case is blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through "hybrid parallel speciation". Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new "nyererei-like" and "pundamilia-like" species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two-thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.

Nano-copper-bearing stainless steel promotes fracture healing by accelerating the callus evolution process.

PubMed

Wang, Lei; Li, Guoyuan; Ren, Ling; Kong, Xiangdong; Wang, Yugang; Han, Xiuguo; Jiang, Wenbo; Dai, Kerong; Yang, Ke; Hao, Yongqiang

2017-01-01

Treatment for fractures requires internal fixation devices, which are mainly produced from stainless steel or titanium alloy without biological functions. Therefore, we developed a novel nano-copper-bearing stainless steel with nano-sized copper-precipitation (317L-Cu SS). Based on previous studies, this work explores the effect of 317L-Cu SS on fracture healing; that is, proliferation, osteogenic differentiation, osteogenesis-related gene expression, and lysyl oxidase activity of human bone mesenchymal stem cells were detected in vitro. Sprague-Dawley rats were used to build an animal fracture model, and fracture healing and callus evolution were investigated by radiology (X-ray and micro-CT), histology (H&E, Masson, and safranin O/fast green staining), and histomorphometry. Further, the Cu 2+ content and Runx2 level in the callus were determined, and local mechanical test of the fracture was performed to assess the healing quality. Our results revealed that 317L-Cu SS did not affect the proliferation of human bone mesenchymal stem cells, but promoted osteogenic differentiation and the expression of osteogenesis-related genes. In addition, 317L-Cu SS upregulated the lysyl oxidase activity. The X-ray and micro-CT results showed that the callus evolution efficiency and fracture healing speed were superior for 317L-Cu SS. Histological staining displayed large amounts of fibrous tissues at 3 weeks, and cartilage and new bone at 6 weeks. Further, histomorphometric analysis indicated that the callus possessed higher osteogenic efficiency at 6 weeks, and a high Cu 2+ content and increased Runx2 expression were observed in the callus for 317L-Cu SS. Besides, the mechanical strength of the fracture site was much better than that of the control group. Overall, we conclude that 317L-Cu SS possesses the ability to increase Cu 2+ content and promote osteogenesis in the callus, which could accelerate the callus evolution process and bone formation to provide faster and better fracture healing.

Nano-copper-bearing stainless steel promotes fracture healing by accelerating the callus evolution process

PubMed Central

Kong, Xiangdong; Wang, Yugang; Han, Xiuguo; Jiang, Wenbo; Dai, Kerong; Yang, Ke; Hao, Yongqiang

2017-01-01

Treatment for fractures requires internal fixation devices, which are mainly produced from stainless steel or titanium alloy without biological functions. Therefore, we developed a novel nano-copper-bearing stainless steel with nano-sized copper-precipitation (317L-Cu SS). Based on previous studies, this work explores the effect of 317L-Cu SS on fracture healing; that is, proliferation, osteogenic differentiation, osteogenesis-related gene expression, and lysyl oxidase activity of human bone mesenchymal stem cells were detected in vitro. Sprague–Dawley rats were used to build an animal fracture model, and fracture healing and callus evolution were investigated by radiology (X-ray and micro-CT), histology (H&E, Masson, and safranin O/fast green staining), and histomorphometry. Further, the Cu2+ content and Runx2 level in the callus were determined, and local mechanical test of the fracture was performed to assess the healing quality. Our results revealed that 317L-Cu SS did not affect the proliferation of human bone mesenchymal stem cells, but promoted osteogenic differentiation and the expression of osteogenesis-related genes. In addition, 317L-Cu SS upregulated the lysyl oxidase activity. The X-ray and micro-CT results showed that the callus evolution efficiency and fracture healing speed were superior for 317L-Cu SS. Histological staining displayed large amounts of fibrous tissues at 3 weeks, and cartilage and new bone at 6 weeks. Further, histomorphometric analysis indicated that the callus possessed higher osteogenic efficiency at 6 weeks, and a high Cu2+ content and increased Runx2 expression were observed in the callus for 317L-Cu SS. Besides, the mechanical strength of the fracture site was much better than that of the control group. Overall, we conclude that 317L-Cu SS possesses the ability to increase Cu2+ content and promote osteogenesis in the callus, which could accelerate the callus evolution process and bone formation to provide faster and better fracture healing. PMID:29225463

On the instability of wave-fields with JONSWAP spectra to inhomogeneous disturbances, and the consequent long-time evolution

NASA Astrophysics Data System (ADS)

Ribal, A.; Stiassnie, M.; Babanin, A.; Young, I.

2012-04-01

The instability of two-dimensional wave-fields and its subsequent evolution in time are studied by means of the Alber equation for narrow-banded random surface-waves in deep water subject to inhomogeneous disturbances. A linear partial differential equation (PDE) is obtained after applying an inhomogeneous disturbance to the Alber's equation and based on the solution of this PDE, the instability of the ocean wave surface is studied for a JONSWAP spectrum, which is a realistic ocean spectrum with variable directional spreading and steepness. The steepness of the JONSWAP spectrum depends on γ and α which are the peak-enhancement factor and energy scale of the spectrum respectively and it is found that instability depends on the directional spreading, α and γ. Specifically, if the instability stops due to the directional spreading, increase of the steepness by increasing α or γ can reactivate it. This result is in qualitative agreement with the recent large-scale experiment and new theoretical results. In the instability area of α-γ plane, a long-time evolution has been simulated by integrating Alber's equation numerically and recurrent evolution is obtained which is the stochastic counterpart of the Fermi-Pasta-Ulam recurrence obtained for the cubic Schrödinger equation.

Convergent evolution as natural experiment: the tape of life reconsidered

PubMed Central

Powell, Russell; Mariscal, Carlos

2015-01-01

Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life. PMID:26640647

Evolution of vertebrate mechanosensory hair cells and inner ears: toward identifying stimuli that select mutation driven altered morphologies

PubMed Central

Fritzsch, Bernd; Straka, Hans

2014-01-01

Among the major distance senses of vertebrates, the ear is unique in its complex morphological changes during evolution. Conceivably, these changes enable the ear to adapt toward sensing various physically well-characterized stimuli. This review develops a scenario that integrates sensory cell with organ evolution. We propose that molecular and cellular evolution of the vertebrate hair cells occurred prior to the formation of the vertebrate ear. We previously proposed that the genes driving hair cell differentiation, were aggregated in the otic region through developmental re-patterning that generated a unique vertebrate embryonic structure, the otic placode. In agreement with the presence of graviceptive receptors in many vertebrate outgroups, it is likely that the vertebrate ear originally functioned as a simple gravity-sensing organ. Based on the rare occurrence of angular acceleration receptors in vertebrate outgroups, we further propose that the canal system evolved with a more sophisticated ear morphogenesis. This evolving morphogenesis obviously turned the initial otocyst into a complex set of canals and recesses, harboring multiple sensory epithelia each adapted to the acquisition of a specific aspect of a given physical stimulus. As support for this evolutionary progression, we provide several details of the molecular basis of ear development. PMID:24281353

Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors.

PubMed

Herrmann, Alexander; Haake, Andrea; Ammerpohl, Ole; Martin-Guerrero, Idoia; Szafranski, Karol; Stemshorn, Kathryn; Nothnagel, Michael; Kotsopoulos, Steve K; Richter, Julia; Warner, Jason; Olson, Jeff; Link, Darren R; Schreiber, Stefan; Krawczak, Michael; Platzer, Matthias; Nürnberg, Peter; Siebert, Reiner; Hampe, Jochen

2011-01-01

Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.

State-transition diagrams for biologists.

PubMed

Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

2012-01-01

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines.

State-Transition Diagrams for Biologists

PubMed Central

Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

2012-01-01

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines. PMID:22844438

Trait-based diversification shifts reflect differential extinction among fossil taxa.

PubMed

Wagner, Peter J; Estabrook, George F

2014-11-18

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

Algorithm for Stabilizing a POD-Based Dynamical System

NASA Technical Reports Server (NTRS)

Kalb, Virginia L.

2010-01-01

This algorithm provides a new way to improve the accuracy and asymptotic behavior of a low-dimensional system based on the proper orthogonal decomposition (POD). Given a data set representing the evolution of a system of partial differential equations (PDEs), such as the Navier-Stokes equations for incompressible flow, one may obtain a low-dimensional model in the form of ordinary differential equations (ODEs) that should model the dynamics of the flow. Temporal sampling of the direct numerical simulation of the PDEs produces a spatial time series. The POD extracts the temporal and spatial eigenfunctions of this data set. Truncated to retain only the most energetic modes followed by Galerkin projection of these modes onto the PDEs obtains a dynamical system of ordinary differential equations for the time-dependent behavior of the flow. In practice, the steps leading to this system of ODEs entail numerically computing first-order derivatives of the mean data field and the eigenfunctions, and the computation of many inner products. This is far from a perfect process, and often results in the lack of long-term stability of the system and incorrect asymptotic behavior of the model. This algorithm describes a new stabilization method that utilizes the temporal eigenfunctions to derive correction terms for the coefficients of the dynamical system to significantly reduce these errors.

Spreading of blood drops over dry porous substrate: complete wetting case.

PubMed

Chao, Tzu Chieh; Arjmandi-Tash, Omid; Das, Diganta B; Starov, Victor M

2015-05-15

The process of dried blood spot sampling involves simultaneous spreading and penetration of blood into a porous filter paper with subsequent evaporation and drying. Spreading of small drops of blood, which is a non-Newtonian liquid, over a dry porous layer is investigated from both theoretical and experimental points of view. A system of two differential equations is derived, which describes the time evolution of radii of both the drop base and the wetted region inside the porous medium. The system of equations does not include any fitting parameters. The predicted time evolutions of both radii are compared with experimental data published earlier. For a given power law dependency of viscosity of blood with different hematocrit level, radii of both drop base and wetted region, and contact angle fell on three universal curves if appropriate scales are used with a plot of the dimensionless radii of the drop base and the wetted region inside the porous layer and dynamic contact angle on dimensionless time. The predicted theoretical relationships are three universal curves accounting satisfactorily for the experimental data. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Unconstrained cranial evolution in Neandertals and modern humans compared to common chimpanzees

PubMed Central

Weaver, Timothy D.; Stringer, Chris B.

2015-01-01

A variety of lines of evidence support the idea that neutral evolutionary processes (genetic drift, mutation) have been important in generating cranial differences between Neandertals and modern humans. But how do Neandertals and modern humans compare with other species? And how do these comparisons illuminate the evolutionary processes underlying cranial diversification? To address these questions, we used 27 standard cranial measurements collected on 2524 recent modern humans, 20 Neandertals and 237 common chimpanzees to estimate split times between Neandertals and modern humans, and between Pan troglodytes verus and two other subspecies of common chimpanzee. Consistent with a neutral divergence, the Neandertal versus modern human split-time estimates based on cranial measurements are similar to those based on DNA sequences. By contrast, the common chimpanzee cranial estimates are much lower than DNA-sequence estimates. Apparently, cranial evolution has been unconstrained in Neandertals and modern humans compared with common chimpanzees. Based on these and additional analyses, it appears that cranial differentiation in common chimpanzees has been restricted by stabilizing natural selection. Alternatively, this restriction could be due to genetic and/or developmental constraints on the amount of within-group variance (relative to effective population size) available for genetic drift to act on. PMID:26468243

Growth and characterization of organic layers deposited on porous-patterned Si surface

NASA Astrophysics Data System (ADS)

Gorbach, Tamara Ya.; Smertenko, Petro S.; Olkhovik, G. P.; Wisz, Grzegorz

2017-01-01

The organic layers with the thickness from a few nanometers up to few micrometers have been deposited from the chemical solution at room temperature on porous patterned Si surfaces using two medical solutions: thiamine diphosphide (pH=1÷2) and metamizole sodium (pH=6÷7). Based on evolution of morphology, structural and compositional features obtained by scanning electron microscopy, X-ray analysis, reflectance high energy electron diffraction the grown mechanisms in thin organic layers are discussed in the terms of terrace-step-kink model whereas self-organized assemblies evaluated more thick layers. Transport mechanism features and possible photovoltaic properties are discussed on the base of differential current-voltage characteristics.

Interplanetary navigation

NASA Technical Reports Server (NTRS)

Stuart, J. R.

1984-01-01

The evolution of NASA's planetary navigation techniques is traced, and radiometric and optical data types are described. Doppler navigation; the Deep Space Network; differenced two-way range techniques; differential very long base interferometry; and optical navigation are treated. The Doppler system enables a spacecraft in cruise at high absolute declination to be located within a total angular uncertainty of 1/4 microrad. The two-station range measurement provides a 1 microrad backup at low declinations. Optical data locate the spacecraft relative to the target to an angular accuracy of 5 microrad. Earth-based radio navigation and its less accurate but target-relative counterpart, optical navigation, thus form complementary measurement sources, which provide a powerful sensory system to produce high-precision orbit estimates.

Origin and thermal evolution of Mars

NASA Technical Reports Server (NTRS)

Schubert, G.; Solomon, Sean C.; Turcotte, D. L.; Drake, M. J.; Sleep, N. H.

1993-01-01

The thermal evolution of Mars is governed by subsolidus mantle convection beneath a thick lithosphere. Models of the interior evolution are developed by parameterizing mantle convective heat transport in terms of mantle viscosity, the superadiabatic temperature rise across the mantle and mantle heat production. Geological, geophysical, and geochemical observations of the composition and structure of the interior and of the timing of major events in Martian evolution, such as global differentiation, atmospheric outgassing and the formation of the hemispherical dichotomy and Tharsis, are used to constrain the model computations. Isotope systematics of SNC meteorites suggest core formation essentially contemporaneously with the completion of accretion. Other aspects of this investigation are discussed.

Culture rather than genes provides greater scope for the evolution of large-scale human prosociality

PubMed Central

Bell, Adrian V.; Richerson, Peter J.; McElreath, Richard

2009-01-01

Whether competition among large groups played an important role in human social evolution is dependent on how variation, whether cultural or genetic, is maintained between groups. Comparisons between genetic and cultural differentiation between neighboring groups show how natural selection on large groups is more plausible on cultural rather than genetic variation. PMID:19822753

No evidence for faster male hybrid sterility in population crosses of an intertidal copepod (Tigriopus californicus).

PubMed

Willett, Christopher S

2008-06-01

Two different forces are thought to contribute to the rapid accumulation of hybrid male sterility that has been observed in many inter-specific crosses, namely the faster male and the dominance theories. For male heterogametic taxa, both faster male and dominance would work in the same direction to cause the rapid evolution of male sterility; however, for taxa lacking differentiated sex chromosomes only the faster male theory would explain the rapid evolution of male hybrid sterility. It is currently unknown what causes the faster evolution of male sterility, but increased sexual selection on males and the sensitivity of genes involved in male reproduction are two hypotheses that could explain the observation. Here, patterns of hybrid sterility in crosses of genetically divergent copepod populations are examined to test potential mechanisms of faster male evolution. The study species, Tigriopus californicus, lacks differentiated, hemizygous sex chromosomes and appears to have low levels of divergence caused by sexual selection acting upon males. Hybrid sterility does not accumulate more rapidly in males than females in these crosses suggesting that in this taxon male reproductive genes are not inherently more prone to disruption in hybrids.

Cognitive algorithms: dynamic logic, working of the mind, evolution of consciousness and cultures

NASA Astrophysics Data System (ADS)

Perlovsky, Leonid I.

2007-04-01

The paper discusses evolution of consciousness driven by the knowledge instinct, a fundamental mechanism of the mind which determines its higher cognitive functions. Dynamic logic mathematically describes the knowledge instinct. It overcomes past mathematical difficulties encountered in modeling intelligence and relates it to mechanisms of concepts, emotions, instincts, consciousness and unconscious. The two main aspects of the knowledge instinct are differentiation and synthesis. Differentiation is driven by dynamic logic and proceeds from vague and unconscious states to more crisp and conscious states, from less knowledge to more knowledge at each hierarchical level of the mind. Synthesis is driven by dynamic logic operating in a hierarchical organization of the mind; it strives to achieve unity and meaning of knowledge: every concept finds its deeper and more general meaning at a higher level. These mechanisms are in complex relationship of symbiosis and opposition, which leads to complex dynamics of evolution of consciousness and cultures. Modeling this dynamics in a population leads to predictions for the evolution of consciousness, and cultures. Cultural predictive models can be compared to experimental data and used for improvement of human conditions. We discuss existing evidence and future research directions.

SaLEM (v1.0) - the Soil and Landscape Evolution Model (SaLEM) for simulation of regolith depth in periglacial environments

NASA Astrophysics Data System (ADS)

Bock, Michael; Conrad, Olaf; Günther, Andreas; Gehrt, Ernst; Baritz, Rainer; Böhner, Jürgen

2018-04-01

We propose the implementation of the Soil and Landscape Evolution Model (SaLEM) for the spatiotemporal investigation of soil parent material evolution following a lithologically differentiated approach. Relevant parts of the established Geomorphic/Orogenic Landscape Evolution Model (GOLEM) have been adapted for an operational Geographical Information System (GIS) tool within the open-source software framework System for Automated Geoscientific Analyses (SAGA), thus taking advantage of SAGA's capabilities for geomorphometric analyses. The model is driven by palaeoclimatic data (temperature, precipitation) representative of periglacial areas in northern Germany over the last 50 000 years. The initial conditions have been determined for a test site by a digital terrain model and a geological model. Weathering, erosion and transport functions are calibrated using extrinsic (climatic) and intrinsic (lithologic) parameter data. First results indicate that our differentiated SaLEM approach shows some evidence for the spatiotemporal prediction of important soil parental material properties (particularly its depth). Future research will focus on the validation of the results against field data, and the influence of discrete events (mass movements, floods) on soil parent material formation has to be evaluated.

The nonlinear evolution of modes on unstable stratified shear layers

NASA Technical Reports Server (NTRS)

Blackaby, Nicholas; Dando, Andrew; Hall, Philip

1993-01-01

The nonlinear development of disturbances in stratified shear flows (having a local Richardson number of value less than one quarter) is considered. Such modes are initially fast growing but, like related studies, we assume that the viscous, non-parallel spreading of the shear layer results in them evolving in a linear fashion until they reach a position where their amplitudes are large enough and their growth rates have diminished sufficiently so that amplitude equations can be derived using weakly nonlinear and non-equilibrium critical-layer theories. Four different basic integro-differential amplitude equations are possible, including one due to a novel mechanism; the relevant choice of amplitude equation, at a particular instance, being dependent on the relative sizes of the disturbance amplitude, the growth rate of the disturbance, its wavenumber, and the viscosity of the fluid. This richness of choice of possible nonlinearities arises mathematically from the indicial Frobenius roots of the governing linear inviscid equation (the Taylor-Goldstein equation) not, in general, differing by an integer. The initial nonlinear evolution of a mode will be governed by an integro-differential amplitude equations with a cubic nonlinearity but the resulting significant increase in the size of the disturbance's amplitude leads on to the next stage of the evolution process where the evolution of the mode is governed by an integro-differential amplitude equations with a quintic nonlinearity. Continued growth of the disturbance amplitude is expected during this stage, resulting in the effects of nonlinearity spreading to outside the critical level, by which time the flow has become fully nonlinear.

Molecular evolution and the latitudinal biodiversity gradient.

PubMed

Dowle, E J; Morgan-Richards, M; Trewick, S A

2013-06-01

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

Protein interactions and ligand binding: from protein subfamilies to functional specificity.

PubMed

Rausell, Antonio; Juan, David; Pazos, Florencio; Valencia, Alfonso

2010-02-02

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.

First-passage times for pattern formation in nonlocal partial differential equations

NASA Astrophysics Data System (ADS)

Cáceres, Manuel O.; Fuentes, Miguel A.

2015-10-01

We describe the lifetimes associated with the stochastic evolution from an unstable uniform state to a patterned one when the time evolution of the field is controlled by a nonlocal Fisher equation. A small noise is added to the evolution equation to define the lifetimes and to calculate the mean first-passage time of the stochastic field through a given threshold value, before the patterned steady state is reached. In order to obtain analytical results we introduce a stochastic multiscale perturbation expansion. This multiscale expansion can also be used to tackle multiplicative stochastic partial differential equations. A critical slowing down is predicted for the marginal case when the Fourier phase of the unstable initial condition is null. We carry out Monte Carlo simulations to show the agreement with our theoretical predictions. Analytic results for the bifurcation point and asymptotic analysis of traveling wave-front solutions are included to get insight into the noise-induced transition phenomena mediated by invading fronts.

First-passage times for pattern formation in nonlocal partial differential equations.

PubMed

Cáceres, Manuel O; Fuentes, Miguel A

2015-10-01

We describe the lifetimes associated with the stochastic evolution from an unstable uniform state to a patterned one when the time evolution of the field is controlled by a nonlocal Fisher equation. A small noise is added to the evolution equation to define the lifetimes and to calculate the mean first-passage time of the stochastic field through a given threshold value, before the patterned steady state is reached. In order to obtain analytical results we introduce a stochastic multiscale perturbation expansion. This multiscale expansion can also be used to tackle multiplicative stochastic partial differential equations. A critical slowing down is predicted for the marginal case when the Fourier phase of the unstable initial condition is null. We carry out Monte Carlo simulations to show the agreement with our theoretical predictions. Analytic results for the bifurcation point and asymptotic analysis of traveling wave-front solutions are included to get insight into the noise-induced transition phenomena mediated by invading fronts.

Social cohesion among kin, gene flow without dispersal and the evolution of population genetic structure in the killer whale (Orcinus orca).

PubMed

Pilot, M; Dahlheim, M E; Hoelzel, A R

2010-01-01

In social species, breeding system and gregarious behavior are key factors influencing the evolution of large-scale population genetic structure. The killer whale is a highly social apex predator showing genetic differentiation in sympatry between populations of foraging specialists (ecotypes), and low levels of genetic diversity overall. Our comparative assessments of kinship, parentage and dispersal reveal high levels of kinship within local populations and ongoing male-mediated gene flow among them, including among ecotypes that are maximally divergent within the mtDNA phylogeny. Dispersal from natal populations was rare, implying that gene flow occurs without dispersal, as a result of reproduction during temporary interactions. Discordance between nuclear and mitochondrial phylogenies was consistent with earlier studies suggesting a stochastic basis for the magnitude of mtDNA differentiation between matrilines. Taken together our results show how the killer whale breeding system, coupled with social, dispersal and foraging behaviour, contributes to the evolution of population genetic structure.

Damage-Based Time-Dependent Modeling of Paraglacial to Postglacial Progressive Failure of Large Rock Slopes

NASA Astrophysics Data System (ADS)

Riva, Federico; Agliardi, Federico; Amitrano, David; Crosta, Giovanni B.

2018-01-01

Large alpine rock slopes undergo long-term evolution in paraglacial to postglacial environments. Rock mass weakening and increased permeability associated with the progressive failure of deglaciated slopes promote the development of potentially catastrophic rockslides. We captured the entire life cycle of alpine slopes in one damage-based, time-dependent 2-D model of brittle creep, including deglaciation, damage-dependent fluid occurrence, and rock mass property upscaling. We applied the model to the Spriana rock slope (Central Alps), affected by long-term instability after Last Glacial Maximum and representing an active threat. We simulated the evolution of the slope from glaciated conditions to present day and calibrated the model using site investigation data and available temporal constraints. The model tracks the entire progressive failure path of the slope from deglaciation to rockslide development, without a priori assumptions on shear zone geometry and hydraulic conditions. Complete rockslide differentiation occurs through the transition from dilatant damage to a compacting basal shear zone, accounting for observed hydraulic barrier effects and perched aquifer formation. Our model investigates the mechanical role of deglaciation and damage-controlled fluid distribution in the development of alpine rockslides. The absolute simulated timing of rock slope instability development supports a very long "paraglacial" period of subcritical rock mass damage. After initial damage localization during the Lateglacial, rockslide nucleation initiates soon after the onset of Holocene, whereas full mechanical and hydraulic rockslide differentiation occurs during Mid-Holocene, supporting a key role of long-term damage in the reported occurrence of widespread rockslide clusters of these ages.

Spitzer observations of NGC 2264: the nature of the disk population

NASA Astrophysics Data System (ADS)

Teixeira, P. S.; Lada, C. J.; Marengo, M.; Lada, E. A.

2012-04-01

Aims: NGC 2264 is a young cluster with a rich circumstellar disk population which makes it an ideal target for studying the evolution of stellar clusters. Our goal is to study the star formation history of NGC 2264 and to analyse the primordial disk evolution of its members. Methods: The study presented is based on data obtained with the Infrared Array Camera (IRAC) and the Multiband Imaging Photometer for Spitzer (MIPS) on board the Spitzer Space Telescope, combined with deep near-infrared (NIR) ground-based FLAMINGOS imaging and previously published optical data. Results: We build NIR dust extinction maps of the molecular cloud associated with the cluster, and determine it to have a mass of 2.1 × 103 M⊙ above an AV of 7 mag. Using a differential Ks-band luminosity function (KLF) of the cluster, we estimate the size of the population of NGC 2264, within the area observed by FLAMINGOS, to be 1436 ± 242 members. The star formation efficiency is ≥ ~25%. We identify the disk population and divide it into 3 groups based on their spectral energy distribution slopes from 3.6 μm to 8 μm and on the 24 μm excess emission: (i) optically thick inner disks, (ii) anaemic inner disks, and (iii) disks with inner holes, or transition disks. We analyse the spatial distribution of these sources and find that sources with thick disks segregate into sub-clusterings, whereas sources with anaemic disks do not. Furthermore, sources with anaemic disks are found to be unembedded (i.e., with AV < 3 mag), whereas the clustered sources with thick disks are still embedded within the parental cloud. Conclusions: NGC 2264 has undergone more than one star-forming event, where the anaemic and extincted thick disk population appear to have formed in separate episodes: the sources with anaemic disks are more evolved and have had time to disperse and populate a halo of the cluster. We also find tentative evidence of triggered star-formation in the Fox Fur Nebula. In terms of disk evolution, our findings support the emerging disk evolution paradigm of two distinct evolutionary paths for primordial optically thick disks: a homologous one where the disk emission decreases uniformly at NIR and mid-infrared (MIR) wavelengths, and a radially differential one where the emission from the inner region of the disk decreases more rapidly than from the outer region (forming transition disks).

Origin and evolution of Petrocosmea (Gesneriaceae) inferred from both DNA sequence and novel findings in morphology with a test of morphology-based hypotheses.

PubMed

Qiu, Zhi-Jing; Lu, Yuan-Xue; Li, Chao-Qun; Dong, Yang; Smith, James F; Wang, Yin-Zheng

2015-07-03

Petrocosmea Oliver (Gesneriaceae) currently comprises 38 species with four non-nominate varieties, nearly all of which have been described solely from herbarium specimens. However, the dried specimens have obscured the full range of extremely diverse morphological variation that exists in the genus and has resulted in a poor subgeneric classification system that does not reflect the evolutionary history of this group. It is important to develop innovative methods to find new morphological traits and reexamine and reevaluate the traditionally used morphological data based on new hypothesis. In addition, Petrocosmea is a mid-sized genus but exhibits extreme diverse floral variants. This makes the genus of particular interest in addressing the question whether there are any key factors that is specifically associated with their evolution and diversification. Here we present the first phylogenetic analyses of the genus based on dense taxonomic sampling and multiple genes combined with a comprehensive morphological investigation. Maximum-parsimony, maximum likelihood and Bayesian analyses of molecular data from two nuclear DNA and six cpDNA regions support the monophyly of Petrocosmea and recover five major clades within the genus, which is strongly corroborated by the reconstruction of ancestral states for twelve new morphological characters directly observed from living material. Ancestral area reconstruction shows that its most common ancestor was likely located east and southeast of the Himalaya-Tibetan plateau. The origin of Petrocosmea from a potentially Raphiocarpus-like ancestor might have involved a series of morphological modifications from caulescent to acaulescent habit as well as from a tetrandrous flower with a long corolla-tube to a diandrous flower with a short corolla-tube, also evident in the vestigial caulescent habit and transitional floral form in clade A that is sister to the remainder of the genus. Among the five clades in Petrocosmea, the patterns of floral morphological differentiation are consistent with discontinuous lineage-associated morphotypes as a repeated adaptive response to alternative environments. Our results suggest that the lineage-specific morphological differentiations reflected in the upper lip, a functional organ for insect pollination, are likely adaptive responses to pollinator shifts. We further recognize that the floral morphological diversification in Petrocosmea involves several evolutionary phenomena, i.e. evolutionary successive specialization, reversals, parallel evolution, and convergent evolution, which are probably associated with adaptation to pollination against the background of heterogeneous abiotic and biotic environments in the eastern wing regions of Himalaya-Tibetan plateau.

Institutional evolution of a community-based programme for malaria control through larval source management in Dar es Salaam, United Republic of Tanzania.

PubMed

Chaki, Prosper P; Kannady, Khadija; Mtasiwa, Deo; Tanner, Marcel; Mshinda, Hassan; Kelly, Ann H; Killeen, Gerry F

2014-06-25

Community-based service delivery is vital to the effectiveness, affordability and sustainability of vector control generally, and to labour-intensive larval source management (LSM) programmes in particular. The institutional evolution of a city-level, community-based LSM programme over 14 years in urban Dar es Salaam, Tanzania, illustrates how operational research projects can contribute to public health governance and to the establishment of sustainable service delivery programmes. Implementation, management and governance of this LSM programme is framed within a nested set of spatially-defined relationships between mosquitoes, residents, government and research institutions that build upward from neighbourhood to city and national scales. The clear hierarchical structure associated with vertical, centralized management of decentralized, community-based service delivery, as well as increasingly clear differentiation of partner roles and responsibilities across several spatial scales, contributed to the evolution and subsequent growth of the programme. The UMCP was based on the principle of an integrated operational research project that evolved over time as the City Council gradually took more responsibility for management. The central role of Dar es Salaam's City Council in coordinating LSM implementation enabled that flexibility; the institutionalization of management and planning in local administrative structures enhanced community-mobilization and funding possibilities at national and international levels. Ultimately, the high degree of program ownership by the City Council and three municipalities, coupled with catalytic donor funding and technical support from expert overseas partners have enabled establishment of a sustainable, internally-funded programme implemented by the National Ministry of Health and Social Welfare and supported by national research and training institutes.

Institutional evolution of a community-based programme for malaria control through larval source management in Dar es Salaam, United Republic of Tanzania

PubMed Central

2014-01-01

Background Community-based service delivery is vital to the effectiveness, affordability and sustainability of vector control generally, and to labour-intensive larval source management (LSM) programmes in particular. Case description The institutional evolution of a city-level, community-based LSM programme over 14 years in urban Dar es Salaam, Tanzania, illustrates how operational research projects can contribute to public health governance and to the establishment of sustainable service delivery programmes. Implementation, management and governance of this LSM programme is framed within a nested set of spatially-defined relationships between mosquitoes, residents, government and research institutions that build upward from neighbourhood to city and national scales. Discussion and evaluation The clear hierarchical structure associated with vertical, centralized management of decentralized, community-based service delivery, as well as increasingly clear differentiation of partner roles and responsibilities across several spatial scales, contributed to the evolution and subsequent growth of the programme. Conclusions The UMCP was based on the principle of an integrated operational research project that evolved over time as the City Council gradually took more responsibility for management. The central role of Dar es Salaam’s City Council in coordinating LSM implementation enabled that flexibility; the institutionalization of management and planning in local administrative structures enhanced community-mobilization and funding possibilities at national and international levels. Ultimately, the high degree of program ownership by the City Council and three municipalities, coupled with catalytic donor funding and technical support from expert overseas partners have enabled establishment of a sustainable, internally-funded programme implemented by the National Ministry of Health and Social Welfare and supported by national research and training institutes. PMID:24964790

Evidence of Adaptive Evolution and Relaxed Constraints in Sex-Biased Genes of South American and West Indies Fruit Flies (Diptera: Tephritidae).

PubMed

Congrains, Carlos; Campanini, Emeline B; Torres, Felipe R; Rezende, Víctor B; Nakamura, Aline M; de Oliveira, Janaína L; Lima, André L A; Chahad-Ehlers, Samira; Sobrinho, Iderval S; de Brito, Reinaldo A

2018-01-01

Several studies have demonstrated that genes differentially expressed between sexes (sex-biased genes) tend to evolve faster than unbiased genes, particularly in males. The reason for this accelerated evolution is not clear, but several explanations have involved adaptive and nonadaptive mechanisms. Furthermore, the differences of sex-biased expression patterns of closely related species are also little explored out of Drosophila. To address the evolutionary processes involved with sex-biased expression in species with incipient differentiation, we analyzed male and female transcriptomes of Anastrepha fraterculus and Anastrepha obliqua, a pair of species that have diverged recently, likely in the presence of gene flow. Using these data, we inferred differentiation indexes and evolutionary rates and tested for signals of selection in thousands of genes expressed in head and reproductive transcriptomes from both species. Our results indicate that sex-biased and reproductive-biased genes evolve faster than unbiased genes in both species, which is due to both adaptive pressure and relaxed constraints. Furthermore, among male-biased genes evolving under positive selection, we identified some related to sexual functions such as courtship behavior and fertility. These findings suggest that sex-biased genes may have played important roles in the establishment of reproductive isolation between these species, due to a combination of selection and drift, and unveil a plethora of genetic markers useful for more studies in these species and their differentiation. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.

PubMed

Schrider, Daniel R; Hahn, Matthew W; Begun, David J

2016-05-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soldiers in a Stingless Bee.

PubMed

Hammel, Benedikt; Vollet-Neto, Ayrton; Menezes, Cristiano; Nascimento, Fabio S; Engels, Wolf; Grüter, Christoph

2016-01-01

The differentiation of workers into morphological subcastes (e.g., soldiers) represents an important evolutionary transition and is thought to improve division of labor in social insects. Soldiers occur in many ant and termite species, where they make up a small proportion of the workforce. A common assumption of worker caste evolution is that soldiers are behavioral specialists. Here, we report the first test of the "rare specialist" hypothesis in a eusocial bee. Colonies of the stingless bee Tetragonisca angustula are defended by a small group of morphologically differentiated soldiers. Contrary to the rare specialist hypothesis, we found that soldiers worked more (+34%-41%) and performed a greater variety of tasks (+23%-34%) than other workers, particularly early in life. Our results suggest a "rare elite" function of soldiers in T. angustula, that is, that they perform a disproportionately large amount of the work. Division of labor was based on a combination of temporal and physical castes, but soldiers transitioned faster from one task to the next. We discuss why the rare specialist assumption might not hold in species with a moderate degree of worker differentiation.

Evolutional Optimization on Material Ordering and Inventory Control of Supply Chain through Incentive Scheme

NASA Astrophysics Data System (ADS)

Prasertwattana, Kanit; Shimizu, Yoshiaki; Chiadamrong, Navee

This paper studied the material ordering and inventory control of supply chain systems. The effect of controlling policies is analyzed under three different configurations of the supply chain systems, and the formulated problem has been solved by using an evolutional optimization method known as Differential Evolution (DE). The numerical results show that the coordinating policy with the incentive scheme outperforms the other policies and can improve the performance of the overall system as well as all members under the concept of supply chain management.

Os isotopes in SNC meteorites and their implications to the early evolution of Mars and Earth

NASA Technical Reports Server (NTRS)

Jagoutz, E.; Luck, J. M.; Othman, D. Ben; Wanke, H.

1993-01-01

A new development on the measurement of the Os isotopic composition by mass spectrometry using negative ions opened a new field of applications. The Re-Os systematic provides time information on the differentiation of the nobel metals. The nobel metals are strongly partitioned into metal and sulphide phases, but also the generation of silicate melts might fractionate the Re-Os system. Compared to the other isotopic systems which are mainly dating the fractionation of the alkalis and alkali-earth elements, the Re-Os system is expected to disclose entirely new information about the geochemistry. Especially the differentiation and early evolution of the planets such as the formation of the core will be elucidated with this method.

Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress.

PubMed

Xu, Yingchun; Wang, Yanjie; Mattson, Neil; Yang, Liu; Jin, Qijiang

2017-12-01

Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato). In this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of d N /d S ratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR. This study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.

Feynman formulae and phase space Feynman path integrals for tau-quantization of some Lévy-Khintchine type Hamilton functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butko, Yana A., E-mail: yanabutko@yandex.ru, E-mail: kinderknecht@math.uni-sb.de; Grothaus, Martin, E-mail: grothaus@mathematik.uni-kl.de; Smolyanov, Oleg G., E-mail: Smolyanov@yandex.ru

2016-02-15

Evolution semigroups generated by pseudo-differential operators are considered. These operators are obtained by different (parameterized by a number τ) procedures of quantization from a certain class of functions (or symbols) defined on the phase space. This class contains Hamilton functions of particles with variable mass in magnetic and potential fields and more general symbols given by the Lévy-Khintchine formula. The considered semigroups are represented as limits of n-fold iterated integrals when n tends to infinity. Such representations are called Feynman formulae. Some of these representations are constructed with the help of another pseudo-differential operator, obtained by the same procedure ofmore » quantization; such representations are called Hamiltonian Feynman formulae. Some representations are based on integral operators with elementary kernels; these are called Lagrangian Feynman formulae. Langrangian Feynman formulae provide approximations of evolution semigroups, suitable for direct computations and numerical modeling of the corresponding dynamics. Hamiltonian Feynman formulae allow to represent the considered semigroups by means of Feynman path integrals. In the article, a family of phase space Feynman pseudomeasures corresponding to different procedures of quantization is introduced. The considered evolution semigroups are represented as phase space Feynman path integrals with respect to these Feynman pseudomeasures, i.e., different quantizations correspond to Feynman path integrals with the same integrand but with respect to different pseudomeasures. This answers Berezin’s problem of distinguishing a procedure of quantization on the language of Feynman path integrals. Moreover, the obtained Lagrangian Feynman formulae allow also to calculate these phase space Feynman path integrals and to connect them with some functional integrals with respect to probability measures.« less

Dissolution-induced preferential flow in a limestone fracture.

PubMed

Liu, Jishan; Polak, Amir; Elsworth, Derek; Grader, Avrami

2005-06-01

Flow in a rock fracture is surprisingly sensitive to the evolution of flow paths that develop as a result of dissolution. Net dissolution may either increase or decrease permeability uniformly within the fracture, or may form a preferential flow path through which most of the injected fluid flows, depending on the prevailing ambient mechanical and chemical conditions. A flow-through test was completed on an artificial fracture in limestone at room temperature under ambient confining stress of 3.5 MPa. The sample was sequentially circulated by water of two different compositions through the 1500 h duration of the experiment; the first 935 h by tap groundwater, followed by 555 h of distilled water. Measurements of differential pressures between the inlet and the outlet, fluid and dissolved mass fluxes, and concurrent X-ray CT imaging and sectioning were used to characterize the evolution of flow paths within the limestone fracture. During the initial circulation of groundwater, the differential pressure increased almost threefold, and was interpreted as a net reduction in permeability as the contacting asperities across the fracture are removed, and the fracture closes. With the circulation of distilled water, permeability initially reduces threefold, and ultimately increases by two orders of magnitude. This spontaneous switch from net decrease in permeability, to net increase occurred with no change in flow rate or applied effective stress, and is attributed to the evolving localization of flow path as evidenced by CT images. Based on the X-ray CT characterizations, a flow path-dependent flow model was developed to simulate the evolution of flow paths within the fracture and its influence on the overall flow behaviors of the injected fluid in the fracture.

Dynamical evolution of differentiated asteroid families

NASA Astrophysics Data System (ADS)

Martins-Filho, W. S.; Carvano, J.; Mothe-Diniz, T.; Roig, F.

2014-10-01

The project aims to study the dynamical evolution of a family of asteroids formed from a fully differentiated parent body, considering family members with different physical properties consistent with what is expected from the break up of a body formed by a metallic nucleus surrounded by a rocky mantle. Initially, we study the effects of variations in density, bond albedo, and thermal inertia in the semi-major axis drift caused by the Yarkovsky effect. The Yarkovsky effect is a non-conservative force caused by the thermal re-radiation of the solar radiation by an irregular body. In Solar System bodies, it is known to cause changes in the orbital motions (Peterson, 1976), eventually bringing asteroids into transport routes to near-Earth space, such as some mean motion resonances. We expressed the equations of variation of the semi-major axis directly in terms of physical properties (such as the mean motion, frequency of rotation, conductivity, thermal parameter, specific heat, obliquity and bond albedo). This development was based on the original formalism for the Yarkovsky effect (i.e., Bottke et al., 2006 and references therein). The derivation of above equations allowed us to closely study the variation of the semi-major axis individually for each physical parameter, clearly showing that the changes in semi-major axis for silicate bodies is twice or three times greater than for metal bodies. The next step was to calculate the orbital elements of a synthetic family after the break-up. That was accomplished assuming that the catastrophic disruption energy is given by the formalism described by Stewart and Leinhardt (2009) and assuming an isotropic distribution of velocities for the fragments of the nucleus and the mantle. Finally, the orbital evolution of the fragments is implemented using a simpletic integrator, and the result compared with the distribution of real asteroid families.

Ancient geographical gaps and paleo-climate shape the phylogeography of an endemic bird in the sky islands of southern India.

PubMed

Robin, V V; Sinha, Anindya; Ramakrishnan, Uma

2010-10-13

Sky islands, formed by the highest reaches of mountain tracts physically isolated from one another, represent one of the biodiversity-rich regions of the world. Comparative studies of geographically isolated populations on such islands can provide valuable insights into the biogeography and evolution of species on these islands. The Western Ghats mountains of southern India form a sky island system, where the relationship between the island structure and the evolution of its species remains virtually unknown despite a few population genetic studies. We investigated how ancient geographic gaps and glacial cycles have partitioned genetic variation in modern populations of a threatened endemic bird, the White-bellied Shortwing Brachypteryx major, across the montane Shola forests on these islands and also inferred its evolutionary history. We used bayesian and maximum likelihood-based phylogenetic and population-genetic analyses on data from three mitochondrial markers and one nuclear marker (totally 2594 bp) obtained from 33 White-bellied Shortwing individuals across five islands. Genetic differentiation between populations of the species correlated with the locations of deep valleys in the Western Ghats but not with geographical distance between these populations. All populations revealed demographic histories consistent with population founding and expansion during the Last Glacial Maximum. Given the level of genetic differentiation north and south of the Palghat Gap, we suggest that these populations be considered two different taxonomic species. Our results show that the physiography and paleo-climate of this region historically resulted in multiple glacial refugia that may have subsequently driven the evolutionary history and current population structure of this bird. The first avian genetic study from this biodiversity hotspot, our results provide insights into processes that may have impacted the speciation and evolution of the endemic fauna of this region.

The evolution of the moon and the terrestrial planets

NASA Technical Reports Server (NTRS)

Toksoez, M. N.; Johnston, D. H.

1974-01-01

The thermal evolutions of the Moon, Mars, Venus and Mercury are calculated theoretically starting from cosmochemical condensation models. An assortment of geological, geochemical and geophysical data are used to constrain both the present day temperatures and the thermal histories of the planets' interiors. Such data imply that the planets were heated during or shortly after formation and that all the terrestrial planets started their differentiations early in their history. The moon, smallest in size, is characterized as a differentiated body with a crust, a thick solid mantle and an interior region which may be partially molten. Mars, intermediate in size, is assumed to have differentiated an Fe-FeS core. Venus is characterized as a planet not unlike the earth in many respects. Core formation has occurred probably during the first billion years after the formation. Mercury, which probably has a large core, may have a 500 km thick solid lithosphere and a partially molten core if it is assumed that some heat sources exist in the core.

Estimation of shear viscosity based on transverse momentum correlations

NASA Astrophysics Data System (ADS)

STAR Collaboration; Sharma, Monika; STAR Collaboration

2009-11-01

Event anisotropy measurements at RHIC suggest the strongly interacting matter created in heavy ion collisions flows with very little shear viscosity. Precise determination of “shear viscosity-to-entropy” ratio is currently a subject of extensive study [S. Gavin and M. Abdel-Aziz, Phys. Rev. Lett. 97 (2006) 162302]. We present preliminary results of measurements of the evolution of transverse momentum correlation function with collision centrality of Au+Au interactions at s=200 GeV. We compare two differential correlation functions, namely inclusive [J. Adams et al. (STAR Collaboration), Phys. Rev. C 72 (2005) 044902] and a differential version of the correlation measure C˜ introduced by Gavin et al. [S. Gavin and M. Abdel-Aziz, Phys. Rev. Lett. 97 (2006) 162302; M. Sharma and C. A. Pruneau, Phys. Rev. C 79 (2009) 024905.]. These observables can be used for the experimental study of the shear viscosity per unit entropy.

At the Edge of Translation – Materials to Program Cells for Directed Differentiation

PubMed Central

Arany, Praveen R; Mooney, David J

2010-01-01

The rapid advancement in basic biology knowledge, especially in the stem cell field, has created new opportunities to develop biomaterials capable of orchestrating the behavior of transplanted and host cells. Based on our current understanding of cellular differentiation, a conceptual framework for the use of materials to program cells in situ is presented, namely a domino versus a switchboard model, to highlight the use of single versus multiple cues in a controlled manner to modulate biological processes. Further, specific design principles of material systems to present soluble and insoluble cues that are capable of recruiting, programming and deploying host cells for various applications are presented. The evolution of biomaterials from simple inert substances used to fill defects, to the recent development of sophisticated material systems capable of programming cells in situ is providing a platform to translate our understanding of basic biological mechanisms to clinical care. PMID:20860763

Analysis of differential selective forces acting on the coat protein (P3) of the plant virus family Luteoviridae.

PubMed

Torres, Marina W; Corrêa, Régis L; Schrago, Carlos G

2005-12-30

The coat protein (CP) of the family Luteoviridae is directly associated with the success of infection. It participates in various steps of the virus life cycle, such as virion assembly, stability, systemic infection, and transmission. Despite its importance, extensive studies on the molecular evolution of this protein are lacking. In the present study, we investigate the action of differential selective forces on the CP coding region using maximum likelihood methods. We found that the protein is subjected to heterogeneous selective pressures and some sites may be evolving near neutrality. Based on the proposed 3-D model of the CP S-domain, we showed that nearly neutral sites are predominantly located in the region of the protein that faces the interior of the capsid, in close contact with the viral RNA, while highly conserved sites are mainly part of beta-strands, in the protein's major framework.

Portent of Heine's Reciprocal Square Root Identity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cohl, H W

Precise efforts in theoretical astrophysics are needed to fully understand the mechanisms that govern the structure, stability, dynamics, formation, and evolution of differentially rotating stars. Direct computation of the physical attributes of a star can be facilitated by the use of highly compact azimuthal and separation angle Fourier formulations of the Green's functions for the linear partial differential equations of mathematical physics.

Phylogeography and alpha taxonomy of the common dolphin (Delphinus sp.).

PubMed

Natoli, A; Cañadas, A; Peddemors, V M; Aguilar, A; Vaquero, C; Fernández-Piqueras, P; Hoelzel, A R

2006-05-01

The resolution of taxonomic classifications for delphinid cetaceans has been problematic, especially for species in the genera Delphinus, Tursiops and Stenella. The frequent lack of correspondence between morphological and genetic differentiation in these species raises questions about the mechanisms responsible for their evolution. In this study we focus on the genus Delphinus, and use molecular markers to address questions about speciation and the evolution of population structure. Delphinus species have a worldwide distribution and show a high degree of morphological variation. Two distinct morphotypes, long-beaked and short-beaked, have been considered different species named D. capensis and D. delphis, respectively. However, genetic differentiation between these two forms has only been demonstrated in the Pacific. We analysed samples from eight different geographical regions, including two morphologically defined long-beaked form populations, and compared these with the eastern North Pacific populations. We found high differentiation among the populations described as long-beaked instead of the expected monophyly, suggesting that these populations may have evolved from independent events converging on the same morphotype. We observed low genetic differentiation among the short-beaked populations across a large geographical scale. We interpret these phylogeographical patterns in the context of life history and population structure in related species.

Evolution of plant growth and defense in a continental introduction.

PubMed

Agrawal, Anurag A; Hastings, Amy P; Bradburd, Gideon S; Woods, Ellen C; Züst, Tobias; Harvey, Jeffrey A; Bukovinszky, Tibor

2015-07-01

Substantial research has addressed adaptation of nonnative biota to novel environments, yet surprisingly little work has integrated population genetic structure and the mechanisms underlying phenotypic differentiation in ecologically important traits. We report on studies of the common milkweed Asclepias syriaca, which was introduced from North America to Europe over the past 400 years and which lacks most of its specialized herbivores in the introduced range. Using 10 populations from each continent grown in a common environment, we identified several growth and defense traits that have diverged, despite low neutral genetic differentiation between continents. We next developed a Bayesian modeling approach to account for relationships between molecular and phenotypic differences, confirming that continental trait differentiation was greater than expected from neutral genetic differentiation. We found evidence that growth-related traits adaptively diverged within and between continents. Inducible defenses triggered by monarch butterfly herbivory were substantially reduced in European populations, and this reduction in inducibility was concordant with altered phytohormonal dynamics, reduced plant growth, and a trade-off with constitutive investment. Freedom from the community of native and specialized herbivores may have favored constitutive over induced defense. Our replicated analysis of plant growth and defense, including phenotypically plastic traits, suggests adaptive evolution following a continental introduction.

Differential expression of non-coding RNAs and continuous evolution of the X chromosome in testicular transcriptome of two mouse species.

PubMed

Homolka, David; Ivanek, Robert; Forejt, Jiri; Jansa, Petr

2011-02-14

Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition.

Tracking Topographic Changes from Multitemporal Stereo Images, Application to the Nili Patera Dune Field

NASA Astrophysics Data System (ADS)

Avouac, J.; Ayoub, F.; Bridges, N. T.; Leprince, S.; Lucas, A.

2012-12-01

The High Resolution Imaging Science Experiment (HiRISE) in orbit around Mars provides images with a nominal ground resolution of 25cm. Its agility allows imaging a same scene with stereo view angles thus allowing for for Digital elevation Model (DEM) extraction through stereo-photogrammetry. This dataset thus offers an exceptional opportunity to measure the topography with high precision and track its eventual evolution with time. In this presentation, we will discuss how multi-temporal acquisitions of HiRISE images of the Nili Patera dune field allow tracking ripples migration, assess sand fluxes and dunes activity. We investigated in particular the use of multi-temporal DEMs to monitor the migration and morphologic evolution of the dune field. We present here the methodology used and the various challenges that must be overcome to best exploit the multi-temporal images. Two DEMs were extracted from two stereo images pairs acquired 390 earth days apart in 2010-2011 using SOCET SET photogrammetry software, with a 1m post-spacing and a vertical accuracy of few tens of centimeters. Prior to comparison the DEMs registration, which was not precise enough out of SOCET-SET, was improved by wrapping the second DEM onto the first one using the bedrock only as a support for registration. The vertical registration residual was estimated at around 40cm RMSE and is mostly due to CCD misalignment and uncorrected spacecraft attitudes. Changes of elevation over time are usually determined from DEMs differentiation: provided that DEMs are perfectly registered and sampled on the same grid, this approach readily quantifies erosion and deposition processes. As the dunes have moved horizontally, they are not physically aligned anymore in the DEMs, and their morphologic evolution cannot be recovered easily from differentiating the DEMs. In this particular setting the topographic evolution is best recovered from correlation of the DEMs. We measure that the fastest dunes have migrated by up to 1meter per Earth year as a result of lee front deposition and stoss slope erosion. DEMs differentiation, after correction for horizontal migration, provides and additional information on dune morphology evolution. Some dunes show a vertical growth over the 390 days spanning the 2 DEMs, but we cannot exclude a bias due to the acquisition parameters. Indeed, the images of the two stereo pairs were acquired 22 and 5 days apart, respectively. During that time, the ripples laying on the dune surface have probably migrated. As the DEMs extraction is based on feature tracking and parallax, this difference in DEMs elevation may be only, or in part, due to the ripple migration between the acquisition times that biased the actual dune elevations.

Angiosperm ovules: diversity, development, evolution

PubMed Central

Endress, Peter K.

2011-01-01

Background Ovules as developmental precursors of seeds are organs of central importance in angiosperm flowers and can be traced back in evolution to the earliest seed plants. Angiosperm ovules are diverse in their position in the ovary, nucellus thickness, number and thickness of integuments, degree and direction of curvature, and histological differentiations. There is a large body of literature on this diversity, and various views on its evolution have been proposed over the course of time. Most recently evo–devo studies have been concentrated on molecular developmental genetics in ovules of model plants. Scope The present review provides a synthetic treatment of several aspects of the sporophytic part of ovule diversity, development and evolution, based on extensive research on the vast original literature and on experience from my own comparative studies in a broad range of angiosperm clades. Conclusions In angiosperms the presence of an outer integument appears to be instrumental for ovule curvature, as indicated from studies on ovule diversity through the major clades of angiosperms, molecular developmental genetics in model species, abnormal ovules in a broad range of angiosperms, and comparison with gymnosperms with curved ovules. Lobation of integuments is not an atavism indicating evolution from telomes, but simply a morphogenetic constraint from the necessity of closure of the micropyle. Ovule shape is partly dependent on locule architecture, which is especially indicated by the occurrence of orthotropous ovules. Some ovule features are even more conservative than earlier assumed and thus of special interest in angiosperm macrosystematics. PMID:21606056

A stochastic evolution model for residue Insertion-Deletion Independent from Substitution.

PubMed

Lèbre, Sophie; Michel, Christian J

2010-12-01

We develop here a new class of stochastic models of gene evolution based on residue Insertion-Deletion Independent from Substitution (IDIS). Indeed, in contrast to all existing evolution models, insertions and deletions are modeled here by a concept in population dynamics. Therefore, they are not only independent from each other, but also independent from the substitution process. After a separate stochastic analysis of the substitution and the insertion-deletion processes, we obtain a matrix differential equation combining these two processes defining the IDIS model. By deriving a general solution, we give an analytical expression of the residue occurrence probability at evolution time t as a function of a substitution rate matrix, an insertion rate vector, a deletion rate and an initial residue probability vector. Various mathematical properties of the IDIS model in relation with time t are derived: time scale, time step, time inversion and sequence length. Particular expressions of the nucleotide occurrence probability at time t are given for classical substitution rate matrices in various biological contexts: equal insertion rate, insertion-deletion only and substitution only. All these expressions can be directly used for biological evolutionary applications. The IDIS model shows a strongly different stochastic behavior from the classical substitution only model when compared on a gene dataset. Indeed, by considering three processes of residue insertion, deletion and substitution independently from each other, it allows a more realistic representation of gene evolution and opens new directions and applications in this research field. Copyright © 2010 Elsevier Ltd. All rights reserved.

Continuum Model for River Networks

NASA Astrophysics Data System (ADS)

Giacometti, Achille; Maritan, Amos; Banavar, Jayanth R.

1995-07-01

The effects of erosion, avalanching, and random precipitation are captured in a simple stochastic partial differential equation for modeling the evolution of river networks. Our model leads to a self-organized structured landscape and to abstraction and piracy of the smaller tributaries as the evolution proceeds. An algebraic distribution of the average basin areas and a power law relationship between the drainage basin area and the river length are found.

Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics

PubMed Central

Klassen, Jonathan L.

2010-01-01

Background Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Methodology/Principal Findings Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. Conclusions/Significance Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a “bramble” model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic “root”. Structural diversification may be constrained (“trimmed”) where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification. PMID:20582313

Bringing Together Evolution on Serpentine and Polyploidy: Spatiotemporal History of the Diploid-Tetraploid Complex of Knautia arvensis (Dipsacaceae)

PubMed Central

Kolář, Filip; Fér, Tomáš; Štech, Milan; Trávníček, Pavel; Dušková, Eva; Schönswetter, Peter; Suda, Jan

2012-01-01

Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb Knautia arvensis (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of K. arvensis allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary ‘dead-ends’ but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes K. arvensis a unique system for addressing general questions of polyploid research. PMID:22792207

Differentiated cell behavior: a multiscale approach using measure theory.

PubMed

Colombi, Annachiara; Scianna, Marco; Tosin, Andrea

2015-11-01

This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving measures, rather than at individual cell paths, we obtain an ensemble representation stemming from the phenomenological behavior of the single component cells. In particular, as a key advantage of our approach, the scale of representation of the system, i.e., microscopic/discrete vs. macroscopic/continuous, can be chosen a posteriori according only to the spatial structure given to the aforesaid measures. The paper focuses in particular on the use of different scales based on the specific functions performed by cells. A two-population hybrid system is considered, where cells with a specialized/differentiated phenotype are treated as a discrete population of point masses while unspecialized/undifferentiated cell aggregates are represented by a continuous approximation. Numerical simulations and analytical investigations emphasize the role of some biologically relevant parameters in determining the specific evolution of such a hybrid cell system.

An almost symmetric Strang splitting scheme for nonlinear evolution equations.

PubMed

Einkemmer, Lukas; Ostermann, Alexander

2014-07-01

In this paper we consider splitting methods for the time integration of parabolic and certain classes of hyperbolic partial differential equations, where one partial flow cannot be computed exactly. Instead, we use a numerical approximation based on the linearization of the vector field. This is of interest in applications as it allows us to apply splitting methods to a wider class of problems from the sciences. However, in the situation described, the classic Strang splitting scheme, while still being a method of second order, is not longer symmetric. This, in turn, implies that the construction of higher order methods by composition is limited to order three only. To remedy this situation, based on previous work in the context of ordinary differential equations, we construct a class of Strang splitting schemes that are symmetric up to a desired order. We show rigorously that, under suitable assumptions on the nonlinearity, these methods are of second order and can then be used to construct higher order methods by composition. In addition, we illustrate the theoretical results by conducting numerical experiments for the Brusselator system and the KdV equation.

An almost symmetric Strang splitting scheme for nonlinear evolution equations☆

PubMed Central

Einkemmer, Lukas; Ostermann, Alexander

2014-01-01

In this paper we consider splitting methods for the time integration of parabolic and certain classes of hyperbolic partial differential equations, where one partial flow cannot be computed exactly. Instead, we use a numerical approximation based on the linearization of the vector field. This is of interest in applications as it allows us to apply splitting methods to a wider class of problems from the sciences. However, in the situation described, the classic Strang splitting scheme, while still being a method of second order, is not longer symmetric. This, in turn, implies that the construction of higher order methods by composition is limited to order three only. To remedy this situation, based on previous work in the context of ordinary differential equations, we construct a class of Strang splitting schemes that are symmetric up to a desired order. We show rigorously that, under suitable assumptions on the nonlinearity, these methods are of second order and can then be used to construct higher order methods by composition. In addition, we illustrate the theoretical results by conducting numerical experiments for the Brusselator system and the KdV equation. PMID:25844017

The Kadomtsev{endash}Petviashvili equation as a source of integrable model equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maccari, A.

1996-12-01

A new integrable and nonlinear partial differential equation (PDE) in 2+1 dimensions is obtained, by an asymptotically exact reduction method based on Fourier expansion and spatiotemporal rescaling, from the Kadomtsev{endash}Petviashvili equation. The integrability property is explicitly demonstrated, by exhibiting the corresponding Lax pair, that is obtained by applying the reduction technique to the Lax pair of the Kadomtsev{endash}Petviashvili equation. This model equation is likely to be of applicative relevance, because it may be considered a consistent approximation of a large class of nonlinear evolution PDEs. {copyright} {ital 1996 American Institute of Physics.}

Differential patterns of acquired virulence genes distinguish Salmonella strains

PubMed Central

Conner, Christopher P.; Heithoff, Douglas M.; Julio, Steven M.; Sinsheimer, Robert L.; Mahan, Michael J.

1998-01-01

Analysis of several Salmonella typhimurium in vivo-induced genes located in regions of atypical base composition has uncovered acquired genetic elements that cumulatively engender pathogenicity. Many of these regions are associated with mobile elements, encode predicted adhesin and invasin-like functions, and are required for full virulence. Some of these regions distinguish broad host range from host-adapted Salmonella serovars and may contribute to inherent differences in host specificity, tissue tropism, and disease manifestation. Maintenance of this archipelago of acquired sequence by selection in specific hosts reveals a fossil record of the evolution of pathogenic species. PMID:9539791

Symmetry analysis of a model for the exercise of a barrier option

NASA Astrophysics Data System (ADS)

O'Hara, J. G.; Sophocleous, C.; Leach, P. G. L.

2013-09-01

A barrier option takes into account the possibility of an unacceptable change in the price of the underlying stock. Such a change could carry considerable financial loss. We examine one model based upon the Black-Scholes-Merton Equation and determine the functional forms of the barrier function and rebate function which are consistent with a solution of the underlying evolution partial differential equation using the Lie Theory of Extended Groups. The solution is consistent with the possibility of no rebate and the barrier function is very similar to one adopted on an heuristic basis.

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

NASA Astrophysics Data System (ADS)

Husa, Sascha; Hinder, Ian; Lechner, Christiane

2006-06-01

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a "rapid prototyping" system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations. Program summaryTitle of program: Kranc Catalogue identifier: ADXS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under Linux Programming language used: Mathematica, C, Fortran 90 Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KB Has the code been vectorized or parallelized: The code is parallelized based on the Cactus framework. Number of bytes in distributed program, including test data, etc.: 1 578 142 Number of lines in distributed program, including test data, etc.: 11 711 Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations. Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface. Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500 3. Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor. Unusual features of the program: based on Mathematica and Cactus

A simulation method for the stability analysis of landscape scenarios by using a NetLogo application in GIS environment

NASA Astrophysics Data System (ADS)

Gobattoni, Federica; Lauro, Giuliana; Leone, Antonio; Monaco, Roberto; Pelorosso, Raffaele

2010-05-01

Landscape continually evolves under the influence of a complex and broad range of natural processes, directly or indirectly determined by land use, but also under the impact of anthropic actions of planning and territorial management. While processes such as earthquakes, landslides, and so on, are manifestations of this evolutionary process, human decisions concerning land government (cropping, urbanization etc.) may affect dramatically the landscape evolution in a complex mechanism of cause-and-effect leading to accelerated erosion phenomena, hydro-geological instability and flood events. To better understand landscape evolution and change in time, several numerical and empirical models have been developed and implemented with the aim to explore and explain such complex processes; reproducing landscape evolution through models and schematic representation of reality could be a powerful and reliable tool for natural resources planning and decision making in land management. Even understanding interactions and relations between the involved variables, predicting how the system will react to external inputs such as political, social or economic constraints, could be strongly difficult. Decision support systems could help in choosing among possible alternatives by integrating different sources of information and "What if" scenarios could be developed as possible future states of the world that represent alternative plausible conditions under different assumptions (Mahmoud M. wt al., 2009). Modelling approaches can be successfully applied to describe and assess both the natural spatial environmental variability and the anthropic impacts at different temporal and spatial scales even if they usually takes into account each aspect of the environmental system separately and without looking directly at landscape as a unique system and without understanding its intrinsic evolution mechanisms (H. Siegrist, 2002, S. Demberel, 2003, A. Brenner, 2005). GIS-based models which could be able to predict the response of the landscape working as a unique system, are expected to advance through a development of sustainable planning strategies and to evaluate the equilibrium-non equilibrium status of landscape evolution and the availability of vital resources in space and time. In this context mathematical models adapted in GIS environment may really give an heavy contribution in such a complex problem- solving, providing a real and concrete Decision System Support. An integrated GIS (Geographic Information System)-based approach was developed (G. Lauro, R. Monaco, 2008) combining an ecological graph model for the analysis of the relationship between spatial pattern and ecological flows and a mathematical model, based on a system of two nonlinear differential equations, that studies meta-stability and bifurcation phenomena. These equations are mainly based on a balance law between a logistic growth of bio-energy and its reduction due to limiting factors coming from environmental constraints. The energy exchange among them will be more or less strong depending on the degree of permeability of the barriers which can obstruct the energy passage from each "landscape unit" to the other. Through NetLogo, a cross-platform multi-agent programmable modelling environment, a completely automatic GIS-based mathematical model, based on the ecological graph and on the cited two differential equations, is presented and discussed here. A study case in Central Italy is analysed to better underline the importance of such a user friendly model in GIS environment.

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

PubMed Central

Galinsky, Kevin J.; Bhatia, Gaurav; Loh, Po-Ru; Georgiev, Stoyan; Mukherjee, Sayan; Patterson, Nick J.; Price, Alkes L.

2016-01-01

Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984∗T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease. PMID:26924531

Nonstationary Extreme Value Analysis in a Changing Climate: A Software Package

NASA Astrophysics Data System (ADS)

Cheng, L.; AghaKouchak, A.; Gilleland, E.

2013-12-01

Numerous studies show that climatic extremes have increased substantially in the second half of the 20th century. For this reason, analysis of extremes under a nonstationary assumption has received a great deal of attention. This paper presents a software package developed for estimation of return levels, return periods, and risks of climatic extremes in a changing climate. This MATLAB software package offers tools for analysis of climate extremes under both stationary and non-stationary assumptions. The Nonstationary Extreme Value Analysis (hereafter, NEVA) provides an efficient and generalized framework for analyzing extremes using Bayesian inference. NEVA estimates the extreme value parameters using a Differential Evolution Markov Chain (DE-MC) which utilizes the genetic algorithm Differential Evolution (DE) for global optimization over the real parameter space with the Markov Chain Monte Carlo (MCMC) approach and has the advantage of simplicity, speed of calculation and convergence over conventional MCMC. NEVA also offers the confidence interval and uncertainty bounds of estimated return levels based on the sampled parameters. NEVA integrates extreme value design concepts, data analysis tools, optimization and visualization, explicitly designed to facilitate analysis extremes in geosciences. The generalized input and output files of this software package make it attractive for users from across different fields. Both stationary and nonstationary components of the package are validated for a number of case studies using empirical return levels. The results show that NEVA reliably describes extremes and their return levels.

Design of a fuzzy differential evolution algorithm to predict non-deposition sediment transport

NASA Astrophysics Data System (ADS)

Ebtehaj, Isa; Bonakdari, Hossein

2017-12-01

Since the flow entering a sewer contains solid matter, deposition at the bottom of the channel is inevitable. It is difficult to understand the complex, three-dimensional mechanism of sediment transport in sewer pipelines. Therefore, a method to estimate the limiting velocity is necessary for optimal designs. Due to the inability of gradient-based algorithms to train Adaptive Neuro-Fuzzy Inference Systems (ANFIS) for non-deposition sediment transport prediction, a new hybrid ANFIS method based on a differential evolutionary algorithm (ANFIS-DE) is developed. The training and testing performance of ANFIS-DE is evaluated using a wide range of dimensionless parameters gathered from the literature. The input combination used to estimate the densimetric Froude number ( Fr) parameters includes the volumetric sediment concentration ( C V ), ratio of median particle diameter to hydraulic radius ( d/R), ratio of median particle diameter to pipe diameter ( d/D) and overall friction factor of sediment ( λ s ). The testing results are compared with the ANFIS model and regression-based equation results. The ANFIS-DE technique predicted sediment transport at limit of deposition with lower root mean square error (RMSE = 0.323) and mean absolute percentage of error (MAPE = 0.065) and higher accuracy ( R 2 = 0.965) than the ANFIS model and regression-based equations.

Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups

PubMed Central

Garcia, Thomas; Brunnet, Leonardo Gregory; De Monte, Silvia

2014-01-01

The evolutionary stability of cooperative traits, that are beneficial to other individuals but costly to their carrier, is considered possible only through the establishment of a sufficient degree of assortment between cooperators. Chimeric microbial populations, characterized by simple interactions between unrelated individuals, restrain the applicability of standard mechanisms generating such assortment, in particular when cells disperse between successive reproductive events such as happens in Dicyostelids and Myxobacteria. In this paper, we address the evolutionary dynamics of a costly trait that enhances attachment to others as well as group cohesion. By modeling cells as self-propelled particles moving on a plane according to local interaction forces and undergoing cycles of aggregation, reproduction and dispersal, we show that blind differential adhesion provides a basis for assortment in the process of group formation. When reproductive performance depends on the social context of players, evolution by natural selection can lead to the success of the social trait, and to the concomitant emergence of sizeable groups. We point out the conditions on the microscopic properties of motion and interaction that make such evolutionary outcome possible, stressing that the advent of sociality by differential adhesion is restricted to specific ecological contexts. Moreover, we show that the aggregation process naturally implies the existence of non-aggregated particles, and highlight their crucial evolutionary role despite being largely neglected in theoretical models for the evolution of sociality. PMID:24586133

Evolution of Karyotypes in Chameleons

PubMed Central

Rovatsos, Michail; Altmanová, Marie; Johnson Pokorná, Martina; Velenský, Petr; Kratochvíl, Lukáš

2017-01-01

The reconstruction of the evolutionary dynamics of karyotypes and sex determining systems in squamate reptiles is precluded by the lack of data in many groups including most chameleons (Squamata: Acrodonta: Chamaeleonidae). We performed cytogenetic analysis in 16 species of chameleons from 8 genera covering the phylogenetic diversity of the family and also phylogenetic reconstruction of karyotype evolution in this group. In comparison to other squamates, chameleons demonstrate rather variable karyotypes, differing in chromosome number, morphology and presence of interstitial telomeric signal (ITS). On the other hand, the location of rDNA is quite conserved among chameleon species. Phylogenetic analysis combining our new results and previously published data tentatively suggests that the ancestral chromosome number for chameleons is 2n = 36, which is the same as assumed for other lineages of the clade Iguania, i.e., agamids and iguanas. In general, we observed a tendency for the reduction of chromosome number during the evolution of chameleons, however, in Rieppeleon brevicaudatus, we uncovered a chromosome number of 2n = 62, very unusual among squamates, originating from a number of chromosome splits. Despite the presence of the highly differentiated ZZ/ZW sex chromosomes in the genus Furcifer, we did not detect any unequivocal sexual differences in the karyotypes of any other studied species of chameleons tested using differential staining and comparative genomic hybridization, suggesting that sex chromosomes in most chameleons are only poorly differentiated. PMID:29231849

Postmating sexual selection: allopatric evolution of sperm competition mechanisms and genital morphology in calopterygid damselflies (Insecta: Odonata).

PubMed

Cordero Rivera, A; Andrés, J A; Córdoba-Aguilar, A; Utzeri, C

2004-02-01

Postmating sexual selection theory predicts that in allopatry reproductive traits diverge rapidly and that the resulting differentiation in these traits may lead to restrictions to gene flow between populations and, eventually, reproductive isolation. In this paper we explore the potential for this premise in a group of damselflies of the family Calopterygidae, in which postmating sexual mechanisms are especially well understood. Particularly, we tested if in allopatric populations the sperm competition mechanisms and genitalic traits involved in these mechanisms have indeed diverged as sexual selection theory predicts. We did so in two different steps. First, we compared the sperm competition mechanisms of two allopatric populations of Calopteryx haemorrhoidalis (one Italian population studied here and one Spanish population previously studied). Our results indicate that in both populations males are able to displace spermathecal sperm, but the mechanism used for sperm removal between both populations is strikingly different. In the Spanish population males seem to empty the spermathecae by stimulating females, whereas in the Italian population males physically remove sperm from the spermathecae. Both populations also exhibit differences in genital morphometry that explain the use of different mechanisms: the male lateral processes are narrower than the spermathecal ducts in the Italian population, which is the reverse in the Spanish population. The estimated degree of phenotypic differentiation between these populations based on the genitalic traits involved in sperm removal was much greater than the differentiation based on a set of other seven morphological variables, suggesting that strong directional postmating sexual selection is indeed the main evolutionary force behind the reproductive differentiation between the studied populations. In a second step, we examined if a similar pattern in genital morphometry emerge in allopatric populations of this and other three species of the same family (Calopteryx splendens, C. virgo and Hetaerina cruentata). Our results suggest that there is geographic variation in the sperm competition mechanisms in all four studied species. Furthermore, genitalic morphology was significantly divergent between populations within species even when different populations were using the same copulatory mechanism. These results can be explained by probable local coadaptation processes that have given rise to an ability or inability to reach and displace spermathecal sperm in different populations. This set of results provides the first direct evidence of intraspecific evolution of genitalic traits shaped by postmating sexual selection.

The origin and evolution of a differentiated Mimas

NASA Astrophysics Data System (ADS)

Neveu, M.; Rhoden, A. R.

2017-11-01

In stark contrast with its neighbor moon Enceladus, Mimas is surprisingly geologically quiet, despite an eccentric orbit and distance to Saturn prone to levels of tidal dissipation 30 times higher. While Mimas' lack of geological activity could be due to a stiff, frigid interior, libration data acquired using the Cassini spacecraft suggest that its interior is not homogeneous. Here, we present one-dimensional models of the thermal, structural, and orbital evolution of Mimas under two accretion scenarios: primordial, undifferentiated formation in the Saturnian sub-nebula, and late, layered formation from a debris ring created by the disruption of one or more previous moons. We find it difficult to reproduce a differentiated, eccentric Mimas under a primordial accretion scenario: either Mimas never differentiates, or the internal warming that leads to differentiation increases tidal dissipation, yielding runaway heating that produces a persistent ocean, thereby circularizing Mimas' orbit. Only if Mimas accretes very early (so that the decay of short-lived radionuclides initiates differentiation) but its rheology is not highly dissipative (in order to stop runaway tidal heating even if the eccentricity is not negligible) can the simulations match the observational constraints. Alternatively, a late, layered accretion scenario yields a present-day Mimas that matches observational constraints, independently of the magnitude of tidal dissipation. Consistent with previous findings, these models do not produce an ocean on Enceladus unless its orbital eccentricity is higher than today's value.

MEVTV Workshop on Early Tectonic and Volcanic Evolution of Mars

NASA Technical Reports Server (NTRS)

Frey, H. (Editor)

1988-01-01

Although not ignored, the problems of the early tectonic and volcanic evolution of Mars have generally received less attention than those later in the evolution of the planet. Specifically, much attention was devoted to the evolution of the Tharsis region of Mars and to the planet itself at the time following the establishment of this major tectonic and volcanic province. By contrast, little attention was directed at fundamental questions, such as the conditions that led to the development of Tharsis and the cause of the basic fundamental dichotomy of the Martian crust. It was to address these and related questions of the earliest evolution of Mars that a workshop was organized under the auspices of the Mars: Evolution of Volcanism, Tectonism, and Volatiles (MEVTV) Program. Four sessions were held: crustal dichotomy; crustal differentiation/volcanism; Tharsis, Elysium, and Valles Marineris; and ridges and fault tectonics.

Differential paralog divergence modulates genome evolution across yeast species

PubMed Central

Lynch, Bryony; Huang, Mei; Alcantara, Erica; DeSevo, Christopher G.; Pai, Dave A.; Hoang, Margaret L.

2017-01-01

Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200–500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution. PMID:28196070

Embryology of the lamprey and evolution of the vertebrate jaw: insights from molecular and developmental perspectives.

PubMed Central

Kuratani, S; Nobusada, Y; Horigome, N; Shigetani, Y

2001-01-01

Evolution of the vertebrate jaw has been reviewed and discussed based on the developmental pattern of the Japanese marine lamprey, Lampetra japonica. Though it never forms a jointed jaw apparatus, the L. japonica embryo exhibits the typical embryonic structure as well as the conserved regulatory gene expression patterns of vertebrates. The lamprey therefore shares the phylotype of vertebrates, the conserved embryonic pattern that appears at pharyngula stage, rather than representing an intermediate evolutionary state. Both gnathostomes and lampreys exhibit a tripartite configuration of the rostral-most crest-derived ectomesenchyme, each part occupying an anatomically equivalent site. Differentiated oral structure becomes apparent in post-pharyngula development. Due to the solid nasohypophyseal plate, the post-optic ectomesenchyme of the lamprey fails to grow rostromedially to form the medial nasal septum as in gnathostomes, but forms the upper lip instead. The gnathostome jaw may thus have arisen through a process of ontogenetic repatterning, in which a heterotopic shift of mesenchyme-epithelial relationships would have been involved. Further identification of shifts in tissue interaction and expression of regulatory genes are necessary to describe the evolution of the jaw fully from the standpoint of evolutionary developmental biology. PMID:11604127

Moran-evolution of cooperation: From well-mixed to heterogeneous complex networks

NASA Astrophysics Data System (ADS)

Sarkar, Bijan

2018-05-01

Configurational arrangement of network architecture and interaction character of individuals are two most influential factors on the mechanisms underlying the evolutionary outcome of cooperation, which is explained by the well-established framework of evolutionary game theory. In the current study, not only qualitatively but also quantitatively, we measure Moran-evolution of cooperation to support an analytical agreement based on the consequences of the replicator equation in a finite population. The validity of the measurement has been double-checked in the well-mixed network by the Langevin stochastic differential equation and the Gillespie-algorithmic version of Moran-evolution, while in a structured network, the measurement of accuracy is verified by the standard numerical simulation. Considering the Birth-Death and Death-Birth updating rules through diffusion of individuals, the investigation is carried out in the wide range of game environments those relate to the various social dilemmas where we are able to draw a new rigorous mathematical track to tackle the heterogeneity of complex networks. The set of modified criteria reveals the exact fact about the emergence and maintenance of cooperation in the structured population. We find that in general, nature promotes the environment of coexistent traits.

Modelling the evolution of a comet subsurface: implications for 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Guilbert-Lepoutre, Aurélie; Rosenberg, Eric D.; Prialnik, Dina; Besse, Sébastien

2016-11-01

Modelling the evolution of comets is a complex task aiming at providing constraints on physical processes and internal properties that are inaccessible to observations, although they could potentially bring key elements to our understanding of the origins of these primitive objects. This field has made a tremendous step forward in the post-Giotto area, owing to detailed space- and ground-based observations, as well as detailed laboratory simulations of comet nuclei. In this paper, we review studies that we believe are significant for interpreting the observations of 67P/Churyumov-Gerasimenko by the ESA/Rosetta mission, and provide new calculations where needed. These studies hold a strong statistical significance, which is exactly what is needed for this comet with an orbital evolution that cannot be traced back accurately for more than hundreds of years. We show that radial and lateral differentiation may have occurred on 67P's chaotic path to the inner Solar system, and that internal inhomogeneities may result in an erratic activity pattern. Finally, we discuss the origins of circular depressions seen on several comets including 67P, and suggest that they could be considered as evidence of the past processing of subsurface layers.

Herbivory as an important selective force in the evolution of floral traits and pollinator shifts

PubMed Central

Overson, Rick P.; Raguso, Robert A.; Skogen, Krissa A.

2017-01-01

Abstract Floral trait evolution is frequently attributed to pollinator-mediated selection but herbivores can play a key role in shaping plant reproductive biology. Here we examine the role of florivores in driving floral trait evolution and pollinator shifts in a recently radiated clade of flowering plants, Oenothera sect. Calylophus. We compare florivory by a specialist, internal feeder, Mompha, on closely related hawkmoth- and bee-pollinated species and document variation in damage based on floral traits within sites, species and among species. Our results show that flowers with longer floral tubes and decreased floral flare have increased Mompha damage. Bee-pollinated flowers, which have substantially smaller floral tubes, experience on average 13% less Mompha florivory than do hawkmoth-pollinated flowers. The positive association between tube length and Mompha damage is evident even within sites of some species, suggesting that Mompha can drive trait differentiation at microevolutionary scales. Given that there are at least two independent shifts from hawkmoth to bee pollination in this clade, florivore-mediated selection on floral traits may have played an important role in facilitating morphological changes associated with transitions from hawkmoth to bee pollination. PMID:28011456

The Discovery of XY Sex Chromosomes in a Boa and Python.

PubMed

Gamble, Tony; Castoe, Todd A; Nielsen, Stuart V; Banks, Jaison L; Card, Daren C; Schield, Drew R; Schuett, Gordon W; Booth, Warren

2017-07-24

For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1-3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7]. Here we demonstrate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromosomes, based on the discovery of male-specific genetic markers in both species. We use these markers, along with transcriptomic and genomic data, to identify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independently in each lineage. This discovery highlights the dynamic evolution of vertebrate sex chromosomes and further enhances the value of snakes as a model for studying sex chromosome evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity.

PubMed

Streelman, J T; Alfaro, M; Westneat, M W; Bellwood, D R; Karl, S A

2002-05-01

The family Scaridae comprises about 90 species of herbivorous coral reef, rock reef, and seagrass fishes. Parrotfishes are important agents of marine bioerosion who rework the substrate with their beaklike oral jaws. Many scarid populations are characterized by complex social systems including highly differentiated sexual stages, territoriality, and the defense of harems. Here, we test a hypothesis of relationships among parrotfish genera derived from nearly 2 kb of nuclear and mitochondrial DNA sequence. The DNA tree is different than a phylogeny based on comparative morphology and leads to important reinterpretations of scarid evolution. The molecular data suggest a split among seagrass and coral reef associated genera with nearly 80% of all species in the coral reef clade. Our phylogenetic results imply an East Tethyan origin of the family and the recurrent evolution of excavating and scraping feeding modes. It is likely that ecomorphological differences played a significant role in the initial divergence of major scarid lineages, but that variation in color and breeding behavior has triggered subsequent diversification. We present a two-phase model of parrotfish evolution to explain patterns of comparative diversity. Finally, we discuss the application of this model to other adaptively radiating clades.

The evolution of the moon and the terrestrial planets

NASA Technical Reports Server (NTRS)

Toksoez, M. N.; Johnston, D. H.

1977-01-01

The thermal evolutions of the Moon, Mars, Venus, and Mercury were calculated theoretically starting from cosmochemical condensation models. An assortment of geological, geochemical, and geophysical data were used to constrain both the present day temperature and the thermal histories of the planets' interiors. Such data imply that the planets were heated during or shortly after formation and that all the terrestrial planets started their differentiations early in their history.

Small-x asymptotics of the quark helicity distribution: Analytic results

DOE PAGES

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2017-06-15

In this Letter, we analytically solve the evolution equations for the small-x asymptotic behavior of the (flavor singlet) quark helicity distribution in the large- N c limit. Here, these evolution equations form a set of coupled integro-differential equations, which previously could only be solved numerically. This approximate numerical solution, however, revealed simplifying properties of the small-x asymptotics, which we exploit here to obtain an analytic solution.

Trait-based diversification shifts reflect differential extinction among fossil taxa

PubMed Central

Wagner, Peter J.; Estabrook, George F.

2014-01-01

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

Constraining cosmic scatter in the Galactic halo through a differential analysis of metal-poor stars

NASA Astrophysics Data System (ADS)

Reggiani, Henrique; Meléndez, Jorge; Kobayashi, Chiaki; Karakas, Amanda; Placco, Vinicius

2017-12-01

Context. The chemical abundances of metal-poor halo stars are important to understanding key aspects of Galactic formation and evolution. Aims: We aim to constrain Galactic chemical evolution with precise chemical abundances of metal-poor stars (-2.8 ≤ [Fe/H] ≤ -1.5). Methods: Using high resolution and high S/N UVES spectra of 23 stars and employing the differential analysis technique we estimated stellar parameters and obtained precise LTE chemical abundances. Results: We present the abundances of Li, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Zn, Sr, Y, Zr, and Ba. The differential technique allowed us to obtain an unprecedented low level of scatter in our analysis, with standard deviations as low as 0.05 dex, and mean errors as low as 0.05 dex for [X/Fe]. Conclusions: By expanding our metallicity range with precise abundances from other works, we were able to precisely constrain Galactic chemical evolution models in a wide metallicity range (-3.6 ≤ [Fe/H] ≤ -0.4). The agreements and discrepancies found are key for further improvement of both models and observations. We also show that the LTE analysis of Cr II is a much more reliable source of abundance for chromium, as Cr I has important NLTE effects. These effects can be clearly seen when we compare the observed abundances of Cr I and Cr II with GCE models. While Cr I has a clear disagreement between model and observations, Cr II is very well modeled. We confirm tight increasing trends of Co and Zn toward lower metallicities, and a tight flat evolution of Ni relative to Fe. Our results strongly suggest inhomogeneous enrichment from hypernovae. Our precise stellar parameters results in a low star-to-star scatter (0.04 dex) in the Li abundances of our sample, with a mean value about 0.4 dex lower than the prediction from standard Big Bang nucleosynthesis; we also study the relation between lithium depletion and stellar mass, but it is difficult to assess a correlation due to the limited mass range. We find two blue straggler stars, based on their very depleted Li abundances. One of them shows intriguing abundance anomalies, including a possible zinc enhancement, suggesting that zinc may have been also produced by a former AGB companion. Tables A.1-A.6 are also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/608/A46

A process model for the heat-affected zone microstructure evolution in duplex stainless steel weldments: Part I. the model

NASA Astrophysics Data System (ADS)

Hemmer, H.; Grong, Ø.

1999-11-01

The present investigation is concerned with modeling of the microstructure evolution in duplex stainless steels under thermal conditions applicable to welding. The important reactions that have been modeled are the dissolution of austenite during heating, subsequent grain growth in the delta ferrite regime, and finally, the decomposition of the delta ferrite to austenite during cooling. As a starting point, a differential formulation of the underlying diffusion problem is presented, based on the internal-state variable approach. These solutions are later manipulated and expressed in terms of the Scheil integral in the cases where the evolution equation is separable or can be made separable by a simple change of variables. The models have then been applied to describe the heat-affected zone microstructure evolution during both thick-plate and thin-plate welding of three commercial duplex stainless steel grades: 2205, 2304, and 2507. The results may conveniently be presented in the form of novel process diagrams, which display contours of constant delta ferrite grain size along with information about dissolution and reprecipitation of austenite for different combinations of weld input energy and peak temperature. These diagrams are well suited for quantitative readings and illustrate, in a condensed manner, the competition between the different variables that lead to structural changes during welding of duplex stainless steels.

The Evolution of the Brain, the Human Nature of Cortical Circuits, and Intellectual Creativity

PubMed Central

DeFelipe, Javier

2011-01-01

The tremendous expansion and the differentiation of the neocortex constitute two major events in the evolution of the mammalian brain. The increase in size and complexity of our brains opened the way to a spectacular development of cognitive and mental skills. This expansion during evolution facilitated the addition of microcircuits with a similar basic structure, which increased the complexity of the human brain and contributed to its uniqueness. However, fundamental differences even exist between distinct mammalian species. Here, we shall discuss the issue of our humanity from a neurobiological and historical perspective. PMID:21647212

Differentiation with Stratification: A Principle of Theoretical Physics in the Tradition of the Memory Art

NASA Astrophysics Data System (ADS)

Pombo, Claudia

2015-10-01

The art of memory started with Aristotle's questions on memory. During its long evolution, it had important contributions from alchemists, was transformed by Ramon Llull and apparently ended with Giordano Bruno, who was considered the best known representative of this art. This tradition did not disappear, but lives in the formulations of our modern scientific theories. From its initial form as a method of keeping information via associations, it became a principle of classification and structuring of knowledge. This principle, which we here name differentiation with stratification, is a structural design behind classical mechanics. Integrating two different traditions of science in one structure, this physical theory became the modern paradigm of science. In this paper, we show that this principle can also be formulated as a set of questions. This is done via an analysis of theories, based on the epistemology of observational realism. A combination of Rudolph Carnap's concept of theory as a system of observational and theoretical languages, with a criterion for separating observational languages, based on analytical psychology, shapes this epistemology. The `nuclear' role of the observational laws and the differentiations from these nucleus, reproducing the general cases of phenomena, reveals the memory art's heritage in the theories. Here in this paper we argue that this design is also present in special relativity and in quantum mechanics.

Size Evolution and Stochastic Models: Explaining Ostracod Size through Probabilistic Distributions

NASA Astrophysics Data System (ADS)

Krawczyk, M.; Decker, S.; Heim, N. A.; Payne, J.

2014-12-01

The biovolume of animals has functioned as an important benchmark for measuring evolution throughout geologic time. In our project, we examined the observed average body size of ostracods over time in order to understand the mechanism of size evolution in these marine organisms. The body size of ostracods has varied since the beginning of the Ordovician, where the first true ostracods appeared. We created a stochastic branching model to create possible evolutionary trees of ostracod size. Using stratigraphic ranges for ostracods compiled from over 750 genera in the Treatise on Invertebrate Paleontology, we calculated overall speciation and extinction rates for our model. At each timestep in our model, new lineages can evolve or existing lineages can become extinct. Newly evolved lineages are assigned sizes based on their parent genera. We parameterized our model to generate neutral and directional changes in ostracod size to compare with the observed data. New sizes were chosen via a normal distribution, and the neutral model selected new sizes differentials centered on zero, allowing for an equal chance of larger or smaller ostracods at each speciation. Conversely, the directional model centered the distribution on a negative value, giving a larger chance of smaller ostracods. Our data strongly suggests that the overall direction of ostracod evolution has been following a model that directionally pushes mean ostracod size down, shying away from a neutral model. Our model was able to match the magnitude of size decrease. Our models had a constant linear decrease while the actual data had a much more rapid initial rate followed by a constant size. The nuance of the observed trends ultimately suggests a more complex method of size evolution. In conclusion, probabilistic methods can provide valuable insight into possible evolutionary mechanisms determining size evolution in ostracods.

Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau.

PubMed

Ren, Guangpeng; Conti, Elena; Salamin, Nicolas

2015-08-16

The historical orogenesis and associated climatic changes of mountain areas have been suggested to partly account for the occurrence of high levels of biodiversity and endemism. However, their effects on dispersal, differentiation and evolution of many groups of plants are still unknown. In this study, we examined the detailed diversification history of Primula sect. Armerina, and used biogeographic analysis and macro-evolutionary modeling to investigate a series of different questions concerning the evolution of the geographical and ecological distribution of the species in this section. We sequenced five chloroplast and one nuclear genes for species of Primula sect. Armerina. Neither chloroplast nor nuclear trees support the monophyly of the section. The major incongruences between the two trees occur among closely related species and may be explained by hybridization. Our dating analyses based on the chloroplast dataset suggest that this section began to diverge from its relatives around 3.55 million years ago, largely coinciding with the last major uplift of the Qinghai-Tibet Plateau (QTP). Biogeographic analysis supports the origin of the section in the Himalayan Mountains and dispersal from the Himalayas to Northeastern QTP, Western QTP and Hengduan Mountains. Furthermore, evolutionary models of ecological niches show that the two P. fasciculata clades have significantly different climatic niche optima and rates of niche evolution, indicating niche evolution under climatic changes and further providing evidence for explaining their biogeographic patterns. Our results support the hypothesis that geologic and climatic events play important roles in driving biological diversification of organisms in the QTP area. The Pliocene uplift of the QTP and following climatic changes most likely promoted both the inter- and intraspecific divergence of Primula sect. Armerina. This study also illustrates how niche evolution under climatic changes influences biogeographic patterns.

Modeling the Long-term Planform Evolution of Meandering Rivers in Confined Alluvial Valleys: Etsch-Adige River, NE Italy.

NASA Astrophysics Data System (ADS)

Zen, S.; Bogoni, M.; Zolezzi, G.; Lanzoni, S.; Scorpio, V.

2016-12-01

We combine the use of a morphodynamic model for river meander planform evolution with a geological dataset to investigate the influence of external confinements on the long-term evolution of a meandering river flowing in an Alpine valley. The analysis focuses on a 100 km reach of the Adige River, NE Italy, which had several sinuous/meandering sections before being extensively channelized in the 1800s. Geological surveys and historical maps revealed that many sections of the study reach impinge on the borders of the valley during its evolution. Moreover, a marked spatial heterogeneity in floodplain vertical accretion rates likely reflects preferential positions of the river channel in the floodplain. Valley confinements are represented by bedrock outcrops and by alluvial fans created by lateral tributaries, and were extracted from the geological and historical maps to build the computational domain for the meander morphodynamic model. The model predicts the long-term planform evolution of a meandering river based on a linear solution of the 2D De St Venant-Exner differential system and can manage changes in floodplain erodibility. Model applications allow to isolate the effects of valley bedrock and of alluvial fans in constraining the lateral channel migration. Modeled river channel persistence maps are compared with the available geological information. The present work allows further insights into the role of external confinements to river meander belts, which have been conducted so far mostly assuming the channel to evolve in unconfined floodplains. Future research shall incorporate model components for floodplain vertical accretion rates and for the advancement of alluvial fans occurring at the same time scale considered for meander evolution.

Spatial evolutionary epidemiology of spreading epidemics

PubMed Central

2016-01-01

Most spatial models of host–parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. PMID:27798295

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

Geologic Evolution of North America: Geologic features suggest that the continent has grown and differentiated through geologic time.

PubMed

Engel, A E

1963-04-12

The oldest decipherable rock complexes within continents (more than 2.5 billion years old) are largely basaltic volcanics and graywacke. Recent and modern analogs are the island arcs formed along and adjacent to the unstable interface of continental and oceanic crusts. The major interfacial reactions (orogenies) incorporate pre-existing sial, oceanic crust, and mantle into crust of a more continental type. Incipient stages of continental evolution, more than 3 billion years ago, remain obscure. They may involve either a cataclysmic granite-forming event or a succession of volcanic-sedimentary and granite-forming cycles. Intermediate and recent stages of continental evolution, as indicated by data for North America, involve accretion of numerous crustal interfaces with fragments of adjacent continental crust and their partial melting, reinjection, elevation, unroofing, and stabilization. Areas of relict provinces defined by ages of granites suggest that continental growth is approximately linear. But the advanced differentiation found in many provinces and the known overlaps permit wide deviation from linearity in the direction of a more explosive early or intermediate growth.

Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snead, Lance; Contescu, Christian I.; Byun, Thak Sang

2016-08-01

The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ~400 *C up to 9.3E25 n/m2 (E > 0.1 MeV). Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free conditions. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significantmore » increase in dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3e40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.« less

Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

DOE PAGES

Snead, Lance L.; Contescu, C. I.; Byun, T. S.; ...

2016-04-23

The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ~400 C up to 9.3x10 25 n/m 2 (E>0.1 MeV.) Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free condition. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significantmore » increase in dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3-40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.« less

Floral Development of Berberidopsis corallina: a Crucial Link in the Evolution of Flowers in the Core Eudicots

PubMed Central

RONSE DE CRAENE, LOUIS P.

2004-01-01

• Background and Aims On the basis of molecular evidence Berberidopsidaceae have been linked with Aextoxicaceae in an order Berberidopsidales at the base of the core Eudicots. The floral development of Berberidopsis is central to the understanding of the evolution of floral configurations at the transition of the basal Eudicots to the core Eudicots. It lies at the transition of trimerous or dimerous, simplified apetalous forms into pentamerous, petaliferous flowers. • Methods The floral ontogeny of Berberidopsis was studied with a scanning electron microscope. • Key Results Flowers are grouped in terminal racemes with variable development. The relationship between the number of tepals, stamens and carpels is more or less fixed and floral initiation follows a strict 2/5 phyllotaxis. Two bracteoles, 12 tepals, eight stamens and three carpels are initiated in a regular sequence. The number of stamens can be increased by a doubling of stamen positions. • Conclusions The floral ontogeny of Berberidopsis provides support for the shift in floral bauplan from the basal Eudicots to the core Eudicots as a transition of a spiral flower with a 2/5 phyllotaxis to pentamerous flowers with two perianth whorls, two stamen whorls and a single carpel whorl. The differentiation of sepals and petals from bracteotepals is discussed and a comparison is made with other Eudicots with a similar configuration and development. Depending on the resolution of the relationships among the basalmost core Eudicots it is suggested that Berberidopsis either represents a critical stage in the evolution of pentamerous flowers of major clades of Eudicots, or has a floral prototype that may be at the base of evolution of flowers of other core Eudicots. The distribution of a floral Bauplan in other clades of Eudicots similar to Berberidopsidales is discussed. PMID:15451722

An evolutionary framework for cultural change: Selectionism versus communal exchange

NASA Astrophysics Data System (ADS)

Gabora, Liane

2013-06-01

Dawkins' replicator-based conception of evolution has led to widespread mis-application of selectionism across the social sciences because it does not address the paradox that necessitated the theory of natural selection in the first place: how do organisms accumulate change when traits acquired over their lifetime are obliterated? This is addressed by von Neumann's concept of a self-replicating automaton (SRA). A SRA consists of a self-assembly code that is used in two distinct ways: (1) actively deciphered during development to construct a self-similar replicant, and (2) passively copied to the replicant to ensure that it can reproduce. Information that is acquired over a lifetime is not transmitted to offspring, whereas information that is inherited during copying is transmitted. In cultural evolution there is no mechanism for discarding acquired change. Acquired change can accumulate orders of magnitude faster than, and quickly overwhelm, inherited change due to differential replication of variants in response to selection. This prohibits a selectionist but not an evolutionary framework for culture and the creative processes that fuel it. The importance non-Darwinian processes in biological evolution is increasingly recognized. Recent work on the origin of life suggests that early life evolved through a non-Darwinian process referred to as communal exchange that does not involve a self-assembly code, and that natural selection emerged from this more haphazard, ancestral evolutionary process. It is proposed that communal exchange provides an evolutionary framework for culture that enables specification of cognitive features necessary for a (real or artificial) societies to evolve culture. This is supported by a computational model of cultural evolution and a conceptual network based program for documenting material cultural history, and it is consistent with high levels of human cooperation.

The fast debris evolution model

NASA Astrophysics Data System (ADS)

Lewis, H. G.; Swinerd, G. G.; Newland, R. J.; Saunders, A.

2009-09-01

The 'particles-in-a-box' (PIB) model introduced by Talent [Talent, D.L. Analytic model for orbital debris environmental management. J. Spacecraft Rocket, 29 (4), 508-513, 1992.] removed the need for computer-intensive Monte Carlo simulation to predict the gross characteristics of an evolving debris environment. The PIB model was described using a differential equation that allows the stability of the low Earth orbit (LEO) environment to be tested by a straightforward analysis of the equation's coefficients. As part of an ongoing research effort to investigate more efficient approaches to evolutionary modelling and to develop a suite of educational tools, a new PIB model has been developed. The model, entitled Fast Debris Evolution (FADE), employs a first-order differential equation to describe the rate at which new objects ⩾10 cm are added and removed from the environment. Whilst Talent [Talent, D.L. Analytic model for orbital debris environmental management. J. Spacecraft Rocket, 29 (4), 508-513, 1992.] based the collision theory for the PIB approach on collisions between gas particles and adopted specific values for the parameters of the model from a number of references, the form and coefficients of the FADE model equations can be inferred from the outputs of future projections produced by high-fidelity models, such as the DAMAGE model. The FADE model has been implemented as a client-side, web-based service using JavaScript embedded within a HTML document. Due to the simple nature of the algorithm, FADE can deliver the results of future projections immediately in a graphical format, with complete user-control over key simulation parameters. Historical and future projections for the ⩾10 cm LEO debris environment under a variety of different scenarios are possible, including business as usual, no future launches, post-mission disposal and remediation. A selection of results is presented with comparisons with predictions made using the DAMAGE environment model. The results demonstrate that the FADE model is able to capture comparable time-series of collisions and number of objects as predicted by DAMAGE in several scenarios. Further, and perhaps more importantly, its speed and flexibility allows the user to explore and understand the evolution of the space debris environment.

Does Angling Technique Selectively Target Fishes Based on Their Behavioural Type?

PubMed Central

Wilson, Alexander D. M.; Brownscombe, Jacob W.; Sullivan, Brittany; Jain-Schlaepfer, Sofia; Cooke, Steven J.

2015-01-01

Recently, there has been growing recognition that fish harvesting practices can have important impacts on the phenotypic distributions and diversity of natural populations through a phenomenon known as fisheries-induced evolution. Here we experimentally show that two common recreational angling techniques (active crank baits versus passive soft plastics) differentially target wild largemouth bass (Micropterus salmoides) and rock bass (Ambloplites rupestris) based on variation in their behavioural tendencies. Fish were first angled in the wild using both techniques and then brought back to the laboratory and tested for individual-level differences in common estimates of personality (refuge emergence, flight-initiation-distance, latency-to-recapture and with a net, and general activity) in an in-lake experimental arena. We found that different angling techniques appear to selectively target these species based on their boldness (as characterized by refuge emergence, a standard measure of boldness in fishes) but not other assays of personality. We also observed that body size was independently a significant predictor of personality in both species, though this varied between traits and species. Our results suggest a context-dependency for vulnerability to capture relative to behaviour in these fish species. Ascertaining the selective pressures angling practices exert on natural populations is an important area of fisheries research with significant implications for ecology, evolution, and resource management. PMID:26284779

New 3D thermal evolution model for icy bodies application to trans-Neptunian objects

NASA Astrophysics Data System (ADS)

Guilbert-Lepoutre, A.; Lasue, J.; Federico, C.; Coradini, A.; Orosei, R.; Rosenberg, E. D.

2011-05-01

Context. Thermal evolution models have been developed over the years to investigate the evolution of thermal properties based on the transfer of heat fluxes or transport of gas through a porous matrix, among others. Applications of such models to trans-Neptunian objects (TNOs) and Centaurs has shown that these bodies could be strongly differentiated from the point of view of chemistry (i.e. loss of most volatile ices), as well as from physics (e.g. melting of water ice), resulting in stratified internal structures with differentiated cores and potential pristine material close to the surface. In this context, some observational results, such as the detection of crystalline water ice or volatiles, remain puzzling. Aims: In this paper, we would like to present a new fully three-dimensional thermal evolution model. With this model, we aim to improve determination of the temperature distribution inside icy bodies such as TNOs by accounting for lateral heat fluxes, which have been proven to be important for accurate simulations. We also would like to be able to account for heterogeneous boundary conditions at the surface through various albedo properties, for example, that might induce different local temperature distributions. Methods: In a departure from published modeling approaches, the heat diffusion problem and its boundary conditions are represented in terms of real spherical harmonics, increasing the numerical efficiency by roughly an order of magnitude. We then compare this new model and another 3D model recently published to illustrate the advantages and limits of the new model. We try to put some constraints on the presence of crystalline water ice at the surface of TNOs. Results: The results obtained with this new model are in excellent agreement with results obtained by different groups with various models. Small TNOs could remain primitive unless they are formed quickly (less than 2 Myr) or are debris from the disruption of larger bodies. We find that, for large objects with a thermal evolution dominated by the decay of long-lived isotopes (objects with a formation period greater than 2 to 3 Myr), the presence of crystalline water ice would require both a large radius (>300 km) and high density (>1500 kg m-3). In particular, objects with intermediate radii and densities would be an interesting transitory population deserving a detailed study of individual fates.

Early evolution of the earth - Accretion, atmosphere formation, and thermal history

NASA Technical Reports Server (NTRS)

Abe, Yutaka; Matsui, Takafumi

1986-01-01

The thermal and atmospheric evolution of the earth growing planetesimal impacts are studied. The generation of an H2O protoatmosphere is examined, and the surface temperatures are estimated. The evolution of an impact-induced H2O atmosphere is analyzed. Consideration is given to the formation time of a 'magma ocean'and internal water budgets. The thermal history of an accreting earth is reviewed. The wet convection and greenhouse effects are discussed, and the role of Fe oxidation on the evolution of an impact-induced H2O atmopshere is described. The relationship between differentiation processes and core segregation, the H2O and FeO content of the mantle, and the origin of the hydrosphere is also examined.

The Fossilized Size Distribution of the Main Asteroid Belt

NASA Astrophysics Data System (ADS)

Bottke, W. F.; Durda, D.; Nesvorny, D.; Jedicke, R.; Morbidelli, A.

2003-05-01

At present, we do not understand how the main asteroid belt evolved into its current state. During the planet formation epoch, the primordial main belt (PMB) contained several Earth masses of material, enough to allow the asteroids to accrete on relatively short timescales (e.g., Weidenschilling 1977). The present-day main belt, however, only contains 5e-4 Earth masses of material (Petit et al. 2002). Constraints on this evolution come from (i) the observed fragments of differentiated asteroids, (ii) meteorites collected from numerous differentiated parent bodies, (iii) the presence of ˜ 10 prominent asteroid families, (iv) the "wavy" size-frequency distribution of the main belt, which has been shown to be a by-product of substantial collisional evolution (e.g., Durda et al. 1997), and (v) the still-intact crust of (4) Vesta. To explain the contradictions in the above constraints, we suggest the PMB evolved in this fashion: Planetesimals and planetary embryos accreted (and differentiated) in the PMB during the first few Myr of the solar system. Gravitational perturbations from these embryos dynamically stirred the main belt, enough to initiate fragmentation. When Jupiter reached its full size, some 10 Myr after the solar system's birth, its perturbations, together with those of the embryos, dynamically depleted the main belt region of ˜ 99% of its bodies. Much of this material was sent to high (e,i) orbits, where it continued to pummel the surviving main belt bodies at high impact velocities for more than 100 Myr. While some differentiated bodies in the PMB were disrupted, most were instead scattered; only small fragments from this population remain. This period of comminution and dynamical evolution in the PMB created, among other things, the main belt's wavy size distribution, such that it can be considered a "fossil" from this violent early epoch. From this time forward, however, relatively little collisional evolution has taken place in the main belt, consistent with the surprising paucity of prominent asteroid families. Preliminary modeling results of this scenario and implications will be presented.

Effect of the stellar spin history on the tidal evolution of close-in planets

NASA Astrophysics Data System (ADS)

Bolmont, E.; Raymond, S. N.; Leconte, J.; Matt, S. P.

2012-08-01

Context. The spin rate of stars evolves substantially during their lifetime, owing to the evolution of their internal structure and to external torques arising from the interaction of stars with their environments and stellar winds. Aims: We investigate how the evolution of the stellar spin rate affects, and is affected by, planets in close orbits via star-planet tidal interactions. Methods: We used a standard equilibrium tidal model to compute the orbital evolution of single planets orbiting both Sun-like stars and very low-mass stars (0.1 M⊙). We tested two stellar spin evolution profiles, one with fast initial rotation (1.2 day rotation period) and one with slow initial rotation (8 day period). We tested the effect of varying the stellar and planetary dissipations, and the planet's mass and initial orbital radius. Results: For Sun-like stars, the different tidal evolution between initially rapidly and slowly rotating stars is only evident for extremely close-in gas giants orbiting highly dissipative stars. However, for very low-mass stars the effect of the initial rotation of the star on the planet's evolution is apparent for less massive (1 M⊕) planets and typical dissipation values. We also find that planetary evolution can have significant effects on the stellar spin history. In particular, when a planet falls onto the star, it can cause the star to spin up. Conclusions: Tidal evolution allows us to differentiate between the early behaviors of extremely close-in planets orbiting either a rapidly rotating star or a slowly rotating star. The early spin-up of the star allows the close-in planets around fast rotators to survive the early evolution. For planets around M-dwarfs, surviving the early evolution means surviving on Gyr timescales, whereas for Sun-like stars the spin-down brings about late mergers of Jupiter planets. In the light of this study, we can say that differentiating one type of spin evolution from another given the present position of planets can be very tricky. Unless we can observe some markers of former evolution, it is nearly impossible to distinguish the two very different spin profiles, let alone intermediate spin-profiles. Nevertheless, some conclusions can still be drawn about statistical distributions of planets around fully convective M-dwarfs. If tidal evolution brings about a merger late in the stellar history, it can also entail a noticeable acceleration of the star at late ages, so that it is possible to have old stars that spin rapidly. This raises the question of how the age of stars can be more tightly constrained.

[Focal lymphoid hyperplasia (pseudolymphoma) of the terminal ileum in adults].

PubMed

Molas, G; Potet, F; Nogig, P

1985-01-01

We report two cases of focal lymphoid hyperplasia (FLH) of terminal ileum in adult patients. Both cases showed identical morphological findings. The first was discovered during cholecystectomy in a 75-year-old woman who complained mild non-specific abdominal discomfort. The second was manifested by right lower quadrant abdominal pain in a 32-year-old man. The surgical specimens revealed a thickened wall, a narrowed lumen and multiple ulcerations. The histologic features were small cell, well differentiated lymphocyte infiltration, with several follicles showing large germinal centers; regional lymph nodes revealed a conspicuous reactive size enlargement. Further clinical investigations revealed no other abnormalities. Clinical course showed benign evolution after 6 and 3 years of respective follow-up. FLH should be differentiated from terminal ileum inflammatory and infectious diseases. It can be differentiated from Crohn's disease by the absence of characteristic histological features; from Yersinia infection by the absence of significant rates of specific serum antibodies. Moreover, FLH can be differentiated from malignant lymphoma by the presence of follicles and enlarged germinal centers and by the long-term benign evolution. The nature of FLH in terminal ileum, as well as those of the stomach and colo-rectum is still to be determined. Several hypothesis are proposed: reactive, benign neoplastic, or prelymphomatous lesion?

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.

PubMed

Samis, Karen E; Murren, Courtney J; Bossdorf, Oliver; Donohue, Kathleen; Fenster, Charles B; Malmberg, Russell L; Purugganan, Michael D; Stinchcombe, John R

2012-06-01

Introduced species frequently show geographic differentiation, and when differentiation mirrors the ancestral range, it is often taken as evidence of adaptive evolution. The mouse-ear cress (Arabidopsis thaliana) was introduced to North America from Eurasia 150-200 years ago, providing an opportunity to study parallel adaptation in a genetic model organism. Here, we test for clinal variation in flowering time using 199 North American (NA) accessions of A. thaliana, and evaluate the contributions of major flowering time genes FRI, FLC, and PHYC as well as potential ecological mechanisms underlying differentiation. We find evidence for substantial within population genetic variation in quantitative traits and flowering time, and putatively adaptive longitudinal differentiation, despite low levels of variation at FRI, FLC, and PHYC and genome-wide reductions in population structure relative to Eurasian (EA) samples. The observed longitudinal cline in flowering time in North America is parallel to an EA cline, robust to the effects of population structure, and associated with geographic variation in winter precipitation and temperature. We detected major effects of FRI on quantitative traits associated with reproductive fitness, although the haplotype associated with higher fitness remains rare in North America. Collectively, our results suggest the evolution of parallel flowering time clines through novel genetic mechanisms.

Differential Expression of Non-Coding RNAs and Continuous Evolution of the X Chromosome in Testicular Transcriptome of Two Mouse Species

PubMed Central

Homolka, David; Ivanek, Robert; Forejt, Jiri; Jansa, Petr

2011-01-01

Background Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. Methodology/Principal Findings Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. Conclusions/Significance The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition. PMID:21347268

New "missing link" genus of the colonial volvocine green algae gives insights into the evolution of oogamy.

PubMed

Nozaki, Hisayoshi; Yamada, Toshihiro K; Takahashi, Fumio; Matsuzaki, Ryo; Nakada, Takashi

2014-03-03

The evolution of oogamy from isogamy, an important biological event, can be summarized as follows: morphologically similar gametes (isogametes) differentiated into small "male" and large "female" motile gametes during anisogamy, from which immotile female gametes (eggs) evolved. The volvocine green algae represent a model lineage to study this type of sex evolution and show two types of gametic unions: conjugation between isogametes outside the parental colonies (external fertilization during isogamy) and fertilization between small motile gametes (sperm) and large gametes (eggs) inside the female colony (internal fertilization during anisogamy and oogamy). Although recent cultural studies on volvocine algae revealed morphological diversity and molecular genetic data of sexual reproduction, an intermediate type of union between these two gametic unions has not been identified. We identified a novel colonial volvocine genus, Colemanosphaera, which produces bundles of spindle-shaped male gametes through successive divisions of colonial cells. Obligately anisogamous conjugation between male and female motile gametes occurred outside the female colony (external fertilization during anisogamy). This new genus contains 16- or 32-celled spheroidal colonies similar to those of the volvocine genera Yamagishiella and Eudorina. However, Colemanosphaera can be clearly distinguished from these two genera based on its sister phylogenetic position to the enigmatic flattened colonial volvocine Platydorina and external fertilization during anisogamy. Two species of Colemanosphaera were found in a Japanese lake; these species are also distributed in European freshwaters based on a published sequence of an Austrian strain and the original description of Pandorina charkowiensis from Ukraine. Based on phylogeny and morphological data, this novel genus exhibits a missing link between Platydorina and the typical spheroidal colonial volvocine members such as Pandorina or Yamagishiella. Considering the external obligate anisogamy, oogamy evolution may have been preceded by the transition from external to internal fertilization during anisogamy within the volvocine green algae.

PHONATION TAKES PRECEDENCE IN DEVELOPMENT AS WELL AS EVOLUTION OF LANGUAGE

PubMed Central

Oller, D. Kimbrough

2014-01-01

Early development of vocalization in humans is characterized by emerging control of phonation, rather than of prosody or supraglottal articulation. This fact offers an opportunity to the authors of the target article to enrich their characterization of the evolution of differential brain mechanisms in human and non-human primates. Phonation, I suggest, is the initial target of human-specific brain changes in sound-making capability upon which language is founded. PMID:25514957

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

PubMed Central

Peng, Duo; Gu, Xi; Xue, Liang-Jiao; Leebens-Mack, James H.; Tsai, Chung-Jui

2014-01-01

Sucrose transporters (SUTs) are essential for the export and efficient movement of sucrose from source leaves to sink organs in plants. The angiosperm SUT family was previously classified into three or four distinct groups, Types I, II (subgroup IIB), and III, with dicot-specific Type I and monocot-specific Type IIB functioning in phloem loading. To shed light on the underlying drivers of SUT evolution, Bayesian phylogenetic inference was undertaken using 41 sequenced plant genomes, including seven basal lineages at key evolutionary junctures. Our analysis supports four phylogenetically and structurally distinct SUT subfamilies, originating from two ancient groups (AG1 and AG2) that diverged early during terrestrial colonization. In both AG1 and AG2, multiple intron acquisition events in the progenitor vascular plant established the gene structures of modern SUTs. Tonoplastic Type III and plasmalemmal Type II represent evolutionarily conserved descendants of AG1 and AG2, respectively. Type I and Type IIB were previously thought to evolve after the dicot-monocot split. We show, however, that divergence of Type I from Type III SUT predated basal angiosperms, likely associated with evolution of vascular cambium and phloem transport. Type I SUT was subsequently lost in monocots along with vascular cambium, and independent evolution of Type IIB coincided with modified monocot vasculature. Both Type I and Type IIB underwent lineage-specific expansion. In multiple unrelated taxa, the newly-derived SUTs exhibit biased expression in reproductive tissues, suggesting a functional link between phloem loading and reproductive fitness. Convergent evolution of Type I and Type IIB for SUT function in phloem loading and reproductive organs supports the idea that differential vascular development in dicots and monocots is a strong driver for SUT family evolution in angiosperms. PMID:25429293

Diversifying mechanisms in the on-farm evolution of crop mixtures.

PubMed

Thomas, Mathieu; Thépot, Stéphanie; Galic, Nathalie; Jouanne-Pin, Sophie; Remoué, Carine; Goldringer, Isabelle

2015-06-01

While modern agriculture relies on genetic homogeneity, diversifying practices associated with seed exchange and seed recycling may allow crops to adapt to their environment. This socio-genetic model is an original experimental evolution design referred to as on-farm dynamic management of crop diversity. Investigating such model can help in understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro-environments. We studied a French farmer-led initiative where a mixture of four wheat landraces called 'Mélange de Touselles' (MDT) was created and circulated within a farmers' network. The 15 sampled MDT subpopulations were simultaneously submitted to diverse environments (e.g. altitude, rainfall) and diverse farmers' practices (e.g. field size, sowing and harvesting date). Twenty-one space-time samples of 80 individuals each were genotyped using 17 microsatellite markers and characterized for their heading date in a 'common-garden' experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network-based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. Rapid differentiation among populations within the mixture was detected, larger at the phenotypic and gene levels than at the neutral genetic level, indicating potential divergent selection. We identified two interacting selection processes: variation in the mixture component frequencies, and evolution of within-variety diversity, that shaped the standing variability available within the mixture. These results confirmed that diversifying practices and environments maintain genetic diversity and allow for crop evolution in the context of global change. Including concrete measurements of farmers' practices is critical to disentangle crop evolution processes. © 2015 John Wiley & Sons Ltd.

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

PubMed

Zhu, Yuan O; Aw, Pauline P K; de Sessions, Paola Florez; Hong, Shuzhen; See, Lee Xian; Hong, Lewis Z; Wilm, Andreas; Li, Chen Hao; Hue, Stephane; Lim, Seng Gee; Nagarajan, Niranjan; Burkholder, William F; Hibberd, Martin

2017-10-27

Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.

Detecting consistent patterns of directional adaptation using differential selection codon models.

PubMed

Parto, Sahar; Lartillot, Nicolas

2017-06-23

Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles. Our differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

Integrative taxonomy reveals cryptic diversity in neotropical grasshoppers: taxonomy, phylogenetics, and evolution of the genus Sphenarium Charpentier, 1842 (Orthoptera: Pyrgomorphidae).

PubMed

Sanabria-Urbán, Salomón; Song, Hojun; Oyama, Ken; González-Rodríguez, Antonio; Castillo, Raúl Cueva Del

2017-06-08

The genus Sphenarium Charpentier, 1842 comprises the most diverse group of the New World Pyrgomorphidae. These grasshoppers show an extensive variation in external morphology, and are culturally and economically important for Mexican people since pre-Hispanic times. Nevertheless, the taxonomy of Sphenarium has been chaotic and remained incompletely resolved until now. Following an integrative taxonomic framework, we infer the number of species in this genus by species delimitation based on morphological, phylogenetic, and geographic information. Based on our results, we revise the genus and redefine 9 species and describe 8 new species (S. adelinae sp.n., S. crypticum sp.n., S. infernalis sp.n., S. miztecum sp.n., S. occidentalis sp.n., S. tarascum sp.n., S. totonacum sp.n. and S. zapotecum sp.n.). Moreover, we update the knowledge of the evolutionary relationships and biogeographic patterns of Sphenarium species. Our results also demonstrate the importance of historic geological and climatic events on the lineage diversification of this genus. Different levels of morphological and genetic differentiation among species suggest a complex interplay between evolutionary forces during the evolution of these neotropical grasshoppers.

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

PubMed

Bergman, C M; Kreitman, M

2001-08-01

Comparative genomic approaches to gene and cis-regulatory prediction are based on the principle that differential DNA sequence conservation reflects variation in functional constraint. Using this principle, we analyze noncoding sequence conservation in Drosophila for 40 loci with known or suspected cis-regulatory function encompassing >100 kb of DNA. We estimate the fraction of noncoding DNA conserved in both intergenic and intronic regions and describe the length distribution of ungapped conserved noncoding blocks. On average, 22%-26% of noncoding sequences surveyed are conserved in Drosophila, with median block length approximately 19 bp. We show that point substitution in conserved noncoding blocks exhibits transition bias as well as lineage effects in base composition, and occurs more than an order of magnitude more frequently than insertion/deletion (indel) substitution. Overall, patterns of noncoding DNA structure and evolution differ remarkably little between intergenic and intronic conserved blocks, suggesting that the effects of transcription per se contribute minimally to the constraints operating on these sequences. The results of this study have implications for the development of alignment and prediction algorithms specific to noncoding DNA, as well as for models of cis-regulatory DNA sequence evolution.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

The Microstructural Evolution and Mechanical Properties of Zr-Based Metallic Glass under Different Strain Rate Compressions

PubMed Central

Chen, Tao-Hsing; Tsai, Chih-Kai

2015-01-01

In this study, the high strain rate deformation behavior and the microstructure evolution of Zr-Cu-Al-Ni metallic glasses under various strain rates were investigated. The influence of strain and strain rate on the mechanical properties and fracture behavior, as well as microstructural properties was also investigated. Before mechanical testing, the structure and thermal stability of the Zr-Cu-Al-Ni metallic glasses were studied with X-ray diffraction (XRD) and differential scanning calorimeter. The mechanical property experiments and microstructural observations of Zr-Cu-Al-Ni metallic glasses under different strain rates ranging from 10−3 to 5.1 × 103 s−1 and at temperatures of 25 °C were investigated using compressive split-Hopkinson bar (SHPB) and an MTS tester. An in situ transmission electron microscope (TEM) nanoindenter was used to carry out compression tests and investigate the deformation behavior arising at nanopillars of the Zr-based metallic glass. The formation and interaction of shear band during the plastic deformation were investigated. Moreover, it was clearly apparent that the mechanical strength and ductility could be enhanced by impeding the penetration of shear bands with reinforced particles. PMID:28788034

A Quasiphysics Intelligent Model for a Long Range Fast Tool Servo

PubMed Central

Liu, Qiang; Zhou, Xiaoqin; Lin, Jieqiong; Xu, Pengzi; Zhu, Zhiwei

2013-01-01

Accurately modeling the dynamic behaviors of fast tool servo (FTS) is one of the key issues in the ultraprecision positioning of the cutting tool. Herein, a quasiphysics intelligent model (QPIM) integrating a linear physics model (LPM) and a radial basis function (RBF) based neural model (NM) is developed to accurately describe the dynamic behaviors of a voice coil motor (VCM) actuated long range fast tool servo (LFTS). To identify the parameters of the LPM, a novel Opposition-based Self-adaptive Replacement Differential Evolution (OSaRDE) algorithm is proposed which has been proved to have a faster convergence mechanism without compromising with the quality of solution and outperform than similar evolution algorithms taken for consideration. The modeling errors of the LPM and the QPIM are investigated by experiments. The modeling error of the LPM presents an obvious trend component which is about ±1.15% of the full span range verifying the efficiency of the proposed OSaRDE algorithm for system identification. As for the QPIM, the trend component in the residual error of LPM can be well suppressed, and the error of the QPIM maintains noise level. All the results verify the efficiency and superiority of the proposed modeling and identification approaches. PMID:24163627

Has snake fang evolution lost its bite? New insights from a structural mechanics viewpoint.

PubMed

Broeckhoven, Chris; du Plessis, Anton

2017-08-01

Venomous snakes-the pinnacle of snake evolution-are characterized by their possession of venom-conducting fangs ranging from grooved phenotypes characterizing multiple lineages of rear-fanged taxa to tubular phenotypes present in elapids, viperids and atractaspidines. Despite extensive research, controversy still exists on the selective pressures involved in fang phenotype diversification. Here, we test the hypothesis that larger fangs and consequently a shift to an anterior position in the maxilla evolved to compensate for the costs of structural changes, i.e. higher stress upon impact in tubular fangs compared to grooved fangs. Direct voxel-based stress simulations conducted on high-resolution µCT scans, analysed within a phylogenetic framework, showed no differences in stress distribution between the three fang phenotypes, despite differences in (relative) fang length. These findings suggest that additional compensatory mechanisms are responsible for the biomechanical optimization and that fang length might instead be related to differential striking behaviour strategies. © 2017 The Author(s).

Nonlinear Evolution of Azimuthally Compact Crossflow-Vortex Packet over a Yawed Cone

NASA Astrophysics Data System (ADS)

Choudhari, Meelan; Li, Fei; Paredes, Pedro; Duan, Lian; NASA Langley Research Center Team; Missouri Univ of Sci; Tech Team

2017-11-01

Hypersonic boundary-layer flows over a circular cone at moderate incidence angle can support strong crossflow instability and, therefore, a likely scenario for laminar-turbulent transition in such flows corresponds to rapid amplification of high-frequency secondary instabilities sustained by finite amplitude stationary crossflow vortices. Direct numerical simulations (DNS) are used to investigate the nonlinear evolution of azimuthally compact crossflow vortex packets over a 7-degree half-angle, yawed circular cone in a Mach 6 free stream. Simulation results indicate that the azimuthal distribution of forcing has a strong influence on the stationary crossflow amplitudes; however, the vortex trajectories are nearly the same for both periodic and localized roughness height distributions. The frequency range, mode shapes, and amplification characteristics of strongly amplified secondary instabilities in the DNS are found to overlap with the predictions of secondary instability theory. The DNS computations also provide valuable insights toward the application of planar, partial-differential-equation based eigenvalue analysis to spanwise inhomogeneous, fully three-dimensional, crossflow-dominated flow configurations.

Turbulence closure for mixing length theories

NASA Astrophysics Data System (ADS)

Jermyn, Adam S.; Lesaffre, Pierre; Tout, Christopher A.; Chitre, Shashikumar M.

2018-05-01

We present an approach to turbulence closure based on mixing length theory with three-dimensional fluctuations against a two-dimensional background. This model is intended to be rapidly computable for implementation in stellar evolution software and to capture a wide range of relevant phenomena with just a single free parameter, namely the mixing length. We incorporate magnetic, rotational, baroclinic, and buoyancy effects exactly within the formalism of linear growth theories with non-linear decay. We treat differential rotation effects perturbatively in the corotating frame using a novel controlled approximation, which matches the time evolution of the reference frame to arbitrary order. We then implement this model in an efficient open source code and discuss the resulting turbulent stresses and transport coefficients. We demonstrate that this model exhibits convective, baroclinic, and shear instabilities as well as the magnetorotational instability. It also exhibits non-linear saturation behaviour, and we use this to extract the asymptotic scaling of various transport coefficients in physically interesting limits.

Investigation of phase evolution of CaCu3Ti4O12 (CCTO) by in situ synchrotron high-temperature powder diffraction

NASA Astrophysics Data System (ADS)

Ouyang, Xin; Huang, Saifang; Zhang, Weijun; Cao, Peng; Huang, Zhaohui; Gao, Wei

2014-03-01

In situ synchrotron X-ray powder diffraction was used to study the high-temperature phase evolution of CaCu3Ti4O12 (CCTO) precursors prepared via solid-state and sol-gel methods. After the precursors are heated to 1225 °C, the CCTO phase is the main phase observed in the calcined powder, with the presence of some minor impurities. Comparing the two precursors, we found that the onset temperature for the CCTO phase formation is 800 °C in the sol-gel precursor, lower than that in the solid-state precursor (875 °C). Intermediate phases were only observed in the sol-gel precursor. Both precursors are able to be calcined to sub-micrometric sized powders. Based on the synchrotron data along with differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA), the phase formation sequence and mechanism during calcination are proposed in this study.

The evolution of floral biology in basal angiosperms

PubMed Central

Endress, Peter K.

2010-01-01

In basal angiosperms (including ANITA grade, magnoliids, Choranthaceae, Ceratophyllaceae) almost all bisexual flowers are dichogamous (with male and female functions more or less separated in time), and nearly 100 per cent of those are protogynous (with female function before male function). Movements of floral parts and differential early abscission of stamens in the male phase are variously associated with protogyny. Evolution of synchronous dichogamy based on the day/night rhythm and anthesis lasting 2 days is common. In a few clades in Magnoliales and Laurales heterodichogamy has also evolved. Beetles, flies and thrips are the major pollinators, with various degrees of specialization up to large beetles and special flies in some large-flowered Nymphaeaceae, Magnoliaceae, Annonaceae and Aristolochiaceae. Unusual structural specializations are involved in floral biological adaptations (calyptras, inner staminodes, synandria and food bodies, and secretory structures on tepals, stamens and staminodes). Numerous specializations that are common in monocots and eudicots are absent in basal angiosperms. Several families are poorly known in their floral biology. PMID:20047868

A Model Parameter Extraction Method for Dielectric Barrier Discharge Ozone Chamber using Differential Evolution

NASA Astrophysics Data System (ADS)

Amjad, M.; Salam, Z.; Ishaque, K.

2014-04-01

In order to design an efficient resonant power supply for ozone gas generator, it is necessary to accurately determine the parameters of the ozone chamber. In the conventional method, the information from Lissajous plot is used to estimate the values of these parameters. However, the experimental setup for this purpose can only predict the parameters at one operating frequency and there is no guarantee that it results in the highest ozone gas yield. This paper proposes a new approach to determine the parameters using a search and optimization technique known as Differential Evolution (DE). The desired objective function of DE is set at the resonance condition and the chamber parameter values can be searched regardless of experimental constraints. The chamber parameters obtained from the DE technique are validated by experiment.

Optimal feature selection using a modified differential evolution algorithm and its effectiveness for prediction of heart disease.

PubMed

Vivekanandan, T; Sriman Narayana Iyengar, N Ch

2017-11-01

Enormous data growth in multiple domains has posed a great challenge for data processing and analysis techniques. In particular, the traditional record maintenance strategy has been replaced in the healthcare system. It is vital to develop a model that is able to handle the huge amount of e-healthcare data efficiently. In this paper, the challenging tasks of selecting critical features from the enormous set of available features and diagnosing heart disease are carried out. Feature selection is one of the most widely used pre-processing steps in classification problems. A modified differential evolution (DE) algorithm is used to perform feature selection for cardiovascular disease and optimization of selected features. Of the 10 available strategies for the traditional DE algorithm, the seventh strategy, which is represented by DE/rand/2/exp, is considered for comparative study. The performance analysis of the developed modified DE strategy is given in this paper. With the selected critical features, prediction of heart disease is carried out using fuzzy AHP and a feed-forward neural network. Various performance measures of integrating the modified differential evolution algorithm with fuzzy AHP and a feed-forward neural network in the prediction of heart disease are evaluated in this paper. The accuracy of the proposed hybrid model is 83%, which is higher than that of some other existing models. In addition, the prediction time of the proposed hybrid model is also evaluated and has shown promising results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species.

PubMed

Tschirren, Barbara; Andersson, Martin; Scherman, Kristin; Westerdahl, Helena; Råberg, Lars

2012-03-01

Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defense may be evolutionarily more dynamic than has previously been appreciated. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Leading-Color Fully Differential Two-Loop Soft Corrections to QCD Dipole Showers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dulat, Falko; Höche, Stefan; Prestel, Stefan

We compute the next-to-leading order corrections to soft-gluon radiation differentially in the one-emission phase space. We show that their contribution to the evolution of color dipoles can be obtained in a modified subtraction scheme, such that both one- and two-emission terms are amenable to Monte-Carlo integration. The two-loop cusp anomalous dimension is recovered naturally upon integration over the full phase space. We present two independent implementations of the new algorithm in the two event generators Pythia and Sherpa, and we compare the resulting fully differential simulation to the CMW scheme.

Simulation of Stochastic Processes by Coupled ODE-PDE

NASA Technical Reports Server (NTRS)

Zak, Michail

2008-01-01

A document discusses the emergence of randomness in solutions of coupled, fully deterministic ODE-PDE (ordinary differential equations-partial differential equations) due to failure of the Lipschitz condition as a new phenomenon. It is possible to exploit the special properties of ordinary differential equations (represented by an arbitrarily chosen, dynamical system) coupled with the corresponding Liouville equations (used to describe the evolution of initial uncertainties in terms of joint probability distribution) in order to simulate stochastic processes with the proscribed probability distributions. The important advantage of the proposed approach is that the simulation does not require a random-number generator.

Osteograft, plastic material for regenerative medicine

NASA Astrophysics Data System (ADS)

Zaidman, A. M.; Korel, A. V.; Shevchenko, A. I.; Shchelkunova, E. I.; Sherman, K. M.; Predein, Yu. A.; Kosareva, O. S.

2016-08-01

Creating tissue-engineering constructs based on the mechanism of cartilage-bone evolution is promising for traumatology and orthopedics. Such a graft was obtained from a chondrograft by transdifferentiation. The hondrograft placed in osteogenic medium is undergoing osteogenic differentiation for 14-30 days. Tissue specificity of the osteograft was studied by morphology, immunohistochemistry, electron microscopy, and the expression of the corresponding genes was estimated. The expression of osteonectin, fibronectin, collagen of type I, izolektin and CD 44 is determined. Alkaline phosphatase and matrix vesicles are determined in osteoblasts. Calcificates are observed in the matrix. Chondrogenic proteins expression is absent. These findings evidence the tissue specificity of the developed osteograft.

Mean Field Games for Stochastic Growth with Relative Utility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Minyi, E-mail: mhuang@math.carleton.ca; Nguyen, Son Luu, E-mail: sonluu.nguyen@upr.edu

This paper considers continuous time stochastic growth-consumption optimization in a mean field game setting. The individual capital stock evolution is determined by a Cobb–Douglas production function, consumption and stochastic depreciation. The individual utility functional combines an own utility and a relative utility with respect to the population. The use of the relative utility reflects human psychology, leading to a natural pattern of mean field interaction. The fixed point equation of the mean field game is derived with the aid of some ordinary differential equations. Due to the relative utility interaction, our performance analysis depends on some ratio based approximation errormore » estimate.« less

Effects of stochastic noise on dynamical decoupling procedures

NASA Astrophysics Data System (ADS)

Bernád, J. Z.; Frydrych, H.

2014-06-01

Dynamical decoupling is an important tool to counter decoherence and dissipation effects in quantum systems originating from environmental interactions. It has been used successfully in many experiments; however, there is still a gap between fidelity improvements achieved in practice compared to theoretical predictions. We propose a model for imperfect dynamical decoupling based on a stochastic Ito differential equation which could explain the observed gap. We discuss the impact of our model on the time evolution of various quantum systems in finite- and infinite-dimensional Hilbert spaces. Analytical results are given for the limit of continuous control, whereas we present numerical simulations and upper bounds for the case of finite control.

Matrix description of the complete topology of three-dimensional cells

PubMed Central

Xue, Weihua; Wang, Hao; Liu, Guoquan; Meng, Li; Xiang, Song; Ma, Guang; Li, Wenwen

2016-01-01

A new, efficient method based on a series of matrices is introduced to completely describe the detailed topology of individual domains and their topology evolution in three-dimensional cellular structures. With this approach, we found a lot of new topological grain forms which are never reported before, i.e., there are total 8 and 32 topological forms for 7- and 8-faced grains respectively, other than the reported 7 and 27. This method is proved to be a practical tool to predict all possible grain forms efficiently. Moreover, a connectivity index of grain forms serves as a new convenient differentiator of different multicellular structures. PMID:27160500

Secular changes of LOD associated with a growth of the inner core

NASA Astrophysics Data System (ADS)

Denis, C.; Rybicki, K. R.; Varga, P.

2006-05-01

From recent estimates of the age of the inner core based on the theory of thermal evolution of the core, we estimate that nowadays the growth of the inner core may perhaps contribute to the observed overall secular increase of LOD caused mainly by tidal friction (i.e., 1.72 ms per century) by a relative decrease of 2 to 7 μs per century. Another, albeit much less plausible, hypothesis is that crystallization of the inner core does not produce any change of LOD, but makes the inner core rotate differentially with respect to the outer core and mantle.

Western classical music development: a statistical analysis of composers similarity, differentiation and evolution.

PubMed

Georges, Patrick

2017-01-01

This paper proposes a statistical analysis that captures similarities and differences between classical music composers with the eventual aim to understand why particular composers 'sound' different even if their 'lineages' (influences network) are similar or why they 'sound' alike if their 'lineages' are different. In order to do this we use statistical methods and measures of association or similarity (based on presence/absence of traits such as specific 'ecological' characteristics and personal musical influences) that have been developed in biosystematics, scientometrics, and bibliographic coupling. This paper also represents a first step towards a more ambitious goal of developing an evolutionary model of Western classical music.

Thermal evolution of a differentiated Ganymede and implications for surface features

NASA Technical Reports Server (NTRS)

Kirk, R. L.; Stevenson, D. J.

1987-01-01

Thermodynamic models are developed for the processes which controlled the evolution of the surface Ganymede, an icy Jovian satellite assumed to have a rock-rich core surrounded by a water-ice mantle. Account is taken of a heat pulse which would have arisen from a Rayleigh-Taylor instability at a deep-seated liquid-solid water interface, rapid fracturing from global stresses imposed by warm ice diapiric upwelling, impacts by large meteorites, and resurfacing by ice flows (rather than core formation). Comparisons are made with existing models for the evolution of Callisto, and the difficulties in defining a mechanism which produced the groove terrain of Ganymede are discussed.

Nonmathematical models for evolution of altruism, and for group selection (peck order-territoriality-ant colony-dual-determinant model-tri-determinant model).

PubMed

Darlington, P J

1972-02-01

Mathematical biologists have failed to produce a satisfactory general model for evolution of altruism, i.e., of behaviors by which "altruists" benefit other individuals but not themselves; kin selection does not seem to be a sufficient explanation of nonreciprocal altruism. Nonmathematical (but mathematically acceptable) models are now proposed for evolution of negative altruism in dual-determinant and of positive altruism in tri-determinant systems. Peck orders, territorial systems, and an ant society are analyzed as examples. In all models, evolution is primarily by individual selection, probably supplemented by group selection. Group selection is differential extinction of populations. It can act only on populations preformed by selection at the individual level, but can either cancel individual selective trends (effecting evolutionary homeostasis) or supplement them; its supplementary effect is probably increasingly important in the evolution of increasingly organized populations.

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest.

PubMed

Bracewell, Ryan R; Bentz, Barbara J; Sullivan, Brian T; Good, Jeffrey M

2017-11-17

Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations. This striking progression of reproductive isolation is coupled with extensive gene specialization, natural selection, and elevated genetic differentiation on both sex chromosomes. Closely related populations isolated by hybrid male sterility also show fixation of alternative neo-Y haplotypes that differ in structure and male-specific gene content. Our results suggest that neo-sex chromosome evolution can drive rapid functional divergence between closely related populations irrespective of ecological drivers of divergence.

The relationship between crustal tectonics and internal evolution in the moon and Mercury

NASA Technical Reports Server (NTRS)

Solomon, S. C.

1977-01-01

The relationship between crustal tectonics and thermal evolution is discussed in terms of the moon and Mercury. Finite strain theory and depth and temperature-dependent thermal expansion are used to evaluate previous conclusions about early lunar history. Factors bringing about core differentiation in the first 0.6 b.y. of Mercurian evolution are described. The influence of concentrating radioactive heat sources located in Mercury's crust on the predicted contraction is outlined. The predicted planetary volume change is explored with regard to quantitative limits on the extent of Mercurian core solidification. Lunar and Mercurian thermal stresses involved in thermal evolution are reviewed, noting the history of surface volcanism. It is concluded that surface faulting and volcanism are closely associated with the thermal evolution of the whole planetary volume. As the planet cools or is heated, several types of tectonic and volcanic effects may be produced by thermal stress occurring in the lithosphere.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bisio, Alessandro; D’Ariano, Giacomo Mauro; Tosini, Alessandro, E-mail: alessandro.tosini@unipv.it

We present a quantum cellular automaton model in one space-dimension which has the Dirac equation as emergent. This model, a discrete-time and causal unitary evolution of a lattice of quantum systems, is derived from the assumptions of homogeneity, parity and time-reversal invariance. The comparison between the automaton and the Dirac evolutions is rigorously set as a discrimination problem between unitary channels. We derive an exact lower bound for the probability of error in the discrimination as an explicit function of the mass, the number and the momentum of the particles, and the duration of the evolution. Computing this bound withmore » experimentally achievable values, we see that in that regime the QCA model cannot be discriminated from the usual Dirac evolution. Finally, we show that the evolution of one-particle states with narrow-band in momentum can be efficiently simulated by a dispersive differential equation for any regime. This analysis allows for a comparison with the dynamics of wave-packets as it is described by the usual Dirac equation. This paper is a first step in exploring the idea that quantum field theory could be grounded on a more fundamental quantum cellular automaton model and that physical dynamics could emerge from quantum information processing. In this framework, the discretization is a central ingredient and not only a tool for performing non-perturbative calculation as in lattice gauge theory. The automaton model, endowed with a precise notion of local observables and a full probabilistic interpretation, could lead to a coherent unification of a hypothetical discrete Planck scale with the usual Fermi scale of high-energy physics. - Highlights: • The free Dirac field in one space dimension as a quantum cellular automaton. • Large scale limit of the automaton and the emergence of the Dirac equation. • Dispersive differential equation for the evolution of smooth states on the automaton. • Optimal discrimination between the automaton evolution and the Dirac equation.« less

Social media enhances languages differentiation: a mathematical description.

PubMed

Vidal-Franco, Ignacio; Guiu-Souto, Jacobo; Muñuzuri, Alberto P

2017-05-01

Understanding and predicting the evolution of competing languages is a topic of high interest in a world with more than 6000 languages competing in a highly connected environment. We consider a reasonable mathematical model describing a situation of competition between two languages and analyse the effect of the speakers' connectivity (i.e. social networks). Surprisingly, instead of homogenizing the system, a high degree of connectivity helps to introduce differentiation for the appropriate parameters.

Large-Scale Impact Cratering and Early Earth Evolution

NASA Technical Reports Server (NTRS)

Grieve, R. A. F.; Cintala, M. J.

1997-01-01

The surface of the Moon attests to the importance of large-scale impact in its early crustal evolution. Previous models of the effects of a massive bombardment on terrestrial crustal evolution have relied on analogies with the Moon, with allowances for the presence of water and a thinner lithosphere. It is now apparent that strict lunar-terrestrial analogies are incorrect because of the "differential scaling" of crater dimensions and melt volumes with event size and planetary gravity. Impact melt volumes and "ancient cavity dimensions for specific impacts were modeled according to previous procedures. In the terrestrial case, the melt volume (V(sub m)) exceeds that of the transient cavity (V(sub tc)) at diameters > or = 400 km. This condition is reached on the Moon only with transient cavity diameters > or = 3000 km, equivalent to whole Moon melting. The melt volumes in these large impact events are minimum estimates, since, at these sizes, the higher temperature of the target rocks at depth will increase melt production. Using the modification-scaling relation of Croft, a transient cavity diameter of about 400 km in the terrestrial environment corresponds to an expected final impact "basin" diameter of about 900 km. Such a "basin" would be comparable in dimensions to the lunar basin Orientale. This 900-km "basin" on the early Earth, however, would not have had the appearance of Orientale. It would have been essentially a melt pool, and, morphologically, would have had more in common with the palimpsests structures on Callisto and Ganymede. With the terrestrial equivalents to the large multiring basins of the Moon being manifested as muted palimpsest-like structures filled with impact melt, it is unlikely they played a role in establishing the freeboard on the early Earth. The composition of the massive impact melt sheets (> 10 (exp 7) cu km) produced in "basin-forming" events on the early Earth would have most likely ranged from basaltic to more mafic for the largest impacts, where the melt volume would have reached well into the mantle. Any contribution from adiabatic melting or shock heating of the asthenosphere would have had similar mafic compositions. The depth of the melt sheets is unknown but would have been in the multilkilometer range. Bodies of basaltic melt > or = 300 m thick differentiate in the terrestrial environment, with the degree of differentiation being a function of the thickness of the body. We therefore expect that these thick, closed-system melt pools would have differentiated into an ultramafic-mafic base and felsic top. If only 10% of the impact melt produced in a single event creating a 400-km diameter transient cavity evolved into felsic differentiates, they would be comparable in volume to the Columbia River basalts. It has been estimated that at least 200 impact events of this size or larger occurred on the early Earth during a period of heavy bombardment. We speculate that these massive differentiated melt sheets may have had a role in the formation of the initial felsic component of the Earth's crust. Additional information is contained in the original.

Variation, differential reproduction and oscillation: the evolution of nucleic acid hybridization.

PubMed

Suárez-Díaz, Edna

2013-01-01

This paper builds upon Hans-Jörg Rheinberger ideas on the oscillation and intercalation of epistemic things and technical objects in experimental systems, to give a fine-grained analysis of what here is called the problems of "adaptation" between our material and cognitive tools and the phenomena of the material world. To do so, it relies on the case-study of the evolution of nucleic acid hybridization and the stabilization of satellite DNA.

[Cranial metastasis of thyroid follicular carcinoma. Report of a case].

PubMed

Calderón-Garcidueñas, A L; González-Schaffinni, M A; Farías-García, R; Rey-Laborde, R

2001-01-01

Thyroid follicular carcinoma is able to produce metastatic lesions before the vanishing of the primary lesion. We present a case of a woman with a lytic, solitary, asymptomatic parietal bone lesion of 2 years of evolution. Autopsy revealed a thyroid gland with two small cystic areas and renal metastasis. Thyroid carcinoma should be included in the differential diagnosis in cases of lytic bone lesions with long evolution in patients 60 years of age or older.

Molecular development of fibular reduction in birds and its evolution from dinosaurs.

PubMed

Botelho, João Francisco; Smith-Paredes, Daniel; Soto-Acuña, Sergio; O'Connor, Jingmai; Palma, Verónica; Vargas, Alexander O

2016-03-01

Birds have a distally reduced, splinter-like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid-related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis-like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo-tibial disparity. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Mitochondria and the evolutionary roots of cancer

NASA Astrophysics Data System (ADS)

Davila, Alfonso F.; Zamorano, Pedro

2013-04-01

Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell.

Evolution of relative drifts and temperature anisotropies in expanding collisionless plasmas—1.5D vs. 2.5D hybrid simulations

NASA Astrophysics Data System (ADS)

Maneva, Y. G.; Poedts, S.; Araneda, J. A.

2016-02-01

We compare the results from 1.5D and 2.5D hybrid simulations (with fluid electrons, and kinetic/particle-in-cell protons and α particles) to investigate the effect of the solar wind expansion on the evolution of ion relative drifts in collisionless fast wind streams. We initialize the system with initial relative drifts and follow its evolution in time within and without the expanding box model, which takes into account the gradual solar wind expansion in the interplanetary medium. The decay of the differential streaming follows similar pattern in the 1.5D and 2.5D non-expanding cases. For the 1.5D studies we find no difference in the evolution of the initial relative drift speed with and without expansion, whereas in the two-dimensional case the differential streaming is further suppressed once the solar wind expansion is taken into account. This implies that a stronger acceleration source is required to compensate for the effect of the expansion and produce the observed solar wind acceleration rate. The 1.5D case shows stronger oscillations in all plasma properties with higher temperature anisotropies for the minor ions in the first few hundred gyro-periods of the simulations. Yet the preferential perpendicular heating for the minor ions is stronger in the 2.5D case with higher temperature anisotropies at the final stage.

CRevolution 2—Origin and evolution of the Colorado River system, workshop abstracts

USGS Publications Warehouse

Beard, L. Sue; Karlstrom, Karl E.; Young, Richard A.; Billingsley, George H.

2011-01-01

A 2010 Colorado River symposium, held in Flagstaff, Arizona, involved 70 participants who engaged in intense debate about the origin and evolution of the Colorado River system. This symposium, built upon two previous decadal scientific meetings, focused on forging scientific consensus, where possible, while articulating continued controversies regarding the Cenozoic evolution of the Colorado River System and the landscapes of the Colorado Plateau-Rocky Mountain region that it drains. New developments involved hypotheses that Neogene mantle flow is driving plateau tilting and differential uplift and new and controversial hypotheses for the pre-6 Ma presence and evolution of ancestral rivers that may be important in the history and birth of the present Colorado River. There is a consensus that plateau tilt and uplift models must be tested with multidisciplinary studies involving differential incision studies and additional geochronology and thermochronology to determine the relative importance of tectonic and geomorphic forces that shape the spectacular landscapes of the Colorado Plateau, Arizona and region. In addition to the scientific goals, the meeting participants emphasized the iconic status of Grand Canyon for geosciences and the importance of good communication between the research community, the geoscience education/interpretation community, the public, and the media. Building on a century-long tradition, this region still provides a globally important natural laboratory for studies of the interactions of erosion and tectonism in shaping the landscape of elevated plateaus.

About Tidal Evolution of Quasi-Periodic Orbits of Satellites

NASA Astrophysics Data System (ADS)

Ershkov, Sergey V.

2017-06-01

Tidal interactions between Planet and its satellites are known to be the main phenomena, which are determining the orbital evolution of the satellites. The modern ansatz in the theory of tidal dissipation in Saturn was developed previously by the international team of scientists from various countries in the field of celestial mechanics. Our applying to the theory of tidal dissipation concerns the investigating of the system of ODE-equations (ordinary differential equations) that govern the orbital evolution of the satellites; such an extremely non-linear system of 2 ordinary differential equations describes the mutual internal dynamics for the eccentricity of the orbit along with involving the semi-major axis of the proper satellite into such a monstrous equations. In our derivation, we have presented the elegant analytical solutions to the system above; so, the motivation of our ansatz is to transform the previously presented system of equations to the convenient form, in which the minimum of numerical calculations are required to obtain the final solutions. Preferably, it should be the analytical solutions; we have presented the solution as a set of quasi- periodic cycles via re-inversing of the proper ultra- elliptical integral. It means a quasi-periodic character of the evolution of the eccentricity, of the semi-major axis for the satellite orbit as well as of the quasi-periodic character of the tidal dissipation in the Planet.

Crack Detection in Concrete Tunnels Using a Gabor Filter Invariant to Rotation.

PubMed

Medina, Roberto; Llamas, José; Gómez-García-Bermejo, Jaime; Zalama, Eduardo; Segarra, Miguel José

2017-07-20

In this article, a system for the detection of cracks in concrete tunnel surfaces, based on image sensors, is presented. Both data acquisition and processing are covered. Linear cameras and proper lighting are used for data acquisition. The required resolution of the camera sensors and the number of cameras is discussed in terms of the crack size and the tunnel type. Data processing is done by applying a new method called Gabor filter invariant to rotation, allowing the detection of cracks in any direction. The parameter values of this filter are set by using a modified genetic algorithm based on the Differential Evolution optimization method. The detection of the pixels belonging to cracks is obtained to a balanced accuracy of 95.27%, thus improving the results of previous approaches.

Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus

PubMed Central

Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S.

2016-01-01

Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites. PMID:27588023

Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus.

PubMed

Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S

2016-01-01

Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

A stochastic differential equation analysis of cerebrospinal fluid dynamics.

PubMed

Raman, Kalyan

2011-01-18

Clinical measurements of intracranial pressure (ICP) over time show fluctuations around the deterministic time path predicted by a classic mathematical model in hydrocephalus research. Thus an important issue in mathematical research on hydrocephalus remains unaddressed--modeling the effect of noise on CSF dynamics. Our objective is to mathematically model the noise in the data. The classic model relating the temporal evolution of ICP in pressure-volume studies to infusions is a nonlinear differential equation based on natural physical analogies between CSF dynamics and an electrical circuit. Brownian motion was incorporated into the differential equation describing CSF dynamics to obtain a nonlinear stochastic differential equation (SDE) that accommodates the fluctuations in ICP. The SDE is explicitly solved and the dynamic probabilities of exceeding critical levels of ICP under different clinical conditions are computed. A key finding is that the probabilities display strong threshold effects with respect to noise. Above the noise threshold, the probabilities are significantly influenced by the resistance to CSF outflow and the intensity of the noise. Fluctuations in the CSF formation rate increase fluctuations in the ICP and they should be minimized to lower the patient's risk. The nonlinear SDE provides a scientific methodology for dynamic risk management of patients. The dynamic output of the SDE matches the noisy ICP data generated by the actual intracranial dynamics of patients better than the classic model used in prior research.

Differential morphology and image processing.

PubMed

Maragos, P

1996-01-01

Image processing via mathematical morphology has traditionally used geometry to intuitively understand morphological signal operators and set or lattice algebra to analyze them in the space domain. We provide a unified view and analytic tools for morphological image processing that is based on ideas from differential calculus and dynamical systems. This includes ideas on using partial differential or difference equations (PDEs) to model distance propagation or nonlinear multiscale processes in images. We briefly review some nonlinear difference equations that implement discrete distance transforms and relate them to numerical solutions of the eikonal equation of optics. We also review some nonlinear PDEs that model the evolution of multiscale morphological operators and use morphological derivatives. Among the new ideas presented, we develop some general 2-D max/min-sum difference equations that model the space dynamics of 2-D morphological systems (including the distance computations) and some nonlinear signal transforms, called slope transforms, that can analyze these systems in a transform domain in ways conceptually similar to the application of Fourier transforms to linear systems. Thus, distance transforms are shown to be bandpass slope filters. We view the analysis of the multiscale morphological PDEs and of the eikonal PDE solved via weighted distance transforms as a unified area in nonlinear image processing, which we call differential morphology, and briefly discuss its potential applications to image processing and computer vision.

Solar radiation and landscape evolution: co-evolution of topography, vegetation, and erosion rates in a semi-arid ecosystem

NASA Astrophysics Data System (ADS)

Istanbulluoglu, Erkan; Yetemen, Omer

2016-04-01

In this study CHILD landscape evolution model (LEM) is used to study the role of solar radiation on the co-evolution of landscape morphology, vegetation patterns, and erosion rates in a central New Mexico catchment. In the study site north facing slopes (NFS) are characterized by steep diffusion-dominated planar hillslopes covered by co-exiting juniper pine and grass vegetation. South facing slopes (SFS) are characterized by shallow slopes and covered by sparse shrub vegetation. Measured short-term and Holocene-averaged erosion rates show higher soil loss on SFS than NFS. In this study CHILD LEM is first confirmed with ecohydrologic field data and used to systematically examine the co-evolution of topography, vegetation pattern, and erosion rates. Aspect- and network-control are identified as the two main topographic drivers of soil moisture and vegetation organization on the landscape. Landscape-scale and long-term implications of solar radiation driven ecohdrologic patterns emerged in modeled landscape: NFS supported denser vegetation cover and became steeper and planar, while on SFS vegetation grew sparser and slopes declined with more fluvial activity. At the landscape scale, these differential erosion processes led to asymmetric development of catchment forms, consistent with regional observations. While the general patterns of vegetation and topography were reproduced by the model using a stationary representation of the current climate, the observed differential Holocene erosion rates were captured by the model only when cyclic climate is used. This suggests sensitivity of Holocene erosion rates to long-term climate fluctuations.

Landslide Kinematical Analysis through Inverse Numerical Modelling and Differential SAR Interferometry

NASA Astrophysics Data System (ADS)

Castaldo, R.; Tizzani, P.; Lollino, P.; Calò, F.; Ardizzone, F.; Lanari, R.; Guzzetti, F.; Manunta, M.

2015-11-01

The aim of this paper is to propose a methodology to perform inverse numerical modelling of slow landslides that combines the potentialities of both numerical approaches and well-known remote-sensing satellite techniques. In particular, through an optimization procedure based on a genetic algorithm, we minimize, with respect to a proper penalty function, the difference between the modelled displacement field and differential synthetic aperture radar interferometry (DInSAR) deformation time series. The proposed methodology allows us to automatically search for the physical parameters that characterize the landslide behaviour. To validate the presented approach, we focus our analysis on the slow Ivancich landslide (Assisi, central Italy). The kinematical evolution of the unstable slope is investigated via long-term DInSAR analysis, by exploiting about 20 years of ERS-1/2 and ENVISAT satellite acquisitions. The landslide is driven by the presence of a shear band, whose behaviour is simulated through a two-dimensional time-dependent finite element model, in two different physical scenarios, i.e. Newtonian viscous flow and a deviatoric creep model. Comparison between the model results and DInSAR measurements reveals that the deviatoric creep model is more suitable to describe the kinematical evolution of the landslide. This finding is also confirmed by comparing the model results with the available independent inclinometer measurements. Our analysis emphasizes that integration of different data, within inverse numerical models, allows deep investigation of the kinematical behaviour of slow active landslides and discrimination of the driving forces that govern their deformation processes.

Flux Transport and the Sun's Global Magnetic Field

NASA Technical Reports Server (NTRS)

Hathaway, David H.

2010-01-01

The Sun s global magnetic field is produced and evolved through the emergence of magnetic flux in active regions and its transport across the solar surface by the axisymmetric differential rotation and meridional flow and the non-axisymmetric convective flows of granulation, supergranulation, and giant cell convection. Maps of the global magnetic field serve as the inner boundary condition for space weather. The photospheric magnetic field and its evolution determine the coronal and solar wind structures through which CMEs must propagate and in which solar energetic particles are accelerated and propagate. Producing magnetic maps which best represent the actual field configuration at any instant requires knowing the magnetic field over the observed hemisphere as well as knowing the flows that transport flux. From our Earth-based vantage point we only observe the front-side hemisphere and each pole is observable for only six months of the year at best. Models for the surface magnetic flux transport can be used to provide updates to the magnetic field configuration in those unseen regions. In this presentation I will describe successes and failures of surface flux transport and present new observations on the structure, the solar cycle variability, and the evolution of the flows involved in magnetic flux transport. I find that supergranules play the dominant role due to their strong flow velocities and long lifetimes. Flux is transported by differential rotation and meridional flow only to the extent that the supergranules participate in those two flows.

Brain, calvarium, cladistics: A new approach to an old question, who are modern humans and Neandertals?

PubMed

Mounier, Aurélien; Balzeau, Antoine; Caparros, Miguel; Grimaud-Hervé, Dominique

2016-03-01

The evolutionary history of the genus Homo is the focus of major research efforts in palaeoanthropology. However, the use of palaeoneurology to infer phylogenies of our genus is rare. Here we use cladistics to test the importance of the brain in differentiating and defining Neandertals and modern humans. The analysis is based on morphological data from the calvarium and endocast of Pleistocene fossils and results in a single most parsimonious cladogram. We demonstrate that the joint use of endocranial and calvarial features with cladistics provides a unique means to understand the evolution of the genus Homo. The main results of this study indicate that: (i) the endocranial features are more phylogenetically informative than the characters from the calvarium; (ii) the specific differentiation of Neandertals and modern humans is mostly supported by well-known calvarial autapomorphies; (iii) the endocranial anatomy of modern humans and Neandertals show strong similarities, which appeared in the fossil record with the last common ancestor of both species; and (iv) apart from encephalisation, human endocranial anatomy changed tremendously during the end of the Middle Pleistocene. This may be linked to major cultural and technological novelties that had happened by the end of the Middle Pleistocene (e.g., expansion of the Middle Stone Age (MSA) in Africa and Mousterian in Europe). The combined study of endocranial and exocranial anatomy offers opportunities to further understand human evolution and the implication for the phylogeny of our genus. Copyright © 2015 Elsevier Ltd. All rights reserved.

Designing manufacturable filters for a 16-band plenoptic camera using differential evolution

NASA Astrophysics Data System (ADS)

Doster, Timothy; Olson, Colin C.; Fleet, Erin; Yetzbacher, Michael; Kanaev, Andrey; Lebow, Paul; Leathers, Robert

2017-05-01

A 16-band plenoptic camera allows for the rapid exchange of filter sets via a 4x4 filter array on the lens's front aperture. This ability to change out filters allows for an operator to quickly adapt to different locales or threat intelligence. Typically, such a system incorporates a default set of 16 equally spaced at-topped filters. Knowing the operating theater or the likely targets of interest it becomes advantageous to tune the filters. We propose using a modified beta distribution to parameterize the different possible filters and differential evolution (DE) to search over the space of possible filter designs. The modified beta distribution allows us to jointly optimize the width, taper and wavelength center of each single- or multi-pass filter in the set over a number of evolutionary steps. Further, by constraining the function parameters we can develop solutions which are not just theoretical but manufacturable. We examine two independent tasks: general spectral sensing and target detection. In the general spectral sensing task we utilize the theory of compressive sensing (CS) and find filters that generate codings which minimize the CS reconstruction error based on a fixed spectral dictionary of endmembers. For the target detection task and a set of known targets, we train the filters to optimize the separation of the background and target signature. We compare our results to the default 16 at-topped non-overlapping filter set which comes with the plenoptic camera and full hyperspectral resolution data which was previously acquired.

High-throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo-Y chromosome of the cricket Eneoptera surinamensis.

PubMed

Palacios-Gimenez, Octavio Manuel; Dias, Guilherme Borges; de Lima, Leonardo Gomes; Kuhn, Gustavo Campos E Silva; Ramos, Érica; Martins, Cesar; Cabral-de-Mello, Diogo Cavalcanti

2017-07-25

Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X 1 X 2 Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses. We found an unusually high number of 45 families of satDNAs, ranging from 4 bp to 517 bp, accounting for about 14% of the genome and showing different modular structures and high diversity of arrays. FISH mapping revealed that satDNAs are located mostly in C-positive pericentromeric regions of the chromosomes. SatDNAs enrichment was also observed in the neo-sex chromosomes in comparison to autosomes. Especially astonishing accumulation of satDNAs loci was found in the highly differentiated neo-Y, including 39 satDNAs over-represented in this chromosome, which is the greatest satDNAs diversity yet reported for sex chromosomes. Our results suggest possible involvement of satDNAs in genome increasing and in molecular differentiation of the neo-sex chromosomes in this species, contributing to the understanding of sex chromosome composition and evolution in Orthoptera.

Coronary artery segmentation in X-ray angiograms using gabor filters and differential evolution.

PubMed

Cervantes-Sanchez, Fernando; Cruz-Aceves, Ivan; Hernandez-Aguirre, Arturo; Solorio-Meza, Sergio; Cordova-Fraga, Teodoro; Aviña-Cervantes, Juan Gabriel

2018-08-01

Segmentation of coronary arteries in X-ray angiograms represents an essential task for computer-aided diagnosis, since it can help cardiologists in diagnosing and monitoring vascular abnormalities. Due to the main disadvantages of the X-ray angiograms are the nonuniform illumination, and the weak contrast between blood vessels and image background, different vessel enhancement methods have been introduced. In this paper, a novel method for blood vessel enhancement based on Gabor filters tuned using the optimization strategy of Differential evolution (DE) is proposed. Because the Gabor filters are governed by three different parameters, the optimal selection of those parameters is highly desirable in order to maximize the vessel detection rate while reducing the computational cost of the training stage. To obtain the optimal set of parameters for the Gabor filters, the area (Az) under the receiver operating characteristics curve is used as objective function. In the experimental results, the proposed method achieves an A z =0.9388 in a training set of 40 images, and for a test set of 40 images it obtains the highest performance with an A z =0.9538 compared with six state-of-the-art vessel detection methods. Finally, the proposed method achieves an accuracy of 0.9423 for vessel segmentation using the test set. In addition, the experimental results have also shown that the proposed method can be highly suitable for clinical decision support in terms of computational time and vessel segmentation performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modeling and 2-D discrete simulation of dislocation dynamics for plastic deformation of metal

NASA Astrophysics Data System (ADS)

Liu, Juan; Cui, Zhenshan; Ou, Hengan; Ruan, Liqun

2013-05-01

Two methods are employed in this paper to investigate the dislocation evolution during plastic deformation of metal. One method is dislocation dynamic simulation of two-dimensional discrete dislocation dynamics (2D-DDD), and the other is dislocation dynamics modeling by means of nonlinear analysis. As screw dislocation is prone to disappear by cross-slip, only edge dislocation is taken into account in simulation. First, an approach of 2D-DDD is used to graphically simulate and exhibit the collective motion of a large number of discrete dislocations. In the beginning, initial grains are generated in the simulation cells according to the mechanism of grain growth and the initial dislocation is randomly distributed in grains and relaxed under the internal stress. During the simulation process, the externally imposed stress, the long range stress contribution of all dislocations and the short range stress caused by the grain boundaries are calculated. Under the action of these forces, dislocations begin to glide, climb, multiply, annihilate and react with each other. Besides, thermal activation process is included. Through the simulation, the distribution of dislocation and the stress-strain curves can be obtained. On the other hand, based on the classic dislocation theory, the variation of the dislocation density with time is described by nonlinear differential equations. Finite difference method (FDM) is used to solve the built differential equations. The dislocation evolution at a constant strain rate is taken as an example to verify the rationality of the model.

Evolution and Christian Faith

NASA Astrophysics Data System (ADS)

Roughgarden, J. E.

2006-12-01

My recent book, Evolution and Christian Faith explores how evolutionary biology can be portrayed from the religious perspective of Christianity. The principal metaphors for evolutionary biology---differential success at breeding and random mutation, probably originate with the dawn of agriculture and clearly occur in the Bible. The central narrative of evolutionary biology can be presented using Biblical passages, providing an account of evolution that is inherently friendly to a Christian perspective. Still, evolutionary biology is far from complete, and problematic areas pertain to species in which the concept of an individual is poorly defined, and to species in which the expression of gender and sexuality depart from Darwin's sexual-selection templates. The present- day controversy in the US about teaching evolution in the schools provides an opportunity to engage the public about science education.

Chayanov and Social Agronomy in Russia (1918).

ERIC Educational Resources Information Center

Sanchez de Puerta, F.

1994-01-01

Chayanov's ideas on rural development (farmer participation in agricultural evolution, increasing the scope and differentiation of extension activities, and using methods adapted to farmers' characteristics) could be usefully applied today in reforming Russian agriculture. (SK)

Long-distance communication by specialized cellular projections during pigment pattern development and evolution

PubMed Central

Eom, Dae Seok; Bain, Emily J; Patterson, Larissa B; Grout, Megan E; Parichy, David M

2015-01-01

Changes in gene activity are essential for evolutionary diversification. Yet, elucidating the cellular behaviors that underlie modifications to adult form remains a profound challenge. We use neural crest-derived adult pigmentation of zebrafish and pearl danio to uncover cellular bases for alternative pattern states. We show that stripes in zebrafish require a novel class of thin, fast cellular projection to promote Delta-Notch signaling over long distances from cells of the xanthophore lineage to melanophores. Projections depended on microfilaments and microtubules, exhibited meandering trajectories, and stabilized on target cells to which they delivered membraneous vesicles. By contrast, the uniformly patterned pearl danio lacked such projections, concomitant with Colony stimulating factor 1-dependent changes in xanthophore differentiation that likely curtail signaling available to melanophores. Our study reveals a novel mechanism of cellular communication, roles for differentiation state heterogeneity in pigment cell interactions, and an unanticipated morphogenetic behavior contributing to a striking difference in adult form. DOI: http://dx.doi.org/10.7554/eLife.12401.001 PMID:26701906

Chronic Lower Leg Pain in Athletes

PubMed Central

Brewer, Rachel Biber; Gregory, Andrew J. M.

2012-01-01

Context: Chronic lower leg pain in athletes can be a frustrating problem for patients and a difficult diagnosis for clinicians. Myriad approaches have been suggested to evaluate these conditions. With the continued evolution of diagnostic studies, evidence-based guidance for a standard approach is unfortunately sparse. Evidence Acquisition: PubMed was searched from January 1980 to May 2011 to identify publications regarding chronic lower leg pain in athletes (excluding conditions related to the foot), including differential diagnosis, clinical presentation, physical examination, history, diagnostic workup, and treatment. Results: Leg pain in athletes can be caused by many conditions, with the most frequent being medial tibial stress syndrome; chronic exertional compartment syndrome, stress fracture, nerve entrapment, and popliteal artery entrapment syndrome are also considerations. Conservative management is the mainstay of care for the majority of causes of chronic lower leg pain; however, surgical intervention may be necessary. Conclusion: Chronic lower extremity pain in athletes includes a wide differential and can pose diagnostic dilemmas for clinicians. PMID:23016078

Comparison of Early Evolutions of Mimas and Enceladus

NASA Astrophysics Data System (ADS)

Czechowski, Leszek; Witek, Piotr

2015-06-01

Thermal history of Mimas and Enceladus is investigated from the beginning of accretion to 400 Myr. The numerical model of convection combined with the parameterized theory is used. The following heat sources are included: short lived and long lived radioactive isotopes, accretion, serpentinization, and phase changes. The heat transfer processes are: conduction, solid state convection, and liquid state convection. We find that temperature of Mimas' interior was significantly lower than that of Enceladus. If Mimas accreted 1.8 Myr after CAI then the internal melting and differentiation did not occur at all. Comparison of thermal models of Mimas and Enceladus indicates that conditions favorable for the start of tidal heating lasted for a short time ( 107 yr) in Mimas and for 108 yr in Enceladus. This could explain the Mimas—Enceladus paradox. In fact, in view of the chronology based on cometary impact rate, one cannot discard a possibility that also Mimas was for some time active and it has the interior differentiated on porous core and icy mantle.

On new classes of solutions of nonlinear partial differential equations in the form of convergent special series

NASA Astrophysics Data System (ADS)

Filimonov, M. Yu.

2017-12-01

The method of special series with recursively calculated coefficients is used to solve nonlinear partial differential equations. The recurrence of finding the coefficients of the series is achieved due to a special choice of functions, in powers of which the solution is expanded in a series. We obtain a sequence of linear partial differential equations to find the coefficients of the series constructed. In many cases, one can deal with a sequence of linear ordinary differential equations. We construct classes of solutions in the form of convergent series for a certain class of nonlinear evolution equations. A new class of solutions of generalized Boussinesque equation with an arbitrary function in the form of a convergent series is constructed.

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

PubMed Central

Wang, Minglei; Yafremava, Liudmila S.; Caetano-Anollés, Derek; Mittenthal, Jay E.; Caetano-Anollés, Gustavo

2007-01-01

The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages. Functional annotation of FSF along these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes the first organismal divide. Reconstruction of phylogenomic trees of proteomes reflects the timeline of architectural diversification in the emerging lineages. Thus, Archaea undertook a minimalist strategy using only a small subset of the full architectural repertoire and then crystallized into a diversified superkingdom late in evolution. Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya. PMID:17908824

Three Substrains of the Cyanobacterium Anabaena sp. Strain PCC 7120 Display Divergence in Genomic Sequences and hetC Function.

PubMed

Wang, Yali; Gao, Yuan; Li, Chao; Gao, Hong; Zhang, Cheng-Cai; Xu, Xudong

2018-07-01

Anabaena sp. strain PCC 7120 is a model strain for molecular studies of cell differentiation and patterning in heterocyst-forming cyanobacteria. Subtle differences in heterocyst development have been noticed in different laboratories working on the same organism. In this study, 360 mutations, including single nucleotide polymorphisms (SNPs), small insertion/deletions (indels; 1 to 3 bp), fragment deletions, and transpositions, were identified in the genomes of three substrains. Heterogeneous/heterozygous bases were also identified due to the polyploidy nature of the genome and the multicellular morphology but could be completely segregated when plated after filament fragmentation by sonication. hetC is a gene upregulated in developing cells during heterocyst formation in Anabaena sp. strain PCC 7120 and found in approximately half of other heterocyst-forming cyanobacteria. Inactivation of hetC in 3 substrains of Anabaena sp. PCC 7120 led to different phenotypes: the formation of heterocysts, differentiating cells that keep dividing, or the presence of both heterocysts and dividing differentiating cells. The expression of P hetZ - gfp in these hetC mutants also showed different patterns of green fluorescent protein (GFP) fluorescence. Thus, the function of hetC is influenced by the genomic background and epistasis and constitutes an example of evolution under way. IMPORTANCE Our knowledge about the molecular genetics of heterocyst formation, an important cell differentiation process for global N 2 fixation, is mostly based on studies with Anabaena sp. strain PCC 7120. Here, we show that rapid microevolution is under way in this strain, leading to phenotypic variations for certain genes related to heterocyst development, such as hetC This study provides an example for ongoing microevolution, marked by multiple heterogeneous/heterozygous single nucleotide polymorphisms (SNPs), in a multicellular multicopy-genome microorganism. Copyright © 2018 American Society for Microbiology.

Thermal Evolution of a Failed Flux Rope Eruption Revealed by Temperature Maps

NASA Astrophysics Data System (ADS)

Song, H.; Zhang, J.; CHEN, Y.

2013-12-01

Flux rope is generally considered to be the fundamental magnetic configuration of a coronal mass ejection (CME). Recent observations suggest that hot channel or blob structures during the eruptions be the direct observational manifestation of flux ropes. In this study, we report our analysis of thermal evolution of a failed solar eruption with an apparent flux rope embedded. The thermal structure of the eruption is revealed through differential emission measure (DEM) analysis technique, which shows detailed temperature maps in both high spatial resolution and high temperature resolution based on SDO/AIA observations. Our results show that the flux rope exists in the corona before the eruption, and its temperature can quickly rise to over 10 MK within one minute of the eruption. The correlation study between the flux rope temperature and the soft x-ray flux suggests that the flux rope should be heated through the direct thermal energy release of magnetic reconnection. Further, we study the kinematic evolution process of the flux rope, in an effort to find the physical mechanism that prevents the magnetic rope eruption to become a full coronal mass ejection. This kind of study using temperature maps might reveal where and when magnetic reconnection takes place during solar eruptions.

Reconstituting the Evolutionary History of Cronobacter Driven by Differentiated CRISPR Activity.

PubMed

Zeng, Haiyan; Zhang, Jumei; Wu, Qingping; He, Wenjing; Wu, Haoming; Ye, Yingwang; Li, Chengsi; Ling, Na; Chen, Moutong; Wang, Juan; Cai, Shuzhen; Lei, Tao; Ding, Yu; Xue, Liang

2018-03-09

Cronobacter strains harboring the CRISPR-Cas system are important foodborne pathogens causing serious neonatal infections. However, the specific role of the CRISPR-Cas system in bacterial evolution remains relatively unexplored. In this study, we investigated the impact of CRISPR-Cas in Cronobacter evolution and obtained 137 new whole-genome sequences of Cronobacter by next-generation sequencing technology. Among the strains examined (n=240), 90.6% (193/213) of prevalent species Cronobacter sakazakii , Cronobacter malonaticus , and Cronobacter dublinensis strains had intact CRISPR-Cas systems. Two rare species, Cronobacter condimenti (n=2) and Cronobacter universalis (n=6), lacked and preserved the CRISPR-Cas system at a low frequency (1/6), respectively. These results suggest that the presence of one CRISPR-Cas system in Cronobacter is important for the species to maintain genome homeostasis for survival. The Cronobacter ancestral strain was likely to harbored both subtype I-E and I-F CRISPR-Cas systems, during the long evolutionary process, subtype I-E was retained, while subtype I-F selectively degenerated in Cronobacter species and was even lost in the major Cronobacter pathovars. Moreover, significantly higher CRISPR activity was observed in plant-associated species C. dublinensis than in the virulence-related species C. sakazakii and C. malonaticus Similar spacers of CRISPR arrays were rarely found among species, suggesting intensive change through adaptive acquisition and loss. Differentiated CRISPR activity appears to be the product of environmental selective pressure and might contribute to the bidirectional divergence and speciation of Cronobacter IMPORTANCE This study reports the evolutionary history of Cronobacter under the selective pressure of the CRISPR-Cas system. One CRISPR-Cas system in Cronobacter is important for maintaining genome homeostasis, whereas two types of systems may be redundant and not conducive for acquiring beneficial DNA for environmental adaption and pathogenicity. Differentiated CRISPR activity has contributed to the bidirectional divergence and genetic diversity of Cronobacter This perspective makes a significant contribution to the literature by providing new insights into CRISPR-Cas systems in general, while further expanding the roles of CRISPR beyond conferring adaptive immunity and demonstrating a link to adaptation and species divergence in a genus. Moreover, our study provides new insights into the balance between genome homeostasis and the uptake of beneficial DNA related to CRISPR-based activity in the evolution of Cronobacter . Copyright © 2018 American Society for Microbiology.

Forecasting SPEI and SPI Drought Indices Using the Integrated Artificial Neural Networks

PubMed Central

Maca, Petr; Pech, Pavel

2016-01-01

The presented paper compares forecast of drought indices based on two different models of artificial neural networks. The first model is based on feedforward multilayer perceptron, sANN, and the second one is the integrated neural network model, hANN. The analyzed drought indices are the standardized precipitation index (SPI) and the standardized precipitation evaporation index (SPEI) and were derived for the period of 1948–2002 on two US catchments. The meteorological and hydrological data were obtained from MOPEX experiment. The training of both neural network models was made by the adaptive version of differential evolution, JADE. The comparison of models was based on six model performance measures. The results of drought indices forecast, explained by the values of four model performance indices, show that the integrated neural network model was superior to the feedforward multilayer perceptron with one hidden layer of neurons. PMID:26880875

Forecasting SPEI and SPI Drought Indices Using the Integrated Artificial Neural Networks.

PubMed

Maca, Petr; Pech, Pavel

2016-01-01

The presented paper compares forecast of drought indices based on two different models of artificial neural networks. The first model is based on feedforward multilayer perceptron, sANN, and the second one is the integrated neural network model, hANN. The analyzed drought indices are the standardized precipitation index (SPI) and the standardized precipitation evaporation index (SPEI) and were derived for the period of 1948-2002 on two US catchments. The meteorological and hydrological data were obtained from MOPEX experiment. The training of both neural network models was made by the adaptive version of differential evolution, JADE. The comparison of models was based on six model performance measures. The results of drought indices forecast, explained by the values of four model performance indices, show that the integrated neural network model was superior to the feedforward multilayer perceptron with one hidden layer of neurons.

Introduction: CRevolution 2: origin and evolution of the Colorado River System II

USGS Publications Warehouse

Karlstrom, Karl E.; Beard, L. Sue; House, P. Kyle; Young, Richard A.; Aslan, Andres; Billingsley, George; Pederson, Joel

2012-01-01

A 2010 Colorado River symposium held in Flagstaff, Arizona, in May 2010, had 70 participants who engaged in intense debate about the origin and evolution of the Colorado River system. This symposium, built on two previous decadal scientific meetings, focused on forging scientific consensus where possible, while also articulating continued controversies regarding the Cenozoic evolution of the Colorado River System and the landscapes of the Colorado Plateau–Rocky Mountain region that it drains. New developments involved hypotheses that Neogene mantle flow is driving plateau tilting and differential uplift, with consensus that multidisciplinary studies involving differential incision studies and additional geochronology and thermochronology are needed to test the relative importance of tectonic and geomorphic forcings in shaping the spectacular landscapes of the Colorado Plateau region. In addition to the scientific goals, the meeting participants emphasized the iconic status of Grand Canyon for geosciences, and the importance of good communication between the research community, the geoscience education/interpretation community, the public, and the media. Building on a century-long tradition, this region still provides a globally important natural laboratory for studies of the interactions of erosion and tectonism in the shaping landscape of elevated plateaus.

Detection of biological threats. A challenge for directed molecular evolution.

PubMed

Petrenko, Valery A; Sorokulova, Iryna B

2004-08-01

The probe technique originated from early attempts of Anton van Leeuwenhoek to contrast microorganisms under the microscope using plant juices, successful staining of tubercle bacilli with synthetic dyes by Paul Ehrlich and discovery of a stain for differentiation of gram-positive and gram-negative bacteria by Hans Christian Gram. The technique relies on the principle that pathogens have unique structural features, which can be recognized by specifically labeled organic molecules. A hundred years of extensive screening efforts led to discovery of a limited assortment of organic probes that are used for identification and differentiation of bacteria. A new challenge--continuous monitoring of biological threats--requires long lasting molecular probes capable of tight specific binding of pathogens in unfavorable conditions. To respond to the challenge, probe technology is being revolutionized by utilizing methods of combinatorial chemistry, phage display and directed molecular evolution. This review describes how molecular evolution methods are applied for development of peptide, antibody and phage probes, and summarizes the author's own data on development of landscape phage probes against Salmonella typhimurium. The performance of the probes in detection of Salmonella is illustrated by a precipitation test, enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cell sorting (FACS) and fluorescent, optical and electron microscopy.

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2003-01-01

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

Artificial selection on brain-expressed genes during the domestication of dog.

PubMed

Li, Yan; Vonholdt, Bridgett M; Reynolds, Andy; Boyko, Adam R; Wayne, Robert K; Wu, Dong-Dong; Zhang, Ya-Ping

2013-08-01

Domesticated dogs have many unique behaviors not found in gray wolves that have augmented their interaction and communication with humans. The genetic basis of such unique behaviors in dogs remains poorly understood. We found that genes within regions highly differentiated between outbred Chinese native dogs (CNs) and wolves show high bias for expression localized to brain tissues, particularly the prefrontal cortex, a specific region responsible for complex cognitive behaviors. In contrast, candidate genes showing high population differentiation between CNs and German Shepherd dogs (GSs) did not demonstrate significant expression bias. These observations indicate that these candidate genes highly expressed in the brain have rapidly evolved. This rapid evolution was probably driven by artificial selection during the primary transition from wolves to ancient dogs and was consistent with the evolution of dog-specific characteristics, such as behavior transformation, for thousands of years.

[Asynchronous asymmetry (sexual and lateral differentiation--a consequence of asynchronous evolution)].

PubMed

Geodakian, V A

1993-01-01

In the paper is presented a unified interpretation of sex differentiation and lateral asymmetry as asynchronous evolution. The operative subsystems, i.e. the male and the left hemisphere of the brain evolutionize earlier than the conservative ones, i.e. the female and the right hemisphere. New functions appear at first in males and after many generations they are transferred to females. The leading centers of their control are at first originated in the left hemisphere, then they are translocated to the right one. The criterion for functions localization in the hemisphere is their evolutionary age: new functions are controlled by the left hemisphere, old functions by the right one. Therefore the left hemisphere is socio-cultural, ethnic, the right one is biological, special. The theory explains from a single standpoint the phenomena of sex, handedness, nervous crossover, as well as many know facts, and predicts the new ones.

Laboratory Annealing Experiments Of Refractory Silicate Grain Analogs Using Differential Scanning Calorimetry

NASA Technical Reports Server (NTRS)

Kimura, Yuki; Nuth, Joseph A., III; Tsukamota, Katsuo; Kaito, Chihiro

2010-01-01

Exothermic reactions during the annealing of laboratory synthesized amorphous magnesium-bearing silicate particles used as grain analogs of cosmic dust were detected by differential scanning calorimetry (DSC) in air. With infrared spectroscopy and transmission electron microscopy, we show that cosmic dust could possibly undergo fusion to larger particles, with oxidation of magnesium silicide and crystallization of forsterite as exothermic reactions in the early solar system. The reactions begin at approximately 425, approximately 625, and approximately 1000 K, respectively, and the reaction energies (enthalpies) are at least 727, 4151, and 160.22 J per gram, respectively. During the crystallization of forsterite particles, the spectral evolution of the 10 micrometer feature from amorphous to crystalline was observed to begin at lower temperature than the crystallization temperature of 1003 K. During spectral evolution at lower temperature, nucleation and/or the formation of nanocrystallites of forsterite at the surface of the grain analogs was observed.

Nature and evolution of the meteorite parent bodies: Evidence from petrology and metallurgy

NASA Technical Reports Server (NTRS)

Wood, J. A.

1978-01-01

The physical as well as chemical properties of the meteorite parent bodies are reviewed and it is concluded that many differentiated meteorites were likely formed in asteroidal-sized parents. A new model is developed for the formation of pallasites at the interface between an iron core and olivine mantle in differentiated bodies only about 10 km in diameter, which are later incorporated into a second generation of larger (100 km) parent bodies.

Woody climbers show greater population genetic differentiation than trees: Insights into the link between ecological traits and diversification.

PubMed

Gianoli, Ernesto; Torres-Díaz, Cristian; Ruiz, Eduardo; Salgado-Luarte, Cristian; Molina-Montenegro, Marco A; Saldaña, Alfredo; Ríos, Rodrigo S

2016-12-01

The climbing habit is a key innovation in plants: climbing taxa have higher species richness than nonclimbing sister groups. We evaluated the hypothesis that climbing plant species show greater among-population genetic differentiation than nonclimber species. We compared the among-population genetic distance in woody climbers (eight species, 30 populations) and trees (seven species, 29 populations) coexisting in nine communities in a temperate rainforest. We also compared within-population genetic diversity in co-occurring woody climbers and trees in two communities. Mean genetic distance between populations of climbers was twice that of trees. Isolation by distance (increase in genetic distance with geographic distance) was greater for climbers. Climbers and trees showed similar within-population genetic diversity. Our longevity estimate suggested that climbers had shorter generation times, while other biological features often associated with diversification (dispersal and pollination syndromes, mating system, size, and metabolic rate) did not show significant differences between groups. We hypothesize that the greater population differentiation in climbers could result from greater evolutionary responses to local selection acting on initially higher within-population genetic diversity, which could be driven by neutral processes associated with shorter generation times. Increased population genetic differentiation could be incorporated as another line of evidence when testing for key innovations. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Timing sexual differentiation: full functional sex reversal achieved through silencing of a single insulin-like gene in the prawn, Macrobrachium rosenbergii.

PubMed

Ventura, Tomer; Manor, Rivka; Aflalo, Eliahu D; Weil, Simy; Rosen, Ohad; Sagi, Amir

2012-03-01

In Crustacea, an early evolutionary group (∼50 000 species) inhabiting most ecological niches, sex differentiation is regulated by a male-specific androgenic gland (AG). The identification of AG-specific insulin-like factors (IAGs) and genomic sex markers offers an opportunity for a deeper understanding of the sexual differentiation mechanism in crustaceans and other arthropods. Here, we report, to our knowledge, the first full and functional sex reversal of male freshwater prawns (Macrobrachium rosenbergii) through the silencing of a single IAG-encoding gene. These "neofemales" produced all-male progeny, as proven by sex-specific genomic markers. This finding offers an insight regarding the biology and evolution of sex differentiation regulation, with a novel perspective for the evolution of insulin-like peptides. Our results demonstrate how temporal intervention with a key regulating gene induces a determinative, extreme phenotypic shift. Our results also carry tremendous ecological and commercial implications. Invasive and pest crustacean species represent genuine concerns worldwide without an apparent solution. Such efforts might, therefore, benefit from sexual manipulations, as has been successfully realized with other arthropods. Commercially, such manipulation would be significant in sexually dimorphic cultured species, allowing the use of nonbreeding, monosex populations while dramatically increasing yield and possibly minimizing the invasion of exotic cultured species into the environment.

Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster

PubMed Central

Schrider, Daniel R.; Hahn, Matthew W.; Begun, David J.

2016-01-01

Genetic differentiation across populations that is maintained in the presence of gene flow is a hallmark of spatially varying selection. In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents. As of yet there has been no genome-wide examination of differentiated copy-number variants (CNVs) in these geographic regions, despite their potential importance for phenotypic variation in Drosophila and other taxa. Here, we present an analysis of geographic variation in CNVs in D. melanogaster. We also present the first genomic analysis of geographic variation for copy-number variation in the sister species, D. simulans, in order to investigate patterns of parallel evolution in these close relatives. In D. melanogaster we find hundreds of CNVs, many of which show parallel patterns of geographic variation on both continents, lending support to the idea that they are influenced by spatially varying selection. These findings support the idea that polymorphic CNVs contribute to local adaptation in D. melanogaster. In contrast, we find very few CNVs in D. simulans that are geographically differentiated in parallel on both continents, consistent with earlier work suggesting that clinal patterns are weaker in this species. PMID:26809315

Adaptive cockroach swarm algorithm

NASA Astrophysics Data System (ADS)

Obagbuwa, Ibidun C.; Abidoye, Ademola P.

2017-07-01

An adaptive cockroach swarm optimization (ACSO) algorithm is proposed in this paper to strengthen the existing cockroach swarm optimization (CSO) algorithm. The ruthless component of CSO algorithm is modified by the employment of blend crossover predator-prey evolution method which helps algorithm prevent any possible population collapse, maintain population diversity and create adaptive search in each iteration. The performance of the proposed algorithm on 16 global optimization benchmark function problems was evaluated and compared with the existing CSO, cuckoo search, differential evolution, particle swarm optimization and artificial bee colony algorithms.

Cloud Model-Based Artificial Immune Network for Complex Optimization Problem

PubMed Central

Wang, Mingan; Li, Jianming; Guo, Dongliang

2017-01-01

This paper proposes an artificial immune network based on cloud model (AINet-CM) for complex function optimization problems. Three key immune operators—cloning, mutation, and suppression—are redesigned with the help of the cloud model. To be specific, an increasing half cloud-based cloning operator is used to adjust the dynamic clone multipliers of antibodies, an asymmetrical cloud-based mutation operator is used to control the adaptive evolution of antibodies, and a normal similarity cloud-based suppressor is used to keep the diversity of the antibody population. To quicken the searching convergence, a dynamic searching step length strategy is adopted. For comparative study, a series of numerical simulations are arranged between AINet-CM and the other three artificial immune systems, that is, opt-aiNet, IA-AIS, and AAIS-2S. Furthermore, two industrial applications—finite impulse response (FIR) filter design and proportional-integral-differential (PID) controller tuning—are investigated and the results demonstrate the potential searching capability and practical value of the proposed AINet-CM algorithm. PMID:28630620