Rugged Metropolis sampling with simultaneous updating of two dynamical variables

NASA Astrophysics Data System (ADS)

Berg, Bernd A.; Zhou, Huan-Xiang

2005-07-01

The rugged Metropolis (RM) algorithm is a biased updating scheme which aims at directly hitting the most likely configurations in a rugged free-energy landscape. Details of the one-variable (RM1) implementation of this algorithm are presented. This is followed by an extension to simultaneous updating of two dynamical variables (RM2) . In a test with the brain peptide Met-Enkephalin in vacuum RM2 improves conventional Metropolis simulations by a factor of about 4. Correlations between three or more dihedral angles appear to prevent larger improvements at low temperatures. We also investigate a multihit Metropolis scheme, which spends more CPU time on variables with large autocorrelation times.

Out to eat: the emergence and evolution of the restaurant in nineteenth-century New York City.

PubMed

Lobel, Cindy R

2010-01-01

Unheard of in the eighteenth century, restaurants became an integral part of New York City's public culture in the antebellum period. This article examines the emergence and development of New York's restaurant sector in the nineteenth century, focusing on three aspects in particular: the close ties between urbanization and the rise of New York's restaurants, the role restaurants played in enforcing the city's class structure and gender mores, and the role of restaurants in shaping the public culture of the growing metropolis.

Experimental and Numerical Investigations on Colloid-facilitated Plutonium Reactive Transport in Fractured Tuffaceous Rocks

NASA Astrophysics Data System (ADS)

Dai, Z.; Wolfsberg, A. V.; Zhu, L.; Reimus, P. W.

2017-12-01

Colloids have the potential to enhance mobility of strongly sorbing radionuclide contaminants in fractured rocks at underground nuclear test sites. This study presents an experimental and numerical investigation of colloid-facilitated plutonium reactive transport in fractured porous media for identifying plutonium sorption/filtration processes. The transport parameters for dispersion, diffusion, sorption, and filtration are estimated with inverse modeling for minimizing the least squares objective function of multicomponent concentration data from multiple transport experiments with the Shuffled Complex Evolution Metropolis (SCEM). Capitalizing on an unplanned experimental artifact that led to colloid formation and migration, we adopt a stepwise strategy to first interpret the data from each experiment separately and then to incorporate multiple experiments simultaneously to identify a suite of plutonium-colloid transport processes. Nonequilibrium or kinetic attachment and detachment of plutonium-colloid in fractures was clearly demonstrated and captured in the inverted modeling parameters along with estimates of the source plutonium fraction that formed plutonium-colloids. The results from this study provide valuable insights for understanding the transport mechanisms and environmental impacts of plutonium in fractured formations and groundwater aquifers.

Nuclear shape evolution based on microscopic level densities

DOE PAGES

Ward, D. E.; Carlsson, B. G.; Døssing, T.; ...

2017-02-27

Here, by combining microscopically calculated level densities with the Metropolis walk method, we develop a consistent framework for treating the energy and angular-momentum dependence of the nuclear shape evolution in the fission process. For each nucleus under consideration, the level density is calculated microscopically for each of more than five million shapes with a recently developed combinatorial method. The method employs the same single-particle levels as those used for the extraction of the pairing and shell contributions to the macroscopic-microscopic deformation-energy surface. Containing no new parameters, the treatment is suitable for elucidating the energy dependence of the dynamics of warmmore » nuclei on pairing and shell effects. It is illustrated for the fission fragment mass distribution for several uranium and plutonium isotopes of particular interest.« less

MEXICAN-AMERICAN STUDY PROJECT. ADVANCE REPORT 8, MEXICAN-AMERICANS IN A MIDWEST METROPOLIS--A STUDY OF EAST CHICAGO.

ERIC Educational Resources Information Center

LAMANNA, RICHARD A.; SAMORA, JULIAN

MEXICAN AMERICANS WHO HAVE MIGRATED TO THE INDUSTRIAL COMPLEX OF EAST CHICAGO ARE ANALYZED TO DETERMINE THE VALIDITY OF A HYPOTHESIS THAT THIS GROUP WAS PROVIDED OPPORTUNITIES NOT AVAILABLE TO THEIR COUNTERPARTS IN THE SOUTHWEST FOR ASSIMILATION INTO THE COMMUNITY. A CONCISE REPORT ON THE HISTORY OF THE MEXICAN-AMERICAN COLONY IN EAST CHICAGO, ITS…

Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms.

PubMed

Mori, Yoshiharu; Okumura, Hisashi

2015-12-05

Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa-Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa-Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa-Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa-Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa-Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa-Todo algorithm when compared with the Metropolis algorithm. © 2015 Wiley Periodicals, Inc.

A Bootstrap Metropolis-Hastings Algorithm for Bayesian Analysis of Big Data.

PubMed

Liang, Faming; Kim, Jinsu; Song, Qifan

2016-01-01

Markov chain Monte Carlo (MCMC) methods have proven to be a very powerful tool for analyzing data of complex structures. However, their computer-intensive nature, which typically require a large number of iterations and a complete scan of the full dataset for each iteration, precludes their use for big data analysis. In this paper, we propose the so-called bootstrap Metropolis-Hastings (BMH) algorithm, which provides a general framework for how to tame powerful MCMC methods to be used for big data analysis; that is to replace the full data log-likelihood by a Monte Carlo average of the log-likelihoods that are calculated in parallel from multiple bootstrap samples. The BMH algorithm possesses an embarrassingly parallel structure and avoids repeated scans of the full dataset in iterations, and is thus feasible for big data problems. Compared to the popular divide-and-combine method, BMH can be generally more efficient as it can asymptotically integrate the whole data information into a single simulation run. The BMH algorithm is very flexible. Like the Metropolis-Hastings algorithm, it can serve as a basic building block for developing advanced MCMC algorithms that are feasible for big data problems. This is illustrated in the paper by the tempering BMH algorithm, which can be viewed as a combination of parallel tempering and the BMH algorithm. BMH can also be used for model selection and optimization by combining with reversible jump MCMC and simulated annealing, respectively.

Embracing equifinality with efficiency: Limits of Acceptability sampling using the DREAM(LOA) algorithm

NASA Astrophysics Data System (ADS)

Vrugt, Jasper A.; Beven, Keith J.

2018-04-01

This essay illustrates some recent developments to the DiffeRential Evolution Adaptive Metropolis (DREAM) MATLAB toolbox of Vrugt (2016) to delineate and sample the behavioural solution space of set-theoretic likelihood functions used within the GLUE (Limits of Acceptability) framework (Beven and Binley, 1992, 2014; Beven and Freer, 2001; Beven, 2006). This work builds on the DREAM(ABC) algorithm of Sadegh and Vrugt (2014) and enhances significantly the accuracy and CPU-efficiency of Bayesian inference with GLUE. In particular it is shown how lack of adequate sampling in the model space might lead to unjustified model rejection.

Activated aging dynamics and effective trap model description in the random energy model

NASA Astrophysics Data System (ADS)

Baity-Jesi, M.; Biroli, G.; Cammarota, C.

2018-01-01

We study the out-of-equilibrium aging dynamics of the random energy model (REM) ruled by a single spin-flip Metropolis dynamics. We focus on the dynamical evolution taking place on time-scales diverging with the system size. Our aim is to show to what extent the activated dynamics displayed by the REM can be described in terms of an effective trap model. We identify two time regimes: the first one corresponds to the process of escaping from a basin in the energy landscape and to the subsequent exploration of high energy configurations, whereas the second one corresponds to the evolution from a deep basin to the other. By combining numerical simulations with analytical arguments we show why the trap model description does not hold in the former but becomes exact in the second.

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

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

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan

In this study we developed an efficient Bayesian inversion framework for interpreting marine seismic amplitude versus angle (AVA) and controlled source electromagnetic (CSEM) data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo (MCMC) sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis (DREAM) and Adaptive Metropolis (AM) samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and CSEM data. The multi-chain MCMC is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration,more » the approach is used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic AVA and CSEM joint inversion provides better estimation of reservoir saturations than the seismic AVA-only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated – reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.« less

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

NASA Astrophysics Data System (ADS)

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan; Huang, Maoyi; Bao, Jie; Swiler, Laura

2017-12-01

In this study we developed an efficient Bayesian inversion framework for interpreting marine seismic Amplitude Versus Angle and Controlled-Source Electromagnetic data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis and Adaptive Metropolis samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and Controlled-Source Electromagnetic data. The multi-chain Markov-chain Monte Carlo is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration, the approach is used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic Amplitude Versus Angle and Controlled-Source Electromagnetic joint inversion provides better estimation of reservoir saturations than the seismic Amplitude Versus Angle only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated - reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.

Attributing runoff changes to climate variability and human activities: uncertainty analysis using four monthly water balance models

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

Li, Shuai; Xiong, Lihua; Li, Hong-Yi

2015-05-26

Hydrological simulations to delineate the impacts of climate variability and human activities are subjected to uncertainties related to both parameter and structure of the hydrological models. To analyze the impact of these uncertainties on the model performance and to yield more reliable simulation results, a global calibration and multimodel combination method that integrates the Shuffled Complex Evolution Metropolis (SCEM) and Bayesian Model Averaging (BMA) of four monthly water balance models was proposed. The method was applied to the Weihe River Basin (WRB), the largest tributary of the Yellow River, to determine the contribution of climate variability and human activities tomore » runoff changes. The change point, which was used to determine the baseline period (1956-1990) and human-impacted period (1991-2009), was derived using both cumulative curve and Pettitt’s test. Results show that the combination method from SCEM provides more skillful deterministic predictions than the best calibrated individual model, resulting in the smallest uncertainty interval of runoff changes attributed to climate variability and human activities. This combination methodology provides a practical and flexible tool for attribution of runoff changes to climate variability and human activities by hydrological models.« less

A stochastic simulation method for the assessment of resistive random access memory retention reliability

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

Berco, Dan, E-mail: danny.barkan@gmail.com; Tseng, Tseung-Yuen, E-mail: tseng@cc.nctu.edu.tw

This study presents an evaluation method for resistive random access memory retention reliability based on the Metropolis Monte Carlo algorithm and Gibbs free energy. The method, which does not rely on a time evolution, provides an extremely efficient way to compare the relative retention properties of metal-insulator-metal structures. It requires a small number of iterations and may be used for statistical analysis. The presented approach is used to compare the relative robustness of a single layer ZrO{sub 2} device with a double layer ZnO/ZrO{sub 2} one, and obtain results which are in good agreement with experimental data.

Bayesian inference of spectral induced polarization parameters for laboratory complex resistivity measurements of rocks and soils

NASA Astrophysics Data System (ADS)

Bérubé, Charles L.; Chouteau, Michel; Shamsipour, Pejman; Enkin, Randolph J.; Olivo, Gema R.

2017-08-01

Spectral induced polarization (SIP) measurements are now widely used to infer mineralogical or hydrogeological properties from the low-frequency electrical properties of the subsurface in both mineral exploration and environmental sciences. We present an open-source program that performs fast multi-model inversion of laboratory complex resistivity measurements using Markov-chain Monte Carlo simulation. Using this stochastic method, SIP parameters and their uncertainties may be obtained from the Cole-Cole and Dias models, or from the Debye and Warburg decomposition approaches. The program is tested on synthetic and laboratory data to show that the posterior distribution of a multiple Cole-Cole model is multimodal in particular cases. The Warburg and Debye decomposition approaches yield unique solutions in all cases. It is shown that an adaptive Metropolis algorithm performs faster and is less dependent on the initial parameter values than the Metropolis-Hastings step method when inverting SIP data through the decomposition schemes. There are no advantages in using an adaptive step method for well-defined Cole-Cole inversion. Finally, the influence of measurement noise on the recovered relaxation time distribution is explored. We provide the geophysics community with a open-source platform that can serve as a base for further developments in stochastic SIP data inversion and that may be used to perform parameter analysis with various SIP models.

Metropolis-Hastings Robbins-Monro Algorithm for Confirmatory Item Factor Analysis

ERIC Educational Resources Information Center

Cai, Li

2010-01-01

Item factor analysis (IFA), already well established in educational measurement, is increasingly applied to psychological measurement in research settings. However, high-dimensional confirmatory IFA remains a numerical challenge. The current research extends the Metropolis-Hastings Robbins-Monro (MH-RM) algorithm, initially proposed for…

Estimating a Noncompensatory IRT Model Using Metropolis within Gibbs Sampling

ERIC Educational Resources Information Center

Babcock, Ben

2011-01-01

Relatively little research has been conducted with the noncompensatory class of multidimensional item response theory (MIRT) models. A Monte Carlo simulation study was conducted exploring the estimation of a two-parameter noncompensatory item response theory (IRT) model. The estimation method used was a Metropolis-Hastings within Gibbs algorithm…

78 FR 59731 - License Amendment Request for Closure of Calcium Fluoride Ponds at Honeywell Metropolis Works...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-27

... NUCLEAR REGULATORY COMMISSION [Docket No. 40-3392; NRC-2011-0143] License Amendment Request for Closure of Calcium Fluoride Ponds at Honeywell Metropolis Works, Honeywell International, Inc. AGENCY... Federal Regulations (10 CFR) to approve the closure of the calcium fluoride ponds in-place, by...

[Study on anemia and vitamin A and vitamin D nutritional status of Chinese urban pregnant women in 2010-2012].

PubMed

Hu, Y C; Chen, J; Li, M; Wang, R; Li, W D; Yang, Y H; Yang, C; Yun, C F; Yang, L C; Yang, X G

2017-02-06

Objective: To evaluate the prevalence of anemia and the nutritional status of vitamins A and D by analyzing hemoglobin, serum retinol, and serum 25-hydroxyvitamin D levels in Chinese urban pregnant women during 2010-2012. Methods: Data were obtained from the China Nutrition and Health Survey in 2010-2012. Using multi-stage stratified sampling and population proportional stratified random sampling, 2 250 pregnant women from 34 metropolis and 41 middle-sized and small cities were included in this study. Information was collected using a questionnaire survey. The blood hemoglobin concentration was determined using the cyanmethemoglobin method, and anemia was determined using the World Health Organization guidelines combined with the elevation correction standard. The serum retinol level was determined using high-performance liquid chromatography, and vitamin A deficiency (VAD) was judged by the related standard recommended by the World Health Organization. The vitamin D level was determined using enzyme-linked immunosorbent assay and vitamin D deficiency was judged by the recommendation standards from the Institute of Medicine of The National Academies. The hemoglobin, serum retinol, and serum 25-hydroxyvitamin D levels were compared, along with differences in the prevalence of anemia, VAD, and the vitamin D deficiency rate (including deficiency and serious deficiency). Results: A total of 1 738 cases of hemoglobin level, 594 cases of serum retinol level, and 1 027 cases of serum 25-hydroxyvitamin D were available for analysis in this study. The overall blood hemoglobin level ( P (50) ( P (25)- P (75))) was 122.70 (114.00-131.10) g/L; 123.70 (115.21-132.00) g/L for metropolis and 122.01 (113.30-130.40) g/L for middle-sized and small cities. The blood hemoglobin level of metropolis residents was significantly higher than that of middle-sized and small city residents ( P= 0.027). The overall prevalence of anemia was 17.0% (295/1 738). The overall serum retinol level ( P (50) ( P (25)- P (75))) was 1.61 (1.20-2.06) μmol/L; 1.50 (1.04-2.06) μmol/L for metropolis and 1.63 (1.31-2.05) μmol/L for middle-sized and small cities. The serum retinol level of metropolis residents was significantly higher than that of middle-sized and small city residents ( P= 0.033). The overall prevalence of VAD was 7.4% (47/639); 11.5% (33/286) for metropolis and 4.0% (14/353) for middle-sized and small cities. A significant difference was observed in the prevalence of VAD between metropolis and middle-sized and small city residents ( P< 0.001). The overall serum 25-hydroxyvitamin D level ( P (50) ( P (25)- P (75))) was 15.41 (11.79-20.23) ng/ml; 14.71 (11.15-19.07) ng/ml for metropolis and 16.02 (12.65-21.36) ng/ml for middle-sized and small cities. A significant difference was observed in the vitamin D level between metropolis and middle-sized and small city residents ( P< 0.001). The overall prevalence of vitamin D deficiency was 74.3% (763/1 027); A significant difference was observed in the prevalence of serious vitamin D deficiency between metropolis (30.64%(144/470)) and middle-sized and small city residents (26%(267/1 027))( P= 0.002). There were no significant differences between blood hemoglobin level and the prevalence of anemia, VAD, and vitamin D deficiency. Conclusion: The prevalence of anemia in Chinese urban pregnant women improved from 2002 to 2012. The prevalence of vitamin D deficiency in pregnant women was generally more serious, while a certain percentage of women had VAD. The prevalence of VAD and serious vitamin D deficiency among pregnant women from metropolis was significantly higher than that of pregnant women from medium and small-sized cities.

Thermodynamics and simulation of hard-sphere fluid and solid: Kinetic Monte Carlo method versus standard Metropolis scheme

NASA Astrophysics Data System (ADS)

Ustinov, E. A.

2017-01-01

The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hard-sphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

PubMed

Chen, Yunjie; Roux, Benoît

2015-08-11

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water.

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

PubMed Central

2015-01-01

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up to 21 times for polyalanine and (AAQAA)3 in water. PMID:26574442

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

DOE PAGES

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan; ...

2017-10-17

In this paper we developed an efficient Bayesian inversion framework for interpreting marine seismic Amplitude Versus Angle and Controlled-Source Electromagnetic data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis and Adaptive Metropolis samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and Controlled-Source Electromagnetic data. The multi-chain Markov-chain Monte Carlo is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration, the approach ismore » used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic Amplitude Versus Angle and Controlled-Source Electromagnetic joint inversion provides better estimation of reservoir saturations than the seismic Amplitude Versus Angle only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated — reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.« less

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

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

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan

In this paper we developed an efficient Bayesian inversion framework for interpreting marine seismic Amplitude Versus Angle and Controlled-Source Electromagnetic data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis and Adaptive Metropolis samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and Controlled-Source Electromagnetic data. The multi-chain Markov-chain Monte Carlo is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration, the approach ismore » used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic Amplitude Versus Angle and Controlled-Source Electromagnetic joint inversion provides better estimation of reservoir saturations than the seismic Amplitude Versus Angle only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated — reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.« less

Examining Work and Family Conflict among Female Bankers in Accra Metropolis, Ghana

ERIC Educational Resources Information Center

Kissi-Abrokwah, Bernard; Andoh-Robertson, Theophilus; Tutu-Danquah, Cecilia; Agbesi, Catherine Selorm

2015-01-01

This study investigated the effects and solutions of work and family conflict among female bankers in Accra Metropolis. Using triangulatory mixed method design, a structured questionnaire was randomly administered to 300 female bankers and 15 female Bankers who were interviewed were also sampled by using convenient sampling technique. The…

Behavioural Problems of Juvenile Street Hawkers in Uyo Metropolis, Nigeria

ERIC Educational Resources Information Center

Udoh, Nsisong A.; Joseph, Eme U.

2012-01-01

The study sought the opinions of Faculty of Education Students of University of Uyo on the behavioural problems of juvenile street hawkers in Uyo metropolis. Five research hypotheses were formulated to guide the study. This cross-sectional survey employed multi-stage random sampling technique in selecting 200 regular undergraduate students in the…

Women in Educational Leadership within the Tamale Metropolis

ERIC Educational Resources Information Center

Segkulu, L.; Gyimah, K.

2016-01-01

Within the Tamale Metropolis, it is observed that only a few women occupy top level management positions within the Ghana Education Service (GES). A descriptive survey was therefore conducted in 2013/2014 academic year to assess the factors affecting the gender disparity in educational leadership within the Service. Specifically, the study sought…

77 FR 64831 - Confirmatory Order; In the Matter of Honeywell International Inc.; Metropolis, Illinois

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-23

... NUCLEAR REGULATORY COMMISSION [Docket No. 40-3392; License No. SUB-526; EA-12-157; NRC-2012-0244] Confirmatory Order; In the Matter of Honeywell International Inc.; Metropolis, Illinois I. Honeywell International Inc. (Honeywell or Licensee) is the holder of Materials License No. SUB-526, issued by the U.S...

High-Dimensional Exploratory Item Factor Analysis by a Metropolis-Hastings Robbins-Monro Algorithm

ERIC Educational Resources Information Center

Cai, Li

2010-01-01

A Metropolis-Hastings Robbins-Monro (MH-RM) algorithm for high-dimensional maximum marginal likelihood exploratory item factor analysis is proposed. The sequence of estimates from the MH-RM algorithm converges with probability one to the maximum likelihood solution. Details on the computer implementation of this algorithm are provided. The…

Environmental Awareness and School Sanitation in Calabar Metropolis of Cross Rivers State, Nigeria

ERIC Educational Resources Information Center

Anijaobi-Idem, F. N.; Ukata, B. N.; Bisong, N. N

2015-01-01

This descriptive survey designed study explored the influence of environmental awareness on secondary school sanitation in Calabar Metropolis. 1 hypothesis was formulated to direct the investigation. 300 subjects made up of 30 principals and 270 teachers constituted the sample drawn from the population of principals and teachers in secondary…

Expectancy Beliefs and English Language Performance of Secondary Schools Students in Maiduguri Metropolis, Borno State, Nigeria

ERIC Educational Resources Information Center

Musa, Alice K. J.; Nwachukwu, Kelechukwu I.; Ali, Domiya Geoffrey

2016-01-01

The study determined Relationship between Students' Expectancy Beliefs and English Language Performance of Students in Maiduguri Metropolis, Borno State, Nigeria. Correlation design was adopted for the study. Four hypotheses which determined the relationships between the components of expectancy beliefs: ability, tasks difficulty, and past…

Accelerated Dimension-Independent Adaptive Metropolis

DOE PAGES

Chen, Yuxin; Keyes, David E.; Law, Kody J.; ...

2016-10-27

This work describes improvements from algorithmic and architectural means to black-box Bayesian inference over high-dimensional parameter spaces. The well-known adaptive Metropolis (AM) algorithm [33] is extended herein to scale asymptotically uniformly with respect to the underlying parameter dimension for Gaussian targets, by respecting the variance of the target. The resulting algorithm, referred to as the dimension-independent adaptive Metropolis (DIAM) algorithm, also shows improved performance with respect to adaptive Metropolis on non-Gaussian targets. This algorithm is further improved, and the possibility of probing high-dimensional (with dimension d 1000) targets is enabled, via GPU-accelerated numerical libraries and periodically synchronized concurrent chains (justimore » ed a posteriori). Asymptotically in dimension, this GPU implementation exhibits a factor of four improvement versus a competitive CPU-based Intel MKL parallel version alone. Strong scaling to concurrent chains is exhibited, through a combination of longer time per sample batch (weak scaling) and yet fewer necessary samples to convergence. The algorithm performance is illustrated on several Gaussian and non-Gaussian target examples, in which the dimension may be in excess of one thousand.« less

Accelerated Dimension-Independent Adaptive Metropolis

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

Chen, Yuxin; Keyes, David E.; Law, Kody J.

This work describes improvements from algorithmic and architectural means to black-box Bayesian inference over high-dimensional parameter spaces. The well-known adaptive Metropolis (AM) algorithm [33] is extended herein to scale asymptotically uniformly with respect to the underlying parameter dimension for Gaussian targets, by respecting the variance of the target. The resulting algorithm, referred to as the dimension-independent adaptive Metropolis (DIAM) algorithm, also shows improved performance with respect to adaptive Metropolis on non-Gaussian targets. This algorithm is further improved, and the possibility of probing high-dimensional (with dimension d 1000) targets is enabled, via GPU-accelerated numerical libraries and periodically synchronized concurrent chains (justimore » ed a posteriori). Asymptotically in dimension, this GPU implementation exhibits a factor of four improvement versus a competitive CPU-based Intel MKL parallel version alone. Strong scaling to concurrent chains is exhibited, through a combination of longer time per sample batch (weak scaling) and yet fewer necessary samples to convergence. The algorithm performance is illustrated on several Gaussian and non-Gaussian target examples, in which the dimension may be in excess of one thousand.« less

Race, Schools and Opportunity Hoarding: Evidence from a Post-War American Metropolis

ERIC Educational Resources Information Center

Rury, John L.; Rife, Aaron Tyler

2018-01-01

Opportunity hoarding is a sociological concept first introduced by Charles Tilly. This article explores its utility for historians by examining efforts to exclude different groups of people in a major American metropolis during the 1960s and seventies. This was a period of significant social change, as the racial composition of big city schools…

Using the Metropolis Algorithm to Calculate Thermodynamic Quantities: An Undergraduate Computational Experiment

ERIC Educational Resources Information Center

Beddard, Godfrey S.

2011-01-01

Thermodynamic quantities such as the average energy, heat capacity, and entropy are calculated using a Monte Carlo method based on the Metropolis algorithm. This method is illustrated with reference to the harmonic oscillator but is particularly useful when the partition function cannot be evaluated; an example using a one-dimensional spin system…

Employee Motivation on the Organisational Growth of Printing Industry in the Kumasi Metropolis

ERIC Educational Resources Information Center

Enninful, Ebenezer Kofi; Boakye-Amponsah, Abraham; Osei-Poku, Patrick

2015-01-01

The printing industry is supposed to be a major contributor to Ghana's development through employment creation and the enhancement of information to the general public. The main purpose of the study was to assess employee motivation on the printing industry within Kumasi Metropolis. The study employed both the quantitative and qualitative surveys…

Instructional Methods and Students' End of Term Achievement in Biology in Selected Secondary Schools in Sokoto Metropolis, Sokoto State Nigeria

ERIC Educational Resources Information Center

Shamsuddeen, Abdulrahman; Amina, Hassan

2016-01-01

This study investigated the Correlation between instructional methods and students end of term achievement in Biology in selected secondary schools in Sokoto Metropolis, Sokoto State Nigeria. The study addressed three Specific objectives. To examine the relationship between; Cooperative learning methods, guided discovery, Simulation Method and…

"Metropolis," The Lights Fantastic: Semiotic Analysis of Lighting Codes in Relation to Character and Theme.

ERIC Educational Resources Information Center

Roth, Lane

Fritz Lang's "Metropolis" (1927) is a seminal film because of its concern, now generic, with the profound impact technological progress has on mankind's social and spiritual progress. As in many later science fiction films, the ascendancy of artifact over nature is depicted not as liberating human beings, but as subjecting and corrupting…

Efficient implementation of the Metropolis-Hastings algorithm, with application to the Cormack?Jolly?Seber model

USGS Publications Warehouse

Link, W.A.; Barker, R.J.

2008-01-01

Judicious choice of candidate generating distributions improves efficiency of the Metropolis-Hastings algorithm. In Bayesian applications, it is sometimes possible to identify an approximation to the target posterior distribution; this approximate posterior distribution is a good choice for candidate generation. These observations are applied to analysis of the Cormack?Jolly?Seber model and its extensions.

Family Background, Sexual Behaviour, and HIV/AIDS Vulnerability of Female Street Hawkers in Lagos Metropolis, Nigeria

ERIC Educational Resources Information Center

Oyefara, John Lekan

2005-01-01

This article examines the sexual behaviour and the HIV/AIDS knowledge and vulnerability of female street hawkers in Lagos metropolis, Nigeria. A total of 126 female street hawkers under 18 were sampled in a cross-sectional survey and six Focus Group Discussions (FGDs) were conducted to generate data from respondents. Data on sexual behaviour…

Analysis of Errors Committed by Physics Students in Secondary Schools in Ilorin Metropolis, Nigeria

ERIC Educational Resources Information Center

Omosewo, Esther Ore; Akanbi, Abdulrasaq Oladimeji

2013-01-01

The study attempt to find out the types of error committed and influence of gender on the type of error committed by senior secondary school physics students in metropolis. Six (6) schools were purposively chosen for the study. One hundred and fifty five students' scripts were randomly sampled for the study. Joint Mock physics essay questions…

Estimation of Contextual Effects through Nonlinear Multilevel Latent Variable Modeling with a Metropolis-Hastings Robbins-Monro Algorithm

ERIC Educational Resources Information Center

Yang, Ji Seung; Cai, Li

2014-01-01

The main purpose of this study is to improve estimation efficiency in obtaining maximum marginal likelihood estimates of contextual effects in the framework of nonlinear multilevel latent variable model by adopting the Metropolis-Hastings Robbins-Monro algorithm (MH-RM). Results indicate that the MH-RM algorithm can produce estimates and standard…

Challenges Pre-School Teachers Face in the Implementation of the Early Childhood Curriculum in the Cape Coast Metropolis

ERIC Educational Resources Information Center

Ntumi, Simon

2016-01-01

The study examined the challenges that pre-school teachers encounter in the implementation of the early childhood curriculum; exploring teaching methods employed by pre-schools teachers in the Cape Coast Metropolis. The study employed descriptive survey as the research design. A convenient sample of 62 pre-school teachers were selected from a…

Students' Perception of Factors Influencing Teaching and Learning of Mathematics in Senior Secondary Schools in Maiduguri Metropolis, Borno State, Nigeria

ERIC Educational Resources Information Center

Dauda, Bala; Jambo, Hyelni Emmanuel; Umar, Muhammad Amin

2016-01-01

This study examined students' perception of factors influencing teaching and learning of mathematics in senior secondary schools in Maiduguri Metropolis of Borno State, Nigeria. The objectives of the study were to determine the extent to which students perceived: qualification, method of teaching, instructional materials and attitude of both…

Putting the Learning in Service Learning: From Soup Kitchen Models to the Black Metropolis Model

ERIC Educational Resources Information Center

Manley, Theodoric, Jr.; Buffa, Avery S.; Dube, Caleb; Reed, Lauren

2006-01-01

Results of the Black Metropolis Model (BMM) of service learning are analyzed and illustrated in this article to explain how to "put the learning in service learning." There are many soup kitchens or nontransforming models of service learning where students are asked to serve needy populations but internalize and learn little about the…

Stakeholders' Perception on Teachers' Assessment Effectiveness in Secondary Schools in Port Harcourt Metropolis in Rivers State

ERIC Educational Resources Information Center

Ogidi, Reuben C.; Udechukwu, Jonathan O.

2017-01-01

The study sought to investigate the perception of stakeholders on teachers' assessment effectiveness in secondary schools in Port Harcourt Metropolis in Rivers State. Three research questions and one hypothesis were formulated to guide the study. The study adopted survey research design. The sample of the study consisted of 20 principles, 30 vice…

Adolescents' Perception of the Psychological Security of School Environment, Emotional Development and Academic Performance in Secondary Schools in Gombe Metropolis

ERIC Educational Resources Information Center

Musa, Alice K. J.; Meshak, Bibi; Sagir, Jummai Ibrahim

2016-01-01

The purpose of the study was to determine adolescents' perceptions of the psychological security of their schools environments and their relationship with their emotional development and academic performance in secondary schools in Gombe Metropolis. A sample of 239 (107 males and 133 females) secondary school students selected via stratified…

Evidence for a magma reservoir beneath the Taipei metropolis of Taiwan from both S-wave shadows and P-wave delays.

PubMed

Lin, Cheng-Horng

2016-12-23

There are more than 7 million people living near the Tatun volcano group in northern Taiwan. For the safety of the Taipei metropolis, in particular, it has been debated for decades whether or not these volcanoes are active. Here I show evidence of a deep magma reservoir beneath the Taipei metropolis from both S-wave shadows and P-wave delays. The reservoir is probably composed of either a thin magma layer overlay or many molten sills within thick partially molten rocks. Assuming that 40% of the reservoir is partially molten, its total volume could be approximately 350 km 3 . The exact location and geometry of the magma reservoir will be obtained after dense seismic arrays are deployed in 2017-2020.

Adaptation, Commissioning, and Evaluation of a 3D Treatment Planning System for High-Resolution Small-Animal Irradiation

PubMed Central

Jeong, Jeho; Chen, Qing; Febo, Robert; Yang, Jie; Pham, Hai; Xiong, Jian-Ping; Zanzonico, Pat B.; Deasy, Joseph O.; Humm, John L.; Mageras, Gig S.

2016-01-01

Although spatially precise systems are now available for small-animal irradiations, there are currently limited software tools available for treatment planning for such irradiations. We report on the adaptation, commissioning, and evaluation of a 3-dimensional treatment planning system for use with a small-animal irradiation system. The 225-kV X-ray beam of the X-RAD 225Cx microirradiator (Precision X-Ray) was commissioned using both ion-chamber and radiochromic film for 10 different collimators ranging in field size from 1 mm in diameter to 40 × 40 mm2. A clinical 3-dimensional treatment planning system (Metropolis) developed at our institution was adapted to small-animal irradiation by making it compatible with the dimensions of mice and rats, modeling the microirradiator beam orientations and collimators, and incorporating the measured beam data for dose calculation. Dose calculations in Metropolis were verified by comparison with measurements in phantoms. Treatment plans for irradiation of a tumor-bearing mouse were generated with both the Metropolis and the vendor-supplied software. The calculated beam-on times and the plan evaluation tools were compared. The dose rate at the central axis ranges from 74 to 365 cGy/min depending on the collimator size. Doses calculated with Metropolis agreed with phantom measurements within 3% for all collimators. The beam-on times calculated by Metropolis and the vendor-supplied software agreed within 1% at the isocenter. The modified 3-dimensional treatment planning system provides better visualization of the relationship between the X-ray beams and the small-animal anatomy as well as more complete dosimetric information on target tissues and organs at risk. It thereby enhances the potential of image-guided microirradiator systems for evaluation of dose–response relationships and for preclinical experimentation generally. PMID:25948321

A comparative study of noise pollution levels in some selected areas in Ilorin Metropolis, Nigeria.

PubMed

Oyedepo, Olayinka S; Saadu, Abdullahi A

2009-11-01

The noise pollution is a major problem for the quality of life in urban areas. This study was conducted to compare the noise pollution levels at busy roads/road junctions, passengers loading parks, commercial, industrial and residential areas in Ilorin metropolis. A total number of 47-locations were selected within the metropolis. Statistical analysis shows significant difference (P < 0.05) in noise pollution levels between industrial areas and low density residential areas, industrial areas and high density areas, industrial areas and passengers loading parks, industrial areas and commercial areas, busy roads/road junctions and low density areas, passengers loading parks and commercial areas and commercial areas and low density areas. There is no significant difference (P > 0.05) in noise pollution levels between industrial areas and busy roads/road junctions, busy roads/road junctions and high density areas, busy roads/road junctions and passengers loading parks, busy roads/road junctions and commercial areas, passengers loading parks and high density areas, passengers loading parks and commercial areas and commercial areas and high density areas. The results show that Industrial areas have the highest noise pollution levels (110.2 dB(A)) followed by busy roads/Road junctions (91.5 dB(A)), Passengers loading parks (87.8 dB(A)) and Commercial areas (84.4 dB(A)). The noise pollution levels in Ilorin metropolis exceeded the recommended level by WHO at 34 of 47 measuring points. It can be concluded that the city is environmentally noise polluted and road traffic and industrial machineries are the major sources of it. Noting the noise emission standards, technical control measures, planning and promoting the citizens awareness about the high noise risk may help to relieve the noise problem in the metropolis.

Water Oxidation Catalysis for NiOOH by a Metropolis Monte Carlo Algorithm.

PubMed

Hareli, Chen; Caspary Toroker, Maytal

2018-05-08

Understanding catalytic mechanisms is important for discovering better catalysts, particularly for water splitting reactions that are of great interest to the renewable energy field. One of the best performing catalysts for water oxidation is nickel oxyhydroxide (NiOOH). However, only one mechanism has been adopted so far for modeling catalysis of the active plane: β-NiOOH(01̅5). In order to understand how a second reaction mechanism affects catalysis, we perform Density Functional Theory + U (DFT+U) calculations of a second mechanism for water oxidation reaction of NiOOH. Then, we use a Metropolis Monte Carlo algorithm to calculate how many catalytic cycles are completed when two reaction mechanisms are competing. We find that within the Metropolis algorithm, the second mechanism has a higher overpotential and is therefore not active even for large applied biases.

Evidence for a magma reservoir beneath the Taipei metropolis of Taiwan from both S-wave shadows and P-wave delays

PubMed Central

Lin, Cheng-Horng

2016-01-01

There are more than 7 million people living near the Tatun volcano group in northern Taiwan. For the safety of the Taipei metropolis, in particular, it has been debated for decades whether or not these volcanoes are active. Here I show evidence of a deep magma reservoir beneath the Taipei metropolis from both S-wave shadows and P-wave delays. The reservoir is probably composed of either a thin magma layer overlay or many molten sills within thick partially molten rocks. Assuming that 40% of the reservoir is partially molten, its total volume could be approximately 350 km3. The exact location and geometry of the magma reservoir will be obtained after dense seismic arrays are deployed in 2017–2020. PMID:28008931

Entanglement complexity in quantum many-body dynamics, thermalization, and localization

NASA Astrophysics Data System (ADS)

Yang, Zhi-Cheng; Hamma, Alioscia; Giampaolo, Salvatore M.; Mucciolo, Eduardo R.; Chamon, Claudio

2017-07-01

Entanglement is usually quantified by von Neumann entropy, but its properties are much more complex than what can be expressed with a single number. We show that the three distinct dynamical phases known as thermalization, Anderson localization, and many-body localization are marked by different patterns of the spectrum of the reduced density matrix for a state evolved after a quantum quench. While the entanglement spectrum displays Poisson statistics for the case of Anderson localization, it displays universal Wigner-Dyson statistics for both the cases of many-body localization and thermalization, albeit the universal distribution is asymptotically reached within very different time scales in these two cases. We further show that the complexity of entanglement, revealed by the possibility of disentangling the state through a Metropolis-like algorithm, is signaled by whether the entanglement spectrum level spacing is Poisson or Wigner-Dyson distributed.

An Improved Nested Sampling Algorithm for Model Selection and Assessment

NASA Astrophysics Data System (ADS)

Zeng, X.; Ye, M.; Wu, J.; WANG, D.

2017-12-01

Multimodel strategy is a general approach for treating model structure uncertainty in recent researches. The unknown groundwater system is represented by several plausible conceptual models. Each alternative conceptual model is attached with a weight which represents the possibility of this model. In Bayesian framework, the posterior model weight is computed as the product of model prior weight and marginal likelihood (or termed as model evidence). As a result, estimating marginal likelihoods is crucial for reliable model selection and assessment in multimodel analysis. Nested sampling estimator (NSE) is a new proposed algorithm for marginal likelihood estimation. The implementation of NSE comprises searching the parameters' space from low likelihood area to high likelihood area gradually, and this evolution is finished iteratively via local sampling procedure. Thus, the efficiency of NSE is dominated by the strength of local sampling procedure. Currently, Metropolis-Hasting (M-H) algorithm and its variants are often used for local sampling in NSE. However, M-H is not an efficient sampling algorithm for high-dimensional or complex likelihood function. For improving the performance of NSE, it could be feasible to integrate more efficient and elaborated sampling algorithm - DREAMzs into the local sampling. In addition, in order to overcome the computation burden problem of large quantity of repeating model executions in marginal likelihood estimation, an adaptive sparse grid stochastic collocation method is used to build the surrogates for original groundwater model.

General Metropolis-Hastings jump diffusions for automatic target recognition in infrared scenes

NASA Astrophysics Data System (ADS)

Lanterman, Aaron D.; Miller, Michael I.; Snyder, Donald L.

1997-04-01

To locate and recognize ground-based targets in forward- looking IR (FLIR) images, 3D faceted models with associated pose parameters are formulated to accommodate the variability found in FLIR imagery. Taking a Bayesian approach, scenes are simulated from the emissive characteristics of the CAD models and compared with the collected data by a likelihood function based on sensor statistics. This likelihood is combined with a prior distribution defined over the set of possible scenes to form a posterior distribution. To accommodate scenes with variable numbers of targets, the posterior distribution is defined over parameter vectors of varying dimension. An inference algorithm based on Metropolis-Hastings jump- diffusion processes empirically samples from the posterior distribution, generating configurations of templates and transformations that match the collected sensor data with high probability. The jumps accommodate the addition and deletion of targets and the estimation of target identities; diffusions refine the hypotheses by drifting along the gradient of the posterior distribution with respect to the orientation and position parameters. Previous results on jumps strategies analogous to the Metropolis acceptance/rejection algorithm, with proposals drawn from the prior and accepted based on the likelihood, are extended to encompass general Metropolis-Hastings proposal densities. In particular, the algorithm proposes moves by drawing from the posterior distribution over computationally tractible subsets of the parameter space. The algorithm is illustrated by an implementation on a Silicon Graphics Onyx/Reality Engine.

Quality assessment of MEG-to-MRI coregistrations

NASA Astrophysics Data System (ADS)

Sonntag, Hermann; Haueisen, Jens; Maess, Burkhard

2018-04-01

For high precision in source reconstruction of magnetoencephalography (MEG) or electroencephalography data, high accuracy of the coregistration of sources and sensors is mandatory. Usually, the source space is derived from magnetic resonance imaging (MRI). In most cases, however, no quality assessment is reported for sensor-to-MRI coregistrations. If any, typically root mean squares (RMS) of point residuals are provided. It has been shown, however, that RMS of residuals do not correlate with coregistration errors. We suggest using target registration error (TRE) as criterion for the quality of sensor-to-MRI coregistrations. TRE measures the effect of uncertainty in coregistrations at all points of interest. In total, 5544 data sets with sensor-to-head and 128 head-to-MRI coregistrations, from a single MEG laboratory, were analyzed. An adaptive Metropolis algorithm was used to estimate the optimal coregistration and to sample the coregistration parameters (rotation and translation). We found an average TRE between 1.3 and 2.3 mm at the head surface. Further, we observed a mean absolute difference in coregistration parameters between the Metropolis and iterative closest point algorithm of (1.9 +/- 15){\\hspace{0pt}}\\circ and (1.1 +/- 9) m. A paired sample t-test indicated a significant improvement in goal function minimization by using the Metropolis algorithm. The sampled parameters allowed computation of TRE on the entire grid of the MRI volume. Hence, we recommend the Metropolis algorithm for head-to-MRI coregistrations.

Hybrid optimization and Bayesian inference techniques for a non-smooth radiation detection problem

DOE PAGES

Stefanescu, Razvan; Schmidt, Kathleen; Hite, Jason; ...

2016-12-12

In this paper, we propose several algorithms to recover the location and intensity of a radiation source located in a simulated 250 × 180 m block of an urban center based on synthetic measurements. Radioactive decay and detection are Poisson random processes, so we employ likelihood functions based on this distribution. Owing to the domain geometry and the proposed response model, the negative logarithm of the likelihood is only piecewise continuous differentiable, and it has multiple local minima. To address these difficulties, we investigate three hybrid algorithms composed of mixed optimization techniques. For global optimization, we consider simulated annealing, particlemore » swarm, and genetic algorithm, which rely solely on objective function evaluations; that is, they do not evaluate the gradient in the objective function. By employing early stopping criteria for the global optimization methods, a pseudo-optimum point is obtained. This is subsequently utilized as the initial value by the deterministic implicit filtering method, which is able to find local extrema in non-smooth functions, to finish the search in a narrow domain. These new hybrid techniques, combining global optimization and implicit filtering address, difficulties associated with the non-smooth response, and their performances, are shown to significantly decrease the computational time over the global optimization methods. To quantify uncertainties associated with the source location and intensity, we employ the delayed rejection adaptive Metropolis and DiffeRential Evolution Adaptive Metropolis algorithms. Finally, marginal densities of the source properties are obtained, and the means of the chains compare accurately with the estimates produced by the hybrid algorithms.« less

Assessment of parametric uncertainty for groundwater reactive transport modeling,

USGS Publications Warehouse

Shi, Xiaoqing; Ye, Ming; Curtis, Gary P.; Miller, Geoffery L.; Meyer, Philip D.; Kohler, Matthias; Yabusaki, Steve; Wu, Jichun

2014-01-01

The validity of using Gaussian assumptions for model residuals in uncertainty quantification of a groundwater reactive transport model was evaluated in this study. Least squares regression methods explicitly assume Gaussian residuals, and the assumption leads to Gaussian likelihood functions, model parameters, and model predictions. While the Bayesian methods do not explicitly require the Gaussian assumption, Gaussian residuals are widely used. This paper shows that the residuals of the reactive transport model are non-Gaussian, heteroscedastic, and correlated in time; characterizing them requires using a generalized likelihood function such as the formal generalized likelihood function developed by Schoups and Vrugt (2010). For the surface complexation model considered in this study for simulating uranium reactive transport in groundwater, parametric uncertainty is quantified using the least squares regression methods and Bayesian methods with both Gaussian and formal generalized likelihood functions. While the least squares methods and Bayesian methods with Gaussian likelihood function produce similar Gaussian parameter distributions, the parameter distributions of Bayesian uncertainty quantification using the formal generalized likelihood function are non-Gaussian. In addition, predictive performance of formal generalized likelihood function is superior to that of least squares regression and Bayesian methods with Gaussian likelihood function. The Bayesian uncertainty quantification is conducted using the differential evolution adaptive metropolis (DREAM(zs)) algorithm; as a Markov chain Monte Carlo (MCMC) method, it is a robust tool for quantifying uncertainty in groundwater reactive transport models. For the surface complexation model, the regression-based local sensitivity analysis and Morris- and DREAM(ZS)-based global sensitivity analysis yield almost identical ranking of parameter importance. The uncertainty analysis may help select appropriate likelihood functions, improve model calibration, and reduce predictive uncertainty in other groundwater reactive transport and environmental modeling.

MontePython 3: Parameter inference code for cosmology

NASA Astrophysics Data System (ADS)

Brinckmann, Thejs; Lesgourgues, Julien; Audren, Benjamin; Benabed, Karim; Prunet, Simon

2018-05-01

MontePython 3 provides numerous ways to explore parameter space using Monte Carlo Markov Chain (MCMC) sampling, including Metropolis-Hastings, Nested Sampling, Cosmo Hammer, and a Fisher sampling method. This improved version of the Monte Python (ascl:1307.002) parameter inference code for cosmology offers new ingredients that improve the performance of Metropolis-Hastings sampling, speeding up convergence and offering significant time improvement in difficult runs. Additional likelihoods and plotting options are available, as are post-processing algorithms such as Importance Sampling and Adding Derived Parameter.

Metis: A Pure Metropolis Markov Chain Monte Carlo Bayesian Inference Library

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

Bates, Cameron Russell; Mckigney, Edward Allen

The use of Bayesian inference in data analysis has become the standard for large scienti c experiments [1, 2]. The Monte Carlo Codes Group(XCP-3) at Los Alamos has developed a simple set of algorithms currently implemented in C++ and Python to easily perform at-prior Markov Chain Monte Carlo Bayesian inference with pure Metropolis sampling. These implementations are designed to be user friendly and extensible for customization based on speci c application requirements. This document describes the algorithmic choices made and presents two use cases.

Approach of Urban Design Elements in Preservation Area Kampung Bandar Senapelan Towards Pekanbaru Metropolitan City

NASA Astrophysics Data System (ADS)

Riza, Yose; Cheris, Rika; Repi

2017-12-01

The development of Pekanbaru City is very rapid, consequently is constantly experiencing changes in buildings, areas or cultural objects that need to be preserved to be disrupted, replaced by economic-oriented development - commercial. The contradiction between the construction of the metropolis will be the beginning of the problem for urban areas. Kampong Bandar Senapelan is an early town of Pekanbaru town located on the banks of the Siak River. The settlement has a typology of Malay and vernacular Malay architecture. The existence of these villages experienced concern as a contradiction of the city's development toward the metropolis which resulted in degradation of the historical value of urban development in this region. This study was conducted to make an important assessment of preserving Kampung Bandar Senapelan as the oldest area and its great influence on the development of metropolis. Preservation of historical and cultural heritage with conservation and preservation measures is one of the urban design elements to be considered for all city stakeholders to safeguard the civilization of a generation. Considerations that will become a benchmark is the history, conservation and urban development towards the metropolis. The importance of awareness of the conservation of the city through conservation and preservation in this area can lead to new characters and values to the building and its environment and will create an atmosphere different from the rapid development (modern style). In addition, this preservation will be evident in a harmonious life with a high tolerance between multi-ethnicity that co-existed in the past.

Exploring equivalence domain in nonlinear inverse problems using Covariance Matrix Adaption Evolution Strategy (CMAES) and random sampling

NASA Astrophysics Data System (ADS)

Grayver, Alexander V.; Kuvshinov, Alexey V.

2016-05-01

This paper presents a methodology to sample equivalence domain (ED) in nonlinear partial differential equation (PDE)-constrained inverse problems. For this purpose, we first applied state-of-the-art stochastic optimization algorithm called Covariance Matrix Adaptation Evolution Strategy (CMAES) to identify low-misfit regions of the model space. These regions were then randomly sampled to create an ensemble of equivalent models and quantify uncertainty. CMAES is aimed at exploring model space globally and is robust on very ill-conditioned problems. We show that the number of iterations required to converge grows at a moderate rate with respect to number of unknowns and the algorithm is embarrassingly parallel. We formulated the problem by using the generalized Gaussian distribution. This enabled us to seamlessly use arbitrary norms for residual and regularization terms. We show that various regularization norms facilitate studying different classes of equivalent solutions. We further show how performance of the standard Metropolis-Hastings Markov chain Monte Carlo algorithm can be substantially improved by using information CMAES provides. This methodology was tested by using individual and joint inversions of magneotelluric, controlled-source electromagnetic (EM) and global EM induction data.

A quantum–quantum Metropolis algorithm

PubMed Central

Yung, Man-Hong; Aspuru-Guzik, Alán

2012-01-01

The classical Metropolis sampling method is a cornerstone of many statistical modeling applications that range from physics, chemistry, and biology to economics. This method is particularly suitable for sampling the thermal distributions of classical systems. The challenge of extending this method to the simulation of arbitrary quantum systems is that, in general, eigenstates of quantum Hamiltonians cannot be obtained efficiently with a classical computer. However, this challenge can be overcome by quantum computers. Here, we present a quantum algorithm which fully generalizes the classical Metropolis algorithm to the quantum domain. The meaning of quantum generalization is twofold: The proposed algorithm is not only applicable to both classical and quantum systems, but also offers a quantum speedup relative to the classical counterpart. Furthermore, unlike the classical method of quantum Monte Carlo, this quantum algorithm does not suffer from the negative-sign problem associated with fermionic systems. Applications of this algorithm include the study of low-temperature properties of quantum systems, such as the Hubbard model, and preparing the thermal states of sizable molecules to simulate, for example, chemical reactions at an arbitrary temperature. PMID:22215584

Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and Invasion

PubMed Central

Andasari, Vivi; Roper, Ryan T.; Swat, Maciej H.; Chaplain, Mark A. J.

2012-01-01

In this paper we present a multiscale, individual-based simulation environment that integrates CompuCell3D for lattice-based modelling on the cellular level and Bionetsolver for intracellular modelling. CompuCell3D or CC3D provides an implementation of the lattice-based Cellular Potts Model or CPM (also known as the Glazier-Graner-Hogeweg or GGH model) and a Monte Carlo method based on the metropolis algorithm for system evolution. The integration of CC3D for cellular systems with Bionetsolver for subcellular systems enables us to develop a multiscale mathematical model and to study the evolution of cell behaviour due to the dynamics inside of the cells, capturing aspects of cell behaviour and interaction that is not possible using continuum approaches. We then apply this multiscale modelling technique to a model of cancer growth and invasion, based on a previously published model of Ramis-Conde et al. (2008) where individual cell behaviour is driven by a molecular network describing the dynamics of E-cadherin and -catenin. In this model, which we refer to as the centre-based model, an alternative individual-based modelling technique was used, namely, a lattice-free approach. In many respects, the GGH or CPM methodology and the approach of the centre-based model have the same overall goal, that is to mimic behaviours and interactions of biological cells. Although the mathematical foundations and computational implementations of the two approaches are very different, the results of the presented simulations are compatible with each other, suggesting that by using individual-based approaches we can formulate a natural way of describing complex multi-cell, multiscale models. The ability to easily reproduce results of one modelling approach using an alternative approach is also essential from a model cross-validation standpoint and also helps to identify any modelling artefacts specific to a given computational approach. PMID:22461894

Monte Carlo sampling in diffusive dynamical systems

NASA Astrophysics Data System (ADS)

Tapias, Diego; Sanders, David P.; Altmann, Eduardo G.

2018-05-01

We introduce a Monte Carlo algorithm to efficiently compute transport properties of chaotic dynamical systems. Our method exploits the importance sampling technique that favors trajectories in the tail of the distribution of displacements, where deviations from a diffusive process are most prominent. We search for initial conditions using a proposal that correlates states in the Markov chain constructed via a Metropolis-Hastings algorithm. We show that our method outperforms the direct sampling method and also Metropolis-Hastings methods with alternative proposals. We test our general method through numerical simulations in 1D (box-map) and 2D (Lorentz gas) systems.

A brief history of the introduction of generalized ensembles to Markov chain Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Berg, Bernd A.

2017-03-01

The most efficient weights for Markov chain Monte Carlo calculations of physical observables are not necessarily those of the canonical ensemble. Generalized ensembles, which do not exist in nature but can be simulated on computers, lead often to a much faster convergence. In particular, they have been used for simulations of first order phase transitions and for simulations of complex systems in which conflicting constraints lead to a rugged free energy landscape. Starting off with the Metropolis algorithm and Hastings' extension, I present a minireview which focuses on the explosive use of generalized ensembles in the early 1990s. Illustrations are given, which range from spin models to peptides.

Exploring first-order phase transitions with population annealing

NASA Astrophysics Data System (ADS)

Barash, Lev Yu.; Weigel, Martin; Shchur, Lev N.; Janke, Wolfhard

2017-03-01

Population annealing is a hybrid of sequential and Markov chain Monte Carlo methods geared towards the efficient parallel simulation of systems with complex free-energy landscapes. Systems with first-order phase transitions are among the problems in computational physics that are difficult to tackle with standard methods such as local-update simulations in the canonical ensemble, for example with the Metropolis algorithm. It is hence interesting to see whether such transitions can be more easily studied using population annealing. We report here our preliminary observations from population annealing runs for the two-dimensional Potts model with q > 4, where it undergoes a first-order transition.

A Bootstrap Metropolis–Hastings Algorithm for Bayesian Analysis of Big Data

PubMed Central

Kim, Jinsu; Song, Qifan

2016-01-01

Markov chain Monte Carlo (MCMC) methods have proven to be a very powerful tool for analyzing data of complex structures. However, their computer-intensive nature, which typically require a large number of iterations and a complete scan of the full dataset for each iteration, precludes their use for big data analysis. In this paper, we propose the so-called bootstrap Metropolis-Hastings (BMH) algorithm, which provides a general framework for how to tame powerful MCMC methods to be used for big data analysis; that is to replace the full data log-likelihood by a Monte Carlo average of the log-likelihoods that are calculated in parallel from multiple bootstrap samples. The BMH algorithm possesses an embarrassingly parallel structure and avoids repeated scans of the full dataset in iterations, and is thus feasible for big data problems. Compared to the popular divide-and-combine method, BMH can be generally more efficient as it can asymptotically integrate the whole data information into a single simulation run. The BMH algorithm is very flexible. Like the Metropolis-Hastings algorithm, it can serve as a basic building block for developing advanced MCMC algorithms that are feasible for big data problems. This is illustrated in the paper by the tempering BMH algorithm, which can be viewed as a combination of parallel tempering and the BMH algorithm. BMH can also be used for model selection and optimization by combining with reversible jump MCMC and simulated annealing, respectively. PMID:29033469

Biased Metropolis Sampling for Rugged Free Energy Landscapes

NASA Astrophysics Data System (ADS)

Berg, Bernd A.

2003-11-01

Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which uses probability densities from a higher temperature to improve the algorithmic performance at a lower temperature. The method is suitable for canonical as well as for generalized ensemble simulations. A simple approximation to the full transformation is tested at room temperature for Met-Enkephalin in vacuum. Integrated autocorrelation times are found to be reduced by factors close to two and a similar improvement due to generalized ensemble methods enters multiplicatively.

Adaptive Metropolis Sampling with Product Distributions

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Lee, Chiu Fan

2005-01-01

The Metropolis-Hastings (MH) algorithm is a way to sample a provided target distribution pi(z). It works by repeatedly sampling a separate proposal distribution T(x,x') to generate a random walk {x(t)}. We consider a modification of the MH algorithm in which T is dynamically updated during the walk. The update at time t uses the {x(t' less than t)} to estimate the product distribution that has the least Kullback-Leibler distance to pi. That estimate is the information-theoretically optimal mean-field approximation to pi. We demonstrate through computer experiments that our algorithm produces samples that are superior to those of the conventional MH algorithm.

Exposure to media content and sexual health behaviour among adolescents in Lagos metropolis, Nigeria.

PubMed

Wusu, Onipede

2013-06-01

The influence of adolescents' exposure to sexual health content of mass media in their sexual health behaviour in Nigeria is still not clear. Data were gathered through a survey conducted among adolescents aged 12-19 years in Lagos metropolis between November 2009 and February 2010. A multistage sampling strategy was adopted in selecting respondents. Logistic regression technique was utilised in the analysis. The results indicate that the respondents were most frequently exposed to TV (male = 92.2; female = 94.9) and radio (male = 88.2; female = 91.7) media. The odds ratios indicate that sexual health content of mass media significantly predicted condom use, multiple sexual relationship, sexual intercourse and self reported occurrence of abortion in the study sample. The findings imply that positive media sexual health content is likely to promote sexual health among adolescents but negative contents can put adolescents' sexual health in danger. In addition, safe sex can be advanced among adolescents if the media provide accurate information on sexuality, emphasising the dangers of risky sexual practices. Finally, this study posits that accurate portrayal of sexuality in the media would contribute immensely to improving public health in the metropolis.

Assessment of radiation protection practices among radiographers in Lagos, Nigeria.

PubMed

Eze, Cletus Uche; Abonyi, Livinus Chibuzo; Njoku, Jerome; Irurhe, Nicholas Kayode; Olowu, Oluwabola

2013-11-01

Use of ionising radiation in diagnostic radiography could lead to hazards such as somatic and genetic damages. Compliance to safe work and radiation protection practices could mitigate such risks. The aim of the study was to assess the knowledge and radiation protection practices among radiographers in Lagos, Nigeria. The study was a prospective cross sectional survey. Convenience sampling technique was used to select four x-ray diagnostic centres in four tertiary hospitals in Lagos metropolis. Data were analysed with Epi- info software, version 3.5.1. Average score on assessment of knowledge was 73%. Most modern radiation protection instruments were lacking in all the centres studied. Application of shielding devices such as gonad shield for protection was neglected mostly in government hospitals. Most x-ray machines were quite old and evidence of quality assurance tests performed on such machines were lacking. Radiographers within Lagos metropolis showed an excellent knowledge of radiation protection within the study period. Adherence to radiation protection practices among radiographers in Lagos metropolis during the period studied was, however, poor. Radiographers in Lagos, Nigeria should embrace current trends in radiation protection and make more concerted efforts to apply their knowledge in protecting themselves and patients from harmful effects of ionising radiation.

Fission dynamics with microscopic level densities

NASA Astrophysics Data System (ADS)

Randrup, Jørgen; Ward, Daniel; Carlsson, Gillis; Døssing, Thomas; Möller, Peter; Åberg, Sven

2018-03-01

Working within the Langevin framework of nuclear shape dynamics, we study the dependence of the evolution on the degree of excitation. As the excitation energy of the fissioning system is increased, the pairing correlations and the shell effects diminish and the effective potential-energy surface becomes ever more liquid-drop like. This feature can be included in the treatment in a formally well-founded manner by using the local level densities as a basis for the shape evolution. This is particularly easy to understand and implement in the Metropolis treatment where the evolution is simulated by means of a random walk on the five-dimensional lattice of shapes for which the potential energy has been tabulated. Because the individual steps between two neighboring lattice sites are decided on the basis of the ratio of the statistical weights, what is needed is the ratio of the local level densities for those shapes, evaluated at the associated local excitation energies. For this purpose, we adapt a recently developed combinatorial method for calculating level densities which employs the same single-particle levels as those that were used for the calculation of the pairing and shell contributions to the macroscopic-microscopic deformation-energy surface. For each nucleus under consideration, the level density (for a fixed total angular momentum) is calculated microscopically for each of the over five million shapes given in the three-quadratic-surface parametrization. This novel treatment, which introduces no new parameters, is illustrated for the fission fragment mass distributions for selected uranium and plutonium cases.

Onset transition to cold nuclear matter from lattice QCD with heavy quarks.

PubMed

Fromm, M; Langelage, J; Lottini, S; Neuman, M; Philipsen, O

2013-03-22

Lattice QCD at finite density suffers from a severe sign problem, which has so far prohibited simulations of the cold and dense regime. Here we study the onset of nuclear matter employing a three-dimensional effective theory derived by combined strong coupling and hopping expansions, which is valid for heavy but dynamical quarks and has a mild sign problem only. Its numerical evaluations agree between a standard Metropolis and complex Langevin algorithm, where the latter is free of the sign problem. Our continuum extrapolated data approach a first order phase transition at μ(B) ≈ m(B) as the temperature approaches zero. An excellent description of the data is achieved by an analytic solution in the strong coupling limit.

Non-proportional odds multivariate logistic regression of ordinal family data.

PubMed

Zaloumis, Sophie G; Scurrah, Katrina J; Harrap, Stephen B; Ellis, Justine A; Gurrin, Lyle C

2015-03-01

Methods to examine whether genetic and/or environmental sources can account for the residual variation in ordinal family data usually assume proportional odds. However, standard software to fit the non-proportional odds model to ordinal family data is limited because the correlation structure of family data is more complex than for other types of clustered data. To perform these analyses we propose the non-proportional odds multivariate logistic regression model and take a simulation-based approach to model fitting using Markov chain Monte Carlo methods, such as partially collapsed Gibbs sampling and the Metropolis algorithm. We applied the proposed methodology to male pattern baldness data from the Victorian Family Heart Study. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Note: A pure-sampling quantum Monte Carlo algorithm with independent Metropolis.

PubMed

Vrbik, Jan; Ospadov, Egor; Rothstein, Stuart M

2016-07-14

Recently, Ospadov and Rothstein published a pure-sampling quantum Monte Carlo algorithm (PSQMC) that features an auxiliary Path Z that connects the midpoints of the current and proposed Paths X and Y, respectively. When sufficiently long, Path Z provides statistical independence of Paths X and Y. Under those conditions, the Metropolis decision used in PSQMC is done without any approximation, i.e., not requiring microscopic reversibility and without having to introduce any G(x → x'; τ) factors into its decision function. This is a unique feature that contrasts with all competing reptation algorithms in the literature. An example illustrates that dependence of Paths X and Y has adverse consequences for pure sampling.

Random Numbers and Monte Carlo Methods

NASA Astrophysics Data System (ADS)

Scherer, Philipp O. J.

Many-body problems often involve the calculation of integrals of very high dimension which cannot be treated by standard methods. For the calculation of thermodynamic averages Monte Carlo methods are very useful which sample the integration volume at randomly chosen points. After summarizing some basic statistics, we discuss algorithms for the generation of pseudo-random numbers with given probability distribution which are essential for all Monte Carlo methods. We show how the efficiency of Monte Carlo integration can be improved by sampling preferentially the important configurations. Finally the famous Metropolis algorithm is applied to classical many-particle systems. Computer experiments visualize the central limit theorem and apply the Metropolis method to the traveling salesman problem.

Note: A pure-sampling quantum Monte Carlo algorithm with independent Metropolis

NASA Astrophysics Data System (ADS)

Vrbik, Jan; Ospadov, Egor; Rothstein, Stuart M.

2016-07-01

Recently, Ospadov and Rothstein published a pure-sampling quantum Monte Carlo algorithm (PSQMC) that features an auxiliary Path Z that connects the midpoints of the current and proposed Paths X and Y, respectively. When sufficiently long, Path Z provides statistical independence of Paths X and Y. Under those conditions, the Metropolis decision used in PSQMC is done without any approximation, i.e., not requiring microscopic reversibility and without having to introduce any G(x → x'; τ) factors into its decision function. This is a unique feature that contrasts with all competing reptation algorithms in the literature. An example illustrates that dependence of Paths X and Y has adverse consequences for pure sampling.

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

PubMed Central

2016-01-01

A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys.2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD–MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD–MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems. PMID:26300709

Study on Law of Groundwater Evolution under Natural and Artificial Forcing with Case study of Haihe River Basin

NASA Astrophysics Data System (ADS)

You, Jinjun; Gan, Hong; Wang, Lin; Bi, Xue; Du, Sisi

2010-05-01

The evolution of groundwater is one of the key problems of water cycle study. It is a result of joint effect of natural condition and human activities, but until now the driving forces of groundwater system evolution were not fully understood due to the complexity of groundwater system structures and the uncertainty of affecting factors. Geology, precipitation and human activity are the main factors affecting the groundwater system evolution and interact each other, but the influence of such three factors on groundwater system are not clarified clearly on a macroscopic scale. The precipitation changes the volume of water recharge and the groundwater pumping effect the discharge of groundwater. Another important factor influencing balance of groundwater storage is the underlaying that affects the renewablility of groundwater. The underlaying is decided mainly by geological attributes but also influenced by human activited. The macroscopic environment of groundwater evolves under the natural and anthropic factors. This paper study the general law of groundwater evolution among the factors based on the case study in Haihe River Basin, a typical area with dramatic groundwater change under natural precipitation attenuation and gradually increase of water suuply. Haihe River Basin is located in north-China, covers an area of 320,041 km2 with over 40% plain areas. The plain area of Haihe Basin is densely populated with many large and medium-sized cities, including metropolis of Beijing and Tianjin, and concentrated irrigated areas, playing important roles in China's economy and food production. It is the unique basin where groundwater occupies majority of total water supply in China. Long-term groundwater over-exploitation causes a series of ecological and environmental problems that threats the sustainable development. In this paper, the historical process of groundwater balance in Haihe Basin is divided into three phases by decrease of rainfall and increase of water pumping. The different problems caused by groundwater shrinkage are summarized. The volume of recharge from natural precipitation and artificial water cycle, natural evaporation and groundwater exploitation are analyzed based on water balance. Through the historical data analysis the changing trend of coefficients of groundwater balance discovers the evolution of groundwater. The general law is concluded with deeper analysis displays the contribution of natural and artificial factors causing deterioration of groundwater balance. A general law of groundwater evolution is put forward to describe the affection of both natural and anthropogenic factors with a relation curve. Considering the water demand of future socio-economic development in Haihe River Basin, the prospective of future vision of groundwater cycle is analyzed by the law of groundwater evolution. Iterated scenario analysis based on comparison of ameliorative function on groundwater balance to point out reasonable control on groundwater exploitation and rational water allocation under the condition of completion of South-to-North Water Transfer Project that could bring more than 7 billion m3 into Haihe River Basin from Yantze River. Finally, the advantages and disadvantages are concluded through the case study and the farther research in this field is pointed out.

Characteristics, determinants, and spatial variations of ambient fungal levels in the subtropical Taipei metropolis

NASA Astrophysics Data System (ADS)

Wu, Yi-Hua; Chan, Chang-Chuan; Rao, Carol Y.; Lee, Chung-Te; Hsu, Hsiao-Hsien; Chiu, Yueh-Hsiu; Chao, H. Jasmine

This study was conducted to investigate the temporal and spatial distributions, compositions, and determinants of ambient aeroallergens in Taipei, Taiwan, a subtropical metropolis. We monitored ambient culturable fungi in Shin-Jhuang City, an urban area, and Shi-Men Township, a rural area, in Taipei metropolis from 2003 to 2004. We collected ambient fungi in the last week of every month during the study period, using duplicate Burkard portable samplers and Malt Extract Agar. The median concentration of total fungi was 1339 colony-forming units m -3 of air over the study period. The most prevalent fungi were non-sporulating fungi, Cladosporium, Penicillium, Curvularia and Aspergillus at both sites. Airborne fungal concentrations and diversity of fungal species were generally higher in urban than in rural areas. Most fungal taxa had significant seasonal variations, with higher levels in summer. Multivariate analyses showed that the levels of ambient fungi were associated positively with temperature, but negatively with ozone and several other air pollutants. Relative humidity also had a significant non-linear relationship with ambient fungal levels. We concluded that the concentrations and the compositions of ambient fungi are diverse in urban and rural areas in the subtropical region. High ambient fungal levels were related to an urban environment and environmental conditions of high temperature and low ozone levels.

Diabetes in the Cape Coast metropolis of Ghana: an assessment of risk factors, nutritional practices and lifestyle changes.

PubMed

Gato, Worlanyo E; Acquah, Samuel; Apenteng, Bettye A; Opoku, Samuel T; Boakye, Blessed K

2017-09-01

Despite the significant increase in the incidence of diabetes in Ghana, research in this area has been lagging. The purpose of the study was to assess the risk factors associated with diabetes in the Cape Coast metropolis of Ghana, and to describe nutritional practices and efforts toward lifestyle change. A convenient sample of 482 adults from the Cape Coast metropolis was surveyed using a self-reported questionnaire. The survey collected information on the demographic, socioeconomic characteristics, health status and routine nutritional practices of respondents. The aims of the study were addressed using multivariable regression analyses. A total of 8% of respondents reported that they had been diagnosed with diabetes. Older age and body weight were found to be independently associated with diabetes. Individuals living with diabetes were no more likely than those without diabetes to have taken active steps at reducing their weight. The percentage of self-reported diabetes in this population was consistent with what has been reported in previous studies in Ghana. The findings from this study highlight the need for more patient education on physical activity and weight management. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Probabilistic learning of nonlinear dynamical systems using sequential Monte Carlo

NASA Astrophysics Data System (ADS)

Schön, Thomas B.; Svensson, Andreas; Murray, Lawrence; Lindsten, Fredrik

2018-05-01

Probabilistic modeling provides the capability to represent and manipulate uncertainty in data, models, predictions and decisions. We are concerned with the problem of learning probabilistic models of dynamical systems from measured data. Specifically, we consider learning of probabilistic nonlinear state-space models. There is no closed-form solution available for this problem, implying that we are forced to use approximations. In this tutorial we will provide a self-contained introduction to one of the state-of-the-art methods-the particle Metropolis-Hastings algorithm-which has proven to offer a practical approximation. This is a Monte Carlo based method, where the particle filter is used to guide a Markov chain Monte Carlo method through the parameter space. One of the key merits of the particle Metropolis-Hastings algorithm is that it is guaranteed to converge to the "true solution" under mild assumptions, despite being based on a particle filter with only a finite number of particles. We will also provide a motivating numerical example illustrating the method using a modeling language tailored for sequential Monte Carlo methods. The intention of modeling languages of this kind is to open up the power of sophisticated Monte Carlo methods-including particle Metropolis-Hastings-to a large group of users without requiring them to know all the underlying mathematical details.

Geo-products of urban areas: Silesian Metropolis, Southern Poland

NASA Astrophysics Data System (ADS)

Chybiorz, Ryszard; Abramowicz, Anna

2017-04-01

Silesian Metropolis is located in the Silesian Voivodeship, in the most important industrial region in Poland. It consist of 14 cities with powiat rights, which create the largest urban center in Poland and one of the largest in Central and Eastern Europe. Almost 2 million people live in its territory. A large concentration of the population is associated with industrialization and especially with the development of the mining industry (Upper Silesian Coal Basin) and the processing industry (steelworks, textile industry) at the end of 19th century. One hundred years later, during the creation of the modern sectors of the economy, processes of metallurgy and mining restructuring have been started. Created mechanisms and conditions for development of post-industrial areas were consistent with the principles of sustainable development and had many new features, including cultural and touristic features. The Industrial Monuments Route was opened for the inhabitants and visitors in October 2006. The route joined the European Route of Industrial Heritage (ERIH) in 2010. Its most interesting mining attractions are located in Silesian Metropolis, and the most frequently visited object on the route is the Guido Historical Coal Mine in Zabrze and the Historical Silver Mine in Tarnowskie Góry. The project, which is realized in Zabrze, will provide for tourists a system of underground corridors, which were used for coal transportation in the 19th century. Visitors will be able to actively explore the work of miners, moving by underground boats, railway and suspension railway. Surface mines are also available for geotourists. The Ecological and Geological Education Center GEOsfera was created in a former Triassic quarry in Jaworzno. Although the area of the Silesian Metropolis is characterized by a very large devastation of the environment, the following objects were created (and are still created) on the basis of inanimate nature and they have a touristic value for the region and the country. Some of them already provide for the implementation of geotouristic purposes.

Posterior uncertainty of GEOS-5 L-band radiative transfer model parameters and brightness temperatures after calibration with SMOS observations

NASA Astrophysics Data System (ADS)

De Lannoy, G. J.; Reichle, R. H.; Vrugt, J. A.

2012-12-01

Simulated L-band (1.4 GHz) brightness temperatures are very sensitive to the values of the parameters in the radiative transfer model (RTM). We assess the optimum RTM parameter values and their (posterior) uncertainty in the Goddard Earth Observing System (GEOS-5) land surface model using observations of multi-angular brightness temperature over North America from the Soil Moisture Ocean Salinity (SMOS) mission. Two different parameter estimation methods are being compared: (i) a particle swarm optimization (PSO) approach, and (ii) an MCMC simulation procedure using the differential evolution adaptive Metropolis (DREAM) algorithm. Our results demonstrate that both methods provide similar "optimal" parameter values. Yet, DREAM exhibits better convergence properties, resulting in a reduced spread of the posterior ensemble. The posterior parameter distributions derived with both methods are used for predictive uncertainty estimation of brightness temperature. This presentation will highlight our model-data synthesis framework and summarize our initial findings.

An integrated uncertainty analysis and data assimilation approach for improved streamflow predictions

NASA Astrophysics Data System (ADS)

Hogue, T. S.; He, M.; Franz, K. J.; Margulis, S. A.; Vrugt, J. A.

2010-12-01

The current study presents an integrated uncertainty analysis and data assimilation approach to improve streamflow predictions while simultaneously providing meaningful estimates of the associated uncertainty. Study models include the National Weather Service (NWS) operational snow model (SNOW17) and rainfall-runoff model (SAC-SMA). The proposed approach uses the recently developed DiffeRential Evolution Adaptive Metropolis (DREAM) to simultaneously estimate uncertainties in model parameters, forcing, and observations. An ensemble Kalman filter (EnKF) is configured with the DREAM-identified uncertainty structure and applied to assimilating snow water equivalent data into the SNOW17 model for improved snowmelt simulations. Snowmelt estimates then serves as an input to the SAC-SMA model to provide streamflow predictions at the basin outlet. The robustness and usefulness of the approach is evaluated for a snow-dominated watershed in the northern Sierra Mountains. This presentation describes the implementation of DREAM and EnKF into the coupled SNOW17 and SAC-SMA models and summarizes study results and findings.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Kyiv Small Rivers in Metropolis Water Objects System

NASA Astrophysics Data System (ADS)

Krelshteyn, P.; Dubnytska, M.

2017-12-01

The article answers the question, what really are the small underground rivers with artificial watercourses: water bodies or city engineering infrastructure objects? The place of such rivers in metropolis water objects system is identified. The ecological state and the degree of urbanization of small rivers, as well as the dynamics of change in these indicators are analysed on the Kiev city example with the help of water objects cadastre. It was found that the registration of small rivers in Kyiv city is not conducted, and the summary information on such water objects is absent and is not taken into account when making managerial decisions at the urban level. To solve this problem, we propose to create some water bodies accounting system (water cadastre).

Gradient-free MCMC methods for dynamic causal modelling

DOE PAGES

Sengupta, Biswa; Friston, Karl J.; Penny, Will D.

2015-03-14

Here, we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density -- albeit at almost 1000% increase in computational time, in comparisonmore » to the most efficient algorithm (i.e., the adaptive MCMC sampler).« less

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Pathologic Analysis of Control Plans for Air Pollution Management in Tehran Metropolis: A Cross-Sectional Study

PubMed Central

Salehi Shahrabi, Narges; Pourezzat, Aliasghar; Mobaraki, Hossein; Mafimoradi, Shiva

2013-01-01

Abstract Background The centralization of human activities is associated with different pollutants which enter into environment easily and cause the urban environment more vulnerable. Regarding the importance of air pollution issue for Tehran metropolis, many plans and regulations have been developed. However, most of them failed to decline the pollution. The purpose of this study was to pathologically analyze air-pollution control plans to offer effective solutions for Tehran metropolis. Methods A Qualitative content analysis in addition to a semi-structured interview with 14 practicing professional were used to identify 1) key sources of Tehran’s air pollution, 2) recognize challenges towards effective performance of pertinent plans and 3), offer effective solutions. Results Related challenges to air-pollution control plans can be divided into two major categories including lack of integrated and organized stewardship and PEST challenges. Conclusion For controlling the air pollution of Tehran effectively, various controlling alternatives were identified as systematization of plan preparation process, standardization and utilization of new technologies & experts, infrastructural development, realization of social justice, developing coordination mechanisms, improving citizens’ participatory capacity and focusing on effective management of fuel and energy. Controlling air pollution in Tehran needs a serious attention of policymakers to make enforcements through applying a systemic cycle of preparation comprehensive plans. Further, implement the enforcements and evaluate the environmental impact of the plans through involving all stakeholders. PMID:26171340

Groundwater fluoride and dental fluorosis in southwestern Nigeria.

PubMed

Gbadebo, A M

2012-10-01

This study was carried out to assess the fluoride levels of groundwater from open wells, consumed by the residents of three communities located in two distinct geological terrains of southwestern Nigeria. Fluoride concentration was determined using spectrophotometric technique, while analysis of other parameters like temperature, pH and total dissolve solids followed standard methods. Results of the analysis indicated that groundwater samples from Abeokuta Metropolis (i.e., basement complex terrain) had fluoride content in the range of 0.65 ± 0.21 and 1.20 ± 0.14. These values were found to be lower than the fluoride contents in the groundwater samples from Ewekoro peri-urban and Lagos metropolis where the values ranged between 1.10 ± 0.14-1.45 ± 0.07 and 0.15 ± 0.07-2.20 ± 1.41 mg/l, respectively. The fluoride contents in almost all locations were generally higher than the WHO recommended 0.6 mg/l. Analysis of Duncan multiple range test indicated that there is similarity in the level of significance of fluoride contents between different locations of same geological terrain at p ≤ 0.05. It was also observed that fluoride distribution of groundwater samples from the different geological terrain was more dependent on factors like pH and TDS than on temperature. The result of the analyzed social demographic characteristics of the residents indicated that the adults (between the age of 20 and >40 years) showed dental decay than the adolescent (<20 years). This signifies incidence of dental fluorosis by the high fluoride content in the drinking water of the populace. Further investigation on all sources of drinking water and other causes of tooth decay in the area is suggested.

Physical Complexity and Cognitive Evolution

NASA Astrophysics Data System (ADS)

Jedlicka, Peter

Our intuition tells us that there is a general trend in the evolution of nature, a trend towards greater complexity. However, there are several definitions of complexity and hence it is difficult to argue for or against the validity of this intuition. Christoph Adami has recently introduced a novel measure called physical complexity that assigns low complexity to both ordered and random systems and high complexity to those in between. Physical complexity measures the amount of information that an organism stores in its genome about the environment in which it evolves. The theory of physical complexity predicts that evolution increases the amount of `knowledge' an organism accumulates about its niche. It might be fruitful to generalize Adami's concept of complexity to the entire evolution (including the evolution of man). Physical complexity fits nicely into the philosophical framework of cognitive biology which considers biological evolution as a progressing process of accumulation of knowledge (as a gradual increase of epistemic complexity). According to this paradigm, evolution is a cognitive `ratchet' that pushes the organisms unidirectionally towards higher complexity. Dynamic environment continually creates problems to be solved. To survive in the environment means to solve the problem, and the solution is an embodied knowledge. Cognitive biology (as well as the theory of physical complexity) uses the concepts of information and entropy and views the evolution from both the information-theoretical and thermodynamical perspective. Concerning humans as conscious beings, it seems necessary to postulate an emergence of a new kind of knowledge - a self-aware and self-referential knowledge. Appearence of selfreflection in evolution indicates that the human brain reached a new qualitative level in the epistemic complexity.

Gradient-free MCMC methods for dynamic causal modelling.

PubMed

Sengupta, Biswa; Friston, Karl J; Penny, Will D

2015-05-15

In this technical note we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density - albeit at almost 1000% increase in computational time, in comparison to the most efficient algorithm (i.e., the adaptive MCMC sampler). Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Kinematic source inversions of teleseismic data based on the QUESO library for uncertainty quantification and prediction

NASA Astrophysics Data System (ADS)

Zielke, O.; McDougall, D.; Mai, P. M.; Babuska, I.

2014-12-01

One fundamental aspect of seismic hazard mitigation is gaining a better understanding of the rupture process. Because direct observation of the relevant parameters and properties is not possible, other means such as kinematic source inversions are used instead. By constraining the spatial and temporal evolution of fault slip during an earthquake, those inversion approaches may enable valuable insights in the physics of the rupture process. However, due to the underdetermined nature of this inversion problem (i.e., inverting a kinematic source model for an extended fault based on seismic data), the provided solutions are generally non-unique. Here we present a statistical (Bayesian) inversion approach based on an open-source library for uncertainty quantification (UQ) called QUESO that was developed at ICES (UT Austin). The approach has advantages with respect to deterministic inversion approaches as it provides not only a single (non-unique) solution but also provides uncertainty bounds with it. Those uncertainty bounds help to qualitatively and quantitatively judge how well constrained an inversion solution is and how much rupture complexity the data reliably resolve. The presented inversion scheme uses only tele-seismically recorded body waves but future developments may lead us towards joint inversion schemes. After giving an insight in the inversion scheme ifself (based on delayed rejection adaptive metropolis, DRAM) we explore the method's resolution potential. For that, we synthetically generate tele-seismic data, add for example different levels of noise and/or change fault plane parameterization and then apply our inversion scheme in the attempt to extract the (known) kinematic rupture model. We conclude with exemplary inverting real tele-seismic data of a recent large earthquake and compare those results with deterministically derived kinematic source models provided by other research groups.

The New Sectionalism: I. Metropolis Without Growth

ERIC Educational Resources Information Center

Alonso, William

1978-01-01

This article suggests that there are three principal sources of metropolitan population decline: the declining birth rate, the reversal of rural-to-urban migration, and inter-metropolitan migration. (Author/AM)

Topics in Bayesian Hierarchical Modeling and its Monte Carlo Computations

NASA Astrophysics Data System (ADS)

Tak, Hyung Suk

The first chapter addresses a Beta-Binomial-Logit model that is a Beta-Binomial conjugate hierarchical model with covariate information incorporated via a logistic regression. Various researchers in the literature have unknowingly used improper posterior distributions or have given incorrect statements about posterior propriety because checking posterior propriety can be challenging due to the complicated functional form of a Beta-Binomial-Logit model. We derive data-dependent necessary and sufficient conditions for posterior propriety within a class of hyper-prior distributions that encompass those used in previous studies. Frequency coverage properties of several hyper-prior distributions are also investigated to see when and whether Bayesian interval estimates of random effects meet their nominal confidence levels. The second chapter deals with a time delay estimation problem in astrophysics. When the gravitational field of an intervening galaxy between a quasar and the Earth is strong enough to split light into two or more images, the time delay is defined as the difference between their travel times. The time delay can be used to constrain cosmological parameters and can be inferred from the time series of brightness data of each image. To estimate the time delay, we construct a Gaussian hierarchical model based on a state-space representation for irregularly observed time series generated by a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian approach jointly infers model parameters via a Gibbs sampler. We also introduce a profile likelihood of the time delay as an approximation of its marginal posterior distribution. The last chapter specifies a repelling-attracting Metropolis algorithm, a new Markov chain Monte Carlo method to explore multi-modal distributions in a simple and fast manner. This algorithm is essentially a Metropolis-Hastings algorithm with a proposal that consists of a downhill move in density that aims to make local modes repelling, followed by an uphill move in density that aims to make local modes attracting. The downhill move is achieved via a reciprocal Metropolis ratio so that the algorithm prefers downward movement. The uphill move does the opposite using the standard Metropolis ratio which prefers upward movement. This down-up movement in density increases the probability of a proposed move to a different mode.

[Problems resulting from the absorption of small towns into urban areas in major Third World cities].

PubMed

Mckee, D L

1985-01-01

The tendency toward hypertrophy of large metropolitan areas in the Third World has been a subject of concern to economists and other social scientists for some time. Inability to absorb vast waves of migrants into the organized labor force or to provide adequate infrastructure and services are serious problems in many growing cities of Asia, Africa, and Latin America. A different phenomenon created by perpetual urban expansion has been relatively neglected: the problems caused when preexisting urban areas are absorbed into the metropolis. The tendency of squatter settlements to constrict normal urban growth and expansion and to impede rational provision of services has been recognized, but the absorption of small cities does not necessarily produce identical problems. Small cities absorbed into a metropolis lose their identity in the successive waves of suburban proliferation. Los Angeles in the US may be considered the prototype of the phenomenon in which multiple preexisting urban zones are absorbed into the same metropolis without formation of any visible center of gravity. In some cases, small cities may be completely engulfed by the encroaching metropolis, if transit routes or availability of land makes them interesting to developers. The livelihood of residents may be threatened if they are no longer able to cultivate gardens or raise small animals. Local services may deteriorate. The youngest and most able residents are likely to abandon such places for the greater opportunities of the city, leaving the aged and less qualified to fend for themselves. Jobs may disappear and traditional commercial relations may be destroyed without being replaced. The future wellbeing of residents depends on their ability to maneuver in the new metropolitan environment, but many will be unable to adjust for lack of training, the weight of immovable property, or diverse personal considerations. Planning could help to reduce the problems that occasional survival of some small entities may pose for rational expansion of transportation and services at the metropolitan level, but many Third World cities lack such planning capacity altogether.

Sero-prevalence and risk factors for hepatitis E virus infection among pregnant women in the Cape Coast Metropolis, Ghana.

PubMed

Obiri-Yeboah, Dorcas; Asante Awuku, Yaw; Adu, Joseph; Pappoe, Faustina; Obboh, Evans; Nsiah, Paul; Amoako-Sakyi, Daniel; Simpore, Jacques

2018-01-01

Hepatitis E virus is an emerging infection in Africa with poor maternal and foetal outcomes. There is scanty data on the sero-prevalence of HEV infection among pregnant women in Ghana. This study highlighted the prevalence and risk factors associated with HEV infection among pregnant women in Cape Coast Metropolis, Central Region of Ghana. A multicenter (3 selected sites) analytical cross sectional study involving 398 pregnant women in the Cape Coast metropolis was conducted. HEV (Anti-HEV IgG and Anti-HEV IgM) ELISA was performed. Sero-positive women had liver chemistries done and data collected on maternal and neonatal outcomes. Data analyses were performed using Stata version 13 software (STATA Corp, Texas USA). Mean age was 28.01 (± 5.93) years. HEV sero-prevalence was 12.2% (n = 48) for IgG and 0.2% (n = 1) for IgM with overall of 12.3%. The odds of being HEV sero-positive for women aged 26-35 years was 3.1 (95% CI: 1.1-8.1), p = 0.02 and ≥36 years it was 10.7 (95% CI; 3.4-33.5), p = 0.0001. Living in urban settlement was associated with lowest odds of HEV infection {OR 0.4 (95% CI; 0.2-0.8), p = 0.01}. Factors with no statistical evidence of association include main source of drinking water and history of blood transfusion. The sero-prevalence of HEV IgG increased progressively across trimesters with the highest among women in their third trimester (55.3%). None of the 49 HEV sero-positive women had elevated ALT level. Ten (N = 41) of the neonates born to sero-positive women developed jaundice in the neonatal period. The mean birth weight was 3.1kg (SD 0.4). HEV sero-prevalence among pregnant women in the Cape Coast Metropolis is high enough to deserve more attention than it has received so far. It is therefore important to conduct further research on the potential impact on maternal and neonatal mortality and morbidity in Ghana.

Evolution of biological complexity

PubMed Central

Adami, Christoph; Ofria, Charles; Collier, Travis C.

2000-01-01

To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural “Maxwell Demon,” within a fixed environment, genomic complexity is forced to increase. PMID:10781045

A sampling algorithm for segregation analysis

PubMed Central

Tier, Bruce; Henshall, John

2001-01-01

Methods for detecting Quantitative Trait Loci (QTL) without markers have generally used iterative peeling algorithms for determining genotype probabilities. These algorithms have considerable shortcomings in complex pedigrees. A Monte Carlo Markov chain (MCMC) method which samples the pedigree of the whole population jointly is described. Simultaneous sampling of the pedigree was achieved by sampling descent graphs using the Metropolis-Hastings algorithm. A descent graph describes the inheritance state of each allele and provides pedigrees guaranteed to be consistent with Mendelian sampling. Sampling descent graphs overcomes most, if not all, of the limitations incurred by iterative peeling algorithms. The algorithm was able to find the QTL in most of the simulated populations. However, when the QTL was not modeled or found then its effect was ascribed to the polygenic component. No QTL were detected when they were not simulated. PMID:11742631

Galactic Metropolis

NASA Image and Video Library

2013-12-18

The collection of red dots seen here show one of several very distant galaxy clusters discovered by combining ground-based optical data from the NOAO Kitt Peak National Observatory with infrared data from NASA Spitzer Space Telescope.

Exact posterior computation in non-conjugate Gaussian location-scale parameters models

NASA Astrophysics Data System (ADS)

Andrade, J. A. A.; Rathie, P. N.

2017-12-01

In Bayesian analysis the class of conjugate models allows to obtain exact posterior distributions, however this class quite restrictive in the sense that it involves only a few distributions. In fact, most of the practical applications involves non-conjugate models, thus approximate methods, such as the MCMC algorithms, are required. Although these methods can deal with quite complex structures, some practical problems can make their applications quite time demanding, for example, when we use heavy-tailed distributions, convergence may be difficult, also the Metropolis-Hastings algorithm can become very slow, in addition to the extra work inevitably required on choosing efficient candidate generator distributions. In this work, we draw attention to the special functions as a tools for Bayesian computation, we propose an alternative method for obtaining the posterior distribution in Gaussian non-conjugate models in an exact form. We use complex integration methods based on the H-function in order to obtain the posterior distribution and some of its posterior quantities in an explicit computable form. Two examples are provided in order to illustrate the theory.

Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells

NASA Astrophysics Data System (ADS)

Fu, Yan; Glaros, Trevor; Zhu, Meng; Wang, Ping; Wu, Zhanghan; Tyson, John; Li, Liwu; Xing, Jianhua

2012-01-01

The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are classic examples of the complex adaptation of innate immune cells. Upon repetitive exposures to different doses of bacterial endotoxin (lipopolysaccharide) or other stimulants, macrophages show either suppressed or augmented inflammatory responses compared to a single exposure to the stimulant. Endotoxin tolerance and priming are critically involved in both immune homeostasis and the pathogenesis of diverse inflammatory diseases. However, the underlying molecular mechanisms are not well understood. By means of a computational search through the parameter space of a coarse-grained three-node network with a two-stage Metropolis sampling approach, we enumerated all the network topologies that can generate priming or tolerance. We discovered three major mechanisms for priming (pathway synergy, suppressor deactivation, activator induction) and one for tolerance (inhibitor persistence). These results not only explain existing experimental observations, but also reveal intriguing test scenarios for future experimental studies to clarify mechanisms of endotoxin priming and tolerance.

Evolution and complexity: the double-edged sword.

PubMed

Miconi, Thomas

2008-01-01

We attempt to provide a comprehensive answer to the question of whether, and when, an arrow of complexity emerges in Darwinian evolution. We note that this expression can be interpreted in different ways, including a passive, incidental growth, or a pervasive bias towards complexification. We argue at length that an arrow of complexity does indeed occur in evolution, which can be most reasonably interpreted as the result of a passive trend rather than a driven one. What, then, is the role of evolution in the creation of this trend, and under which conditions will it emerge? In the later sections of this article we point out that when certain proper conditions (which we attempt to formulate in a concise form) are met, Darwinian evolution predictably creates a sustained trend of increase in maximum complexity (that is, an arrow of complexity) that would not be possible without it; but if they are not, evolution will not only fail to produce an arrow of complexity, but may actually prevent any increase in complexity altogether. We conclude that, with regard to the growth of complexity, evolution is very much a double-edged sword.

78 FR 962 - Sunshine Act Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-07

.... (Metropolis Works Uranium Conversion Facility), Docket No. 40-3392, Petition for Review of LBP-12-6 (Mar. 22...--Tentative Thursday, February 7, 2013 1:00 p.m. Briefing on Steam Generator Tube Degradation (Public Meeting...

Delhi, India

NASA Image and Video Library

2008-01-17

Delhi is the second largest metropolis in India, with a population of 16 million and is located in northern India along the banks of the Yamuna River. This image was acquired by NASA Terra satellite on September 22, 2003.

Bayesian forecasting and uncertainty quantifying of stream flows using Metropolis-Hastings Markov Chain Monte Carlo algorithm

NASA Astrophysics Data System (ADS)

Wang, Hongrui; Wang, Cheng; Wang, Ying; Gao, Xiong; Yu, Chen

2017-06-01

This paper presents a Bayesian approach using Metropolis-Hastings Markov Chain Monte Carlo algorithm and applies this method for daily river flow rate forecast and uncertainty quantification for Zhujiachuan River using data collected from Qiaotoubao Gage Station and other 13 gage stations in Zhujiachuan watershed in China. The proposed method is also compared with the conventional maximum likelihood estimation (MLE) for parameter estimation and quantification of associated uncertainties. While the Bayesian method performs similarly in estimating the mean value of daily flow rate, it performs over the conventional MLE method on uncertainty quantification, providing relatively narrower reliable interval than the MLE confidence interval and thus more precise estimation by using the related information from regional gage stations. The Bayesian MCMC method might be more favorable in the uncertainty analysis and risk management.

Modelling maximum river flow by using Bayesian Markov Chain Monte Carlo

NASA Astrophysics Data System (ADS)

Cheong, R. Y.; Gabda, D.

2017-09-01

Analysis of flood trends is vital since flooding threatens human living in terms of financial, environment and security. The data of annual maximum river flows in Sabah were fitted into generalized extreme value (GEV) distribution. Maximum likelihood estimator (MLE) raised naturally when working with GEV distribution. However, previous researches showed that MLE provide unstable results especially in small sample size. In this study, we used different Bayesian Markov Chain Monte Carlo (MCMC) based on Metropolis-Hastings algorithm to estimate GEV parameters. Bayesian MCMC method is a statistical inference which studies the parameter estimation by using posterior distribution based on Bayes’ theorem. Metropolis-Hastings algorithm is used to overcome the high dimensional state space faced in Monte Carlo method. This approach also considers more uncertainty in parameter estimation which then presents a better prediction on maximum river flow in Sabah.

Fault zone structure and inferences on past activities of the active Shanchiao Fault in the Taipei metropolis, northern Taiwan

NASA Astrophysics Data System (ADS)

Chen, C.; Lee, J.; Chan, Y.; Lu, C.

2010-12-01

The Taipei Metropolis, home to around 10 million people, is subject to seismic hazard originated from not only distant faults or sources scattered throughout the Taiwan region, but also active fault lain directly underneath. Northern Taiwan including the Taipei region is currently affected by post-orogenic (Penglai arc-continent collision) processes related to backarc extension of the Ryukyu subduction system. The Shanchiao Fault, an active normal fault outcropping along the western boundary of the Taipei Basin and dipping to the east, is investigated here for its subsurface structure and activities. Boreholes records in the central portion of the fault were analyzed to document the stacking of post- Last Glacial Maximum growth sediments, and a tulip flower structure is illuminated with averaged vertical slip rate of about 3 mm/yr. Similar fault zone architecture and post-LGM tectonic subsidence rate is also found in the northern portion of the fault. A correlation between geomorphology and structural geology in the Shanchiao Fault zone demonstrates an array of subtle geomorphic scarps corresponds to the branch fault while the surface trace of the main fault seems to be completely erased by erosion and sedimentation. Such constraints and knowledge are crucial in earthquake hazard evaluation and mitigation in the Taipei Metropolis, and in understanding the kinematics of transtensional tectonics in northern Taiwan. Schematic 3D diagram of the fault zone in the central portion of the Shanchiao Fault, displaying regional subsurface geology and its relation to topographic features.

Wheelchair accessibility to public buildings in the Kumasi metropolis, Ghana.

PubMed

Yarfi, Cosmos; Ashigbi, Evans Y K; Nakua, Emmanuel K

2017-01-01

Accessibility implies making public places accessible to every individual, irrespective of his or her disability or special need, ensuring the integration of the wheelchair user into the society and thereby granting them the capability of participating in activities of daily living and ensuring equality in daily life. This study was carried out to assess the accessibility of the physical infrastructures (public buildings) in the Kumasi metropolis to wheelchairs after the passage of the Ghanaian Disability Law (Act 716, 2006). Eighty-four public buildings housing education facilities, health facilities, ministries, departments and agencies, sports and recreation, religious groups and banks were assessed. The routes, entrances, height of steps, grade of ramps, sinks, entrance to washrooms, toilets, urinals, automated teller machines and tellers' counters were measured and computed. Out of a total of 84 buildings assessed, only 34 (40.5%) of the buildings, 52.3% of the entrances and 87.4% of the routes of the buildings were accessible to wheelchair users. A total of 25% (13 out of 52) of the public buildings with more than one floor were fitted with elevators to connect the different levels of floors. The results of this study show that public buildings in the Kumasi metropolis are not wheelchair accessible. An important observation made during this study was that there is an intention to improve accessibility when buildings are being constructed or renovated, but there are no laid down guidelines as how to make the buildings accessible for wheelchair users.

Ocular Health and Safety Assessment among Mechanics of the Cape Coast Metropolis, Ghana.

PubMed

Abu, Emmanuel Kwasi; Boadi-Kusi, Samuel Bert; Opuni, Prince Quarcoo; Kyei, Samuel; Owusu-Ansah, Andrew; Darko-Takyi, Charles

2016-01-01

To conduct an ocular health and safety assessment among mechanics in the Cape Coast Metropolis, Ghana. This descriptive cross sectional study included 500 mechanics using multistage sampling. All participants filled a structured questionnaire on demographic data, occupational history and ocular health history. Study participants underwent determination of visual acuity (VA) using LogMAR chart, external eye examination with a handheld slit lamp biomicroscope, dilated fundus examination, applanation tonometry and refraction. Out of 500 mechanics, 433 were examined (response rate, 87%) comprised of 408 (94.2%) male and 25 (5.8%) female subjects. The prevalence of visual impairment (i.e. presenting VA < 6/18) among the respondents was 2.1%. Eye injuries were reported in 171 (39.5%) mechanics probably due to the large number of workers, 314 (72.5%), who did not use eye protective devices. Mechanics in the auto welding category were at the highest risk of sustaining an eye injury (odds ratio [OR], 13.4; P < 0.001). Anterior segment ocular disorders were mostly pterygia while posterior segment eye disorders included glaucoma suspects and retinochoroidal lesions. The development of pterygia was associated with the number of years a mechanic stayed on the job. Eye care seeking behavior among the participants was poor. Eye injuries were prevalent among the mechanics as the use of eye protection was low. Eye safety should be made an integral part of the public health agenda in the Cape Coast Metropolis.

Wheelchair accessibility to public buildings in the Kumasi metropolis, Ghana

PubMed Central

Ashigbi, Evans Y.K.

2017-01-01

Background Accessibility implies making public places accessible to every individual, irrespective of his or her disability or special need, ensuring the integration of the wheelchair user into the society and thereby granting them the capability of participating in activities of daily living and ensuring equality in daily life. Objective This study was carried out to assess the accessibility of the physical infrastructures (public buildings) in the Kumasi metropolis to wheelchairs after the passage of the Ghanaian Disability Law (Act 716, 2006). Methods Eighty-four public buildings housing education facilities, health facilities, ministries, departments and agencies, sports and recreation, religious groups and banks were assessed. The routes, entrances, height of steps, grade of ramps, sinks, entrance to washrooms, toilets, urinals, automated teller machines and tellers’ counters were measured and computed. Results Out of a total of 84 buildings assessed, only 34 (40.5%) of the buildings, 52.3% of the entrances and 87.4% of the routes of the buildings were accessible to wheelchair users. A total of 25% (13 out of 52) of the public buildings with more than one floor were fitted with elevators to connect the different levels of floors. Conclusion The results of this study show that public buildings in the Kumasi metropolis are not wheelchair accessible. An important observation made during this study was that there is an intention to improve accessibility when buildings are being constructed or renovated, but there are no laid down guidelines as how to make the buildings accessible for wheelchair users. PMID:29062761

Awareness and knowledge of National School Health Policy and School Health Programme among public secondary school teachers in Ibadan metropolis

PubMed Central

Obembe, Taiwo A.; Osungbade, Kayode O.; Ademokun, Oluwakemi M.

2016-01-01

Background: The awareness, knowledge, and involvement of teachers in the implementation of School Health Programme (SHP) in secondary schools are essential in ensuring the effectiveness and overall success of the School Health Policy. This study assessed the awareness and knowledge of teachers on SHP in Ibadan metropolis. Methods: A descriptive cross-sectional study was carried out using a two-stage sampling technique to select 426 secondary school teachers across all the five Urban Local Government Areas (LGAs) in Ibadan metropolis by balloting. Pretested semi-structured questionnaires were used to collect data from 426 teachers. Quantitative data were analyzed using descriptive statistics, Chi-square, and logistics regression tests at 5% level of significance. Results: About one-third of the respondents had heard of National School Health Policy (NSHP); however, few had seen the document. About half of the respondents were aware of the SHP in their schools. Many of the respondents had a good knowledge of SHP. Age and level of education of participants significantly influenced the knowledge of SHP. Above 50 years of age and postgraduate qualification were the significant predictors for the good knowledge of SHP. Conclusions: Awareness of the NSHP was low despite the good knowledge of SHP. This could be due to the tertiary education that most of the respondents had. Concerted efforts of stakeholders are required to intensify the health education awareness campaign to improve teachers’ knowledge based on NSHP. PMID:27630385

1995 Bicycle and Pedestrian Safety Report

DOT National Transportation Integrated Search

1995-03-01

This report provides a review of the current data on bicycle and pedestrian : safety across the United States, finding that safety and education : programs could significantly improve bicycle and pedestrian safety in the : Dallas-Fort Worth Metropoli...

The evolution of complex life.

PubMed

Billingham, J

1989-01-01

In considering the probabilities that intelligent life might exist elsewhere in the Universe, it is important to ask questions about the factors governing the emergence of complex living organisms in the context of evolutionary biology, planetary environments and events in space. Two important problems arise. First, what can be learned about the general laws governing the evolution of complex life anywhere in space by studying its history on the Earth? Second, how is the evolution of complex life affected by events in space? To address these problems, a series of Science Workshops on the Evolution of Complex Life was held at the Ames Research Center. Included in this paper are highlights of those workshops, with particular emphasis on the first question, namely the evolution of complex extraterrestrial life.

Analyzing the Velocity of Urban Dynamic Over Northeastern China Using Dmsp-Ols Night-Time Lights

NASA Astrophysics Data System (ADS)

Zhou, Y.

2017-09-01

Stable night-time lights (NTL) data from the Defense Meteorological Satellite Program Operational Line-scan System (DMSPOLS) can serve as a good proxy for anthropogenic development. Here DMSP-OLS NTL data was used to detect the urban development status in northeastern China. The spatial and temporal gradients are combined to depict the velocity of urban expanding process. This velocity index represents the instantaneous local velocity along the Earth's surface needed to maintain constant NTL condition, and has a mean of 0.36 km/yr for northeastern China. The velocity change of NTL is lower in the urban center and its near regions, and the suburbs show a relatively high value. The connecting zones between satellite cities and metropolis have also a rapid rate of NTL evolution. The dynamic process of urbanization over the study area is mainly in a manner of spreading from urban cores to edges. The rank size of the velocity for the prefectures is analyzed and a long tail distribution is found. The velocity index can provide insights for the future pattern of urban sprawl.

Bayesian Inference for Source Reconstruction: A Real-World Application

PubMed Central

Yee, Eugene; Hoffman, Ian; Ungar, Kurt

2014-01-01

This paper applies a Bayesian probabilistic inferential methodology for the reconstruction of the location and emission rate from an actual contaminant source (emission from the Chalk River Laboratories medical isotope production facility) using a small number of activity concentration measurements of a noble gas (Xenon-133) obtained from three stations that form part of the International Monitoring System radionuclide network. The sampling of the resulting posterior distribution of the source parameters is undertaken using a very efficient Markov chain Monte Carlo technique that utilizes a multiple-try differential evolution adaptive Metropolis algorithm with an archive of past states. It is shown that the principal difficulty in the reconstruction lay in the correct specification of the model errors (both scale and structure) for use in the Bayesian inferential methodology. In this context, two different measurement models for incorporation of the model error of the predicted concentrations are considered. The performance of both of these measurement models with respect to their accuracy and precision in the recovery of the source parameters is compared and contrasted. PMID:27379292

A Bayesian Uncertainty Framework for Conceptual Snowmelt and Hydrologic Models Applied to the Tenderfoot Creek Experimental Forest

NASA Astrophysics Data System (ADS)

Smith, T.; Marshall, L.

2007-12-01

In many mountainous regions, the single most important parameter in forecasting the controls on regional water resources is snowpack (Williams et al., 1999). In an effort to bridge the gap between theoretical understanding and functional modeling of snow-driven watersheds, a flexible hydrologic modeling framework is being developed. The aim is to create a suite of models that move from parsimonious structures, concentrated on aggregated watershed response, to those focused on representing finer scale processes and distributed response. This framework will operate as a tool to investigate the link between hydrologic model predictive performance, uncertainty, model complexity, and observable hydrologic processes. Bayesian methods, and particularly Markov chain Monte Carlo (MCMC) techniques, are extremely useful in uncertainty assessment and parameter estimation of hydrologic models. However, these methods have some difficulties in implementation. In a traditional Bayesian setting, it can be difficult to reconcile multiple data types, particularly those offering different spatial and temporal coverage, depending on the model type. These difficulties are also exacerbated by sensitivity of MCMC algorithms to model initialization and complex parameter interdependencies. As a way of circumnavigating some of the computational complications, adaptive MCMC algorithms have been developed to take advantage of the information gained from each successive iteration. Two adaptive algorithms are compared is this study, the Adaptive Metropolis (AM) algorithm, developed by Haario et al (2001), and the Delayed Rejection Adaptive Metropolis (DRAM) algorithm, developed by Haario et al (2006). While neither algorithm is truly Markovian, it has been proven that each satisfies the desired ergodicity and stationarity properties of Markov chains. Both algorithms were implemented as the uncertainty and parameter estimation framework for a conceptual rainfall-runoff model based on the Probability Distributed Model (PDM), developed by Moore (1985). We implement the modeling framework in Stringer Creek watershed in the Tenderfoot Creek Experimental Forest (TCEF), Montana. The snowmelt-driven watershed offers that additional challenge of modeling snow accumulation and melt and current efforts are aimed at developing a temperature- and radiation-index snowmelt model. Auxiliary data available from within TCEF's watersheds are used to support in the understanding of information value as it relates to predictive performance. Because the model is based on lumped parameters, auxiliary data are hard to incorporate directly. However, these additional data offer benefits through the ability to inform prior distributions of the lumped, model parameters. By incorporating data offering different information into the uncertainty assessment process, a cross-validation technique is engaged to better ensure that modeled results reflect real process complexity.

[Study on vitamin A nutritional status of Chinese urban elderly residents in 2010-2012].

PubMed

Chen, J; Hu, Y C; Yang, C; Yun, C F; Wang, R; Mao, D Q; Li, W D; Yang, Y H; Yang, X G; Yang, L C

2017-02-06

Objective: To assess the vitamin A nutritional status of the Chinese urban elderly population by analyzing serum retinol level in 2010-2012. Methods: Data were collected from the Chinese National Nutrition and Health Survey in 2010-2012. Using the multi-stage stratified cluster sampling method, serum samples from elderly residents aged ≥60 years old were obtained from 34 metropolis and 41 middle-sized and small cities. Demographic data were collected using a questionnaire survey. The serum retinol concentration was determined by high-performance liquid chromatography. Vitamin A deficiency (VAD) was determined using the World Health Organization guidelines. A total of 3 200 elderly residents were included in the study. The serum retinol levels and prevalence of VAD and marginal VAD were also compared. Results: The serum retinol concentration ( P (50)( P (25)- P (75))) of Chinese urban elderly residents was 1.83 (1.37-2.39) μmoL/L. Compared with middle-sized and small cities (1.91 (1.47-2.48) μmol/L), the retinol level of senior citizens in metropolis (1.70 (1.25-2.25) μmol/L) was significantly lower ( P< 0.001). The serum retinol levels of elderly male (1.89 (1.37-2.47) μmoL/L) was significantly higher than that of female (1.80 (1.36-2.28) μmoL/L) ( P= 0.001). The serum retinol concentration was 1.87 (1.42-2.43), 1.78 (1.32-2.33), and 1.71 (1.24-2.24) μmol/L for 60-69, 70-79, and ≥80 years olds, respectively. The retinol level in elderly people ≥70 years olds was significantly lower than that of 60-69 years olds ( P< 0.001). The overall prevalence of VAD among Chinese urban elderly residents was 4.22% (135/3 200); 6.00% (81/1 350) for metropolis residents and 2.92% (54/1 850) for middle-sized and small city residents. The overall marginal VAD rate of Chinese urban elderly residents was 8.19% (262/3 200); 10.51% (142/1 350) for metropolis residents and 6.49% (120/1 850) for medium-sized and small city residents. The prevalence of VAD and marginal VAD for males was 3.87% (61/1 577) and 8.24% (130/1 577), respectively ( P< 0.05). The prevalence of VAD according to age group was 3.65% (72/1 975), 4.96% (50/1 008), and 5.99% (13/217), respectively( P =0.097). The prevalence of marginal VAD according to age group was 6.99% (138/1 975), 9.82% (99/1 008), and 11.52% (25/217), respectively( P =0.05). Conclusion: Chinese urban elderly residents showed various levels of VAD, although marginal VAD was quite common. As VAD was more common in metropolis residents and older residents, specific strategies should target these populations.

Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

PubMed Central

Ord, Terry J.; Garcia-Porta, Joan

2012-01-01

Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

Galactic City at the Edge of the Universe

NASA Image and Video Library

2011-01-12

Astronomers have discovered a massive cluster of young galaxies forming in the distant universe. The growing galactic metropolis is known as COSMOS-AzTEC3. This image was taken Japan Subaru telescope atop Mauna Kea in Hawaii.

Rainforest metropolis casts 1,000-km defaunation shadow.

PubMed

Tregidgo, Daniel J; Barlow, Jos; Pompeu, Paulo S; de Almeida Rocha, Mayana; Parry, Luke

2017-08-08

Tropical rainforest regions are urbanizing rapidly, yet the role of emerging metropolises in driving wildlife overharvesting in forests and inland waters is unknown. We present evidence of a large defaunation shadow around a rainforest metropolis. Using interviews with 392 rural fishers, we show that fishing has severely depleted a large-bodied keystone fish species, tambaqui ( Colossoma macropomum ), with an impact extending over 1,000 km from the rainforest city of Manaus (population 2.1 million). There was strong evidence of defaunation within this area, including a 50% reduction in body size and catch rate (catch per unit effort). Our findings link these declines to city-based boats that provide rural fishers with reliable access to fish buyers and ice and likely impact rural fisher livelihoods and flooded forest biodiversity. This empirical evidence that urban markets can defaunate deep into rainforest wilderness has implications for other urbanizing socioecological systems.

Lung Cancer Pathological Image Analysis Using a Hidden Potts Model

PubMed Central

Li, Qianyun; Yi, Faliu; Wang, Tao; Xiao, Guanghua; Liang, Faming

2017-01-01

Nowadays, many biological data are acquired via images. In this article, we study the pathological images scanned from 205 patients with lung cancer with the goal to find out the relationship between the survival time and the spatial distribution of different types of cells, including lymphocyte, stroma, and tumor cells. Toward this goal, we model the spatial distribution of different types of cells using a modified Potts model for which the parameters represent interactions between different types of cells and estimate the parameters of the Potts model using the double Metropolis-Hastings algorithm. The double Metropolis-Hastings algorithm allows us to simulate samples approximately from a distribution with an intractable normalizing constant. Our numerical results indicate that the spatial interaction between the lymphocyte and tumor cells is significantly associated with the patient’s survival time, and it can be used together with the cell count information to predict the survival of the patients. PMID:28615918

Optimized nested Markov chain Monte Carlo sampling: theory

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

Coe, Joshua D; Shaw, M Sam; Sewell, Thomas D

2009-01-01

Metropolis Monte Carlo sampling of a reference potential is used to build a Markov chain in the isothermal-isobaric ensemble. At the endpoints of the chain, the energy is reevaluated at a different level of approximation (the 'full' energy) and a composite move encompassing all of the intervening steps is accepted on the basis of a modified Metropolis criterion. By manipulating the thermodynamic variables characterizing the reference system we maximize the average acceptance probability of composite moves, lengthening significantly the random walk made between consecutive evaluations of the full energy at a fixed acceptance probability. This provides maximally decorrelated samples ofmore » the full potential, thereby lowering the total number required to build ensemble averages of a given variance. The efficiency of the method is illustrated using model potentials appropriate to molecular fluids at high pressure. Implications for ab initio or density functional theory (DFT) treatment are discussed.« less

An Investigation of the Influence of Urban Areas on Rainfall Using the TRMM Satellite and a Cloud-Mesoscale Model

NASA Technical Reports Server (NTRS)

Shepherd, J. Marshall; OCStarr, David (Technical Monitor)

2002-01-01

A recent paper by Shepherd and Pierce (in press at Journal of Applied Meteorology) used rainfall data from the Precipitation Radar on NASA's Tropical Rainfall Measuring Mission's (TRMM) satellite to identify warm season rainfall anomalies downwind of major urban areas. Data (PR) were employed to identify warm season rainfall (1998-2000) patterns around Atlanta, Montgomery, Nashville, San Antonio, Waco, and Dallas. Results reveal an average increase of approx. 28% in monthly rainfall rates within 30-60 kilometers downwind of the metropolis with a modest increase of 5.6% over the metropolis. Portions of the downwind area exhibit increases as high as 51%. The percentage changes are relative to an upwind control area. It was also found that maximum rainfall rates in the downwind impact area exceeded the mean value in the upwind control area by 48%-116%. The maximum value was generally found at an average distance of 39 km from the edge of the urban center or 64 km from the center of the city. Results are consistent with METROMEX studies of St. Louis almost two decades ago and with more recent studies near Atlanta. A convective-mesoscale model with extensive land-surface processes is currently being employed to (a) determine if an urban heat island (UHI) thermal perturbation can induce a dynamic response to affect rainfall processes and (b) quantify the impact of the following three factors on the evolution of rainfall: (1) urban surface roughness, (2) magnitude of the UHI temperature anomaly, and (3) physical size of the UHI temperature anomaly. The sensitivity experiments are achieved by inserting a slab of land with urban properties (e.g. roughness length, albedo, thermal character) within a rural surface environment and varying the appropriate lower boundary condition parameters. The study will discuss the feasibility of utilizing satellite-based rainfall estimates for examining rainfall modification by urban areas on global scales and over longer time periods. The talk also introduces very preliminary results from the modeling component of the study. Such research has implications for weather forecasting, urban planning, water resource management, and understanding human impact on the environment and climate.

Stochastic evaluation of second-order many-body perturbation energies.

PubMed

Willow, Soohaeng Yoo; Kim, Kwang S; Hirata, So

2012-11-28

With the aid of the Laplace transform, the canonical expression of the second-order many-body perturbation correction to an electronic energy is converted into the sum of two 13-dimensional integrals, the 12-dimensional parts of which are evaluated by Monte Carlo integration. Weight functions are identified that are analytically normalizable, are finite and non-negative everywhere, and share the same singularities as the integrands. They thus generate appropriate distributions of four-electron walkers via the Metropolis algorithm, yielding correlation energies of small molecules within a few mE(h) of the correct values after 10(8) Monte Carlo steps. This algorithm does away with the integral transformation as the hotspot of the usual algorithms, has a far superior size dependence of cost, does not suffer from the sign problem of some quantum Monte Carlo methods, and potentially easily parallelizable and extensible to other more complex electron-correlation theories.

The evolution of life cycle complexity in aphids: Ecological optimization or historical constraint?

PubMed

Hardy, Nate B; Peterson, Daniel A; von Dohlen, Carol D

2015-06-01

For decades, biologists have debated why many parasites have obligate multihost life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, that is, change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (nonaphidines)-groups that differ in the intensity of their relationships with primary hosts. Next, we test specific mechanisms by which life cycle complexity could be adaptive or a constraint. We find that among aphidines there is a strong association between complex life cycles and polyphagy but only a weak correlation between life cycle complexity and reproductive mode. In contrast, among nonaphidines the relationship between life cycle complexity and host breadth is weak but the association between complex life cycles and sexual reproduction is strong. Thus, although the adaptiveness of life cycle complexity appears to be lineage specific, across aphids, life cycle evolution appears to be tightly linked with the evolution of other important natural history traits. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Quality of life of deaf and hard of hearing students in Ibadan metropolis, Nigeria

PubMed Central

2018-01-01

Quality of Life encompasses an individual’s well-being and health, social participation and satisfaction with functional daily living. Disabilities such as deafness can impact on the quality of life with spatial variance to the environment. Deafness causes communicative problems with significant consequences in cognitive, social, and emotional well-being of affected individuals. However, information relating to the quality of life of deaf and hard of hearing individuals, especially students in developing countries like Nigeria, which could be used to design special health-related interventions is sparse. This study examined the quality of life of deaf and hard of hearing students in Ibadan metropolis, Nigeria. One hundred and ten deaf and hard of hearing students participated in this cross-sectional study. Participants were drawn from all four secondary schools for the Deaf in Ibadan metropolis. The 26 item Brief version of the WHO Quality of Life questionnaire was used for data collection. The data was analyzed using descriptive and inferential statistics at statistical significance of p<0.05. Majority (57.8%) of the deaf and hard of hearing students had poor quality of life. Attending the special school for the Deaf, upper socio-economic status and age (≥17years) are significantly associated with better quality of life. However, gender and age at onset of hearing loss had no significant influence on the quality of life. The Deaf community available in the special school appeared to protect against stigma and discrimination, while also promoting social interactions between deaf and hard of hearing individuals. PMID:29293560

Quality of life of deaf and hard of hearing students in Ibadan metropolis, Nigeria.

PubMed

Jaiyeola, Mofadeke T; Adeyemo, Adebolajo A

2018-01-01

Quality of Life encompasses an individual's well-being and health, social participation and satisfaction with functional daily living. Disabilities such as deafness can impact on the quality of life with spatial variance to the environment. Deafness causes communicative problems with significant consequences in cognitive, social, and emotional well-being of affected individuals. However, information relating to the quality of life of deaf and hard of hearing individuals, especially students in developing countries like Nigeria, which could be used to design special health-related interventions is sparse. This study examined the quality of life of deaf and hard of hearing students in Ibadan metropolis, Nigeria. One hundred and ten deaf and hard of hearing students participated in this cross-sectional study. Participants were drawn from all four secondary schools for the Deaf in Ibadan metropolis. The 26 item Brief version of the WHO Quality of Life questionnaire was used for data collection. The data was analyzed using descriptive and inferential statistics at statistical significance of p<0.05. Majority (57.8%) of the deaf and hard of hearing students had poor quality of life. Attending the special school for the Deaf, upper socio-economic status and age (≥17years) are significantly associated with better quality of life. However, gender and age at onset of hearing loss had no significant influence on the quality of life. The Deaf community available in the special school appeared to protect against stigma and discrimination, while also promoting social interactions between deaf and hard of hearing individuals.

Simulating evolution of protein complexes through gene duplication and co-option.

PubMed

Haarsma, Loren; Nelesen, Serita; VanAndel, Ethan; Lamine, James; VandeHaar, Peter

2016-06-21

We present a model of the evolution of protein complexes with novel functions through gene duplication, mutation, and co-option. Under a wide variety of input parameters, digital organisms evolve complexes of 2-5 bound proteins which have novel functions but whose component proteins are not independently functional. Evolution of complexes with novel functions happens more quickly as gene duplication rates increase, point mutation rates increase, protein complex functional probability increases, protein complex functional strength increases, and protein family size decreases. Evolution of complexity is inhibited when the metabolic costs of making proteins exceeds the fitness gain of having functional proteins, or when point mutation rates get so large the functional proteins undergo deleterious mutations faster than new functional complexes can evolve. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Weaver, Brian Phillip

The purpose of this document is to describe the statistical modeling effort for gas concentrations in WIPP storage containers. The concentration (in ppm) of CO 2 in the headspace volume of standard waste box (SWB) 68685 is shown. A Bayesian approach and an adaptive Metropolis-Hastings algorithm were used.

Undecidability and Irreducibility Conditions for Open-Ended Evolution and Emergence.

PubMed

Hernández-Orozco, Santiago; Hernández-Quiroz, Francisco; Zenil, Hector

2018-01-01

Is undecidability a requirement for open-ended evolution (OEE)? Using methods derived from algorithmic complexity theory, we propose robust computational definitions of open-ended evolution and the adaptability of computable dynamical systems. Within this framework, we show that decidability imposes absolute limits on the stable growth of complexity in computable dynamical systems. Conversely, systems that exhibit (strong) open-ended evolution must be undecidable, establishing undecidability as a requirement for such systems. Complexity is assessed in terms of three measures: sophistication, coarse sophistication, and busy beaver logical depth. These three complexity measures assign low complexity values to random (incompressible) objects. As time grows, the stated complexity measures allow for the existence of complex states during the evolution of a computable dynamical system. We show, however, that finding these states involves undecidable computations. We conjecture that for similar complexity measures that assign low complexity values, decidability imposes comparable limits on the stable growth of complexity, and that such behavior is necessary for nontrivial evolutionary systems. We show that the undecidability of adapted states imposes novel and unpredictable behavior on the individuals or populations being modeled. Such behavior is irreducible. Finally, we offer an example of a system, first proposed by Chaitin, that exhibits strong OEE.

Nutrition and Metabolic Correlates of Obesity and Inflammation: Clinical Considerations123

PubMed Central

Johnson, Amy R; Makowski, Liza

2015-01-01

Since 1980, the global prevalence of obesity has doubled; in the United States, it has almost tripled. Billions of people are overweight and obese; the WHO reports that >65% of the world’s population die of diseases related to overweight rather than underweight. Obesity is a complex disease that can be studied from “metropolis to metabolite”—that is, beginning at the policy and the population level through epidemiology and intervention studies; to bench work including preclinical models, tissue, and cell culture studies; to biochemical assays; and to metabolomics. Metabolomics is the next research frontier because it provides a real-time snapshot of biochemical building blocks and products of cellular processes. This report comments on practical considerations when conducting metabolomics research. The pros and cons and important study design concerns are addressed to aid in increasing metabolomics research in the United States. The link between metabolism and inflammation is an understudied phenomenon that has great potential to transform our understanding of immunometabolism in obesity, diabetes, cancer, and other diseases; metabolomics promises to be an important tool in understanding the complex relations between factors contributing to such diseases. PMID:25833891

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

NASA Astrophysics Data System (ADS)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield a significant speedup.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

PubMed

Suh, Donghyuk; Radak, Brian K; Chipot, Christophe; Roux, Benoît

2018-01-07

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield a significant speedup.

Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

PubMed

Chen, Yunjie; Roux, Benoît

2014-09-21

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct equilibrium probability distribution with this prescription.

Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

NASA Astrophysics Data System (ADS)

Chen, Yunjie; Roux, Benoît

2014-09-01

Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct equilibrium probability distribution with this prescription.

Sterilisation: characteristics of vasectomy acceptors in Delhi.

PubMed

Sarkar, N N

1993-01-01

The place of vasectomy within the sterilisation programme in Delhi over the period 1983-88 is reviewed and data on vasectomy acceptance and characteristics of acceptors are analysed. Findings suggest a need to improve the strategy for the promotion of vasectomy within the metropolis.

High-risk of obstructive sleep apnea and excessive daytime sleepiness among commercial intra-city drivers in Lagos metropolis

PubMed Central

Ozoh, Obianuju B.; Okubadejo, Njideka U.; Akanbi, Maxwell O.; Dania, Michelle G.

2013-01-01

Background: The burden of obstructive sleep apnea among commercial drivers in Nigeria is not known. Aim: To assess the prevalence of high risk of obstructive sleep apnea (OSA) and excessive daytime sleepiness (EDS) among intra-city commercial drivers. Setting and Design: A descriptive cross-sectional study in three major motor parks in Lagos metropolis. Materials and Methods: Demographic, anthropometric and historical data was obtained. The risk of OSA and EDS was assessed using the STOP BANG questionnaire and the Epworth Sleepiness Scale, respectively. Statistical Analysis: The relationship between the OSA risk, EDS risk and past road traffic accident (RTA) was explored using the Pearson's chi square. Independent determinants of OSA risk, EDS risk and past RTA, respectively, were assessed by multiple logistic regression models. Result: Five hundred male commercial drivers (mean age (years) ±SD = 42.36 ± 11.17 and mean BMI (kg/m2) ±SD = 25.68 ± 3.79) were recruited. OSA risk was high in 244 (48.8%) drivers and 72 (14.4%) had EDS. There was a positive relationship between OSA risk and the risk of EDS (Pearson's X2 = 28.2, P < 0.001). Sixty-one (12.2%) drivers had a past history of RTA but there was no significant relationship between a past RTA and either OSA risk (X2 = 2.05, P = 0.15) or EDS risk (X2 = 2.7, P = 0.1), respectively. Abdominal adiposity, regular alcohol use and EDS were independent determinants of OSA risk while the use of cannabis and OSA risk were independent determinants of EDS. No independent risk factor for past RTA was identified. Conclusion: A significant proportion of commercial drivers in Lagos metropolis are at high risk of OSA and EDS. PMID:24249946

Adolescent pregnancy and the risk of Plasmodium falciparum malaria and anaemia-a pilot study from Sekondi-Takoradi metropolis, Ghana.

PubMed

Orish, Verner N; Onyeabor, Onyekachi S; Boampong, Johnson N; Aforakwah, Richmond; Nwaefuna, Ekene; Iriemenam, Nnaemeka C

2012-09-01

The problem of malaria in adolescence has been surpassed by the immense burden of malaria in children, most especially less than 5. A substantial amount of work done on malaria in pregnancy in endemic regions has not properly considered the adolescence. The present study therefore aimed at evaluating the prevalence of Plasmodium falciparum and anaemia infection in adolescent pregnant girls in the Sekondi-Takoradi metropolis, Ghana. The study was carried out at four hospitals in the Sekondi-Takoradi metropolis of the western region of Ghana from January 2010 to October 2010. Structured questionnaires were administered to the consenting pregnant women during their antenatal care visits. Information on education, age, gravidae, occupation and socio-demographic characteristics were recorded. Venous bloods were screened for malaria using RAPID response antibody kit and Geimsa staining while haemoglobin estimations were done by cyanmethemoglobin method. The results revealed that adolescent pregnant girls were more likely to have malaria infection than the adult pregnant women (34.6% verses 21.3%, adjusted OR 1.65, 95% CI, 1.03-2.65, P=0.039). In addition, adolescent pregnant girls had higher odds of anaemia than their adult pregnant women equivalent (43.9% versus 33.2%; adjusted OR 1.63, 95% CI, 1.01-2.62, P=0.046). Taken together, these data suggest that adolescent pregnant girls were more likely to have malaria and anaemia compared to their adult pregnant counterpart. Results from this study shows that proactive adolescent friendly policies and control programmes for malaria and anaemia are needed in this region in order to protect this vulnerable group of pregnant women. Copyright © 2012 Elsevier B.V. All rights reserved.

The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units

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

Hall, Clifford; School of Physics, Astronomy, and Computational Sciences, George Mason University, 4400 University Dr., Fairfax, VA 22030; Ji, Weixiao

2014-02-01

We present a CPU–GPU system for runtime acceleration of large molecular simulations using GPU computation and memory swaps. The memory architecture of the GPU can be used both as container for simulation data stored on the graphics card and as floating-point code target, providing an effective means for the manipulation of atomistic or molecular data on the GPU. To fully take advantage of this mechanism, efficient GPU realizations of algorithms used to perform atomistic and molecular simulations are essential. Our system implements a versatile molecular engine, including inter-molecule interactions and orientational variables for performing the Metropolis Monte Carlo (MMC) algorithm,more » which is one type of Markov chain Monte Carlo. By combining memory objects with floating-point code fragments we have implemented an MMC parallel engine that entirely avoids the communication time of molecular data at runtime. Our runtime acceleration system is a forerunner of a new class of CPU–GPU algorithms exploiting memory concepts combined with threading for avoiding bus bandwidth and communication. The testbed molecular system used here is a condensed phase system of oligopyrrole chains. A benchmark shows a size scaling speedup of 60 for systems with 210,000 pyrrole monomers. Our implementation can easily be combined with MPI to connect in parallel several CPU–GPU duets. -- Highlights: •We parallelize the Metropolis Monte Carlo (MMC) algorithm on one CPU—GPU duet. •The Adaptive Tempering Monte Carlo employs MMC and profits from this CPU—GPU implementation. •Our benchmark shows a size scaling-up speedup of 62 for systems with 225,000 particles. •The testbed involves a polymeric system of oligopyrroles in the condensed phase. •The CPU—GPU parallelization includes dipole—dipole and Mie—Jones classic potentials.« less

Drivers and Pattern of Social Vulnerability to Flood in Metropolitan Lagos, Nigeria

NASA Astrophysics Data System (ADS)

Fasona, M.

2016-12-01

Lagos is Africa's second largest city and a city-state in southwest Nigeria. Population and economic activities in the city are concentrated in the greater Lagos metropolitan area - a group of barrier islands less than a thousand square kilometer. Several physical factors and critical human-environmental conditions contribute to high flood vulnerability across the city. Flood impact is highly denominated and the poor tend to suffer more due to higher risk of exposure and poor adaptive capacity. In this study we present the pattern of social vulnerability to flooding across the Lagos metropolis and argued that the pattern substantially reflects the pattern and severity of flooding impact on people across the metropolis. Twenty nine social indicators and experiences including poverty profile, housing conditions, education, population and demography, social network, and communication, among others, were considered. The data were collated through field survey and subjected to principal component analysis. The results were processed into raster surfaces using GIS for social vulnerability characterization at neighborhood levels. The results suggest the social status indicators, neighborhood standing and social networks indictors, the indicators of emergency responses and security, and the neighborhood conditions, in that order, are the most important determinants of social vulnerability. Six of the 16 LGAs in metropolitan Lagos have high social vulnerability. Neighborhoods that combine poor social status indicators and poor neighborhood standing and social networks are found to have high social vulnerability whereas other poor neighborhoods with strong social networks performed better. We conclude that improved human living condition and social network and communication in poor urban neighborhoods are important to reducing social vulnerability to flooding in the metropolis.

Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms

PubMed Central

2016-01-01

A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance. Because of this relationship, many theories invoke a role for population size in the evolution of complexity. Such theories are difficult to test empirically because of the time required for the evolution of complexity in biological populations. Here, we used digital experimental evolution to test whether large or small asexual populations tend to evolve greater complexity. We find that both small and large—but not intermediate-sized—populations are favored to evolve larger genomes, which provides the opportunity for subsequent increases in phenotypic complexity. However, small and large populations followed different evolutionary paths towards these novel traits. Small populations evolved larger genomes by fixing slightly deleterious insertions, while large populations fixed rare beneficial insertions that increased genome size. These results demonstrate that genetic drift can lead to the evolution of complexity in small populations and that purifying selection is not powerful enough to prevent the evolution of complexity in large populations. PMID:27923053

Does standard Monte Carlo give justice to instantons?

NASA Astrophysics Data System (ADS)

Fucito, F.; Solomon, S.

1984-01-01

The results of the standard local Monte Carlo are changed by offering instantons as candidates in the Metropolis procedure. We also define an O(3) topological charge with no contribution from planar dislocations. The RG behavior is still not recovered. Bantrell Fellow in Theoretical Physics.

Who Cares? Pre and Post Abortion Experiences among Young Females in Cape Coast Metropolis, Ghana.

PubMed

Esia-Donkoh, Kobina; Darteh, Eugene K M; Blemano, Harriet; Asare, Hagar

2015-06-01

Issues of abortion are critical in Ghana largely due to its consequences on sexual and reproductive health. The negative perception society attaches to it makes it difficult for young females to access services and share their experiences. This paper examines the pre and post abortion experiences of young females; a subject scarcely researched in the country. Twenty-one clients of Planned Parenthood Association of Ghana (PPAG) clinic at Cape Coast were interviewed. Guided by the biopsychosocial model, the study revealed that fear of societal stigma, shame, and rejection by partners, as well as self-imposed stigma constituted some of the pre and post abortion experiences the respondents. Other experiences reported were bleeding, severe abdominal pain and psychological pain. The Ghana Health Services (GHS) and other service providers should partner the PPAG clinic to integrate psychosocial treatment in its abortion services while intensifying behaviour change communication and community-based stigma-reduction education in the Metropolis.

Quantifying parameter uncertainty in stochastic models using the Box Cox transformation

NASA Astrophysics Data System (ADS)

Thyer, Mark; Kuczera, George; Wang, Q. J.

2002-08-01

The Box-Cox transformation is widely used to transform hydrological data to make it approximately Gaussian. Bayesian evaluation of parameter uncertainty in stochastic models using the Box-Cox transformation is hindered by the fact that there is no analytical solution for the posterior distribution. However, the Markov chain Monte Carlo method known as the Metropolis algorithm can be used to simulate the posterior distribution. This method properly accounts for the nonnegativity constraint implicit in the Box-Cox transformation. Nonetheless, a case study using the AR(1) model uncovered a practical problem with the implementation of the Metropolis algorithm. The use of a multivariate Gaussian jump distribution resulted in unacceptable convergence behaviour. This was rectified by developing suitable parameter transformations for the mean and variance of the AR(1) process to remove the strong nonlinear dependencies with the Box-Cox transformation parameter. Applying this methodology to the Sydney annual rainfall data and the Burdekin River annual runoff data illustrates the efficacy of these parameter transformations and demonstrate the value of quantifying parameter uncertainty.

Irreversible Local Markov Chains with Rapid Convergence towards Equilibrium.

PubMed

Kapfer, Sebastian C; Krauth, Werner

2017-12-15

We study the continuous one-dimensional hard-sphere model and present irreversible local Markov chains that mix on faster time scales than the reversible heat bath or Metropolis algorithms. The mixing time scales appear to fall into two distinct universality classes, both faster than for reversible local Markov chains. The event-chain algorithm, the infinitesimal limit of one of these Markov chains, belongs to the class presenting the fastest decay. For the lattice-gas limit of the hard-sphere model, reversible local Markov chains correspond to the symmetric simple exclusion process (SEP) with periodic boundary conditions. The two universality classes for irreversible Markov chains are realized by the totally asymmetric SEP (TASEP), and by a faster variant (lifted TASEP) that we propose here. We discuss how our irreversible hard-sphere Markov chains generalize to arbitrary repulsive pair interactions and carry over to higher dimensions through the concept of lifted Markov chains and the recently introduced factorized Metropolis acceptance rule.

Irreversible Local Markov Chains with Rapid Convergence towards Equilibrium

NASA Astrophysics Data System (ADS)

Kapfer, Sebastian C.; Krauth, Werner

2017-12-01

We study the continuous one-dimensional hard-sphere model and present irreversible local Markov chains that mix on faster time scales than the reversible heat bath or Metropolis algorithms. The mixing time scales appear to fall into two distinct universality classes, both faster than for reversible local Markov chains. The event-chain algorithm, the infinitesimal limit of one of these Markov chains, belongs to the class presenting the fastest decay. For the lattice-gas limit of the hard-sphere model, reversible local Markov chains correspond to the symmetric simple exclusion process (SEP) with periodic boundary conditions. The two universality classes for irreversible Markov chains are realized by the totally asymmetric SEP (TASEP), and by a faster variant (lifted TASEP) that we propose here. We discuss how our irreversible hard-sphere Markov chains generalize to arbitrary repulsive pair interactions and carry over to higher dimensions through the concept of lifted Markov chains and the recently introduced factorized Metropolis acceptance rule.

Animal Management at the Ancient Metropolis of Teotihuacan, Mexico: Stable Isotope Analysis of Leporid (Cottontail and Jackrabbit) Bone Mineral.

PubMed

Somerville, Andrew D; Sugiyama, Nawa; Manzanilla, Linda R; Schoeninger, Margaret J

2016-01-01

Human-animal interactions have played crucial roles in the development of complex societies across the globe. This study examines the human-leporid (cottontail and jackrabbit) relationship at the pre-Hispanic (AD 1-550) city of Teotihuacan in the Basin of Mexico and tests the hypothesis that leporids were managed or bred for food and secondary products within the urban core. We use stable isotope analysis (δ13Capatite and δ18Oapatite) of 134 leporid specimens from five archaeological contexts within the city and 13 modern specimens from across central Mexico to quantify aspects of leporid diet and ecology. The results demonstrate that leporids from Oztoyahualco, a residential complex associated with a unique rabbit sculpture and archaeological traces of animal butchering, exhibit the highest δ13Capatite values of the sample. These results imply greater consumption of human-cultivated foods, such as maize (Zea mays), by cottontails and jackrabbits at this complex and suggest practices of human provisioning. A lack of significant differences in δ18Oapatite values between ancient and modern leporids and between Oztoyahualco and other locations within Teotihuacan indicates generally similar relative humidity from sampled contexts. Results of this study support the notion that residents provisioned, managed, or bred leporids during the height of the city, and provide new evidence for mammalian animal husbandry in the ancient New World.

Animal Management at the Ancient Metropolis of Teotihuacan, Mexico: Stable Isotope Analysis of Leporid (Cottontail and Jackrabbit) Bone Mineral

PubMed Central

Somerville, Andrew D.; Sugiyama, Nawa; Manzanilla, Linda R.; Schoeninger, Margaret J.

2016-01-01

Human-animal interactions have played crucial roles in the development of complex societies across the globe. This study examines the human-leporid (cottontail and jackrabbit) relationship at the pre-Hispanic (AD 1–550) city of Teotihuacan in the Basin of Mexico and tests the hypothesis that leporids were managed or bred for food and secondary products within the urban core. We use stable isotope analysis (δ13Capatite and δ18Oapatite) of 134 leporid specimens from five archaeological contexts within the city and 13 modern specimens from across central Mexico to quantify aspects of leporid diet and ecology. The results demonstrate that leporids from Oztoyahualco, a residential complex associated with a unique rabbit sculpture and archaeological traces of animal butchering, exhibit the highest δ13Capatite values of the sample. These results imply greater consumption of human-cultivated foods, such as maize (Zea mays), by cottontails and jackrabbits at this complex and suggest practices of human provisioning. A lack of significant differences in δ18Oapatite values between ancient and modern leporids and between Oztoyahualco and other locations within Teotihuacan indicates generally similar relative humidity from sampled contexts. Results of this study support the notion that residents provisioned, managed, or bred leporids during the height of the city, and provide new evidence for mammalian animal husbandry in the ancient New World. PMID:27532515

The evolution of genital complexity and mating rates in sexually size dimorphic spiders.

PubMed

Kuntner, Matjaž; Cheng, Ren-Chung; Kralj-Fišer, Simona; Liao, Chen-Pan; Schneider, Jutta M; Elgar, Mark A

2016-11-09

Genital diversity may arise through sexual conflict over polyandry, where male genital features function to manipulate female mating frequency against her interest. Correlated genital evolution across animal groups is consistent with this view, but a link between genital complexity and mating rates remains to be established. In sexually size dimorphic spiders, golden orbweaving spiders (Nephilidae) males mutilate their genitals to form genital plugs, but these plugs do not always prevent female polyandry. In a comparative framework, we test whether male and female genital complexity coevolve, and how these morphologies, as well as sexual cannibalism, relate to the evolution of mating systems. Using a combination of comparative tests, we show that male genital complexity negatively correlates with female mating rates, and that levels of sexual cannibalism negatively correlate with male mating rates. We also confirm a positive correlation between male and female genital complexity. The macroevolutionary trajectory is consistent with a repeated evolution from polyandry to monandry coinciding with the evolution towards more complex male genitals. These results are consistent with the predictions from sexual conflict theory, although sexual conflict may not be the only mechanism responsible for the evolution of genital complexity and mating systems. Nevertheless, our comparative evidence suggests that in golden orbweavers, male genital complexity limits female mating rates, and sexual cannibalism by females coincides with monogyny.

Energy model for rumor propagation on social networks

NASA Astrophysics Data System (ADS)

Han, Shuo; Zhuang, Fuzhen; He, Qing; Shi, Zhongzhi; Ao, Xiang

2014-01-01

With the development of social networks, the impact of rumor propagation on human lives is more and more significant. Due to the change of propagation mode, traditional rumor propagation models designed for word-of-mouth process may not be suitable for describing the rumor spreading on social networks. To overcome this shortcoming, we carefully analyze the mechanisms of rumor propagation and the topological properties of large-scale social networks, then propose a novel model based on the physical theory. In this model, heat energy calculation formula and Metropolis rule are introduced to formalize this problem and the amount of heat energy is used to measure a rumor’s impact on a network. Finally, we conduct track experiments to show the evolution of rumor propagation, make comparison experiments to contrast the proposed model with the traditional models, and perform simulation experiments to study the dynamics of rumor spreading. The experiments show that (1) the rumor propagation simulated by our model goes through three stages: rapid growth, fluctuant persistence and slow decline; (2) individuals could spread a rumor repeatedly, which leads to the rumor’s resurgence; (3) rumor propagation is greatly influenced by a rumor’s attraction, the initial rumormonger and the sending probability.

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

Vrugt, Jasper A; Robinson, Bruce A; Ter Braak, Cajo J F

In recent years, a strong debate has emerged in the hydrologic literature regarding what constitutes an appropriate framework for uncertainty estimation. Particularly, there is strong disagreement whether an uncertainty framework should have its roots within a proper statistical (Bayesian) context, or whether such a framework should be based on a different philosophy and implement informal measures and weaker inference to summarize parameter and predictive distributions. In this paper, we compare a formal Bayesian approach using Markov Chain Monte Carlo (MCMC) with generalized likelihood uncertainty estimation (GLUE) for assessing uncertainty in conceptual watershed modeling. Our formal Bayesian approach is implemented usingmore » the recently developed differential evolution adaptive metropolis (DREAM) MCMC scheme with a likelihood function that explicitly considers model structural, input and parameter uncertainty. Our results demonstrate that DREAM and GLUE can generate very similar estimates of total streamflow uncertainty. This suggests that formal and informal Bayesian approaches have more common ground than the hydrologic literature and ongoing debate might suggest. The main advantage of formal approaches is, however, that they attempt to disentangle the effect of forcing, parameter and model structural error on total predictive uncertainty. This is key to improving hydrologic theory and to better understand and predict the flow of water through catchments.« less

Implement Method for Automated Testing of Markov Chain Convergence into INVERSE for ORNL12-RS-108J: Advanced Multi-Dimensional Forward and Inverse Modeling

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

Bledsoe, Keith C.

2015-04-01

The DiffeRential Evolution Adaptive Metropolis (DREAM) method is a powerful optimization/uncertainty quantification tool used to solve inverse transport problems in Los Alamos National Laboratory’s INVERSE code system. The DREAM method has been shown to be adept at accurate uncertainty quantification, but it can be very computationally demanding. Previously, the DREAM method in INVERSE performed a user-defined number of particle transport calculations. This placed a burden on the user to guess the number of calculations that would be required to accurately solve any given problem. This report discusses a new approach that has been implemented into INVERSE, the Gelman-Rubin convergence metric.more » This metric automatically detects when an appropriate number of transport calculations have been completed and the uncertainty in the inverse problem has been accurately calculated. In a test problem with a spherical geometry, this method was found to decrease the number of transport calculations (and thus time required) to solve a problem by an average of over 90%. In a cylindrical test geometry, a 75% decrease was obtained.« less

Evolution of complex adaptations in molecular systems

PubMed Central

Pál, Csaba; Papp, Balázs

2017-01-01

A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular ’springboards’, such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths. PMID:28782044

Maximum Likelihood Estimation of Nonlinear Structural Equation Models.

ERIC Educational Resources Information Center

Lee, Sik-Yum; Zhu, Hong-Tu

2002-01-01

Developed an EM type algorithm for maximum likelihood estimation of a general nonlinear structural equation model in which the E-step is completed by a Metropolis-Hastings algorithm. Illustrated the methodology with results from a simulation study and two real examples using data from previous studies. (SLD)

Comparing Three Estimation Methods for the Three-Parameter Logistic IRT Model

ERIC Educational Resources Information Center

Lamsal, Sunil

2015-01-01

Different estimation procedures have been developed for the unidimensional three-parameter item response theory (IRT) model. These techniques include the marginal maximum likelihood estimation, the fully Bayesian estimation using Markov chain Monte Carlo simulation techniques, and the Metropolis-Hastings Robbin-Monro estimation. With each…

Regional cooperation and bike/ped and transit connections : a regional models of cooperation peer exchange summary report

DOT National Transportation Integrated Search

2016-10-01

This report summarizes the presentations, key themes, and recommendations identified at a Regional Models of Cooperation peer exchange on October 24, 2016 in Salt Lake City, Utah. The Utah Transit Authority hosted peers from the Los Angeles Metropoli...

Sexual selection and the evolution of genital shape and complexity in water striders.

PubMed

Rowe, Locke; Arnqvist, Göran

2012-01-01

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Towards physical principles of biological evolution

NASA Astrophysics Data System (ADS)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice for adequate modeling of the biological level of complexity, and new developments within physics itself are likely to be required.

Bayesian Analysis of Nonlinear Structural Equation Models with Nonignorable Missing Data

ERIC Educational Resources Information Center

Lee, Sik-Yum

2006-01-01

A Bayesian approach is developed for analyzing nonlinear structural equation models with nonignorable missing data. The nonignorable missingness mechanism is specified by a logistic regression model. A hybrid algorithm that combines the Gibbs sampler and the Metropolis-Hastings algorithm is used to produce the joint Bayesian estimates of…

BOOK REVIEW: HANDBOOK OF URBAN HEALTH: POPULATIONS, METHODS AND PRACTICE

EPA Science Inventory

In Clifford D. Simak's 1952 science fiction classic, City, the metropolis is dead by the end of the 20th century. Cheap atomic power and ubiquitous private helicopters have made concentrated human existence a quaint memory. Simak could not have been more wrong, of course. About h...

Art off the Beaten Track

ERIC Educational Resources Information Center

Fogg, Piper

2007-01-01

When the nearest metropolis is hundreds of miles away, cultural enrichment is not always easy to come by. Arts programs have evolved to reflect the needs of such regions, providing a rich diet for culture-starved residents. Some colleges have created choirs or theater groups that welcome local participation, while others have developed elaborate…

Stochastic Approximation Methods for Latent Regression Item Response Models

ERIC Educational Resources Information Center

von Davier, Matthias; Sinharay, Sandip

2010-01-01

This article presents an application of a stochastic approximation expectation maximization (EM) algorithm using a Metropolis-Hastings (MH) sampler to estimate the parameters of an item response latent regression model. Latent regression item response models are extensions of item response theory (IRT) to a latent variable model with covariates…

School Choice, Gentrification, and the Variable Significance of Racial Stratification in Urban Neighborhoods

ERIC Educational Resources Information Center

Pearman, Francis A., III; Swain, Walker A.

2017-01-01

Racial and socioeconomic stratification have long governed patterns of residential sorting in the American metropolis. However, recent expansions of school choice policies that allow parents to select schools outside their neighborhood raise questions as to whether this weakening of the neighborhood-school connection might influence the…

Verification Techniques for Parameter Selection and Bayesian Model Calibration Presented for an HIV Model

NASA Astrophysics Data System (ADS)

Wentworth, Mami Tonoe

Uncertainty quantification plays an important role when making predictive estimates of model responses. In this context, uncertainty quantification is defined as quantifying and reducing uncertainties, and the objective is to quantify uncertainties in parameter, model and measurements, and propagate the uncertainties through the model, so that one can make a predictive estimate with quantified uncertainties. Two of the aspects of uncertainty quantification that must be performed prior to propagating uncertainties are model calibration and parameter selection. There are several efficient techniques for these processes; however, the accuracy of these methods are often not verified. This is the motivation for our work, and in this dissertation, we present and illustrate verification frameworks for model calibration and parameter selection in the context of biological and physical models. First, HIV models, developed and improved by [2, 3, 8], describe the viral infection dynamics of an HIV disease. These are also used to make predictive estimates of viral loads and T-cell counts and to construct an optimal control for drug therapy. Estimating input parameters is an essential step prior to uncertainty quantification. However, not all the parameters are identifiable, implying that they cannot be uniquely determined by the observations. These unidentifiable parameters can be partially removed by performing parameter selection, a process in which parameters that have minimal impacts on the model response are determined. We provide verification techniques for Bayesian model calibration and parameter selection for an HIV model. As an example of a physical model, we employ a heat model with experimental measurements presented in [10]. A steady-state heat model represents a prototypical behavior for heat conduction and diffusion process involved in a thermal-hydraulic model, which is a part of nuclear reactor models. We employ this simple heat model to illustrate verification techniques for model calibration. For Bayesian model calibration, we employ adaptive Metropolis algorithms to construct densities for input parameters in the heat model and the HIV model. To quantify the uncertainty in the parameters, we employ two MCMC algorithms: Delayed Rejection Adaptive Metropolis (DRAM) [33] and Differential Evolution Adaptive Metropolis (DREAM) [66, 68]. The densities obtained using these methods are compared to those obtained through the direct numerical evaluation of the Bayes' formula. We also combine uncertainties in input parameters and measurement errors to construct predictive estimates for a model response. A significant emphasis is on the development and illustration of techniques to verify the accuracy of sampling-based Metropolis algorithms. We verify the accuracy of DRAM and DREAM by comparing chains, densities and correlations obtained using DRAM, DREAM and the direct evaluation of Bayes formula. We also perform similar analysis for credible and prediction intervals for responses. Once the parameters are estimated, we employ energy statistics test [63, 64] to compare the densities obtained by different methods for the HIV model. The energy statistics are used to test the equality of distributions. We also consider parameter selection and verification techniques for models having one or more parameters that are noninfluential in the sense that they minimally impact model outputs. We illustrate these techniques for a dynamic HIV model but note that the parameter selection and verification framework is applicable to a wide range of biological and physical models. To accommodate the nonlinear input to output relations, which are typical for such models, we focus on global sensitivity analysis techniques, including those based on partial correlations, Sobol indices based on second-order model representations, and Morris indices, as well as a parameter selection technique based on standard errors. A significant objective is to provide verification strategies to assess the accuracy of those techniques, which we illustrate in the context of the HIV model. Finally, we examine active subspace methods as an alternative to parameter subset selection techniques. The objective of active subspace methods is to determine the subspace of inputs that most strongly affect the model response, and to reduce the dimension of the input space. The major difference between active subspace methods and parameter selection techniques is that parameter selection identifies influential parameters whereas subspace selection identifies a linear combination of parameters that impacts the model responses significantly. We employ active subspace methods discussed in [22] for the HIV model and present a verification that the active subspace successfully reduces the input dimensions.

Simulation of phase equilibria

NASA Astrophysics Data System (ADS)

Martin, Marcus Gary

The focus of this thesis is on the use of configurational bias Monte Carlo in the Gibbs ensemble. Unlike Metropolis Monte Carlo, which is reviewed in chapter I, configurational bias Monte Carlo uses an underlying Markov chain transition matrix which is asymmetric in such a way that it is more likely to attempt to move to a molecular conformation which has a lower energy than to one with a higher energy. Chapter II explains how this enables efficient simulation of molecules with complex architectures (long chains and branched molecules) for coexisting fluid phases (liquid, vapor, or supercritical), and also presents several of our recent extensions to this method. In chapter III we discuss the development of the Transferable Potentials for Phase Equilibria United Atom (TraPPE-UA) force field which accurately describes the fluid phase coexistence for linear and branched alkanes. Finally, in the fourth chapter the methods and the force field are applied to systems ranging from supercritical extraction to gas chromatography to illustrate the power and versatility of our approach.

Model selection and Bayesian inference for high-resolution seabed reflection inversion.

PubMed

Dettmer, Jan; Dosso, Stan E; Holland, Charles W

2009-02-01

This paper applies Bayesian inference, including model selection and posterior parameter inference, to inversion of seabed reflection data to resolve sediment structure at a spatial scale below the pulse length of the acoustic source. A practical approach to model selection is used, employing the Bayesian information criterion to decide on the number of sediment layers needed to sufficiently fit the data while satisfying parsimony to avoid overparametrization. Posterior parameter inference is carried out using an efficient Metropolis-Hastings algorithm for high-dimensional models, and results are presented as marginal-probability depth distributions for sound velocity, density, and attenuation. The approach is applied to plane-wave reflection-coefficient inversion of single-bounce data collected on the Malta Plateau, Mediterranean Sea, which indicate complex fine structure close to the water-sediment interface. This fine structure is resolved in the geoacoustic inversion results in terms of four layers within the upper meter of sediments. The inversion results are in good agreement with parameter estimates from a gravity core taken at the experiment site.

Fast Proton Titration Scheme for Multiscale Modeling of Protein Solutions.

PubMed

Teixeira, Andre Azevedo Reis; Lund, Mikael; da Silva, Fernando Luís Barroso

2010-10-12

Proton exchange between titratable amino acid residues and the surrounding solution gives rise to exciting electric processes in proteins. We present a proton titration scheme for studying acid-base equilibria in Metropolis Monte Carlo simulations where salt is treated at the Debye-Hückel level. The method, rooted in the Kirkwood model of impenetrable spheres, is applied on the three milk proteins α-lactalbumin, β-lactoglobulin, and lactoferrin, for which we investigate the net-charge, molecular dipole moment, and charge capacitance. Over a wide range of pH and salt conditions, excellent agreement is found with more elaborate simulations where salt is explicitly included. The implicit salt scheme is orders of magnitude faster than the explicit analog and allows for transparent interpretation of physical mechanisms. It is shown how the method can be expanded to multiscale modeling of aqueous salt solutions of many biomolecules with nonstatic charge distributions. Important examples are protein-protein aggregation, protein-polyelectrolyte complexation, and protein-membrane association.

Urban Renewal Mega Projects and Residents' Quality of Life: Evidence from Historical Religious Center of Mashhad Metropolis.

PubMed

Forouhar, Amir; Hasankhani, Mahnoosh

2018-04-01

Urban decay is the process by which a historical city center, or an old part of a city, falls into decrepitude and faces serious problems. Urban management, therefore, implements renewal mega projects with the goal of physical and functional revitalization, retrieval of socioeconomic capacities, and improving of quality of life of residents. Ignoring the complexities of these large-scale interventions in the old and historical urban fabrics may lead to undesirable consequences, including an additional decline of quality of life. Thus, the present paper aims to assess the impact of renewal mega projects on residents' subjective quality of life, in the historical religious district of the holy city of Mashhad (Samen District). A combination of quantitative and qualitative methods of impact assessment, including questionnaires, semi-structured personal interviews, and direct observation, is used in this paper. The results yield that the Samen Renewal Project has significantly reduced the resident's subjective quality of life, due to its undesirable impacts on physical, socio-cultural, and economic environments.

Modeling association among demographic parameters in analysis of open population capture-recapture data.

PubMed

Link, William A; Barker, Richard J

2005-03-01

We present a hierarchical extension of the Cormack-Jolly-Seber (CJS) model for open population capture-recapture data. In addition to recaptures of marked animals, we model first captures of animals and losses on capture. The parameter set includes capture probabilities, survival rates, and birth rates. The survival rates and birth rates are treated as a random sample from a bivariate distribution, thus the model explicitly incorporates correlation in these demographic rates. A key feature of the model is that the likelihood function, which includes a CJS model factor, is expressed entirely in terms of identifiable parameters; losses on capture can be factored out of the model. Since the computational complexity of classical likelihood methods is prohibitive, we use Markov chain Monte Carlo in a Bayesian analysis. We describe an efficient candidate-generation scheme for Metropolis-Hastings sampling of CJS models and extensions. The procedure is illustrated using mark-recapture data for the moth Gonodontis bidentata.

Hydrogen storage and evolution catalysed by metal hydride complexes.

PubMed

Fukuzumi, Shunichi; Suenobu, Tomoyoshi

2013-01-07

The storage and evolution of hydrogen are catalysed by appropriate metal hydride complexes. Hydrogenation of carbon dioxide by hydrogen is catalysed by a [C,N] cyclometalated organoiridium complex, [Ir(III)(Cp*)(4-(1H-pyrazol-1-yl-κN(2))benzoic acid-κC(3))(OH(2))](2)SO(4) [Ir-OH(2)](2)SO(4), under atmospheric pressure of H(2) and CO(2) in weakly basic water (pH 7.5) at room temperature. The reverse reaction, i.e., hydrogen evolution from formate, is also catalysed by [Ir-OH(2)](+) in acidic water (pH 2.8) at room temperature. Thus, interconversion between hydrogen and formic acid in water at ambient temperature and pressure has been achieved by using [Ir-OH(2)](+) as an efficient catalyst in both directions depending on pH. The Ir complex [Ir-OH(2)](+) also catalyses regioselective hydrogenation of the oxidised form of β-nicotinamide adenine dinucleotide (NAD(+)) to produce the 1,4-reduced form (NADH) under atmospheric pressure of H(2) at room temperature in weakly basic water. In weakly acidic water, the complex [Ir-OH(2)](+) also catalyses the reverse reaction, i.e., hydrogen evolution from NADH to produce NAD(+) at room temperature. Thus, interconversion between NADH (and H(+)) and NAD(+) (and H(2)) has also been achieved by using [Ir-OH(2)](+) as an efficient catalyst and by changing pH. The iridium hydride complex formed by the reduction of [Ir-OH(2)](+) by H(2) and NADH is responsible for the hydrogen evolution. Photoirradiation (λ > 330 nm) of an aqueous solution of the Ir-hydride complex produced by the reduction of [Ir-OH(2)](+) with alcohols resulted in the quantitative conversion to a unique [C,C] cyclometalated Ir-hydride complex, which can catalyse hydrogen evolution from alcohols in a basic aqueous solution (pH 11.9). The catalytic mechanisms of the hydrogen storage and evolution are discussed by focusing on the reactivity of Ir-hydride complexes.

Residents' Yard Choices and Rationales in a Desert City: Social Priorities, Ecological Impacts, and Decision Tradeoffs

NASA Astrophysics Data System (ADS)

Larson, Kelli L.; Casagrande, David; Harlan, Sharon L.; Yabiku, Scott T.

2009-11-01

As a dominant land use in urban ecosystems, residential yards impact water and other environmental resources. Converting thirsty lawns into alternative landscapes is one approach to water conservation, yet barriers such as cultural norms reinforce the traditional lawn. Meanwhile, the complex social and ecological implications of yard choices complicate programs aimed at changing grass and other yard features for particular purposes. In order to better understand individual landscape decisions, we qualitatively examined residents’ rationales for their preferred yard types in the desert metropolis of Phoenix, Arizona. After briefly presenting landscape choices across two survey samples, the dominant reasons for preferences are discussed: appearance, maintenance, environment, recreation, microclimate, familiarity, and health/safety. Three broader analytical themes emerged from these descriptive codes: (1) residents’ desires for attractive, comfortable landscapes of leisure encompassing pluralistic tastes, lifestyles, and perceptions; (2) the association of environmental benefits and impacts with different landscape types involving complex social and ecological tradeoffs; and (3) the cultural legacies evident in modern landscape choices, especially in terms of a dichotomous human-nature worldview among long-time residents of the Phoenix oasis. Given these findings, programs aimed at landscape change must recognize diverse preferences and rationalization processes, along with the perceived versus actual impacts and tradeoffs of varying yard alternatives.

Evolution of disorder in Mediator complex and its functional relevance

PubMed Central

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K.

2016-01-01

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. PMID:26590257

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Synaptic scaffold evolution generated components of vertebrate cognitive complexity

PubMed Central

Nithianantharajah, J.; Komiyama, N.H.; McKechanie, A.; Johnstone, M.; Blackwood, D. H.; St Clair, D.; Emes, R.D.; van de Lagemaat, L. N.; Saksida, L.M.; Bussey, T.J.; Grant, S.G.N.

2014-01-01

The origins and evolution of higher cognitive functions including complex forms of learning, attention and executive functions are unknown. A potential mechanism driving the evolution of vertebrate cognition early in the vertebrate lineage (550 My ago) was genome duplication and subsequent diversification of postsynaptic genes. Here we report the first genetic analysis of a vertebrate gene family in cognitive functions measured using computerized touchscreens. Comparison of mice carrying mutations in all four Dlg paralogs show simple associative learning required Dlg4, while Dlg2 and Dlg3 diversified to play opposing roles in complex cognitive processes. Exploiting the translational utility of touchscreens in humans and mice, testing Dlg2 mutations in both species showed Dlg2’s role in complex learning, cognitive flexibility and attention has been highly conserved over 100 My. Dlg family mutations underlie psychiatric disorders suggesting genome evolution expanded the complexity of vertebrate cognition at the cost of susceptibility to mental illness. PMID:23201973

Manifestations of Dyslexia and Dyscalculia

ERIC Educational Resources Information Center

Osisanya, Ayo; Lazarus, Kelechi; Adewunmi, Abiodun

2013-01-01

This study examined the prevalence of dyslexia and dyscalculia among persons with academic deficits in English Language and Mathematics in public primary schools in Ibadan metropolis. A correlational survey study, sampling 477 pupils who were between the ages of eight and 12 years, and in 4th and 5th grades with the use of four research…

Engaging Suburban Students in Dialogues on Diversity in a Segregated Metropolitan Area

ERIC Educational Resources Information Center

Checkoway, Barry; Lipa, Todd; Vivyan, Erika; Zurvalec, Sue

2017-01-01

What are some strategies for engaging suburban students in dialogues on diversity in new American metropolis? This question is important, especially at a time when some suburbs are changing from "segregated" to "segregated and diverse," and scholarship is needed to guide their discussion. This article analyzes efforts by a…

Urbanization and Spatial Organization: Hospital and Orphanage Location in Chicago, 1848-1916

ERIC Educational Resources Information Center

Britton, Marcus; Ocasio, William

2007-01-01

What factors affect where organizations locate facilities in local communities? This paper examines how urban development influenced the neighborhood location of two very different types of facilities, general hospitals and orphanages, over the 70-year period during which Chicago emerged as an urban metropolis. Our results suggest that the human…

Mapping Language Ideologies in Multi-Ethnic Urban Europe: The Case of Parisian French

ERIC Educational Resources Information Center

Stewart, Christopher Michael

2012-01-01

Although the modern multicultural European metropolis has brought previously disparate groups into close contact, little research has focused on the effect of these shifting demographic patterns on language attitudes and ideologies. This is probably due to the sensitive nature of issues relating to immigration which may evoke contexts of…

Community of Inquiry Method and Language Skills Acquisition: Empirical Evidence

ERIC Educational Resources Information Center

Preece, Abdul Shakhour Duncan

2015-01-01

The study investigates the effectiveness of community of inquiry method in preparing students to develop listening and speaking skills in a sample of junior secondary school students in Borno state, Nigeria. A sample of 100 students in standard classes was drawn in one secondary school in Maiduguri metropolis through stratified random sampling…

Can Learning in Informal Settings Mitigate Disadvantage and Promote Urban Sustainability? School Gardens in Washington, DC

ERIC Educational Resources Information Center

Fisher-Maltese, Carley; Fisher, Dana R.; Ray, Rashawn

2018-01-01

This article explores how school gardens provide learning opportunities for school-aged children while concurrently helping cities achieve sustainability. The authors analyse this process in Washington, DC, a particularly innovative metropolis in the United States. This national capital city boasts two of the most progressive examples of…

Extended Mixed-Efects Item Response Models with the MH-RM Algorithm

ERIC Educational Resources Information Center

Chalmers, R. Philip

2015-01-01

A mixed-effects item response theory (IRT) model is presented as a logical extension of the generalized linear mixed-effects modeling approach to formulating explanatory IRT models. Fixed and random coefficients in the extended model are estimated using a Metropolis-Hastings Robbins-Monro (MH-RM) stochastic imputation algorithm to accommodate for…

Battle in Los Angeles: Conflict Escalates as Charter Schools Thrive

ERIC Educational Resources Information Center

Whitmire, Richard

2016-01-01

Throughout the 1990s and well into the new millennium, the massive Los Angeles Unified School District barely noticed the many charter schools that were springing up around the metropolis. But Los Angeles parents certainly took notice, and started enrolling their children. In 2008, five charter-management organizations announced plans to…

Challenges of Attending E-Learning Studies in Nigeria

ERIC Educational Resources Information Center

Bugi, Stephan Z.

2012-01-01

This study set out to find out what challenges the E-leaner faces in the Nigerian environment. Survey research design was used to obtain the opinion of 200 randomly selected E-learners in Kaduna metropolis. Their responses revealed that the most prominent challenges they face are, Inadequate Power supply, Internet connectivity problems, Efficacy…

From Mountain to Metropolis: Appalachian Migrants in American Cities.

ERIC Educational Resources Information Center

Borman, Kathryn M., Ed.; Obermiller, Phillip J., Ed.

This book consists of 14 essays that focus on the condition of urban Appalachians (former migrants to cities from Appalachia and their descendants). Chapters address issues of health, environment, education, and cultural identity in an urban Appalachian context, and are meant to be a resource for educators and health and human service…

No Safe Place: Environmental Hazards & Injustice along Mexico's Northern Border

ERIC Educational Resources Information Center

Grineski, Sara E.; Collins, Timothy W.; Aguilar, Maria de Lourdes Romo; Aldouri, Raed

2010-01-01

This article examines spatial relationships between environmental hazards (i.e., pork feed lots, brick kilns, final assembly plants and a rail line) and markers of social marginality in Ciudad Juarez, Mexico. Juarez represents an opportunity for researchers to test for patterns of injustice in a recently urbanizing metropolis of the Global South.…

The Efficacies of Secretarial Profession by Ghana Education Service and Higher Education Institutions

ERIC Educational Resources Information Center

Adam, Abdul-Kahar

2015-01-01

This project is carried out by employing an empirical method through questionnaire design and administration and tapped the perceptions and knowledge of the target elements of this study. The research frame was about Ghana Education Service office workers within the Accra Metropolis including higher education institutions. A qualitative data…

Comparison of sampling techniques for Bayesian parameter estimation

NASA Astrophysics Data System (ADS)

Allison, Rupert; Dunkley, Joanna

2014-02-01

The posterior probability distribution for a set of model parameters encodes all that the data have to tell us in the context of a given model; it is the fundamental quantity for Bayesian parameter estimation. In order to infer the posterior probability distribution we have to decide how to explore parameter space. Here we compare three prescriptions for how parameter space is navigated, discussing their relative merits. We consider Metropolis-Hasting sampling, nested sampling and affine-invariant ensemble Markov chain Monte Carlo (MCMC) sampling. We focus on their performance on toy-model Gaussian likelihoods and on a real-world cosmological data set. We outline the sampling algorithms themselves and elaborate on performance diagnostics such as convergence time, scope for parallelization, dimensional scaling, requisite tunings and suitability for non-Gaussian distributions. We find that nested sampling delivers high-fidelity estimates for posterior statistics at low computational cost, and should be adopted in favour of Metropolis-Hastings in many cases. Affine-invariant MCMC is competitive when computing clusters can be utilized for massive parallelization. Affine-invariant MCMC and existing extensions to nested sampling naturally probe multimodal and curving distributions.

Estimating ground-level PM(10) in a Chinese city by combining satellite data, meteorological information and a land use regression model.

PubMed

Meng, Xia; Fu, Qingyan; Ma, Zongwei; Chen, Li; Zou, Bin; Zhang, Yan; Xue, Wenbo; Wang, Jinnan; Wang, Dongfang; Kan, Haidong; Liu, Yang

2016-01-01

Development of exposure assessment model is the key component for epidemiological studies concerning air pollution, but the evidence from China is limited. Therefore, a linear mixed effects (LME) model was established in this study in a Chinese metropolis by incorporating aerosol optical depth (AOD), meteorological information and the land use regression (LUR) model to predict ground PM10 levels on high spatiotemporal resolution. The cross validation (CV) R(2) and the RMSE of the LME model were 0.87 and 19.2 μg/m(3), respectively. The relative prediction error (RPE) of daily and annual mean predicted PM10 concentrations were 19.1% and 7.5%, respectively. This study was the first attempt in China to estimate both short-term and long-term variation of PM10 levels with high spatial resolution in a Chinese metropolis with the LME model. The results suggested that the LME model could provide exposure assessment for short-term and long-term epidemiological studies in China. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hazardous waste management and weight-based indicators--the case of Haifa Metropolis.

PubMed

Elimelech, E; Ayalon, O; Flicstein, B

2011-01-30

The quantity control of hazardous waste in Israel relies primarily on the Environmental Services Company (ESC) reports. With limited management tools, the Ministry of Environmental Protection (MoEP) has no applicable methodology to confirm or monitor the actual amounts of hazardous waste produced by various industrial sectors. The main goal of this research was to develop a method for estimating the amounts of hazardous waste produced by various sectors. In order to achieve this goal, sector-specific indicators were tested on three hazardous waste producing sectors in the Haifa Metropolis: petroleum refineries, dry cleaners, and public hospitals. The findings reveal poor practice of hazardous waste management in the dry cleaning sector and in the public hospitals sector. Large discrepancies were found in the dry cleaning sector, between the quantities of hazardous waste reported and the corresponding indicator estimates. Furthermore, a lack of documentation on hospitals' pharmaceutical and chemical waste production volume was observed. Only in the case of petroleum refineries, the reported amount was consistent with the estimate. Copyright © 2010 Elsevier B.V. All rights reserved.

Markov Chain Monte Carlo in the Analysis of Single-Molecule Experimental Data

NASA Astrophysics Data System (ADS)

Kou, S. C.; Xie, X. Sunney; Liu, Jun S.

2003-11-01

This article provides a Bayesian analysis of the single-molecule fluorescence lifetime experiment designed to probe the conformational dynamics of a single DNA hairpin molecule. The DNA hairpin's conformational change is initially modeled as a two-state Markov chain, which is not observable and has to be indirectly inferred. The Brownian diffusion of the single molecule, in addition to the hidden Markov structure, further complicates the matter. We show that the analytical form of the likelihood function can be obtained in the simplest case and a Metropolis-Hastings algorithm can be designed to sample from the posterior distribution of the parameters of interest and to compute desired estiamtes. To cope with the molecular diffusion process and the potentially oscillating energy barrier between the two states of the DNA hairpin, we introduce a data augmentation technique to handle both the Brownian diffusion and the hidden Ornstein-Uhlenbeck process associated with the fluctuating energy barrier, and design a more sophisticated Metropolis-type algorithm. Our method not only increases the estimating resolution by several folds but also proves to be successful for model discrimination.

Audit of sharp weapon deaths in metropolis of Karachi--an autopsy based study.

PubMed

Mirza, Farhat Hussain; Hasan, Qudsia; Memon, Akhtar Amin; Adil, Syeda Ezz-e-Rukhshan

2010-01-01

Sharp weapons are one of the most violent and abhorrent means of deaths. This study assesses the frequency of sharp weapon deaths in Karachi. This was a cross sectional study, and involves the deaths by sharp weapons autopsied in Karachi during Mar 2008-Feb 2009. This study reports that the frequency of sharp weapon deaths in Karachi is similar to some other studies conducted in different regions of Pakistan, yet it is very high as the population of Karachi is way more than any other metropolis of Pakistan. Our study reported that out of 2090 medico-legal deaths in Karachi during the study period, 91 deaths were due to sharp weapons, including 73 (80.2%) males and 18 (19.8%) females. 100% of the deaths were homicides, so none were suicides. Deaths were more frequent in age group ranging from 20-39 years (59.3%). Sharp weapon deaths continue to be a means of quite a number of deaths in Karachi. Such violence depicts intolerant and frustrated nature of the citizens.

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms.

PubMed

Yedid, G; Ofria, C A; Lenski, R E

2008-09-01

Re-evolution of complex biological features following the extinction of taxa bearing them remains one of evolution's most interesting phenomena, but is not amenable to study in fossil taxa. We used communities of digital organisms (computer programs that self-replicate, mutate and evolve), subjected to periods of low resource availability, to study the evolution, loss and re-evolution of a complex computational trait, the function EQU (bit-wise logical equals). We focused our analysis on cases where the pre-extinction EQU clade had surviving descendents at the end of the extinction episode. To see if these clades retained the capacity to re-evolve EQU, we seeded one set of multiple subreplicate 'replay' populations using the most abundant survivor of the pre-extinction EQU clade, and another set with the actual end-extinction ancestor of the organism in which EQU re-evolved following the extinction episode. Our results demonstrate that stochastic, historical, genomic and ecological factors can lead to constraints on further adaptation, and facilitate or hinder re-evolution of a complex feature.

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

PubMed Central

Hibbett, David S; Binder, Manfred

2002-01-01

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes. PMID:12396494

Time evolution of complexity in Abelian gauge theories

NASA Astrophysics Data System (ADS)

Hashimoto, Koji; Iizuka, Norihiro; Sugishita, Sotaro

2017-12-01

Quantum complexity is conjectured to probe inside of black hole horizons (or wormholes) via gauge gravity correspondence. In order to have a better understanding of this correspondence, we study time evolutions of complexities for Abelian pure gauge theories. For this purpose, we discretize the U (1 ) gauge group as ZN and also the continuum spacetime as lattice spacetime, and this enables us to define a universal gate set for these gauge theories and to evaluate time evolutions of the complexities explicitly. We find that to achieve a large complexity ˜exp (entropy), which is one of the conjectured criteria necessary to have a dual black hole, the Abelian gauge theory needs to be maximally nonlocal.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

PubMed

Kapheim, Karen M; Pan, Hailin; Li, Cai; Salzberg, Steven L; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M; Hudson, Matthew E; Venkat, Aarti; Fischman, Brielle J; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D; Kemp, William P; Bosch, Jordi; Waterhouse, Robert M; Zdobnov, Evgeny M; Stolle, Eckart; Kraus, F Bernhard; Helbing, Sophie; Moritz, Robin F A; Glastad, Karl M; Hunt, Brendan G; Goodisman, Michael A D; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D; Barribeau, Seth M; Johnson, Reed M; Massey, Jonathan H; Southey, Bruce R; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J Spencer; Hanrahan, Shawn J; Kocher, Sarah D; Wang, Jun; Robinson, Gene E; Zhang, Guojie

2015-06-05

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. Copyright © 2015, American Association for the Advancement of Science.

The metropolis of Tokyo.

PubMed

Russoff, D

1986-04-01

The Tokyo metropolis houses 11,892,016 people, 1/10 of the Japanese population. In recent years, Tokyo's population growth has slowed as the birthrate has fallen from a 1947 postwar high of 31.5/1000 to 11.4/1000 in 1983. 5.9 million males and 5.8 million females, composing 4 1/2 million households, live in Tokyo's 2160 square kilometers. Within the metropolis' 23 wards, density per square kilometer was 14,023 persons in 1983, with Toshima ward containing 21,844 people per square kilometer. Wards around the city's center held 71% of the population in 1983, but had only 27% of its land mass; outlying cities, towns, and villages held 28% of the population on 54% of the land. 50% of Tokyo's population is aged 25-59; those 65 or over will rise from 1980's 9% to 15.6% of the population in 2000. In 40 years, Japan will have more elderly people than any other advanced country. In 1983, Tokyo had over 150,000 housing starts, high by Japanese and international standards. Nearly 1/4 of Tokyo households each contain a married couple with 2 children, but single person households predominate, reflecting Tokyo's student, working bachelor, and elderly populations. Young, single Japanese workers spend 1/3 of their income on leisure, entertainment, cultural activities and education; couples marry late and, with 2 incomes, can purchase many nonessentials. Nearly 3.25 million students attend Tokyo's fiercely competitive schools and colleges; Japan is almost 100% literate. Of the 6 million people working in Tokyo, half work in the service and retail sector, 25% in manufacturing, 12% in transportation and communication, 9% in finance and insurance, and 8% work in construction. Tokyo workers earn nearly 20% more than the average Japanese worker. Japan now faces job shortages and will see many unemployment problems by 1990. To help absorb new workers, government planners recommend increasing vacation time, training workers as specialists rather than generalists, and encouraging job sharing and part-time work.

From Internet of Things to Smart Data for Smart Urban Monitoring

NASA Astrophysics Data System (ADS)

Gastaud, E.

2017-09-01

Cities are facing some of the major challenges of our time: global warming, pollution, waste management, energy efficiency. The territory of the Metropolis of Lyon, France, which brings together 59 municipalities, for a total of 1.3 million inhabitants, has launched a smart city policy aimed, among other things, at finding solutions for these issues. The data platform set up in 2013 is one of the cornerstones of this policy. In this context, the Metropolis of Lyon is deploying solutions that will enable, through the collection of new data, to implement monitoring and action tools in several fields. As part of a European innovation project called "bIoTope", focused on the development of new services based on the Internet of Things, a multidisciplinary team is implementing a system to mitigate the effects of global warming in the city. Thanks to various connected objects allowing a true monitoring of the trees, and by using different data sources, an automatic and intelligent irrigation system is developed. In the field of waste management, several hundred containers in which the inhabitants throw away their used glass for recycling will soon be equipped with fill rate sensors. The main objective is to have this network of sensors interact easily with the container collection trucks. Expected results are an optimization of the collection, thus less fuel consumed, less noise, less traffic jam. The Metropolis of Lyon also participates in the "Smarter Together" project, focused on the development of intelligent duplicable solutions for cities, in the field of energy. A digital tool for analysing consumption and energy production at the level of a neighbourhood is currently being developed. This requires both interfaces with multiple partners, the development of a data model reflecting the reality of the terrain, from the sensors to the buildings, and the implementation of a visualization tool.

Childhood epilepsy: knowledge and attitude of primary school teachers in Port Harcourt, Nigeria.

PubMed

Alikor, E A D; Essien, A A

2005-01-01

This study was conducted to determine the knowledge of primary school teachers in Port Harcourt metropolis of epilepsy, their knowledge of the management of an attack of epilepsy and the attitude of these teachers towards epilepsy in children. This is a questionnaire-based, cross-sectional study of 118 school teachers from five randomly selected primary schools in Port Harcourt metropolis, Nigeria. Ten percent (12) of the 118 teachers were graded "Good", 45% (54) "Fair" and 43% (52) "Poor" in overall knowledge score. Sixty six teachers (56%) accept applying crude oil on the body as useful in stopping epileptic attacks in children. There was no significant association between overall knowledge score and sex, year of experience as a teacher and experience with a child with epilepsy. Only 10% of the teachers studied were classified as having overall good knowledge of epilepsy. Sixty nine teachers (58.5%) were graded as having good knowledge of cause of epilepsy. Only 38 (32%) disagree that the saliva drooled during an epileptic attack is contagious; one hundred (84.8%) and 65 (55.1%) agree that some childhood illnesses can cause epilepsy and that it runs in families respectively. Overall, 54 teachers (45.8%) had a cumulative score of negative attitude towards epilepsy. Eighty three teachers (73.3%) would want all children with epilepsy put in a special school whilst 57 (48%) agree that children with epilepsy should be withdrawn from schools. The longer the teacher's professional experience, the more the likelihood of positive attitude towards epilepsy but the association did not reach statistically significant level (p = 0.076). Attitude was not statistically associated with sex and educational qualification. The overall knowledge of primary school teachers in Port Harcourt metropolis of epilepsy and the first-aid management of an epileptic attack is poor. The attitude of these teachers towards epilepsy is negative. Education of the primary school teacher and general public on epilepsy is recommended.

Evolution of complexity following a quantum quench in free field theory

NASA Astrophysics Data System (ADS)

Alves, Daniel W. F.; Camilo, Giancarlo

2018-06-01

Using a recent proposal of circuit complexity in quantum field theories introduced by Jefferson and Myers, we compute the time evolution of the complexity following a smooth mass quench characterized by a time scale δ t in a free scalar field theory. We show that the dynamics has two distinct phases, namely an early regime of approximately linear evolution followed by a saturation phase characterized by oscillations around a mean value. The behavior is similar to previous conjectures for the complexity growth in chaotic and holographic systems, although here we have found that the complexity may grow or decrease depending on whether the quench increases or decreases the mass, and also that the time scale for saturation of the complexity is of order δ t (not parametrically larger).

Darwinian evolution in the light of genomics

PubMed Central

Koonin, Eugene V.

2009-01-01

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future. PMID:19213802

Evolution of disorder in Mediator complex and its functional relevance.

PubMed

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K

2016-02-29

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of 'junction-MoRF' has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein-protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster

PubMed Central

Kroiss, Matthias; Schultz, Jörg; Wiesner, Julia; Chari, Ashwin; Sickmann, Albert; Fischer, Utz

2008-01-01

In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran Drosophila melanogaster contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction per se, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction. PMID:18621711

Complex quantum network geometries: Evolution and phase transitions

NASA Astrophysics Data System (ADS)

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Complex quantum network geometries: Evolution and phase transitions.

PubMed

Bianconi, Ginestra; Rahmede, Christoph; Wu, Zhihao

2015-08-01

Networks are topological and geometric structures used to describe systems as different as the Internet, the brain, or the quantum structure of space-time. Here we define complex quantum network geometries, describing the underlying structure of growing simplicial 2-complexes, i.e., simplicial complexes formed by triangles. These networks are geometric networks with energies of the links that grow according to a nonequilibrium dynamics. The evolution in time of the geometric networks is a classical evolution describing a given path of a path integral defining the evolution of quantum network states. The quantum network states are characterized by quantum occupation numbers that can be mapped, respectively, to the nodes, links, and triangles incident to each link of the network. We call the geometric networks describing the evolution of quantum network states the quantum geometric networks. The quantum geometric networks have many properties common to complex networks, including small-world property, high clustering coefficient, high modularity, and scale-free degree distribution. Moreover, they can be distinguished between the Fermi-Dirac network and the Bose-Einstein network obeying, respectively, the Fermi-Dirac and Bose-Einstein statistics. We show that these networks can undergo structural phase transitions where the geometrical properties of the networks change drastically. Finally, we comment on the relation between quantum complex network geometries, spin networks, and triangulations.

Mobilizing Practice: Engaging Space, Technology and Design from a Thai Metropolis

ERIC Educational Resources Information Center

Williams, Amanda Marisa

2009-01-01

The project of ubiquitous computing aims to embed computation into everyday spaces. As a practice that is heavily concerned with space and place, its stance towards mobility is sometimes conflicted--treating mobility by turns as a disruption or as an opportunity--and almost always conceiving of it as free and empowered. Conducted in industrial and…

Psycho-Demographic Correlates of Behaviour towards Seeking Counselling Intervention among Workers in Lagos, Nigeria

ERIC Educational Resources Information Center

Gesinde, Abiodun Matthew; Sanu, Oluwafunto Jolade

2015-01-01

This study sought to examine the impact which age, gender and psychological adjustment have on behaviour towards seeking professional counselling intervention. Multistage sampling technique was employed to select a total of three hundred workers across Lagos metropolis. The ex post facto research design was adopted for the study. Inventory of…

Factors That Inform Students' Choice of Study and Career

ERIC Educational Resources Information Center

Theresa, Lawer Dede

2015-01-01

The research was conducted to find out factors that informed second cycle students' choices of programmes of study and career in the Kumasi Metropolis of Ghana. The descriptive survey was used for the study, and both questionnaire and interview guide were used in gathering the data. The questionnaire was administered on the students while the…

Urban Inequality: Evidence from Four Cities. A Volume in the Multi-City Study of Urban Inequality.

ERIC Educational Resources Information Center

O'Connor, Alice, Ed.; Tilly, Chris, Ed.; Bobo, Lawrence D., Ed.

This collection of papers focuses on urban inequalities in Atlanta, Boston, Detroit, and Los Angeles. There are 11 chapters in 3 parts. The book begins with an introduction, "Understanding Inequality in the Late Twentieth-Century Metropolis: New Perspectives on the Enduring Racial Divide" (Alice O'Connor) and chapter 1,…

Exploring In-Service Teachers' Self-Efficacy in the Kindergarten Classrooms in Ghana

ERIC Educational Resources Information Center

Boateng, Philip; Sekyere, Frank Owusu

2018-01-01

The study explored in-service teachers' efficacy beliefs in pupil engagement. The sample size was 299 kindergarten teachers selected from both public and private kindergarten schools in the Kumasi metropolis of Ghana. The study adopted and used pupil engagement subscale of the Ohio State Teacher Efficacy Scale (OSTES) developed by Tschannen-Moran…

Utility of University Curricula in Contemporary Times: Perspectives of Employers in the Cape Coast Metropolis

ERIC Educational Resources Information Center

Dodoo, Joana Eva; Kuupole, Domwini Dabire

2017-01-01

The majority of studies and reports on university education in Africa have focused mainly on issues related to access, quality, teaching and learning environment, and so on. Although these issues are undoubtedly critical, even more germane to the discourse is the desired utility of university education to society. The authors present the…

Perceiving the Metropolis: Seeing the City through a Prism of Race

ERIC Educational Resources Information Center

Krysan, Maria; Bader, Michael

2007-01-01

Investigating the role of preferences in causing persistent patterns of racial residential segregation in the United States has a long history. In this paper, we bring a new perspective--and new data from the 2004 Detroit Area Study--to the question of how best to characterize black and white preferences toward living in neighborhoods with people…

Effects of Goal-Setting Skills on Students'academic Performance in English Language in Enugu Nigeria

ERIC Educational Resources Information Center

Abe, Iyabo Idowu; Ilogu, Guy Chibuzoh; Madueke, Ify Louisa

2014-01-01

The study investigated the effectiveness of goal-setting skills among Senior Secondary II students' academic performance in English language in Enugu Metropolis, Enugu state, Nigeria. Quasi-experimental pre-test, post-test control group design was adopted for the study. The initial sample was 147 participants (male and female) Senior Secondary…

Technology Instructional Package Mediated Instruction and Senior Secondary School Students' Academic Performance in Biology Concepts

ERIC Educational Resources Information Center

Yaki, Akawo Angwal; Babagana, Mohammed

2016-01-01

The paper examined the effects of a Technological Instructional Package (TIP) on secondary school students' performance in biology. The study adopted a pre-test, post-test experimental control group design. The sample size of the study was 80 students from Minna metropolis, Niger state, Nigeria; the samples were randomly assigned into treatment…

Beyond the Metropolis: The Forgotten History of Small-Town Teachers' Unions

ERIC Educational Resources Information Center

Scribner, Campbell F.

2015-01-01

This article examines the legal and political significance of teacher unionization in rural and suburban school districts between 1960 and 1975. While most historians focus on the growth of unions in urban areas, strikes in outlying districts played a determinative role in the development of public sector labor law, particularly in the arbitration…

Stochastic Approximation Methods for Latent Regression Item Response Models. Research Report. ETS RR-09-09

ERIC Educational Resources Information Center

von Davier, Matthias; Sinharay, Sandip

2009-01-01

This paper presents an application of a stochastic approximation EM-algorithm using a Metropolis-Hastings sampler to estimate the parameters of an item response latent regression model. Latent regression models are extensions of item response theory (IRT) to a 2-level latent variable model in which covariates serve as predictors of the…

Normative Value Conceptions of Modern Parents, Teachers, and Educators (Analysis of Moral Value Judgments)

ERIC Educational Resources Information Center

Shelina, S. L.; Mitina, O. V.

2015-01-01

The article presents the results of an analysis of the moral value judgments of adults (parents, teachers, educators) that directly concern the socialization process of the young generation in the modern metropolis. This paper follows the model study by Jean Piaget that investigated the moral value judgments of children. A comparative analysis of…

Bayesian Estimation of Multidimensional Item Response Models. A Comparison of Analytic and Simulation Algorithms

ERIC Educational Resources Information Center

Martin-Fernandez, Manuel; Revuelta, Javier

2017-01-01

This study compares the performance of two estimation algorithms of new usage, the Metropolis-Hastings Robins-Monro (MHRM) and the Hamiltonian MCMC (HMC), with two consolidated algorithms in the psychometric literature, the marginal likelihood via EM algorithm (MML-EM) and the Markov chain Monte Carlo (MCMC), in the estimation of multidimensional…

Development and Validation of Social Provision Scale on First Year Undergraduate Psychological Adjustment

ERIC Educational Resources Information Center

Oluwatomiwo, Oladunmoye Enoch

2015-01-01

This study examined the development and validation of socio provision scale on first year undergraduates adjustment among institution in Ibadan metropolis. The study adopted a descriptive survey design. A sample of 300 participants was randomly selected across institutions in Ibadan. Data were collected using socio provision scale (a =0.76),…

Ecology, Literature and Environmental Education

ERIC Educational Resources Information Center

Tsekos, Christos A.; Tsekos, Evangelos A.; Christoforidou, Elena I.

2012-01-01

The first part of this article refers to the initial attempt to relate Nature to Literature since the age of Hellenistic Alexandria in Egypt. Alexandria was a metropolis of its time with a quite lively character of urban life. Influenced by that character Theocritus was the first to lay the foundations of what is defined as pastoral poetry. In the…

Firoz Uncle: A "Reluctant" Educationist in a Mumbai Ghetto

ERIC Educational Resources Information Center

Murali, Sreejith

2017-01-01

This article focuses on the educational efforts of Syed Firoz Ashraf in the East Jogeshwari area of Mumbai and places his work in the context of the increasing communalisation of social life and education in a poor working class suburb in Mumbai city. Muslim community has been ghettoised in the metropolis to specific areas especially since the…

Determinants of Differing Teacher Attitudes towards Inclusive Education Practice

ERIC Educational Resources Information Center

Gyimah, Emmanuel K.; Ackah, Francis R., Jr.; Yarquah, John A.

2010-01-01

An examination of literature reveals that teacher attitude is fundamental to the practice of inclusive education. In order to verify the extent to which the assertion is applicable in Ghana, 132 teachers were selected from 16 regular schools in the Cape Coast Metropolis using purposive and simple random sampling techniques to respond to a four…

Environmental Influence on the Evolution of Morphological Complexity in Machines

PubMed Central

Auerbach, Joshua E.; Bongard, Josh C.

2014-01-01

Whether, when, how, and why increased complexity evolves in biological populations is a longstanding open question. In this work we combine a recently developed method for evolving virtual organisms with an information-theoretic metric of morphological complexity in order to investigate how the complexity of morphologies, which are evolved for locomotion, varies across different environments. We first demonstrate that selection for locomotion results in the evolution of organisms with morphologies that increase in complexity over evolutionary time beyond what would be expected due to random chance. This provides evidence that the increase in complexity observed is a result of a driven rather than a passive trend. In subsequent experiments we demonstrate that morphologies having greater complexity evolve in complex environments, when compared to a simple environment when a cost of complexity is imposed. This suggests that in some niches, evolution may act to complexify the body plans of organisms while in other niches selection favors simpler body plans. PMID:24391483

Time-ordered exponential on the complex plane and Gell-Mann—Low formula as a mathematical theorem

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

Futakuchi, Shinichiro; Usui, Kouta

2016-04-15

The time-ordered exponential representation of a complex time evolution operator in the interaction picture is studied. Using the complex time evolution, we prove the Gell-Mann—Low formula under certain abstract conditions, in mathematically rigorous manner. We apply the abstract results to quantum electrodynamics with cutoffs.

Acquisition of Complex Systemic Thinking: Mental Models of Evolution

ERIC Educational Resources Information Center

d'Apollonia, Sylvia T.; Charles, Elizabeth S.; Boyd, Gary M.

2004-01-01

We investigated the impact of introducing college students to complex adaptive systems on their subsequent mental models of evolution compared to those of students taught in the same manner but with no reference to complex systems. The students' mental models (derived from similarity ratings of 12 evolutionary terms using the pathfinder algorithm)…

Ornament Complexity Is Correlated with Sexual Selection: (A Comment on Raia et al., "Cope's Rule and the Universal Scaling Law of Ornament Complexity").

PubMed

Holman, Luke; Bro-Jørgensen, Jakob

2016-08-01

Raia et al. propose that the evolution of the shape and complexity of animal ornaments (e.g., deer antlers) can be explained by interspecific variation in body size and is not influenced by sexual selection. They claim to show that ornament complexity is related to body size by an 0.25-power law and argue that this finding precludes a role for sexual selection in the evolution of ornament complexity. However, their study does not test alternative hypotheses and mismeasures antler shape allometry by omitting much of the published data. We show that an index of sexual selection (sexual size dimorphism) is positively correlated with size-corrected antler complexity and that the allometric slope of complexity is substantially greater than 0.25, contra Raia et al. We conclude that sexual selection and physical constraints both affect the evolution of antler shape.

Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

PubMed

Speijer, Dave

2011-05-01

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

Spectral analysis of finite-time correlation matrices near equilibrium phase transitions

NASA Astrophysics Data System (ADS)

Vinayak; Prosen, T.; Buča, B.; Seligman, T. H.

2014-10-01

We study spectral densities for systems on lattices, which, at a phase transition display, power-law spatial correlations. Constructing the spatial correlation matrix we prove that its eigenvalue density shows a power law that can be derived from the spatial correlations. In practice time series are short in the sense that they are either not stationary over long time intervals or not available over long time intervals. Also we usually do not have time series for all variables available. We shall make numerical simulations on a two-dimensional Ising model with the usual Metropolis algorithm as time evolution. Using all spins on a grid with periodic boundary conditions we find a power law, that is, for large grids, compatible with the analytic result. We still find a power law even if we choose a fairly small subset of grid points at random. The exponents of the power laws will be smaller under such circumstances. For very short time series leading to singular correlation matrices we use a recently developed technique to lift the degeneracy at zero in the spectrum and find a significant signature of critical behavior even in this case as compared to high temperature results which tend to those of random matrix models.

Active heat pulse sensing of 3-D-flow fields in streambeds

NASA Astrophysics Data System (ADS)

Banks, Eddie W.; Shanafield, Margaret A.; Noorduijn, Saskia; McCallum, James; Lewandowski, Jörg; Batelaan, Okke

2018-03-01

Profiles of temperature time series are commonly used to determine hyporheic flow patterns and hydraulic dynamics in the streambed sediments. Although hyporheic flows are 3-D, past research has focused on determining the magnitude of the vertical flow component and how this varies spatially. This study used a portable 56-sensor, 3-D temperature array with three heat pulse sources to measure the flow direction and magnitude up to 200 mm below the water-sediment interface. Short, 1 min heat pulses were injected at one of the three heat sources and the temperature response was monitored over a period of 30 min. Breakthrough curves from each of the sensors were analysed using a heat transport equation. Parameter estimation and uncertainty analysis was undertaken using the differential evolution adaptive metropolis (DREAM) algorithm, an adaption of the Markov chain Monte Carlo method, to estimate the flux and its orientation. Measurements were conducted in the field and in a sand tank under an extensive range of controlled hydraulic conditions to validate the method. The use of short-duration heat pulses provided a rapid, accurate assessment technique for determining dynamic and multi-directional flow patterns in the hyporheic zone and is a basis for improved understanding of biogeochemical processes at the water-streambed interface.

The Role of Reticulate Evolution in Creating Innovation and Complexity

PubMed Central

Swithers, Kristen S.; Soucy, Shannon M.; Gogarten, J. Peter

2012-01-01

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity. PMID:22844638

Exponential evolution: implications for intelligent extraterrestrial life.

PubMed

Russell, D A

1983-01-01

Some measures of biologic complexity, including maximal levels of brain development, are exponential functions of time through intervals of 10(6) to 10(9) yrs. Biological interactions apparently stimulate evolution but physical conditions determine the time required to achieve a given level of complexity. Trends in brain evolution suggest that other organisms could attain human levels within approximately 10(7) yrs. The number (N) and longevity (L) terms in appropriate modifications of the Drake Equation, together with trends in the evolution of biological complexity on Earth, could provide rough estimates of the prevalence of life forms at specified levels of complexity within the Galaxy. If life occurs throughout the cosmos, exponential evolutionary processes imply that higher intelligence will soon (10(9) yrs) become more prevalent than it now is. Changes in the physical universe become less rapid as time increases from the Big Bang. Changes in biological complexity may be most rapid at such later times. This lends a unique and symmetrical importance to early and late universal times.

The evolution of resistance genes in multi-protein plant resistance systems.

PubMed

Friedman, Aaron R; Baker, Barbara J

2007-12-01

The genomic perspective aids in integrating the analysis of single resistance (R-) genes into a higher order model of complex plant resistance systems. The majority of R-genes encode a class of proteins with nucleotide binding (NB) and leucine-rich repeat (LRR) domains. Several R-proteins act in multi-protein R-complexes that mediate interaction with pathogen effectors to induce resistance signaling. The complexity of these systems seems to have resulted from multiple rounds of plant-pathogen co-evolution. R-gene evolution is thought to be facilitated by the formation of R-gene clusters, which permit sequence exchanges via recombinatorial mispairing and generate high haplotypic diversity. This pattern of evolution may also generate diversity at other loci that contribute to the R-complex. The rate of recombination at R-clusters is not necessarily homogeneous or consistent over evolutionary time: recent evidence suggests that recombination at R-clusters is increased following pathogen infection, suggesting a mechanism that induces temporary genome instability in response to extreme stress. DNA methylation and chromatin modifications may allow this instability to be conditionally regulated and targeted to specific genome regions. Knowledge of natural R-gene evolution may contribute to strategies for artificial evolution of novel resistance specificities.

Complexity and the Arrow of Time

NASA Astrophysics Data System (ADS)

Lineweaver, Charles H.; Davies, Paul C. W.; Ruse, Michael

2013-08-01

1. What is complexity? Is it increasing? Charles H. Lineweaver, Paul C. W. Davies and Michael Ruse; 2. Directionality principles from cancer to cosmology Paul C. W. Davies; 3. A simple treatment of complexity: cosmological entropic boundary conditions on increasing complexity Charles H. Lineweaver; 4. Using complexity science to search for unity in the natural sciences Eric J. Chaisson; 5. On the spontaneous generation of complexity in the universe Seth Lloyd; 6. Emergent spatiotemporal complexity in field theory Marcelo Gleiser; 7. Life: the final frontier for complexity? Simon Conway Morris; 8. Evolution beyond Newton, Darwin, and entailing law: the origin of complexity in the evolving biosphere Stuart A. Kauffman; 9. Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere D. Eric Smith; 10. The inferential evolution of biological complexity: forgetting nature by learning to nurture David C. Krakauer; 11. Information width: a way for the second law to increase complexity David Wolpert; 12. Wrestling with biological complexity: from Darwin to Dawkins Michael Ruse; 13. The role of generative entrenchment and robustness in the evolution of complexity William C. Wimsatt; 14. On the plurality of complexity-producing mechanisms Philip Clayton; Index.

Evolution of complex dynamics

NASA Astrophysics Data System (ADS)

Wilds, Roy; Kauffman, Stuart A.; Glass, Leon

2008-09-01

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.

Complex Homology and the Evolution of Nervous Systems

PubMed Central

Liebeskind, Benjamin J.; Hillis, David M.; Zakon, Harold H.; Hofmann, Hans A.

2016-01-01

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states. PMID:26746806

Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

PubMed Central

Esteve-Altava, Borja; Boughner, Julia C.; Diogo, Rui; Villmoare, Brian A.; Rasskin-Gutman, Diego

2015-01-01

Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates. PMID:25992690

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

PubMed Central

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-01-01

Abstract Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. PMID:28685813

Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid

PubMed Central

Pankey, M. Sabrina; Minin, Vladimir N.; Imholte, Greg C.; Suchard, Marc A.; Oakley, Todd H.

2014-01-01

Despite contingency in life’s history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species’ photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them. PMID:25336755

Genomic signatures of evolutionary transitions from solitary to group living

PubMed Central

Kapheim, Karen M.; Pan, Hailin; Li, Cai; Salzberg, Steven L.; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M.; Hudson, Matthew E.; Venkat, Aarti; Fischman, Brielle J.; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D.; Kemp, William P.; Bosch, Jordi; Waterhouse, Robert M.; Zdobnov, Evgeny M.; Stolle, Eckart; Kraus, F. Bernhard; Helbing, Sophie; Moritz, Robin F. A.; Glastad, Karl M.; Hunt, Brendan G.; Goodisman, Michael A. D.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D.; Barribeau, Seth M.; Johnson, Reed M.; Massey, Jonathan H.; Southey, Bruce R.; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F.; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J. Spencer; Hanrahan, Shawn J.; Kocher, Sarah D.; Wang, Jun; Robinson, Gene E.; Zhang, Guojie

2017-01-01

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. PMID:25977371

A Hierarchical Multivariate Bayesian Approach to Ensemble Model output Statistics in Atmospheric Prediction

DTIC Science & Technology

2017-09-01

efficacy of statistical post-processing methods downstream of these dynamical model components with a hierarchical multivariate Bayesian approach to...Bayesian hierarchical modeling, Markov chain Monte Carlo methods , Metropolis algorithm, machine learning, atmospheric prediction 15. NUMBER OF PAGES...scale processes. However, this dissertation explores the efficacy of statistical post-processing methods downstream of these dynamical model components

Effects of Lecture Method Supplemented with Music and Computer Animation on Senior Secondary School Students' Academic Achievement in Electrochemistry

ERIC Educational Resources Information Center

Akpoghol, T. V.; Ezeudu, F. O.; Adzape, J. N.; Otor, E. E.

2016-01-01

The study investigated the effects of Lecture Method Supplemented with Music (LMM) and Computer Animation (LMC) on senior secondary school students' academic achievement in electrochemistry in Makurdi metropolis. Six research questions and six hypotheses guided the study. The design of the study was quasi experimental, specifically the pre-test,…

Relative Effect of Lecture Method Supplemented with Music and Computer Animation on Senior Secondary School Students' Retention in Electrochemistry

ERIC Educational Resources Information Center

Akpoghol, T. V.; Ezeudu, F. O.; Adzape, J. N.; Otor, E. E.

2016-01-01

The study investigated the effects of Lecture Method Supplemented with Music (LMM) and Computer Animation (LMC) on senior secondary school students' retention in electrochemistry in Makurdi metropolis. Three research questions and three hypotheses guided the study. The design of the study was quasi experimental, specifically the pre-test,…

Factors Related to under Achievement in Science, Technology and Mathematics Education (STME) in Secondary Schools in Rivers State, Nigeria

ERIC Educational Resources Information Center

Obomanu, B. J.; Adaramola, M. O.

2011-01-01

We report a research into factors related to underachievement in science, technology and mathematics (STM) education in schools in Rivers State, Nigeria. The study investigated 240 Nigerian secondary school students, 100 parents, 140 STM teachers and 20 government officials from Port Harcourt Metropolis. Five (5) research questions and one…

The Vitality of a City: Challenge to Higher Education; Challenge to Education: A New Approach.

ERIC Educational Resources Information Center

Johnson, Byron

The US higher education system adopted the European pattern of separating the university from the city. This pattern has changed somewhat in the last few decades, when new universities or branches of older ones have appeared in the metropolis. But frequently these institutions are unconcerned with finding ways to contribute toward improving urban…

Teachers' Level of Awareness of 21st Century Occupational Roles in Rivers State Secondary Schools

ERIC Educational Resources Information Center

Uche, Chineze M.; Kaegon, Leesi E. S. P.; Okata, Fanny Chiemezie

2016-01-01

This study investigated the teachers' level of awareness of 21st century occupational roles in Rivers state secondary schools. Three research questions and three hypotheses guided the study. The population of study comprised of 247 public secondary schools and 57 private secondary schools in Port Harcourt metropolis of Rivers state which gave a…

Testing a Moderated Model of Satisfaction with Urban Living Using Data for Brisbane-South East Queensland, Australia

ERIC Educational Resources Information Center

Mccrea, Rod; Stimson, Robert; Western, John

2005-01-01

Using survey data collected from households living in the Brisbane-South East Queensland region, a rapidly growing metropolis in Australia, path analysis is used to test links between urban residents' assessment of various urban attributes and their level of satisfaction in three urban domains--housing, neighbourhood or local area, and the wider…

Effect of Improvised Instructional Materials on Students' Achievement in Geometry at the Upper Basic Education Level in Makurdi Metropolis, Benue State, Nigeria

ERIC Educational Resources Information Center

Iji, C. O.; Ogbole, P. O.; Uka, N. K.

2014-01-01

Among all approaches aimed at reducing poor mathematics achievement among the students, adoption of appropriate methods of teaching appears to be more rewarding. In this study, improvised instructional materials were used to ascertain students' geometry achievement at the upper basic education one. Two research questions were asked with associated…

Assessment of the Implementation of the Reading Component of the English Language Curriculum for Basic Education in Nigeria

ERIC Educational Resources Information Center

Yusuf, Hanna Onyi

2014-01-01

This study assessed the implementation of the reading component of the Junior Secondary School English Language Curriculum for Basic Education in Nigeria. Ten (10) randomly selected public and private secondary schools from Kaduna metropolis in Kaduna State of Nigeria were used for the study. Among the factors assessed in relation to the…

33 CFR 165.801 - Annual fireworks displays and other events in the Eighth Coast Guard District requiring safety...

Code of Federal Regulations, 2014 CFR

2014-07-01

... representatives include commissioned, warrant, and petty officers of the U.S. Coast Guard. (d) Informational...-90.5 (West Virginia). 9. 1 day—Third or fourth of July Harrah's Casino/Metropolis Fireworks... Mississippi River mile marker 518.0 to 519.0 (Iowa). 27. 1 day—4th of July weekend Harrah's Casino and Hotel...

Performance of Higher National Diploma of Building Technology Graduates in the Construction Industry: A Tracer Study in Kumasi Metropolis, Ghana

ERIC Educational Resources Information Center

Awere, E.; Edu-Buandoh, K. B. M.; Dadzie, D. K.; Aboagye, J. A.

2016-01-01

Building Technology graduates from Ghanaian Polytechnics seek employment in the construction industry, yet little information is known as to whether their tertiary education is really related to and meeting the actual needs of their prospective employers in the construction industry. The tracer study was conducted to ascertain the performance of…

STS-61A earth observations

NASA Image and Video Library

1985-10-30

61A-31-005 (30 Oct 1985) --- This almost vertical view, photographed from Earth-orbit by an STS-61A crew member, centers on the metropolis of Milwaukee, Wisconsin, and some of the adjacent Lake Michigan shoreline, southward toward the Illinois border. The 70mm frame was photographed on the first day of the Spacelab D-1 mission with a handheld Hasselblad camera.

Achieving Quality Education in Ghana: The Spotlight on Primary Education within the Kumasi Metropolis

ERIC Educational Resources Information Center

Boakye-Amponsah, Abraham; Enninful, Ebenezer Kofi; Anin, Emmanuel Kwabena; Vanderpuye, Patience

2015-01-01

Background: Ghana being a member of the United Nations, committed to the Universal Primary Education initiative in 2000 and has since implemented series of educational reforms to meet the target for the Millennium Development Goal (MDG) 2. Despite the numerous government interventions to achieve the MDG 2, many children in Ghana have been denied…

Structural Dimensions and Functions of Student Centers in the Open Education Faculty Practices: Three Metropolis Samplings--Istanbul, Ankara and Izmir

ERIC Educational Resources Information Center

Tunckan, Ergun

2007-01-01

The Open Education Faculty Students Centers have been offering many services to students in Turkey since 1982. Building up bridges between students and faculties, student centers have had technological improvements since 1998 and thereafter quality of services have been increased and services given to students at the student center have been…

Estimation of a Ramsay-Curve Item Response Theory Model by the Metropolis-Hastings Robbins-Monro Algorithm. CRESST Report 834

ERIC Educational Resources Information Center

Monroe, Scott; Cai, Li

2013-01-01

In Ramsay curve item response theory (RC-IRT, Woods & Thissen, 2006) modeling, the shape of the latent trait distribution is estimated simultaneously with the item parameters. In its original implementation, RC-IRT is estimated via Bock and Aitkin's (1981) EM algorithm, which yields maximum marginal likelihood estimates. This method, however,…

Estimation of a Ramsay-Curve Item Response Theory Model by the Metropolis-Hastings Robbins-Monro Algorithm

ERIC Educational Resources Information Center

Monroe, Scott; Cai, Li

2014-01-01

In Ramsay curve item response theory (RC-IRT) modeling, the shape of the latent trait distribution is estimated simultaneously with the item parameters. In its original implementation, RC-IRT is estimated via Bock and Aitkin's EM algorithm, which yields maximum marginal likelihood estimates. This method, however, does not produce the…

Visual defects and commercial motorcycle accidents in south eastern Nigeria.

PubMed

Achigbu, E O; Fiebai, B

2013-01-01

Commercial motorcyclists are a regular part of our highways, especially with the decrease in the number and quality of good roads. This study is aimed at determining the role of vision if any in the increasing number of road traffic accidents (RTA's) among commercial motorcyclists in Enugu metropolis, Nigeria. A cross sectional survey with a multi stage random sampling design was used to select the 615 commercial motorcyclists in Enugu metropolis enrolled in the study. Out of the 615 motorcyclists, seven (1.14% +/- 0.70%) motorcyclists had visual impairment (< 6/18-3/60). Visual field defect was noted in 2.3% +/- 0.98% while 2.6% +/- 0.98% had colour vision defect. The prevalence of road traffic accident (RTA) was 57.7%. Visual impairment was not significantly associated with RTA (P = 0.333) while visual field defect (P = 0.000), and colour vision defect (P = 0.003) were positively associated with RTA. Inexperienced riders had significantly more RTAs than their counterparts (P = 0.000). CONCLUSION; Visual field defect, and colour vision defect were significantly associated with RTA but this finding is in the backdrop of poor training, and inexperience which also significantly affected RTA among the predominantly young riders involved in RTA.

Spatial patterns monitoring of road traffic injuries in Karachi metropolis.

PubMed

Lateef, Muhammad U

2011-06-01

This article aims to assess the pattern of road traffic injuries (RTIs) and fatalities in Karachi metropolis. Assessing the pattern of RTIs in Karachi at this juncture is important for many reasons. The rapid motorisation in the recent years due to the availability of credit has significantly increased the traffic volume of the city. Since then, the roads of Karachi have continuously developed at a rapid pace. This development has come with a high human loss, because the construction of multilevel flyovers, signal-free corridors and the resulting high-speed traffic ultimately increase the severity of injuries. The reasons for this high proportion are inadequate infrastructure, poor enforcement of safety regulations, high crash severity index and greater population of vulnerable road user groups (riders and pedestrians). This research is the first of its kind in the country to have a geocoded database of fatalities and injuries in a geographical information system for the entire city of Karachi. In fact, road crashes are both predictable and preventable. Developing countries should learn from the experience of highly motorised nations to avoid the high burden of RTIs by adopting road safety and prevention measures.

Strategic guidelines of a megalopolis’s development: new industrialization and ecological tension

NASA Astrophysics Data System (ADS)

Lavrikova, Yulia; Akberdina, Victoria; Mezentseva, Elena

2017-06-01

The article is devoted to the integration of environmental concerns in the development strategy of the metropolis. The authors substantiate the relationship of the new industrialization and reduce the burden on the environment. For example, a large city in Russia - Ekaterinburg - projections and strategic directions of ecological development of the city for the period up to 2035. The basis for the forecast were the methods of aggregation of economic sectors, functional relationship and forecasting algorithms. The article describes three scenarios for the development of Ekaterinburg, the results of calculations by the author’s method. The authors have shown the relationship of industrial development of the metropolis and the anthropogenic load, which is assessed using such indicators as emissions of harmful substances into the atmosphere, discharges of sewage, green spaces per inhabitant. The authors note that the ecological security of the residents is directly related to the improvement of controllability of the municipal economy, the increased control in the field of the environment, reduction of environmental burden on humans and the environment, zoning of the city with a goal differential application of indicators of the quality of the environment.

Offal dumping sites influence the relative abundance and roosting site selection of Black Kites (Milvus migrans govinda) in urban landscape: a study from Kolkata metropolis, India.

PubMed

Mazumdar, Subhendu; Ghose, Dipankar; Saha, Goutam Kumar

2017-12-14

Although Black Kites (Milvus migrans govinda) serve as major scavenging raptor in most of the urban areas, scientific studies on this important ecosystem service provider are almost non-existent in Indian context. The present study was carried out in a metropolis in eastern India to find out the factors influencing relative abundance and roosting site selection of Black Kites. Separate generalized linear models (GLMs) were performed considering encounter rate and roosting Black Kite abundance as response variables. The study conclusively indicated that encounter rates of Black Kites were significantly influenced by the presence of garbage dumps in its vicinity. Numbers of Black Kites were also higher in the roosting sites situated closer to garbage dumps and open spaces. In addition, expected counts of Black Kites significantly increased in roosting sites situated away from buildings and water bodies. However, built-up area and tree cover around the roosting sites had no influence on the abundance of Black Kites therein. With rapid urbanization and changing offal disposal patterns, our findings would be useful to ensure continued availability of food and roosting sites of Black Kites in urban areas.

Cure fraction model with random effects for regional variation in cancer survival.

PubMed

Seppä, Karri; Hakulinen, Timo; Kim, Hyon-Jung; Läärä, Esa

2010-11-30

Assessing regional differences in the survival of cancer patients is important but difficult when separate regions are small or sparsely populated. In this paper, we apply a mixture cure fraction model with random effects to cause-specific survival data of female breast cancer patients collected by the population-based Finnish Cancer Registry. Two sets of random effects were used to capture the regional variation in the cure fraction and in the survival of the non-cured patients, respectively. This hierarchical model was implemented in a Bayesian framework using a Metropolis-within-Gibbs algorithm. To avoid poor mixing of the Markov chain, when the variance of either set of random effects was close to zero, posterior simulations were based on a parameter-expanded model with tailor-made proposal distributions in Metropolis steps. The random effects allowed the fitting of the cure fraction model to the sparse regional data and the estimation of the regional variation in 10-year cause-specific breast cancer survival with a parsimonious number of parameters. Before 1986, the capital of Finland clearly stood out from the rest, but since then all the 21 hospital districts have achieved approximately the same level of survival. Copyright © 2010 John Wiley & Sons, Ltd.

Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics — Monte Carlo Canonical Propagation Algorithm

PubMed Central

Weare, Jonathan; Dinner, Aaron R.; Roux, Benoît

2016-01-01

A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method. PMID:26918826

The Emerging Spatial Organization of the Metropolis: Zones of Diversity and Minority Enclaves in Chicago

PubMed Central

Zhang, Wenquan; Logan, John R.

2018-01-01

The rapid growth of Asian and Hispanic populations in urban areas is superceding traditional classifications of neighborhoods (for example as white, transitional, or minority). The “global neighborhood” that includes all groups (white, black, Hispanic and Asian) is one important new category. We examine the emerging spatial pattern of racial/ethnic composition in the Chicago metropolis, documenting an expansion of all-minority neighborhoods in the city and just beyond its borders, a shrinking set of all-white neighborhoods in the outer suburbs, and more diverse neighborhoods including whites mainly in between. The most novel element of this pattern is how large the zone of diversity has become and how far it extends into suburbia, upending the old dichotomy of “chocolate city” and “vanilla suburbs.” In addition to comparing the distance of different kinds of neighborhoods from the urban core, we also analyze their adjacency to neighborhoods of the same type or other types. There is a strong tendency toward spatial clustering of each neighborhood type and also for transitions on the boundaries of clusters either to expand or to contract their territory. PMID:29430517

Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.

PubMed

Turoňová, Beata; Marsalek, Lukas; Davidovič, Tomáš; Slusallek, Philipp

2015-03-01

Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts. Copyright © 2015 Elsevier Inc. All rights reserved.

Predicting the evolution of sex on complex fitness landscapes.

PubMed

Misevic, Dusan; Kouyos, Roger D; Bonhoeffer, Sebastian

2009-09-01

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, Delta Var(HD), also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. Delta Var(HD) is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction.

Predicting the Evolution of Sex on Complex Fitness Landscapes

PubMed Central

Misevic, Dusan; Kouyos, Roger D.; Bonhoeffer, Sebastian

2009-01-01

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, ΔVarHD, also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. ΔVarHD is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction. PMID:19763171

The long story of mitochondrial DNA and respiratory complex I.

PubMed

Degli Esposti, Mauro

2017-01-01

This article examines the long story of the relationship between mitochondrial DNA (mtDNA) and respiratory complex I, NADH:Ubiquinone Oxidoreductase, from its beginning  in the genome of the bacterial endosymbiont which then evolved into the mitochondria of our cells. The story begins with the evolution of ancient forms of bacterial complex I into the Nuo14 complex I that was present in the alpha proteobacterial ancestor of mitochondria. The story then becomes complicated in the diversity of eukaryotic organisms that are currently recognized. Therefore, it does not have a clear end, because currently available information shows different situations of metabolic adaptation and gene loss, indicating cases of de-evolution of the original protonmotive complex into a system that may fundamentally assist [FeFe]-hydrogenases in re-oxidising metabolically produced NADH under anaerobic conditions. The history of complex I is thus a never ending story of molecular and physiological evolution producing new perspectives for studying the enzyme complex that occupies the largest proportion of mitochondrial DNA.

"Synergistic selection": a Darwinian frame for the evolution of complexity.

PubMed

Corning, Peter A; Szathmáry, Eörs

2015-04-21

Non-Darwinian theories about the emergence and evolution of complexity date back at least to Lamarck, and include those of Herbert Spencer and the "emergent evolution" theorists of the later nineteenth and early twentieth centuries. In recent decades, this approach has mostly been espoused by various practitioners in biophysics and complexity theory. However, there is a Darwinian alternative - in essence, an economic theory of complexity - proposing that synergistic effects of various kinds have played an important causal role in the evolution of complexity, especially in the "major transitions". This theory is called the "synergism hypothesis". We posit that otherwise unattainable functional advantages arising from various cooperative phenomena have been favored over time in a dynamic that the late John Maynard Smith characterized and modeled as "synergistic selection". The term highlights the fact that synergistic "wholes" may become interdependent "units" of selection. We provide some historical perspective on this issue, as well as a brief explication of the underlying theory and the concept of synergistic selection, and we describe two relevant models. Copyright © 2015 Elsevier Ltd. All rights reserved.

Highly efficient photocatalytic hydrogen evolution from nickel quinolinethiolate complexes under visible light irradiation

NASA Astrophysics Data System (ADS)

Rao, Heng; Yu, Wen-Qian; Zheng, Hui-Qin; Bonin, Julien; Fan, Yao-Ting; Hou, Hong-Wei

2016-08-01

Earth-abundant metal complexes have emerged as promising surrogates of platinum for catalyzing the hydrogen evolution reaction (HER). In this study, we report the design and synthesis of two novel nickel quinolinethiolate complexes, namely [Ni(Hqt)2(4, 4‧-Z-2, 2‧-bpy)] (Hqt = 8-quinolinethiol, Z = sbnd H [1] or sbnd CH3 [2], bpy = bipyridine). An efficient three-component photocatalytic homogeneous system for hydrogen generation working under visible light irradiation was constructed by using the target complexes as catalysts, triethylamine (TEA) as sacrificial electron donor and xanthene dyes as photosensitizer. We obtain turnover numbers (TON, vs. catalyst) for H2 evolution of 5923/7634 under the optimal conditions with 5.0 × 10-6 M complex 1/2 respectively, 1.0 × 10-3 M fluorescein and 5% (v/v) TEA at pH 12.3 in EtOH/H2O (1:1, v/v) mixture after 8 h irradiation (λ > 420 nm). We discuss the mechanism of H2 evolution in the homogeneous photocatalytic system based on fluorescence spectrum and cyclic voltammetry data.

Detection of timescales in evolving complex systems

PubMed Central

Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

2016-01-01

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system. PMID:28004820

Distribution of physical therapists working on public and private establishments in different levels of complexity of health care in Brazil.

PubMed

Costa, Larissa R; Costa, José L R; Oishi, Jorge; Driusso, Patricia

2012-01-01

The Brazilian Health System is organized on a regional and hierarchical form with three levels of complexity of health care. The Primary Care represents the first element of a continuing health care process, complemented by specialized actions. However, the centrality of the specialized care is still a problem in Brazil, especially in the private sector. Studies on the distribution of professionals in the health system allowing the formulation of appropriate policies are needed. To investigate the distribution of physical therapists in the levels of complexity of health care and between public and private establishments, according to data from the National Register of Health Service Providers (NRHSP). A descriptive cross-sectional study was performed considering NRHSP-national bank data collected in March 2010 and demographic census 2010 data. Data were analyzed through descriptive statistics techniques. We identified 53,181 registries of physical therapists, 60% linked to the private sector. Only 13% of all entries were linked to primary care. The predominance in specialized care occurred in the public sector (65%) and private sector (100%). The specialized establishments of private sector linked to the southeast region (16,043) were the main sites of physical therapists. Only the public sector in the south had a majority in the Primary Care. When considering the sizes of the cities, there is focus on specialist care in bigger cities. This study identified the concentration of physical therapists in the specialized care, mostly in metropolis and big cities and in the private sector, with restricted to participation in the primary care.

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.

Complex Homology and the Evolution of Nervous Systems.

PubMed

Liebeskind, Benjamin J; Hillis, David M; Zakon, Harold H; Hofmann, Hans A

2016-02-01

We examine the complex evolution of animal nervous systems and discuss the ramifications of this complexity for inferring the nature of early animals. Although reconstructing the origins of nervous systems remains a central challenge in biology, and the phenotypic complexity of early animals remains controversial, a compelling picture is emerging. We now know that the nervous system and other key animal innovations contain a large degree of homoplasy, at least on the molecular level. Conflicting hypotheses about early nervous system evolution are due primarily to differences in the interpretation of this homoplasy. We highlight the need for explicit discussion of assumptions and discuss the limitations of current approaches for inferring ancient phenotypic states. Copyright © 2015. Published by Elsevier Ltd.

Modification of feeding circuits in the evolution of social behavior.

PubMed

Fischer, Eva K; O'Connell, Lauren A

2017-01-01

Adaptive trade-offs between foraging and social behavior intuitively explain many aspects of individual decision-making. Given the intimate connection between social behavior and feeding/foraging at the behavioral level, we propose that social behaviors are linked to foraging on a mechanistic level, and that modifications of feeding circuits are crucial in the evolution of complex social behaviors. In this Review, we first highlight the overlap between mechanisms underlying foraging and parental care and then expand this argument to consider the manipulation of feeding-related pathways in the evolution of other complex social behaviors. We include examples from diverse taxa to highlight that the independent evolution of complex social behaviors is a variation on the theme of feeding circuit modification. © 2017. Published by The Company of Biologists Ltd.

The Evolution of Biological Complexity in Digital Organisms

NASA Astrophysics Data System (ADS)

Ofria, Charles

2013-03-01

When Darwin first proposed his theory of evolution by natural selection, he realized that it had a problem explaining the origins of traits of ``extreme perfection and complication'' such as the vertebrate eye. Critics of Darwin's theory have latched onto this perceived flaw as a proof that Darwinian evolution is impossible. In anticipation of this issue, Darwin described the perfect data needed to understand this process, but lamented that such data are ``scarcely ever possible'' to obtain. In this talk, I will discuss research where we use populations of digital organisms (self-replicating and evolving computer programs) to elucidate the genetic and evolutionary processes by which new, highly-complex traits arise, drawing inspiration directly from Darwin's wistful thinking and hypotheses. During the process of evolution in these fully-transparent computational environments we can measure the incorporation of new information into the genome, a process akin to a natural Maxwell's Demon, and identify the original source of any such information. We show that, as Darwin predicted, much of the information used to encode a complex trait was already in the genome as part of simpler evolved traits, and that many routes must be possible for a new complex trait to have a high probability of successfully evolving. In even more extreme examples of the evolution of complexity, we are now using these same principles to examine the evolutionary dynamics the drive major transitions in evolution; that is transitions to higher-levels of organization, which are some of the most complex evolutionary events to occur in nature. Finally, I will explore some of the implications of this research to other aspects of evolutionary biology and as well as ways that these evolutionary principles can be applied toward solving computational and engineering problems.

Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

PubMed

Kim, Inhae; Lee, Heetak; Han, Seong Kyu; Kim, Sanguk

2014-10-01

The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.

Life history, cognition and the evolution of complex foraging niches.

PubMed

Schuppli, Caroline; Graber, Sereina M; Isler, Karin; van Schaik, Carel P

2016-03-01

Animal species that live in complex foraging niches have, in general, improved access to energy-rich and seasonally stable food sources. Because human food procurement is uniquely complex, we ask here which conditions may have allowed species to evolve into such complex foraging niches, and also how niche complexity is related to relative brain size. To do so, we divided niche complexity into a knowledge-learning and a motor-learning dimension. Using a sample of 78 primate and 65 carnivoran species, we found that two life-history features are consistently correlated with complex niches: slow, conservative development or provisioning of offspring over extended periods of time. Both act to buffer low energy yields during periods of learning, and may thus act as limiting factors for the evolution of complex niches. Our results further showed that the knowledge and motor dimensions of niche complexity were correlated with pace of development in primates only, and with the length of provisioning in only carnivorans. Accordingly, in primates, but not carnivorans, living in a complex foraging niche requires enhanced cognitive abilities, i.e., a large brain. The patterns in these two groups of mammals show that selection favors evolution into complex niches (in either the knowledge or motor dimension) in species that either develop more slowly or provision their young for an extended period of time. These findings help to explain how humans constructed by far the most complex niche: our ancestors managed to combine slow development (as in other primates) with systematic provisioning of immatures and even adults (as in carnivorans). This study also provides strong support for the importance of ecological factors in brain size evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Black Metropolis and Mental Life: Beyond the "Burden of "Acting White"" Toward a Third Wave of Critical Racial Studies

ERIC Educational Resources Information Center

Akom, A. A.

2008-01-01

In this article, I reflect on Signithia Fordham and John Ogbu's classic research on the "burden of "acting White"" to develop a long overdue dialogue between Africana studies and critical white studies. It highlights the dialectical nature of Fordham and Ogbu's philosophy of race and critical race theory by locating the origins of the "burden of…

Effect of Field Trip on Students' Academic Performance in Basic Technology in Ilorin Metropolis, Nigeria

ERIC Educational Resources Information Center

Amosa, Abdul Ganiyu Alasela; Ogunlade, Oyeronke Olufunmilola; Atobatele, Adunni Suliat

2015-01-01

The use of field trip in teaching and learning helps to bring about effective and efficient learning in Basic Technology. Field trip is a group excursion away from the normal education environment for firsthand experience of an historic site or place of special interest. This study therefore was geared towards finding out the effect of field trip…

The Relationship between the Quality of Teachers and Pupils Academic Performance in the STMA Junior High Schools of the Western Region of Ghana

ERIC Educational Resources Information Center

Bonney, Ebenezer Appah; Amoah, Daniel F.; Micah, Sophia A.; Ahiamenyo, Comfort; Lemaire, Margaret B.

2015-01-01

The study investigated into the relationship between the quality of teachers and students' academic performance in Sekondi Takoradi Metropolitan Assembly (STMA) Junior High Schools. Descriptive survey design was used and the target population was Junior High School teachers and pupils in the metropolis. Five educational circuits in the metropolis…

The Implementation of the Basic School English Curriculum: The Case of the Cape Coast Metropolis in Ghana

ERIC Educational Resources Information Center

Torto, Gertrude Afiba

2017-01-01

The English language curriculum for primary schools in Ghana spells out the various aspects, topics and sub topics that teachers must teach the child within a specified time. The syllabus again specifies the various topics and sub topics that should be taught in an integrated manner so as to enhance meaningful learning. For this meaningful…

Area Handbook Series: Paraguay: A Country Study

DTIC Science & Technology

1988-12-01

fattening period for steers. Artificial insemination was increasingly common. To a certain extent, cattle raising reflected the dispari- ties in agriculture...metropolis and satellite . Joseph had no constituency in Spanish America. Without a king, the entire colonial system lost its legitimacy, and the colonists...generally more dependable than local service because it used a microwave and satellite transmission system. Telex ser- vices also were available through

How Confident Are Kindergarten Teachers in Their Ability to Keep Order in the Classroom? A Study of Teacher Efficacy in Classroom Management

ERIC Educational Resources Information Center

Cobbold, Cosmas; Boateng, Philip

2016-01-01

The objective of the study was to investigate kindergarten teachers' efficacy beliefs in classroom management. The sample size was 299 teachers drawn from both public and private kindergarten schools in the Kumasi Metropolis of Ghana. The efficacy beliefs of the teachers with respect to their classroom management practices were measured on a…

An Examination of the Extent to Which School Outdoor Activities Could Enhance Senior Secondary Two Students' Achievement in Ecology

ERIC Educational Resources Information Center

Achor, Emmanuel E.; Amadu, Samuel O.

2015-01-01

This study examined the extent to which school outdoor activities could enhance senior secondary (SS) two students' achievement in ecology. Non randomized pre test post test control group Quasi-experimental design was adopted. A sample of 160 SS II students from 4 co-educational schools in Jalingo metropolis, Taraba State Nigeria was used. A 40…

Teacher Self-Efficacy Enhancement and School Location: Implication for Students' Achievement in Economics in Senior Secondary School in Ibadan, Oyo State, Nigeria

ERIC Educational Resources Information Center

Durowoju, Esther O.; Onuka, Adams O. U.

2015-01-01

The paper investigated the effect of teacher self-efficacy enhancement and school location on students' achievement in Economics in Senior Secondary School in Ibadan Metropolis of Oyo State, Nigeria. Three hypotheses were tested at 0.05 level of significance. Multi-stage sampling technique was adopted in the study. Four Local Government Areas (two…

Rise and fall of political complexity in island South-East Asia and the Pacific.

PubMed

Currie, Thomas E; Greenhill, Simon J; Gray, Russell D; Hasegawa, Toshikazu; Mace, Ruth

2010-10-14

There is disagreement about whether human political evolution has proceeded through a sequence of incremental increases in complexity, or whether larger, non-sequential increases have occurred. The extent to which societies have decreased in complexity is also unclear. These debates have continued largely in the absence of rigorous, quantitative tests. We evaluated six competing models of political evolution in Austronesian-speaking societies using phylogenetic methods. Here we show that in the best-fitting model political complexity rises and falls in a sequence of small steps. This is closely followed by another model in which increases are sequential but decreases can be either sequential or in bigger drops. The results indicate that large, non-sequential jumps in political complexity have not occurred during the evolutionary history of these societies. This suggests that, despite the numerous contingent pathways of human history, there are regularities in cultural evolution that can be detected using computational phylogenetic methods.

Lake on life support: Evaluating urban lake management measures by using a coupled 1D-modelling approach

NASA Astrophysics Data System (ADS)

Ladwig, Robert; Kirillin, Georgiy; Hinkelmann, Reinhard; Hupfer, Michael

2017-04-01

Urban surface water systems and especially lakes are heavily stressed and modified systems to comply with water management goals and expectations. In this study we focus on Lake Tegel in Berlin, Germany, as a representative of heavily modified urban lakes. In the 20th century, Lake Tegel received increased loadings of nutrients and leached heavy metals from an upstream sewage farm resulting in severe eutrophication problems. The construction of two upstream treatment plants caused a lowering of nutrient concentrations and a re-oligotrophication of the lake. Additionally, artificial aerators, to keep the hypolimnion oxic, and a lake pipeline, to bypass water for maintaining a minimum discharge, went into operation. Lake Tegel is still heavily used for drinking water extraction by bank filtration. These interacting management measures make the system vulnerable to changing climate conditions and pollutant loads. Past modelling studies have shown the complex hydrodynamics of the lake. Here, we are following a simplified approach by using a less computational time consuming vertical 1D-model to simulate the hydrodynamics and the ecological interactions of the system by coupling the General Lake Model to the Aquatic Ecodynamics Model Library 2. For calibration of the multidimensional parameter space we applied the Covariance Matrix Adaption-Evolution Strategy algorithm. The model is able to sufficiently replicate the vertical field temperature profiles of Lake Tegel as well as to simulate similar concentration ranges of phosphate, dissolved oxygen and nitrate. The calibrated model is used to run an uncertainty analysis by sampling the simulated data within the meaning of the Metropolis-Hastings algorithm. Finally, we are evaluating different scenarios: (1) changing air temperatures, precipitation and wind speed due to effects of climate change, (2) decreased discharges into the lake due to bypassing treated effluents into a near stream instead of Lake Tegel, and (3) increased nutrient elimination at the upstream treatment plants. We are focusing on quantifying the impact of these scenarios on lake stability as well as the abundance and distribution of nutrients.

Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.

PubMed

Villarreal A, Juan Carlos; Crandall-Stotler, Barbara J; Hart, Michelle L; Long, David G; Forrest, Laura L

2016-03-01

We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament-less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization. © 2015 Royal Botanic Garden Edinburgh. New Phytologist © 2015 New Phytologist Trust.

Prediction in complex systems: The case of the international trade network

NASA Astrophysics Data System (ADS)

Vidmer, Alexandre; Zeng, An; Medo, Matúš; Zhang, Yi-Cheng

2015-10-01

Predicting the future evolution of complex systems is one of the main challenges in complexity science. Based on a current snapshot of a network, link prediction algorithms aim to predict its future evolution. We apply here link prediction algorithms to data on the international trade between countries. This data can be represented as a complex network where links connect countries with the products that they export. Link prediction techniques based on heat and mass diffusion processes are employed to obtain predictions for products exported in the future. These baseline predictions are improved using a recent metric of country fitness and product similarity. The overall best results are achieved with a newly developed metric of product similarity which takes advantage of causality in the network evolution.

Information-theoretic metamodel of organizational evolution

NASA Astrophysics Data System (ADS)

Sepulveda, Alfredo

2011-12-01

Social organizations are abstractly modeled by holarchies---self-similar connected networks---and intelligent complex adaptive multiagent systems---large networks of autonomous reasoning agents interacting via scaled processes. However, little is known of how information shapes evolution in such organizations, a gap that can lead to misleading analytics. The research problem addressed in this study was the ineffective manner in which classical model-predict-control methods used in business analytics attempt to define organization evolution. The purpose of the study was to construct an effective metamodel for organization evolution based on a proposed complex adaptive structure---the info-holarchy. Theoretical foundations of this study were holarchies, complex adaptive systems, evolutionary theory, and quantum mechanics, among other recently developed physical and information theories. Research questions addressed how information evolution patterns gleamed from the study's inductive metamodel more aptly explained volatility in organization. In this study, a hybrid grounded theory based on abstract inductive extensions of information theories was utilized as the research methodology. An overarching heuristic metamodel was framed from the theoretical analysis of the properties of these extension theories and applied to business, neural, and computational entities. This metamodel resulted in the synthesis of a metaphor for, and generalization of organization evolution, serving as the recommended and appropriate analytical tool to view business dynamics for future applications. This study may manifest positive social change through a fundamental understanding of complexity in business from general information theories, resulting in more effective management.

Comparison of different uncertainty techniques in urban stormwater quantity and quality modelling.

PubMed

Dotto, Cintia B S; Mannina, Giorgio; Kleidorfer, Manfred; Vezzaro, Luca; Henrichs, Malte; McCarthy, David T; Freni, Gabriele; Rauch, Wolfgang; Deletic, Ana

2012-05-15

Urban drainage models are important tools used by both practitioners and scientists in the field of stormwater management. These models are often conceptual and usually require calibration using local datasets. The quantification of the uncertainty associated with the models is a must, although it is rarely practiced. The International Working Group on Data and Models, which works under the IWA/IAHR Joint Committee on Urban Drainage, has been working on the development of a framework for defining and assessing uncertainties in the field of urban drainage modelling. A part of that work is the assessment and comparison of different techniques generally used in the uncertainty assessment of the parameters of water models. This paper compares a number of these techniques: the Generalized Likelihood Uncertainty Estimation (GLUE), the Shuffled Complex Evolution Metropolis algorithm (SCEM-UA), an approach based on a multi-objective auto-calibration (a multialgorithm, genetically adaptive multi-objective method, AMALGAM) and a Bayesian approach based on a simplified Markov Chain Monte Carlo method (implemented in the software MICA). To allow a meaningful comparison among the different uncertainty techniques, common criteria have been set for the likelihood formulation, defining the number of simulations, and the measure of uncertainty bounds. Moreover, all the uncertainty techniques were implemented for the same case study, in which the same stormwater quantity and quality model was used alongside the same dataset. The comparison results for a well-posed rainfall/runoff model showed that the four methods provide similar probability distributions of model parameters, and model prediction intervals. For ill-posed water quality model the differences between the results were much wider; and the paper provides the specific advantages and disadvantages of each method. In relation to computational efficiency (i.e. number of iterations required to generate the probability distribution of parameters), it was found that SCEM-UA and AMALGAM produce results quicker than GLUE in terms of required number of simulations. However, GLUE requires the lowest modelling skills and is easy to implement. All non-Bayesian methods have problems with the way they accept behavioural parameter sets, e.g. GLUE, SCEM-UA and AMALGAM have subjective acceptance thresholds, while MICA has usually problem with its hypothesis on normality of residuals. It is concluded that modellers should select the method which is most suitable for the system they are modelling (e.g. complexity of the model's structure including the number of parameters), their skill/knowledge level, the available information, and the purpose of their study. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evolution of complexity following a global quench

NASA Astrophysics Data System (ADS)

Moosa, Mudassir

2018-03-01

The rate of complexification of a quantum state is conjectured to be bounded from above by the average energy of the state. A different conjecture relates the complexity of a holographic CFT state to the on-shell gravitational action of a certain bulk region. We use `complexity equals action' conjecture to study the time evolution of the complexity of the CFT state after a global quench. We find that the rate of growth of complexity is not only consistent with the conjectured bound, but it also saturates the bound soon after the system has achieved local equilibrium.

The spatiotemporal system dynamics of acquired resistance in an engineered microecology.

PubMed

Datla, Udaya Sree; Mather, William H; Chen, Sheng; Shoultz, Isaac W; Täuber, Uwe C; Jones, Caroline N; Butzin, Nicholas C

2017-11-22

Great strides have been made in the understanding of complex networks; however, our understanding of natural microecologies is limited. Modelling of complex natural ecological systems has allowed for new findings, but these models typically ignore the constant evolution of species. Due to the complexity of natural systems, unanticipated interactions may lead to erroneous conclusions concerning the role of specific molecular components. To address this, we use a synthetic system to understand the spatiotemporal dynamics of growth and to study acquired resistance in vivo. Our system differs from earlier synthetic systems in that it focuses on the evolution of a microecology from a killer-prey relationship to coexistence using two different non-motile Escherichia coli strains. Using empirical data, we developed the first ecological model emphasising the concept of the constant evolution of species, where the survival of the prey species is dependent on location (distance from the killer) or the evolution of resistance. Our simple model, when expanded to complex microecological association studies under varied spatial and nutrient backgrounds may help to understand the complex relationships between multiple species in intricate natural ecological networks. This type of microecological study has become increasingly important, especially with the emergence of antibiotic-resistant pathogens.

Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits.

PubMed

Wang, Yaqiong; Ma, Hong

2015-09-01

Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

PubMed

Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

2014-10-01

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Modified unified kinetic scheme for all flow regimes.

PubMed

Liu, Sha; Zhong, Chengwen

2012-06-01

A modified unified kinetic scheme for the prediction of fluid flow behaviors in all flow regimes is described. The time evolution of macrovariables at the cell interface is calculated with the idea that both free transport and collision mechanisms should be considered. The time evolution of macrovariables is obtained through the conservation constraints. The time evolution of local Maxwellian distribution is obtained directly through the one-to-one mapping from the evolution of macrovariables. These improvements provide more physical realities in flow behaviors and more accurate numerical results in all flow regimes especially in the complex transition flow regime. In addition, the improvement steps introduce no extra computational complexity.

Analyzing complex networks evolution through Information Theory quantifiers

NASA Astrophysics Data System (ADS)

Carpi, Laura C.; Rosso, Osvaldo A.; Saco, Patricia M.; Ravetti, Martín Gómez

2011-01-01

A methodology to analyze dynamical changes in complex networks based on Information Theory quantifiers is proposed. The square root of the Jensen-Shannon divergence, a measure of dissimilarity between two probability distributions, and the MPR Statistical Complexity are used to quantify states in the network evolution process. Three cases are analyzed, the Watts-Strogatz model, a gene network during the progression of Alzheimer's disease and a climate network for the Tropical Pacific region to study the El Niño/Southern Oscillation (ENSO) dynamic. We find that the proposed quantifiers are able not only to capture changes in the dynamics of the processes but also to quantify and compare states in their evolution.

Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

PubMed

Pallen, M J; Gophna, U

2007-01-01

Bacterial flagella at first sight appear uniquely sophisticated in structure, so much so that they have even been considered 'irreducibly complex' by the intelligent design movement. However, a more detailed analysis reveals that these remarkable pieces of molecular machinery are the product of processes that are fully compatible with Darwinian evolution. In this chapter we present evidence for such processes, based on a review of experimental studies, molecular phylogeny and microbial genomics. Several processes have played important roles in flagellar evolution: self-assembly of simple repeating subunits, gene duplication with subsequent divergence, recruitment of elements from other systems ('molecular bricolage'), and recombination. We also discuss additional tentative new assignments of homology (FliG with MgtE, FliO with YscJ). In conclusion, rather than providing evidence of intelligent design, flagellar and non-flagellar Type III secretion systems instead provide excellent case studies in the evolution of complex systems from simpler components.

The Evolution of ICT Markets: An Agent-Based Model on Complex Networks

NASA Astrophysics Data System (ADS)

Zhao, Liangjie; Wu, Bangtao; Chen, Zhong; Li, Li

Information and communication technology (ICT) products exhibit positive network effects.The dynamic process of ICT markets evolution has two intrinsic characteristics: (1) customers are influenced by each others’ purchasing decision; (2) customers are intelligent agents with bounded rationality.Guided by complex systems theory, we construct an agent-based model and simulate on complex networks to examine how the evolution can arise from the interaction of customers, which occur when they make expectations about the future installed base of a product by the fraction of neighbors who are using the same product in his personal network.We demonstrate that network effects play an important role in the evolution of markets share, which make even an inferior product can dominate the whole market.We also find that the intensity of customers’ communication can influence whether the best initial strategy for firms is to improve product quality or expand their installed base.

The Monitoring and Spatial-Temporal Evolution Characteristic Analysis for Land Subsidence in Beijing

NASA Astrophysics Data System (ADS)

Zhou, Q.; Zhao, W.; Yu, J.

2018-05-01

At present the land subsidence has been the main geological disaster in the plain area of China, and became one of the most serious disaster that restrict the social and economic sustainable development, it also is an important content in the project of national geographic conditions monitoring. With the development of economy and society, Beijing as the capital of China has experienced significant population growth in the last few decades which led to over-exploitation of the ground water to meet the water demand of more than 20 million inhabitants, especially in the urban region with high population density. However, the rainfall and surface runoff can't satisfy the need of aquifer recharge that product the land subsidence. As China's political center and a metropolis, there are a lot of large constructions, underground traffic projects and complicated municipal pipeline network, and Beijing is also an important traffic hub for national railway and highway network, all of them would be threatened by the land subsidence disaster. In this article the author used twenty ENVISAT Synthetic Aperture Radar (SAR) images acquired in 2008 June-2010 August and ten TerraSAR images acquired in 2011 June-2012 September were processed with Small Baseline Subset SAR Interferometry (SBAS-InSAR) techniques, to investigate spatial and temporal patterns of land subsidence in the urban area of Beijing.

Effects of snowmelt on watershed transit time distributions

NASA Astrophysics Data System (ADS)

Fang, Z.; Carroll, R. W. H.; Harman, C. J.; Wilusz, D. C.; Schumer, R.

2017-12-01

Snowmelt is the principal control of the timing and magnitude of water flow through alpine watersheds, but the streamflow generated may be displaced groundwater. To quantify this effect, we use a rank StorAge Selection (rSAS) model to estimate time-dependent travel time distributions (TTDs) for the East River Catchment (ERC, 84 km2) - a headwater basin of the Colorado River, and newly designated as the Lawrence Berkeley National Laboratory's Watershed Function Science Focus Area (SFA). Through the SFA, observational networks related to precipitation and stream fluxes have been established with a focus on environmental tracers and stable isotopes. The United Stated Geological Survey Precipitation Runoff Modeling System (PRMS) was used to estimate spatially- and temporally-variable boundary fluxes of effective precipitation (snowmelt & rain), evapotranspiration, and subsurface storage. The DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm was used to calibrate the rSAS model to observed stream isotopic concentration data and quantify uncertainty. The sensitivity of the simulated TTDs to systematic changes in the boundary fluxes was explored. Different PRMS and rSAS model parameters setup were tested to explore how they affect the relationship between input precipitation, especially snowmelt, and the estimated TTDs. Wavelet Coherence Analysis (WCA) was applied to investigate the seasonality of TTD simulations. Our ultimate goal is insight into how the Colorado River headwater catchments store and route water, and how sensitive flow paths and transit times are to climatic changes.

A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms

PubMed Central

Grabowski, Laura M.; Bryson, David M.; Dyer, Fred C.; Pennock, Robert T.; Ofria, Charles

2013-01-01

Investigating the evolution of animal behavior is difficult. The fossil record leaves few clues that would allow us to recapitulate the path that evolution took to build a complex behavior, and the large population sizes and long time scales required prevent us from re-evolving such behaviors in a laboratory setting. We present results of a study in which digital organisms–self-replicating computer programs that are subject to mutations and selection–evolved in different environments that required information about past experience for fitness-enhancing behavioral decisions. One population evolved a mechanism for step-counting, a surprisingly complex odometric behavior that was only indirectly related to enhancing fitness. We examine in detail the operation of the evolved mechanism and the evolutionary transitions that produced this striking example of a complex behavior. PMID:23577113

Progress on Complex Langevin simulations of a finite density matrix model for QCD

NASA Astrophysics Data System (ADS)

Bloch, Jacques; Glesaaen, Jonas; Verbaarschot, Jacobus; Zafeiropoulos, Savvas

2018-03-01

We study the Stephanov model, which is an RMT model for QCD at finite density, using the Complex Langevin algorithm. Naive implementation of the algorithm shows convergence towards the phase quenched or quenched theory rather than to intended theory with dynamical quarks. A detailed analysis of this issue and a potential resolution of the failure of this algorithm are discussed. We study the effect of gauge cooling on the Dirac eigenvalue distribution and time evolution of the norm for various cooling norms, which were specifically designed to remove the pathologies of the complex Langevin evolution. The cooling is further supplemented with a shifted representation for the random matrices. Unfortunately, none of these modifications generate a substantial improvement on the complex Langevin evolution and the final results still do not agree with the analytical predictions.

Surface Segregation in Ternary Alloys

NASA Technical Reports Server (NTRS)

Good, Brian; Bozzolo, Guillermo H.; Abel, Phillip B.

2000-01-01

Surface segregation profiles of binary (Cu-Ni, Au-Ni, Cu-Au) and ternary (Cu-Au-Ni) alloys are determined via Monte Carlo-Metropolis computer simulations using the BFS method for alloys for the calculation of the energetics. The behavior of Cu or Au in Ni is contrasted with their behavior when both are present. The interaction between Cu and Au and its effect on the segregation profiles for Cu-Au-Ni alloys is discussed.

Life Styles of African Women [And] A Swimming Pool for Mansa Musa's Wife [And] A Yoruba Naming Ceremony [And] Metropolis: African and American Style. Mini-Modules.

ERIC Educational Resources Information Center

African-American Inst., New York, NY. School Services Div.

Four modules dealing with African culture are combined in this document. The first module discusses various life-styles of African women, including warrior, queen, ruler, and matriarch. A lesson plan uses a question-and-answer format to encourage discussion of the effects of tradition, society, and nation upon African women. Questions asked…

Assessing the Impact of Environment on Life Styles and Life Chances among out of School Youths in Lagos Metropolis

ERIC Educational Resources Information Center

Wahab, E. O.; Ajiboye, O. E.; Atere, A. A.

2011-01-01

This research is motivated as a result of rapid changes in the lifestyle of our youths and the increasing deterioration of their welfare in terms of the increase in the number of out of school youth in the country, high incidence of child participation in economic activities and incidence of street children in Nigeria. Although, many researches…

The Effect of Performance Assessment-Driven Instruction on the Attitude and Achievement of Senior High School Students in Mathematics in Cape Coast Metropolis, Ghana

ERIC Educational Resources Information Center

Arhin, Ato Kwamina

2015-01-01

The study was a quasi-experimental research project conducted to investigate the effect of performance assessment-driven instructions on the attitude and achievement in mathematics of senior high school students in Ghana at Ghana National College in Cape Coast. Two Form 1 science classes were used for the study and were assigned as experimental…

Receiver discriminability drives the evolution of complex sexual signals by sexual selection.

PubMed

Cui, Jianguo; Song, Xiaowei; Zhu, Bicheng; Fang, Guangzhan; Tang, Yezhong; Ryan, Michael J

2016-04-01

A hallmark of sexual selection by mate choice is the evolution of exaggerated traits, such as longer tails in birds and more acoustic components in the calls of birds and frogs. Trait elaboration can be opposed by costs such as increased metabolism and greater predation risk, but cognitive processes of the receiver can also put a brake on trait elaboration. For example, according to Weber's Law traits of a fixed absolute difference will be more difficult to discriminate as the absolute magnitude increases. Here, we show that in the Emei music frog (Babina daunchina) increases in the fundamental frequency between successive notes in the male advertisement call, which increases the spectral complexity of the call, facilitates the female's ability to compare the number of notes between calls. These results suggest that female's discriminability provides the impetus to switch from enhancement of signaling magnitude (i.e., adding more notes into calls) to employing a new signal feature (i.e., increasing frequency among notes) to increase complexity. We suggest that increasing the spectral complexity of notes ameliorates some of the effects of Weber's Law, and highlights how perceptual and cognitive biases of choosers can have important influences on the evolution of courtship signals. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Evolution of weighted complex bus transit networks with flow

NASA Astrophysics Data System (ADS)

Huang, Ailing; Xiong, Jie; Shen, Jinsheng; Guan, Wei

2016-02-01

Study on the intrinsic properties and evolutional mechanism of urban public transit networks (PTNs) has great significance for transit planning and control, particularly considering passengers’ dynamic behaviors. This paper presents an empirical analysis for exploring the complex properties of Beijing’s weighted bus transit network (BTN) based on passenger flow in L-space, and proposes a bi-level evolution model to simulate the development of transit routes from the view of complex network. The model is an iterative process that is driven by passengers’ travel demands and dual-controlled interest mechanism, which is composed of passengers’ spatio-temporal requirements and cost constraint of transit agencies. Also, the flow’s dynamic behaviors, including the evolutions of travel demand, sectional flow attracted by a new link and flow perturbation triggered in nearby routes, are taken into consideration in the evolutional process. We present the numerical experiment to validate the model, where the main parameters are estimated by using distribution functions that are deduced from real-world data. The results obtained have proven that our model can generate a BTN with complex properties, such as the scale-free behavior or small-world phenomenon, which shows an agreement with our empirical results. Our study’s results can be exploited to optimize the real BTN’s structure and improve the network’s robustness.

Monte Carlo Bayesian inference on a statistical model of sub-gridcolumn moisture variability using high-resolution cloud observations. Part 1: Method.

PubMed

Norris, Peter M; da Silva, Arlindo M

2016-07-01

A method is presented to constrain a statistical model of sub-gridcolumn moisture variability using high-resolution satellite cloud data. The method can be used for large-scale model parameter estimation or cloud data assimilation. The gridcolumn model includes assumed probability density function (PDF) intra-layer horizontal variability and a copula-based inter-layer correlation model. The observables used in the current study are Moderate Resolution Imaging Spectroradiometer (MODIS) cloud-top pressure, brightness temperature and cloud optical thickness, but the method should be extensible to direct cloudy radiance assimilation for a small number of channels. The algorithm is a form of Bayesian inference with a Markov chain Monte Carlo (MCMC) approach to characterizing the posterior distribution. This approach is especially useful in cases where the background state is clear but cloudy observations exist. In traditional linearized data assimilation methods, a subsaturated background cannot produce clouds via any infinitesimal equilibrium perturbation, but the Monte Carlo approach is not gradient-based and allows jumps into regions of non-zero cloud probability. The current study uses a skewed-triangle distribution for layer moisture. The article also includes a discussion of the Metropolis and multiple-try Metropolis versions of MCMC.

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

Hou Fengji; Hogg, David W.; Goodman, Jonathan

Markov chain Monte Carlo (MCMC) proves to be powerful for Bayesian inference and in particular for exoplanet radial velocity fitting because MCMC provides more statistical information and makes better use of data than common approaches like chi-square fitting. However, the nonlinear density functions encountered in these problems can make MCMC time-consuming. In this paper, we apply an ensemble sampler respecting affine invariance to orbital parameter extraction from radial velocity data. This new sampler has only one free parameter, and does not require much tuning for good performance, which is important for automatization. The autocorrelation time of this sampler is approximatelymore » the same for all parameters and far smaller than Metropolis-Hastings, which means it requires many fewer function calls to produce the same number of independent samples. The affine-invariant sampler speeds up MCMC by hundreds of times compared with Metropolis-Hastings in the same computing situation. This novel sampler would be ideal for projects involving large data sets such as statistical investigations of planet distribution. The biggest obstacle to ensemble samplers is the existence of multiple local optima; we present a clustering technique to deal with local optima by clustering based on the likelihood of the walkers in the ensemble. We demonstrate the effectiveness of the sampler on real radial velocity data.« less

Monte Carlo Bayesian Inference on a Statistical Model of Sub-Gridcolumn Moisture Variability Using High-Resolution Cloud Observations. Part 1: Method

NASA Technical Reports Server (NTRS)

Norris, Peter M.; Da Silva, Arlindo M.

2016-01-01

A method is presented to constrain a statistical model of sub-gridcolumn moisture variability using high-resolution satellite cloud data. The method can be used for large-scale model parameter estimation or cloud data assimilation. The gridcolumn model includes assumed probability density function (PDF) intra-layer horizontal variability and a copula-based inter-layer correlation model. The observables used in the current study are Moderate Resolution Imaging Spectroradiometer (MODIS) cloud-top pressure, brightness temperature and cloud optical thickness, but the method should be extensible to direct cloudy radiance assimilation for a small number of channels. The algorithm is a form of Bayesian inference with a Markov chain Monte Carlo (MCMC) approach to characterizing the posterior distribution. This approach is especially useful in cases where the background state is clear but cloudy observations exist. In traditional linearized data assimilation methods, a subsaturated background cannot produce clouds via any infinitesimal equilibrium perturbation, but the Monte Carlo approach is not gradient-based and allows jumps into regions of non-zero cloud probability. The current study uses a skewed-triangle distribution for layer moisture. The article also includes a discussion of the Metropolis and multiple-try Metropolis versions of MCMC.

Monte Carlo Bayesian inference on a statistical model of sub-gridcolumn moisture variability using high-resolution cloud observations. Part 1: Method

PubMed Central

Norris, Peter M.; da Silva, Arlindo M.

2018-01-01

A method is presented to constrain a statistical model of sub-gridcolumn moisture variability using high-resolution satellite cloud data. The method can be used for large-scale model parameter estimation or cloud data assimilation. The gridcolumn model includes assumed probability density function (PDF) intra-layer horizontal variability and a copula-based inter-layer correlation model. The observables used in the current study are Moderate Resolution Imaging Spectroradiometer (MODIS) cloud-top pressure, brightness temperature and cloud optical thickness, but the method should be extensible to direct cloudy radiance assimilation for a small number of channels. The algorithm is a form of Bayesian inference with a Markov chain Monte Carlo (MCMC) approach to characterizing the posterior distribution. This approach is especially useful in cases where the background state is clear but cloudy observations exist. In traditional linearized data assimilation methods, a subsaturated background cannot produce clouds via any infinitesimal equilibrium perturbation, but the Monte Carlo approach is not gradient-based and allows jumps into regions of non-zero cloud probability. The current study uses a skewed-triangle distribution for layer moisture. The article also includes a discussion of the Metropolis and multiple-try Metropolis versions of MCMC. PMID:29618847

Solubility classification of airborne uranium products collected at the perimeter of the Allied Chemical Plant, Metropolis, Illinois

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

Kalkwarf, D.R.

1980-05-01

Airborne uranium products were collected at the perimeter of the uranium-conversion plant operated by the Allied Chemical Corporation at Metropolis, Illinois, and the dissolution rates of these products were classified in terms of the ICRP Task Group Lung Model. Assignments were based on measurements of the dissolution half-times exhibited by uranium components of the dust samples as they dissolved in simulated lung fluid at 37/sup 0/C. Based on three trials, the dissolution behavior of dust with aerodynamic equivalent diameter (AED) less than 5.5 ..mu..m and collected nearest the closest residence to the plant was classified 0.40 D, 0.60 Y. Basedmore » on two trials, the dissolution behavior of dust with AED greater than 5.5 ..mu..m and collected at this location was classified 0.37 D, 0.63 Y. Based on one trial, the dissolution behavior of dust with AED less than 5.5 ..mu..m and collected at a location on the opposite side of the plant was classified 0.68 D, 0.32 Y. There was some evidence for adsorption of dissolved uranium onto other dust components during dissolution, and preliminary dissolution trials are recommended for future samples in order to optimize the fluid replacement schedule.« less

Rainfall Modification by Major Urban Areas: Observations from Spaceborne Rain Radar on the TRMM Satellite.

NASA Astrophysics Data System (ADS)

Shepherd, J. Marshall; Pierce, Harold; Negri, Andrew J.

2002-07-01

Data from the Tropical Rainfall Measuring Mission (TRMM) satellite's precipitation radar (PR) were employed to identify warm-season rainfall (1998-2000) patterns around Atlanta, Georgia; Montgomery, Alabama; Nashville, Tennessee; and San Antonio, Waco, and Dallas, Texas. Results reveal an average increase of about 28% in monthly rainfall rates within 30-60 km downwind of the metropolis, with a modest increase of 5.6% over the metropolis. Portions of the downwind area exhibit increases as high as 51%. The percentage changes are relative to an upwind control area. It was also found that maximum rainfall rates in the downwind impact area exceeded the mean value in the upwind control area by 48%-116%. The maximum value was generally found at an average distance of 39 km from the edge of the urban center or 64 km from the center of the city. Results are consistent with the Metropolitan Meteorological Experiment (METROMEX) studies of St. Louis, Missouri, almost two decades ago and with more recent studies near Atlanta. The study establishes the possibility of utilizing satellite-based rainfall estimates for examining rainfall modification by urban areas on global scales and over longer time periods. Such research has implications for weather forecasting, urban planning, water resource management, and understanding human impact on the environment and climate.

Determinants of parents' decisions on childhood immunisations at Kumasi Metropolis in Ghana.

PubMed

Hagan, Doris; Phethlu, Deliwe R

2016-07-29

To describe factors that influence parents' decisions on childhood immunisations at Kumasi Metropolis in Ghana. Quantitative cross-sectional survey. A sample of 303 parents was obtained from a monthly accessible population of 1420 individuals from the five district hospitals through convenience sampling of respondents at immunisation sessions in Kumasi. Data obtained from the survey were analysed with SPSS version 21 software. Most parents were aware of child immunisations, but they had limited knowledge on vaccines and immunisation schedules. Antenatal nurses constituted the most accessible source of vaccine information. The study established a high percentage of complete immunisation, influenced by parents' fear of their children contracting vaccine-preventable diseases. Remarkably, some parents indicated that they immunised their children because they wanted to know the weight of their children. Forgetfulness and lack of personnel or vaccine at the centres were the reasons given by the few parents who could not complete immunisation schedules for their children, whereas the socio-demographic variables considered did not influence parents' decision on immunisation. Knowledge on immunisation could not influence immunisation decisions but parents' fear of vaccine-preventable diseases, awareness on the benefits of immunisations and sources of vaccine information were the main factors that influenced immunisation decision at Kumasi in Ghana.

Volatility modeling for IDR exchange rate through APARCH model with student-t distribution

NASA Astrophysics Data System (ADS)

Nugroho, Didit Budi; Susanto, Bambang

2017-08-01

The aim of this study is to empirically investigate the performance of APARCH(1,1) volatility model with the Student-t error distribution on five foreign currency selling rates to Indonesian rupiah (IDR), including the Swiss franc (CHF), the Euro (EUR), the British pound (GBP), Japanese yen (JPY), and the US dollar (USD). Six years daily closing rates over the period of January 2010 to December 2016 for a total number of 1722 observations have analysed. The Bayesian inference using the efficient independence chain Metropolis-Hastings and adaptive random walk Metropolis methods in the Markov chain Monte Carlo (MCMC) scheme has been applied to estimate the parameters of model. According to the DIC criterion, this study has found that the APARCH(1,1) model under Student-t distribution is a better fit than the model under normal distribution for any observed rate return series. The 95% highest posterior density interval suggested the APARCH models to model the IDR/JPY and IDR/USD volatilities. In particular, the IDR/JPY and IDR/USD data, respectively, have significant negative and positive leverage effect in the rate returns. Meanwhile, the optimal power coefficient of volatility has been found to be statistically different from 2 in adopting all rate return series, save the IDR/EUR rate return series.

Bacteriological quality of the wastewater used for irrigation at the vegetable farms in Korle-bu Teaching Hospital, Accra Metropolis, Ghana.

PubMed

Pesewu, George A; Bentum, Daniel; Olu-Taiwo, Michael A; Glover, Kathreen K; Yirenya-Tawiah, Dzidzo R

2017-01-01

Many developing countries, including Ghana, are water stressed. As such, farmers, particularly those in urban areas, have adopted the use of wastewater for irrigation. This study evaluated the bacteriological water quality of the wastewater used for irrigation in the vegetable farms at Korle-Bu Teaching Hospital (KBTH), Accra Metropolis, Ghana. In all, 40 wastewater samples were collected and analysed bacteriologically using the total aerobic plate count method. The isolated bacteria were identified biochemically using Bergey's manual for determinative bacteriology. Mean total bacterial colony count values in the range of 2.75-4.44 × 10 5 CFU/100 mL were isolated which far exceeds values of 1 × 10 3 /100 mL recommended by the World Health Organization (WHO) for unrestricted irrigation of crops likely to be eaten raw. Enterobacter cloacae (51.4%), Klebsiella sp. (24.1%), Pseudomonas aeruginosa (11.3%), Salmonella typhi (10.6%), Escherichia coli (2.2%) and Proteus sp. (0.4%) were the predominant bacteria isolated. Growers should use treated wastewater for farming while processors and consumers should minimize contamination risks of produce from the vegetable farms/garden to the plate. © The Author(s) 2016.

Maternal depression does not affect complementary feeding indicators or stunting status of young children (6-23 months) in Northern Ghana.

PubMed

Wemakor, Anthony; Iddrisu, Habib

2018-06-25

Maternal depression may affect child feeding practice which is an important determinant of child nutritional status. The objective of this study was to explore the association between maternal depression and WHO complementary feeding indicators [minimum dietary diversity (MDD), minimum meal frequency (MMF) and minimum acceptable diet (MAD)] or stunting status of children (6-23 months) in Tamale Metropolis, Ghana. A community-based cross-sectional study was carried out involving 200 mother-child pairs randomly sampled from three communities in Tamale Metropolis, Ghana. The prevalence of MDD, MMF, and MAD were 56.5, 65.0, and 44.0% respectively and 41.0% of the children sampled were stunted. A third of the mothers (33.5%) screened positive for depression. Maternal depression did not influence significantly MDD (p = 0.245), MMF (p = 0.442), and MAD (p = 0.885) or children's risk of stunting (p = 0.872). In conclusion maternal depression and child stunting are prevalent in Northern Ghana but there is a lack of evidence of an association between maternal depression and child feeding practices or nutritional status in this study population. Further research is needed to assess the effect of maternal depression on feeding practices and growth of young children.

Exposure to coarse and fine particulate matter at and around major intra-urban traffic intersections of Ilorin metropolis, Nigeria

NASA Astrophysics Data System (ADS)

Adeniran, J. A.; Yusuf, R. O.; Olajire, A. A.

2017-10-01

This study aims to determine the seasonal variations and composition of suspended particulate matter in different sizes PM1.0, PM2.5, PM10 and the total suspended particles (TSP) emitted at major intra-urban traffic intersections (TIs) of Ilorin metropolis. The concentration levels of PM (PM1.0, PM2.5, PM10) obtained at the TIs during the rush hours (45.1, 77.9, and 513 μg/m3) are higher than the levels obtained for the non-rush hour periods (42.3, 62.7, and 390 μg/m3). The average on-road respiratory deposition dose (RDD) rates of PM1.0, PM2.5 and PM10 during the dry period at TIs types was found to be about 24%, 9% and 25% higher than those obtained during the wet period. Based on EF values calculated, Pb and Zn were anthropogenically-derived while Fe, Mn, Cr, Cu and Mg were of crustal source. Principal component analysis (PCA) has been applied to a set of PM data in order to determine the contribution of different sources. It was found that the main principal factors extracted from particulate emission data were related to exhaust and non-exhaust emissions such as tyre wears, oil and fuel combustion sources.

Water budget analysis and management for Bangkok Metropolis, Thailand.

PubMed

Singkran, Nuanchan

2017-09-01

The water budget of the Bangkok Metropolis system was analyzed using a material flow analysis model. Total imported flows into the system were 80,080 million m 3 per year (Mm 3 y -1 ) including inflows from the Chao Phraya and Mae Klong rivers and rainwater. Total exported flows out of the system were 78,528 Mm 3 y -1 including outflow into the lower Chao Phraya River and tap water (TW) distributed to suburbs. Total rates of stock exchange (1,552 Mm 3 y -1 ) were found in the processes of water recycling, TW distribution, domestic use, swine farming, aquaculture, and paddy fields. Only 21% of the total amount of wastewater (1,255 Mm 3 y -1 ) was collected, with insufficient treatment capacity of about 415 Mm 3 y -1 . Domestic and business (industrial and commercial sectors) areas were major point sources, whereas paddy fields were a major non-point source of wastewater. To manage Bangkok's water budget, critical measures have to be considered. Wastewater treatment capacity and efficiency of wastewater collection should be improved. On-site wastewater treatment plants for residential areas should be installed. Urban planning and land use zoning are suggested to control land use activities. Green technology should be supported to reduce wastewater from farming.

Carbon in the Universe

NASA Technical Reports Server (NTRS)

Allamandola, Louis J.

2013-01-01

Over the past few decades, NASA missions have revealed that we live in a Universe that is not a hydrogen-dominated, physicist's paradise, but in a molecular Universe with complex molecules directly interwoven into its fabric. These missions have shown that molecules are an abundant and important component of astronomical objects at all stages of their evolution and that they play a key role in many processes that dominate the structure and evolution of galaxies. Closer to home in our galaxy, the Milky Way, they have revealed a unique and complex organic inventory of regions of star and planet formation that may well represent some of the prebiotic roots to life. Astrobiology emerges from the great interest in understanding astrochemical evolution from simple to complex molecules, especially those with biogenic potential and the roles they may play as primordial seeds in the origin of life on habitable worlds. The first part of this talk will highlight how infrared spectroscopic studies of interstellar space, combined with dedicated laboratory simulations, have revealed the widespread presence of complex organics across deep space. The remainder of the presentation will focus on the evolution of these materials and astrobiology.

Beverton-Holt discrete pest management models with pulsed chemical control and evolution of pesticide resistance

NASA Astrophysics Data System (ADS)

Liang, Juhua; Tang, Sanyi; Cheke, Robert A.

2016-07-01

Pest resistance to pesticides is usually managed by switching between different types of pesticides. The optimal switching time, which depends on the dynamics of the pest population and on the evolution of the pesticide resistance, is critical. Here we address how the dynamic complexity of the pest population, the development of resistance and the spraying frequency of pulsed chemical control affect optimal switching strategies given different control aims. To do this, we developed novel discrete pest population growth models with both impulsive chemical control and the evolution of pesticide resistance. Strong and weak threshold conditions which guarantee the extinction of the pest population, based on the threshold values of the analytical formula for the optimal switching time, were derived. Further, we addressed switching strategies in the light of chosen economic injury levels. Moreover, the effects of the complex dynamical behaviour of the pest population on the pesticide switching times were also studied. The pesticide application period, the evolution of pesticide resistance and the dynamic complexity of the pest population may result in complex outbreak patterns, with consequent effects on the pesticide switching strategies.

The systematics and independent evolution of cave ecomorphology in distantly related clades of Bent-toed Geckos (Genus Cyrtodactylus Gray, 1827) from the Mekong Delta and islands in the Gulf of Thailand.

PubMed

Grismer, L Lee; Wood, P L Jr; Tri, Ngo Van; Murdoch, Matthew L

2015-06-26

An integrative taxonomic analysis of the distantly related Cyrtodactylus condorensis and intermedius species complexes of the Mekong Delta revealed that C. paradoxus is a junior synonym of C. condorensis and that C. thochuensis is a junior synonym of C. leegrismeri. Additionally, the analysis revealed that a cave-dwelling ecomorpholgy has evolved independently early on in the evolution of both complexes (represented by C. hontreensis in the intermedius complex and C. grismeri and C. eisenmani in the condorensis complex) and cave ecomorphs exist in sympatry-but not syntopy-with general scansorial ecomorphs. Multiple, recent, cyclical, glacioeustatic driven changes in sea levels across the Sunda Shelf are hypothesized to account for the evolution and distribution of the widely separated, conspecific insular populations of C. condorensis and C. leegrismeri. The independent evolution of cave ecomorphology is proposed to have been driven by competition avoidance. Habitat islands across the Mekong Delta are an important source of endemism and in need of protection.

Hierarchical coordinate systems for understanding complexity and its evolution, with applications to genetic regulatory networks.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Beyond complexity measures, sometimes it is worthwhile in addition to investigate how complexity changes structurally, especially in artificial systems where we have complete knowledge about the evolutionary process. Hierarchical decomposition is a useful way of assessing structural complexity changes of organisms modeled as automata, and we show how recently developed computational tools can be used for this purpose, by computing holonomy decompositions and holonomy complexity. To gain insight into the evolution of complexity, we investigate the smoothness of the landscape structure of complexity under minimal transitions. As a proof of concept, we illustrate how the hierarchical complexity analysis reveals symmetries and irreversible structure in biological networks by applying the methods to the lac operon mechanism in the genetic regulatory network of Escherichia coli.

The evolution of complex and higher organisms

NASA Technical Reports Server (NTRS)

Milne, D. (Editor); Raup, D. (Editor); Billingham, J. (Editor); Niklaus, K. (Editor); Padian, K. (Editor)

1985-01-01

The evolution of Phanerozoic life has probably been influenced by extraterrestrial events and properties of the Earth-Moon system that have not, until now, been widely recognized. Tide range, gravitational strength, the Earth's axial tilt, and other planetary properties provide background conditions whose effects on evolution may be difficult to distinguish. Solar flares, asteroid impacts, supernovae, and passage of the solar system through galactic clouds can provide catastrophic changes on the Earth with consequent characteristic extinctions. Study of the fossil record and the evolution of complex Phanerozoic life can reveal evidence of past disturbances in space near the Earth. Conversely, better understanding of environmental influences caused by extraterrestrial factors and properties of the solar system can clarify aspects of evolution, and may aid in visualizing life on other planets with different properties.

Complexities’ day-to-day dynamic evolution analysis and prediction for a Didi taxi trip network based on complex network theory

NASA Astrophysics Data System (ADS)

Zhang, Lin; Lu, Jian; Zhou, Jialin; Zhu, Jinqing; Li, Yunxuan; Wan, Qian

2018-03-01

Didi Dache is the most popular taxi order mobile app in China, which provides online taxi-hailing service. The obtained big database from this app could be used to analyze the complexities’ day-to-day dynamic evolution of Didi taxi trip network (DTTN) from the level of complex network dynamics. First, this paper proposes the data cleaning and modeling methods for expressing Nanjing’s DTTN as a complex network. Second, the three consecutive weeks’ data are cleaned to establish 21 DTTNs based on the proposed big data processing technology. Then, multiple topology measures that characterize the complexities’ day-to-day dynamic evolution of these networks are provided. Third, these measures of 21 DTTNs are calculated and subsequently explained with actual implications. They are used as a training set for modeling the BP neural network which is designed for predicting DTTN complexities evolution. Finally, the reliability of the designed BP neural network is verified by comparing with the actual data and the results obtained from ARIMA method simultaneously. Because network complexities are the basis for modeling cascading failures and conducting link prediction in complex system, this proposed research framework not only provides a novel perspective for analyzing DTTN from the level of system aggregated behavior, but can also be used to improve the DTTN management level.

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking

PubMed Central

Madaoui, Hocine; Guerois, Raphaël

2008-01-01

Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. Capturing how selection pressure acts at the interfaces of protein–protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein–protein complex structures. Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact. PMID:18511568

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

PubMed Central

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained. PMID:24999297

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

PubMed

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

Cope's Rule and the Universal Scaling Law of Ornament Complexity.

PubMed

Raia, Pasquale; Passaro, Federico; Carotenuto, Francesco; Maiorino, Leonardo; Piras, Paolo; Teresi, Luciano; Meiri, Shai; Itescu, Yuval; Novosolov, Maria; Baiano, Mattia Antonio; Martínez, Ricard; Fortelius, Mikael

2015-08-01

Luxuriant, bushy antlers, bizarre crests, and huge, twisting horns and tusks are conventionally understood as products of sexual selection. This view stems from both direct observation and from the empirical finding that the size of these structures grows faster than body size (i.e., ornament size shows positive allometry). We contend that the familiar evolutionary increase in the complexity of ornaments over time in many animal clades is decoupled from ornament size evolution. Increased body size comes with extended growth. Since growth scales to the quarter power of body size, we predicted that ornament complexity should scale according to the quarter power law as well, irrespective of the role of sexual selection in the evolution and function of the ornament. To test this hypothesis, we selected three clades (ammonites, deer, and ceratopsian dinosaurs) whose species bore ornaments that differ in terms of the importance of sexual selection to their evolution. We found that the exponent of the regression of ornament complexity to body size is the same for the three groups and is statistically indistinguishable from 0.25. We suggest that the evolution of ornament complexity is a by-product of Cope's rule. We argue that although sexual selection may control size in most ornaments, it does not influence their shape.

Evolution of Brain and Language

ERIC Educational Resources Information Center

Schoenemann, P. Thomas

2009-01-01

The evolution of language and the evolution of the brain are tightly interlinked. Language evolution represents a special kind of adaptation, in part because language is a complex behavior (as opposed to a physical feature) but also because changes are adaptive only to the extent that they increase either one's understanding of others, or one's…

Searching for Genotype-Phenotype Structure: Using Hierarchical Log-Linear Models in Crohn Disease

PubMed Central

Chapman, Juliet M.; Onnie, Clive M.; Prescott, Natalie J.; Fisher, Sheila A.; Mansfield, John C.; Mathew, Christopher G.; Lewis, Cathryn M.; Verzilli, Claudio J.; Whittaker, John C.

2009-01-01

There has been considerable recent success in the detection of gene-disease associations. We consider here the development of tools that facilitate the more detailed characterization of the effect of a genetic variant on disease. We replace the simplistic classification of individuals according to a single binary disease indicator with classification according to a number of subphenotypes. This more accurately reflects the underlying biological complexity of the disease process, but it poses additional analytical difficulties. Notably, the subphenotypes that make up a particular disease are typically highly associated, and it becomes difficult to distinguish which genes might be causing which subphenotypes. Such problems arise in many complex diseases. Here, we concentrate on an application to Crohn disease (CD). We consider this problem as one of model selection based upon log-linear models, fitted in a Bayesian framework via reversible-jump Metropolis-Hastings approach. We evaluate the performance of our suggested approach with a simple simulation study and then apply the method to a real data example in CD, revealing a sparse disease structure. Most notably, the associated NOD2.908G→R mutation appears to be directly related to more severe disease behaviors, whereas the other two associated NOD2 variants, 1007L→FS and 702R→W, are more generally related to disease in the small bowel (ileum and jejenum). The ATG16L1.300T→A variant appears to be directly associated with only disease of the small bowel. PMID:19185283

Natural vs. Human forcing: the new challenge for the Earth science community in the Anthropocene

NASA Astrophysics Data System (ADS)

Tarolli, Paolo

2014-05-01

From the analysis of Earth surface, we are able to learn a lot about its history and processes. Indeed, different landforms bear the signs of different ages, but also of climate and tectonic forcing. In addition to these processes, also the biota forcing has a role in shaping the landscape, of course at different scale and magnitude if compared with geology. In biotic landscapes the vegetation through the roots influences the soil formation and surface erosion. Biota affect also climate, and as a consequence the mechanisms and erosion rates that control the landscape evolution. However, the question is, if we can suppose that there is an evidence of biota forcing, what is the role of humans? Human activities, more than vegetation, are leaving a significant signature on the Earth, by altering its morphology and ecosystems. Also in this case, the temporal and spatial scale (and also the magnitude) are different respect to geological forcing, but the development of the society during the Holocene was significant (from hunting-gathering to farming to complex societies and metropolis): the increase of the population was related to a progressively increase of intensive agriculture and urbanization. This anthropogenic forcing deeply affected the environment, inducing or reducing erosion, and changing the equilibrium of several ecosystems. The recognition and the analysis of the human induced changes, signatures and processes represent a real challenge for the scientific community to better understand the evolution of our Planet. This analysis can help in scheduling a suitable environmental planning for a sustainable development, and to mitigate the consequences of anthropogenic alteration. Wider multidisciplinary groups based on these studies could be able to understand better the evolution of landscapes and ecosystems during the human era, providing a full dataset of multidisciplinary information that can be used by land managers and local authorities, and by the scientific community as well. The recent remotely sensed technologies (e.g. LIDAR, SAR, SfM) might help to reach part of the mentioned goals. High-resolution topography could really play a strategic and helpful role in the recognition of human-induced geomorphic and anthropogenic features, and the connected erosion. Among the most evident landscape signatures of the human fingerprint, for example, road networks and agricultural practices such as terracing deserve a great importance since significantly affect the erosional processes. A better recognition of these signatures is at the basis to improve the knowledge of the related induced processes. In addition to this, it is necessary to improve, through historical data (e.g. hydrogeological, meteorological, stratigraphy, also archeological data) and modeling, the understanding about the land use changes occurred during the last centuries, focusing on the reasoning behind these changes, and on the analysis of their effects on landscape and processes. Human society relies on the vast diversity of benefits provided by the environment. Soil biodiversity and conservation are part of the driving force behind its regulation. At the same time, human society is deeply affecting the environment with consequences on the landscape. It is therefore fundamental to establish greater management control over the Earth's rapidly changing ecosystems.

Lower bound on the time complexity of local adiabatic evolution

NASA Astrophysics Data System (ADS)

Chen, Zhenghao; Koh, Pang Wei; Zhao, Yan

2006-11-01

The adiabatic theorem of quantum physics has been, in recent times, utilized in the design of local search quantum algorithms, and has been proven to be equivalent to standard quantum computation, that is, the use of unitary operators [D. Aharonov in Proceedings of the 45th Annual Symposium on the Foundations of Computer Science, 2004, Rome, Italy (IEEE Computer Society Press, New York, 2004), pp. 42-51]. Hence, the study of the time complexity of adiabatic evolution algorithms gives insight into the computational power of quantum algorithms. In this paper, we present two different approaches of evaluating the time complexity for local adiabatic evolution using time-independent parameters, thus providing effective tests (not requiring the evaluation of the entire time-dependent gap function) for the time complexity of newly developed algorithms. We further illustrate our tests by displaying results from the numerical simulation of some problems, viz. specially modified instances of the Hamming weight problem.

Progress on Complex Langevin simulations of a finite density matrix model for QCD

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

Bloch, Jacques; Glesaan, Jonas; Verbaarschot, Jacobus

We study the Stephanov model, which is an RMT model for QCD at finite density, using the Complex Langevin algorithm. Naive implementation of the algorithm shows convergence towards the phase quenched or quenched theory rather than to intended theory with dynamical quarks. A detailed analysis of this issue and a potential resolution of the failure of this algorithm are discussed. We study the effect of gauge cooling on the Dirac eigenvalue distribution and time evolution of the norm for various cooling norms, which were specifically designed to remove the pathologies of the complex Langevin evolution. The cooling is further supplementedmore » with a shifted representation for the random matrices. Unfortunately, none of these modifications generate a substantial improvement on the complex Langevin evolution and the final results still do not agree with the analytical predictions.« less

Evolution of an ancient protein function involved in organized multicellularity in animals.

PubMed

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-07

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which - the evolution of GKPID's capacity to bind the cortical marker protein - can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals.

The impact of polyploidy on the evolution of a complex NB-LRR resistance gene cluster in soybean

USDA-ARS?s Scientific Manuscript database

A comparative genomics approach was used to investigate the evolution of a complex NB-LRR gene cluster found in soybean (Glycine max), common bean (Phaseolus vulgaris), and other legumes. In soybean, the cluster is associated with several disease resistance (R) genes of known function including Rpg1...

Evolution and the complexity of bacteriophages.

PubMed

Serwer, Philip

2007-03-13

The genomes of both long-genome (> 200 Kb) bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions. Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1) Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2) Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection). (3) The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection). (4) The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems. I propose testing this hypothesis by controlled evolution in microbial communities to (1) determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2) find the environmental conditions that select for the presence of cellular gene homologs, (3) determine which, if any, bacteriophage genes were selected for maintaining the homologs and (4) determine the dynamics of homolog evolution. This hypothesis is an explanation of evolutionary leaps in general. If accurate, it will assist both understanding and influencing the evolution of microbes and their communities. Analysis of evolutionary complexity increase for at least prokaryotes should include analysis of genomes of long-genome bacteriophages.

Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes.

PubMed

Price, Samantha A; Tavera, Jose J; Near, Thomas J; Wainwright, Peter C

2013-02-01

The relationship between habitat complexity and species richness is well established but comparatively little is known about the evolution of morphological diversity in complex habitats. Reefs are structurally complex, highly productive shallow-water marine ecosystems found in tropical (coral reefs) and temperate zones (rocky reefs) that harbor exceptional levels of biodiversity. We investigated whether reef habitats promote the evolution of morphological diversity in the feeding and locomotion systems of grunts (Haemulidae), a group of predominantly nocturnal fishes that live on both temperate and tropical reefs. Using phylogenetic comparative methods and statistical analyses that take into account uncertainty in phylogeny and the evolutionary history of reef living, we demonstrate that rates of morphological evolution are faster in reef-dwelling haemulids. The magnitude of this effect depends on the type of trait; on average, traits involved in the functional systems for prey capture and processing evolve twice as fast on reefs as locomotor traits. This result, along with the observation that haemulids do not exploit unique feeding niches on reefs, suggests that fine-scale trophic niche partitioning and character displacement may be driving higher rates of morphological evolution. Whatever the cause, there is growing evidence that reef habitats stimulate morphological and functional diversification in teleost fishes. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Nanothermodynamics Applied to Thermal Processes in Heterogeneous Materials

DTIC Science & Technology

2012-08-03

models agree favorably with a wide range of measurements of local thermal and dynamic properties. Progress in understanding basic thermodynamic...Monte- Carlo (MC) simulations of the Ising model .7 The solid black lines in Fig. 4 show results using the uncorrected (Metropolis) algorithm on the...parameter g=0.5 (green, dash-dot), g=1 (black, solid ), and g=2 (blue, dash-dot-dot). Note the failure of the standard Ising model (g=0) to match

Nicholas Metropolis Award Talk for Outstanding Doctoral Thesis Work in Computational Physics: Computational biophysics and multiscale modeling of blood cells and blood flow in health and disease

NASA Astrophysics Data System (ADS)

Fedosov, Dmitry

2011-03-01

Computational biophysics is a large and rapidly growing area of computational physics. In this talk, we will focus on a number of biophysical problems related to blood cells and blood flow in health and disease. Blood flow plays a fundamental role in a wide range of physiological processes and pathologies in the organism. To understand and, if necessary, manipulate the course of these processes it is essential to investigate blood flow under realistic conditions including deformability of blood cells, their interactions, and behavior in the complex microvascular network. Using a multiscale cell model we are able to accurately capture red blood cell mechanics, rheology, and dynamics in agreement with a number of single cell experiments. Further, this validated model yields accurate predictions of the blood rheological properties, cell migration, cell-free layer, and hemodynamic resistance in microvessels. In addition, we investigate blood related changes in malaria, which include a considerable stiffening of red blood cells and their cytoadherence to endothelium. For these biophysical problems computational modeling is able to provide new physical insights and capabilities for quantitative predictions of blood flow in health and disease.

The Full Monte Carlo: A Live Performance with Stars

NASA Astrophysics Data System (ADS)

Meng, Xiao-Li

2014-06-01

Markov chain Monte Carlo (MCMC) is being applied increasingly often in modern Astrostatistics. It is indeed incredibly powerful, but also very dangerous. It is popular because of its apparent generality (from simple to highly complex problems) and simplicity (the availability of out-of-the-box recipes). It is dangerous because it always produces something but there is no surefire way to verify or even diagnosis that the “something” is remotely close to what the MCMC theory predicts or one hopes. Using very simple models (e.g., conditionally Gaussian), this talk starts with a tutorial of the two most popular MCMC algorithms, namely, the Gibbs Sampler and the Metropolis-Hasting Algorithm, and illustratestheir good, bad, and ugly implementations via live demonstration. The talk ends with a story of how a recent advance, the Ancillary-Sufficient Interweaving Strategy (ASIS) (Yu and Meng, 2011, http://www.stat.harvard.edu/Faculty_Content/meng/jcgs.2011-article.pdf)reduces the danger. It was discovered almost by accident during a Ph.D. student’s (Yaming Yu) struggle with fitting a Cox process model for detecting changes in source intensity of photon counts observed by the Chandra X-ray telescope from a (candidate) neutron/quark star.

Geometrically Constructed Markov Chain Monte Carlo Study of Quantum Spin-phonon Complex Systems

NASA Astrophysics Data System (ADS)

Suwa, Hidemaro

2013-03-01

We have developed novel Monte Carlo methods for precisely calculating quantum spin-boson models and investigated the critical phenomena of the spin-Peierls systems. Three significant methods are presented. The first is a new optimization algorithm of the Markov chain transition kernel based on the geometric weight allocation. This algorithm, for the first time, satisfies the total balance generally without imposing the detailed balance and always minimizes the average rejection rate, being better than the Metropolis algorithm. The second is the extension of the worm (directed-loop) algorithm to non-conserved particles, which cannot be treated efficiently by the conventional methods. The third is the combination with the level spectroscopy. Proposing a new gap estimator, we are successful in eliminating the systematic error of the conventional moment method. Then we have elucidated the phase diagram and the universality class of the one-dimensional XXZ spin-Peierls system. The criticality is totally consistent with the J1 -J2 model, an effective model in the antiadiabatic limit. Through this research, we have succeeded in investigating the critical phenomena of the effectively frustrated quantum spin system by the quantum Monte Carlo method without the negative sign. JSPS Postdoctoral Fellow for Research Abroad

A brief introduction to computer-intensive methods, with a view towards applications in spatial statistics and stereology.

PubMed

Mattfeldt, Torsten

2011-04-01

Computer-intensive methods may be defined as data analytical procedures involving a huge number of highly repetitive computations. We mention resampling methods with replacement (bootstrap methods), resampling methods without replacement (randomization tests) and simulation methods. The resampling methods are based on simple and robust principles and are largely free from distributional assumptions. Bootstrap methods may be used to compute confidence intervals for a scalar model parameter and for summary statistics from replicated planar point patterns, and for significance tests. For some simple models of planar point processes, point patterns can be simulated by elementary Monte Carlo methods. The simulation of models with more complex interaction properties usually requires more advanced computing methods. In this context, we mention simulation of Gibbs processes with Markov chain Monte Carlo methods using the Metropolis-Hastings algorithm. An alternative to simulations on the basis of a parametric model consists of stochastic reconstruction methods. The basic ideas behind the methods are briefly reviewed and illustrated by simple worked examples in order to encourage novices in the field to use computer-intensive methods. © 2010 The Authors Journal of Microscopy © 2010 Royal Microscopical Society.

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

PubMed Central

Rockenbach, Kate; Havird, Justin C.; Monroe, J. Grey; Triant, Deborah A.; Taylor, Douglas R.; Sloan, Daniel B.

2016-01-01

Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i.e., relaxed purifying selection) is a source of ongoing controversy. To address this, we have taken advantage of the multiple independent accelerations that have occurred within the genus Silene (Caryophyllaceae) by examining phylogenetic and population genetic variation in the nuclear genes that encode subunits of the CLP and ACCase complexes. We found that, in species with accelerated plastid genome evolution, the nuclear-encoded subunits in the CLP and ACCase complexes are also evolving rapidly, especially those involved in direct physical interactions with plastid-encoded proteins. A massive excess of nonsynonymous substitutions between species relative to levels of intraspecific polymorphism indicated a history of strong positive selection (particularly in CLP genes). Interestingly, however, some species are likely undergoing loss of the native (heteromeric) plastid ACCase and putative functional replacement by a duplicated cytosolic (homomeric) ACCase. Overall, the patterns of molecular evolution in these plastid–nuclear complexes are unusual for anciently conserved enzymes. They instead resemble cases of antagonistic coevolution between pathogens and host immune genes. We discuss a possible role of plastid–nuclear conflict as a novel cause of accelerated evolution. PMID:27707788

Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

PubMed Central

Dibrova, Daria V.; Cherepanov, Dmitry A.; Galperin, Michael Y.; Skulachev, Vladimir P.; Mulkidjanian, Armen Y.

2013-01-01

This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. PMID:23871937

The Evolution and Increasing Complexity of the Resident Assistant Role in the United States from Colonial to Modern Times

ERIC Educational Resources Information Center

Boone, Katherine B.; Davidson, Denise L.; Bauman, Mark

2016-01-01

The evolution of the resident assistant position and its history are important to understanding its increasing complexities. In this article we examine how court cases and federal legislation, along with changes in popular culture, have altered and shaped the role of the resident assistant. Our premise is that this role, originally relatively…

Geometry of Quantum Computation with Qudits

PubMed Central

Luo, Ming-Xing; Chen, Xiu-Bo; Yang, Yi-Xian; Wang, Xiaojun

2014-01-01

The circuit complexity of quantum qubit system evolution as a primitive problem in quantum computation has been discussed widely. We investigate this problem in terms of qudit system. Using the Riemannian geometry the optimal quantum circuits are equivalent to the geodetic evolutions in specially curved parametrization of SU(dn). And the quantum circuit complexity is explicitly dependent of controllable approximation error bound. PMID:24509710

Evolution of mixing width induced by general Rayleigh-Taylor instability.

PubMed

Zhang, You-Sheng; He, Zhi-Wei; Gao, Fu-Jie; Li, Xin-Liang; Tian, Bao-Lin

2016-06-01

Turbulent mixing induced by Rayleigh-Taylor (RT) instability occurs ubiquitously in many natural phenomena and engineering applications. As the simplest and primary descriptor of the mixing process, the evolution of mixing width of the mixing zone plays a notable role in the flows. The flows generally involve complex varying acceleration histories and widely varying density ratios, two dominant factors affecting the evolution of mixing width. However, no satisfactory theory for predicting the evolution has yet been established. Here a theory determining the evolution of mixing width in general RT flows is established to reproduce, first, all of the documented experiments conducted for diverse (i.e., constant, impulsive, oscillating, decreasing, increasing, and complex) acceleration histories and all density ratios. The theory is established in terms of the conservation principle, with special consideration given to the asymmetry of the volume-averaged density fields occurring in actual flows. The results reveal the sensitivity or insensitivity of the evolution of a mixing front of a neighboring light or heavy fluid to the degree of asymmetry and thus explain the distinct evolutions in two experiments with the same configurations.

ComplexContact: a web server for inter-protein contact prediction using deep learning.

PubMed

Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

2018-05-22

ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

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

The evolution of the neocortex in mammals: intrinsic and extrinsic contributions to the cortical phenotype.

PubMed

Karlen, Sarah J; Krubitzer, Leah

2006-01-01

The neocortex is that portion of the brain that is involved in volitional motor control, perception, cognition and a number of other complex behaviours exhibited by mammals, including humans. Indeed, the increase in the size of the cortical sheet and cortical field number is one of the hallmarks of human brain evolution. Fossil records and comparative studies of the neocortex indicate that early mammalian neocortices were composed of only a few parts or cortical fields, and that in some lineages such as primates, the neocortex expanded dramatically. More significantly, the number of cortical fields increased and the connectivity between cortical fields became more complex. While we do not know the exact transformation between this type of increase in cortical field number and connectivity; and the emergence of complex behaviours like those mentioned above, we know that species that have large neocorticies with multiple parts generally have more complex behaviours, both overt and covert. Although a number of inroads have been made into understanding how neurons in the neocortex respond to a variety of stimuli, the micro and macro circuitry of particular neocortical fields, and the molecular developmental events that construct current organization, very little is known about how more cortical fields are added in evolution. In particular, we do not know the rules of change, nor the constraints imposed on evolving nervous systems that dictate the particular phenotype that will ultimately emerge. One reason why these issues are unresolved is that the brain is a compromise between existing genetic constraints and the need to adapt. Thus, the functions that the brain generates are absolutely imperfect, although functionally optimized. This makes it very difficult to determine the rules of construction, to generate viable computational models of brain evolution, and to predict the direction of changes that may occur over time. Despite these obstacles, it is still possible to study the evolution of the neocortex. One way is to study the products of the evolutionary process--extant mammal brains-and to make inferences about the process. The second way to study brain evolution is to examine the developmental mechanisms that give rise to complex brains. We have begun to test our theories regarding cortical evolution, generated from comparative studies, by 'tweaking' in a developing nervous system what we believe is naturally being modified in evolution. Our goals are to identify the constraints imposed on the evolving neocortex, to disentangle the genetic and activity dependent mechanisms that give rise to complex brains, and ultimately to produce a cortical phenotype that is consistent with what would naturally occur in evolution.

Synergy from reproductive division of labor and genetic complexity drive the evolution of sex.

PubMed

Jaffe, Klaus

2018-04-16

Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating. Looking at the evolution of sex as a complex system through individual-based simulations explains better the diversity of sexual strategies known to exist in nature, compared to classical analytical models.

Evolution of the social network of scientific collaborations

NASA Astrophysics Data System (ADS)

Barabasi, Albert-Laszlo; Jeong, Hawoong; Neda, Zoltan; Ravasz, Erzsebet; Schubert, Andras; Vicsek, Tamas

2002-03-01

The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer the dynamic and the structural mechanisms that govern the evolution and topology of this complex system. First, empirical measurements allow us to uncover the topological measures that characterize the network at a given moment, as well as the time evolution of these quantities. The results indicate that the network is scale-free, and that the network evolution is governed by preferential attachment, affecting both internal and external links. However, in contrast with most model predictions the average degree increases in time, and the node separation decreases. Second, we propose a simple model that captures the network's time evolution. Third, numerical simulations are used to uncover the behavior of quantities that could not be predicted analytically.

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

ERIC Educational Resources Information Center

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

2016-01-01

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…

Emergence of life: Physical chemistry changes the paradigm.

PubMed

Spitzer, Jan; Pielak, Gary J; Poolman, Bert

2015-06-10

Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of 'what is life?'. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life's emergence: (1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents. (3) Earth's overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states. (4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization. We discuss these premises in relation to current 'constructive' (non-evolutionary) paradigm of origins research - the process of complexification of chemical matter 'from the simple to the complex'. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

Family feuds: social competition and sexual conflict in complex societies

PubMed Central

Rubenstein, Dustin R.

2012-01-01

Darwin was initially puzzled by the processes that led to ornamentation in males—what he termed sexual selection—and those that led to extreme cooperation and altruism in complex animal societies—what was later termed kin selection. Here, I explore the relationships between sexual and kin selection theory by examining how social competition for reproductive opportunities—particularly in females—and sexual conflict over mating partners are inherent and critical parts of complex altruistic societies. I argue that (i) patterns of reproductive sharing within complex societies can drive levels of social competition and reproductive conflict not only in males but also in females living in social groups, and ultimately the evolution of female traits such as ornaments and armaments; (ii) mating conflict over female choice of sexual partners can influence kin structure within groups and drive the evolution of complex societies; and (iii) patterns of reproductive sharing and conflict among females may also drive the evolution of complex societies by influencing kin structure within groups. Ultimately, complex societies exhibiting altruistic behaviour appear to have only arisen in taxa where social competition over reproductive opportunities and sexual conflict over mating partners were low. Once such societies evolved, there were important selective feedbacks on traits used to regulate and mediate intra-sexual competition over reproductive opportunities, particularly in females. PMID:22777018

Family feuds: social competition and sexual conflict in complex societies.

PubMed

Rubenstein, Dustin R

2012-08-19

Darwin was initially puzzled by the processes that led to ornamentation in males-what he termed sexual selection-and those that led to extreme cooperation and altruism in complex animal societies-what was later termed kin selection. Here, I explore the relationships between sexual and kin selection theory by examining how social competition for reproductive opportunities-particularly in females-and sexual conflict over mating partners are inherent and critical parts of complex altruistic societies. I argue that (i) patterns of reproductive sharing within complex societies can drive levels of social competition and reproductive conflict not only in males but also in females living in social groups, and ultimately the evolution of female traits such as ornaments and armaments; (ii) mating conflict over female choice of sexual partners can influence kin structure within groups and drive the evolution of complex societies; and (iii) patterns of reproductive sharing and conflict among females may also drive the evolution of complex societies by influencing kin structure within groups. Ultimately, complex societies exhibiting altruistic behaviour appear to have only arisen in taxa where social competition over reproductive opportunities and sexual conflict over mating partners were low. Once such societies evolved, there were important selective feedbacks on traits used to regulate and mediate intra-sexual competition over reproductive opportunities, particularly in females.

Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations.

PubMed

Austerlitz, Frédéric; Heyer, Evelyne

2018-06-01

Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.

Towards Complex Abiotic Systems for Chemical and Biological Sensing

DTIC Science & Technology

2009-11-01

such as phage display, cell surface display, and Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Other processes necessary to...Directed evolution by in vitro compartmentalization. Nat Methods 2006, 3, 561-570. l7Chelliserrykattil, J.; Ellington, A.D. Evolution of a T7 RNA

Applicability of land use models for the Houston area test site

NASA Technical Reports Server (NTRS)

Petersburg, R. K.; Bradford, L. H.

1973-01-01

Descriptions of land use models are presented which were considered for their applicability to the Houston Area Test Site. These models are representative both of the prevailing theories of land use dynamics and of basic approaches to simulation. The models considered are: a model of metropolis, land use simulation model, emperic land use forecasting model, a probabilistic model for residential growth, and the regional environmental management allocation process. Sources of environmental/resource information are listed.

Rainfall Modification by Urban Areas: New Perspectives from TRMM

NASA Technical Reports Server (NTRS)

Shepherd, J. Marshall; Pierce, Harold F.; Negri, Andrew

2002-01-01

Data from the Tropical Rainfall Measuring Mission's (TRMM) Precipitation Radar (PR) were employed to identify warm season rainfall (1998-2000) patterns around Atlanta, Montgomery, Nashville, San Antonio, Waco, and Dallas. Results reveal an average increase of -28% in monthly rainfall rates within 30-60 kilometers downwind of the metropolis with a modest increase of 5.6% over the metropolis. Portions of the downwind area exhibit increases as high as 51%. The percentage changes are relative to an upwind control area. It was also found that maximum rainfall rates in the downwind impact area exceeded the mean value in the upwind control area by 48% - 116%. The maximum value was generally found at an average distance of 39 km from the edge of the urban center or 64 km from the center of the city. Results are consistent with METROMEX studies of St. Louis almost two decades ago and with more recent studies near Atlanta. Future work is extending the investigation to Phoenix, Arizona, an arid U.S. city, and several international cities like Mexico City, Johannesburg, and Brasilia. The study establishes the possibility of utilizing satellite-based rainfall estimates for examining rainfall modification by urban areas on global scales and over longer time periods. Such research has implications for weather forecasting, urban planning, water resource management, and understanding human impact on the environment and climate.

The prevalence and incidence of COPD among urban older persons of Bangkok Metropolis.

PubMed

Maranetra, Khun Nanta; Chuaychoo, Benjamas; Dejsomritrutai, Wanchai; Chierakul, Nitipatana; Nana, Arth; Lertakyamanee, Jariya; Naruman, Chana; Suthamsmai, Tasneeya; Sangkaew, Sutee; Sreelum, Wichean; Aksornin, Montchai; Dechapol, Jaroon; Sathet, Wichean

2002-11-01

COPD substantially affects the national healthcare resource and healthcare cost especially among the older persons. Identifying the accurate prevalence and incidence reflects the scale of problem posed by COPD. This epidemiological study using the criteria for diagnosing COPD based on ratio of FEV1.0/FVC less than 70 per cent and the reversibility of less than 15 per cent increase of post bronchodilator FEV1.0 in the absence of parenchymal lesions and cardiomegaly in CXR (PA and lateral view) revealed the prevalence (1998) of COPD among the 3094 older persons aged 60 years and over in the communities of Bangkok Metropolis 10 km around Siriraj Hospital was 7.11 per cent (95% CI: 6.21-8.01), whereas the incidence (1999) of COPD was 3.63 per cent (95% CI: 2.83-4.43). Both the prevalence and the incidence were increased with increasing age. The disease occurred predominantly among male smokers. The distribution of mild : moderate : severe COPD in the prevalence study was 5.6:2.2:1. The current findings also suggest that tobacco smoking is the prime important cause of COPD and the indoor pollution especially cooking smoke is not significant. In particular, the unexpectedly high incidence compared with prevalence in this population probably represents the warning message to the national policy maker for prompt and effective health promotion and disease prevention to prevent further social and economic loss.

Influence of education on HIV infection among pregnant women attending their antenatal care in Sekondi-Takoradi metropolis, Ghana.

PubMed

Orish, Verner N; Onyeabor, Onyekachi S; Boampong, Johnson N; Afoakwah, Richmond; Nwaefuna, Ekene; Acquah, Samuel; Orish, Esther O; Sanyaolu, Adekunle O; Iriemenam, Nnaemeka C

2014-08-01

This study investigated the influence of the level of education on HIV infection among pregnant women attending antenatal care in Sekondi-Takoradi, Ghana. A cross-sectional study was conducted at four hospitals in the Sekondi-Takoradi metropolis. The study group comprised 885 consenting pregnant women attending antenatal care clinics. Questionnaires were administered and venous blood samples were screened for HIV and other parameters. Multivariable logistic regression analyses were performed to determine the association between the level of education attained by the pregnant women and their HIV statuses. The data showed that 9.83% (87/885) of the pregnant women were HIV seropositive while 90.17% (798/885) were HIV seronegative. There were significant differences in mean age (years) between the HIV seropositive women (27.45 ± 5.5) and their HIV seronegative (26.02 ± 5.6) counterparts (p = .026) but the inference disappeared after adjustment (p = .22). Multivariable logistic regression analysis revealed that pregnant women with secondary/tertiary education were less likely to have HIV infection compared with those with none/primary education (adjusted OR, 0.53; 95% CI, 0.30-0.91; p = .022). Our data showed an association with higher level of education and HIV statuses of the pregnant women. It is imperative to encourage formal education among pregnant women in this region.

Urban transformation of a metropolis and its environmental impacts: a case study in Shanghai.

PubMed

Tian, Zhan; Cao, Guiying; Shi, Jun; McCallum, Ian; Cui, Linli; Fan, Dongli; Li, Xinhu

2012-06-01

The aim of this paper is to understand the sustainability of urban spatial transformation in the process of rapid urbanization, and calls for future research on the demographic and economic dimensions of climate change. Shanghai towards its transformation to a metropolis has experienced vast socioeconomic and ecological change and calls for future research on the impacts of demographic and economic dimensions on climate change. We look at the major questions (1) to explore economic and demographic growth, land use and land-cover changes in the context of rapid economic and city growth, and (2) to analyze how the demography and economic growth have been associated with the local air temperature and vegetation. We examine urban growth, land use and land-cover changes in the context of rapid economic development and urbanization. We assess the impact of urban expansion on local air temperature and vegetation. The analysis is based on time series data of land use, normalized difference vegetation index (NDVI), and meteorological, demographic and economic data. The results indicate that urban growth has been driven by mass immigration; as a consequence of economic growth and urban expansion, a large amount of farmland has been converted to paved road and residential buildings. Furthermore, the difference between air temperature in urban and exurban areas has increased rapidly. The decrease of high mean annual NDVI has mainly occurred around the dense urban areas.

Finite Adaptation and Multistep Moves in the Metropolis-Hastings Algorithm for Variable Selection in Genome-Wide Association Analysis

PubMed Central

Peltola, Tomi; Marttinen, Pekka; Vehtari, Aki

2012-01-01

High-dimensional datasets with large amounts of redundant information are nowadays available for hypothesis-free exploration of scientific questions. A particular case is genome-wide association analysis, where variations in the genome are searched for effects on disease or other traits. Bayesian variable selection has been demonstrated as a possible analysis approach, which can account for the multifactorial nature of the genetic effects in a linear regression model. Yet, the computation presents a challenge and application to large-scale data is not routine. Here, we study aspects of the computation using the Metropolis-Hastings algorithm for the variable selection: finite adaptation of the proposal distributions, multistep moves for changing the inclusion state of multiple variables in a single proposal and multistep move size adaptation. We also experiment with a delayed rejection step for the multistep moves. Results on simulated and real data show increase in the sampling efficiency. We also demonstrate that with application specific proposals, the approach can overcome a specific mixing problem in real data with 3822 individuals and 1,051,811 single nucleotide polymorphisms and uncover a variant pair with synergistic effect on the studied trait. Moreover, we illustrate multimodality in the real dataset related to a restrictive prior distribution on the genetic effect sizes and advocate a more flexible alternative. PMID:23166669

Markov Chain Monte Carlo Inference of Parametric Dictionaries for Sparse Bayesian Approximations

PubMed Central

Chaspari, Theodora; Tsiartas, Andreas; Tsilifis, Panagiotis; Narayanan, Shrikanth

2016-01-01

Parametric dictionaries can increase the ability of sparse representations to meaningfully capture and interpret the underlying signal information, such as encountered in biomedical problems. Given a mapping function from the atom parameter space to the actual atoms, we propose a sparse Bayesian framework for learning the atom parameters, because of its ability to provide full posterior estimates, take uncertainty into account and generalize on unseen data. Inference is performed with Markov Chain Monte Carlo, that uses block sampling to generate the variables of the Bayesian problem. Since the parameterization of dictionary atoms results in posteriors that cannot be analytically computed, we use a Metropolis-Hastings-within-Gibbs framework, according to which variables with closed-form posteriors are generated with the Gibbs sampler, while the remaining ones with the Metropolis Hastings from appropriate candidate-generating densities. We further show that the corresponding Markov Chain is uniformly ergodic ensuring its convergence to a stationary distribution independently of the initial state. Results on synthetic data and real biomedical signals indicate that our approach offers advantages in terms of signal reconstruction compared to previously proposed Steepest Descent and Equiangular Tight Frame methods. This paper demonstrates the ability of Bayesian learning to generate parametric dictionaries that can reliably represent the exemplar data and provides the foundation towards inferring the entire variable set of the sparse approximation problem for signal denoising, adaptation and other applications. PMID:28649173

Metropolis revisited: the evolving role of librarians in informatics education for the health professions

PubMed Central

King, Samuel B.; Lapidus, Mariana

2015-01-01

Objective: The authors' goal was to assess changes in the role of librarians in informatics education from 2004 to 2013. This is a follow-up to “Metropolis Redux: The Unique Importance of Library Skills in Informatics,” a 2004 survey of informatics programs. Methods: An electronic survey was conducted in January 2013 and sent to librarians via the MEDLIB-L email discussion list, the library section of the American Association of Colleges of Pharmacy, the Medical Informatics Section of the Medical Library Association, the Information Technology Interest Group of the Association of College and Research Libraries/New England Region, and various library directors across the country. Results: Librarians from fifty-five institutions responded to the survey. Of these respondents, thirty-four included librarians in nonlibrary aspects of informatics training. Fifteen institutions have librarians participating in leadership positions in their informatics programs. Compared to the earlier survey, the role of librarians has evolved. Conclusions: Librarians possess skills that enable them to participate in informatics programs beyond a narrow library focus. Librarians currently perform significant leadership roles in informatics education. There are opportunities for librarian interdisciplinary collaboration in informatics programs. Implications: Informatics is much more than the study of technology. The information skills that librarians bring to the table enrich and broaden the study of informatics in addition to adding value to the library profession itself. PMID:25552939

Metropolis revisited: the evolving role of librarians in informatics education for the health professions.

PubMed

King, Samuel B; Lapidus, Mariana

2015-01-01

The authors' goal was to assess changes in the role of librarians in informatics education from 2004 to 2013. This is a follow-up to "Metropolis Redux: The Unique Importance of Library Skills in Informatics," a 2004 survey of informatics programs. An electronic survey was conducted in January 2013 and sent to librarians via the MEDLIB-L email discussion list, the library section of the American Association of Colleges of Pharmacy, the Medical Informatics Section of the Medical Library Association, the Information Technology Interest Group of the Association of College and Research Libraries/New England Region, and various library directors across the country. Librarians from fifty-five institutions responded to the survey. Of these respondents, thirty-four included librarians in nonlibrary aspects of informatics training. Fifteen institutions have librarians participating in leadership positions in their informatics programs. Compared to the earlier survey, the role of librarians has evolved. Librarians possess skills that enable them to participate in informatics programs beyond a narrow library focus. Librarians currently perform significant leadership roles in informatics education. There are opportunities for librarian interdisciplinary collaboration in informatics programs. Informatics is much more than the study of technology. The information skills that librarians bring to the table enrich and broaden the study of informatics in addition to adding value to the library profession itself.

Current studies on bacterospermia the leading cause of male infertility: a protégé and potential threat towards mans extinction.

PubMed

Isaiah, Ibeh Nnana; Nche, Bikwe Thomas; Nwagu, Ibeh Georgina; Nnanna, Ibeh Isaiah

2011-12-01

The current rise of male infertility associated with bacterospermia and urogenital infection has been on the increase amongst adult married males in Benin metropolis and a major cause of concern to male fertility and reproduction in Nigeria. To microbiologically isolate and study the infectious agent that has led to male infertility and also to study the percentage occurrence of bacteropsermia and urogenital caused infertility in adult married males in Benin metropolis using standard microbiological methods of isolating and identifying the organism, specimen was collected and processed which includes the susceptibility profile of isolates and sperm quality. In this study a total of 140 sperm samples was collected from patient who were referred from the consultant outpatient department of the University of Benin Teaching Hospital and then evaluated bacteriologically using standard bacterial cultural methods Among the total cases, 92 (65.7%) showed at least one pathogen. Staphylococcus aureus (28.3%), Staphylococcus Saprophyticus (13.0%), Pseudomonas aerouginosa (6.5%), Escherichia Coli (19.6%) Proteus mirabilis (10.8%) Klebsiella spp (10.8%) and Proteus vulgaris (10.8%). There was an outstanding significant relationship between bacteriospermia and the rate of total motility and morphologically abnormal sperms, The percentage of morphologically normal sperm was lower in this study. Staphylococcus aureus Staphylococcus saprohyticus and Escherichia coli were the most common pathogen having negative effects on sperm motility and morphology in this study.

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

PubMed

Osada, Naoki; Akashi, Hiroshi

2012-01-01

Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.

Influence of chemical disorder on energy dissipation and defect evolution in concentrated solid solution alloys

DOE PAGES

Zhang, Yanwen; Stocks, George Malcolm; Jin, Ke; ...

2015-10-28

A long-standing objective in materials research is to understand how energy is dissipated in both the electronic and atomic subsystems in irradiated materials, and how related non-equilibrium processes may affect defect dynamics and microstructure evolution. Here we show that alloy complexity in concentrated solid solution alloys having both an increasing number of principal elements and altered concentrations of specific elements can lead to substantial reduction in the electron mean free path and thermal conductivity, which has a significant impact on energy dissipation and consequentially on defect evolution during ion irradiation. Enhanced radiation resistance with increasing complexity from pure nickel tomore » binary and to more complex quaternary solid solutions is observed under ion irradiation up to an average damage level of 1 displacement per atom. Understanding how materials properties can be tailored by alloy complexity and their influence on defect dynamics may pave the way for new principles for the design of radiation tolerant structural alloys.« less

Big cats as a model system for the study of the evolution of intelligence.

PubMed

Borrego, Natalia

2017-08-01

Currently, carnivores, and felids in particular, are vastly underrepresented in cognitive literature, despite being an ideal model system for tests of social and ecological intelligence hypotheses. Within Felidae, big cats (Panthera) are uniquely suited to studies investigating the evolutionary links between social, ecological, and cognitive complexity. Intelligence likely did not evolve in a unitary way but instead evolved as the result of mutually reinforcing feedback loops within the physical and social environments. The domain-specific social intelligence hypothesis proposes that social complexity drives only the evolution of cognitive abilities adapted only to social domains. The domain-general hypothesis proposes that the unique demands of social life serve as a bootstrap for the evolution of superior general cognition. Big cats are one of the few systems in which we can directly address conflicting predictions of the domain-general and domain-specific hypothesis by comparing cognition among closely related species that face roughly equivalent ecological complexity but vary considerably in social complexity. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolution of an ancient protein function involved in organized multicellularity in animals

PubMed Central

Anderson, Douglas P; Whitney, Dustin S; Hanson-Smith, Victor; Woznica, Arielle; Campodonico-Burnett, William; Volkman, Brian F; King, Nicole; Thornton, Joseph W; Prehoda, Kenneth E

2016-01-01

To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals. DOI: http://dx.doi.org/10.7554/eLife.10147.001 PMID:26740169

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

PubMed

Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

2016-01-01

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.

Evolution for Young Victorians

ERIC Educational Resources Information Center

Lightman, Bernard

2012-01-01

Evolution was a difficult topic to tackle when writing books for the young in the wake of the controversies over Darwin's "Origin of Species." Authors who wrote about evolution for the young experimented with different ways of making the complex concepts of evolutionary theory accessible and less controversial. Many authors depicted presented…

Thermodynamical Arguments against Evolution

ERIC Educational Resources Information Center

Rosenhouse, Jason

2017-01-01

The argument that the second law of thermodynamics contradicts the theory of evolution has recently been revived by anti-evolutionists. In its basic form, the argument asserts that whereas evolution implies that there has been an increase in biological complexity over time, the second law, a fundamental principle of physics, shows this to be…

Voids and the Cosmic Web: cosmic depression & spatial complexity

NASA Astrophysics Data System (ADS)

van de Weygaert, Rien

2016-10-01

Voids form a prominent aspect of the Megaparsec distribution of galaxies and matter. Not only do theyrepresent a key constituent of the Cosmic Web, they also are one of the cleanest probesand measures of global cosmological parameters. The shape and evolution of voids are highly sensitive tothe nature of dark energy, while their substructure and galaxy population provides a direct key to thenature of dark matter. Also, the pristine environment of void interiors is an important testing groundfor our understanding of environmental influences on galaxy formation and evolution. In this paper, we reviewthe key aspects of the structure and dynamics ofvoids, with a particular focus on the hierarchical evolution of the void population. We demonstratehow the rich structural pattern of the Cosmic Web is related to the complex evolution and buildupof voids.

Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

PubMed

Remington, David L

2015-12-01

Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Time-evolution of quantum systems via a complex nonlinear Riccati equation. I. Conservative systems with time-independent Hamiltonian

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

Cruz, Hans, E-mail: hans@ciencias.unam.mx; Schuch, Dieter; Castaños, Octavio, E-mail: ocasta@nucleares.unam.mx

2015-09-15

The sensitivity of the evolution of quantum uncertainties to the choice of the initial conditions is shown via a complex nonlinear Riccati equation leading to a reformulation of quantum dynamics. This sensitivity is demonstrated for systems with exact analytic solutions with the form of Gaussian wave packets. In particular, one-dimensional conservative systems with at most quadratic Hamiltonians are studied.

Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces

PubMed Central

Andreani, Jessica; Faure, Guilhem; Guerois, Raphaël

2012-01-01

Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity. Nonetheless, the elementary interactions which compose the interface are highly versatile throughout evolution. Understanding and characterizing interface plasticity across evolution is a fundamental issue which could provide new insights into protein-protein interaction prediction. Using a database of 1,024 couples of close and remote heteromeric structural interologs, we studied protein-protein interactions from a structural and evolutionary point of view. We systematically and quantitatively analyzed the conservation of different types of interface contacts. Our study highlights astonishing plasticity regarding polar contacts at complex interfaces. It also reveals that up to a quarter of the residues switch out of the interface when comparing two homologous complexes. Despite such versatility, we identify two important interface descriptors which correlate with an increased conservation in the evolution of interfaces: apolar patches and contacts surrounding anchor residues. These observations hold true even when restricting the dataset to transiently formed complexes. We show that a combination of six features related either to sequence or to geometric properties of interfaces can be used to rank positions likely to share similar contacts between two interologs. Altogether, our analysis provides important tracks for extracting meaningful information from multiple sequence alignments of conserved binding partners and for discriminating near-native interfaces using evolutionary information. PMID:22952442

Biogeography predicts macro-evolutionary patterning of gestural display complexity in a passerine family.

PubMed

Miles, Meredith C; Cheng, Samantha; Fuxjager, Matthew J

2017-05-01

Gestural displays are incorporated into the signaling repertoire of numerous animal species. These displays range from complex signals that involve impressive and challenging maneuvers, to simpler displays or no gesture at all. The factors that drive this evolution remain largely unclear, and we therefore investigate this issue in New World blackbirds by testing how factors related to a species' geographical distribution and social mating system predict macro-evolutionary patterns of display elaboration. We report that species inhabiting temperate regions produce more complex displays than species living in tropical regions, and we attribute this to (i) ecological factors that increase the competitiveness of the social environment in temperate regions, and (ii) different evolutionary and geological contexts under which species in temperate and tropical regions evolved. Meanwhile, we find no evidence that social mating system predicts species differences in display complexity, which is consistent with the idea that gestural displays evolve independently of social mating system. Together, these results offer some of the first insight into the role played by geographic factors and evolutionary context in the evolution of the remarkable physical displays of birds and other vertebrates. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Estimation and impact assessment of input and parameter uncertainty in predicting groundwater flow with a fully distributed model

NASA Astrophysics Data System (ADS)

Touhidul Mustafa, Syed Md.; Nossent, Jiri; Ghysels, Gert; Huysmans, Marijke

2017-04-01

Transient numerical groundwater flow models have been used to understand and forecast groundwater flow systems under anthropogenic and climatic effects, but the reliability of the predictions is strongly influenced by different sources of uncertainty. Hence, researchers in hydrological sciences are developing and applying methods for uncertainty quantification. Nevertheless, spatially distributed flow models pose significant challenges for parameter and spatially distributed input estimation and uncertainty quantification. In this study, we present a general and flexible approach for input and parameter estimation and uncertainty analysis of groundwater models. The proposed approach combines a fully distributed groundwater flow model (MODFLOW) with the DiffeRential Evolution Adaptive Metropolis (DREAM) algorithm. To avoid over-parameterization, the uncertainty of the spatially distributed model input has been represented by multipliers. The posterior distributions of these multipliers and the regular model parameters were estimated using DREAM. The proposed methodology has been applied in an overexploited aquifer in Bangladesh where groundwater pumping and recharge data are highly uncertain. The results confirm that input uncertainty does have a considerable effect on the model predictions and parameter distributions. Additionally, our approach also provides a new way to optimize the spatially distributed recharge and pumping data along with the parameter values under uncertain input conditions. It can be concluded from our approach that considering model input uncertainty along with parameter uncertainty is important for obtaining realistic model predictions and a correct estimation of the uncertainty bounds.

Improving and Evaluating Nested Sampling Algorithm for Marginal Likelihood Estimation

NASA Astrophysics Data System (ADS)

Ye, M.; Zeng, X.; Wu, J.; Wang, D.; Liu, J.

2016-12-01

With the growing impacts of climate change and human activities on the cycle of water resources, an increasing number of researches focus on the quantification of modeling uncertainty. Bayesian model averaging (BMA) provides a popular framework for quantifying conceptual model and parameter uncertainty. The ensemble prediction is generated by combining each plausible model's prediction, and each model is attached with a model weight which is determined by model's prior weight and marginal likelihood. Thus, the estimation of model's marginal likelihood is crucial for reliable and accurate BMA prediction. Nested sampling estimator (NSE) is a new proposed method for marginal likelihood estimation. The process of NSE is accomplished by searching the parameters' space from low likelihood area to high likelihood area gradually, and this evolution is finished iteratively via local sampling procedure. Thus, the efficiency of NSE is dominated by the strength of local sampling procedure. Currently, Metropolis-Hasting (M-H) algorithm is often used for local sampling. However, M-H is not an efficient sampling algorithm for high-dimensional or complicated parameter space. For improving the efficiency of NSE, it could be ideal to incorporate the robust and efficient sampling algorithm - DREAMzs into the local sampling of NSE. The comparison results demonstrated that the improved NSE could improve the efficiency of marginal likelihood estimation significantly. However, both improved and original NSEs suffer from heavy instability. In addition, the heavy computation cost of huge number of model executions is overcome by using an adaptive sparse grid surrogates.

Tourism and the Hispanicization of race in Jim Crow Miami, 1945-1965.

PubMed

Rose, Chanelle N

2012-01-01

This article examines how Miami's significant presence of Anglo Caribbean blacks and Spanish-speaking tourists critically influenced the evolution of race relations before and after the watershed 1959 Cuban Revolution. The convergence of people from the American South and North, the Caribbean, and Latin America created a border culture in a city where the influx of Bahamian blacks and Spanish-speakers, especially tourists, had begun to alter the racial landscape. To be sure, Miami had many parallels with other parts of the South in regard to how blackness was understood and enforced by whites during the first half of the twentieth century. However, I argue that the city's post-WWII meteoric tourist growth, along with its emergence as a burgeoning Pan-American metropolis, complicated the traditional southern black-white dichotomy. The purchasing power of Spanish-speaking visitors during the postwar era transformed a tourist economy that had traditionally catered to primarily wealthy white transplanted Northerners. This significant change to the city's tourist industry significantly influenced white civic leaders' decision to occasionally modify Jim Crow practices for Latin American vacationers. In effect, Miami's early Latinization had a profound impact on the established racial order as speaking Spanish became a form of currency that benefited Spanish-speaking tourists—even those of African descent. Paradoxically, this ostensibly peculiar racial climate aided the local struggle by highlighting the idiosyncrasies of Jim Crow while perpetuating the second-class status of native-born blacks.

Optimization of canopy conductance models from concurrent measurements of sap flow and stem water potential on Drooping Sheoak in South Australia

NASA Astrophysics Data System (ADS)

Wang, Hailong; Guan, Huade; Deng, Zijuan; Simmons, Craig T.

2014-07-01

Canopy conductance (gc) is a critical component in hydrological modeling for transpiration estimate. It is often formulated as functions of environmental variables. These functions are climate and vegetation specific. Thus, it is important to determine the appropriate functions in gc models and corresponding parameter values for a specific environment. In this study, sap flow, stem water potential, and microclimatic variables were measured for three Drooping Sheoak (Allocasuarina verticillata) trees in year 2011, 2012, and 2014. Canopy conductance was calculated from the inversed Penman-Monteith (PM) equation, which was then used to examine 36 gc models that comprise different response functions. Parameters were optimized using the DiffeRential Evolution Adaptive Metropolis (DREAM) model based on a training data set in 2012. Use of proper predawn stem water potential function, vapor pressure deficit function, and temperature function improves model performance significantly, while no pronounced difference is observed between models that differ in solar radiation functions. The best model gives a correlation coefficient of 0.97, and root-mean-square error of 0.0006 m/s in comparison to the PM-calculated gc. The optimized temperature function shows different characteristics from its counterparts in other similar studies. This is likely due to strong interdependence between air temperature and vapor pressure deficit in the study area or Sheoak tree physiology. Supported by the measurements and optimization results, we suggest that the effects of air temperature and vapor pressure deficit on canopy conductance should be represented together.

Complex networks generated by the Penna bit-string model: Emergence of small-world and assortative mixing

NASA Astrophysics Data System (ADS)

Li, Chunguang; Maini, Philip K.

2005-10-01

The Penna bit-string model successfully encompasses many phenomena of population evolution, including inheritance, mutation, evolution, and aging. If we consider social interactions among individuals in the Penna model, the population will form a complex network. In this paper, we first modify the Verhulst factor to control only the birth rate, and introduce activity-based preferential reproduction of offspring in the Penna model. The social interactions among individuals are generated by both inheritance and activity-based preferential increase. Then we study the properties of the complex network generated by the modified Penna model. We find that the resulting complex network has a small-world effect and the assortative mixing property.

Testing calibration routines for LISFLOOD, a distributed hydrological model

NASA Astrophysics Data System (ADS)

Pannemans, B.

2009-04-01

Traditionally hydrological models are considered as difficult to calibrate: their highly non-linearity results in rugged and rough response surfaces were calibration algorithms easily get stuck in local minima. For the calibration of distributed hydrological models two extra factors play an important role: on the one hand they are often costly on computation, thus restricting the feasible number of model runs; on the other hand their distributed nature smooths the response surface, thus facilitating the search for a global minimum. Lisflood is a distributed hydrological model currently used for the European Flood Alert System - EFAS (Van der Knijff et al, 2008). Its upcoming recalibration over more then 200 catchments, each with an average runtime of 2-3 minutes, proved a perfect occasion to put several existing calibration algorithms to the test. The tested routines are Downhill Simplex (DHS, Nelder and Mead, 1965), SCEUA (Duan et Al. 1993), SCEM (Vrugt et al., 2003) and AMALGAM (Vrugt et al., 2008), and they were evaluated on their capability to efficiently converge onto the global minimum and on the spread in the found solutions in repeated runs. The routines were let loose on a simple hyperbolic function, on a Lisflood catchment using model output as observation, and on two Lisflood catchments using real observations (one on the river Inn in the Alps, the other along the downstream stretch of the Elbe). On the mathematical problem and on the catchment with synthetic observations DHS proved to be the fastest and the most efficient in finding a solution. SCEUA and AMALGAM are a slower, but while SCEUA keeps converging on the exact solution, AMALGAM slows down after about 600 runs. For the Lisflood models with real-time observations AMALGAM (hybrid algorithm that combines several other algorithms, we used CMA, PSO and GA) came as fastest out of the tests, and giving comparable results in consecutive runs. However, some more work is needed to tweak the stopping criteria. SCEUA is a bit slower, but has very transparent stopping rules. Both have closed in on the minima after about 600 runs. DHS equals only SCEUA on convergence speed. The stopping criteria we applied so far are too strict, causing it to stop too early. SCEM converges 5-6 times slower. This is a high price for the parameter uncertainty analysis that is simultaneously done. The ease with which all algorithms find the same optimum suggests that we are dealing with a smooth and relatively simple response surface. This leaves room for other deterministic calibration algorithms being smarter than DHS in sliding downhill. PEST seems promising but sofar we haven't managed to get it running with LISFLOOD. • Duan, Q.; Gupta, V. & Sorooshian, S., 1993, Shuffled complex evolution approach for effective and efficient global minimization, J Optim Theory Appl, Kluwer Academic Publishers-Plenum Publishers, 76, 501-521 • Nelder, J. & Mead, R., 1965, A simplex method for function minimization, Comput. J., 7, 308-313 • Van Der Knijff, J. M.; Younis, J. & De Roo, A. P. J., 2008, LISFLOOD: a GIS-based distributed model for river basin scale water balance and flood simulation, International Journal of Geographical Information Science, • Vrugt, J.; Gupta, H.; Bouten, W. & Sorooshian, S., 2003, A Shuffled Complex Evolution Metropolis algorithm for optimization and uncertainty assessment of hydrologic model parameters, Water Resour. Res., 39 • Vrugt, J.; Robinson, B. & Hyman, J., 2008, Self-Adaptive Multimethod Search for Global Optimization in Real-Parameter Spaces, IEEE Trans Evol Comput, IEEE,

Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway.

PubMed

Hagey, Lee R; Møller, Peter R; Hofmann, Alan F; Krasowski, Matthew D

2010-01-01

Bile salts are the major end metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates.

Self-determined mechanisms in complex networks

NASA Astrophysics Data System (ADS)

Liu, Yang; Yuan, Jian; Shan, Xiuming; Ren, Yong; Ma, Zhengxin

2008-03-01

Self-organized networks are pervasive in communication systems such as the Internet, overlay networks, peer-to-peer networks, and cluster-based services. These networks evolve into complex topologies, under specific driving forces, i.e. user demands, technological innovations, design objectives and so on. Our study focuses on the driving forces behind individual evolutions of network components, and their stimulation and domination to the self-organized networks which are defined as self-determined mechanisms in this paper. Understanding forces underlying the evolution of networks should enable informed design decisions and help to avoid unwanted surprises, such as congestion collapse. A case study on the macroscopic evolution of the Internet topology of autonomous systems under a specific driving force is then presented. Using computer simulations, it is found that the power-law degree distribution can originate from a connection preference to larger numbers of users, and that the small-world property can be caused by rapid growth in the number of users. Our results provide a new feasible perspective to understand intrinsic fundamentals in the topological evolution of complex networks.

Evolution of the transcription complex during sporulation of Bacillus subtilis.

PubMed

Brevet, J

1976-01-01

Ribonucleic acid polymerase activity in partially purified extract of cells of Bacillus subtilis harvested at different times (t-1, to, t1, and t2) was studied by zone centrifugation. During the course of sporulation, vegetative sigma-factor activity decreased and the transcription complex lost some of its affinity for active sigma factor. The complex underwent a two-stage change in sedimentation value, from 14.5S in vegetative growth phase to a 13S species very early in sporulation to a 16S species at later times. Two SpoO mutants have been studied by zone centrifugation. One strain, a rifampin-resistant (RfmR) mutant, failed to show any modification of the transcription complex, whereas the other, a Rfms strain, underwent a partial evolution of the transcription complex after to.

The protein-protein interface evolution acts in a similar way to antibody affinity maturation.

PubMed

Li, Bohua; Zhao, Lei; Wang, Chong; Guo, Huaizu; Wu, Lan; Zhang, Xunming; Qian, Weizhu; Wang, Hao; Guo, Yajun

2010-02-05

Understanding the evolutionary mechanism that acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for delineating the macromolecular complexes and networks responsible for regulation and complexity in biological systems. To investigate whether the evolution of protein-protein interface acts in a similar way as antibody affinity maturation, we incorporated evolutionary information derived from antibody affinity maturation with common simulation techniques to evaluate prediction success rates of the computational method in affinity improvement in four different systems: antibody-receptor, antibody-peptide, receptor-membrane ligand, and receptor-soluble ligand. It was interesting to find that the same evolutionary information could improve the prediction success rates in all the four protein-protein complexes with an exceptional high accuracy (>57%). One of the most striking findings in our present study is that not only in the antibody-combining site but in other protein-protein interfaces almost all of the affinity-enhancing mutations are located at the germline hotspot sequences (RGYW or WA), indicating that DNA hot spot mechanisms may be widely used in the evolution of protein-protein interfaces. Our data suggest that the evolution of distinct protein-protein interfaces may use the same basic strategy under selection pressure to maintain interactions. Additionally, our data indicate that classical simulation techniques incorporating the evolutionary information derived from in vivo antibody affinity maturation can be utilized as a powerful tool to improve the binding affinity of protein-protein complex with a high accuracy.

Complex Pattern Formation from Current-Driven Dynamics of Single-Layer Homoepitaxial Islands on Crystalline Conducting Substrates

NASA Astrophysics Data System (ADS)

Kumar, Ashish; Dasgupta, Dwaipayan; Maroudas, Dimitrios

2017-07-01

We report a systematic study of complex pattern formation resulting from the driven dynamics of single-layer homoepitaxial islands on surfaces of face-centered-cubic (fcc) crystalline conducting substrates under the action of an externally applied electric field. The analysis is based on an experimentally validated nonlinear model of mass transport via island edge atomic diffusion, which also accounts for edge diffusional anisotropy. We analyze the morphological stability and simulate the field-driven evolution of rounded islands for an electric field oriented along the fast edge diffusion direction. For larger-than-critical island sizes on {110 } and {100 } fcc substrates, we show that multiple necking instabilities generate complex island patterns, including not-simply-connected void-containing islands mediated by sequences of breakup and coalescence events and distributed symmetrically with respect to the electric field direction. We analyze the dependence of the formed patterns on the original island size and on the duration of application of the external field. Starting from a single large rounded island, we characterize the evolution of the number of daughter islands and their average size and uniformity. The evolution of the average island size follows a universal power-law scaling relation, and the evolution of the total edge length of the islands in the complex pattern follows Kolmogorov-Johnson-Mehl-Avrami kinetics. Our study makes a strong case for the use of electric fields, as precisely controlled macroscopic forcing, toward surface patterning involving complex nanoscale features.

Ising model simulation in directed lattices and networks

NASA Astrophysics Data System (ADS)

Lima, F. W. S.; Stauffer, D.

2006-01-01

On directed lattices, with half as many neighbours as in the usual undirected lattices, the Ising model does not seem to show a spontaneous magnetisation, at least for lower dimensions. Instead, the decay time for flipping of the magnetisation follows an Arrhenius law on the square and simple cubic lattice. On directed Barabási-Albert networks with two and seven neighbours selected by each added site, Metropolis and Glauber algorithms give similar results, while for Wolff cluster flipping the magnetisation decays exponentially with time.

Historical changes to Lake Washington and route of the Lake Washington Ship Canal, King County, Washington

USGS Publications Warehouse

Chrzastowski, Michael J.

1983-01-01

Lake Washington, in the midst of the greater Seattle metropolitan area of the Puget Sound region (fig. 1), is an exceptional commercial, recreational, and esthetic resource for the region . In the past 130 years, Lake Washington has been changed from a " wild " lake in a wilderness setting to a regulated lake surrounded by a growing metropolis--a transformation that provides an unusual opportunity to study changes to a lake's shoreline and hydrologic characteristics -resulting from urbanization.

Transition records of stationary Markov chains.

PubMed

Naudts, Jan; Van der Straeten, Erik

2006-10-01

In any Markov chain with finite state space the distribution of transition records always belongs to the exponential family. This observation is used to prove a fluctuation theorem, and to show that the dynamical entropy of a stationary Markov chain is linear in the number of steps. Three applications are discussed. A known result about entropy production is reproduced. A thermodynamic relation is derived for equilibrium systems with Metropolis dynamics. Finally, a link is made with recent results concerning a one-dimensional polymer model.

[Marketing as a tool in the medical institution management].

PubMed

Petrova, N G; Balokhina, S A

2009-01-01

The contemporary social economic conditions dictate the necessity to change tactics and strategy of functioning of medical institutions of different property forms. Marketing, alongside with management is to become a leading concept of administration of medical institutions. It should be a framework for systematic collection, registration and analysis of data relevant to the medical services market. The issues of the implementation of marketing concept in the practical everyday activities of commercial medical organization providing cosmetology services to population of metropolis.

Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics

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

Kube, Susanna; Lasser, Caroline; Weber, Marcus

2009-04-01

The article addresses the achievable accuracy for a Monte Carlo sampling of Wigner functions in combination with a surface hopping algorithm for non-adiabatic quantum dynamics. The approximation of Wigner functions is realized by an adaption of the Metropolis algorithm for real-valued functions with disconnected support. The integration, which is necessary for computing values of the Wigner function, uses importance sampling with a Gaussian weight function. The numerical experiments agree with theoretical considerations and show an error of 2-3%.

Experimental implementation of local adiabatic evolution algorithms by an NMR quantum information processor.

PubMed

Mitra, Avik; Ghosh, Arindam; Das, Ranabir; Patel, Apoorva; Kumar, Anil

2005-12-01

Quantum adiabatic algorithm is a method of solving computational problems by evolving the ground state of a slowly varying Hamiltonian. The technique uses evolution of the ground state of a slowly varying Hamiltonian to reach the required output state. In some cases, such as the adiabatic versions of Grover's search algorithm and Deutsch-Jozsa algorithm, applying the global adiabatic evolution yields a complexity similar to their classical algorithms. However, using the local adiabatic evolution, the algorithms given by J. Roland and N.J. Cerf for Grover's search [J. Roland, N.J. Cerf, Quantum search by local adiabatic evolution, Phys. Rev. A 65 (2002) 042308] and by Saurya Das, Randy Kobes, and Gabor Kunstatter for the Deutsch-Jozsa algorithm [S. Das, R. Kobes, G. Kunstatter, Adiabatic quantum computation and Deutsh's algorithm, Phys. Rev. A 65 (2002) 062301], yield a complexity of order N (where N=2(n) and n is the number of qubits). In this paper, we report the experimental implementation of these local adiabatic evolution algorithms on a 2-qubit quantum information processor, by Nuclear Magnetic Resonance.

Assembly and function of the major histocompatibility complex (MHC) I peptide-loading complex are conserved across higher vertebrates.

PubMed

Hinz, Andreas; Jedamzick, Johanna; Herbring, Valentina; Fischbach, Hanna; Hartmann, Jessica; Parcej, David; Koch, Joachim; Tampé, Robert

2014-11-28

Antigen presentation to cytotoxic T lymphocytes via major histocompatibility complex class I (MHC I) molecules depends on the heterodimeric transporter associated with antigen processing (TAP). For efficient antigen supply to MHC I molecules in the ER, TAP assembles a macromolecular peptide-loading complex (PLC) by recruiting tapasin. In evolution, TAP appeared together with effector cells of adaptive immunity at the transition from jawless to jawed vertebrates and diversified further within the jawed vertebrates. Here, we compared TAP function and interaction with tapasin of a range of species within two classes of jawed vertebrates. We found that avian and mammalian TAP1 and TAP2 form heterodimeric complexes across taxa. Moreover, the extra N-terminal domain TMD0 of mammalian TAP1 and TAP2 as well as avian TAP2 recruits tapasin. Strikingly, however, only TAP1 and TAP2 from the same taxon can form a functional heterodimeric translocation complex. These data demonstrate that the dimerization interface between TAP1 and TAP2 and the tapasin docking sites for PLC assembly are conserved in evolution, whereas elements of antigen translocation diverged later in evolution and are thus taxon specific. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Modelling the evolution of complex conductivity during calcite precipitation on glass beads

NASA Astrophysics Data System (ADS)

Leroy, Philippe; Li, Shuai; Jougnot, Damien; Revil, André; Wu, Yuxin

2017-04-01

When pH and alkalinity increase, calcite frequently precipitates and hence modifies the petrophysical properties of porous media. The complex conductivity method can be used to directly monitor calcite precipitation in porous media because it is sensitive to the evolution of the mineralogy, pore structure and its connectivity. We have developed a mechanistic grain polarization model considering the electrochemical polarization of the Stern and diffuse layers surrounding calcite particles. Our complex conductivity model depends on the surface charge density of the Stern layer and on the electrical potential at the onset of the diffuse layer, which are computed using a basic Stern model of the calcite/water interface. The complex conductivity measurements of Wu et al. on a column packed with glass beads where calcite precipitation occurs are reproduced by our surface complexation and complex conductivity models. The evolution of the size and shape of calcite particles during the calcite precipitation experiment is estimated by our complex conductivity model. At the early stage of the calcite precipitation experiment, modelled particles sizes increase and calcite particles flatten with time because calcite crystals nucleate at the surface of glass beads and grow into larger calcite grains. At the later stage of the calcite precipitation experiment, modelled sizes and cementation exponents of calcite particles decrease with time because large calcite grains aggregate over multiple glass beads and only small calcite crystals polarize.

How does higher frequency monitoring data affect the calibration of a process-based water quality model?

NASA Astrophysics Data System (ADS)

Jackson-Blake, Leah; Helliwell, Rachel

2015-04-01

Process-based catchment water quality models are increasingly used as tools to inform land management. However, for such models to be reliable they need to be well calibrated and shown to reproduce key catchment processes. Calibration can be challenging for process-based models, which tend to be complex and highly parameterised. Calibrating a large number of parameters generally requires a large amount of monitoring data, spanning all hydrochemical conditions. However, regulatory agencies and research organisations generally only sample at a fortnightly or monthly frequency, even in well-studied catchments, often missing peak flow events. The primary aim of this study was therefore to investigate how the quality and uncertainty of model simulations produced by a process-based, semi-distributed catchment model, INCA-P (the INtegrated CAtchment model of Phosphorus dynamics), were improved by calibration to higher frequency water chemistry data. Two model calibrations were carried out for a small rural Scottish catchment: one using 18 months of daily total dissolved phosphorus (TDP) concentration data, another using a fortnightly dataset derived from the daily data. To aid comparability, calibrations were carried out automatically using the Markov Chain Monte Carlo - DiffeRential Evolution Adaptive Metropolis (MCMC-DREAM) algorithm. Calibration to daily data resulted in improved simulation of peak TDP concentrations and improved model performance statistics. Parameter-related uncertainty in simulated TDP was large when fortnightly data was used for calibration, with a 95% credible interval of 26 μg/l. This uncertainty is comparable in size to the difference between Water Framework Directive (WFD) chemical status classes, and would therefore make it difficult to use this calibration to predict shifts in WFD status. The 95% credible interval reduced markedly with the higher frequency monitoring data, to 6 μg/l. The number of parameters that could be reliably auto-calibrated was lower for the fortnightly data, with a physically unrealistic TDP simulation being produced when too many parameters were allowed to vary during model calibration. Parameters should not therefore be varied spatially for models such as INCA-P unless there is solid evidence that this is appropriate, or there is a real need to do so for the model to fulfil its purpose. This study highlights the potential pitfalls of using low frequency timeseries of observed water quality to calibrate complex process-based models. For reliable model calibrations to be produced, monitoring programmes need to be designed which capture system variability, in particular nutrient dynamics during high flow events. In addition, there is a need for simpler models, so that all model parameters can be included in auto-calibration and uncertainty analysis, and to reduce the data needs during calibration.

Structural Evolutions of STOCK Markets Controlled by Generalized Entropy Principles of Complex Systems

NASA Astrophysics Data System (ADS)

Wang, Yi Jiao; Feng, Qing Yi; Chai, Li He

As one of the most important financial markets and one of the main parts of economic system, the stock market has become the research focus in economics. The stock market is a typical complex open system far from equilibrium. Many available models that make huge contribution to researches on market are strong in describing the market however, ignoring strong nonlinear interactions among active agents and weak in reveal underlying dynamic mechanisms of structural evolutions of market. From econophysical perspectives, this paper analyzes the complex interactions among agents and defines the generalized entropy in stock markets. Nonlinear evolutionary dynamic equation for the stock markets is then derived from Maximum Generalized Entropy Principle. Simulations are accordingly conducted for a typical case with the given data, by which the structural evolution of the stock market system is demonstrated. Some discussions and implications are finally provided.

Evolution and development of brain networks: from Caenorhabditis elegans to Homo sapiens.

PubMed

Kaiser, Marcus; Varier, Sreedevi

2011-01-01

Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes involving a limited amount of tasks and modalities to complex functional and behavioral processing integrating different kinds of information from highly specialized tissue. However, studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. 'Small-world' topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms. In conclusion, evolutionary divergence leads to greater complexity while following essential developmental constraints.

From Evolutionary Allometry to Sexual Display: (A Reply to Holman and Bro-Jørgensen).

PubMed

Raia, Pasquale; Passaro, Federico; Carotenuto, Francesco; Meiri, Shai; Piras, Paolo

2016-08-01

Conventional wisdom holds that the complex shapes of deer antlers are produced under the sole influence of sexual selection. We questioned this view by demonstrating that trends for increased body size evolution passively yield more-complex ornaments, even in organisms where no effect of sexual selection is possible, with similar allometric slopes. Recent investigations suggest that sexual selection on antlers of larger deer species is stronger than that in smaller species; hence, the use of conspicuous antlers for display in large male deer is a secondary function driven by especially intense sexual selection on these large-bodied species. Since ancestral deer were small and had very simple antlers, such an intense selection on antlers shape was probably absent in early deer. Therefore, the evolution of complex ornaments is coupled with body size evolution, even in deer.

Linguistics: evolution and language change.

PubMed

Bowern, Claire

2015-01-05

Linguists have long identified sound changes that occur in parallel. Now novel research shows how Bayesian modeling can capture complex concerted changes, revealing how evolution of sounds proceeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

PubMed Central

Garvin, Michael R.; Bielawski, Joseph P.; Gharrett, Anthony J.

2011-01-01

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm. PMID:21969854

Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon.

PubMed

Garvin, Michael R; Bielawski, Joseph P; Gharrett, Anthony J

2011-01-01

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm.

T Cell Adaptive Immunity Proceeds through Environment-Induced Adaptation from the Exposure of Cryptic Genetic Variation

PubMed Central

Whitacre, James M.; Lin, Joseph; Harding, Angus

2011-01-01

Evolution is often characterized as a process involving incremental genetic changes that are slowly discovered and fixed in a population through genetic drift and selection. However, a growing body of evidence is finding that changes in the environment frequently induce adaptations that are much too rapid to occur by an incremental genetic search process. Rapid evolution is hypothesized to be facilitated by mutations present within the population that are silent or “cryptic” within the first environment but are co-opted or “exapted” to the new environment, providing a selective advantage once revealed. Although cryptic mutations have recently been shown to facilitate evolution in RNA enzymes, their role in the evolution of complex phenotypes has not been proven. In support of this wider role, this paper describes an unambiguous relationship between cryptic genetic variation and complex phenotypic responses within the immune system. By reviewing the biology of the adaptive immune system through the lens of evolution, we show that T cell adaptive immunity constitutes an exemplary model system where cryptic alleles drive rapid adaptation of complex traits. In naive T cells, normally cryptic differences in T cell receptor reveal diversity in activation responses when the cellular population is presented with a novel environment during infection. We summarize how the adaptive immune response presents a well studied and appropriate experimental system that can be used to confirm and expand upon theoretical evolutionary models describing how seemingly small and innocuous mutations can drive rapid cellular evolution. PMID:22363338

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems

PubMed Central

Yoshida, M. A.; Ogura, A.; Ikeo, K.; Shigeno, S.; Moritaki, T.; Winters, G. C.; Kohn, A. B.; Moroz, L. L.

2015-01-01

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called “evolutionary tinkering” or “co-option”, and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the “camera” eye from nautilus’ “pinhole” eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids’ opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. PMID:26002349

Netgram: Visualizing Communities in Evolving Networks

PubMed Central

Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

2015-01-01

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems. PMID:26356538

Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy

PubMed Central

Sheehan, Oliver; Gray, Russell D.; Atkinson, Quentin D.

2018-01-01

One of the defining trends of the Holocene has been the emergence of complex societies. Two essential features of complex societies are intensive resource use and sociopolitical hierarchy. Although it is widely agreed that these two phenomena are associated cross-culturally and have both contributed to the rise of complex societies, the causality underlying their relationship has been the subject of longstanding debate. Materialist theories of cultural evolution tend to view resource intensification as driving the development of hierarchy, but the reverse order of causation has also been advocated, along with a range of intermediate views. Phylogenetic methods have the potential to test between these different causal models. Here we report the results of a phylogenetic study that modeled the coevolution of one type of resource intensification—the development of landesque capital intensive agriculture—with political complexity and social stratification in a sample of 155 Austronesian-speaking societies. We found support for the coevolution of landesque capital with both political complexity and social stratification, but the contingent and nondeterministic nature of both of these relationships was clear. There was no indication that intensification was the “prime mover” in either relationship. Instead, the relationship between intensification and social stratification was broadly reciprocal, whereas political complexity was more of a driver than a result of intensification. These results challenge the materialist view and emphasize the importance of both material and social factors in the evolution of complex societies, as well as the complex and multifactorial nature of cultural evolution. PMID:29555760

Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

PubMed

Beck, Emily A; Llopart, Ana

2015-11-25

Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

Divide and conquer: intermediate levels of population fragmentation maximize cultural accumulation.

PubMed

Derex, Maxime; Perreault, Charles; Boyd, Robert

2018-04-05

Identifying the determinants of cumulative cultural evolution is a key issue in the interdisciplinary field of cultural evolution. A widely held view is that large and well-connected social networks facilitate cumulative cultural evolution because they promote the spread of useful cultural traits and prevent the loss of cultural knowledge through factors such as drift. This view stems from models that focus on the transmission of cultural information, without considering how new cultural traits actually arise. In this paper, we review the literature from various fields that suggest that, under some circumstances, increased connectedness can decrease cultural diversity and reduce innovation rates. Incorporating this idea into an agent-based model, we explore the effect of population fragmentation on cumulative culture and show that, for a given population size, there exists an intermediate level of population fragmentation that maximizes the rate of cumulative cultural evolution. This result is explained by the fact that fully connected, non-fragmented populations are able to maintain complex cultural traits but produce insufficient variation and so lack the cultural diversity required to produce highly complex cultural traits. Conversely, highly fragmented populations produce a variety of cultural traits but cannot maintain complex ones. In populations with intermediate levels of fragmentation, cultural loss and cultural diversity are balanced in a way that maximizes cultural complexity. Our results suggest that population structure needs to be taken into account when investigating the relationship between demography and cumulative culture.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Prebiotic coordination chemistry: The potential role of transition-metal complexes in the chemical evolution

NASA Technical Reports Server (NTRS)

Beck, M.

1979-01-01

In approaching the extremely involved and complex problem of the origin of life, consideration of the coordination chemistry appeared not only as a possibility but as a necessity. The first model experiments appear to be promising because of prebiotic-type synthesis by means of transition-metal complexes. It is especially significant that in some instances various types of vitally important substances (nucleic bases, amino acids) are formed simultaneously. There is ground to hope that systematic studies in this field will clarify the role of transition-metal complexes in the organizatorial phase of chemical evolution. It is obvious that researchers working in the fields of the chemistry of cyano and carbonyl complexes, and of the catalytic effect of transition-metal complexes are best suited to study these aspects of the attractive and interesting problem of the origin of life.

The natural science underlying big history.

PubMed

Chaisson, Eric J

2014-01-01

Nature's many varied complex systems-including galaxies, stars, planets, life, and society-are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density-contrasting with information content or entropy production-is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated.

The Natural Science Underlying Big History

PubMed Central

Chaisson, Eric J.

2014-01-01

Nature's many varied complex systems—including galaxies, stars, planets, life, and society—are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density—contrasting with information content or entropy production—is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated. PMID:25032228

The Manipulative Complexity of Lower Paleolithic Stone Toolmaking

PubMed Central

Faisal, Aldo; Stout, Dietrich; Apel, Jan; Bradley, Bruce

2010-01-01

Background Early stone tools provide direct evidence of human cognitive and behavioral evolution that is otherwise unavailable. Proper interpretation of these data requires a robust interpretive framework linking archaeological evidence to specific behavioral and cognitive actions. Methodology/Principal Findings Here we employ a data glove to record manual joint angles in a modern experimental toolmaker (the 4th author) replicating ancient tool forms in order to characterize and compare the manipulative complexity of two major Lower Paleolithic technologies (Oldowan and Acheulean). To this end we used a principled and general measure of behavioral complexity based on the statistics of joint movements. Conclusions/Significance This allowed us to confirm that previously observed differences in brain activation associated with Oldowan versus Acheulean technologies reflect higher-level behavior organization rather than lower-level differences in manipulative complexity. This conclusion is consistent with a scenario in which the earliest stages of human technological evolution depended on novel perceptual-motor capacities (such as the control of joint stiffness) whereas later developments increasingly relied on enhanced mechanisms for cognitive control. This further suggests possible links between toolmaking and language evolution. PMID:21072164

High Selection Pressure Promotes Increase in Cumulative Adaptive Culture

PubMed Central

Vegvari, Carolin; Foley, Robert A.

2014-01-01

The evolution of cumulative adaptive culture has received widespread interest in recent years, especially the factors promoting its occurrence. Current evolutionary models suggest that an increase in population size may lead to an increase in cultural complexity via a higher rate of cultural transmission and innovation. However, relatively little attention has been paid to the role of natural selection in the evolution of cultural complexity. Here we use an agent-based simulation model to demonstrate that high selection pressure in the form of resource pressure promotes the accumulation of adaptive culture in spite of small population sizes and high innovation costs. We argue that the interaction of demography and selection is important, and that neither can be considered in isolation. We predict that an increase in cultural complexity is most likely to occur under conditions of population pressure relative to resource availability. Our model may help to explain why culture change can occur without major environmental change. We suggest that understanding the interaction between shifting selective pressures and demography is essential for explaining the evolution of cultural complexity. PMID:24489724

Knowing the Natural World: The Construction of Knowledge about Evolution in and out of the Classroom

ERIC Educational Resources Information Center

Perkins, Alison Emily Havard

2009-01-01

Evolution is a central underlying concept to a significant number of discourses in civilized society, but the complexity of understanding basic tenets of this important theory is just now coming to light. Knowledge about evolution is constructed from both formal and "free-choice" opportunities, like television. Nature programs are commonly…

Bioprosthetic Mesh in Abdominal Wall Reconstruction

PubMed Central

Baumann, Donald P.; Butler, Charles E.

2012-01-01

Mesh materials have undergone a considerable evolution over the last several decades. There has been enhancement of biomechanical properties, improvement in manufacturing processes, and development of antiadhesive laminate synthetic meshes. The evolution of bioprosthetic mesh materials has markedly changed our indications and methods for complex abdominal wall reconstruction. The authors review the optimal properties of bioprosthetic mesh materials, their evolution over time, and their indications for use. The techniques to optimize outcomes are described using bioprosthetic mesh for complex abdominal wall reconstruction. Bioprosthetic mesh materials clearly have certain advantages over other implantable mesh materials in select indications. Appropriate patient selection and surgical technique are critical to the successful use of bioprosthetic materials for abdominal wall repair. PMID:23372454

[The evolution of human cultural behavior: notes on Darwinism and complexity].

PubMed

Peric, Mikael; Murrieta, Rui Sérgio Sereni

2015-12-01

The article analyzes three schools that can be understood as central in studies of the evolution of human behavior within the paradigm of evolution by natural selection: human behavioral ecology (HBE), evolutionary psychology, and dual inheritance. These three streams of thought are used to depict the Darwinist landscape and pinpoint its strong suits and limitations. Theoretical gaps were identified that seem to reduce these schools' ability to account for the diversity of human evolutionary behavior. Their weak points include issues related to the concept of reproductive success, types of adaptation, and targets of selection. An interdisciplinary approach is proposed as the solution to this dilemma, where complex adaptive systems would serve as a source.

Evolution of radiation resistance in a complex microenvironment

NASA Astrophysics Data System (ADS)

Kim, So Hyun; Austin, Robert; Mehta, Monal; Kahn, Atif

2013-03-01

Radiation treatment responses in brain cancers are typically associated with short progression-free intervals in highly lethal malignancies such as glioblastomas. Even as patients routinely progress through second and third line salvage therapies, which are usually empirically selected, surprisingly little information exists on how cancer cells evolve resistance. We will present experimental results showing how in the presence of complex radiation gradients evolution of resistance to radiation occurs. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

Irradiation-induced damage evolution in concentrated Ni-based alloys

DOE PAGES

Velisa, Gihan; Ullah, Mohammad Wali; Xue, Haizhou; ...

2017-06-06

Understanding the effects of chemical complexity from the number, type and concentration of alloying elements in single-phase concentred solid-solution alloys (SP-CSAs) on defect dynamics and microstructure evolution is pivotal for developing next-generation radiation-tolerant structural alloys. A specially chosen set of SP-CSAs with different chemical complexity (Ni 80Fe 20, Ni 80Cr 20 and Ni 40Fe 40Cr 20) are investigated using 1.5 MeV Mn ions over a wide fluence range, from 2 × 10 13 to 1 × 10 16 ions cm –2 at room temperature. Based on an integrated study of Rutherford backscattering spectroscopy in channeling geometry and molecular dynamics simulations,more » the results demonstrate that Ni 40Fe 40Cr 20 is more radiation tolerant than Ni 80Fe 20, Ni 80Cr 20 and elemental Ni in the low fluence regime. While chemical complexity of this set of SP-CSAs is clearly demonstrated to affect defect evolution through suppressed defect production and enhanced recombination at early stages, the effect of the mixed ferro- and anti-ferromagnetic interactions is not the only controlling factor responsible for the improved radiation performance. As a result, the observed strong alloying effect on defect evolution is attributed to the altered defect migration mobilities of defect clusters in these alloys, an intrinsic characteristic of the complex energy landscapes in CSAs.« less

Irradiation-induced damage evolution in concentrated Ni-based alloys

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

Velisa, Gihan; Ullah, Mohammad Wali; Xue, Haizhou

Understanding the effects of chemical complexity from the number, type and concentration of alloying elements in single-phase concentred solid-solution alloys (SP-CSAs) on defect dynamics and microstructure evolution is pivotal for developing next-generation radiation-tolerant structural alloys. A specially chosen set of SP-CSAs with different chemical complexity (Ni 80Fe 20, Ni 80Cr 20 and Ni 40Fe 40Cr 20) are investigated using 1.5 MeV Mn ions over a wide fluence range, from 2 × 10 13 to 1 × 10 16 ions cm –2 at room temperature. Based on an integrated study of Rutherford backscattering spectroscopy in channeling geometry and molecular dynamics simulations,more » the results demonstrate that Ni 40Fe 40Cr 20 is more radiation tolerant than Ni 80Fe 20, Ni 80Cr 20 and elemental Ni in the low fluence regime. While chemical complexity of this set of SP-CSAs is clearly demonstrated to affect defect evolution through suppressed defect production and enhanced recombination at early stages, the effect of the mixed ferro- and anti-ferromagnetic interactions is not the only controlling factor responsible for the improved radiation performance. As a result, the observed strong alloying effect on defect evolution is attributed to the altered defect migration mobilities of defect clusters in these alloys, an intrinsic characteristic of the complex energy landscapes in CSAs.« less

Evolution of the PWWP-domain encoding genes in the plant and animal lineages

PubMed Central

2012-01-01

Background Conserved domains are recognized as the building blocks of eukaryotic proteins. Domains showing a tendency to occur in diverse combinations (‘promiscuous’ domains) are involved in versatile architectures in proteins with different functions. Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity. Alternative models using domain-based phylogenetic trees propose that domains have become promiscuous independently in different lineages through convergent evolution and are, thus, random with no functional or structural preferences. Here we test whether complex protein architectures have occurred by accretion from simpler systems and whether the appearance of multidomain combinations parallels organismal complexity. As a model, we analyze the modular evolution of the PWWP domain and ask whether its appearance in combinations with other domains into multidomain architectures is linked with the occurrence of more complex life-forms. Whether high-level combinations of domains are conserved and transmitted as stable units (cassettes) through evolution is examined in the genomes of plant or metazoan species selected for their established position in the evolution of the respective lineages. Results Using the domain-tree approach, we analyze the evolutionary origins and distribution patterns of the promiscuous PWWP domain to understand the principles of its modular evolution and its existence in combination with other domains in higher-level protein architectures. We found that as a single module the PWWP domain occurs only in proteins with a limited, mainly, species-specific distribution. Earlier, it was suggested that domain promiscuity is a fast-changing (volatile) feature shaped by natural selection and that only a few domains retain their promiscuity status throughout evolution. In contrast, our data show that most of the multidomain PWWP combinations in extant multicellular organisms (humans or land plants) are present in their unicellular ancestral relatives suggesting they have been transmitted through evolution as conserved linear arrangements (‘cassettes’). Among the most interesting biologically relevant results is the finding that the genes of the two plant Trithorax family subgroups (ATX1/2 and ATX3/4/5) have different phylogenetic origins. The two subgroups occur together in the earliest land plants Physcomitrella patens and Selaginella moellendorffii. Conclusion Gain/loss of a single PWWP domain is observed throughout evolution reflecting dynamic lineage- or species-specific events. In contrast, higher-level protein architectures involving the PWWP domain have survived as stable arrangements driven by evolutionary descent. The association of PWWP domains with the DNA methyltransferases in O. tauri and in the metazoan lineage seems to have occurred independently consistent with convergent evolution. Our results do not support models wherein more complex protein architectures involving the PWWP domain occur with the appearance of more evolutionarily advanced life forms. PMID:22734652

Sex markets and sexual opportunity structures of behaviorally bisexual latino men in the urban metropolis of new york city.

PubMed

Garcia, Jonathan; Muñoz-Laboy, Miguel; Parker, Richard; Wilson, Patrick A

2014-04-01

Sex markets (the spatially and culturally bounded arenas) that shape bisexual behavior among Latino men have been utilized as a deterministic concept without a sufficient focus on the ability of individuals to make autonomous decisions within such arenas. We nuance the theory of sex markets using the concept of sexual opportunity structures to investigate the ways in which behaviorally bisexual Latino men in the urban metropolis of New York City navigate sexual geographies, cultural meaning systems, sexual scripts, and social institutions to configure their bisexual behaviors. Drawing on 60 in-depth interviews with bisexual Latino men in New York City, we first describe and analyze venues that constitute sexual geographies that facilitate and impede sexual interaction. These also allow for a degree of autonomy in decision-making, as men travel throughout the urban sexual landscape and sometimes even manage to reject norms, such as those imposed by Christian religion. We explore some of the cultural meaning systems and social institutions that regulate sex markets and influence individual decision-making. Secrecy and discretion-regulated by the family, masculinity, migration, and religion-only partially shaped sexual behavior and relationships. These factors create a flux in "equilibrium" in bisexual sex markets in which sociocultural-economic structures constantly interplay with human agency. This article contributes to the literature in identifying dynamic spaces for sexual health interventions that draw on individual agency and empowerment.

On Rainfall Modification by Major Urban Areas. Part 1; Observations from Space-borne Rain Radar on TRMM

NASA Technical Reports Server (NTRS)

Shepherd, J. Marshall; Pierce, Harold; Starr, David OC. (Technical Monitor)

2001-01-01

This study represents one of the first published attempts to identify rainfall modification by urban areas using satellite-based rainfall measurements. Data from the first space-based rain-radar, the Tropical Rainfall Measuring Mission's (TRMM) Precipitation Radar, are employed. Analysis of the data enables identification of rainfall patterns around Atlanta, Montgomery, Nashville, San Antonio, Waco, and Dallas during the warm season. Results reveal an average increase of -28% in monthly rainfall rates within 30-60 kilometers downwind of the metropolis with a modest increase of 5.6% over the metropolis. Portions of the downwind area exhibit increases as high as 51%. The percentage chances are relative to an upwind CONTROL area. It was also found that maximum rainfall rates in the downwind impact area can exceed the mean value in the upwind CONTROL area by 48%-116%. The maximum value was generally found at an average distance of 39 km from the edge of the urban center or 64 km from the center of the city. These results are consistent with METROMEX studies of St. Louis almost two decades ago and more recent studies near Atlanta. Future work will investi(yate hypothesized factors causing rainfall modification by urban areas. Additional work is also needed to provide more robust validation of space-based rain estimates near major urban areas. Such research has implications for urban planning, water resource management, and understanding human impact on the environment.

Sex Markets and Sexual Opportunity Structures of Behaviorally Bisexual Latino Men in the Urban Metropolis of New York City

PubMed Central

Garcia, Jonathan; Muñoz-Laboy, Miguel; Parker, Richard; Wilson, Patrick A.

2013-01-01

Sex markets (the spatially and culturally bounded arenas) that shape bisexual behavior among Latino men have been utilized as a deterministic concept without a sufficient focus on the ability of individuals to make autonomous decisions within such arenas. We nuance the theory of sex markets using the concept of sexual opportunity structures to investigate the ways in which behaviorally bisexual Latino men in the urban metropolis of New York City navigate sexual geographies, cultural meaning systems, sexual scripts, and social institutions to configure their bisexual behaviors. Drawing on 60 in-depth interviews with bisexual Latino men in New York city, we first describe and analyze venues that constitute sexual geographies that facilitate and impede sexual interaction. These also allow for a degree of autonomy in decision-making, as men travel throughout the urban sexual landscape and sometimes even manage to reject norms, such as those imposed by Christian religion. We explore some of the cultural meaning systems and social institutions that regulate sex markets and influence individual decision-making. Secrecy and discretion—regulated by the family, masculinity, migration, and religion—only partially shaped sexual behavior and relationships. These factors create a flux in “equilibrium” in bisexual sex markets in which sociocultural-economic structures constantly interplay with human agency. This article contributes to the literature in identifying dynamic spaces for sexual health interventions that draw on individual agency and empowerment. PMID:23479357

Current studies on bacterospermia the leading cause of male infertility: a protégé and potential threat towards mans extinction

PubMed Central

Isaiah, Ibeh Nnana; Nche, Bikwe Thomas; Nwagu, Ibeh Georgina; Nnanna, Ibeh Isaiah

2011-01-01

Background: The current rise of male infertility associated with bacterospermia and urogenital infection has been on the increase amongst adult married males in Benin metropolis and a major cause of concern to male fertility and reproduction in Nigeria. Aim: To microbiologically isolate and study the infectious agent that has led to male infertility and also to study the percentage occurrence of bacteropsermia and urogenital caused infertility in adult married males in Benin metropolis Material and Method: using standard microbiological methods of isolating and identifying the organism, specimen was collected and processed which includes the susceptibility profile of isolates and sperm quality. In this study a total of 140 sperm samples was collected from patient who were referred from the consultant outpatient department of the University of Benin Teaching Hospital and then evaluated bacteriologically using standard bacterial cultural methods Results: Among the total cases, 92 (65.7%) showed at least one pathogen. Staphylococcus aureus (28.3%), Staphylococcus Saprophyticus (13.0%), Pseudomonas aerouginosa (6.5%), Escherichia Coli (19.6%) Proteus mirabilis (10.8%) Klebsiella spp (10.8%) and Proteus vulgaris (10.8%). Conclusion: There was an outstanding significant relationship between bacteriospermia and the rate of total motility and morphologically abnormal sperms, The percentage of morphologically normal sperm was lower in this study. Staphylococcus aureus Staphylococcus saprohyticus and Escherichia coli were the most common pathogen having negative effects on sperm motility and morphology in this study. PMID:22363079

Chlorine treatment effectiveness and physico-chemical and bacteriological characteristics of treated water supplies in distribution networks of Accra-Tema Metropolis, Ghana

NASA Astrophysics Data System (ADS)

Karikari, A. Y.; Ampofo, J. A.

2013-06-01

Drinking water quality from two major treatment plants in Ghana; Kpong and Weija Plants, and distribution networks in the Accra-Tema Metropolis were monitored monthly for a year at fifteen different locations. The study determined the relationship between chlorine residual, other physico-chemical qualities of the treated water, and, bacteria regrowth. Results indicated that the treated water at the Kpong and Weija Treatment Plants conformed to WHO guidelines for potable water. However, the water quality deteriorated bacteriologically, from the plants to the delivery points with high numbers of indicator and opportunistic pathogens. This could be due to inadequate disinfection residual, biofilms or accidental point source contamination by broken pipes, installation and repair works. The mean turbidity ranged from 1.6 to 2.4 NTU; pH varied from 6.8 to 7.4; conductivity fluctuated from 71.1 to 293 μS/cm. Chlorine residual ranged from 0.13 to 1.35 mg/l. High residual chlorine was observed at the treatment plants, which decreased further from the plants. Results showed that additional chlorination does not take place at the booster stations. Chlorine showed inverse relationship with microbial counts. Total coliform bacteria ranged from 0 to 248 cfu/100 ml, and faecal coliform values varied from 0 to 128 cfu/100 ml. Other microorganisms observed in the treated water included Aeromonas spp., Clostridium spp. and Pseudomonas spp. Boiling water in the household before consumption will reduce water-related health risks.

Nonlinear stochastic interacting dynamics and complexity of financial gasket fractal-like lattice percolation

NASA Astrophysics Data System (ADS)

Zhang, Wei; Wang, Jun

2018-05-01

A novel nonlinear stochastic interacting price dynamics is proposed and investigated by the bond percolation on Sierpinski gasket fractal-like lattice, aim to make a new approach to reproduce and study the complexity dynamics of real security markets. Fractal-like lattices correspond to finite graphs with vertices and edges, which are similar to fractals, and Sierpinski gasket is a well-known example of fractals. Fractional ordinal array entropy and fractional ordinal array complexity are introduced to analyze the complexity behaviors of financial signals. To deeper comprehend the fluctuation characteristics of the stochastic price evolution, the complexity analysis of random logarithmic returns and volatility are preformed, including power-law distribution, fractional sample entropy and fractional ordinal array complexity. For further verifying the rationality and validity of the developed stochastic price evolution, the actual security market dataset are also studied with the same statistical methods for comparison. The empirical results show that this stochastic price dynamics can reconstruct complexity behaviors of the actual security markets to some extent.

Star-Forming Regions in Orion as a Dust Evolution Laboratory

NASA Astrophysics Data System (ADS)

Wiebe, D.; Murga, M.; Sivkova, E.

2017-06-01

Star-forming regions (SFR) represent a convenient opportunity to study various processes related both to dust growth and to dust destruction. While extragalactic SFRs allow considering these processes in a wide range of metallicities, UV field intensities, etc., the Orion star-forming complex opens up a possibility to observe dust evolution with an unprecedented angular resolution. We review various observations related to dust evolution in some most prominent Orion regions, paying special attention to organic dust evolution, and introduce a new model of organic dust evolution.

Population aging and its impacts: strategies of the health-care system in Taipei.

PubMed

Lin, Ming-Hsien; Chou, Ming-Yueh; Liang, Chih-Kuang; Peng, Li-Ning; Chen, Liang-Kung

2010-11-01

Taiwan is one of the fastest aging countries in the world. As such, the government has developed various strategies to promote an age-friendly health-care system. Health services are supported by National Health Insurance (NHI), which insures over 97% of citizens and over 99% of health-care institutes. The current health-care system has difficulties in caring for older patients with multiple comorbidities, complex care needs, functional impairments, and post-acute care needs. Taipei, an international metropolis with a well-preserved tradition of filial piety in Chinese societies, has developed various strategies to overcome the aforementioned barriers to an age-friendly health-care system. These include an emphasis on general medical care and a holistic approach in all specialties, development of a geriatrics specialty training program, development of post-acute services, and strengthening of linkages between health and social care services. Despite achievements thus far, challenges still include creating a more extensive integration between medical specialties, promotion of an interdisciplinary care model across specialties and health-care settings, and integration of health and social care services. The experiences of Taipei in developing an age-friendly health-care service system may be a culturally appropriate model for other Chinese and Asian communities. Copyright © 2010 Elsevier B.V. All rights reserved.

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

Gencaga, Deniz; Knuth, Kevin H.; Carbon, Duane F.

Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This ismore » a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.« less

Modeling of protein-anion exchange resin interaction for the human growth hormone charge variants.

PubMed

Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E

2015-12-01

Modeling ion exchange chromatography (IEC) behavior has generated significant interest because of the wide use of IEC as an analytical technique as well as a preparative protein purification process; indeed there is a need for better understanding of what drives the unique behavior of protein charge variants. We hypothesize that a complex protein molecule, which contains both hydrophobic and charged moieties, would interact strongly with an in silico designed resin through charged electrostatic patches on the surface of the protein. In the present work, variants of recombinant human growth hormone that mimic naturally-occurring deamidation products were produced and characterized in silico. The study included these four variants: rhGH, N149D, N152D, and N149D/N152D. Poisson-Boltzmann calculations were used to determine surface electrostatic potential. Metropolis Monte Carlo simulations were carried out with the resulting variants to simulate IEC systems, examining the free energy of the interaction of the protein with an in silico anion exchange column represented by polylysine polypeptide. The results show that the charge variants have different average binding energies and the free energy of interaction can be used to predict the retention time for the different variants. Copyright © 2015 Elsevier B.V. All rights reserved.

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

PubMed

Chodera, John D; Shirts, Michael R

2011-11-21

The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in discovering new ways to enhance the phase space mixing of these protocols in order to improve sampling of uncorrelated configurations. Here, we demonstrate how both of these classes of algorithms can be considered as special cases of Gibbs sampling within a Markov chain Monte Carlo framework. Gibbs sampling is a well-studied scheme in the field of statistical inference in which different random variables are alternately updated from conditional distributions. While the update of the conformational degrees of freedom by Metropolis Monte Carlo or molecular dynamics unavoidably generates correlated samples, we show how judicious updating of the thermodynamic state indices--corresponding to thermodynamic parameters such as temperature or alchemical coupling variables--can substantially increase mixing while still sampling from the desired distributions. We show how state update methods in common use can lead to suboptimal mixing, and present some simple, inexpensive alternatives that can increase mixing of the overall Markov chain, reducing simulation times necessary to obtain estimates of the desired precision. These improved schemes are demonstrated for several common applications, including an alchemical expanded ensemble simulation, parallel tempering, and multidimensional replica exchange umbrella sampling.

The Manhattan Frame Model-Manhattan World Inference in the Space of Surface Normals.

PubMed

Straub, Julian; Freifeld, Oren; Rosman, Guy; Leonard, John J; Fisher, John W

2018-01-01

Objects and structures within man-made environments typically exhibit a high degree of organization in the form of orthogonal and parallel planes. Traditional approaches utilize these regularities via the restrictive, and rather local, Manhattan World (MW) assumption which posits that every plane is perpendicular to one of the axes of a single coordinate system. The aforementioned regularities are especially evident in the surface normal distribution of a scene where they manifest as orthogonally-coupled clusters. This motivates the introduction of the Manhattan-Frame (MF) model which captures the notion of an MW in the surface normals space, the unit sphere, and two probabilistic MF models over this space. First, for a single MF we propose novel real-time MAP inference algorithms, evaluate their performance and their use in drift-free rotation estimation. Second, to capture the complexity of real-world scenes at a global scale, we extend the MF model to a probabilistic mixture of Manhattan Frames (MMF). For MMF inference we propose a simple MAP inference algorithm and an adaptive Markov-Chain Monte-Carlo sampling algorithm with Metropolis-Hastings split/merge moves that let us infer the unknown number of mixture components. We demonstrate the versatility of the MMF model and inference algorithm across several scales of man-made environments.

The Evolution of the Exponent of Zipf's Law in Language Ontogeny

PubMed Central

Baixeries, Jaume; Elvevåg, Brita; Ferrer-i-Cancho, Ramon

2013-01-01

It is well-known that word frequencies arrange themselves according to Zipf's law. However, little is known about the dependency of the parameters of the law and the complexity of a communication system. Many models of the evolution of language assume that the exponent of the law remains constant as the complexity of a communication systems increases. Using longitudinal studies of child language, we analysed the word rank distribution for the speech of children and adults participating in conversations. The adults typically included family members (e.g., parents) or the investigators conducting the research. Our analysis of the evolution of Zipf's law yields two main unexpected results. First, in children the exponent of the law tends to decrease over time while this tendency is weaker in adults, thus suggesting this is not a mere mirror effect of adult speech. Second, although the exponent of the law is more stable in adults, their exponents fall below 1 which is the typical value of the exponent assumed in both children and adults. Our analysis also shows a tendency of the mean length of utterances (MLU), a simple estimate of syntactic complexity, to increase as the exponent decreases. The parallel evolution of the exponent and a simple indicator of syntactic complexity (MLU) supports the hypothesis that the exponent of Zipf's law and linguistic complexity are inter-related. The assumption that Zipf's law for word ranks is a power-law with a constant exponent of one in both adults and children needs to be revised. PMID:23516390

Dehydration-driven evolution of topological complexity in ethylamonium uranyl selenates

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

Gurzhiy, Vladislav V., E-mail: vladgeo17@mail.ru; Krivovichev, Sergey V.; Tananaev, Ivan G.

Single crystals of four novel uranyl selenate and selenite-selenate oxysalts with protonated ethylamine molecules, (C{sub 2}H{sub 8}N){sub 2}[(UO{sub 2})(SeO{sub 4}){sub 2}(H{sub 2}O)](H{sub 2}O) (I), (C{sub 2}H{sub 8}N){sub 3}[(UO{sub 2})(SeO{sub 4}){sub 2}(HSeO{sub 4})] (II), (C{sub 2}H{sub 8}N)[(UO{sub 2})(SeO{sub 4})(HSeO{sub 3})] (III), and (C{sub 2}H{sub 8}N)(H{sub 3}O)[(UO{sub 2})(SeO{sub 4}){sub 2}(H{sub 2}O)] (IV) have been prepared by isothermal evaporation from aqueous solutions. Uranyl-containing 1D and 2D units have been investigated using topological approach and information-based complexity measurements that demonstrate the evolution of structural units and the increase of topological complexity with the decrease of H{sub 2}O content. - Graphical abstract: Single crystals ofmore » four novel uranyl selenate and selenite-selenate oxysalts with protonated ethylamine molecules have been prepared by isothermal evaporation from aqueous solutions. Structural analysis and information-based topological complexity calculations points to the possible sequence of crystalline phases formation, showing both topological and structural branches of evolution. - Highlights: • Single crystals of four novel uranyl oxysalts were prepared by evaporation method. • The graph theory was used for investigation of topologies of structural units. • Dehydration processes drives the evolution of topological complexity of 1D and 2D structural units.« less

Evolution of complex higher brain centers and behaviors: behavioral correlates of mushroom body elaboration in insects.

PubMed

Farris, Sarah M

2013-01-01

Large, complex higher brain centers have evolved many times independently within the vertebrates, but the selective pressures driving these acquisitions have been difficult to pinpoint. It is well established that sensory brain centers become larger and more structurally complex to accommodate processing of a particularly important sensory modality. When higher brain centers such as the cerebral cortex become greatly expanded in a particular lineage, it is likely to support the coordination and execution of more complex behaviors, such as those that require flexibility, learning, and social interaction, in response to selective pressures that made these new behaviors advantageous. Vertebrate studies have established a link between complex behaviors, particularly those associated with sociality, and evolutionary expansions of telencephalic higher brain centers. Enlarged higher brain centers have convergently evolved in groups such as the insects, in which multimodal integration and learning and memory centers called the mushroom bodies have become greatly elaborated in at least four independent lineages. Is it possible that similar selective pressures acting on equivalent behavioral outputs drove the evolution of large higher brain centers in all bilaterians? Sociality has greatly impacted brain evolution in vertebrates such as primates, but it has not been a major driver of higher brain center enlargement in insects. However, feeding behaviors requiring flexibility and learning are associated with large higher brain centers in both phyla. Selection for the ability to support behavioral flexibility appears to be a common thread underlying the evolution of large higher brain centers, but the precise nature of these computations and behaviors may vary. © 2013 S. Karger AG, Basel.

Effect of self-interaction on the evolution of cooperation in complex topologies

NASA Astrophysics Data System (ADS)

Wu, Yu'e.; Zhang, Zhipeng; Chang, Shuhua

2017-09-01

Self-interaction, as a significant mechanism explaining the evolution of cooperation, has attracted great attention both theoretically and experimentally. In this text, we consider a new self-interaction mechanism in the two typical pairwise models including the prisoner's dilemma and the snowdrift games, where the cooperative agents will gain extra bonus for their selfless behavior. We find that under the mechanism the collective cooperation is elevated to a very high level especially after adopting the finite population analogue of replicator dynamics for evolution. The robustness of the new mechanism is tested for different complex topologies for the prisoner's dilemma game. All the presented results demonstrate that the enhancement effects are independent of the structure of the applied spatial networks and the potential evolutionary games, and thus showing a high degree of universality. Our conclusions might shed light on the understanding of the evolution of cooperation in the real world.

Directed Evolution as a Powerful Synthetic Biology Tool

PubMed Central

Cobb, Ryan E.; Sun, Ning; Zhao, Huimin

2012-01-01

At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels. PMID:22465795

Extended evolution: A conceptual framework for integrating regulatory networks and niche construction

PubMed Central

Renn, Jürgen

2015-01-01

ABSTRACT This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path‐dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 565–577, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26097188

Creationism and intelligent design.

PubMed

Pennock, Robert T

2003-01-01

Creationism, the rejection of evolution in favor of supernatural design, comes in many varieties besides the common young-earth Genesis version. Creationist attacks on science education have been evolving in the last few years through the alliance of different varieties. Instead of calls to teach "creation science," one now finds lobbying for "intelligent design" (ID). Guided by the Discovery Institute's "Wedge strategy," the ID movement aims to overturn evolution and what it sees as a pernicious materialist worldview and to renew a theistic foundation to Western culture, in which human beings are recognized as being created in the image of God. Common ID arguments involving scientific naturalism, "irreducible complexity," "complex specified information," and "icons of evolution," have been thoroughly examined and refuted. Nevertheless, from Kansas to Ohio to the U.S. Congress, ID continues lobbying to teach the controversy, and scientists need to be ready to defend good evolution education.

Unraveling the Complexity of the Evolution of the Sun's Photospheric Magnetic Field

NASA Astrophysics Data System (ADS)

Hathaway, David H.

2016-10-01

Given the emergence of tilted, bipolar active regions, surface flux transport has been shown to reproduce much of the complex evolution of the Sun's photospheric magnetic field. Surface flux is transported by flows in the surface shear layer - the axisymmetric differential rotation and meridional flow and the non-axisymmetric convective motions (granules, supergranules, and giant cells). We have measured these flows by correlation tracking of the magnetic elements themselves, correlation tracking of the Doppler features (supergranules), and by direct Doppler measurements using SDO/HMI data. These measurements fully constrain (with no free parameters) the flows used in our surface flux transport code - the Advective Flux Transport or AFT code. Here we show the up-to-date evolution of these flows, their impact on the detailed evolution of the Sun's photospheric magnetic field, and predictions for what the polar fields will be at the next minimum in 2020.

Radiation damage buildup and dislocation evolution in Ni and equiatomic multicomponent Ni-based alloys

NASA Astrophysics Data System (ADS)

Levo, E.; Granberg, F.; Fridlund, C.; Nordlund, K.; Djurabekova, F.

2017-07-01

Single-phase multicomponent alloys of equal atomic concentrations ("equiatomic") have proven to exhibit promising mechanical and corrosion resistance properties, that are sought after in materials intended for use in hazardous environments like next-generation nuclear reactors. In this article, we investigate the damage production and dislocation mobility by simulating irradiation of elemental Ni and the alloys NiCo, NiCoCr, NiCoFe and NiFe, to assess the effect of elemental composition. We compare the defect production and the evolution of dislocation networks in the simulation cells of two different sizes, for all five studied materials. We find that the trends in defect evolution are in good agreement between the different cell sizes. The damage is generally reduced with increased alloy complexity, and the dislocation evolution is specific to each material, depending on its complexity. We show that increasing complexity of the alloys does not always lead to decreased susceptibility to damage accumulation under irradiation. We show that, for instance, the NiCo alloy behaves very similarly to Ni, while presence of Fe or Cr in the alloy even as a third component reduces the saturated level of damage substantially. Moreover, we linked the defect evolution with the dislocation transformations in the alloys. Sudden drops in defect number and large defect fluctuations from the continuous irradiation can be explained from the dislocation activity.

Measuring the Evolution of Ontology Complexity: The Gene Ontology Case Study

PubMed Central

Dameron, Olivier; Bettembourg, Charles; Le Meur, Nolwenn

2013-01-01

Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent branches, i.e. biological processes (BP), cellular components (CC) and molecular functions (MF). For each case, we measured complexity by computing metrics related to the size, the nodes connectivity and the hierarchical structure. The number of classes and relations increased monotonously for each branch, with different growth rates. BP and CC had similar connectivity, superior to that of MF. Connectivity increased monotonously for BP, decreased for CC and remained stable for MF, with a marked increase for the three branches in November and December 2012. Hierarchy-related measures showed that CC and MF had similar proportions of leaves, average depths and average heights. BP had a lower proportion of leaves, and a higher average depth and average height. For BP and MF, the late 2012 increase of connectivity resulted in an increase of the average depth and average height and a decrease of the proportion of leaves, indicating that a major enrichment effort of the intermediate-level hierarchy occurred. The variation of the number of classes and relations in an ontology does not provide enough information about the evolution of its complexity. However, connectivity and hierarchy-related metrics revealed different patterns of values as well as of evolution for the three branches of the Gene Ontology. CC was similar to BP in terms of connectivity, and similar to MF in terms of hierarchy. Overall, BP complexity increased, CC was refined with the addition of leaves providing a finer level of annotations but decreasing slightly its complexity, and MF complexity remained stable. PMID:24146805

The macroevolution of size and complexity in insect male genitalia

PubMed Central

Rudoy, Andrey

2016-01-01

The evolution of insect male genitalia has received much attention, but there is still a lack of data on the macroevolutionary origin of its extraordinary variation. We used a calibrated molecular phylogeny of 71 of the 150 known species of the beetle genus Limnebius to study the evolution of the size and complexity of the male genitalia in its two subgenera, Bilimneus, with small species with simple genitalia, and Limnebius s.str., with a much larger variation in size and complexity. We reconstructed ancestral values of complexity (perimeter and fractal dimension of the aedeagus) and genital and body size with Bayesian methods. Complexity evolved more in agreement with a Brownian model, although with evidence of weak directional selection to a decrease or increase in complexity in the two subgenera respectively, as measured with an excess of branches with negative or positive change. On the contrary, aedeagus size, the variable with the highest rates of evolution, had a lower phylogenetic signal, without significant differences between the two subgenera in the average change of the individual branches of the tree. Aedeagus size also had a lower correlation with time and no evidence of directional selection. Rather than to directional selection, it thus seems that the higher diversity of the male genitalia in Limnebius s.str. is mostly due to the larger variance of the phenotypic change in the individual branches of the tree for all measured variables. PMID:27114865

Benchmarking wide swath altimetry-based river discharge estimation algorithms for the Ganges river system

NASA Astrophysics Data System (ADS)

Bonnema, Matthew G.; Sikder, Safat; Hossain, Faisal; Durand, Michael; Gleason, Colin J.; Bjerklie, David M.

2016-04-01

The objective of this study is to compare the effectiveness of three algorithms that estimate discharge from remotely sensed observables (river width, water surface height, and water surface slope) in anticipation of the forthcoming NASA/CNES Surface Water and Ocean Topography (SWOT) mission. SWOT promises to provide these measurements simultaneously, and the river discharge algorithms included here are designed to work with these data. Two algorithms were built around Manning's equation, the Metropolis Manning (MetroMan) method, and the Mean Flow and Geomorphology (MFG) method, and one approach uses hydraulic geometry to estimate discharge, the at-many-stations hydraulic geometry (AMHG) method. A well-calibrated and ground-truthed hydrodynamic model of the Ganges river system (HEC-RAS) was used as reference for three rivers from the Ganges River Delta: the main stem of Ganges, the Arial-Khan, and the Mohananda Rivers. The high seasonal variability of these rivers due to the Monsoon presented a unique opportunity to thoroughly assess the discharge algorithms in light of typical monsoon regime rivers. It was found that the MFG method provides the most accurate discharge estimations in most cases, with an average relative root-mean-squared error (RRMSE) across all three reaches of 35.5%. It is followed closely by the Metropolis Manning algorithm, with an average RRMSE of 51.5%. However, the MFG method's reliance on knowledge of prior river discharge limits its application on ungauged rivers. In terms of input data requirement at ungauged regions with no prior records, the Metropolis Manning algorithm provides a more practical alternative over a region that is lacking in historical observations as the algorithm requires less ancillary data. The AMHG algorithm, while requiring the least prior river data, provided the least accurate discharge measurements with an average wet and dry season RRMSE of 79.8% and 119.1%, respectively, across all rivers studied. This poor performance is directly traced to poor estimation of AMHG via a remotely sensed proxy, and results improve commensurate with MFG and MetroMan when prior AMHG information is given to the method. Therefore, we cannot recommend use of AMHG without inclusion of this prior information, at least for the studied rivers. The dry season discharge (within-bank flow) was captured well by all methods, while the wet season (floodplain flow) appeared more challenging. The picture that emerges from this study is that a multialgorithm approach may be appropriate during flood inundation periods in Ganges Delta.

Playing evolution in the laboratory: From the first major evolutionary transition to global warming

NASA Astrophysics Data System (ADS)

Fragata, Inês; Simões, Pedro; Matos, Margarida; Szathmáry, Eörs; Santos, Mauro

2018-05-01

Experimental evolution allows testing hypotheses derived from theory or from observed patterns in nature. We have designed a droplet-based microfluidic “evolution machine” to test how transient compartmentalization (“trait-groups”) of independent molecular replicators (likely a critical step in the origin of life) could have prevented the spread of parasitic mutants; that is, inactive RNAs that have been reported to spoil a system of free replicators. In remarkable agreement with the theory, we show that this simple population structure was sufficient to prevent takeover by inactive RNAs. A more complex scenario arises when we use experimental evolution to test field-derived hypotheses; for instance, the idea that temperature is driving genetic spatiotemporal patterns of climate change. In the fly Drosophila subobscura, latitudinal clines in gene arrangement frequencies occur worldwide, and more equatorial gene arrangements are becoming more frequent at higher latitudes as a correlated response to climate change. However, the evolution at different constant temperatures in the laboratory was not consistent with patterns in nature, suggesting some limitations of experimental evolution. Finally, also in D. subobscura, we show that repeatability in experimental evolution is staggeringly consistent for life history traits, making evolution quite predictable and suggesting that laboratory selection can quickly erase differences between populations. Yet, the genetic paths used to attain the same adaptive phenotypes are complex and unpredictable. Contribution to the Focus Issue Evolutionary Modeling and Experimental Evolution edited by José Cuesta, Joachim Krug and Susanna Manrubia.

Transforming Misconceptions: Using Transformative Experience to Promote Positive Affect and Conceptual Change in Students Learning about Biological Evolution

ERIC Educational Resources Information Center

Heddy, Benjamin C.; Sinatra, Gale M.

2013-01-01

Teaching and learning about complex scientific content, such as biological evolution, is challenging in part because students have a difficult time seeing the relevance of evolution in their everyday lives. The purpose of this study was to explore the effectiveness of the Teaching for Transformative Experiences in Science (TTES) model (Pugh, 2002)…

Active Cocatalysts for Photocatalytic Hydrogen Evolution Derived from Nickel or Cobalt Amine Complexes.

PubMed

Huang, Yi; Zhang, Bin

2017-11-20

A cost-effective and robust strategy for the anchoring of molecular hydrogen evolution cocatalysts onto semiconductors has recently been reported. The composite materials were highly efficient and stable towards photocatalytic H 2 evolution. This study provides guidance for the design and construction of highly active heterogeneous photocatalysts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems.

PubMed

Yoshida, M A; Ogura, A; Ikeo, K; Shigeno, S; Moritaki, T; Winters, G C; Kohn, A B; Moroz, L L

2015-12-01

Coleoid cephalopods show remarkable evolutionary convergence with vertebrates in their neural organization, including (1) eyes and visual system with optic lobes, (2) specialized parts of the brain controlling learning and memory, such as vertical lobes, and (3) unique vasculature supporting such complexity of the central nervous system. We performed deep sequencing of eye transcriptomes of pygmy squids (Idiosepius paradoxus) and chambered nautiluses (Nautilus pompilius) to decipher the molecular basis of convergent evolution in cephalopods. RNA-seq was complemented by in situ hybridization to localize the expression of selected genes. We found three types of genomic innovations in the evolution of complex brains: (1) recruitment of novel genes into morphogenetic pathways, (2) recombination of various coding and regulatory regions of different genes, often called "evolutionary tinkering" or "co-option", and (3) duplication and divergence of genes. Massive recruitment of novel genes occurred in the evolution of the "camera" eye from nautilus' "pinhole" eye. We also showed that the type-2 co-option of transcription factors played important roles in the evolution of the lens and visual neurons. In summary, the cephalopod convergent morphological evolution of the camera eyes was driven by a mosaic of all types of gene recruitments. In addition, our analysis revealed unexpected variations of squids' opsins, retinochromes, and arrestins, providing more detailed information, valuable for further research on intra-ocular and extra-ocular photoreception of the cephalopods. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Coevolution of landesque capital intensive agriculture and sociopolitical hierarchy.

PubMed

Sheehan, Oliver; Watts, Joseph; Gray, Russell D; Atkinson, Quentin D

2018-04-03

One of the defining trends of the Holocene has been the emergence of complex societies. Two essential features of complex societies are intensive resource use and sociopolitical hierarchy. Although it is widely agreed that these two phenomena are associated cross-culturally and have both contributed to the rise of complex societies, the causality underlying their relationship has been the subject of longstanding debate. Materialist theories of cultural evolution tend to view resource intensification as driving the development of hierarchy, but the reverse order of causation has also been advocated, along with a range of intermediate views. Phylogenetic methods have the potential to test between these different causal models. Here we report the results of a phylogenetic study that modeled the coevolution of one type of resource intensification-the development of landesque capital intensive agriculture-with political complexity and social stratification in a sample of 155 Austronesian-speaking societies. We found support for the coevolution of landesque capital with both political complexity and social stratification, but the contingent and nondeterministic nature of both of these relationships was clear. There was no indication that intensification was the "prime mover" in either relationship. Instead, the relationship between intensification and social stratification was broadly reciprocal, whereas political complexity was more of a driver than a result of intensification. These results challenge the materialist view and emphasize the importance of both material and social factors in the evolution of complex societies, as well as the complex and multifactorial nature of cultural evolution. Copyright © 2018 the Author(s). Published by PNAS.

Digest: Context matters: The effects of light environment and female presence on the structure of wolf spider courtship displays.

PubMed

Fialko, Kristina

2018-05-01

Does variation in the environment in which a signal is presented affect the components of a complex, ritualized animal display? Using a signal phenotype network, Rosenthal et al. (2018) found that light and female presence alter the structure of wolf spider courtship displays, providing evidence that complex signaling behaviors may be modified depending on the social and environmental context. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

PubMed Central

He, Yi-Ming; Ma, Bin-Guang

2016-01-01

Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions. PMID:27220911

Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

NASA Astrophysics Data System (ADS)

He, Yi-Ming; Ma, Bin-Guang

2016-05-01

Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii

PubMed Central

Ratcliff, William C.; Herron, Matthew D.; Howell, Kathryn; Pentz, Jennifer T.; Rosenzweig, Frank; Travisano, Michael

2013-01-01

The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. Here we show that multicellular complexity, including development from a single cell, can evolve rapidly in a unicellular organism that has never had a multicellular ancestor. We subject the alga Chlamydomonas reinhardtii to conditions that favour multicellularity, resulting in the evolution of a multicellular life cycle in which clusters reproduce via motile unicellular propagules. While a single-cell genetic bottleneck during ontogeny is widely regarded as an adaptation to limit among-cell conflict, its appearance very early in this transition suggests that it did not evolve for this purpose. Instead, we find that unicellular propagules are adaptive even in the absence of intercellular conflict, maximizing cluster-level fecundity. These results demonstrate that the unicellular bottleneck, a trait essential for evolving multicellular complexity, can arise rapidly via co-option of the ancestral unicellular form. PMID:24193369

Models and observations of Arctic melt ponds

NASA Astrophysics Data System (ADS)

Golden, K. M.

2016-12-01

During the Arctic melt season, the sea ice surface undergoes a striking transformation from vast expanses of snow covered ice to complex mosaics of ice and melt ponds. Sea ice albedo, a key parameter in climate modeling, is largely determined by the complex evolution of melt pond configurations. In fact, ice-albedo feedback has played a significant role in the recent declines of the summer Arctic sea ice pack. However, understanding melt pond evolution remains a challenge to improving climate projections. It has been found that as the ponds grow and coalesce, the fractal dimension of their boundaries undergoes a transition from 1 to about 2, around a critical length scale of 100 square meters in area. As the ponds evolve they take complex, self-similar shapes with boundaries resembling space-filling curves. I will outline how mathematical models of composite materials and statistical physics, such as percolation and Ising models, are being used to describe this evolution and predict key geometrical parameters that agree very closely with observations.

Complex temporal topic evolution modelling using the Kullback-Leibler divergence and the Bhattacharyya distance.

PubMed

Andrei, Victor; Arandjelović, Ognjen

2016-12-01

The rapidly expanding corpus of medical research literature presents major challenges in the understanding of previous work, the extraction of maximum information from collected data, and the identification of promising research directions. We present a case for the use of advanced machine learning techniques as an aide in this task and introduce a novel methodology that is shown to be capable of extracting meaningful information from large longitudinal corpora and of tracking complex temporal changes within it. Our framework is based on (i) the discretization of time into epochs, (ii) epoch-wise topic discovery using a hierarchical Dirichlet process-based model, and (iii) a temporal similarity graph which allows for the modelling of complex topic changes. More specifically, this is the first work that discusses and distinguishes between two groups of particularly challenging topic evolution phenomena: topic splitting and speciation and topic convergence and merging, in addition to the more widely recognized emergence and disappearance and gradual evolution. The proposed framework is evaluated on a public medical literature corpus.

LMC: Logarithmantic Monte Carlo

NASA Astrophysics Data System (ADS)

Mantz, Adam B.

2017-06-01

LMC is a Markov Chain Monte Carlo engine in Python that implements adaptive Metropolis-Hastings and slice sampling, as well as the affine-invariant method of Goodman & Weare, in a flexible framework. It can be used for simple problems, but the main use case is problems where expensive likelihood evaluations are provided by less flexible third-party software, which benefit from parallelization across many nodes at the sampling level. The parallel/adaptive methods use communication through MPI, or alternatively by writing/reading files, and mostly follow the approaches pioneered by CosmoMC (ascl:1106.025).

Simulating the Rayleigh-Taylor instability with the Ising model

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

Ball, Justin R.; Elliott, James B.

2011-08-26

The Ising model, implemented with the Metropolis algorithm and Kawasaki dynamics, makes a system with its own physics, distinct from the real world. These physics are sophisticated enough to model behavior similar to the Rayleigh-Taylor instability and by better understanding these physics, we can learn how to modify the system to better re ect reality. For example, we could add a v x and a v y to each spin and modify the exchange rules to incorporate them, possibly using two body scattering laws to construct a more realistic system.

Lattice QCD calculation using VPP500

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

Kim, Seyong; Ohta, Shigemi

1995-02-01

A new vector parallel supercomputer, Fujitsu VPP500, was installed at RIKEN earlier this year. It consists of 30 vector computers, each with 1.6 GFLOPS peak speed and 256 MB memory, connected by a crossbar switch with 400 MB/s peak data transfer rate each way between any pair of nodes. The authors developed a Fortran lattice QCD simulation code for it. It runs at about 1.1 GFLOPS sustained per node for Metropolis pure-gauge update, and about 0.8 GFLOPS sustained per node for conjugate gradient inversion of staggered fermion matrix.

Publications of the exobiology program for 1984: A special bibliography

NASA Technical Reports Server (NTRS)

Wallace, J. S. (Compiler); Devincenzi, D. L. (Compiler)

1986-01-01

A bibliography of NASA exobiology programs is given. Planetary environments; chemical evolution; organic geochemistry; extraterrestrial intelligence; and the effect of planetary solar and astrophysical phenomena on the evolution of complex life in the universe are among the topics listed.

Computational complexity of the landscape II-Cosmological considerations

NASA Astrophysics Data System (ADS)

Denef, Frederik; Douglas, Michael R.; Greene, Brian; Zukowski, Claire

2018-05-01

We propose a new approach for multiverse analysis based on computational complexity, which leads to a new family of "computational" measure factors. By defining a cosmology as a space-time containing a vacuum with specified properties (for example small cosmological constant) together with rules for how time evolution will produce the vacuum, we can associate global time in a multiverse with clock time on a supercomputer which simulates it. We argue for a principle of "limited computational complexity" governing early universe dynamics as simulated by this supercomputer, which translates to a global measure for regulating the infinities of eternal inflation. The rules for time evolution can be thought of as a search algorithm, whose details should be constrained by a stronger principle of "minimal computational complexity". Unlike previously studied global measures, ours avoids standard equilibrium considerations and the well-known problems of Boltzmann Brains and the youngness paradox. We also give various definitions of the computational complexity of a cosmology, and argue that there are only a few natural complexity classes.

Do women prefer more complex music around ovulation?

PubMed

Charlton, Benjamin D; Filippi, Piera; Fitch, W Tecumseh

2012-01-01

The evolutionary origins of music are much debated. One theory holds that the ability to produce complex musical sounds might reflect qualities that are relevant in mate choice contexts and hence, that music is functionally analogous to the sexually-selected acoustic displays of some animals. If so, women may be expected to show heightened preferences for more complex music when they are most fertile. Here, we used computer-generated musical pieces and ovulation predictor kits to test this hypothesis. Our results indicate that women prefer more complex music in general; however, we found no evidence that their preference for more complex music increased around ovulation. Consequently, our findings are not consistent with the hypothesis that a heightened preference/bias in women for more complex music around ovulation could have played a role in the evolution of music. We go on to suggest future studies that could further investigate whether sexual selection played a role in the evolution of this universal aspect of human culture.

Evaluation of AA5052 alloy anode in alkaline electrolyte with organic rare-earth complex additives for aluminium-air batteries

NASA Astrophysics Data System (ADS)

Wang, Dapeng; Li, Heshun; Liu, Jie; Zhang, Daquan; Gao, Lixin; Tong, Lin

2015-10-01

Behaviours of the AA5052 aluminium alloy anode of the alkaline aluminium-air battery are studied by the hydrogen evolution test, the electrochemical measurements and the surface analysis method. The combination of amino-acid and rare earth as electrolyte additives effectively retards the self-corrosion of AA5052 aluminium alloy in 4 M NaOH solution. It shows that the combination of L-cysteine and cerium nitrate has a synergistic effect owing to the formation of a complex film on AA5052 alloy surface. The organic rare-earth complex can decrease the anodic polarisation, suppress the hydrogen evolution and increase the anodic utilization rate.

Simple versus complex models of trait evolution and stasis as a response to environmental change

NASA Astrophysics Data System (ADS)

Hunt, Gene; Hopkins, Melanie J.; Lidgard, Scott

2015-04-01

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.

PubMed

Fukasawa, Yoshinori; Oda, Toshiyuki; Tomii, Kentaro; Imai, Kenichiro

2017-07-01

Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases' evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A tool for exploring the dynamics of innovative interventions for public health: the critical event card.

PubMed

Figueiro, Ana Claudia; de Araújo Oliveira, Sydia Rosana; Hartz, Zulmira; Couturier, Yves; Bernier, Jocelyne; do Socorro Machado Freire, Maria; Samico, Isabella; Medina, Maria Guadalupe; de Sa, Ronice Franco; Potvin, Louise

2017-03-01

Public health interventions are increasingly represented as complex systems. Research tools for capturing the dynamic of interventions processes, however, are practically non-existent. This paper describes the development and proof of concept process of an analytical tool, the critical event card (CEC), which supports the representation and analysis of complex interventions' evolution, based on critical events. Drawing on the actor-network theory (ANT), we developed and field-tested the tool using three innovative health interventions in northeastern Brazil. Interventions were aimed to promote health equity through intersectoral approaches; were engaged in participatory evaluation and linked to professional training programs. The CEC developing involve practitioners and researchers from projects. Proof of concept was based on document analysis, face-to-face interviews and focus groups. Analytical categories from CEC allow identifying and describing critical events as milestones in the evolution of complex interventions. Categories are (1) event description; (2) actants (human and non-human) involved; (3) interactions between actants; (4) mediations performed; (5) actions performed; (6) inscriptions produced; and (7) consequences for interventions. The CEC provides a tool to analyze and represent intersectoral internvetions' complex and dynamic evolution.

Advanced Large Scale Cross Domain Temporal Topic Modeling Algorithms to Infer the Influence of Recent Research on IPCC Assessment Reports

NASA Astrophysics Data System (ADS)

Sleeman, J.; Halem, M.; Finin, T.; Cane, M. A.

2016-12-01

Approximately every five years dating back to 1989, thousands of climate scientists, research centers and government labs volunteer to prepare comprehensive Assessment Reports for the Intergovernmental Panel on Climate Change. These are highly curated reports distributed to 200 nation policy makers. There have been five IPCC Assessment Reports to date, the latest leading to a Paris Agreement in Dec. 2016 signed thus far by 172 nations to limit the amount of global Greenhouse gases emitted to producing no more than a 20 C warming of the atmosphere. These reports are a living evolving big data collection tracing 30 years of climate science research, observations, and model scenario intercomparisons. They contain more than 200,000 citations over a 30 year period that trace the evolution of the physical basis of climate science, the observed and predicted impact, risk and adaptation to increased greenhouse gases and mitigation approaches, pathways, policies for climate change. Document-topic and topic-term probability distributions are built from the vocabularies of the respective assessment report chapters and citations. Using Microsoft Bing, we retrieve 150,000 citations referenced across chapters and convert those citations to text. Using a word n-gram model based on a heterogeneous set of climate change terminology, lemmatization, noise filtering and stopword elimination, we calculate word frequencies for chapters and citations. Temporal document sets are built based on the assessment period. In addition to topic modeling, we employ cross domain correlation measures. Using the Jensen-Shannon divergence and Pearson correlation we build correlation matrices for chapter and citations topics. The shared vocabulary acts as the bridge between domains resulting in chapter-citation point pairs in space. Pairs are established based on a document-topic probability distribution. Each chapter and citation is associated with a vector of topics and based on the n most probable topics, we establish which chapter-citation pairs are most similar. We will perform posterior inferences based on Hastings -Metropolis simulated annealing MCMC algorithm to infer, from the evolution of topics starting from AR1 to AR4, assertions of topics for AR5 and potentially AR6.

Model-independent limits and constraints on extended theories of gravity from cosmic reconstruction techniques

NASA Astrophysics Data System (ADS)

de la Cruz-Dombriz, Álvaro; Dunsby, Peter K. S.; Luongo, Orlando; Reverberi, Lorenzo

2016-12-01

The onset of dark energy domination depends on the particular gravitational theory driving the cosmic evolution. Model independent techniques are crucial to test the both the present ΛCDM cosmological paradigm and alternative theories, making the least possible number of assumptions about the Universe. In this paper we investigate whether cosmography is able to distinguish between different gravitational theories, by determining bounds on model parameters for three different extensions of General Relativity, namely quintessence, F(𝒯) and f(R) gravitational theories. We expand each class of theories in powers of redshift z around the present time, making no additional assumptions. This procedure is an extension of previous work and can be seen as the most general approach for testing extended theories of gravity through the use of cosmography. In the case of F(𝒯) and f(R) theories, we show that some assumptions on model parameters often made in previous works are superfluous or even unjustified. We use data from the Union 2.1 supernovae catalogue, baryonic acoustic oscillation data and H(z) differential age compilations, which probe cosmology on different scales of the cosmological evolution. We perform a Monte Carlo analysis using a Metropolis-Hastings algorithm with a Gelman-Rubin convergence criterion, reporting 1-σ and 2-σ confidence levels. To do so, we perform two distinct fits, assuming only data within z < 1 first and then without limitations in redshift. We obtain the corresponding numerical intervals in which coefficients span, and find that the data is compatible the ΛCDM limit of all three theories at the 1-σ level, while still compatible with quite a large portion of parameter space. We compare our results to the truncated ΛCDM paradigm, demonstrating that our bounds divert from the expectations of previous works, showing that the permitted regions of coefficients are significantly modified and in general widened with respect to values usually reported in the existing literature. Finally, we test the extended theories through the Bayesian selection criteria AIC and BIC.

Model-independent limits and constraints on extended theories of gravity from cosmic reconstruction techniques

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

Cruz-Dombriz, Álvaro de la; Dunsby, Peter K.S.; Luongo, Orlando

The onset of dark energy domination depends on the particular gravitational theory driving the cosmic evolution. Model independent techniques are crucial to test the both the present ΛCDM cosmological paradigm and alternative theories, making the least possible number of assumptions about the Universe. In this paper we investigate whether cosmography is able to distinguish between different gravitational theories, by determining bounds on model parameters for three different extensions of General Relativity, namely quintessence, F (Τ) and f ( R ) gravitational theories. We expand each class of theories in powers of redshift z around the present time, making no additionalmore » assumptions. This procedure is an extension of previous work and can be seen as the most general approach for testing extended theories of gravity through the use of cosmography. In the case of F (Τ) and f ( R ) theories, we show that some assumptions on model parameters often made in previous works are superfluous or even unjustified. We use data from the Union 2.1 supernovae catalogue, baryonic acoustic oscillation data and H ( z ) differential age compilations, which probe cosmology on different scales of the cosmological evolution. We perform a Monte Carlo analysis using a Metropolis-Hastings algorithm with a Gelman-Rubin convergence criterion, reporting 1-σ and 2-σ confidence levels. To do so, we perform two distinct fits, assuming only data within z < 1 first and then without limitations in redshift. We obtain the corresponding numerical intervals in which coefficients span, and find that the data is compatible the ΛCDM limit of all three theories at the 1-σ level, while still compatible with quite a large portion of parameter space. We compare our results to the truncated ΛCDM paradigm, demonstrating that our bounds divert from the expectations of previous works, showing that the permitted regions of coefficients are significantly modified and in general widened with respect to values usually reported in the existing literature. Finally, we test the extended theories through the Bayesian selection criteria AIC and BIC.« less

Disentangling the Correlated Evolution of Monogamy and Cooperation.

PubMed

Dillard, Jacqueline R; Westneat, David F

2016-07-01

Lifetime genetic monogamy, by increasing sibling relatedness, has been proposed as an important causal factor in the evolution of altruism. Monogamy, however, could influence the subsequent evolution of cooperation in other ways. We present several alternative, non-mutually exclusive, evolutionary processes that could explain the correlated evolution of monogamy and cooperation. Our analysis of these possibilities reveals that many ecological or social factors can affect all three variables of Hamilton's Rule simultaneously, thus calling for a more holistic, systems-level approach to studying the evolution of social traits. This perspective reveals novel dimensions to coevolutionary relationships and provides solutions for assigning causality in complex cases of correlated social trait evolution, such as the sequential evolution of monogamy and cooperation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Networks of lexical borrowing and lateral gene transfer in language and genome evolution

PubMed Central

List, Johann-Mattis; Nelson-Sathi, Shijulal; Geisler, Hans; Martin, William

2014-01-01

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution. PMID:24375688

Bayesian Atmospheric Radiative Transfer (BART): Model, Statistics Driver, and Application to HD 209458b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Blecic, Jasmina; Stemm, Madison M.; Lust, Nate B.; Foster, Andrew S.; Rojo, Patricio M.; Loredo, Thomas J.

2014-11-01

Multi-wavelength secondary-eclipse and transit depths probe the thermo-chemical properties of exoplanets. In recent years, several research groups have developed retrieval codes to analyze the existing data and study the prospects of future facilities. However, the scientific community has limited access to these packages. Here we premiere the open-source Bayesian Atmospheric Radiative Transfer (BART) code. We discuss the key aspects of the radiative-transfer algorithm and the statistical package. The radiation code includes line databases for all HITRAN molecules, high-temperature H2O, TiO, and VO, and includes a preprocessor for adding additional line databases without recompiling the radiation code. Collision-induced absorption lines are available for H2-H2 and H2-He. The parameterized thermal and molecular abundance profiles can be modified arbitrarily without recompilation. The generated spectra are integrated over arbitrary bandpasses for comparison to data. BART's statistical package, Multi-core Markov-chain Monte Carlo (MC3), is a general-purpose MCMC module. MC3 implements the Differental-evolution Markov-chain Monte Carlo algorithm (ter Braak 2006, 2009). MC3 converges 20-400 times faster than the usual Metropolis-Hastings MCMC algorithm, and in addition uses the Message Passing Interface (MPI) to parallelize the MCMC chains. We apply the BART retrieval code to the HD 209458b data set to estimate the planet's temperature profile and molecular abundances. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.