WorldWideScience

Sample records for reproducible community dynamics

  1. Building Consensus on Community Standards for Reproducible Science

    Science.gov (United States)

    Lehnert, K. A.; Nielsen, R. L.

    2015-12-01

    As geochemists, the traditional model by which standard methods for generating, presenting, and using data have been generated relied on input from the community, the results of seminal studies, a variety of authoritative bodies, and has required a great deal of time. The rate of technological and related policy change has accelerated to the point that this historical model does not satisfy the needs of the community, publishers, or funders. The development of a new mechanism for building consensus raises a number of questions: Which aspects of our data are the focus of reproducibility standards? Who sets the standards? How do we subdivide the development of the consensus? We propose an open, transparent, and inclusive approach to the development of data and reproducibility standards that is organized around specific sub-disciplines and driven by the community of practitioners in those sub-disciplines. It should involve editors, program managers, and representatives of domain data facilities as well as professional societies, but avoid any single group to be the final authority. A successful example of this model is the Editors Roundtable, a cross section of editors, funders, and data facility managers that discussed and agreed on leading practices for the reporting of geochemical data in publications, including accessibility and format of the data, data quality information, and metadata and identifiers for samples (Goldstein et al., 2014). We argue that development of data and reproducibility standards needs to heavily rely on representatives from the community of practitioners to set priorities and provide perspective. Groups of editors, practicing scientists, and other stakeholders would be assigned the task of reviewing existing practices and recommending changes as deemed necessary. They would weigh the costs and benefits of changing the standards for that community, propose appropriate tools to facilitate those changes, work through the professional societies

  2. Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

    Directory of Open Access Journals (Sweden)

    Andrea Maesani

    2015-11-01

    Full Text Available The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.

  3. Static and Dynamic Handgrip Strength Endurance: Test-Retest Reproducibility.

    Science.gov (United States)

    Gerodimos, Vassilis; Karatrantou, Konstantina; Psychou, Dimitra; Vasilopoulou, Theodora; Zafeiridis, Andreas

    2017-03-01

    This study investigated the reliability of static and dynamic handgrip strength endurance using different protocols and indicators for the assessment of strength endurance. Forty young, healthy men and women (age, 18-22 years) performed 2 handgrip strength endurance protocols: a static protocol (sustained submaximal contraction at 50% of maximal voluntary contraction) and a dynamic one (8, 10, and 12 maximal repetitions). The participants executed each protocol twice to assess the test-retest reproducibility. Total work and total time were used as indicators of strength endurance in the static protocol; the strength recorded at each maximal repetition, the percentage change, and fatigue index were used as indicators of strength endurance in the dynamic protocol. The static protocol showed high reliability irrespective of sex and hand for total time and work. The 12-repetition dynamic protocol exhibited moderate-high reliability for repeated maximal repetitions and percentage change; the 8- and 10-repetition protocols demonstrated lower reliability irrespective of sex and hand. The fatigue index was not a reliable indicator for the assessment of dynamic handgrip endurance. Static handgrip endurance can be measured reliably using the total time and total work as indicators of strength endurance. For the evaluation of dynamic handgrip endurance, the 12-repetition protocol is recommended, using the repeated maximal repetitions and percentage change as indicators of strength endurance. Practitioners should consider the static (50% maximal voluntary contraction) and dynamic (12 repeated maximal repetitions) protocols as reliable for the assessment of handgrip strength endurance. The evaluation of static endurance in conjunction with dynamic endurance would provide more complete information about hand function. Copyright © 2017 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

  4. Predictability in community dynamics

    DEFF Research Database (Denmark)

    Blonder, Benjamin; Moulton, Derek E; Blois, Jessica

    2017-01-01

    prominent in disequilibrium ecology, proposing that communities track climate change following a fixed function or with a time delay. However, more complex dynamics are possible and may lead to memory effects and alternate unstable states. We develop graphical and analytic methods for assessing...

  5. Using the UM dynamical cores to reproduce idealised 3D flows

    CERN Document Server

    Mayne, N J; Acreman, David M; Smith, Chris; Wood, Nigel; Amundsen, David Skålid; Thuburn, John; Jackson, David R

    2013-01-01

    We demonstrate that both the current (New Dynamics), and next generation (ENDGame) dynamical cores of the UK Met Office global circulation model, the UM, reproduce consistently, the long-term, large-scale flows found in several published idealised tests. The cases presented are the Held-Suarez test, a simplified model of Earth (including a stratosphere), and a hypothetical tidally locked Earth. Furthermore, we show that using simplifications to the dynamical equations, which are expected to be justified for the physical domains and flow regimes we have studied, and which are supported by the ENDGame dynamical core, also produces matching long-term, large-scale flows. Finally, we present evidence for differences in the detail of the planetary flows and circulations resulting from improvements in the ENDGame formulation over New Dynamics.

  6. A force-based model to reproduce stop-and-go waves in pedestrian dynamics

    CERN Document Server

    Chraibi, Mohcine; Schadschneider, Andreas

    2015-01-01

    Stop-and-go waves in single-file movement are a phenomenon that is ob- served empirically in pedestrian dynamics. It manifests itself by the co-existence of two phases: moving and stopping pedestrians. We show analytically based on a simplified one-dimensional scenario that under some conditions the system can have instable homogeneous solutions. Hence, oscillations in the trajectories and in- stabilities emerge during simulations. To our knowledge there exists no force-based model which is collision- and oscillation-free and meanwhile can reproduce phase separation. We develop a new force-based model for pedestrian dynamics able to reproduce qualitatively the phenomenon of phase separation. We investigate analytically the stability condition of the model and define regimes of parameter values where phase separation can be observed. We show by means of simulations that the predefined conditions lead in fact to the expected behavior and validate our model with respect to empirical findings.

  7. Learning the Inverse Dynamics of Robotic Manipulators in Structured Reproducing Kernel Hilbert Space.

    Science.gov (United States)

    Cheng, Ching-An; Huang, Han-Pang; Hsu, Huan-Kun; Lai, Wei-Zh; Cheng, Chih-Chun

    2016-07-01

    We investigate the modeling of inverse dynamics without prior kinematic information for holonomic rigid-body robots. Despite success in compensating robot dynamics and friction, general inverse dynamics models are nontrivial. Rigid-body models are restrictive or inefficient; learning-based models are generalizable yet require large training data. The structured kernels address the dilemma by embedding the robot dynamics in reproducing kernel Hilbert space. The proposed kernels autonomously converge to rigid-body models but require fewer samples; with a semi-parametric framework that incorporates additional parametric basis for friction, the structured kernels can efficiently model general rigid-body robots. We tested the proposed scheme in simulations and experiments; the models that consider the structure of function space are more accurate.

  8. Dynamic cerebral autoregulation: different signal processing methods without influence on results and reproducibility.

    Science.gov (United States)

    Gommer, Erik D; Shijaku, Eri; Mess, Werner H; Reulen, Jos P H

    2010-12-01

    Cerebral autoregulation controls cerebral blood flow under changing cerebral perfusion pressure. Standards for measurement and analysis of dynamic cerebral autoregulation (dCA) are lacking. In this study, dCA reproducibility, quantified by intraclass correlation coefficient, is evaluated for different methodological approaches of transfer function analysis (TFA) and compared with multimodal pressure flow analysis (MMPF). dCA parameters were determined in 19 healthy volunteers during three 15-min lasting epochs of spontaneous breathing. Every spontaneous breathing epoch was followed by 5 min of paced breathing at 6 cycles/min. These six measurements were performed in both a morning and an afternoon session. Analysis compared raw data pre-processing by mean subtraction versus smoothness priors detrending. The estimation of spectral density was either performed by averaging of subsequent time windows or by smoothing the spectrum of the whole recording. No significant influence of pre-processing and spectral estimation on dCA parameters was found. Therefore, there seems to be no need to prescribe a specific signal-processing regime. Poor reproducibility of gain and phase was found for TFA as well as for MMPF. Based on reproducibility, no preference can be made for morning versus afternoon measurements, neither for spontaneous versus paced breathing. Finally, reproducibility results are not in favour of TFA or MMPF.

  9. CHRONIC MEDICAL CONDITIONS AND REPRODUCIBILITY OF SELF-REPORTED AGE AT MENOPAUSE AMONG COMMUNITY DWELLING WOMEN

    Science.gov (United States)

    de Vries, Heather F.; Northington, Gina M.; Kaye, Elise M.; Bogner, Hillary R.

    2011-01-01

    OBJECTIVE To examine the association between chronic medical conditions and reproducibility of self-reported age at menopause among community-dwelling women. METHOD Age at menopause was assessed in a population-based longitudinal survey of 240 women twice, in 1993 and 2004. Women who recalled age at menopause in 2004 within one year or less of the age at menopause recalled in 1993 (concordant) were compared with women who did not recall of age at menopause in 2004 within 1 year of age at menopause recalled in 1993 (discordant). Type of menopause (surgical or natural) and chronic medical conditions were assessed by self-report. RESULTS One hundred and forty three women (59.6%) reported surgical menopause and 97 (40.4%) reported natural menopause. In all, 130 (54.2%) of women recalled age at menopause in 2004 within one year or less of recalled age at menopause in 1994 while 110 (45.8%) women did not recall age at menopause in 2004 within one year or less of recalled age at menopause in 1994. Among women with surgical menopause, women with three or more medical conditions were less likely to have concordant recall of age at menopause than women with less than three chronic medical conditions (adjusted odds ratio (OR) = 0.36, 95% confidence interval (CI) [0.15, 0.91]) in multivariate models controlling for potentially influential characteristics including cognition and years from menopause. CONCLUSIONS Among women who underwent surgical menopause, the presence of three or more medical conditions is associated with decreased reproducibility of self-reported age at menopause. PMID:21971208

  10. Dynamical detection of network communities

    Science.gov (United States)

    Quiles, Marcos G.; Macau, Elbert E. N.; Rubido, Nicolás

    2016-05-01

    A prominent feature of complex networks is the appearance of communities, also known as modular structures. Specifically, communities are groups of nodes that are densely connected among each other but connect sparsely with others. However, detecting communities in networks is so far a major challenge, in particular, when networks evolve in time. Here, we propose a change in the community detection approach. It underlies in defining an intrinsic dynamic for the nodes of the network as interacting particles (based on diffusive equations of motion and on the topological properties of the network) that results in a fast convergence of the particle system into clustered patterns. The resulting patterns correspond to the communities of the network. Since our detection of communities is constructed from a dynamical process, it is able to analyse time-varying networks straightforwardly. Moreover, for static networks, our numerical experiments show that our approach achieves similar results as the methodologies currently recognized as the most efficient ones. Also, since our approach defines an N-body problem, it allows for efficient numerical implementations using parallel computations that increase its speed performance.

  11. On the reproducibility of spatiotemporal traffic dynamics with microscopic traffic models

    CERN Document Server

    Knorr, Florian

    2012-01-01

    Traffic flow is a very prominent example of a driven non-equilibrium system. A characteristic phenomenon of traffic dynamics is the spontaneous and abrupt drop of the average velocity on a stretch of road leading to congestion. Such a traffic breakdown corresponds to a boundary-induced phase transition from free flow to congested traffic. In this paper, we study the ability of selected microscopic traffic models to reproduce a traffic breakdown, and we investigate its spatiotemporal dynamics. For our analysis, we use empirical traffic data from stationary loop detectors on a German Autobahn showing a spontaneous breakdown. We then present several methods to assess the results and compare the models with each other. In addition, we will also discuss some important modeling aspects and their impact on the resulting spatiotemporal pattern. The investigation of different downstream boundary conditions, for example, shows that the physical origin of the traffic breakdown may be artificially induced by the setup of...

  12. On the reproducibility of spatiotemporal traffic dynamics with microscopic traffic models

    Science.gov (United States)

    Knorr, Florian; Schreckenberg, Michael

    2012-10-01

    Traffic flow is a very prominent example of a driven non-equilibrium system. A characteristic phenomenon of traffic dynamics is the spontaneous and abrupt drop of the average velocity on a stretch of road leading to congestion. Such a traffic breakdown corresponds to a boundary-induced phase transition from free flow to congested traffic. In this paper, we study the ability of selected microscopic traffic models to reproduce a traffic breakdown, and we investigate its spatiotemporal dynamics. For our analysis, we use empirical traffic data from stationary loop detectors on a German Autobahn showing a spontaneous breakdown. We then present several methods to assess the results and compare the models with each other. In addition, we will also discuss some important modeling aspects and their impact on the resulting spatiotemporal pattern. The investigation of different downstream boundary conditions, for example, shows that the physical origin of the traffic breakdown may be artificially induced by the setup of the boundaries.

  13. Dynamic provisioning for community services

    CERN Document Server

    Qi, Li

    2013-01-01

    Dynamic Provisioning for Community Services outlines a dynamic provisioning and maintenance mechanism in a running distributed system, e.g. the grid, which can be used to maximize the utilization of computing resources and user demands. The book includes a complete and reliable maintenance system solution for the large-scale distributed system and an interoperation mechanism for the grid middleware deployed in the United States, Europe, and China. The experiments and evaluations have all been practically implemented for ChinaGrid, and the best practices established can help readers to construc

  14. Epistemic communities and cluster dynamics

    DEFF Research Database (Denmark)

    Håkanson, Lars

    2003-01-01

    This paper questions the prevailing notions that firms within industrial clusters have privi-leged access to `tacit knowledge' that is unavailable - or available only at high cost - to firms located elsewhere, and that such access provides competitive advantages that help to explain the growth...... and development of both firms and regions. It outlines a model of cluster dynam-ics emphasizing two mutually interdependent processes: the concentration of specialized and complementary epistemic communities, on the one hand, and entrepreneurship and a high rate of new firm formation on the other....

  15. Bayesian Overlapping Community Detection in Dynamic Networks

    CERN Document Server

    Ghorbani, Mahsa; Khodadadi, Ali

    2016-01-01

    Detecting community structures in social networks has gained considerable attention in recent years. However, lack of prior knowledge about the number of communities, and their overlapping nature have made community detection a challenging problem. Moreover, many of the existing methods only consider static networks, while most of real world networks are dynamic and evolve over time. Hence, finding consistent overlapping communities in dynamic networks without any prior knowledge about the number of communities is still an interesting open research problem. In this paper, we present an overlapping community detection method for dynamic networks called Dynamic Bayesian Overlapping Community Detector (DBOCD). DBOCD assumes that in every snapshot of network, overlapping parts of communities are dense areas and utilizes link communities instead of common node communities. Using Recurrent Chinese Restaurant Process and community structure of the network in the last snapshot, DBOCD simultaneously extracts the numbe...

  16. Identifying Community Structures in Dynamic Networks

    CERN Document Server

    Alvari, Hamidreza; Sukthankar, Gita; Lakkaraju, Kiran

    2016-01-01

    Most real-world social networks are inherently dynamic, composed of communities that are constantly changing in membership. To track these evolving communities, we need dynamic community detection techniques. This article evaluates the performance of a set of game theoretic approaches for identifying communities in dynamic networks. Our method, D-GT (Dynamic Game Theoretic community detection), models each network node as a rational agent who periodically plays a community membership game with its neighbors. During game play, nodes seek to maximize their local utility by joining or leaving the communities of network neighbors. The community structure emerges after the game reaches a Nash equilibrium. Compared to the benchmark community detection methods, D-GT more accurately predicts the number of communities and finds community assignments with a higher normalized mutual information, while retaining a good modularity.

  17. A Semi-Analytic dynamical friction model that reproduces core stalling

    CERN Document Server

    Petts, James A; Read, Justin I

    2015-01-01

    We present a new semi-analytic model for dynamical friction based on Chandrasekhar's formalism. The key novelty is the introduction of physically motivated, radially varying, maximum and minimum impact parameters. With these, our model gives an excellent match to full N-body simulations for isotropic background density distributions, both cuspy and shallow, without any fine-tuning of the model parameters. In particular, we are able to reproduce the dramatic core-stalling effect that occurs in shallow/constant density cores, for the first time. This gives us new physical insight into the core-stalling phenomenon. We show that core stalling occurs in the limit in which the product of the Coulomb logarithm and the local fraction of stars with velocity lower than the infalling body tends to zero. For cuspy backgrounds, this occurs when the infalling mass approaches the enclosed background mass. For cored backgrounds, it occurs at larger distances from the centre, due to a combination of a rapidly increasing minim...

  18. Some aspects of animal behavior and community dynamics

    Directory of Open Access Journals (Sweden)

    Vikas Rai

    2011-09-01

    Full Text Available We simulate the dynamical behavior of a few two - dimensional predator - prey systems in two - dimensional parameter spaces to gain insight into how functional responses affect community dynamics. The insight gained helps us design three dimensional systems. We construct models for a few ecosystems with three species and study them using computer simulations. The models have been developed by linking food chains which have both kinds of predators: specialist as well as generalist. The linking functions are weakly non-linear. The three dimensional model ecosystems have sexually reproducing top - predators. We perform extensive simulations to figure out dynamics of dynamical possibilities caused by changes in animal behavior. The animals change the foraging strategies and behave differently in different environments. At the end of the paper, we examine how diseases can govern transitions in meandering of dynamical models in bounded volume of their phase spaces.

  19. Omics Pipe: a community-based framework for reproducible multi-omics data analysis.

    Science.gov (United States)

    Fisch, Kathleen M; Meißner, Tobias; Gioia, Louis; Ducom, Jean-Christophe; Carland, Tristan M; Loguercio, Salvatore; Su, Andrew I

    2015-06-01

    Omics Pipe (http://sulab.scripps.edu/omicspipe) is a computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. The goal of Omics Pipe is to democratize next-generation sequencing analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results. Using Omics Pipe, we analyzed 100 TCGA breast invasive carcinoma paired tumor-normal datasets based on the latest UCSC hg19 RefSeq annotation. Omics Pipe automatically downloaded and processed the desired TCGA samples on a high throughput compute cluster to produce a results report for each sample. We aggregated the individual sample results and compared them to the analysis in the original publications. This comparison revealed high overlap between the analyses, as well as novel findings due to the use of updated annotations and methods. Source code for Omics Pipe is freely available on the web (https://bitbucket.org/sulab/omics_pipe). Omics Pipe is distributed as a standalone Python package for installation (https://pypi.python.org/pypi/omics_pipe) and as an Amazon Machine Image in Amazon Web Services Elastic Compute Cloud that contains all necessary third-party software dependencies and databases (https://pythonhosted.org/omics_pipe/AWS_installation.html). © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model.

    Science.gov (United States)

    Rouger, Amélie; Remenant, Benoit; Prévost, Hervé; Zagorec, Monique

    2017-04-17

    Influenced by production and storage processes and by seasonal changes the diversity of meat products microbiota can be very variable. Because microbiotas influence meat quality and safety, characterizing and understanding their dynamics during processing and storage is important for proposing innovative and efficient storage conditions. Challenge tests are usually performed using meat from the same batch, inoculated at high levels with one or few strains. Such experiments do not reflect the true microbial situation, and the global ecosystem is not taken into account. Our purpose was to constitute live stocks of chicken meat microbiotas to create standard and reproducible ecosystems. We searched for the best method to collect contaminating bacterial communities from chicken cuts to store as frozen aliquots. We tested several methods to extract DNA of these stored communities for subsequent PCR amplification. We determined the best moment to collect bacteria in sufficient amounts during the product shelf life. Results showed that the rinsing method associated to the use of Mobio DNA extraction kit was the most reliable method to collect bacteria and obtain DNA for subsequent PCR amplification. Then, 23 different chicken meat microbiotas were collected using this procedure. Microbiota aliquots were stored at -80°C without important loss of viability. Their characterization by cultural methods confirmed the large variability (richness and abundance) of bacterial communities present on chicken cuts. Four of these bacterial communities were used to estimate their ability to regrow on meat matrices. Challenge tests performed on sterile matrices showed that these microbiotas were successfully inoculated and could overgrow the natural microbiota of chicken meat. They can therefore be used for performing reproducible challenge tests mimicking a true meat ecosystem and enabling the possibility to test the influence of various processing or storage conditions on complex meat

  1. [Reproducibility of quantifying Timed Up and Go test, measured with smartphone accelerometers in older people living in the community].

    Science.gov (United States)

    Campillay Guzmán, Jorge; Guzmán Silva, Ricardo; Guzmán-Venegas, Rodrigo

    Inertial Measurement Units (IMU) incorporated in smartphones can provide records that match registers obtained by laboratory instruments. This means that the use of smartphones would be feasible for recording three-dimensional kinematics parameters like velocity and acceleration, enabling more robust analyses, such as the Timed Up and Go (TUG) test, that assess the risk of falls older people (OP) living in the community. The study included 35 female OP, users of the Family Health Centres (CESFAM) Juan Pablo II and Corvallis from Antofagasta city, Chile. They were evaluated with the TUG, with linear and angular acceleration and velocity being recorded simultaneously using a smartphone equipped with a three-dimensional IMU. Using a computer macro application, the start and end time of each sub-stage of the test was determined by two independent observers. Reproducibility of the times of each sub-stage of TUG was assessed using the Intraclass Correlation Coefficient (ICC). The ICC gave values of 0.78 to 0.99, with an acceptable confidence interval, (0.45-1.00), thus providing a reproducible and reliable recording. The reproducibility of the times of the sub-stages of TUG, recorded with inertial measurement units from a smartphone enables it to be used in clinical practices with OP groups, in order to improve the evaluation and prevention of the risk of falls. Copyright © 2017 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.

  2. A new fast algorithm for reproducing complex networks with community structure

    CERN Document Server

    Kowalczyk, Mateusz; Fronczak, Agata

    2016-01-01

    In this paper, we introduce a new algorithm allowing for generation of networks with heterogeneity of both node degrees and community sizes. The quality and efficiency of the algorithm is analyzed and compared to the other, so far the most popular algorithm which was proposed by Lancichinetti et al. We discuss the advantages and shortcomings of both algorithms indicating the areas of their potential application.

  3. Reproducibility of dynamic contrast-enhanced MRI and dynamic susceptibility contrast MRI in the study of brain gliomas: a comparison of data obtained using different commercial software.

    Science.gov (United States)

    Conte, Gian Marco; Castellano, Antonella; Altabella, Luisa; Iadanza, Antonella; Cadioli, Marcello; Falini, Andrea; Anzalone, Nicoletta

    2017-04-01

    Dynamic susceptibility contrast MRI (DSC) and dynamic contrast-enhanced MRI (DCE) are useful tools in the diagnosis and follow-up of brain gliomas; nevertheless, both techniques leave the open issue of data reproducibility. We evaluated the reproducibility of data obtained using two different commercial software for perfusion maps calculation and analysis, as one of the potential sources of variability can be the software itself. DSC and DCE analyses from 20 patients with gliomas were tested for both the intrasoftware (as intraobserver and interobserver reproducibility) and the intersoftware reproducibility, as well as the impact of different postprocessing choices [vascular input function (VIF) selection and deconvolution algorithms] on the quantification of perfusion biomarkers plasma volume (Vp), volume transfer constant (K (trans)) and rCBV. Data reproducibility was evaluated with the intraclass correlation coefficient (ICC) and Bland-Altman analysis. For all the biomarkers, the intra- and interobserver reproducibility resulted in almost perfect agreement in each software, whereas for the intersoftware reproducibility the value ranged from 0.311 to 0.577, suggesting fair to moderate agreement; Bland-Altman analysis showed high dispersion of data, thus confirming these findings. Comparisons of different VIF estimation methods for DCE biomarkers resulted in ICC of 0.636 for K (trans) and 0.662 for Vp; comparison of two deconvolution algorithms in DSC resulted in an ICC of 0.999. The use of single software ensures very good intraobserver and interobservers reproducibility. Caution should be taken when comparing data obtained using different software or different postprocessing within the same software, as reproducibility is not guaranteed anymore.

  4. "This is My Community": Reproducing and Resisting Boundaries of Exclusion in Contested Public Spaces.

    Science.gov (United States)

    Toolis, Erin E; Hammack, Phillip L

    2015-12-01

    The way that public space is structured has significant implications for identity, social interaction, and participation in society. For those experiencing homelessness, with no or limited private space, survival hinges on the accessibility and livability of public space. However, the increasing privatization of public space in the United States has contributed to the implementation of anti-homeless ordinances in cities, restricting sitting, standing, panhandling, and sleeping in public. This study analyzes data from interviews with housed and unhoused community members, text from a local policy document, and ethnographic observations to explore how boundaries between "insiders" and "outsiders" are drawn in public space and mediated through individual discourse. Our findings suggest that boundaries of exclusion are constructed through dominant narratives that portray the unhoused as a threat to safety and economic vitality, thus justifying the need for regulation and punishment through the criminalization of homelessness. Yet, informants also demonstrate resistance to this narrative by discussing how criminalization of homelessness perpetuates dehumanization, violence, and economic inequality. Policy implications for the regulation of public space are discussed.

  5. Understanding Microbial Communities: Function, Structure and Dynamics

    Science.gov (United States)

    2015-02-11

    microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014

  6. Can a stepwise steady flow computational fluid dynamics model reproduce unsteady particulate matter separation for common unit operations?

    Science.gov (United States)

    Pathapati, Subbu-Srikanth; Sansalone, John J

    2011-07-01

    Computational fluid dynamics (CFD) is emerging as a model for resolving the fate of particulate matter (PM) by unit operations subject to rainfall-runoff loadings. However, compared to steady flow CFD models, there are greater computational requirements for unsteady hydrodynamics and PM loading models. Therefore this study examines if integrating a stepwise steady flow CFD model can reproduce PM separation by common unit operations loaded by unsteady flow and PM loadings, thereby reducing computational effort. Utilizing monitored unit operation data from unsteady events as a metric, this study compares the two CFD modeling approaches for a hydrodynamic separator (HS), a primary clarifier (PC) tank, and a volumetric clarifying filtration system (VCF). Results indicate that while unsteady CFD models reproduce PM separation of each unit operation, stepwise steady CFD models result in significant deviation for HS and PC models as compared to monitored data; overestimating the physical size requirements of each unit required to reproduce monitored PM separation results. In contrast, the stepwise steady flow approach reproduces PM separation by the VCF, a combined gravitational sedimentation and media filtration unit operation that provides attenuation of turbulent energy and flow velocity.

  7. Interobserver and Intraobserver Reproducibility with Volume Dynamic Contrast Enhanced Computed Tomography (DCE-CT) in Gastroesophageal Junction Cancer

    DEFF Research Database (Denmark)

    Lundsgaard Hansen, Martin; Fallentin, Eva; Axelsen, Thomas;

    2016-01-01

    The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT) measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal ...... were narrower for 3D analysis compared to 2D analysis. Three-dimensional volume DCE-CT analysis of gastroesophageal junction cancer provides higher inter- and intra-observer reproducibility with narrower limits of agreement between readers compared to 2D analysis.......The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT) measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal...... for each observation. Inter- and intra-observer variability were assessed by Intraclass Correlation Coefficient (ICC) and Bland-Altman statistics. Interobserver ICC was excellent for arterial flow (0.88), for blood volume (0.89) and for permeability (0.91) with 3D-VOI analysis. The 95% limits of agreement...

  8. Biologically plausible learning in recurrent neural networks reproduces neural dynamics observed during cognitive tasks.

    Science.gov (United States)

    Miconi, Thomas

    2017-02-23

    Neural activity during cognitive tasks exhibits complex dynamics that flexibly encode task-relevant variables. Chaotic recurrent networks, which spontaneously generate rich dynamics, have been proposed as a model of cortical computation during cognitive tasks. However, existing methods for training these networks are either biologically implausible, and/or require a continuous, real-time error signal to guide learning. Here we show that a biologically plausible learning rule can train such recurrent networks, guided solely by delayed, phasic rewards at the end of each trial. Networks endowed with this learning rule can successfully learn nontrivial tasks requiring flexible (context-dependent) associations, memory maintenance, nonlinear mixed selectivities, and coordination among multiple outputs. The resulting networks replicate complex dynamics previously observed in animal cortex, such as dynamic encoding of task features and selective integration of sensory inputs. We conclude that recurrent neural networks offer a plausible model of cortical dynamics during both learning and performance of flexible behavior.

  9. Ecological communities with Lotka-Volterra dynamics

    Science.gov (United States)

    Bunin, Guy

    2017-04-01

    Ecological communities in heterogeneous environments assemble through the combined effect of species interaction and migration. Understanding the effect of these processes on the community properties is central to ecology. Here we study these processes for a single community subject to migration from a pool of species, with population dynamics described by the generalized Lotka-Volterra equations. We derive exact results for the phase diagram describing the dynamical behaviors, and for the diversity and species abundance distributions. A phase transition is found from a phase where a unique globally attractive fixed point exists to a phase where multiple dynamical attractors exist, leading to history-dependent community properties. The model is shown to possess a symmetry that also establishes a connection with other well-known models.

  10. Reproducibility blues.

    Science.gov (United States)

    Pulverer, Bernd

    2015-11-12

    Research findings advance science only if they are significant, reliable and reproducible. Scientists and journals must publish robust data in a way that renders it optimally reproducible. Reproducibility has to be incentivized and supported by the research infrastructure but without dampening innovation.

  11. Chronic medical conditions and reproducibility of self-reported age at menopause among community-dwelling women.

    Science.gov (United States)

    de Vries, Heather F; Northington, Gina M; Kaye, Elise M; Bogner, Hillary R

    2011-12-01

    The aim of this study was to examine the association between chronic medical conditions and reproducibility of self-reported age at menopause among community-dwelling women. Age at menopause was assessed in a population-based longitudinal survey of 240 women twice, in 1993 and 2004. Women who recalled age at menopause in 2004 within 1 year or less of age at menopause recalled in 1993 (concordant) were compared with women who did not recall age at menopause in 2004 within 1 year of age at menopause recalled in 1993 (discordant). Type of menopause (surgical or natural) and chronic medical conditions were assessed by self-report. One hundred forty-three women (59.6%) reported surgical menopause, and 97 (40.4%) reported natural menopause. In all, 130 (54.2%) women recalled age at menopause in 2004 within 1 year or less of recalled age at menopause in 1994, whereas 110 (45.8%) women did not recall age at menopause in 2004 within 1 year or less of recalled age at menopause in 1994. Among the women with surgical menopause, the women with three or more medical conditions were less likely to have concordant recall of age at menopause than the women with less than three chronic medical conditions (adjusted odds ratio, 0.36; 95% CI, 0.15-0.91) in multivariate models controlling for potentially influential characteristics including cognition and years since menopause. Among women who underwent surgical menopause, the presence of three or more medical conditions is associated with decreased reproducibility of self-reported age at menopause.

  12. Simple and Flexible Self-Reproducing Structures in Asynchronous Cellular Automata and Their Dynamics

    Science.gov (United States)

    Huang, Xin; Lee, Jia; Yang, Rui-Long; Zhu, Qing-Sheng

    2013-03-01

    Self-reproduction on asynchronous cellular automata (ACAs) has attracted wide attention due to the evident artifacts induced by synchronous updating. Asynchronous updating, which allows cells to undergo transitions independently at random times, might be more compatible with the natural processes occurring at micro-scale, but the dark side of the coin is the increment in the complexity of an ACA in order to accomplish stable self-reproduction. This paper proposes a novel model of self-timed cellular automata (STCAs), a special type of ACAs, where unsheathed loops are able to duplicate themselves reliably in parallel. The removal of sheath cannot only allow various loops with more flexible and compact structures to replicate themselves, but also reduce the number of cell states of the STCA as compared to the previous model adopting sheathed loops [Y. Takada, T. Isokawa, F. Peper and N. Matsui, Physica D227, 26 (2007)]. The lack of sheath, on the other hand, often tends to cause much more complicated interactions among loops, when all of them struggle independently to stretch out their constructing arms at the same time. In particular, such intense collisions may even cause the emergence of a mess of twisted constructing arms in the cellular space. By using a simple and natural method, our self-reproducing loops (SRLs) are able to retract their arms successively, thereby disentangling from the mess successfully.

  13. A Phenomenological and Dynamic View of Homology: Homologs as Persistently Reproducible Modules.

    Science.gov (United States)

    Suzuki, Daichi G; Tanaka, Senji

    2017-01-01

    Homology is a fundamental concept in biology. However, the metaphysical status of homology, especially whether a homolog is a part of an individual or a member of a natural kind, is still a matter of intense debate. The proponents of the individuality view of homology criticize the natural kind view of homology by pointing out that homologs are subject to evolutionary transformation, and natural kinds do not change in the evolutionary process. Conversely, some proponents of the natural kind view of homology argue that a homolog can be construed both as a part of an individual and a member of a natural kind. They adopt the Homeostatic Property Cluster (HPC) theory of natural kinds, and the theory seems to strongly support their construal. Note that this construal implies the acceptance of essentialism. However, looking back on the history of the concept of homology, we should not overlook the fact that the individuality view was proposed to reject the essentialist interpretation of homology. Moreover, the essentialist notions of natural kinds can, in our view, mislead biologists about the phenomena of homology. Consequently, we need a non-essentialist view of homology, which we name the "persistently reproducible module" (PRM) view. This view highlights both the individual-like and kind-like aspects of homologs while stripping down both essentialist and anti-essentialist interpretations of homology. In this article, we articulate the PRM view of homology and explain why it is recommended over the other two views.

  14. Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

    Science.gov (United States)

    Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

    2017-05-07

    A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

  15. Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

    Science.gov (United States)

    Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

    2017-05-01

    A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

  16. Cellular automaton model with dynamical 2D speed-gap relation reproduces empirical and experimental features of traffic flow

    CERN Document Server

    Tian, Junfang; Ma, Shoufeng; Zhu, Chenqiang; Jiang, Rui; Ding, YaoXian

    2015-01-01

    This paper proposes an improved cellular automaton traffic flow model based on the brake light model, which takes into account that the desired time gap of vehicles is remarkably larger than one second. Although the hypothetical steady state of vehicles in the deterministic limit corresponds to a unique relationship between speeds and gaps in the proposed model, the traffic states of vehicles dynamically span a two-dimensional region in the plane of speed versus gap, due to the various randomizations. It is shown that the model is able to well reproduce (i) the free flow, synchronized flow, jam as well as the transitions among the three phases; (ii) the evolution features of disturbances and the spatiotemporal patterns in a car-following platoon; (iii) the empirical time series of traffic speed obtained from NGSIM data. Therefore, we argue that a model can potentially reproduce the empirical and experimental features of traffic flow, provided that the traffic states are able to dynamically span a 2D speed-gap...

  17. Dynamic Social Community Detection and Its Applications

    Science.gov (United States)

    Nguyen, Nam P.; Dinh, Thang N.; Shen, Yilin; Thai, My T.

    2014-01-01

    Community structure is one of the most commonly observed features of Online Social Networks (OSNs) in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs) and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA), an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1) A social-aware message forwarding strategy in MANETs, and (2) worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods. PMID:24722164

  18. Dynamic social community detection and its applications.

    Directory of Open Access Journals (Sweden)

    Nam P Nguyen

    Full Text Available Community structure is one of the most commonly observed features of Online Social Networks (OSNs in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA, an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1 A social-aware message forwarding strategy in MANETs, and (2 worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods.

  19. Dynamic social community detection and its applications.

    Science.gov (United States)

    Nguyen, Nam P; Dinh, Thang N; Shen, Yilin; Thai, My T

    2014-01-01

    Community structure is one of the most commonly observed features of Online Social Networks (OSNs) in reality. The knowledge of this feature is of great advantage: it not only provides helpful insights into developing more efficient social-aware solutions but also promises a wide range of applications enabled by social and mobile networking, such as routing strategies in Mobile Ad Hoc Networks (MANETs) and worm containment in OSNs. Unfortunately, understanding this structure is very challenging, especially in dynamic social networks where social interactions are evolving rapidly. Our work focuses on the following questions: How can we efficiently identify communities in dynamic social networks? How can we adaptively update the network community structure based on its history instead of recomputing from scratch? To this end, we present Quick Community Adaptation (QCA), an adaptive modularity-based framework for not only discovering but also tracing the evolution of network communities in dynamic OSNs. QCA is very fast and efficient in the sense that it adaptively updates and discovers the new community structure based on its history together with the network changes only. This flexible approach makes QCA an ideal framework applicable for analyzing large-scale dynamic social networks due to its lightweight computing-resource requirement. To illustrate the effectiveness of our framework, we extensively test QCA on both synthesized and real-world social networks including Enron, arXiv e-print citation, and Facebook networks. Finally, we demonstrate the applicability of QCA in real applications: (1) A social-aware message forwarding strategy in MANETs, and (2) worm propagation containment in OSNs. Competitive results in comparison with other methods reveal that social-based techniques employing QCA as a community detection core outperform current available methods.

  20. Efficient and reproducible folding simulations of the Trp-case protein with multiscale molecular dynamics

    Institute of Scientific and Technical Information of China (English)

    XIA XueFeng; ZHANG Song; HUANG go; ZHOU Yun; SUN ZhiRong

    2008-01-01

    Folding simulations are often time-consuming or highly sensitive to the initial conformation of the simulation even for mini protein like the Trp-cage. Here, we present a multiscale molecular dynamics method which appears to be both efficient and insensitive to the starting conformation based on the testing results from the Trp-cage protein. In this method the simulated system is simultaneously modeled on atoms and coarse-grained particles with incremental coarsening levels. The dynamics of coarse-grained particles are adapted to the recent trajectories of finer-grained particles instead of fixed and parameterized energy functions as used in previous coarse-grained models. In addition, the compositions of coarse-grained particles are allowed to be updated automatically based on the coherence during its history. Starting from the fully extended conformation and other several different conformations of the Trp-cage protein, our method successfully finds out the native-like conformations of the Trp-cage protein in the largest cluster of the trajectories in all of the eight performed simulations within at most 10 ns simulation time. The results show that approaches based on multiscale modeling are promising for ab initio protein structure prediction.

  1. Seasonal dynamics of plankton communities coupled with ...

    African Journals Online (AJOL)

    Seasonal dynamics of plankton communities coupled with environmental factors ... In this study, we studied the influence of the physical-chemical and biological ... which are well related to changes in algae diversity and abundance, noting that ... The “top-down” effect of planktivorous fish on the zooplankton is a significant ...

  2. Single-cell protein dynamics reproduce universal fluctuations in cell populations

    CERN Document Server

    Brenner, Naama; Rotella, James S; Salman, Hanna

    2015-01-01

    Protein fluctuations in cell populations have recently been shown to exhibit a universal distribution shape under a broad range of biological realizations. Here, measuring protein content in individual bacteria continuously over ~70 generations, we show that single-cell trajectories fluctuate around their average with the same distribution shape as the population, i.e. their relative fluctuations are ergodic. Analysis of these temporal trajectories reveals that one effective random variable, sampled once each cell cycle, suffices to reconstruct the distribution from the trajectory. This in turn implies that cellular microscopic processes are strongly buffered and population-level protein distributions are insensitive to details of the intracellular dynamics. Probing them thus requires searching for novel universality-breaking experimental perturbations.

  3. Automatic determination of the arterial input function in dynamic susceptibility contrast MRI: comparison of different reproducible clustering algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Jiandong; Yang, Jiawen; Guo, Qiyong [Shengjing Hospital of China Medical University, Department of Radiology, Shenyang (China)

    2015-05-01

    Arterial input function (AIF) plays an important role in the quantification of cerebral hemodynamics. The purpose of this study was to select the best reproducible clustering method for AIF detection by comparing three algorithms reported previously in terms of detection accuracy and computational complexity. First, three reproducible clustering methods, normalized cut (Ncut), hierarchy (HIER), and fast affine propagation (FastAP), were applied independently to simulated data which contained the true AIF. Next, a clinical verification was performed where 42 subjects participated in dynamic susceptibility contrast MRI (DSC-MRI) scanning. The manual AIF and AIFs based on the different algorithms were obtained. The performance of each algorithm was evaluated based on shape parameters of the estimated AIFs and the true or manual AIF. Moreover, the execution time of each algorithm was recorded to determine the algorithm that operated more rapidly in clinical practice. In terms of the detection accuracy, Ncut and HIER method produced similar AIF detection results, which were closer to the expected AIF and more accurate than those obtained using FastAP method; in terms of the computational efficiency, the Ncut method required the shortest execution time. Ncut clustering appears promising because it facilitates the automatic and robust determination of AIF with high accuracy and efficiency. (orig.)

  4. Interobserver and Intraobserver Reproducibility with Volume Dynamic Contrast Enhanced Computed Tomography (DCE-CT in Gastroesophageal Junction Cancer

    Directory of Open Access Journals (Sweden)

    Martin Lundsgaard Hansen

    2016-02-01

    Full Text Available The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal junction cancer were selected from a previous longitudinal study. Three radiologists independently reviewed all scans, and one repeated the analysis eight months later for intraobserver analysis. Review of the scans consisted of three analysis methods: (I Four, fixed small sized regions of interest (2-dimensional (2D fixed ROIs placed in the tumor periphery, (II 2-dimensional regions of interest (2D-ROI along the tumor border in the tumor center, and (III 3-dimensional volumes of interest (3D-VOI containing the entire tumor volume. Arterial flow, blood volume and permeability (ktrans were recorded for each observation. Inter- and intra-observer variability were assessed by Intraclass Correlation Coefficient (ICC and Bland-Altman statistics. Interobserver ICC was excellent for arterial flow (0.88, for blood volume (0.89 and for permeability (0.91 with 3D-VOI analysis. The 95% limits of agreement were narrower for 3D analysis compared to 2D analysis. Three-dimensional volume DCE-CT analysis of gastroesophageal junction cancer provides higher inter- and intra-observer reproducibility with narrower limits of agreement between readers compared to 2D analysis.

  5. Interobserver and Intraobserver Reproducibility with Volume Dynamic Contrast Enhanced Computed Tomography (DCE-CT) in Gastroesophageal Junction Cancer.

    Science.gov (United States)

    Lundsgaard Hansen, Martin; Fallentin, Eva; Axelsen, Thomas; Lauridsen, Carsten; Norling, Rikke; Svendsen, Lars Bo; Nielsen, Michael Bachmann

    2016-02-01

    The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT) measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal junction cancer were selected from a previous longitudinal study. Three radiologists independently reviewed all scans, and one repeated the analysis eight months later for intraobserver analysis. Review of the scans consisted of three analysis methods: (I) Four, fixed small sized regions of interest (2-dimensional (2D) fixed ROIs) placed in the tumor periphery, (II) 2-dimensional regions of interest (2D-ROI) along the tumor border in the tumor center, and (III) 3-dimensional volumes of interest (3D-VOI) containing the entire tumor volume. Arterial flow, blood volume and permeability (k(trans)) were recorded for each observation. Inter- and intra-observer variability were assessed by Intraclass Correlation Coefficient (ICC) and Bland-Altman statistics. Interobserver ICC was excellent for arterial flow (0.88), for blood volume (0.89) and for permeability (0.91) with 3D-VOI analysis. The 95% limits of agreement were narrower for 3D analysis compared to 2D analysis. Three-dimensional volume DCE-CT analysis of gastroesophageal junction cancer provides higher inter- and intra-observer reproducibility with narrower limits of agreement between readers compared to 2D analysis.

  6. Intra-Rater Reproducibility and Validity of Nintendo Wii Balance Testing in Community-Dwelling Older Adults

    DEFF Research Database (Denmark)

    Jørgensen, Martin Grønbech; Laessoe, Uffe; Hendriksen, Carsten

    2014-01-01

    The aims of the current study were to (1) examine the intra-rater inter-session reproducibility of the Nintendo Wii Agility and Stillness tests and (2) explore the concurrent validity in relation to 'gold-standard' force plate analysis. Within-day inter-session reproducibility was examined in 30...

  7. Intra-Rater Reproducibility and Validity of Nintendo Wii Balance Testing in Community-Dwelling Older Adults

    DEFF Research Database (Denmark)

    Jørgensen, Martin Grønbech; Laessoe, Uffe; Hendriksen, Carsten;

    2014-01-01

    The aims of the current study were to (1) examine the intra-rater inter-session reproducibility of the Nintendo Wii Agility and Stillness tests and (2) explore the concurrent validity in relation to 'gold-standard' force plate analysis. Within-day inter-session reproducibility was examined in 30...

  8. Global change and terrestrial plant community dynamics.

    Science.gov (United States)

    Franklin, Janet; Serra-Diaz, Josep M; Syphard, Alexandra D; Regan, Helen M

    2016-04-05

    Anthropogenic drivers of global change include rising atmospheric concentrations of carbon dioxide and other greenhouse gasses and resulting changes in the climate, as well as nitrogen deposition, biotic invasions, altered disturbance regimes, and land-use change. Predicting the effects of global change on terrestrial plant communities is crucial because of the ecosystem services vegetation provides, from climate regulation to forest products. In this paper, we present a framework for detecting vegetation changes and attributing them to global change drivers that incorporates multiple lines of evidence from spatially extensive monitoring networks, distributed experiments, remotely sensed data, and historical records. Based on a literature review, we summarize observed changes and then describe modeling tools that can forecast the impacts of multiple drivers on plant communities in an era of rapid change. Observed responses to changes in temperature, water, nutrients, land use, and disturbance show strong sensitivity of ecosystem productivity and plant population dynamics to water balance and long-lasting effects of disturbance on plant community dynamics. Persistent effects of land-use change and human-altered fire regimes on vegetation can overshadow or interact with climate change impacts. Models forecasting plant community responses to global change incorporate shifting ecological niches, population dynamics, species interactions, spatially explicit disturbance, ecosystem processes, and plant functional responses. Monitoring, experiments, and models evaluating multiple change drivers are needed to detect and predict vegetation changes in response to 21st century global change.

  9. Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range

    Science.gov (United States)

    Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin; Sun, Shangjin; Rice, David; Hoch, Jeffrey C.; Rovnyak, David

    2014-01-01

    Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C, 15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high-quality artifact-free datasets. PMID:24752819

  10. Sensitivity Gains, Linearity, and Spectral Reproducibility in Nonuniformly Sampled Multidimensional MAS NMR Spectra of High Dynamic Range.

    Energy Technology Data Exchange (ETDEWEB)

    Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin; Sun, Shangjin; Rice, David M.; Hoch, Jeffrey C.; Rovnyak, David S.; Polenova, Tatyana E.

    2014-04-22

    Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C,15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high quality artifact-free datasets.

  11. Astaxanthin dynamics in Baltic Sea mesozooplankton communities

    Science.gov (United States)

    Snoeijs, Pauline; Häubner, Norbert

    2014-01-01

    The red pigment astaxanthin is a powerful antioxidant, which occurs in eggs and body tissues of crustaceans and fish. It is produced by crustaceans from algal carotenoids. In a two-year field study we assessed natural concentrations and dynamics of astaxanthin in mesozooplankton communities in the brackish Baltic Sea area. Astaxanthin levels varied between 0.37 and 36 ng L- 1. They increased with salinity along the Baltic Sea gradient and were linked to zooplankton biomass and phytoplankton community composition. Astaxanthin concentrations showed typical seasonal patterns and varied from 0.2 to 5.1 ng ind- 1, 0.2 to 3.4 ng (μg C)- 1 and 6 to 100 ng mm- 3. These concentrations were inversely related to water temperature and strongly linked to zooplankton community composition. Communities dominated by the calanoid copepods Temora longicornis, Pseudocalanus acuspes and Eurytemora spp. generally held the highest concentrations. With increasing cladocerans:copepods biomass ratios community astaxanthin concentrations decreased and with higher relative biomass of Acartia spp. the proportion of astaxanthin diesters decreased. Diesters prevailed in the cold season and they are thought to improve the antioxidant protection of storage lipids during winter. Climate change causes higher temperature and lower salinity in the Baltic Sea proper. This modifies zooplankton community composition, but not necessarily into a community with lower concentrations of astaxanthin since T. longicornis (high concentrations) has been reported to increase with higher temperature. However, decreased astaxanthin production in the ecosystem is expected if a basin-wide increase in the cladocerans:copepods biomass ratios would occur with further climate change.

  12. Jellyfish modulate bacterial dynamic and community structure.

    Science.gov (United States)

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

  13. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  14. Disturbance and the dynamics of fynbos biome communities

    CSIR Research Space (South Africa)

    Cowling, RM

    1987-01-01

    Full Text Available exclusively on fire regime effects. The chapters include contributions on fire regimes, life history strategies, canopy-and soil-stored seed bank dynamics, small mammal community dynamics and ecosystem nutrient dynamics. Most chapters address the effect...

  15. Intra-rater reproducibility and validity of Nintendo Wii Balance Tests in community-dwelling Older Adults

    DEFF Research Database (Denmark)

    Jørgensen, Martin; Læssøe, Uffe; Hendriksen, C

    2014-01-01

    The aims of the current study were to examine the intrarater intersession reproducibility of the Nintendo Wii agility and stillness tests and explore the concurrent validity in relation to gold-standard force-plate analysis. Within-day intersession reproducibility was examined in 30 older adults......% of 17.9%. Likewise for the Wii agility test ICC was .73 (95% CI 0.50-0.86), CV 5.3%, LOA 1.8, and LOA% of 14.6%. Wii stillness scores correlated to force plate measures (r = .65-.82, p

  16. Elusive reproducibility.

    Science.gov (United States)

    Gori, Gio Batta

    2014-08-01

    Reproducibility remains a mirage for many biomedical studies because inherent experimental uncertainties generate idiosyncratic outcomes. The authentication and error rates of primary empirical data are often elusive, while multifactorial confounders beset experimental setups. Substantive methodological remedies are difficult to conceive, signifying that many biomedical studies yield more or less plausible results, depending on the attending uncertainties. Real life applications of those results remain problematic, with important exceptions for counterfactual field validations of strong experimental signals, notably for some vaccines and drugs, and for certain safety and occupational measures. It is argued that industrial, commercial and public policies and regulations could not ethically rely on unreliable biomedical results; rather, they should be rationally grounded on transparent cost-benefit tradeoffs.

  17. Market dynamics of community pharmacies in Minnesota.

    Science.gov (United States)

    Schommer, Jon C; Singh, Reshmi L; Cline, Richard R; Hadsall, Ronald S

    2006-09-01

    From a pharmacist workforce perspective, an understanding of pharmacy location is important for monitoring access points for pharmacist services such as medication dispensing, medication counseling, medication therapy management, and disease management. To understand access to community pharmacies, our goal was to describe changes in pharmacy mix (independent vs chain) between 1992 and 2002 for 87 counties in Minnesota. Study objectives were to describe the association of (1) change in population density, (2) metropolitan designation, change in (3) proportion of nonwhite population, (4) proportion of elderly population, and (5) household income with change in (a) number of community pharmacies overall, (b) number of chain pharmacies, (c) number of independent pharmacies, and (d) the independent-to-total community pharmacy ratio. Records from the State of Minnesota Board of Pharmacy were used to examine changes in the community pharmacy mix from 1992 to 2002. Data on county level demographics in 1990 and 2000 were obtained from the US Census Bureau and Datanet. Chi-square analysis was used to test the relationships between the independent and dependent variables. As of 2002, every county in Minnesota had at least one pharmacy as was the case in 1992. The ratio of independent to chain pharmacies changed from approximately 2:1 in 1992 to approximately 1:1 in 2002. Chi-square results revealed that change in population density was significantly associated with change in the number of community pharmacies overall (Pchain pharmacies (P=0.03). The findings revealed an interesting u-shaped pattern for the association between population density and change in independent pharmacies. It appears that chain pharmacies follow changes in population density for making decisions about market entry and exit. The results suggest that some independent pharmacies might be closing due to chain competition in high population density growth areas. However, there was also evidence to

  18. Identifying communities by influence dynamics in social networks

    CERN Document Server

    Stanoev, Angel; Kocarev, Ljupco

    2011-01-01

    Communities are not static; they evolve, split and merge, appear and disappear, i.e. they are product of dynamical processes that govern the evolution of the network. A good algorithm for community detection should not only quantify the topology of the network, but incorporate the dynamical processes that take place on the network. We present a novel algorithm for community detection that combines network structure with processes that support creation and/or evolution of communities. The algorithm does not embrace the universal approach but instead tries to focus on social networks and model dynamic social interactions that occur on those networks. It identifies leaders, and communities that form around those leaders. It naturally supports overlapping communities by associating each node with a membership vector that describes node's involvement in each community. This way, in addition to overlapping communities, we can identify nodes that are good followers to their leader, and also nodes with no clear commu...

  19. Enabling dynamic access to dynamic petascale Earth Systems and Environmental data collections is easy: citing and reproducing the actual data extracts used in research publications is NOT

    Science.gov (United States)

    Wyborn, L. A.; Wang, J.; Si, W.; Druken, K. A.; Evans, B. J. K.; Klump, J. F.; Car, N. J.; Trenham, C.

    2015-12-01

    The National Computational Infrastructure (NCI) at the Australian National University (ANU) has collocated over 10 PB of national and international Earth Systems and Environmental data assets within a HPC facility to create the National Environmental Research Data Interoperability Platform (NERDIP). Data are replicated to, or are produced at, NCI: in many cases they are processed to higher-level data products. Individual data sets within these collections can range from multi-petabyte climate models and large volume raster arrays, down to gigabyte size, ultra-high resolution data sets. All data are quality assured to being 'published' and made accessible as services. Persistent identifiers are assigned during publishing at both the collection and data set level: the granularity and version control on persistent identifiers depend on the dataset. However, most NERDIP collections are dynamic: either new data is being appended, or else models/derivative products are being revised with new data, or changed as processing methods are improved. Further, because the data are accessible as services, researchers can log in and dynamically create user-defined subsets for specific research projects: inevitably such extracts underpin traditional 'publications'. Being able to reproduce these exact data extracts can be difficult and for the very larger data sets preserving a copy of large data extracts is out of the question. A solution is for the researcher to use provenance workflows that at a minimum capture the version of the data set used, the query and the time of extraction. In parallel, the data provider needs to implement version controls on the data and deploy tracking systems that time stamp when new data are appended, or when modifications are made to existing data and record what these changes are. Where, when and how persistent identifiers are minted on these large and dynamically changing data sets is still open to debate.

  20. Tissue oximetry: a comparison of mean values of regional tissue saturation, reproducibility and dynamic range of four NIRS-instruments on the human forearm

    DEFF Research Database (Denmark)

    Hyttel-Sørensen, Simon; Sorensen, Line C; Riera, Joan

    2011-01-01

    We compared absolute values of regional tissue hemoglobin saturation (StO(2)), reproducibility, and dynamic range of four different instruments on the forearm of adults. The sensors were repositioned 10 times on each subject. Dynamic range was estimated by exercise with subsequent arterial...... occlusion. Mean StO(2) was 70.1% ± 6.7 with INVOS 5100, 69.4% ± 5.0 with NIRO 200 NX, 63.4% ± 4.5 with NIRO 300, and 60.8% ± 3.6 with OxyPrem. The corresponding reproducibility S(w) was 5.4% (CI 4.4-6.9), 4.4% (CI 3.5-5.2), 4.1% (CI 3.3-4.9), and 2.7% (CI 2.2-3.2), respectively. The dynamic ranges ¿StO(2......) were 45.0%, 46.8%, 44.8%, and 27.8%, respectively. In conclusion, the three commercial NIRS instruments showed different absolute values, whereas reproducibility and dynamic range were quite similar....

  1. Tissue oximetry: a comparison of mean values of regional tissue saturation, reproducibility and dynamic range of four NIRS-instruments on the human forearm

    DEFF Research Database (Denmark)

    Hyttel-Sørensen, Simon; Sorensen, Line C; Riera, Joan

    2011-01-01

    We compared absolute values of regional tissue hemoglobin saturation (StO(2)), reproducibility, and dynamic range of four different instruments on the forearm of adults. The sensors were repositioned 10 times on each subject. Dynamic range was estimated by exercise with subsequent arterial...... occlusion. Mean StO(2) was 70.1% ± 6.7 with INVOS 5100, 69.4% ± 5.0 with NIRO 200 NX, 63.4% ± 4.5 with NIRO 300, and 60.8% ± 3.6 with OxyPrem. The corresponding reproducibility S(w) was 5.4% (CI 4.4-6.9), 4.4% (CI 3.5-5.2), 4.1% (CI 3.3-4.9), and 2.7% (CI 2.2-3.2), respectively. The dynamic ranges ΔStO(2......) were 45.0%, 46.8%, 44.8%, and 27.8%, respectively. In conclusion, the three commercial NIRS instruments showed different absolute values, whereas reproducibility and dynamic range were quite similar....

  2. SCOUT: simultaneous time segmentation and community detection in dynamic networks

    CERN Document Server

    Hulovatyy, Yuriy

    2016-01-01

    Many evolving complex systems can be modeled via dynamic networks. An important problem in dynamic network research is community detection, which identifies groups of topologically related nodes. Typically, this problem is approached by assuming either that each time point has a distinct community organization or that all time points share one community organization. In reality, the truth likely lies between these two extremes, since some time periods can have community organization that evolves while others can have community organization that stays the same. To find the compromise, we consider community detection in the context of the problem of segment detection, which identifies contiguous time periods with consistent network structure. Consequently, we formulate a combined problem of segment community detection (SCD), which simultaneously partitions the network into contiguous time segments with consistent community organization and finds this community organization for each segment. To solve SCD, we int...

  3. A Dynamic Metadata Community Profile for CUAHSI

    Science.gov (United States)

    Bermudez, L.; Piasecki, M.

    2004-12-01

    Common Metadata standards typically lack of domain specific elements, have limited extensibility and do not always resolve semantic heterogeneities that could occur in the annotations. To facilitate the use and extension of metadata specifications a methodology called Dynamic Community Profiles, DCP, is presented. The methodology allows to overwrite elements definitions and to specify core elements as metadata tree paths. DCP uses the Web Ontology Language (OWL), the Resource Description Framework (RDF) and XML syntax to formalize specifications and to create controlled vocabularies in ontologies, which enhances interoperability. This methodology was employed to create a metadata profile for the Consortium of Universities for the Advancement of Hydrologic Science Inc. (CUAHSI). The profile was created by extending ISO-19115:2003 geographic metadata standard and restricting the permissible values of some elements. The values used as controlled vocabularies were inferred from hydrologic keywords found in the Global Change Master Directory (GCMD) and from measurement units found in the Hydrologic Handbook. Also, a core metadata set for CUAHSI was formally expressed as tree paths, containing the ISO core set plus additional elements. Finally a tool was developed to test the extension and to allow creation of metadata instances in RDF/XML which conforms to the profile. Also this tool is able to export the core elements to other schema formats such as Metadata Template Files (MTF).

  4. Inter-reader reproducibility of dynamic contrast-enhanced magnetic resonance imaging in patients with non-small cell lung cancer treated with bevacizumab and erlotinib.

    Science.gov (United States)

    van den Boogaart, Vivian E M; de Lussanet, Quido G; Houben, Ruud M A; de Ruysscher, Dirk; Groen, Harry J M; Marcus, J Tim; Smit, Egbert F; Dingemans, Anne-Marie C; Backes, Walter H

    2016-03-01

    Objectives When evaluating anti-tumor treatment response by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) it is necessary to assure its validity and reproducibility. This has not been well addressed in lung tumors. Therefore we have evaluated the inter-reader reproducibility of response classification by DCE-MRI in patients with non-small cell lung cancer (NSCLC) treated with bevacizumab and erlotinib enrolled in a multicenter trial. Twenty-one patients were scanned before and 3 weeks after start of treatment with DCE-MRI in a multicenter trial. The scans were evaluated by two independent readers. The primary lung tumor was used for response assessment. Responses were assessed in terms of relative changes in tumor mean trans endothelial transfer rate (K(trans)) and its heterogeneity in terms of the spatial standard deviation. Reproducibility was expressed by the inter-reader variability, intra-class correlation coefficient (ICC) and dichotomous response classification. The inter-reader variability and ICC for the relative K(trans) were 5.8% and 0.930, respectively. For tumor heterogeneity the inter-reader variability and ICC were 0.017 and 0.656, respectively. For the two readers the response classification for relative K(trans) was concordant in 20 of 21 patients (k=0.90, preader variability and reproducibility of response classification by the two readers of lung cancer DCE-MRI scans. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. A new dynamic null model for phylogenetic community structure.

    Science.gov (United States)

    Pigot, Alex L; Etienne, Rampal S

    2015-02-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.

  6. Evolution properties of the community members for dynamic networks

    Science.gov (United States)

    Yang, Kai; Guo, Qiang; Li, Sheng-Nan; Han, Jing-Ti; Liu, Jian-Guo

    2017-03-01

    The collective behaviors of community members for dynamic social networks are significant for understanding evolution features of communities. In this Letter, we empirically investigate the evolution properties of the new community members for dynamic networks. Firstly, we separate data sets into different slices, and analyze the statistical properties of new members as well as communities they joined in for these data sets. Then we introduce a parameter φ to describe community evolution between different slices and investigate the dynamic community properties of the new community members. The empirical analyses for the Facebook, APS, Enron and Wiki data sets indicate that both the number of new members and joint communities increase, the ratio declines rapidly and then becomes stable over time, and most of the new members will join in the small size communities that is s ≤ 10. Furthermore, the proportion of new members in existed communities decreases firstly and then becomes stable and relatively small for these data sets. Our work may be helpful for deeply understanding the evolution properties of community members for social networks.

  7. Intraobserver reproducibility of parameters of standard and 2D speckle tracking echocardiography, dynamics of global longitudinal strain I in patients with acute primary anterior STEMI

    Science.gov (United States)

    Kercheva, M.; Ryabova, T.; Ryabov, V.; Karpov, R.

    2015-11-01

    The aim of this study was to assess the intraobserver reproducibility of parameters of standard and 2 dimensional speckle tracking echocardiography, dynamics of global longitudinal strain in patients with acute primary anterior STEMI. The study included 24 patients, mean age 58.46±10.2. Echocardiography with 2D speckle tracking imaging was performed on the 1st (T1), 7th (T2), 14th days (T3) after STEMI («Vivid E9»). Analysis of echocardiographic images was performed offline at the different periods by the two independent observers (EchoPac) - experienced and inexperienced. In order to assess the agreement between standard and 2D speckle tracking echocardiography, a correlation analysis (Pearson correlation, Spearman's rank correlation coefficient) and Bland-Altman analysis were undertaken. The 23 patients had urgent reperfusion therapy, 6 patients underwent primary PCI, 16 patients - PCI after successful fibrinolysis (68%). GLS and WMSI had the best intraobsever reproducibility. Dynamics of EDV LV, ESV LV, EF LV was without significant differences. Nevertheless, it was found positive dynamic of GLS: - 12.65±3.53 (T1), -13.61±3.81 (T2), -14.27±4.1 (T3), pspeckle-tracking and standard echocardiography was revealed in GLS and WMSI. The modern management of STEMI patients limits adverse postinfarction remodeling and preserves of global left ventricular contractility detected by the EF LV. However, GLS had the positive dynamics and improved to the 14th day.

  8. On the frequency and reproducibility of orthostatic blood pressure changes in healthy community-dwelling elderly during 60-degree head-up tilt.

    Science.gov (United States)

    Patel, A; Maloney, A; Damato, A N

    1993-07-01

    The postural effects of 20 minutes of 60-degree head-up tilt on systolic, diastolic, and mean arterial blood pressures (BPs), heart rate, and rhythm were studied in 70 healthy, community-dwelling volunteer subjects of both sexes, divided into three age groups. Group A consisted of 30 subjects, with a mean age of 76 years (range 65 to 95 years); group B had 19 subjects, with a mean age of 54 years (range 45 to 64 years); and group C had 21 subjects, with a mean age of 33 years (range 24 to 44 years). To qualify, subjects had to have a systolic BP of 150 mm Hg or less and a diastolic BP of 20 mm Hg (p < 0.05). The mean time for the systolic blood pressure drops in group A was 9.2 minutes. Results were reproducible upon retesting after 1 week.

  9. Dynamics and control of diseases in networks with community structure.

    Directory of Open Access Journals (Sweden)

    Marcel Salathé

    2010-04-01

    Full Text Available The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc. depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.

  10. Benefit sharing and community participation dynamics in forest management

    DEFF Research Database (Denmark)

    Antony, Bindu; Treue, Thorsten; Salim, Shyam S.;

    2014-01-01

    Community forestry has a significant role in the lives of people in Nepal as it serves the livelihood security of people to a greater extent. It is central in ensuring community participation in all the stages of CF (Community forestry) process and thus reach the objectives of sustainable forest...... on the dynamics of participation in forest management, especially on the link between distribution of benefits, and the level of participation of members, by exploring the process of institutional management and community governance. The study was undertaken in 178 households of Kankali community forestry...

  11. Marine reserve designation, trophic cascades and altered community dynamics

    National Research Council Canada - National Science Library

    David O’Sullivan; Mark Emmerson

    2011-01-01

    Marine ecosystems and their associated populations are increasingly at risk from the cumulative impacts of many anthropogenic threats that increase the likelihood of species extinction and altered community dynamics...

  12. A new dynamic null model for phylogenetic community structure

    NARCIS (Netherlands)

    Pigot, Alex L; Etienne, Rampal S

    2015-01-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by

  13. Reproducing morphologies of disorderly self-assembling planar molecules with static and dynamic simulation methods by matching density

    Science.gov (United States)

    Bumstead, M.; Arnold, B.; Turak, A.

    2017-04-01

    Monte Carlo and molecular dynamics simulations are the two main numerical approaches to modeling molecular self-assembly and ordering. Conceptually, however, each method explores different paths through the thermodynamic landscape. Molecular dynamics depends on the position and momentum terms. Monte Carlo is a static set, and thus the momentum term is replaced with an energy term that is dependent on the volume and entropy. Until now, it was unclear if a stochastic process of densifying particles would have the same internal structure as morphologies produced from classical mechanics. This paper provides a systematic (i.e., statistical) analysis of the outcomes of 4032 simulations for hard-core circular objects as a function of the number of molecules and the boundary conditions. Structural classification of the resultant ensembles (averaged pair correlation function, bond-order parameter, translational order parameter, and Voronoi diagrams) shows that stochastic and dynamic approaches do not alter the morphology of the steric molecules. We conclude that when the probability density of covering area fractions are matched, the ensembles produced from the two methods will show the same level of structural disorder and positional patterns. The resultant morphology from both models, therefore, is not a product of dynamic unrest, but that of the relaxation of entropic frustration from macromolecular crowding. Although statistically the two methods produce similar configurations, nuances arise from the static and dynamic nature of modeling. As a result, Monte Carlo is slightly better suited to modeling systems when the desired morphology is represented by a metastable state; molecular dynamics on the other hand is more suited to finding defects that can arise in morphologies. Regardless, a fixed density will result in similar morphologies from both techniques, driven by similar configurational entropy.

  14. Dynamics and comparative statics of mutualistic communities

    Energy Technology Data Exchange (ETDEWEB)

    Travis, C.C.; Post, W.M. III

    1979-01-01

    The sensitivity of mutualistic communities to perturbations from equilibrium is examined, and the factors which regulate this sensitivity are discussed in both biological and mathematical terms. The response of equilibrium population densities to changes in environmental and biological parameters is also investigated. These investigations are then extended to include communities which allow for a limited form of competition. The results are discussed in terms of the familiar two species Lotka-Volterra equations.

  15. A computational model incorporating neural stem cell dynamics reproduces glioma incidence across the lifespan in the human population.

    Directory of Open Access Journals (Sweden)

    Roman Bauer

    Full Text Available Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.

  16. Assessment of reproducibility and stability of different breath-hold maneuvres by dynamic MRI: comparison between healthy adults and patients with pulmonary hypertension

    Energy Technology Data Exchange (ETDEWEB)

    Plathow, Christian [German Cancer Research Center Heidelberg, Department of Radiology, Heidelberg (Germany); Eberhard-Karls-University Tuebingen, Department of Diagnostic Radiology, Tuebingen (Germany); Ley, Sebastian; Zaporozhan, Julia; Puderbach, Michael; Eichinger, Monika; Zuna, Ivan; Kauczor, Hans-Ulrich [German Cancer Research Center Heidelberg, Department of Radiology, Heidelberg (Germany); Schoebinger, Max; Meinzer, Hans-Peter [German Cancer Research Center Heidelberg, Department of Medical and Biological Informatics, Heidelberg (Germany); Gruenig, Ekkehard [University of Heidelberg, Department of Internal Medicine III, Heidelberg (Germany)

    2006-01-01

    To assess the stability and reproducibility of different breath-hold levels in healthy volunteers and patients using dynamic MRI (dMRI). In ten healthy volunteers and ten patients with pulmonary hypertension (PH) and normal lung function craniocaudal intrathoracic distances (CCD) were measured during inspiratory and expiratory breath-hold (15 s) (in healthy volunteers additionally at a self-chosen mid-inspiratory breath-hold) using dMRI (trueFISP, three images/s). To evaluate stability and intraobserver reproducibility of the different breath-hold levels, CCDs, time-distance curves, confidence intervals (CIs), Mann-Witney U test and regression equations were calculated. In healthy volunteers there was a substantial decrease of the CCD during the inspiratory breath-hold in contrast to the expiratory breath-hold. The CI at inspiration was 2.84{+-}1.28 in the right and 2.1{+-}0.68 in the left hemithorax. At expiration the CI was 2.54{+-}1.18 and 2.8{+-}1.48. Patients were significantly less able to hold their breath at inspiration than controls (P<0.05). In patients CI was 4.53{+-}4.06 and 3.46{+-}2.21 at inspiration and 4.45{+-}4.23 and 4.76{+-}3.73 at expiration. Intraobserver variability showed no significant differences either in patients or in healthy subjects. Reproducibility was significantly lower at a self-chosen breath-hold level of the healthy volunteers. DMRI is able to differentiate stability and reproducibility of different breath-hold levels. Expiratory breath-hold proved to be more stable than inspiratory breath-hold in healthy volunteers and patients. (orig.)

  17. Demonstration of the reproducibility of free-breathing diffusion-weighted MRI and dynamic contrast enhanced MRI in children with solid tumours: a pilot study

    Energy Technology Data Exchange (ETDEWEB)

    Miyazaki, Keiko; Jerome, Neil P.; Collins, David J.; Orton, Matthew R.; D' Arcy, James A.; Leach, Martin O. [Cancer Research UK Cancer Imaging Centre at The Institute of Cancer Research, London (United Kingdom); Wallace, Toni; Koh, Dow-Mu [Royal Marsden Hospital, Department of Radiology, London, England (United Kingdom); Moreno, Lucas [The Institute of Cancer Research, Paediatric Drug Development Team, Divisions of Cancer Therapeutics and Clinical Studies, London (United Kingdom); Spanish National Cancer Research Centre (CNIO), Clinical Research Programme, Madrid (Spain); The Royal Marsden NHS Foundation Trust, Paediatric Drug Development Unit, Children and Young People' s Unit, Sutton (United Kingdom); Pearson, Andrew D.J.; Marshall, Lynley V.; Carceller, Fernando; Zacharoulis, Stergios [The Institute of Cancer Research, Paediatric Drug Development Team, Divisions of Cancer Therapeutics and Clinical Studies, London (United Kingdom); The Royal Marsden NHS Foundation Trust, Paediatric Drug Development Unit, Children and Young People' s Unit, Sutton (United Kingdom)

    2015-09-15

    The objectives are to examine the reproducibility of functional MR imaging in children with solid tumours using quantitative parameters derived from diffusion-weighted (DW-) and dynamic contrast enhanced (DCE-) MRI. Patients under 16-years-of age with confirmed diagnosis of solid tumours (n = 17) underwent free-breathing DW-MRI and DCE-MRI on a 1.5 T system, repeated 24 hours later. DW-MRI (6 b-values, 0-1000 sec/mm{sup 2}) enabled monoexponential apparent diffusion coefficient estimation using all (ADC{sub 0-1000}) and only ≥100 sec/mm{sup 2} (ADC{sub 100-1000}) b-values. DCE-MRI was used to derive the transfer constant (K{sup trans}), the efflux constant (k{sub ep}), the extracellular extravascular volume (v{sub e}), and the plasma fraction (v{sub p}), using a study cohort arterial input function (AIF) and the extended Tofts model. Initial area under the gadolinium enhancement curve and pre-contrast T{sub 1} were also calculated. Percentage coefficients of variation (CV) of all parameters were calculated. The most reproducible cohort parameters were ADC{sub 100-1000} (CV = 3.26 %), pre-contrast T{sub 1} (CV = 6.21 %), and K{sup trans} (CV = 15.23 %). The ADC{sub 100-1000} was more reproducible than ADC{sub 0-1000}, especially extracranially (CV = 2.40 % vs. 2.78 %). The AIF (n = 9) derived from this paediatric population exhibited sharper and earlier first-pass and recirculation peaks compared with the literature's adult population average. Free-breathing functional imaging protocols including DW-MRI and DCE-MRI are well-tolerated in children aged 6 - 15 with good to moderate measurement reproducibility. (orig.)

  18. Seasonal sediment dynamics shape temperate bedrock reef communities

    Science.gov (United States)

    Figurski, Jared D.; Freiwald, Jan; Lonhart, Steve I.; Storlazzi, Curt

    2016-01-01

    Mobilized seafloor sediment can impact benthic reef communities through burial, scour, and turbidity. These processes are ubiquitous in coastal oceans and, through their influence on the survival, fitness, and interactions of species, can alter the structure and function of benthic communities. In northern Monterey Bay, California, USA, as much as 30% of the seafloor is buried or exposed seasonally, making this an ideal location to test how subtidal temperate rocky reef communities vary in the presence and absence of chronic sediment-based disturbances. Designated dynamic plots were naturally inundated by sediment in summer (50 to 100% cover) and swept clean in winter, whereas designated stable plots remained free of sediment during our study. Multivariate analyses indicated significant differences in the structure of sessile and mobile communities between dynamic and stable reef habitats. For sessile species, community structure in disturbed plots was less variable in space and time than in stable plots due to the maintenance of an early successional state. In contrast, community structure of mobile species varied more in disturbed plots than in stable plots, reflecting how mobile species distribute in response to sediment dynamics. Some species were found only in these disturbed areas, suggesting that the spatial mosaic of disturbance could increase regional diversity. We discuss how the relative ability of species to tolerate disturbance at different life history stages and their ability to colonize habitat translate into community-level differences among habitats, and how this response varies between mobile and sessile communities.

  19. A novel dynamical community detection algorithm based on weighting scheme

    Science.gov (United States)

    Li, Ju; Yu, Kai; Hu, Ke

    2015-12-01

    Network dynamics plays an important role in analyzing the correlation between the function properties and the topological structure. In this paper, we propose a novel dynamical iteration (DI) algorithm, which incorporates the iterative process of membership vector with weighting scheme, i.e. weighting W and tightness T. These new elements can be used to adjust the link strength and the node compactness for improving the speed and accuracy of community structure detection. To estimate the optimal stop time of iteration, we utilize a new stability measure which is defined as the Markov random walk auto-covariance. We do not need to specify the number of communities in advance. It naturally supports the overlapping communities by associating each node with a membership vector describing the node's involvement in each community. Theoretical analysis and experiments show that the algorithm can uncover communities effectively and efficiently.

  20. Fungal community dynamics and driving factors during agricultural waste composting.

    Science.gov (United States)

    Yu, Man; Zhang, Jiachao; Xu, Yuxin; Xiao, Hua; An, Wenhao; Xi, Hui; Xue, Zhiyong; Huang, Hongli; Chen, Xiaoyang; Shen, Alin

    2015-12-01

    This study was conducted to identify the driving factors behind fungal community dynamics during agricultural waste composting. Fungal community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis combined with DNA sequencing. The effects of physico-chemical parameters on fungal community abundance and structure were evaluated by least significant difference tests and redundancy analysis. The results showed that Cladosporium bruhnei, Hanseniaspora uvarum, Scytalidium thermophilum, Tilletiopsis penniseti, and Coprinopsis altramentaria were prominent during the composting process. The greatest variation in the distribution of fungal community structure was statistically explained by pile temperature and total organic carbon (TOC) (P composting.

  1. Opinion Dynamics on Complex Networks with Communities

    Science.gov (United States)

    Wang, Ru; Chi, Li-Ping

    2008-04-01

    The Ising or Potts models of ferromagnetism have been widely used to describe locally interacting social or economic systems. We consider a related model, introduced by Sznajd to describe the evolution of consensus in the scale-free networks with the tunable strength (noted by Q) of community structure. In the Sznajd model, the opinion or state of any spins can only be changed by the influence of neighbouring pairs of similar connection spins. Such pairs can polarize their neighbours. Using asynchronous updating, it is found that the smaller the community strength Q, the larger the slope of the exponential relaxation time distribution. Then the effect of the initial up- spin concentration p as a function of the final all up probability E is investigated by taking different initialization strategies, the random node-chosen initialization strategy has no difference under different community strengths, while the strategies of community node-chosen initialization and hub node-chosen initialization are different in final probability under different Q, and the latter one is more effective in reaching final state.

  2. Opinion Dynamics on Complex Networks with Communities

    Institute of Scientific and Technical Information of China (English)

    WANG Ru; CHI Li-Ping; CAI Xu

    2008-01-01

    @@ The Ising or Ports models of ferromagnetism have been widely used to describe locally interacting social or economic systems. We consider a related model, introduced by Sznajd to describe the evolution of consensus in the scale-free networks with the tunable strength (noted by Q) of community structure. In the Sznajd model, the opinion or state of any spins can only be changed by the influence of neighbouring pairs of similar connection spins.Such pairs can polarize their neighbours. Using asynchronous updating, it is found that the smaller the community strength Q, the larger the slope of the exponential relaxation time distribution. Then the effect of the initial upspin concentration p as a function of the final all up probability E is investigated by taking different initialization strategies, the random node-chosen initialization strategy has no difference under different community strengths,while the strategies of community node-chosen initialization and hub node-chosen initialization are different in final probability under different Q, and the latter one is more effective in reaching final state.

  3. Emergence of structured communities through evolutionary dynamics.

    Science.gov (United States)

    Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

    2015-10-21

    Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Trait diversity promotes stability of community dynamics

    DEFF Research Database (Denmark)

    Zhang, Lai; Thygesen, Uffe Høgsbro; Knudsen, Kim;

    2013-01-01

    The theoretical exploration of how diversity influences stability has traditionally been approached by species-centric methods. Here we offer an alternative approach to the diversity–stability problem by examining the stability and dynamics of size and trait distributions of individuals. The anal...

  5. Identification of Nonlinear Spatiotemporal Dynamical Systems With Nonuniform Observations Using Reproducing-Kernel-Based Integral Least Square Regulation.

    Science.gov (United States)

    Ning, Hanwen; Qing, Guangyan; Jing, Xingjian

    2016-11-01

    The identification of nonlinear spatiotemporal dynamical systems given by partial differential equations has attracted a lot of attention in the past decades. Several methods, such as searching principle-based algorithms, partially linear kernel methods, and coupled lattice methods, have been developed to address the identification problems. However, most existing methods have some restrictions on sampling processes in that the sampling intervals should usually be very small and uniformly distributed in spatiotemporal domains. These are actually not applicable for some practical applications. In this paper, to tackle this issue, a novel kernel-based learning algorithm named integral least square regularization regression (ILSRR) is proposed, which can be used to effectively achieve accurate derivative estimation for nonlinear functions in the time domain. With this technique, a discretization method named inverse meshless collocation is then developed to realize the dimensional reduction of the system to be identified. Thereafter, with this novel inverse meshless collocation model, the ILSRR, and a multiple-kernel-based learning algorithm, a multistep identification method is systematically proposed to address the identification problem of spatiotemporal systems with pointwise nonuniform observations. Numerical studies for benchmark systems with necessary discussions are presented to illustrate the effectiveness and the advantages of the proposed method.

  6. Modeling community structure and topics in dynamic text networks

    CERN Document Server

    Henry, Teague; Chai, Christine; Owens-Oas, Derek

    2016-01-01

    The last decade has seen great progress in both dynamic network modeling and topic modeling. This paper draws upon both areas to create a Bayesian method that allows topic discovery to inform the latent network model and the network structure to facilitate topic identification. We apply this method to the 467 top political blogs of 2012. Our results find complex community structure within this set of blogs, where community membership depends strongly upon the set of topics in which the blogger is interested.

  7. Estimating cyanobacteria community dynamics and its relationship with environmental factors.

    Science.gov (United States)

    Luo, Wenhuai; Chen, Huirong; Lei, Anping; Lu, Jun; Hu, Zhangli

    2014-01-20

    The cyanobacteria community dynamics in two eutrophic freshwater bodies (Tiegang Reservoir and Shiyan Reservoir) was studied with both a traditional microscopic counting method and a PCR-DGGE genotyping method. Results showed that cyanobacterium Phormidium tenue was the predominant species; twenty-six cyanobacteria species were identified in water samples collected from the two reservoirs, among which fourteen were identified with the morphological method and sixteen with the PCR-DGGE method. The cyanobacteria community composition analysis showed a seasonal fluctuation from July to December. The cyanobacteria population peaked in August in both reservoirs, with cell abundances of 3.78 × 10(8) cells L(-1) and 1.92 × 10(8) cells L(-1) in the Tiegang and Shiyan reservoirs, respectively. Canonical Correspondence Analysis (CCA) was applied to further investigate the correlation between cyanobacteria community dynamics and environmental factors. The result indicated that the cyanobacteria community dynamics was mostly correlated with pH, temperature and total nitrogen. This study demonstrated that data obtained from PCR-DGGE combined with a traditional morphological method could reflect cyanobacteria community dynamics and its correlation with environmental factors in eutrophic freshwater bodies.

  8. Estimating Cyanobacteria Community Dynamics and its Relationship with Environmental Factors

    Science.gov (United States)

    Luo, Wenhuai; Chen, Huirong; Lei, Anping; Lu, Jun; Hu, Zhangli

    2014-01-01

    The cyanobacteria community dynamics in two eutrophic freshwater bodies (Tiegang Reservoir and Shiyan Reservoir) was studied with both a traditional microscopic counting method and a PCR-DGGE genotyping method. Results showed that cyanobacterium Phormidium tenue was the predominant species; twenty-six cyanobacteria species were identified in water samples collected from the two reservoirs, among which fourteen were identified with the morphological method and sixteen with the PCR-DGGE method. The cyanobacteria community composition analysis showed a seasonal fluctuation from July to December. The cyanobacteria population peaked in August in both reservoirs, with cell abundances of 3.78 × 108 cells L-1 and 1.92 × 108 cells L-1 in the Tiegang and Shiyan reservoirs, respectively. Canonical Correspondence Analysis (CCA) was applied to further investigate the correlation between cyanobacteria community dynamics and environmental factors. The result indicated that the cyanobacteria community dynamics was mostly correlated with pH, temperature and total nitrogen. This study demonstrated that data obtained from PCR-DGGE combined with a traditional morphological method could reflect cyanobacteria community dynamics and its correlation with environmental factors in eutrophic freshwater bodies. PMID:24448632

  9. Semiotic Dynamics in Online Social Communities

    Science.gov (United States)

    Cattuto, C.

    2007-11-01

    A distributed classification paradigm known as collaborative tagging has been successfully deployed in large-scale web applications designed to manage and share diverse online resources. Users of these applications organize resources by associating with them freely chosen text labels, or tags. Here we regard tags as basic dynamical entities and study the semiotic dynamics underlying collaborative tagging. We collect data from a popular system and focus on tags associated with a given resource. We find that the frequencies of tags obey to a generalized Zipf's law and show that a Yule-Simon process with memory can be used to explain the observed frequency distributions in terms of a simple model of user behavior.

  10. Dynamic Changes of Microbial Community for Degradation of Lignocellulose

    Institute of Scientific and Technical Information of China (English)

    LI Wenzhe; LIU Shuang; WANG Chunying; ZHENG Guoxiang

    2010-01-01

    Dynamic changes of a microbial community for lignocellulose degradation were explored in details.Community composition and development were investigated by the means of denaturing gradient gel electrophoresis(DGGE),and results showed that the microbial community was constituted of 14 kinds of bacteria and presented the fluctuation in some degrees with fermentation.Furthmore,the result of cluster analysis of DGGE pattern was accordant with growth curve,and the degradation process was divided into three stages: initial stage(0-12 h),intermediate stage(24-144 h)and end stage(144-216 h).

  11. Benefit sharing and community participation dynamics in forest management

    DEFF Research Database (Denmark)

    Antony, Bindu; Treue, Thorsten; Salim, Shyam S.

    2014-01-01

    on the dynamics of participation in forest management, especially on the link between distribution of benefits, and the level of participation of members, by exploring the process of institutional management and community governance. The study was undertaken in 178 households of Kankali community forestry......Community forestry has a significant role in the lives of people in Nepal as it serves the livelihood security of people to a greater extent. It is central in ensuring community participation in all the stages of CF (Community forestry) process and thus reach the objectives of sustainable forest......, in Chitwan district of Nepal. The results revealed that availabilty of the benefits do not have direct relation with neither paricipation in activities nor in decision making. Though motivation is a prerequisite to activate participation of people in any activity, other methods of persuasion is also vital...

  12. SCOUT: simultaneous time segmentation and community detection in dynamic networks

    Science.gov (United States)

    Hulovatyy, Yuriy; Milenković, Tijana

    2016-11-01

    Many evolving complex real-world systems can be modeled via dynamic networks. An important problem in dynamic network research is community detection, which finds groups of topologically related nodes. Typically, this problem is approached by assuming either that each time point has a distinct community organization or that all time points share a single community organization. The reality likely lies between these two extremes. To find the compromise, we consider community detection in the context of the problem of segment detection, which identifies contiguous time periods with consistent network structure. Consequently, we formulate a combined problem of segment community detection (SCD), which simultaneously partitions the network into contiguous time segments with consistent community organization and finds this community organization for each segment. To solve SCD, we introduce SCOUT, an optimization framework that explicitly considers both segmentation quality and partition quality. SCOUT addresses limitations of existing methods that can be adapted to solve SCD, which consider only one of segmentation quality or partition quality. In a thorough evaluation, SCOUT outperforms the existing methods in terms of both accuracy and computational complexity. We apply SCOUT to biological network data to study human aging.

  13. Next generation dynamic global vegetation models: learning from community ecology (Invited)

    Science.gov (United States)

    Scheiter, S.; Higgins, S.; Langan, L.

    2013-12-01

    Dynamic global vegetation models are a powerful tool to project past, current and future vegetation patterns and the associated biogeochemical cycles. However, most models are limited by their representation of vegetation by using static and pre-defined plant functional types and by their simplistic representation of competition. We discuss how concepts from community assembly theory and coexistence theory can help to improve dynamic vegetation models. We present a trait- and individual-based dynamic vegetation model, the aDGVM2, that allows individual plants to adopt a unique combination of trait values. These traits define how individual plants grow, compete and reproduce under the given biotic and abiotic conditions. A genetic optimization algorithm is used to simulate trait inheritance and reproductive isolation between individuals. These model properties allow the assembly of plant communities that are adapted to biotic and abiotic conditions. We show (1) that the aDGVM2 can simulate coarse vegetation patterns in Africa, (2) that changes in the environmental conditions and disturbances strongly influence trait diversity and the assembled plant communities by influencing traits such as leaf phenology and carbon allocation patterns of individual plants and (3) that communities do not necessarily return to the initial state when environmental conditions return to the initial state. The aDGVM2 deals with functional diversity and competition fundamentally differently from current models and allows novel insights as to how vegetation may respond to climate change. We believe that the aDGVM2 approach could foster collaborations between research communities that focus on functional plant ecology, plant competition, plant physiology and Earth system science.

  14. Global dynamic topography: geoscience communities requirements

    Science.gov (United States)

    Dewez, T.; Costeraste, J.

    2012-04-01

    The advent of free-of-charge global topographic data sets SRTM and Aster GDEM have enabled testing a host of geoscience hypotheses. This is because they first revealed the relief of previously unavailable earth landscapes, enabled quantitative geomorphometric analyses across entire landscapes and improved the resolution of measurements. Availability of such data is now considered standard, and though resolved at 30-m to 90-m pixel, which is amazing seeing where we come from, they are now regarded as mostly obsolete given the sub-meter imagery coming through web services like Google Earth. Geoscientists now appear to desire two additional features: field-scale-compatible elevation datasets (i.e. meter-scale digital models and sub-meter elevation precision) and dispose of regularly updated topography to retrieve earth surface changes, while retaining the key for success: data availability at no charge. A new satellite instrument is currently under phase 0 study at CNES, the French space agency, to fulfil these aims. The scientific community backing this demand is that of natural hazards, glaciology and to a lesser extent the biomass community. The system under study combines a native stereo imager and a lidar profiler. This combination provides spatially resolved elevation swaths together with absolute along-track elevation control point profiles. Data generated through this system, designed for revisit time better than a year, is intended to produce not only single acquisition digital surface models, colour orthoimages and small footprint full-wave-form lidar profiles to update existing topographic coverages, but also time series of them. This enables 3D change detection with centimetre-scale planimetric precision and metric vertical precision, in complement of classical spectral change appoaches. The purpose of this contribution, on behalf of the science team, is to present the mission concepts and philosophy and the scientific needs for such instrument including

  15. Intrinsic dynamics of the regional community.

    Science.gov (United States)

    Ricklefs, Robert E

    2015-06-01

    Patterns of diversity within large regional biotas express the outcomes of processes, operating on both regional and local scales, that influence evolutionary diversification as well as the distribution and abundance of species. Regional analyses of species distributions suggest that neither ecological sorting of species based on their adaptations to the physical environment, nor interactions between competing species, adequately explain patterns of species richness. Potentially competing species appear to utilise broadly overlapping resources with similar proficiency. Phylogenetic and phylogeographic analyses reveal that species abundances and distributions within regions vary independently of evolutionary relationship. This implies the existence of dynamic, species-specific controls on population growth, as could be applied by specialised pathogens or other antagonists. Here, I argue that the changing balance of coevolved interactions between hosts and their antagonists shapes the distribution and abundance of individual host populations as well as patterns of local species richness. Geographical expansion creates allopatric populations and thereby could promote diversification; contraction ultimately leads to extinction. This taxon-cycle dynamic links regional diversity and distribution to intrinsic biological interactions independently of extrinsic ecological conditions. These hypotheses emphasise the central importance of investigating the impacts of pathogens on species abundance and distribution, and the potential consequences of coevolutionary changes in pathogen-host relationships for species formation and extinction.

  16. Metagenomics meets time series analysis: unraveling microbial community dynamics

    NARCIS (Netherlands)

    Faust, K.; Lahti, L.M.; Gonze, D.; Vos, de W.M.; Raes, J.

    2015-01-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic

  17. Fractal groups: Emergent dynamics in on-line learning communities

    Directory of Open Access Journals (Sweden)

    Junia de Carvalho Fidelis Braga

    Full Text Available Drawing on complexity theory, this work discusses the complex dynamics and emergent patterns of on-line learning communities based on a doctoral study in the area of Applied Linguistics. The analysis will center on the interlocutions of fifty students who interacted in small groups without the teacher's direct intervention, in an undergraduate course offered by the School of Languages and Literature at the Federal University of Minas Gerais. By analyzing the data, I demonstrate that out of the interactions among the peers of autonomous on-line learning communities arise opportunities for the construction of shared meaning, distributed leadership, as well as other dynamics. I also demonstrate the fractal nature of these communities. Moreover, I discuss how these findings shed light on the creation and development of course designs for large groups.

  18. Next generation dynamic global vegetation models: learning from community ecology

    Science.gov (United States)

    Scheiter, Simon; Higgins, Steven; Langan, Liam

    2013-04-01

    Dynamic global vegetation models are a powerful tool to project the past, current and future distribution of vegetation and associated water and carbon fluxes. However, most models are limited by how they define vegetation and by their simplistic representation of competition. We discuss how concepts from community assembly theory and coexistence theory can help to improve vegetation models. We further present a new trait- and individual-based dynamic vegetation model (the aDGVM2) that allows each individual plant to adopt a unique combination of trait values. These traits define how each individual plant grows and competes with other plants under given environmental conditions. The performance of individual plants in turn drives the assembly of a plant community. A genetic optimisation algorithm is used to simulate the inheritance of traits and different levels of reproductive isolation between individuals. Together these model properties allow the assembly of plant communities that are well adapted to a site's biotic and abiotic conditions. Simulated communities can be classified into different plant functional types or biome types by using trait data bases. We illustrate that the aDGVM2 can simulate (1) how environmental conditions and changes in these conditions influence the trait spectra of assembled plant communities, (2) that fire selects for traits that enhance fire protection and reduces trait diversity, and (3) the emergence of communities dominated by life history strategies that are suggestive of colonisation-competition trade-offs. The aDGVM2 deals with functional diversity and competition fundamentally differently from current dynamic vegetation models. We argue that this approach will yield novel insights as to how vegetation may respond to climate change and we believe that it could foster fruitful collaborations between research communities that focus on plant functional traits, plant competition, plant physiology, systems ecology and earth system

  19. Temporal dynamics of restored communities in ecological engineering works

    Science.gov (United States)

    Jaunatre, Renaud; Rey, Freddy

    2015-04-01

    Among the numerous applications of ecological engineering are the creation of engineering structures made of living materials, of which objective is to perform a function (for instance, erosion mitigation). One distinctive characteristic of these living materials is that they have their own dynamics. Within a plant community constituting an engineering structure, diversity and species abundance may change. It is well-known that changes of the community structure can have a significant effect on the whole functioning, and the provided services. This is therefore of primary concern to determine if spontaneous dynamics of these engineering structures allows the preservation of expected services. Our questions are: (i) How vegetation develops on these structures? (ii) How community functional traits are changing with time? and (iii) Is sedimentation control expected service still efficient after 12 years. The study site is the Durance catchment on Jurassic black marls where erosion has led to bare gullies. Since 2002, about 2000 ecological engineering structures have been made up in order to control sedimentation. In spring 2014, we sampled 664 of on which vegetation was recorded on 1m² plot. Plant community traits were a community weighted mean calculated from 13 species representing >60% of overall abundances for which we had values related to erosion control. Sediment control markers were also measured on each structures. NMDS and RDA were used to determine the effect of age on plant communities, traits and sediment control. The results show that during the first years age does not have an effect on plant community dynamics, functional traits related to erosion or erosion control markers of engineering structures. From the fields, stochastic events (decanal floods, small land slides, etc.) seems to play a more major role.

  20. A local algorithm for detecting community structures in dynamic networks

    CERN Document Server

    Massaro, Emanuele; Guazzini, Andrea; Passarella, Andrea; Bagnoli, Franco

    2013-01-01

    The emergence and the global adaptation of mobile devices has influenced human interactions at the individual, community, and social levels leading to the so called Cyber-Physical World (CPW) convergence scenario [1]. One of the most important features of CPW is the possibility of exploiting information about the structure of social communities of users, that manifest through joint movement patterns and frequency of physical co-location: mobile devices of users that belong to the same social community are likely to "see" each other (and thus be able to communicate through ad hoc networking techniques) more frequently and regularly than devices outside of the community. In mobile opportunistic networks, this fact can be exploited, for example, to optimize networking operations such as forwarding and dissemination of messages. In this paper we present a novel local cognitive-inspired algorithm for revealing the structure of these dynamic social networks by exploiting information about physical encounters, logge...

  1. Towards Reproducibility in Computational Hydrology

    Science.gov (United States)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei

    2016-04-01

    The ability to reproduce published scientific findings is a foundational principle of scientific research. Independent observation helps to verify the legitimacy of individual findings; build upon sound observations so that we can evolve hypotheses (and models) of how catchments function; and move them from specific circumstances to more general theory. The rise of computational research has brought increased focus on the issue of reproducibility across the broader scientific literature. This is because publications based on computational research typically do not contain sufficient information to enable the results to be reproduced, and therefore verified. Given the rise of computational analysis in hydrology over the past 30 years, to what extent is reproducibility, or a lack thereof, a problem in hydrology? Whilst much hydrological code is accessible, the actual code and workflow that produced and therefore documents the provenance of published scientific findings, is rarely available. We argue that in order to advance and make more robust the process of hypothesis testing and knowledge creation within the computational hydrological community, we need to build on from existing open data initiatives and adopt common standards and infrastructures to: first make code re-useable and easy to find through consistent use of metadata; second, publish well documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; finally, use unique persistent identifiers (e.g. DOIs) to reference re-useable and reproducible code, thereby clearly showing the provenance of published scientific findings. Whilst extra effort is require to make work reproducible, there are benefits to both the individual and the broader community in doing so, which will improve the credibility of the science in the face of the need for societies to adapt to changing hydrological environments.

  2. Forest fragmentation and bird community dynamics: inference at regional scales

    Science.gov (United States)

    Boulinier, T.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Flather, C.H.; Pollock, K.H.

    2001-01-01

    With increasing fragmentation of natural areas and a dramatic reduction of forest cover in several parts of the world, quantifying the impact of such changes on species richness and community dynamics has been a subject of much concern. Here, we tested whether in more fragmented landscapes there was a lower number of area-sensitive species and higher local extinction and turnover rates, which could explain higher temporal variability in species richness. To investigate such potential landscape effects at a regional scale, we merged two independent, large-scale monitoring efforts: the North American Breeding Bird Survey (BBS) and the Land Use and Land Cover Classification data from the U.S. Geological Survey. We used methods that accounted for heterogeneity in the probability of detecting species to estimate species richness and temporal changes in the bird communities for BBS routes in three mid-Atlantic U.S. states. Forest breeding bird species were grouped prior to the analyses into area-sensitive and non-area-sensitive species according to previous studies. We tested predictions relating measures of forest structure at one point in time (1974) to species richness at that time and to parameters of forest bird community change over the following 22-yr-period (1975-1996). We used the mean size of forest patches to characterize landscape structure, as high correlations among landscape variables did not allow us to disentangle the relative roles of habitat fragmentation per se and habitat loss. As predicted, together with lower species richness for area-sensitive species on routes surrounded by landscapes with lower mean forest-patch size, we found higher mean year-to-year rates of local extinction. Moreover, the mean year-to-year rates of local turnover (proportion of locally new species) for area-sensitive species were also higher in landscapes with lower mean forest-patch size. These associations were not observed for the non-area-sensitive species group. These

  3. Trust and community: Exploring the meanings, contexts and dynamics of community renewable energy

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Gordon, E-mail: g.p.walker@lancaster.ac.u [University of Lancaster, Department of Geography, Lancaster LA1 4YN (United Kingdom); Devine-Wright, Patrick [University of Manchester, School of Environment and Development, Humanities Bridgeford Street Building, Oxford Road, Manchester M13 9PL (United Kingdom); Hunter, Sue; High, Helen; Evans, Bob [University of Lancaster, Department of Geography, Lancaster LA1 4YN (United Kingdom); University of Manchester, School of Environment and Development, Humanities Bridgeford Street Building, Oxford Road, Manchester M13 9PL (United Kingdom)

    2010-06-15

    Community renewable energy projects have recently been promoted and supported in the UK by government policy. A community approach, it is argued in the rhetoric of both government and grassroots activists will change the experience and outcomes of the energy sustainable technology implementation. In this paper, we consider how interpersonal and social trust is implicated in the different meanings given to community in RE programmes and projects, and in the qualities and outcomes that are implied or assumed by taking a community approach. We examine how these meanings play out in examples of projects on the ground, focusing on two contrasting cases in which the relationships between those involved locally have exhibited different patterns of cohesiveness and fracture. We argue that trust does have a necessary part to play in the contingencies and dynamics of community RE projects and in the outcomes they can achieve. Trust between local people and groups that take projects forward is part of the package of conditions which can help projects work. Whilst trust may therefore be functional for the development of community RE and potentially can be enhanced by the adoption of a community approach, this cannot be either assured or assumed under the wide diversity of contexts, conditions and arrangements under which community RE is being pursued and practiced.

  4. The Dynamics of Concepts in a Homogeneous Community

    Directory of Open Access Journals (Sweden)

    Eugene Khmelnitsky

    2013-05-01

    Full Text Available The paper addresses informational interactions in a community and considers the dynamics of concepts that represent distribution of knowledge among the individuals. The evolution of a set of concepts maintained by a community is derived by the use of the concepts’ significance in the communication between “cognoscenti” and “dilettanti” and of birth-death processes. The dynamics of concepts depend on the allocation of communication resources and can be governed by an informational principle that requires minimum self-information of the set of concepts over a time horizon. With respect to that principle, the introduction of a new concept into a community’s disposal is shown to lead to a steady-state self-information, which is smaller than that before the introduction of the new concept.

  5. The Need for Reproducibility

    Energy Technology Data Exchange (ETDEWEB)

    Robey, Robert W. [Los Alamos National Laboratory

    2016-06-27

    The purpose of this presentation is to consider issues of reproducibility, specifically it determines whether bitwise reproducible computation is possible, if computational research in DOE improves its publication process, and if reproducible results can be achieved apart from the peer review process?

  6. Opening Reproducible Research

    Science.gov (United States)

    Nüst, Daniel; Konkol, Markus; Pebesma, Edzer; Kray, Christian; Klötgen, Stephanie; Schutzeichel, Marc; Lorenz, Jörg; Przibytzin, Holger; Kussmann, Dirk

    2016-04-01

    Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we not only mean access to papers, research data being collected, or data being generated, but also access to the data used and the procedures carried out in the research paper. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method (Pebesma, Nüst and Bivand, 2012). As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects. We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents. The DFG-funded experimental project Opening Reproducible Research (ORR) aims for the main aspects of open access, by improving the exchange of, by facilitating productive access to, and by simplifying reuse of research results that are published over the Internet. Central to the project is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to

  7. Probabilistic models to describe the dynamics of migrating microbial communities.

    Directory of Open Access Journals (Sweden)

    Joanna L Schroeder

    Full Text Available In all but the most sterile environments bacteria will reside in fluid being transported through conduits and some of these will attach and grow as biofilms on the conduit walls. The concentration and diversity of bacteria in the fluid at the point of delivery will be a mix of those when it entered the conduit and those that have become entrained into the flow due to seeding from biofilms. Examples include fluids through conduits such as drinking water pipe networks, endotracheal tubes, catheters and ventilation systems. Here we present two probabilistic models to describe changes in the composition of bulk fluid microbial communities as they are transported through a conduit whilst exposed to biofilm communities. The first (discrete model simulates absolute numbers of individual cells, whereas the other (continuous model simulates the relative abundance of taxa in the bulk fluid. The discrete model is founded on a birth-death process whereby the community changes one individual at a time and the numbers of cells in the system can vary. The continuous model is a stochastic differential equation derived from the discrete model and can also accommodate changes in the carrying capacity of the bulk fluid. These models provide a novel Lagrangian framework to investigate and predict the dynamics of migrating microbial communities. In this paper we compare the two models, discuss their merits, possible applications and present simulation results in the context of drinking water distribution systems. Our results provide novel insight into the effects of stochastic dynamics on the composition of non-stationary microbial communities that are exposed to biofilms and provides a new avenue for modelling microbial dynamics in systems where fluids are being transported.

  8. Metagenomics meets time series analysis: unraveling microbial community dynamics.

    Science.gov (United States)

    Faust, Karoline; Lahti, Leo; Gonze, Didier; de Vos, Willem M; Raes, Jeroen

    2015-06-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.

  9. Analytic solution of Hubbell's model of local community dynamics

    CERN Document Server

    McKane, A; Sole, R; Kane, Alan Mc; Alonso, David; Sole, Ricard

    2003-01-01

    Recent theoretical approaches to community structure and dynamics reveal that many large-scale features of community structure (such as species-rank distributions and species-area relations) can be explained by a so-called neutral model. Using this approach, species are taken to be equivalent and trophic relations are not taken into account explicitly. Here we provide a general analytic solution to the local community model of Hubbell's neutral theory of biodiversity by recasting it as an urn model i.e.a Markovian description of states and their transitions. Both stationary and time-dependent distributions are analysed. The stationary distribution -- also called the zero-sum multinomial -- is given in closed form. An approximate form for the time-dependence is obtained by using an expansion of the master equation. The temporal evolution of the approximate distribution is shown to be a good representation for the true temporal evolution for a large range of parameter values.

  10. Ananke: temporal clustering reveals ecological dynamics of microbial communities

    Directory of Open Access Journals (Sweden)

    Michael W. Hall

    2017-09-01

    Full Text Available Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.

  11. Dynamic changes in microbial community structure and function in phenol-degrading microcosms inoculated with cells from a contaminated aquifer.

    Science.gov (United States)

    Elliott, David R; Scholes, Julie D; Thornton, Steven F; Rizoulis, Athanasios; Banwart, Steven A; Rolfe, Stephen A

    2010-02-01

    Contamination of aquifers by organic pollutants threatens groundwater supplies and the environment. In situ biodegradation of organic pollutants by microbial communities is important for the remediation of contaminated sites, but our understanding of the relationship between microbial development and pollutant biodegradation is poor. A particular challenge is understanding the in situ status of microorganisms attached to solid surfaces, but not accessible via conventional sampling of groundwater. We have developed novel flow-through microcosms and examined dynamic changes in microbial community structure and function in a phenol-degrading system. Inoculation of these microcosms with a complex microbial community from a plume in a phenol-contaminated aquifer led to the initial establishment of a population dominated by a few species, most attached to the solid substratum. Initially, phenol biodegradation was incomplete, but as the microbial community structure became more complex, phenol biodegradation was more extensive and complete. These results were replicated between independent microcosms, indicating a deterministic succession of species. This work demonstrates the importance of examining community dynamics when assessing the potential for microbial biodegradation of organic pollutants. It provides a novel system in which such measurements can be made readily and reproducibly to study the temporal development and spatial succession of microbial communities during biodegradation of organic pollutants at interfaces within such environments.

  12. Dynamics of Bacterial Community Composition in the Malaria Mosquito's Epithelia.

    Science.gov (United States)

    Tchioffo, Majoline T; Boissière, Anne; Abate, Luc; Nsango, Sandrine E; Bayibéki, Albert N; Awono-Ambéné, Parfait H; Christen, Richard; Gimonneau, Geoffrey; Morlais, Isabelle

    2015-01-01

    The Anopheles midgut hosts diverse bacterial communities and represents a complex ecosystem. Several evidences indicate that mosquito midgut microbiota interferes with malaria parasite transmission. However, the bacterial composition of salivary glands and ovaries, two other biologically important tissues, has not been described so far. In this study, we investigated the dynamics of the bacterial communities in the mosquito tissues from emerging mosquitoes until 8 days after a blood meal containing Plasmodium falciparum gametocytes and described the temporal colonization of the mosquito epithelia. Bacterial communities were identified in the midgut, ovaries, and salivary glands of individual mosquitoes using pyrosequencing of the 16S rRNA gene. We found that the mosquito epithelia share a core microbiota, but some bacteria taxa were more associated with one or another tissue at a particular time point. The bacterial composition in the tissues of emerging mosquitoes varied according to the breeding site, indicating that some bacteria are acquired from the environment. Our results revealed temporal variations in the bacterial community structure, possibly as a result of the mosquito physiological changes. The abundance of Serratia significantly correlated with P. falciparum infection both in the midgut and salivary glands of malaria challenged mosquitoes, which suggests that interactions occur between microbes and parasites. These bacteria may represent promising targets for vector control strategies. Overall, this study points out the importance of characterizing bacterial communities in malaria mosquito vectors.

  13. SIS model of epidemic spreading on dynamical networks with community

    Institute of Scientific and Technical Information of China (English)

    Chengyi XIA; Shiwen SUN; Feng RAO; Junqing SUN; Jinsong WANG; Zengqiang CHEN

    2009-01-01

    We present a new epidemic Susceptible-Infected-Susceptible (SIS) model to investigate the spreading behav-ior on networks with dynamical topology and community structure. Individuals in the model are mobile agents who are allowed to perform the inter-community (i.e., long-range) motion with the probability p. The mean-field theory is uti-lized to derive the critical threshold (λ_C) of epidemic spread-ing inside separate communities and the influence of the long-range motion on the epidemic spreading. The results indicate that λ_C is only related with the population density within the community, and the long-range motion will make the original disease-free community become the endemic state. Large-scale numerical simulations also demonstrate the theoretical approximations based on our new epidemic model. The current model and analysis will help us to fur-ther understand the propagation behavior of real epidemics taking place on social networks.

  14. Compliant bipedal model with the center of pressure excursion associated with oscillatory behavior of the center of mass reproduces the human gait dynamics.

    Science.gov (United States)

    Jung, Chang Keun; Park, Sukyung

    2014-01-03

    Although the compliant bipedal model could reproduce qualitative ground reaction force (GRF) of human walking, the model with a fixed pivot showed overestimations in stance leg rotation and the ratio of horizontal to vertical GRF. The human walking data showed a continuous forward progression of the center of pressure (CoP) during the stance phase and the suspension of the CoP near the forefoot before the onset of step transition. To better describe human gait dynamics with a minimal expense of model complexity, we proposed a compliant bipedal model with the accelerated pivot which associated the CoP excursion with the oscillatory behavior of the center of mass (CoM) with the existing simulation parameter and leg stiffness. Owing to the pivot acceleration defined to emulate human CoP profile, the arrival of the CoP at the limit of the stance foot over the single stance duration initiated the step-to-step transition. The proposed model showed an improved match of walking data. As the forward motion of CoM during single stance was partly accounted by forward pivot translation, the previously overestimated rotation of the stance leg was reduced and the corresponding horizontal GRF became closer to human data. The walking solutions of the model ranged over higher speed ranges (~1.7 m/s) than those of the fixed pivoted compliant bipedal model (~1.5m/s) and exhibited other gait parameters, such as touchdown angle, step length and step frequency, comparable to the experimental observations. The good matches between the model and experimental GRF data imply that the continuous pivot acceleration associated with CoM oscillatory behavior could serve as a useful framework of bipedal model.

  15. The interaction of cannibalism and omnivory: consequences for community dynamics.

    Science.gov (United States)

    Rudolf, Volker H W

    2007-11-01

    Although cannibalism is ubiquitous in food webs and frequent in systems where a predator and its prey also share a common resource (intraguild predation, IGP), its impacts on species interactions and the dynamics and structure of communities are still poorly understood. In addition, the few existing studies on cannibalism have generally focused on cannibalism in the top-predator, ignoring that it is frequent at intermediate trophic levels. A set of structured models shows that cannibalism can completely alter the dynamics and structure of three-species IGP systems depending on the trophic position where cannibalism occurs. Contrary to the expectations of simple models, the IG predator can exploit the resources more efficiently when it is cannibalistic, enabling the predator to persist at lower resource densities than the IG prey. Cannibalism in the IG predator can also alter the effect of enrichment, preventing predator-mediated extinction of the IG prey at high productivities predicted by simple models. Cannibalism in the IG prey can reverse the effect of top-down cascades, leading to an increase in the resource with decreasing IG predator density. These predictions are consistent with current data. Overall, cannibalism promotes the coexistence of the IG predator and IG prey. These results indicate that including cannibalism in current models can overcome the discrepancy between theory and empirical data. Thus, we need to measure and account for cannibalistic interactions to reliably predict the structure and dynamics of communities.

  16. Bacterial community dynamics during the ensilage of wilted grass.

    Science.gov (United States)

    McEniry, J; O'Kiely, P; Clipson, N J W; Forristal, P D; Doyle, E M

    2008-08-01

    Grass silage is the product formed by a natural lactic acid bacterial fermentation when grass is stored under anaerobic conditions, and represents an important ruminant feedstuff on farms during winter. Of the two commonly employed methods of ensiling forage, baled silage composition frequently differs from that of comparable precision-chop silage reflecting a different ensiling environment. The aim of this study was to investigate the dynamics of the silage fermentation in wilted grass and between ensiling systems. Fermentation dynamics were examined using traditional methods of silage analyses, including microbial enumeration and analysis of fermentation products, and culture-independent terminal restriction fragment length polymorphism (T-RFLP). A successful fermentation was achieved in both systems, with the fermentation (increase in lactic acid bacteria and lactic acid concentration, decrease in pH) proceeding rapidly once the herbage was ensiled. Under controlled conditions, little difference in silage quality and microbial composition were observed between ensiling systems and this was further reflected in the T-RFLP community analysis. T-RFLP proved a potentially useful tool to study the ensilage process and could provide valid support to traditional methods, or a viable alternative to these methods, for investigating the dynamics of the bacterial community over the course of the fermentation.

  17. Exploring Twitter communication dynamics with evolving community analysis

    Directory of Open Access Journals (Sweden)

    Konstantinos Konstantinidis

    2017-02-01

    Full Text Available Online Social Networks (OSNs have been widely adopted as a means of news dissemination, event reporting, opinion expression and discussion. As a result, news and events are being constantly reported and discussed online through OSNs such as Twitter. However, the variety and scale of all the information renders manual analysis extremely cumbersome, and therefore creating a storyline for an event or news story is an effort-intensive task. The main challenge pertains to the magnitude of data to be analyzed. To this end, we propose a framework for ranking the resulting communities and their metadata on the basis of structural, contextual and evolutionary characteristics such as community centrality, textual entropy, persistence and stability. We apply the proposed framework on three Twitter datasets and demonstrate that the analysis that followed enables the extraction of new insights with respect to influential user accounts, topics of discussion and emerging trends. These insights could primarily assist the work of social and political analysis scientists and the work of journalists in their own story telling, but also highlight the limitations of existing analysis methods and pose new research questions. To our knowledge, this study is the first to investigate the ranking of dynamic communities. In addition, our findings suggest future work regarding the determination of the general context of the communities based on structure and evolutionary behavior alone.

  18. Methane dynamics regulated by microbial community response to permafrost thaw.

    Science.gov (United States)

    McCalley, Carmody K; Woodcroft, Ben J; Hodgkins, Suzanne B; Wehr, Richard A; Kim, Eun-Hae; Mondav, Rhiannon; Crill, Patrick M; Chanton, Jeffrey P; Rich, Virginia I; Tyson, Gene W; Saleska, Scott R

    2014-10-23

    Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

  19. Fire, flow and dynamic equilibrium in stream macroinvertebrate communities

    Science.gov (United States)

    Arkle, R.S.; Pilliod, D.S.; Strickler, K.

    2010-01-01

    The complex effects of disturbances on ecological communities can be further complicated by subsequent perturbations within an ecosystem. We investigated how wildfire interacts with annual variations in peak streamflow to affect the stability of stream macroinvertebrate communities in a central Idaho wilderness, USA. We conducted a 4-year retrospective analysis of unburned (n = 7) and burned (n = 6) catchments, using changes in reflectance values (??NBR) from satellite imagery to quantify the percentage of each catchment's riparian and upland vegetation that burned at high and low severity. For this wildland fire complex, increasing riparian burn severity and extent were associated with greater year-to-year variation, rather than a perennial increase, in sediment loads, organic debris, large woody debris (LWD) and undercut bank structure. Temporal changes in these variables were correlated with yearly peak flow in burned catchments but not in unburned reference catchments, indicating that an interaction between fire and flow can result in decreased habitat stability in burned catchments. Streams in more severely burned catchments exhibited increasingly dynamic macroinvertebrate communities and did not show increased similarity to reference streams over time. Annual variability in macroinvertebrates was attributed, predominantly, to the changing influence of sediment, LWD, riparian cover and organic debris, as quantities of these habitat components fluctuated annually depending on burn severity and annual peak streamflows. These analyses suggest that interactions among fire, flow and stream habitat may increase inter-annual habitat variability and macroinvertebrate community dynamics for a duration approaching the length of the historic fire return interval of the study area. ?? 2009 Blackwell Publishing Ltd.

  20. Complex brain networks: From topological communities to clustered dynamics

    Indian Academy of Sciences (India)

    Lucia Zemanová; Gorka Zamora-López; Changsong Zhou; Jürgen Kurths

    2008-06-01

    Recent research has revealed a rich and complicated network topology in the cortical connectivity of mammalian brains. A challenging task is to understand the implications of such network structures on the functional organisation of the brain activities. We investigate synchronisation dynamics on the corticocortical network of the cat by modelling each node of the network (cortical area) with a subnetwork of interacting excitable neurons. We find that this network of networks displays clustered synchronisation behaviour and the dynamical clusters closely coincide with the topological community structures observed in the anatomical network. The correlation between the firing rate of the areas and the areal intensity is additionally examined. Our results provide insights into the relationship between the global organisation and the functional specialisation of the brain cortex.

  1. A right to reproduce?

    Science.gov (United States)

    Quigley, Muireann

    2010-10-01

    How should we conceive of a right to reproduce? And, morally speaking, what might be said to justify such a right? These are just two questions of interest that are raised by the technologies of assisted reproduction. This paper analyses the possible legitimate grounds for a right to reproduce within the two main theories of rights; interest theory and choice theory.

  2. Magni Reproducibility Example

    DEFF Research Database (Denmark)

    2016-01-01

    An example of how to use the magni.reproducibility package for storing metadata along with results from a computational experiment. The example is based on simulating the Mandelbrot set.......An example of how to use the magni.reproducibility package for storing metadata along with results from a computational experiment. The example is based on simulating the Mandelbrot set....

  3. The dynamics of the bacterial communities developed in maize silage.

    Science.gov (United States)

    Gharechahi, Javad; Kharazian, Zohreh Akhavan; Sarikhan, Sajjad; Jouzani, Gholamreza Salehi; Aghdasi, Mahnaz; Hosseini Salekdeh, Ghasem

    2017-07-11

    Ensilage provides an effective means of conserving summer-grown green forage to supply as winter feed to ruminants. The fermentation process involved in the ensilage process relies on lactic acid bacteria (LAB). Here, 16S ribosomal DNA amplicon pyrosequencing was used to follow the dynamic behaviour of the LAB community during the ensilage of maize biomass, with a view to identify the key species involved in the process. The biomass used for ensilage was a single-cross maize hybrid, harvested at the milk-line stage. The crop was grown at three contrasting locations. Aspects of the physico-chemical composition of the material and the LAB species present were sampled at 0, 3, 6, 14, 21 and 32 days after ensilage was initiated. In all three cases, members of the Leuconostocaceae family dominated the epiphytic bacterial community, notably Leuconostoc and Weissella, but some variation was noted in the abundance of certain Leuconostocaceae and Lactobacillaceae species, as well as that of some Acetobacteraceae, Enterobacteriaceae and Moraxellaceae species. The constellation of the microbiome which developed during the ensilage process differed markedly from that of the epiphytic one, with Lactobacillaceae, particularly Lactobacillus and Pediococcus spp. dominating. The abundance of heterofermentative Leuconostocaceae spp. in the epiphytic community and the extent of the transition from hetero- to homo-fermentation during the initial ensilage period are important factors in determining silage quality. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  4. Reproducibility in Seismic Imaging

    Directory of Open Access Journals (Sweden)

    González-Verdejo O.

    2012-04-01

    Full Text Available Within the field of exploration seismology, there is interest at national level of integrating reproducibility in applied, educational and research activities related to seismic processing and imaging. This reproducibility implies the description and organization of the elements involved in numerical experiments. Thus, a researcher, teacher or student can study, verify, repeat, and modify them independently. In this work, we document and adapt reproducibility in seismic processing and imaging to spread this concept and its benefits, and to encourage the use of open source software in this area within our academic and professional environment. We present an enhanced seismic imaging example, of interest in both academic and professional environments, using Mexican seismic data. As a result of this research, we prove that it is possible to assimilate, adapt and transfer technology at low cost, using open source software and following a reproducible research scheme.

  5. Scalably Revealing the Dynamics of Soft Community Structure in Complex Networks

    Institute of Scientific and Technical Information of China (English)

    LI Huijia; LI Huiying

    2016-01-01

    Revealing the dynamics of community structure is of great concern for scientists from many fields.Specifically,how to quantify the dynamic details of soft community structure is a very interesting topic.In this paper,the authors propose a novel framework to study the scalable dynamic behavior of the soft community structure.First,the authors model the Potts dynamics to detect community structure using a "soft" Markov process.Then the soft stability of in a multiscale view is proposed to naturally uncover the local uniform behavior of spin values across multiple hierarchical levels.Finally,a new partition index is developed to detect fuzzy communities based on the stability and the dynamical information.Experiments on the both synthetically generated and real-world networks verify that the framework can be used to uncover hierarchical community structures effectively and efficiently.

  6. Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

    Energy Technology Data Exchange (ETDEWEB)

    Mosher, Jennifer J.; Drake, Meghan M.; Carroll, Susan L.; Yang, Zamin K.; Schadt, Christopher W.; Brown, Stephen D.; Podar, Mircea; Hazen, Terry C.; Arkin, Adam P.; Phelps, Tommy J.; Palumbo, Anthony V.; Faybishenko, Boris A.; Elias, Dwayne A.

    2010-05-01

    The Department of Energy site at Hanford, WA, has been historically impacted by U and Cr from the nuclear weapons industry. In an attempt to stimulate microbial remediation of these metals, in-situ lactate enrichment experiments are ongoing. In order to bridge the gap from the laboratory to the field, we inoculated triplicate anaerobic, continuous-flow glass reactors with groundwater collected from well Hanford 100-H in order to obtain a stable, enriched community while selecting for metal-reducing bacteria. Each reactor was fed from a single carboy containing defined media with 30 mM lactate at a rate of 0.223 ml/min under continuous nitrogen flow at 9 ml/min. Cell counts, organic acids, gDNA (for qPCR and pyrosequencing) and gases were sampled during the experiment. Cell counts remained low (less than 1x107 cells/ml) during the first two weeks of the experiment, but by day 20, had reached a density greater than 1x108 cells/ml. Metabolite analysis showed a decrease in the lactate concentrations over time. Pyruvate concentrations ranged from 20-40 uM the first week of the experiment then was undetectable after day 10. Likewise, formate appeared in the reactors during the first week with concentrations of 1.48-1.65 mM at day 7 then the concentrations decreased to 0.69-0.95 on day 10 and were undetectable on day 15. Acetate was present in low amounts on day 3 (0.15-0.33 mM) and steadily increased to 3.35-5.22 mM over time. Similarly, carbon dioxide was present in low concentrations early on and increased to 0.28-0.35 mM as the experiment progressed. We also were able to detect low amounts of methane (10-20 uM) during the first week of the experiment, but by day 10 the methane was undetectable. From these results and pyrosequencing analysis, we conclude that a shift in the microbial community dynamics occurred over time to eventually form a stable and enriched microbial community. Comprehensive investigations such as these allow for the examination of not only which

  7. Learning Reproducibility with a Yearly Networking Contest

    KAUST Repository

    Canini, Marco

    2017-08-10

    Better reproducibility of networking research results is currently a major goal that the academic community is striving towards. This position paper makes the case that improving the extent and pervasiveness of reproducible research can be greatly fostered by organizing a yearly international contest. We argue that holding a contest undertaken by a plurality of students will have benefits that are two-fold. First, it will promote hands-on learning of skills that are helpful in producing artifacts at the replicable-research level. Second, it will advance the best practices regarding environments, testbeds, and tools that will aid the tasks of reproducibility evaluation committees by and large.

  8. Learning from the past: Trends and dynamics in livelihoods of Bolivian forest communities

    NARCIS (Netherlands)

    Zenteno, M.; Jong, de W.; Boot, R.; Zuidema, P.A.

    2014-01-01

    We use social ecological systems theory (SES) to analyse change in forest communities in the northern Bolivian Amazon. SES characterizes interdependent dynamics of social and ecological systems and we hypothesized it to be a useful frame to grasp dynamics of forest communities affected by changes in

  9. Reproducibility of quantitative measures of binding potential in rat striatum: A test re-test study using DTBZ dynamic PET studies

    Energy Technology Data Exchange (ETDEWEB)

    Avendaño-Estrada, A., E-mail: avilarod@uwalumni.com; Lara-Camacho, V. M., E-mail: avilarod@uwalumni.com; Ávila-García, M. C., E-mail: avilarod@uwalumni.com; Ávila- Rodríguez, M. A., E-mail: avilarod@uwalumni.com [Unidad PET, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, México, D.F. (Mexico)

    2014-11-07

    There is great interest in the study of dopamine (DA) pathways due to the increasing number of patients with illnesses related to the dopaminergic system and molecular imaging based in Positron Emission Tomography (PET) has been proven helpful for this task. Among the different radiopharmaceuticals available to study DA interaction, [{sup 11}C]Dihydrotetrabenazine (DTBZ) has a high affinity for the vesicular monoamine transporter type 2 (VMAT2) and its binding potential (BP) is a marker of DA terminal integrity. This paper reports on the intersubject reproducibility of BP measurements in rat striatum with [11C]DTBZ using the Logańs method.

  10. The reproducibility of different metabolic markers for muscle fiber type distributions investigated by functional {sup 31}P-MRS during dynamic exercise

    Energy Technology Data Exchange (ETDEWEB)

    Rzanny, Reinhard; Hiepe, Patrick; Gussew, Alexander; Reichenbach, Juergen R. [Univ. Hospital Jena (Germany). Medical Physics Group, Inst. of Diagnostics and Interventional Radiology; Stutzig, Norman [Univ. of Stuttgart (Germany). Exercise Science, Inst. of Sport and Movement Science; Thorhauer, Hans-Alexander [Friedrich-Schiller-Univ. Jena (Germany). Exercise Science, Inst. of Sports Science

    2016-07-01

    The objective of the study was to investigate the reproducibility of exercise induced pH-heterogeneity by splitting of the inorganic phosphate (Pi) signal in the corresponding {sup 31}P-MRS spectra and to compare results of this approach with other fiber-type related markers, like phosphocreatine/adenosine triphosphate (PCr/ATP) ratio, and PCr-recovery parameters. Subjects (N = 3) with different sportive background were tested in 10 test sessions separated by at least 3 days. A MR-compatible pedal ergometer was used to perform the exercise and to induce a pH-based splitting of the Pi-signal in {sup 31}P-MR spectra of the medial gastrocnemius muscle. The PCr recovery was analyzed using a non-negative least square algorithm (NNLS) and multi-exponential regression analysis to estimate the number of non-exponential components as well as their amplitude and time constant. The reproducibility of the estimated metabolic marker and the resulting fiber-type distributions between the 10 test sessions were compared. The reproducibility (standard deviation between measurements) based on (1) Pi components varied from 2% to 4%, (2) PCr recovery time components varied from 10% to 12% and (3) phosphate concentrations at rest varied from 8% to 11% between test sessions. Due to the sportive activity differences between the 3 subjects were expected in view of fiber type distribution. All estimated markers indicate the highest type I percentage for volunteer 3 medium for volunteer 2 and the lowest for volunteer 1. The relative high reproducibility of pH dependent Pi components during exercise indicates a high potential of this method to estimate muscle fiber-type distributions in vivo. To make this method usable not only to detect differences in muscle fiber distributions but also to determine individual fiber-type volume contents it is therefore recommended to validate this marker by histological methods and to reveal the effects of muscle fiber recruitments and fiber-type specific

  11. An approach of community evolution based on gravitational relationship refactoring in dynamic networks

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Guisheng; Chi, Kuo, E-mail: chik89769@hrbeu.edu.cn; Dong, Yuxin; Dong, Hongbin

    2017-04-25

    In this paper, an approach of community evolution based on gravitational relationship refactoring between the nodes in a dynamic network is proposed, and it can be used to simulate the process of community evolution. A static community detection algorithm and a dynamic community evolution algorithm are included in the approach. At first, communities are initialized by constructing the core nodes chains, the nodes can be iteratively searched and divided into corresponding communities via the static community detection algorithm. For a dynamic network, an evolutionary process is divided into three phases, and behaviors of community evolution can be judged according to the changing situation of the core nodes chain in each community. Experiments show that the proposed approach can achieve accuracy and availability in the synthetic and real world networks. - Highlights: • The proposed approach considers both the static community detection and dynamic community evolution. • The approach of community evolution can identify the whole 6 common evolution events. • The proposed approach can judge the evolutionary events according to the variations of the core nodes chains.

  12. Thou Shalt Be Reproducible! A Technology Perspective

    Directory of Open Access Journals (Sweden)

    Patrick Mair

    2016-07-01

    Full Text Available This article elaborates on reproducibility in psychology from a technological viewpoint. Modernopen source computational environments are shown and explained that foster reproducibilitythroughout the whole research life cycle, and to which emerging psychology researchers shouldbe sensitized, are shown and explained. First, data archiving platforms that make datasets publiclyavailable are presented. Second, R is advocated as the data-analytic lingua franca in psychologyfor achieving reproducible statistical analysis. Third, dynamic report generation environments forwriting reproducible manuscripts that integrate text, data analysis, and statistical outputs such asfigures and tables in a single document are described. Supplementary materials are provided inorder to get the reader started with these technologies.

  13. Dynamics of bacterial community in the gut of Cornu aspersum

    Directory of Open Access Journals (Sweden)

    ZDRAVKA KOLEVA

    2015-12-01

    Full Text Available The dynamics of the bacterial community in the intestinal tract of Cornu aspersum was investigated during different states of its life cycle. Two approaches were applied – culture and non-culture. The non-culture approach was performed by ARDRA of 16S rDNA using two of the six tested endonucleases. Data were analyzed by hierarchical cluster analysis. The restriction of 16S rDNA samples from the snail of different physiological states with endonucleases HinfI and Csp6I resulted in generation of different profiles depending on the snail states. By the culture approach we found that the total number of cultivable bacteria, representatives of Enterobacteriaceae, lactic acid bacteria, amylolitic and cellulolytic bacteria were the most abundant in active state of the snails. Cellulolytic bacteria were not detected in juveniles of C. aspersum. Escherichia coli, Clostridium perfringens as well as bacteria from the genus Salmonella, Shigella and Pseudomonas were not detected. Bacteria of the genus Aeromonas were found in juveniles of C. aspersum, after that their number decrease and were not found in hibernating snails. On the base of the two applied approaches this study shows that the bacterial flora in the intestinal tract of C. aspersum is affected by the seasonal and environmental variations and undergoes quantitative and qualitative changes during the different states of the life cycle. The snails harbor in their gut intestinal bacteria, which possess biochemical potentiality to degrade the plant components.

  14. Microbial community dynamics in the forefield of glaciers.

    Science.gov (United States)

    Bradley, James A; Singarayer, Joy S; Anesio, Alexandre M

    2014-11-22

    Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

  15. Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics.

    Science.gov (United States)

    Ge, Yuan; Schimel, Joshua P; Holden, Patricia A

    2014-01-01

    Bar-coded pyrosequencing has been increasingly used due to its fine taxonomic resolution and high throughput. Yet, concerns arise regarding the reproducibility of bar-coded pyrosequencing. We evaluated the run-to-run variation of bar-coded pyrosequencing in detecting bacterial community shifts and taxa dynamics. Our results demonstrate that pyrosequencing is reproducible in evaluating community shifts within a run, but not between runs. Also, the reproducibility of pyrosequencing in detecting individual taxa increased as a function of taxa abundance. Based on our findings: (1) for studies with modest sequencing depth, it is doubtful that data from different pyrosequencing runs can be considered comparable; (2) if multiple pyrosequencing runs are needed to increase the sequencing depth, additional sequencing efforts should be applied to all samples, rather than to selected samples; (3) if pyrosequencing is used for estimating bacterial population dynamics, only the abundant taxa should be considered; (4) for less-abundant taxa, the sequencing depth should be increased to ensure an accurate evaluation of taxon variation trends across samples.

  16. Game theory and extremal optimization for community detection in complex dynamic networks.

    Directory of Open Access Journals (Sweden)

    Rodica Ioana Lung

    Full Text Available The detection of evolving communities in dynamic complex networks is a challenging problem that recently received attention from the research community. Dynamics clearly add another complexity dimension to the difficult task of community detection. Methods should be able to detect changes in the network structure and produce a set of community structures corresponding to different timestamps and reflecting the evolution in time of network data. We propose a novel approach based on game theory elements and extremal optimization to address dynamic communities detection. Thus, the problem is formulated as a mathematical game in which nodes take the role of players that seek to choose a community that maximizes their profit viewed as a fitness function. Numerical results obtained for both synthetic and real-world networks illustrate the competitive performance of this game theoretical approach.

  17. Game theory and extremal optimization for community detection in complex dynamic networks.

    Science.gov (United States)

    Lung, Rodica Ioana; Chira, Camelia; Andreica, Anca

    2014-01-01

    The detection of evolving communities in dynamic complex networks is a challenging problem that recently received attention from the research community. Dynamics clearly add another complexity dimension to the difficult task of community detection. Methods should be able to detect changes in the network structure and produce a set of community structures corresponding to different timestamps and reflecting the evolution in time of network data. We propose a novel approach based on game theory elements and extremal optimization to address dynamic communities detection. Thus, the problem is formulated as a mathematical game in which nodes take the role of players that seek to choose a community that maximizes their profit viewed as a fitness function. Numerical results obtained for both synthetic and real-world networks illustrate the competitive performance of this game theoretical approach.

  18. Reproducible research in palaeomagnetism

    Science.gov (United States)

    Lurcock, Pontus; Florindo, Fabio

    2015-04-01

    The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined

  19. Communities recognition in the Chesapeake Bay ecosystem by dynamical clustering algorithms based on different oscillators systems

    CERN Document Server

    Pluchino, Alessandro; Latora, Vito

    2008-01-01

    We have recently introduced an efficient method for the detection and identification of modules in complex networks, based on the de-synchronization properties (dynamical clustering) of phase oscillators. In this paper we apply the dynamical clustering tecnique to the identification of communities of marine organisms living in the Chesapeake Bay food web. We show that our algorithm is able to perform a very reliable classification of the real communities existing in this ecosystem by using different kinds of dynamical oscillators. We compare also our results with those of other methods for the detection of community structures in complex networks.

  20. Microbial Community Dynamics During Biogas Slurry and Cow Manure Compost

    Institute of Scientific and Technical Information of China (English)

    ZHAO Hong-yan; LI Jie; LIU Jing-jing; L Yu-cai; WANG Xiao-fen; CUI Zong-jun

    2013-01-01

    This study evaluated the microbial community dynamics and maturation time of two compost systems: biogas slurry compost and cow manure compost, with the aim of evaluating the potential utility of a biogas slurry compost system. Denaturing gradient gel electrophoresis (DGGE), gene clone library, temperature, C/N ratio, and the germination index were employed for the investigation, cow manure compost was used as the control. Results showed that the basic strip and dominant strips of the DGGE bands for biogas slurry compost were similar to those of cow manure compost, but the brightness of the respective strips for each system were different. Shannon-Weaver indices of the two compost systems differed, possessing only 22%similarity in the primary and maturity stages of the compost process. Using bacterial 16S rRNA gene clone library analysis, 88 bacterial clones were detected. Further, 18 and 13 operational taxonomic units (OTUs) were present in biogas slurry and cow manure compost, respectively. The 18 OTUs of the biogas slurry compost belonged to nine bacterial genera, of which the dominant strains were Bacillus sp. and Carnobacterium sp.;the 13 OTUs of the cow manure compost belonged to eight bacterial genera, of which the dominant strains were Psychrobacter sp., Pseudomonas sp., and Clostridium sp. Results demonstrated that the duration of the thermophilic phase (more than 50°C) for biogas slurry compost was 8 d less than the according duration for cow manure compost, and the maturation times for biogas slurry and cow manure compost were 45 and 60 d, respectively. It is an effective biogas slurry assimilate technology by application of biogas slurry as nitrogen additives in the manufacture of organic fertilizer.

  1. Dynamic community detection based on network structural perturbation and topological similarity

    Science.gov (United States)

    Wang, Peizhuo; Gao, Lin; Ma, Xiaoke

    2017-01-01

    Community detection in dynamic networks has been extensively studied since it sheds light on the structure-function relation of the overall complex systems. Recently, it has been demonstrated that the structural perturbation in static networks is excellent in characterizing the topology. In order to investigate the perturbation structural theory in dynamic networks, we extend the theory by considering the dynamic variation information between networks of consecutive time. Then a novel similarity is proposed by combing structural perturbation and topological features. Finally, we present an evolutionary clustering algorithm to detect dynamic communities under the temporal smoothness framework. Experimental results on both artificial and real dynamic networks demonstrate that the proposed similarity is promising in dynamic community detection since it improves the clustering accuracy compared with state-of-the-art methods, indicating the superiority of the presented similarity measure.

  2. Ammonia oxidizing bacteria community dynamics in a pilot-scale wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Xiaohui Wang

    Full Text Available BACKGROUND: Chemoautotrophic ammonia oxidizing bacteria (AOB have the metabolic ability to oxidize ammonia to nitrite aerobically. This metabolic feature has been widely used, in combination with denitrification, to remove nitrogen from wastewater in wastewater treatment plants (WWTPs. However, the relative influence of specific deterministic environmental factors to AOB community dynamics in WWTP is uncertain. The ecological principles underlying AOB community dynamics and nitrification stability and how they are related are also poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: The community dynamics of ammonia oxidizing bacteria (AOB in a pilot-scale WWTP were monitored over a one-year period by Terminal Restriction Fragment Length Polymorphism (T-RFLP. During the study period, the effluent ammonia concentrations were almost below 2 mg/L, except for the first 60 days, indicting stable nitrification. T-RFLP results showed that, during the test period with stable nitrification, the AOB community structures were not stable, and the average change rate (every 15 days of AOB community structures was 10% ± 8%. The correlations between T-RFLP profiles and 10 operational and environmental parameters were tested by Canonical Correlation Analysis (CCA and Mantel test. The results indicated that the dynamics of AOB community correlated most strongly with Dissolved Oxygen (DO, effluent ammonia, effluent Biochemical Oxygen Demand (BOD and temperature. CONCLUSIONS/SIGNIFICANCE: This study suggests that nitrification stability is not necessarily accompanied by a stable AOB community, and provides insight into parameters controlling the AOB community dynamics within bioreactors with stable nitrification.

  3. Joint community and anomaly tracking in dynamic networks

    CERN Document Server

    Baingana, Brian

    2015-01-01

    Most real-world networks exhibit community structure, a phenomenon characterized by existence of node clusters whose intra-edge connectivity is stronger than edge connectivities between nodes belonging to different clusters. In addition to facilitating a better understanding of network behavior, community detection finds many practical applications in diverse settings. Communities in online social networks are indicative of shared functional roles, or affiliation to a common socio-economic status, the knowledge of which is vital for targeted advertisement. In buyer-seller networks, community detection facilitates better product recommendations. Unfortunately, reliability of community assignments is hindered by anomalous user behavior often observed as unfair self-promotion, or "fake" highly-connected accounts created to promote fraud. The present paper advocates a novel approach for jointly tracking communities while detecting such anomalous nodes in time-varying networks. By postulating edge creation as the ...

  4. Information dynamics algorithm for detecting communities in networks

    Science.gov (United States)

    Massaro, Emanuele; Bagnoli, Franco; Guazzini, Andrea; Lió, Pietro

    2012-11-01

    The problem of community detection is relevant in many scientific disciplines, from social science to statistical physics. Given the impact of community detection in many areas, such as psychology and social sciences, we have addressed the issue of modifying existing well performing algorithms by incorporating elements of the domain application fields, i.e. domain-inspired. We have focused on a psychology and social network-inspired approach which may be useful for further strengthening the link between social network studies and mathematics of community detection. Here we introduce a community-detection algorithm derived from the van Dongen's Markov Cluster algorithm (MCL) method [4] by considering networks' nodes as agents capable to take decisions. In this framework we have introduced a memory factor to mimic a typical human behavior such as the oblivion effect. The method is based on information diffusion and it includes a non-linear processing phase. We test our method on two classical community benchmark and on computer generated networks with known community structure. Our approach has three important features: the capacity of detecting overlapping communities, the capability of identifying communities from an individual point of view and the fine tuning the community detectability with respect to prior knowledge of the data. Finally we discuss how to use a Shannon entropy measure for parameter estimation in complex networks.

  5. ITK: Enabling Reproducible Research and Open Science

    Directory of Open Access Journals (Sweden)

    Matthew Michael McCormick

    2014-02-01

    Full Text Available Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature.Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification.This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

  6. Randomised reproducing graphs

    CERN Document Server

    Jordan, Jonathan

    2011-01-01

    We introduce a model for a growing random graph based on simultaneous reproduction of the vertices. The model can be thought of as a generalisation of the reproducing graphs of Southwell and Cannings and Bonato et al to allow for a random element, and there are three parameters, $\\alpha$, $\\beta$ and $\\gamma$, which are the probabilities of edges appearing between different types of vertices. We show that as the probabilities associated with the model vary there are a number of phase transitions, in particular concerning the degree sequence. If $(1+\\alpha)(1+\\gamma)1$ then the degree of a typical vertex grows to infinity, and the proportion of vertices having any fixed degree $d$ tends to zero. We also give some results on the number of edges and on the spectral gap.

  7. Epiphytic lichen community dynamics in deciduous forests around a phosphorus fertiliser factory in Central Lithuania

    Energy Technology Data Exchange (ETDEWEB)

    Motiejunaite, Jurga [Department of Mycology, Institute of Botany, LT-08406 Vilnius 21 (Lithuania)]. E-mail: mikojm@botanika.lt

    2007-03-15

    The detailed dynamics of epiphytic lichen communities were observed while studying permanent quadrats in the zone of influence of a phosphorus fertiliser factory in central Lithuania. The most significant changes were induced by several factors: changes in macroenvironment (increase of illumination), bark scaling, succession processes, individual growth characteristics of the community members, and influence of fungal infection and invertebrate grazing. None of these changes could be directly linked with air pollution. These observations have shown that in conditions of more or less stable pollution, epiphytic community dynamics should be evaluated with care, the best indicators of the characteristics of the communities being species richness and presence/absence and abundance of indicator (nitrophilous or acidophilous) species. - Biotic factors are important when evaluating dynamics of epiphytic communities in polluted areas.

  8. POPULATION DYNAMICS OF AMBIENT AND ALTERED EARTHWORM COMMUNITIES IN ROW-CROP AGROECOSYSTEMS IN OHIO, USA

    Science.gov (United States)

    Although earthworms are known to influence agroecosystem processes, there are relatively few long-term studies addressing population dynamics under cropping systems in which earthworm populations were intentionally altered. We assessed earthworm communities from fall 1994 to spr...

  9. Communities of Inquiry: Politics, Power and Group Dynamics

    Science.gov (United States)

    Burgh, Gilbert; Yorshansky, Mor

    2011-01-01

    The notion of a community of inquiry has been treated by many of its proponents as being an exemplar of democracy in action. We argue that the assumptions underlying this view present some practical and theoretical difficulties, particularly in relation to distribution of power among the members of a community of inquiry. We identify two…

  10. A quantitative model for assessing community dynamics of pleistocene mammals.

    Science.gov (United States)

    Lyons, S Kathleen

    2005-06-01

    Previous studies have suggested that species responded individualistically to the climate change of the last glaciation, expanding and contracting their ranges independently. Consequently, many researchers have concluded that community composition is plastic over time. Here I quantitatively assess changes in community composition over broad timescales and assess the effect of range shifts on community composition. Data on Pleistocene mammal assemblages from the FAUNMAP database were divided into four time periods (preglacial, full glacial, postglacial, and modern). Simulation analyses were designed to determine whether the degree of change in community composition is consistent with independent range shifts, given the distribution of range shifts observed. Results indicate that many of the communities examined in the United States were more similar through time than expected if individual range shifts were completely independent. However, in each time transition examined, there were areas of nonanalogue communities. I conducted sensitivity analyses to explore how the results were affected by the assumptions of the null model. Conclusions about changes in mammalian distributions and community composition are robust with respect to the assumptions of the model. Thus, whether because of biotic interactions or because of common environmental requirements, community structure through time is more complex than previously thought.

  11. Bacterial Community Dynamics and Polycyclic Aromatic Hydrocarbon Degradation during Bioremediation of Heavily Creosote-Contaminated Soil

    OpenAIRE

    Viñas, Marc; Sabaté, Jordi; Espuny, María José; Solanas, Anna M.

    2005-01-01

    Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87...

  12. Information dynamics algorithm for detecting communities in networks

    CERN Document Server

    Massaro, E; Bagnoli, F; Liò, P

    2011-01-01

    The problem of community detection is relevant in many scientific disciplines, from social science to statistical physics. Given the impact of community detection in many areas, such as psychology and social sciences, we have addressed the issue of modifying existing well performing algorithms by incorporating elements of the domain application fields, i.e. domain-inspired. We have focused on a psychology and social network - inspired approach which may be useful for further strengthening the link between social network studies and mathematics of community detection. Here we introduce a community-detection algorithm derived from the van Dongen's Markov Cluster algorithm (MCL) method by considering networks' nodes as agents capable to take decisions. In this framework we have introduced a memory factor to mimic a typical human behavior such as the oblivion effect. The method is based on information diffusion and it includes a non-linear processing phase. We test our method on two classical community benchmark ...

  13. Multi-Relational Characterization of Dynamic Social Network Communities

    Science.gov (United States)

    Lin, Yu-Ru; Sundaram, Hari; Kelliher, Aisling

    The emergence of the mediated social web - a distributed network of participants creating rich media content and engaging in interactive conversations through Internet-based communication technologies - has contributed to the evolution of powerful social, economic and cultural change. Online social network sites and blogs, such as Facebook, Twitter, Flickr and LiveJournal, thrive due to their fundamental sense of "community". The growth of online communities offers both opportunities and challenges for researchers and practitioners. Participation in online communities has been observed to influence people's behavior in diverse ways ranging from financial decision-making to political choices, suggesting the rich potential for diverse applications. However, although studies on the social web have been extensive, discovering communities from online social media remains challenging, due to the interdisciplinary nature of this subject. In this article, we present our recent work on characterization of communities in online social media using computational approaches grounded on the observations from social science.

  14. Reproducibility in Data-Scarce Environments

    Science.gov (United States)

    Darch, P. T.

    2016-12-01

    Among the usual requirements for reproducibility are large volumes of data and computationally intensive methods. Many fields within earth sciences, however, do not meet these requirements. Data are scarce and data-intensive methods are not well established. How can science be reproducible under these conditions? What changes, both infrastructural and cultural, are needed to advance reproducibility? This paper presents findings from a long-term social scientific case study of an emergent and data scarce field, the deep subseafloor biosphere. This field studies interactions between microbial communities living in the seafloor and the physical environments they inhabit. Factors such as these make reproducibility seem a distant goal for this community: - The relative newness of the field. Serious study began in the late 1990s; - The highly multidisciplinary nature of the field. Researchers come from a range of physical and life science backgrounds; - Data scarcity. Domain researchers produce much of these data in their own onshore laboratories by analyzing cores from international ocean drilling expeditions. Allocation of cores is negotiated between researchers from many fields. These factors interact in multiple ways to inhibit reproducibility: - Incentive structures emphasize producing new data and new knowledge rather than reanalysing extant data; - Only a few steps of laboratory analyses can be reproduced - such as analysis of DNA sequences, but not extraction of DNA from cores -, due to scarcity of cores; - Methodological heterogeneity is a consequence of multidisciplinarity, as researchers bring different techniques from diverse fields. - Few standards for data collection or analysis are available at this early stage of the field; - While datasets from multiple biological and physical phenomena can be integrated into a single workflow, curation tends to be divergent. Each type of dataset may be subject to different disparate policies and contributed to different

  15. Dynamics of Individual Specialization and Global Diversification in Communities

    CERN Document Server

    Borkar, V S; Rangarajan, G; Borkar, Vivek S.; Jain, Sanjay; Rangarajan, Govindan

    1998-01-01

    We discuss a model of an economic community consisting of $N$ interacting agents. The state of each agent at any time is characterized, in general, by a mixed strategy profile drawn from a space of $s$ pure strategies. The community evolves as agents update their strategy profiles in response to payoffs received from other agents. The evolution equation is a generalization of the replicator equation. We argue that when $N$ is sufficiently large and the payoff matrix elements satisfy suitable inequalities, the community evolves to retain the full diversity of available strategies even as individual agents specialize to pure strategies.

  16. Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

    KAUST Repository

    Zhang, Weipeng

    2014-04-14

    Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

  17. DyCoNet: a Gephi plugin for community detection in dynamic complex networks.

    Directory of Open Access Journals (Sweden)

    Julie Kauffman

    Full Text Available Community structure detection has proven to be important in revealing the underlying organisation of complex networks. While most current analyses focus on static networks, the detection of communities in dynamic data is both challenging and timely. An analysis and visualisation procedure for dynamic networks is presented here, which identifies communities and sub-communities that persist across multiple network snapshots. An existing method for community detection in dynamic networks is adapted, extended, and implemented. We demonstrate the applicability of this method to detect communities in networks where individuals tend not to change their community affiliation very frequently. When stability of communities cannot be assumed, we show that the sub-community model may be a better alternative. This is illustrated through test cases of social and biological networks. A plugin for Gephi, an open-source software program used for graph visualisation and manipulation, named "DyCoNet", was created to execute the algorithm and is freely available from https://github.com/juliemkauffman/DyCoNet.

  18. Dynamics of seawater bacterial communities in a shellfish hatchery.

    Science.gov (United States)

    Powell, S M; Chapman, C C; Bermudes, M; Tamplin, M L

    2013-08-01

    Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.

  19. Building a Community of Research Practice: Intragroup Team Social Dynamics in Interdisciplinary Mixed Methods

    Science.gov (United States)

    Hemmings, Annette; Beckett, Gulbahar; Kennerly, Susan; Yap, Tracey

    2013-01-01

    This article explicates the intragroup social dynamics and work of a nursing and education research team as a community of research practice interested in organizational cultures and occupational subcultures. Dynamics were characterized by processes of socialization through reeducation and group social identity formation that enabled members to…

  20. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant.

    Science.gov (United States)

    Flowers, Jason J; Cadkin, Tracey A; McMahon, Katherine D

    2013-12-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = -0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Local community detection as pattern restoration by attractor dynamics of recurrent neural networks.

    Science.gov (United States)

    Okamoto, Hiroshi

    2016-08-01

    Densely connected parts in networks are referred to as "communities". Community structure is a hallmark of a variety of real-world networks. Individual communities in networks form functional modules of complex systems described by networks. Therefore, finding communities in networks is essential to approaching and understanding complex systems described by networks. In fact, network science has made a great deal of effort to develop effective and efficient methods for detecting communities in networks. Here we put forward a type of community detection, which has been little examined so far but will be practically useful. Suppose that we are given a set of source nodes that includes some (but not all) of "true" members of a particular community; suppose also that the set includes some nodes that are not the members of this community (i.e., "false" members of the community). We propose to detect the community from this "imperfect" and "inaccurate" set of source nodes using attractor dynamics of recurrent neural networks. Community detection by the proposed method can be viewed as restoration of the original pattern from a deteriorated pattern, which is analogous to cue-triggered recall of short-term memory in the brain. We demonstrate the effectiveness of the proposed method using synthetic networks and real social networks for which correct communities are known.

  2. Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil.

    Science.gov (United States)

    Santalahti, Minna; Sun, Hui; Jumpponen, Ari; Pennanen, Taina; Heinonsalo, Jussi

    2016-11-01

    Fungal communities are important for carbon (C) transformations in boreal forests that are one of the largest C pools in terrestrial ecosystems, warranting thus further investigation of fungal community dynamics in time and space. We investigated fungal diversity and community composition seasonally and across defined soil horizons in boreal Scots pine forest in Finland using 454 pyrosequencing. We collected a total of 120 samples from five vertical soil horizons monthly from March to October; in March, under snow. Boreal forest soil generally harbored diverse fungal communities across soil horizons. The communities shifted drastically and rapidly over time. In late winter, saprotrophs dominated the community and were replaced by ectomycorrhizal fungi during the growing season. Our studies are among the first to dissect the spatial and temporal dynamics in boreal forest ecosystems and highlights the ecological importance of vertically distinct communities and their rapid seasonal dynamics. As climate change is predicted to result in warmer and longer snow-free winter seasons, as well as increase the rooting depth of trees in boreal forest, the seasonal and vertical distribution of fungal communities may change. These changes are likely to affect the organic matter decomposition by the soil-inhabiting fungi and thus alter organic C pools. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Community Detection in Dynamic Social Networks Based on Multiobjective Immune Algorithm

    Institute of Scientific and Technical Information of China (English)

    Mao-Guo Gong; Ling-Jun Zhang; Jing-Jing Ma; Li-Cheng Jiao

    2012-01-01

    Community structure is one of the most important properties in social networks,and community detection has received an enormous amount of attention in recent years.In dynamic networks,the communities may evolve over time so that pose more challenging tasks than in static ones.Community detection in dynamic networks is a problem which can naturally be formulated with two contradictory objectives and consequently be solved by multiobjective optimization algorithms.In this paper,a novel multiobjective immune algorithm is proposed to solve the community detection problem in dynamic networks.It employs the framework of nondominated neighbor immune algorithm to simultaneously optimize the modularity and normalized mutual information,which quantitatively measure the quality of the community partitions and temporal cost,respectively.The problem-specific knowledge is incorporated in genetic operators and local search to improve the effectiveness and efficiency of our method.Experimental studies based on four synthetic datasets and two real-world social networks demonstrate that our algorithm can not only find community structure and capture community evolution more accurately but also be more steadily than the state-of-the-art algorithms.

  4. COPEWELL: A Conceptual Framework and System Dynamics Model for Predicting Community Functioning and Resilience After Disasters.

    Science.gov (United States)

    Links, Jonathan M; Schwartz, Brian S; Lin, Sen; Kanarek, Norma; Mitrani-Reiser, Judith; Sell, Tara Kirk; Watson, Crystal R; Ward, Doug; Slemp, Cathy; Burhans, Robert; Gill, Kimberly; Igusa, Tak; Zhao, Xilei; Aguirre, Benigno; Trainor, Joseph; Nigg, Joanne; Inglesby, Thomas; Carbone, Eric; Kendra, James M

    2017-06-21

    Policy-makers and practitioners have a need to assess community resilience in disasters. Prior efforts conflated resilience with community functioning, combined resistance and recovery (the components of resilience), and relied on a static model for what is inherently a dynamic process. We sought to develop linked conceptual and computational models of community functioning and resilience after a disaster. We developed a system dynamics computational model that predicts community functioning after a disaster. The computational model outputted the time course of community functioning before, during, and after a disaster, which was used to calculate resistance, recovery, and resilience for all US counties. The conceptual model explicitly separated resilience from community functioning and identified all key components for each, which were translated into a system dynamics computational model with connections and feedbacks. The components were represented by publicly available measures at the county level. Baseline community functioning, resistance, recovery, and resilience evidenced a range of values and geographic clustering, consistent with hypotheses based on the disaster literature. The work is transparent, motivates ongoing refinements, and identifies areas for improved measurements. After validation, such a model can be used to identify effective investments to enhance community resilience.(Disaster Med Public Health Preparedness. 2017;page 1 of 11).

  5. Research Reproducibility in Geosciences: Current Landscape, Practices and Perspectives

    Science.gov (United States)

    Yan, An

    2016-04-01

    Reproducibility of research can gauge the validity of its findings. Yet currently we lack understanding of how much of a problem research reproducibility is in geosciences. We developed an online survey on faculty and graduate students in geosciences, and received 136 responses from research institutions and universities in Americas, Asia, Europe and other parts of the world. This survey examined (1) the current state of research reproducibility in geosciences by asking researchers' experiences with unsuccessful replication work, and what obstacles that lead to their replication failures; (2) the current reproducibility practices in community by asking what efforts researchers made to try to reproduce other's work and make their own work reproducible, and what the underlying factors that contribute to irreproducibility are; (3) the perspectives on reproducibility by collecting researcher's thoughts and opinions on this issue. The survey result indicated that nearly 80% of respondents who had ever reproduced a published study had failed at least one time in reproducing. Only one third of the respondents received helpful feedbacks when they contacted the authors of a published study for data, code, or other information. The primary factors that lead to unsuccessful replication attempts are insufficient details of instructions in published literature, and inaccessibility of data, code and tools needed in the study. Our findings suggest a remarkable lack of research reproducibility in geoscience. Changing the incentive mechanism in academia, as well as developing policies and tools that facilitate open data and code sharing are the promising ways for geosciences community to alleviate this reproducibility problem.

  6. Relationship between diversity of forest plant and community dynamics in eastern mountain area of Heilongjiang Province, China

    Institute of Scientific and Technical Information of China (English)

    WANG Qing-gui; XING Ya-juan; ZHOU Xiao-feng; HAN Shi-jie

    2006-01-01

    The biodiversity was studied in 26 communities with different structures in Maoershan National Park and Liangshui Natural Reserve of Northeast Forestry University in Heilongjiang Province, China. Composition index (CI) was taken as a parameter to quantify the community dynamics, which can nicely describe forest community dynamics, meanwhile, the relationship between diversity and community dynamics were also investigated and analyzed. Results showed that the total number species of community, richness, evenness, and Shannon-Wiener diversity index were obviously different in every community. The richness decreased with the increasing CI of every community, which means richness was in inverse proportion to community dynamics. The Shannon-Wiener index of every community increased from the initial stage to the middle stage of succession, and then decreased in the climax stage. The coverage weighted foliage-height diversity index increased along with the increase of CI, which was similar as the pattern diversity.

  7. Vegetation Dynamics and Community Assembly in Post-Agricultural Heathland

    DEFF Research Database (Denmark)

    Kepfer Rojas, Sebastian

    for the proximity to external seed sources, was an important factor affecting different components of the structure of the vegetation, demonstrating the importance of dispersal in the development of the community. My results indicate that the effect of the biotic interactions varies along abiotic gradients (e...

  8. Bacterial Invasion Dynamics in Zebrafish Gut Microbial Communities

    Science.gov (United States)

    Logan, Savannah; Jemielita, Matthew; Wiles, Travis; Schlomann, Brandon; Hammer, Brian; Guillemin, Karen; Parthasarathy, Raghuveer

    Microbial communities residing in the vertebrate intestine play an important role in host development and health. These communities must be in part shaped by interactions between microbial species as they compete for resources in a physically constrained system. To better understand these interactions, we use light sheet microscopy and zebrafish as a model organism to image established gut microbial communities as they are invaded by robustly-colonizing challengers. We demonstrate that features of the challenger, including motility and spatial distribution, impact success in invasion and in outcompeting the original community. We also show that physical characteristics of the host, such as the motility of the gut, play important roles in mediating inter-species competition. Finally, we examine the influence of the contact-dependent type VI secretion system (T6SS), which is used by specific bacteria to cause cell lysis by injecting toxic effector proteins into competitors. Our findings provide insights into the determinants of microbial success in the complex ecosystems found in the gut.

  9. Vegetation Dynamics and Community Assembly in Post-Agricultural Heathland

    DEFF Research Database (Denmark)

    Kepfer Rojas, Sebastian

    for the proximity to external seed sources, was an important factor affecting different components of the structure of the vegetation, demonstrating the importance of dispersal in the development of the community. My results indicate that the effect of the biotic interactions varies along abiotic gradients (e...

  10. Unscrambling cyanobacteria community dynamics related to environmental factors

    Directory of Open Access Journals (Sweden)

    Mireia eBertos-Fortis

    2016-05-01

    Full Text Available Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a two-year monthly time-series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An epidemic population structure (dominance of a single cluster was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this cluster simultaneously occurred with opportunistic clusters/OTUs e.g. Nodularia spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formed a consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocyanobacteria and

  11. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    Directory of Open Access Journals (Sweden)

    Zak Frentz

    2015-10-01

    Full Text Available Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  12. Incremental Density-Based Link Clustering Algorithm for Community Detection in Dynamic Networks

    Directory of Open Access Journals (Sweden)

    Fanrong Meng

    2016-01-01

    Full Text Available Community detection in complex networks has become a research hotspot in recent years. However, most of the existing community detection algorithms are designed for the static networks; namely, the connections between the nodes are invariable. In this paper, we propose an incremental density-based link clustering algorithm for community detection in dynamic networks, iDBLINK. This algorithm is an extended version of DBLINK which is proposed in our previous work. It can update the local link community structure in the current moment through the change of similarity between the edges at the adjacent moments, which includes the creation, growth, merging, deletion, contraction, and division of link communities. Extensive experimental results demonstrate that iDBLINK not only has a great time efficiency, but also maintains a high quality community detection performance when the network topology is changing.

  13. Detectability Thresholds and Optimal Algorithms for Community Structure in Dynamic Networks

    Science.gov (United States)

    Ghasemian, Amir; Zhang, Pan; Clauset, Aaron; Moore, Cristopher; Peel, Leto

    2016-07-01

    The detection of communities within a dynamic network is a common means for obtaining a coarse-grained view of a complex system and for investigating its underlying processes. While a number of methods have been proposed in the machine learning and physics literature, we lack a theoretical analysis of their strengths and weaknesses, or of the ultimate limits on when communities can be detected. Here, we study the fundamental limits of detecting community structure in dynamic networks. Specifically, we analyze the limits of detectability for a dynamic stochastic block model where nodes change their community memberships over time, but where edges are generated independently at each time step. Using the cavity method, we derive a precise detectability threshold as a function of the rate of change and the strength of the communities. Below this sharp threshold, we claim that no efficient algorithm can identify the communities better than chance. We then give two algorithms that are optimal in the sense that they succeed all the way down to this threshold. The first uses belief propagation, which gives asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm, based on linearizing the belief propagation equations. These results extend our understanding of the limits of community detection in an important direction, and introduce new mathematical tools for similar extensions to networks with other types of auxiliary information.

  14. Dynamical evolution of the community structure of complex earthquake network

    CERN Document Server

    Abe, Sumiyoshi

    2012-01-01

    Earthquake network is known to be complex in the sense that it is scale-free, small-world, hierarchically organized and assortatively mixed. Here, the time evolution of earthquake networks is analyzed around main shocks in the context of the community structure. It is found that the maximum of the modularity measure quantifying existence of communities exhibits a peculiar behavior: its maximum value stays at a large value before a main shock, suddenly drops to a small values at the main shock, and then increases to relax to a large value again relatively slowly. In this way, a main shock is characterized in the language of theory of complex networks. The result is also interpreted in terms of the clustering structure of the earthquake network.

  15. Short-term community dynamics in seasonal and hyperseasonal cerrados

    Directory of Open Access Journals (Sweden)

    MV. Cianciaruso

    Full Text Available In South America, the largest seasonal savanna region is the Brazilian cerrado. Our aim was to study temporal changes in some community descriptors, such as floristic composition, richness, species density, plant density, and cylindrical volume, in a seasonal cerrado, comparing it to a nearby hyperseasonal cerrado. In four different seasons, we placed randomly ten 1 m² quadrats in each vegetation form and sampled all the vascular plants. Seasonal changes in floristic composition, species density, and plant density were less pronounced in the seasonal than in the hyperseasonal cerrado. Floristic similarity between the vegetation forms was lower when the hyperseasonal cerrado was waterlogged. Richness and species density were higher in the seasonal cerrado, which reached its biomass peak at mid rainy season. The hyperseasonal cerrado, in turn, reached its biomass peak at early rainy season and, despite the waterlogging, maintained it until late rainy season. In the hyperseasonal cerrado, waterlogging acts as an environmental filter restricting the number of cerrado species able to withstand it. The seasonal cerrado community was more stable than the hyperseasonal one. Our results corroborated the idea that changes in the environmental filters will affect floristic composition and community structure in savannas.

  16. Decomposition-Based Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Social Networks

    Directory of Open Access Journals (Sweden)

    Jingjing Ma

    2014-01-01

    Full Text Available Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.

  17. Decomposition-based multiobjective evolutionary algorithm for community detection in dynamic social networks.

    Science.gov (United States)

    Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng

    2014-01-01

    Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.

  18. Plant toxicity, adaptive herbivory, and plant community dynamics

    Science.gov (United States)

    Zhilan Feng; Rongsong Liu; Donald L. DeAngelis; John P. Bryant; Knut Kielland; F. Stuart Chapin; Robert K. Swihart

    2009-01-01

    We model effects of interspecific plant competition, herbivory, and a plant's toxic defenses against herbivores on vegetation dynamics. The model predicts that, when a generalist herbivore feeds in the absence of plant toxins, adaptive foraging generally increases the probability of coexistence of plant species populations, because the herbivore switches more of...

  19. Communities recognition in the Chesapeake Bay ecosystem by dynamical clustering algorithms based on different oscillators systems

    Science.gov (United States)

    Pluchino, A.; Rapisarda, A.; Latora, V.

    2008-10-01

    We have recently introduced [Phys. Rev. E 75, 045102(R) (2007); AIP Conference Proceedings 965, 2007, p. 323] an efficient method for the detection and identification of modules in complex networks, based on the de-synchronization properties (dynamical clustering) of phase oscillators. In this paper we apply the dynamical clustering tecnique to the identification of communities of marine organisms living in the Chesapeake Bay food web. We show that our algorithm is able to perform a very reliable classification of the real communities existing in this ecosystem by using different kinds of dynamical oscillators. We compare also our results with those of other methods for the detection of community structures in complex networks.

  20. Dynamical origins of the community structure of multi-layer societies

    CERN Document Server

    Klimek, Peter; Eguiluz, Victor; Miguel, Maxi San; Thurner, Stefan

    2016-01-01

    Social structures emerge as a result of individuals managing a variety of different of social relationships. Societies can be represented as highly structured dynamic multiplex networks. Here we study the dynamical origins of the specific community structures of a large-scale social multiplex network of a human society that interacts in a virtual world of a massive multiplayer online game. There we find substantial differences in the community structures of different social actions, represented by the various network layers in the multiplex. Community size distributions are either similar to a power-law or appear to be centered around a size of 50 individuals. To understand these observations we propose a voter model that is built around the principle of triadic closure. It explicitly models the co-evolution of node- and link-dynamics across different layers of the multiplex. Depending on link- and node fluctuation rates, the model exhibits an anomalous shattered fragmentation transition, where one layer frag...

  1. A New Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Complex Networks

    Directory of Open Access Journals (Sweden)

    Guoqiang Chen

    2013-01-01

    Full Text Available Community detection in dynamic networks is an important research topic and has received an enormous amount of attention in recent years. Modularity is selected as a measure to quantify the quality of the community partition in previous detection methods. But, the modularity has been exposed to resolution limits. In this paper, we propose a novel multiobjective evolutionary algorithm for dynamic networks community detection based on the framework of nondominated sorting genetic algorithm. Modularity density which can address the limitations of modularity function is adopted to measure the snapshot cost, and normalized mutual information is selected to measure temporal cost, respectively. The characteristics knowledge of the problem is used in designing the genetic operators. Furthermore, a local search operator was designed, which can improve the effectiveness and efficiency of community detection. Experimental studies based on synthetic datasets show that the proposed algorithm can obtain better performance than the compared algorithms.

  2. Detectability thresholds and optimal algorithms for community structure in dynamic networks

    CERN Document Server

    Ghasemian, Amir; Clauset, Aaron; Moore, Cristopher; Peel, Leto

    2015-01-01

    We study the fundamental limits on learning latent community structure in dynamic networks. Specifically, we study dynamic stochastic block models where nodes change their community membership over time, but where edges are generated independently at each time step. In this setting (which is a special case of several existing models), we are able to derive the detectability threshold exactly, as a function of the rate of change and the strength of the communities. Below this threshold, we claim that no algorithm can identify the communities better than chance. We then give two algorithms that are optimal in the sense that they succeed all the way down to this limit. The first uses belief propagation (BP), which gives asymptotically optimal accuracy, and the second is a fast spectral clustering algorithm, based on linearizing the BP equations. We verify our analytic and algorithmic results via numerical simulation, and close with a brief discussion of extensions and open questions.

  3. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience

    Energy Technology Data Exchange (ETDEWEB)

    Niu, Qigui; Takemura, Yasuyuki; Kubota, Kengo [Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Li, Yu-You, E-mail: yyli@epl1.civil.tohoku.ac.jp [Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi’an University of Architecture and Technology, Xi’an (China)

    2015-09-15

    Highlights: • Microbial community dynamics and process functional resilience were investigated. • The threshold of TAN in mesophilic reactor was higher than the thermophilic reactor. • The recoverable archaeal community dynamic sustained the process resilience. • Methanosarcina was more sensitive than Methanoculleus on ammonia inhibition. • TAN and FA effects the dynamic of hydrolytic and acidogenic bacteria obviously. - Abstract: While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000 mg/L with free ammonia (FA) 2000 mg/L compared to 16,000 mg/L (FA1500 mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gV S{sub in} in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.

  4. Abrupt community transitions and cyclic evolutionary dynamics in complex food webs☆

    Science.gov (United States)

    Takahashi, Daisuke; Brännström, Åke; Mazzucco, Rupert; Yamauchi, Atsushi; Dieckmann, Ulf

    2013-01-01

    Understanding the emergence and maintenance of biodiversity ranks among the most fundamental challenges in evolutionary ecology. While processes of community assembly have frequently been analyzed from an ecological perspective, their evolutionary dimensions have so far received less attention. To elucidate the eco-evolutionary processes underlying the long-term build-up and potential collapse of community diversity, here we develop and examine an individual-based model describing coevolutionary dynamics driven by trophic interactions and interference competition, of a pair of quantitative traits determining predator and prey niches. Our results demonstrate the (1) emergence of communities with multiple trophic levels, shown here for the first time for stochastic models with linear functional responses, and (2) intermittent and cyclic evolutionary transitions between two alternative community states. In particular, our results indicate that the interplay of ecological and evolutionary dynamics often results in extinction cascades that remove the entire trophic level of consumers from a community. Finally, we show the (3) robustness of our results under variations of model assumptions, underscoring that processes of consumer collapse and subsequent rebound could be important elements of understanding biodiversity dynamics in natural communities. PMID:23948552

  5. Modeling the population dynamics and community impacts of Ambystoma tigrinum: A case study of phenotype plasticity.

    Science.gov (United States)

    McCarthy, Maeve L; Wallace, Dorothy; Whiteman, Howard H; Rheingold, Evan T; Dunham, Ann M; Prosper, Olivia; Chen, Michelle; Hu-Wang, Eileen

    2017-06-01

    . There appears to be a mathematical basis to the general tenet of spatiotemporal variation being important for the maintenance of polyphenisms, and our results suggest that such variation may have cascading effects on population, community, and perhaps ecosystem dynamics because it drives the production of a keystone, cannibalistic predator. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles

    Science.gov (United States)

    Ebrahimi, Ali; Or, Dani

    2016-04-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Mechanistic models of microbial processes in unsaturated aggregate pore networks revealed dynamic interplay between oxic and anoxic microsites that are jointly shaped by hydration and by aerobic and anaerobic microbial communities. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support significant anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3-D angular pore networks with profiles of water, carbon, and oxygen that vary with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain biogeochemical fluxes over the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of interest for hydrological and climate models.

  7. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Maren Stella Müller

    Full Text Available Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG, pyrrolnitrin (PRN and hydrogen cyanide (HCN in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks, as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  8. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Science.gov (United States)

    Müller, Maren Stella; Scheu, Stefan; Jousset, Alexandre

    2013-01-01

    Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  9. Arctic microbial community dynamics influenced by elevated CO2 levels

    Directory of Open Access Journals (Sweden)

    K. Schulz

    2012-09-01

    Full Text Available The Arctic Ocean ecosystem is particular vulnerable for ocean acidification (OA related alterations due to the relatively high CO2 solubility and low carbonate saturation states of its cold surface waters. Thus far, however, there is only little known about the consequences of OA on the base of the food web. In a mesocosm CO2-enrichment experiment (overall CO2 levels ranged from ∼180 to 1100 μatm in the Kongsfjord off Svalbard, we studied the consequences of OA on a natural pelagic microbial community. The most prominent finding of our study is the profound effect of OA on the composition and growth of the Arctic phytoplankton community, i.e. the picoeukaryotic photoautotrophs and to a lesser extent the nanophytoplankton prospered. A shift towards the smallest phytoplankton as a result of OA will have direct consequences for the structure and functioning of the pelagic food web and thus for the biogeochemical cycles. Furthermore, the dominant pico- and nanophytoplankton groups were found prone to viral lysis, thereby shunting the carbon accumulation in living organisms into the dissolved pools of organic carbon and subsequently affecting the efficiency of the biological pump in these Arctic waters.

  10. Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

    Science.gov (United States)

    Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

    2016-11-01

    Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

  11. Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring.

    Science.gov (United States)

    Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

    2017-05-01

    Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

  12. Temporal dynamics of microbial communities in microcosms in response to pollutants.

    Science.gov (United States)

    Jiao, Shuo; Zhang, Zhengqing; Yang, Fan; Lin, Yanbing; Chen, Weimin; Wei, Gehong

    2017-02-01

    Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.

  13. Pervasive influence of large-scale climate in the dynamics of a terrestrial vertebrate community

    Directory of Open Access Journals (Sweden)

    Forchhammer Mads C

    2001-12-01

    Full Text Available Abstract Background Large-scale climatic variability has been implicated in the population dynamics of many vertebrates throughout the Northern Hemisphere, but has not been demonstrated to directly influence dynamics at multiple trophic levels of any single system. Using data from Isle Royale, USA, comprising time series on the long-term dynamics at three trophic levels (wolves, moose, and balsam fir, we analyzed the relative contributions of density dependence, inter-specific interactions, and climate to the dynamics of each level of the community. Results Despite differences in dynamic complexity among the predator, herbivore, and vegetation levels, large-scale climatic variability influenced dynamics directly at all three levels. The strength of the climatic influence on dynamics was, however, strongest at the top and bottom trophic levels, where density dependence was weakest. Conclusions Because of the conflicting influences of environmental variability and intrinsic processes on population stability, a direct influence of climate on the dynamics at all three levels suggests that climate change may alter stability of this community. Theoretical considerations suggest that if it does, such alteration is most likely to result from changes in stability at the top or bottom trophic levels, where the influence of climate was strongest.

  14. Metagenomic insights into the dynamics of microbial communities in food.

    Science.gov (United States)

    Kergourlay, Gilles; Taminiau, Bernard; Daube, Georges; Champomier Vergès, Marie-Christine

    2015-11-20

    Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs, skin). DNA sequencing techniques are becoming increasingly popular and less and less expensive. Given that high-throughput DNA sequencing approaches have only recently started to be used to decipher food microbial ecosystems, there is a significant growth potential for such technologies in the field of food microbiology. The aim of this review is to present a survey of recent food investigations via metagenomics and to illustrate how this approach can be a valuable tool in the better characterization of foods and their transformation, storage and safety. Traditional food in particular has been thoroughly explored by global approaches in order to provide information on multi-species and multi-organism communities.

  15. Market dynamics of community pharmacies in Minnesota, U.S. from 1992 through 2012.

    Science.gov (United States)

    Schommer, Jon C; Yusuf, Akeem A; Hadsall, Ronald S

    2014-01-01

    An understanding of community pharmacy market dynamics is important for monitoring access points for pharmacist services. The purpose of this study was to describe (1) changes in pharmacy mix (independent versus chain) between 1992 and 2002 and between 2002 and 2012 for 87 counties in Minnesota (state in U.S.) and (2) the number (and proportion) of community pharmacies in Minnesota for the years 1992, 2002, and 2012 using a new categorization method developed specifically for this study. Data included licensure records for 1992, 2002, and 2012 from the State of Minnesota Board of Pharmacy and county level demographics for 1990, 2000 and 2010 from the US Census Bureau. Descriptive statistics were used to summarize findings over time and to describe associations between study variables. The ratio of independent pharmacies to chain pharmacies changed from approximately 2:1 in 1992 to 1:2 in 2012. The primary market factors associated with changes in the number of community pharmacies per county were (1) the metropolitan designation of the county and (2) whether the population density (persons/square mile) was increasing or decreasing. The face of community pharmacy in Minnesota changed between 1992 and 2012. By 2012, pharmacies were located in traditional retail pharmacies, mass merchandiser outlets, supermarkets, and clinics/medical centers. Furthermore, specialty pharmacies grew in proportion to meet patient needs. Between 1992 and 2012, the market dynamics of community pharmacies in Minnesota was characterized by vigorous market entry and exit. In light of recent health reform that is exhibiting characteristics such as continuity-of-care models, performance-based payment, technology advances, and the care of patients becoming more "ambulatory" (versus in-patient), we suggest that the market dynamics of community pharmacies will continue to exhibit vigorous market entry and exit in this new environment. It is proposed that the community pharmacy categories developed

  16. Oceanographic gradients and seabird prey community dynamics in glacial fjords

    Science.gov (United States)

    Arimitsu, Mayumi L.; Piatt, John F.; Madison, Erica N.; Conaway, Jeff; Hillgruber, N.

    2012-01-01

    Glacial fjord habitats are undergoing rapid change as a result of contemporary global warming, yet little is known about how glaciers influence marine ecosystems. These ecosystems provide important feeding, breeding and rearing grounds for a wide variety of marine organisms, including seabirds of management concern. To characterize ocean conditions and marine food webs near tidewater glaciers, we conducted monthly surveys of oceanographic variables, plankton, fish and seabirds in Kenai Fjords, Alaska, from June to August of 2007 and 2008. We also measured tidal current velocities near glacial features. We found high sediment load from glacial river runoff played a major role in structuring the fjord marine ecosystem. Submerged moraines (sills) isolated cool, fresh, stratified and silt-laden inner fjord habitats from oceanic influence. Near tidewater glaciers, surface layers of turbid glacial runoff limited availability of light to phytoplankton, but macrozooplankton were abundant in surface waters, perhaps due to the absence of a photic cue for diel migration. Fish and zooplankton community structure varied along an increasing temperature gradient throughout the summer. Acoustic measurements indicated that low density patches of fish and zooplankton were available in the surface waters near glacial river outflows. This is the foraging habitat occupied most by Kittlitz's murrelet (Brachyramphus brevirostris), a rare seabird that appears to be specialized for life in glacially influenced environments. Kittlitz's murrelets were associated with floating glacial ice, and they were more likely to occur near glaciers, in deeper water, and in areas with high acoustic backscatter. Kittlitz's murrelet at-sea distribution was limited to areas influenced by turbid glacial outflows, and where prey was concentrated near the surface in waters with low light penetration. Tidewater glaciers impart unique hydrographic characteristics that influence marine plankton and fish

  17. Completely reproducible description of digital sound data with cellular automata

    Energy Technology Data Exchange (ETDEWEB)

    Wada, Masato; Kuroiwa, Jousuke; Nara, Shigetoshi

    2002-12-30

    A novel method of compressive and completely reproducible description of digital sound data by means of rule dynamics of CA (cellular automata) is proposed. The digital data of spoken words and music recorded with the standard format of a compact disk are reproduced completely by this method with use of only two rules in a one-dimensional CA without loss of information.

  18. Contextual sensitivity in scientific reproducibility.

    Science.gov (United States)

    Van Bavel, Jay J; Mende-Siedlecki, Peter; Brady, William J; Reinero, Diego A

    2016-06-07

    In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.

  19. Force-Based Incremental Algorithm for Mining Community Structure in Dynamic Network

    Institute of Scientific and Technical Information of China (English)

    Bo Yang; Da-You Liu

    2006-01-01

    Community structure is an important property of network. Being able to identify communities can provide invaluable help in exploiting and understanding both social and non-social networks. Several algorithms have been developed up till now. However, all these algorithms can work well only with small or moderate networks with vertexes of order 104.Besides, all the existing algorithms are off-line and cannot work well with highly dynamic networks such as web, in which web pages are updated frequently. When an already clustered network is updated, the entire network including original and incremental parts has to be recalculated, even though only slight changes are involved. To address this problem, an incremental algorithm is proposed, which allows for mining community structure in large-scale and dynamic networks. Based on the community structure detected previously, the algorithm takes little time to reclassify the entire network including both the original and incremental parts. Furthermore, the algorithm is faster than most of the existing algorithms such as Girvan and Newman's algorithm and its improved versions. Also, the algorithm can help to visualize these community structures in network and provide a new approach to research on the evolving process of dynamic networks.

  20. Community structure and seasonal dynamics of diatom biofilms and associated grazers in intertidal mudflats

    NARCIS (Netherlands)

    Sahan, E.; Sabbe, K.; Creach, V.; Hernandez-Raquet, G.; Vyverman, W.; Stal, L.J.; Muyzer, G.

    2007-01-01

    The composition and seasonal dynamics of biofilm-associated eukaryotic communities were analysed at the metre and kilometre scale along a salinity gradient in the Westerschelde estuary (The Netherlands), using microscopy and a genetic fingerprinting technique (PCR-DGGE). Microphytobenthic biomass, m

  1. Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor

    DEFF Research Database (Denmark)

    Ziegler, Anja Sloth; McIlroy, Simon Jon; Larsen, Poul

    2016-01-01

    into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics...

  2. The adaptive dynamic community detection algorithm based on the non-homogeneous random walking

    Science.gov (United States)

    Xin, Yu; Xie, Zhi-Qiang; Yang, Jing

    2016-05-01

    With the changing of the habit and custom, people's social activity tends to be changeable. It is required to have a community evolution analyzing method to mine the dynamic information in social network. For that, we design the random walking possibility function and the topology gain function to calculate the global influence matrix of the nodes. By the analysis of the global influence matrix, the clustering directions of the nodes can be obtained, thus the NRW (Non-Homogeneous Random Walk) method for detecting the static overlapping communities can be established. We design the ANRW (Adaptive Non-Homogeneous Random Walk) method via adapting the nodes impacted by the dynamic events based on the NRW. The ANRW combines the local community detection with dynamic adaptive adjustment to decrease the computational cost for ANRW. Furthermore, the ANRW treats the node as the calculating unity, thus the running manner of the ANRW is suitable to the parallel computing, which could meet the requirement of large dataset mining. Finally, by the experiment analysis, the efficiency of ANRW on dynamic community detection is verified.

  3. From Static Content to Dynamic Communities: The Evolution of Networked Educational Resources.

    Science.gov (United States)

    Jacobs, Neil; Huxley, Lesly

    2002-01-01

    Discusses Web-based educational resources in the United Kingdom, focusing on current challenges of linking content with community and static information with dynamic news. Describes the evolution of three social sciences resources and examines sustainability, the need for collaboration, and data protection and privacy concerns. (Author/LRW)

  4. [Effect of agrochemicals and bio-control productions on soil nematode community dynamics].

    Science.gov (United States)

    Zhang, Wanmin; Duan, Yuxi; Chen, Lijie; Liang, Chen

    2002-05-01

    Dynamics of soil nematode communities amended with agrochemicals and bio-control preparations were investigated in a soybean field. The results showed that the frequency of plant non-parasitic nematodes were obviously higher in soil amended with bio-control preparations (Doufeng 1) than with urea and herbicide, however, that of plant parasitic nematodes exhibited an inverse trend.

  5. PISCATOR, an individual-based model to analyze the dynamics of lake fish communities

    NARCIS (Netherlands)

    Nes, van E.H.; Lammens, E.H.R.R.; Scheffer, M.

    2002-01-01

    Unraveling the mechanisms that drive dynamics of multi-species fish communities is notoriously difficult. Not only are the interactions between fish populations complex, but also the functional niche of individual animals changes profoundly as they grow, making variation in size within populations a

  6. Detecting community structure in networks via consensus dynamics and spatial transformation

    Science.gov (United States)

    Yang, Bo; He, He; Hu, Xiaoming

    2017-10-01

    We present a novel clustering algorithm for community detection, based on the dynamics towards consensus and spatial transformation. The community detection problem is translated to a clustering problem in the N-dimensional Euclidean space by three stages: (1) the dynamics running on a network is emulated to a procedure of gas diffusion in a finite space; (2) the pressure distribution vectors are used to describe the influence that each node exerts on the whole network; (3) the similarity measures between two nodes are quantified in the N-dimensional Euclidean space by k-Nearest Neighbors method. After such steps, we could merge clusters according to their similarity distances and show the community structure of a network by a hierarchical clustering tree. Tests on several benchmark networks are presented and the results show the effectiveness and reliability of our algorithm.

  7. [Dynamics of parasite communities in an age series of Arctic Cisco Coregonus migratorius (Georgi, 1775)].

    Science.gov (United States)

    Dugarov, Zh N; Pronin, N M

    2013-01-01

    Parasite communities of Arctic cisco from Chivyrkui Bay of Lake Baikal have been analyzed at levels of a host individual (infracommunity), a individual age group of a host-(assemblages of infracommunities), and a host population (component community). Significant positive correlations of parameters of species richness (number of parasite species, Margalef and Menhinick indices) with the age of Arctic cisco were recorded only at the level of parasite inffacommunities. The absence of linear positive correlations between the parameters of species richness and the age of Arctic cisco at the level of assemblages of parasite infracommunities were revealed for the first time for fish of Lake Baikal. The peculiarity of the dynamics of parasite communities of. Arctic cisco is determined by specific features of the host physiology and ecology, primarily by the age dynamics of the feeding spectrum.

  8. Reproducibility of a test for the functional evaluation of dynamic and agility in elderly people = Reproducibilidad de una prueba para la evaluación funcional del balance dinámico y la agilidad del adulto mayor

    Directory of Open Access Journals (Sweden)

    Fonseca, Adriana Angarita

    2014-09-01

    Full Text Available Background: The 8 foot up & go test assesses the dynamic balance and agility in elderly people. Its reproducibility has been evaluated in American population, but it is unknown whether it would work similarly in a different population like the Colombian. Objective: To evaluate the test-retest reliability and agreement level of the 8 foot up & go test in a sample of older adults from Bucaramanga, Colombia. Materials and methods: An evaluation of diagnostic tests was done in 114 elderly individuals. In the analysis, we assessed the test-retest reliability of the 8 foot up & go test by the Intraclass Correlation Coefficient (ICC 2.1 with their respective confidence intervals at 95% (95% CI. The agreement level was established by the Bland-Altman method. Results: The test-retest reliability of the 8 foot up & go test was very good (ICC: 0.98; 95% CI: 0.98- 0.99. The agreement was good in females (mean difference [MD] = 0.04 seconds and limits of agreement [LA]: -1.27; 1.36 seconds, and in elderly institutionalized (MD = 0.04 seconds [LA]: -3.18; 3.27 seconds. Conclusion: The 8 foot up & go test has very good reliability and good agreement in Colombian local elderly population.

  9. Plant toxicity, adaptive herbivory, and plant community dynamics

    Science.gov (United States)

    Feng, Z.; Liu, R.; DeAngelis, D.L.; Bryant, J.P.; Kielland, K.; Stuart, Chapin F.; Swihart, R.K.

    2009-01-01

    We model effects of interspecific plant competition, herbivory, and a plant's toxic defenses against herbivores on vegetation dynamics. The model predicts that, when a generalist herbivore feeds in the absence of plant toxins, adaptive foraging generally increases the probability of coexistence of plant species populations, because the herbivore switches more of its effort to whichever plant species is more common and accessible. In contrast, toxin-determined selective herbivory can drive plant succession toward dominance by the more toxic species, as previously documented in boreal forests and prairies. When the toxin concentrations in different plant species are similar, but species have different toxins with nonadditive effects, herbivores tend to diversify foraging efforts to avoid high intakes of any one toxin. This diversification leads the herbivore to focus more feeding on the less common plant species. Thus, uncommon plants may experience depensatory mortality from herbivory, reducing local species diversity. The depensatory effect of herbivory may inhibit the invasion of other plant species that are more palatable or have different toxins. These predictions were tested and confirmed in the Alaskan boreal forest. ?? 2009 Springer Science+Business Media, LLC.

  10. Community dynamics in the mouse gut microbiota: a possible role for IRF9-regulated genes in community homeostasis.

    Directory of Open Access Journals (Sweden)

    Claire L Thompson

    Full Text Available BACKGROUND: Gut microbial communities of mammals are thought to show stable differences between individuals. This means that the properties imparted by the gut microbiota become a unique and constant characteristic of the host. Manipulation of the microbiota has been proposed as a useful tool in health care, but a greater understanding of mechanisms which lead to community stability is required. Here we have examined the impact of host immunoregulatory phenotype on community dynamics. METHODS AND FINDINGS: Denaturing gradient gel electrophoresis was used to analyse the faecal bacterial community of BALB/c and C57BL/6 mice and C57BL/6 mice deficient for either type I interferon (IFN signalling (IRF9 KO mice or type I and type II IFN signalling (STAT1 KO mice. Temporal variation was found in all mouse strains. A measure of the ability for a community structure characteristic of the host to be maintained over time, the individuality index, varied between mouse strains and available data from pigs and human models. IRF9 KO mice had significantly higher temporal variation, and lower individuality, than other mouse strains. Examination of the intestinal mucosa of the IRF9 KO mice revealed an increased presence of T-cells and neutrophils in the absence of inflammation. SIGNIFICANCE: The high temporal variation observed in the gut microbiota of inbred laboratory mice has implications for their use as experimental models for the human gut microbiota. The distinct IRF9 and STAT1 phenotypes suggest a role for IRF9 in immune regulation within the gut mucosa and that further study of interferon responsive genes is necessary to understand host-gut microbe relationships.

  11. Microbial community dynamics in mesophilic anaerobic co-digestion of mixed waste.

    Science.gov (United States)

    Supaphol, Savaporn; Jenkins, Sasha N; Intomo, Pichamon; Waite, Ian S; O'Donnell, Anthony G

    2011-03-01

    This paper identifies key components of the microbial community involved in the mesophilic anaerobic co-digestion (AD) of mixed waste at Rayong Biogas Plant, Thailand. The AD process is separated into three stages: front end treatment (FET); feed holding tank and the main anaerobic digester. The study examines how the microbial community structure was affected by the different stages and found that seeding the waste at the beginning of the process (FET) resulted in community stability. Also, co-digestion of mixed waste supported different bacterial and methanogenic pathways. Typically, acetoclastic methanogenesis was the major pathway catalysed by Methanosaeta but hydrogenotrophs were also supported. Finally, the three-stage AD process means that hydrolysis and acidogenesis is initiated prior to entering the main digester which helps improve the bioconversion efficiency. This paper demonstrates that both resource availability (different waste streams) and environmental factors are key drivers of microbial community dynamics in mesophilic, anaerobic co-digestion.

  12. Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils.

    Directory of Open Access Journals (Sweden)

    Michele C Pereira E Silva

    Full Text Available BACKGROUND: Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. METHODOLOGY/PRINCIPAL FINDINGS: In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K, indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. CONCLUSIONS: Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.

  13. Dynamic structure of stock communities: a comparative study between stock returns and turnover rates

    Science.gov (United States)

    Su, Li-Ling; Jiang, Xiong-Fei; Li, Sai-Ping; Zhong, Li-Xin; Ren, Fei

    2017-07-01

    The detection of community structure in stock market is of theoretical and practical significance for the study of financial dynamics and portfolio risk estimation. We here study the community structures in Chinese stock markets from the aspects of both price returns and turnover rates, by using a combination of the PMFG and infomap methods based on a distance matrix. An empirical study using the overall data set shows that for both returns and turnover rates the largest communities are composed of specific industrial or conceptional sectors and the correlation inside a sector is generally larger than the correlation between different sectors. However, the community structure for turnover rates is more complex than that for returns, which indicates that the interactions between stocks revealed by turnover rates may contain more information. This conclusion is further confirmed by the analysis of the changes in the dynamics of community structures over five sub-periods. Sectors like banks, real estate, health care and New Shanghai take turns to comprise a few of the largest communities in different sub-periods, and more interestingly several specific sectors appear in the communities with different rank orders for returns and turnover rates even in the same sub-period. To better understand their differences, a comparison between the evolution of the returns and turnover rates of the stocks from these sectors is conducted. We find that stock prices only had large changes around important events while turnover rates surged after each of these events relevant to specific sectors, which shows strong evidence that the turnover rates are more susceptible to exogenous shocks than returns and its measurement for community detection may contain more useful information about market structure.

  14. Methanogenic community dynamics in anaerobic co-digestion of fruit and vegetable waste and food waste

    Institute of Scientific and Technical Information of China (English)

    Jia Lin; Jiane Zuo; Ruofan Ji; Xiaojie Chen; Fenglin Liu; Kaijun Wang; Yunfeng Yang

    2012-01-01

    A lab-scale continuously-stirred tank reactor (CSTR),used for anaerobic co-digestion of fruit and vegetable waste (FVW) and food waste (FW) at different mixture ratios,was operated for 178 days at the organic loading rate of 3 kg VS (volatile solids)/(m3.day).The dynamics of the Archaeal community and the correlations between environmental variables and methanogenic community structure were analyzed by polymerase chain reactions - denaturing gradient gel electrophoresis (PCR-DGGE) and redundancy analysis (RDA),respectively.PCR-DGGE results demonstrated that the mixture ratio of FVW to FW altered the community composition of Aachaea.As the FVW/FW ratio increased,Methanoculleus,Methanosaeta and Methanosarcina became the predominant methanogens in the community.Redundancy analysis results indicated that the shift of the methanogenic community was significantly correlated with the composition of acidogenic products and methane production yield.Different mixture ratios of substrates led to different compositions of intermediate metabolites,which may affect the methanogenic community.These results suggested that the analysis of microbial communities could be used to diagnose anaerobic processes.

  15. [Spatial and temporal dynamics of the weed community in the Zoysia matrella lawn].

    Science.gov (United States)

    Liu, Jia-Qi; Li, You-Han; Zeng, Ying; Xie, Xin-Ming

    2014-02-01

    The heterogeneity of species composition is one of the main attributes in weed community dynamics. Based on species frequency and power law, this paper studied the variations of weed community species composition and spatial heterogeneity in a Zoysia matrella lawn in Guangzhou at different time. The results showed that there were 43 weed species belonging to 19 families in the Z. matrella lawn from 2007 to 2009, in which Gramineae, Compositae, Cyperaceae and Rubiaceae had a comparative advantage. Perennial weeds accounted for the largest proportion of weeds and increased gradually in the three years. Weed communities distributed in higher heterogeneity than in a random model. Dominant weeds varied with season and displayed regularity in the order of 'dicotyledon-monocotyledon-dicotyledon weeds' and 'perennial-annual-perennial weeds'. The spatial heterogeneity of weed community in Z. matrella lawn was higher in summer than in winter. The diversity and evenness of weed community were higher in summer and autumn than in winter and spring. The number of weed species with high heterogeneity in summer was higher than in the other seasons. The spatial heterogeneity and diversity of weed community had no significant change in the three years, while the evenness of weed community had the tendency to decline gradually.

  16. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

    Science.gov (United States)

    Ziganshin, Ayrat M; Liebetrau, Jan; Pröter, Jürgen; Kleinsteuber, Sabine

    2013-06-01

    The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors' operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

  17. Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

    Science.gov (United States)

    Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

    2016-01-01

    ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study

  18. Dynamic changes of microbial community diversity in a photohydrogen producing reactor monitored by PCR-DGGE

    Institute of Scientific and Technical Information of China (English)

    YING Yanling; LV Zhenmei; MIN Hang; CHENG Jun

    2008-01-01

    A PCR-DGGE (denaturing gradient gel electrophoresis of polymerase chain reaction) protocol was used for monitoring the dynamic changes in the microbial population during photohydrogen production. Total DNA was extracted directly from the mixed bacterial community in the reactor and subjected to PCR with V3-16S rDNA and pufM gene primers, and the amplifications were then analyzed by DGGE. The DGGE patterns demonstrated the dynamics of community structure and the shift of microbial diversity, which corresponded to different running periods of the reactor. The optimal hydrogen producing community formed on day 10. Using DGGE analysis with the pufM gene fragments was superior to V3-16S rDNA region genes for detecting the dynamic variations of the photosynthetic bacteria population during hydrogen production. The comparative sequence analysis of excised DGGE bands showed the relationship between specific population structures and system performance. Rhodopseudomonas palustris was presumed as one of the dominant community members for hydrogen production in the reactor. The PCR-DGGE protocol was proven to be a good tool for monitoring the photohydrogen production in real time and offered the available information to improve the photohydrogen producing system.

  19. Dynamical origins of the community structure of an online multi-layer society

    Science.gov (United States)

    Klimek, Peter; Diakonova, Marina; Eguíluz, Víctor M.; San Miguel, Maxi; Thurner, Stefan

    2016-08-01

    Social structures emerge as a result of individuals managing a variety of different social relationships. Societies can be represented as highly structured dynamic multiplex networks. Here we study the dynamical origins of the specific community structures of a large-scale social multiplex network of a human society that interacts in a virtual world of a massive multiplayer online game. There we find substantial differences in the community structures of different social actions, represented by the various layers in the multiplex network. Community sizes distributions are either fat-tailed or appear to be centered around a size of 50 individuals. To understand these observations we propose a voter model that is built around the principle of triadic closure. It explicitly models the co-evolution of node- and link-dynamics across different layers of the multiplex network. Depending on link and node fluctuation probabilities, the model exhibits an anomalous shattered fragmentation transition, where one layer fragments from one large component into many small components. The observed community size distributions are in good agreement with the predicted fragmentation in the model. This suggests that several detailed features of the fragmentation in societies can be traced back to the triadic closure processes.

  20. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B.; Gentry, Terry J. [Texas A and M Univ., College Station, TX (United States). Dept. of Soil and Crop Sciences; Forrest, Andrea K.; Holtzapple, Mark T. [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering; Wilkinson, Heather H.; Ebbole, Daniel J. [Texas A and M Univ., College Station, TX (United States). Dept. of Plant Pathology and Microbiology; Malfatti, Stephanie A.; Tringe, Susannah G. [DOE Joint Genome Institute, Walnut Creek, CA (United States)

    2010-09-15

    The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 C) and thermophilic (55 C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and {gamma}-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform's microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes. (orig.)

  1. Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor.

    Directory of Open Access Journals (Sweden)

    Anja S Ziegler

    Full Text Available Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans, Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm.

  2. Community dynamics of a montane Fagus engleriana–Cyclobalanopsis multiervis mixed forest in Shennongjia, Hubei, China

    Directory of Open Access Journals (Sweden)

    Jielin Ge

    2012-11-01

    Full Text Available Montane evergreen and deciduous broad-leaved mixed forests are some of the main vegetation types in China. Specifically, the Fagus–Cyclobalanopsis mixed forest is a dominant forest community in themountainous region of Shennongjia. Using three datasets (2001, 2006, and 2010 from a permanent 120 m ×80 m plot in the montane evergreen and deciduous broad-leaved mixed forest in Shengnongjia, we analyzedthe dynamics of tree species composition and community structure for individual trees (DBH ≥ 4 cm. We found that total species number increased from 81 in 2001 to 84 in 2006, and then decreased to 83 in 2010. Dominant species remained constant throughout the study period, including Cyclobalanopsis multiervis, Fagus engleriana, Rhododendron hypoglaucum and Lithocarpus henryi. Stem number and basal area followed the same trend with an initial increase, followed by a decline. The mortality and recruitment of this survey plot changed substantially over the nine-year study period. Although an ice storm in 2008 had some impact on the community, the species richness and community structure did not alter significantly and the community appeared to be in a state of dynamic equilibrium with strong resilience to external disturbances.

  3. Characterization of bacterial community dynamics in a full-scale drinking water treatment plant.

    Science.gov (United States)

    Li, Cuiping; Ling, Fangqiong; Zhang, Minglu; Liu, Wen-Tso; Li, Yuxian; Liu, Wenjun

    2017-01-01

    Understanding the spatial and temporal dynamics of microbial communities in drinking water systems is vital to securing the microbial safety of drinking water. The objective of this study was to comprehensively characterize the dynamics of microbial biomass and bacterial communities at each step of a full-scale drinking water treatment plant in Beijing, China. Both bulk water and biofilm samples on granular activated carbon (GAC) were collected over 9months. The proportion of cultivable cells decreased during the treatment processes, and this proportion was higher in warm season than cool season, suggesting that treatment processes and water temperature probably had considerable impact on the R2A cultivability of total bacteria. 16s rRNA gene based 454 pyrosequencing analysis of the bacterial community revealed that Proteobacteria predominated in all samples. The GAC biofilm harbored a distinct population with a much higher relative abundance of Acidobacteria than water samples. Principle coordinate analysis and one-way analysis of similarity indicated that the dynamics of the microbial communities in bulk water and biofilm samples were better explained by the treatment processes rather than by sampling time, and distinctive changes of the microbial communities in water occurred after GAC filtration. Furthermore, 20 distinct OTUs contributing most to the dissimilarity among samples of different sampling locations and 6 persistent OTUs present in the entire treatment process flow were identified. Overall, our findings demonstrate the significant effects that treatment processes have on the microbial biomass and community fluctuation and provide implications for further targeted investigation on particular bacteria populations. Copyright © 2016. Published by Elsevier B.V.

  4.  Marine derived dinoflagellates in Antarctic saline lakes: Community composition and annual dynamics

    DEFF Research Database (Denmark)

    Rengefors, K.; Layborn-Parry, L.; Logares, R.

    2008-01-01

    The saline lakes of the Vestfold Hills in Antarctica offer a remarkable natural laboratory where the adaptation of planktonic protists to a range of evolving physiochemical conditions can be investigated. This study illustrates how an ancestral marine community has undergone radical simplification...... leaving a small number of well-adapted species. Our objective was to investigate the species composition and annual dynamics of dinoflagellate communities in three saline Antarctic lakes. We observed that dinoflagellates occur year-round despite extremely low PAR during the southern winter, which suggests...

  5. Challenges in microbial ecology: Building predictive understanding of community function and dynamics

    DEFF Research Database (Denmark)

    Widder, Stefanie; Allen, Rosalind J.; Pfeiffer, Thomas

    2016-01-01

    The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly...... complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development...

  6. Complexity and dynamics of topological and community structure in complex networks

    Science.gov (United States)

    Berec, Vesna

    2017-07-01

    Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

  7. Research of the diurnal soil respiration dynamic in two typical vegetation communities in Tianjin estuarine wetland

    Science.gov (United States)

    Zhang, Q.; Meng, W. Q.; Li, H. Y.

    2016-08-01

    Understanding the differences and diurnal variations of soil respiration in different vegetation communities in coastal wetland is to provide basic reliable scientific evidence for the carbon "source" function of wetland ecosystems in Tianjin.Measured soil respiration rate which changed during a day between two typical vegetation communities (Phragmites australis, Suaeda salsa) in coastal wetland in October, 2015. Soil temperature and moisture were measured at the same time. Each of the diurnal curves of soil temperature in two communities had a single peak value, and the diurnal variations of soil moisture showed a "two peak-one valley" trend. The diurnal dynamic of soil respiration under the two communities had obvious volatility which showed a single peak form with its maximum between 12:00-14:00 and minimum during 18:00. The diurnal average of soil respiration rate in Phragmites australis communities was 3.37 times of that in Suaeda salsa communities. Significant relationships were found by regression analysis among soil temperature, soil moisture and soil respiration rate in Suaeda salsa communities. There could be well described by exponential models which was y = -0.245e0.105t between soil respiration rate and soil temperature, by quadratic models which was y = -0.276×2 + 15.277× - 209.566 between soil respiration rate and soil moisture. But the results of this study showed that there were no significant correlations between soil respiration and soil temperature and soil moisture in Phragmites australis communities (P > 0.05). Therefore, under the specific wetland environment conditions in Tianjin, soil temperature and moisture were not main factors influencing the diurnal variations of soil respiration rate in Phragmites australis communities.

  8. Reproducibility of magnetic resonance perfusion imaging.

    Directory of Open Access Journals (Sweden)

    Xiaomeng Zhang

    Full Text Available Dynamic MR biomarkers (T2*-weighted or susceptibility-based and T1-weighted or relaxivity-enhanced have been applied to assess tumor perfusion and its response to therapies. A significant challenge in the development of reliable biomarkers is a rigorous assessment and optimization of reproducibility. The purpose of this study was to determine the measurement reproducibility of T1-weighted dynamic contrast-enhanced (DCE-MRI and T2*-weighted dynamic susceptibility contrast (DSC-MRI with two contrast agents (CA of different molecular weight (MW: gadopentetate (Gd-DTPA, 0.5 kDa and Gadomelitol (P792, 6.5 kDa. Each contrast agent was tested with eight mice that had subcutaneous MDA-MB-231 breast xenograft tumors. Each mouse was imaged with a combined DSC-DCE protocol three times within one week to achieve measures of reproducibility. DSC-MRI results were evaluated with a contrast to noise ratio (CNR efficiency threshold. There was a clear signal drop (>95% probability threshold in the DSC of normal tissue, while signal changes were minimal or non-existent (<95% probability threshold in tumors. Mean within-subject coefficient of variation (wCV of relative blood volume (rBV in normal tissue was 11.78% for Gd-DTPA and 6.64% for P792. The intra-class correlation coefficient (ICC of rBV in normal tissue was 0.940 for Gd-DTPA and 0.978 for P792. The inter-subject correlation coefficient was 0.092. Calculated K(trans from DCE-MRI showed comparable reproducibility (mean wCV, 5.13% for Gd-DTPA, 8.06% for P792. ICC of K(trans showed high intra-subject reproducibility (ICC = 0.999/0.995 and inter-subject heterogeneity (ICC = 0.774. Histograms of K(trans distributions for three measurements had high degrees of overlap (sum of difference of the normalized histograms <0.01. These results represent homogeneous intra-subject measurement and heterogeneous inter-subject character of biological population, suggesting that perfusion MRI could be an imaging biomarker to

  9. Long-term successional forest dynamics: species and community responses to climatic variability

    Energy Technology Data Exchange (ETDEWEB)

    Kardol, Paul [ORNL; Todd Jr, Donald E [ORNL; Hanson, Paul J [ORNL; Mulholland, Patrick J [ORNL

    2010-01-01

    Question: Are tree dynamics sensitive to climatic variability, and do tree species differ in their responses to climatic variability? Hence, is vulnerability of forest communities to climatic variability depending on stand composition? Location: Mixed young forest at Walker Branch Watershed near Oak Ridge, East-Tennessee, USA. Methods: Using a long-term data set (1967-2006), we analyzed temporal forest dynamics at the tree and species level, and we analyzed community dynamics for forest stands that different in their initial species composition (i.e., Chestnut Oak, Oak-Hickory, Pine, and Yellow poplar stands). Using summer drought and growing season temperature as defined climate drivers, we evaluated relationships between forest dynamics and climate across levels of organization. Results: Over the 4-decade studied period, forest communities underwent successional change and substantially increased their biomass. Variation in summer drought and growing season temperature contributed to temporal biomass dynamics for some tree species, but not for others. Stand-level responses to climatic variability were shown to be related to responses of specific component species; however, not for Pine stands. Pinus echinata, the dominant species in stands initially identified as Pine stands, decreased over time due to periodical outbreaks of the pine bark beetle (Dendroctonus frontalis). The outbreaks on Walker Branch could not be directly related to climatic conditions. Conclusions: Our results imply that vulnerability of developing forests to predicted climate conditions is stand-type dependent, and hence, is a function of species composition. Autogenic successional processes (or insect outbreaks) were found to prevail over climatic variability in determining long-term forest dynamics for stands dominated by sensitive species, emphasizing the importance of studying interactions between forest succession and climate change.

  10. Reproducible Research in Speech Sciences

    Directory of Open Access Journals (Sweden)

    Kandaacute;lmandaacute;n Abari

    2012-11-01

    Full Text Available Reproducible research is the minimum standard of scientific claims in cases when independent replication proves to be difficult. With the special combination of available software tools, we provide a reproducibility recipe for the experimental research conducted in some fields of speech sciences. We have based our model on the triad of the R environment, the EMU-format speech database, and the executable publication. We present the use of three typesetting systems (LaTeX, Markdown, Org, with the help of a mini research.

  11. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

    Science.gov (United States)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

    2016-01-01

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

  12. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

    2016-09-29

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

  13. Exploring the dynamics of ownership in community-oriented design projects

    DEFF Research Database (Denmark)

    Light, Ann; Hansen, Nicolai Brodersen; Halskov, Kim

    2013-01-01

    : what motivates ownership; how ownership transitions; structures to support ownership; and facilitating efficacy among participants. Specifically, we study the contribution of a Danish research team to the production of a media façade for a Swedish municipality and how British researchers engaged......This paper contributes an exploration of ownership as a dynamic process in community-oriented projects. We use case study accounts of two design projects to consider participation in contexts where social structure is relevant to design outcomes. In studying these dynamics, we consider four aspects...... community groups in making internet radio podcasts to share insight. We examine the complexity of the social process involved and trace patterns of change, before concluding with pragmatic and ethical reasons for technology design to pay attention to ownership issues....

  14. A shift from exploitation to interference competition with increasing density affects population and community dynamics

    OpenAIRE

    Holdridge, Erica M.; Cuellar‐Gempeler, Catalina; terHorst, Casey P.

    2016-01-01

    Abstract Intraspecific competition influences population and community dynamics and occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. We grew experimental microcosms of ...

  15. Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

    OpenAIRE

    Laureys, David; De Vuyst, Luc

    2014-01-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the...

  16. Dynamics of Bacterial Community Abundance and Structure in Horizontal Subsurface Flow Wetland Mesocosms Treating Municipal Wastewater

    Directory of Open Access Journals (Sweden)

    Kristjan Oopkaup

    2016-10-01

    Full Text Available Dynamics of bacterial community abundance and structure of a newly established horizontal subsurface flow (HSSF pilot-scale wetland were studied using high-throughput sequencing and quantitative polymerase chain reaction (PCR methods. Bacterial community abundance increased rapidly within one month and stabilised thereafter in three replicate HSSF constructed wetland (CW mesocosms. The most dominant phylum was Proteobacteria, followed by Bacteroidetes in wetland media biofilms and Firmicutes in influent wastewater. CW bacterial community diversity increased over time and was positively related to the wastewater treatment efficiency. Increase in the abundance of total bacteria in the community was accompanied with the abundance of denitrifying bacteria that promoted nitrate and nitrite removal from the wastewater. During the 150-day study period, similar patterns of bacterial community successions were observed in replicate HSSF CW mesocosms. The data indicate that successions in the bacterial community in HSSF CW are shaped by biotic interactions, with a significant contribution made by external abiotic factors such as influent chemical parameters. Network analysis of the bacterial community revealed that organic matter and nitrogen removal in HSSF CW could be, in large part, allocated to a small subset of tightly interconnected bacterial species. The diversity of bacterial community and abundance of denitrifiers were good predictors of the removal efficiency of ammonia, nitrate and total organic C in HSSF CW mesocosms, while the removal of the seven-day biochemical oxygen demand (BOD7 was best predicted by the abundance of a small set of bacterial phylotypes. The results suggest that nitrogen removal in HSSF CW consist of two main pathways. The first is heterotrophic nitrification, which is coupled with aerobic denitrification and mediated by mixotrophic nitrite-oxidizers. The second pathway is anaerobic denitrification, which leads to gaseous

  17. Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

    Directory of Open Access Journals (Sweden)

    Stephanie Turner

    2017-05-01

    Full Text Available Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR and community composition (pyrosequencing as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand. Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate, O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR and community patterns (T-RFLP were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to

  18. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  19. Evaluation of multichannel reproduced sound

    DEFF Research Database (Denmark)

    Choisel, Sylvain; Wickelmaier, Florian Maria

    2007-01-01

    A study was conducted with the goal of quantifying auditory attributes which underlie listener preference for multichannel reproduced sound. Short musical excerpts were presented in mono, stereo and several multichannel formats to a panel of forty selected listeners. Scaling of auditory attributes...

  20. [Reproducibility of subjective refraction measurement].

    Science.gov (United States)

    Grein, H-J; Schmidt, O; Ritsche, A

    2014-11-01

    Reproducibility of subjective refraction measurement is limited by various factors. The main factors affecting reproducibility include the characteristics of the measurement method and of the subject and the examiner. This article presents the results of a study on this topic, focusing on the reproducibility of subjective refraction measurement in healthy eyes. The results of previous studies are not all presented in the same way by the respective authors and cannot be fully standardized without consulting the original scientific data. To the extent that they are comparable, the results of our study largely correspond largely with those of previous investigations: During repeated subjective refraction measurement, 95% of the deviation from the mean value was approximately ±0.2 D to ±0.65 D for the spherical equivalent and cylindrical power. The reproducibility of subjective refraction measurement in healthy eyes is limited, even under ideal conditions. Correct assessment of refraction results is only feasible after identifying individual variability. Several measurements are required. Refraction cannot be measured without a tolerance range. The English full-text version of this article is available at SpringerLink (under supplemental).

  1. Reproducible research in computational science.

    Science.gov (United States)

    Peng, Roger D

    2011-12-02

    Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.

  2. Habitat heterogeneity determines climate impact on zooplankton community structure and dynamics.

    Directory of Open Access Journals (Sweden)

    Saskia A Otto

    Full Text Available Understanding and predicting species distribution in space and time and consequently community structure and dynamics is an important issue in ecology, and particularly in climate change research. A crucial factor determining the composition and dynamics of animal populations is habitat heterogeneity, i.e., the number of structural elements in a given locality. In the marine pelagic environment habitat heterogeneity is represented by the distribution of physical oceanographic parameters such as temperature, salinity and oxygen that are closely linked to atmospheric conditions. Little attention has been given, however, to the role of habitat heterogeneity in modulating the response of animal communities to external climate forcing. Here we investigate the long-term dynamics of Acartia spp., Temora longicornis, and Pseudocalanus acuspes, three dominant zooplankton species inhabiting different pelagic habitats in the Central Baltic Sea (CBS. We use the three copepods as indicator species for changes in the CBS zooplankton community and apply non-linear statistical modeling techniques to compare spatial population trends and to identify their drivers. We demonstrate that effects of climate variability and change depend strongly on species-specific habitat utilization, being more direct and pronounced at the upper water layer. We propose that the differential functional response to climate-related drivers in relation to strong habitat segregation is due to alterations of the species' environmental niches. We stress the importance of understanding how anticipated climate change will affect ecological niches and habitats in order to project spatio-temporal changes in species abundance and distribution.

  3. Colonisation processes and the role of coralline algae in rocky shore community dynamics

    Science.gov (United States)

    Asnaghi, Valentina; Thrush, Simon F.; Hewitt, Judi E.; Mangialajo, Luisa; Cattaneo-Vietti, Riccardo; Chiantore, Mariachiara

    2015-01-01

    Recovery from disturbance is an important attribute of community dynamics. Temperate rocky shores will experience increases in both the type and intensity of impacts under future expected global change. To gauge the community response to these potential changes in the disturbance regime it is important to assess space occupancy and the temporal dynamics of key species over the recovery process. We experimentally disturbed replicated 1 m2 plots in the lower intertidal at 5 sites along the Ligurian rocky coast (North-western Mediterranean) and assessed early succession processes over 18 months. To identify colonisation processes and role of key species in affecting species richness on recovery trajectories, we monitored species composition at the cm-scale along fixed transects within the plots. Our results highlighted the role of a limited number of taxa in driving the recovery of species richness across sites, despite site variation in community composition. Settlement of new propagules and overgrowth were the principal pathway of space occupancy. We detected an important role for coralline algae, particularly the articulated Corallina elongata, in promoting the colonisation of a diverse range of colonists. The present study highlights the important role played by calcifying coralline macroalgae as substrate providers for later colonists, favouring recovery of biodiversity after disturbance. This pivotal role may be compromised in a future scenario of elevated cumulative disturbance, where ocean acidification will likely depress the role of coralline algae in recovery, leading to a general loss in biodiversity and community complexity.

  4. Spatial variation in an avian host community: implications for disease dynamics.

    Science.gov (United States)

    States, Sarah L; Hochachka, Wesley M; Dhondt, André A

    2009-12-01

    Because many pathogens can infect multiple host species within a community, disease dynamics in a focal host species can be affected by the composition of the host community. We examine the extent to which spatial variation in species' abundances in an avian host community may contribute to geographically varying prevalence of a recently emerged wildlife pathogen. Mycoplasma gallisepticum is a pathogen novel to songbirds that has caused substantial mortality in house finches (Carpodacus mexicanus) in eastern North America. Though the house finch is the primary host species for M. gallisepticum, the American goldfinch (Spinus tristis) and northern cardinal (Cardinalis cardinalis) are alternate hosts, and laboratory experiments have demonstrated M. gallisepticum transmission between house finches and goldfinches. Still unknown is the real world impact on disease dynamics of variation in abundances of the three hosts. We analyzed data from winter-long bird and disease surveys in the northeastern United States. We found that higher disease prevalence in house finches was associated with higher numbers of northern cardinals and American goldfinches, although only the effect of cardinal abundance was statistically significant. Nevertheless, our results indicate that spatial variation in bird communities has the potential to cause geographic variation in disease prevalence in house finches.

  5. The structure and dynamics of a rhinolophid bat community of Latium (Central Italy (Chiroptera

    Directory of Open Access Journals (Sweden)

    Pierangelo Crucitti

    1998-12-01

    Full Text Available Abstract The present paper summarizes the results of 3 years of observation made at six month intervals for six months at a time (18 field surveys in a man-made cave in Northern Latium (Central Italy from April 1992 to April 1995. Its aim is to analyze the main structural and dynamic features of a bat community which hibernates at the shelter. Rhinolophus ferrumequinum and especially Rhinolophus euryale are the most abundant species. Population dynamics of both species as well as that of Rhinoluphus hipposideros show higher levels of abundance between December and February of each semester. In mid-winter, large and sometimes mixed aggregations of Rhinolophus ferrumequinum and Rhinolophus euryale in deep hypothermia occur. A small number of Rhinolophus hipposideros, mainly adult males, was observed. The paper compares the structure of this community to the structure of another community of the same district which has been previously analyzed, in which Vespertilionidae, especially Miniopterus schreibersi, are much more abundant. Despite the difference in species composition, body size was found to be a significant and common feature (as highlighted by forearm length, of the dominant species in both communities, Rhinolophus euryale and Miniopterus schreibersi respectively.

  6. A shift from exploitation to interference competition with increasing density affects population and community dynamics.

    Science.gov (United States)

    Holdridge, Erica M; Cuellar-Gempeler, Catalina; terHorst, Casey P

    2016-08-01

    Intraspecific competition influences population and community dynamics and occurs via two mechanisms. Exploitative competition is an indirect effect that occurs through use of a shared resource and depends on resource availability. Interference competition occurs by obstructing access to a resource and may not depend on resource availability. Our study tested whether the strength of interference competition changes with protozoa population density. We grew experimental microcosms of protozoa and bacteria under different combinations of protozoan density and basal resource availability. We then solved a dynamic predator-prey model for parameters of the functional response using population growth rates measured in our experiment. As population density increased, competition shifted from exploitation to interference, and competition was less dependent on resource levels. Surprisingly, the effect of resources was weakest when competition was the most intense. We found that at low population densities, competition was largely exploitative and resource availability had a large effect on population growth rates, but the effect of resources was much weaker at high densities. This shift in competitive mechanism could have implications for interspecific competition, trophic interactions, community diversity, and natural selection. We also tested whether this shift in the mechanism of competition with protozoa density affected the structure of the bacterial prey community. We found that both resources and protozoa density affected the structure of the bacterial prey community, suggesting that competitive mechanism may also affect trophic interactions.

  7. A trait based dynamic energy budget approach to explore emergent microalgal community structure

    Science.gov (United States)

    Cheng, Y.; Bouskill, N.; Karaoz, U.; Geng, H.; Lane, T.; Pett-Ridge, J.; Mayali, X.; Brodie, E.

    2015-12-01

    Microalgae play important roles in the global carbon budget. Phytoplankton, including microalgae, are responsible for around 50% of global primary production, and also hold promise as a viable renewable biofuel source. Research has been underway for decades to realize the full potential of algal biofuels at the commercial scale, however, uni-algal ponds are typically threatened by collapse due to microalgal grazing and parasite invasions. Recently, it has been proposed that functionally diverse microalgal-bacterial communities can achieve high biomass and/or lipid yields, and are more stable (less susceptible to invasion) than a monoculture. Similar positive diversity-productivity relationships have been observed in a wide range of ecosystem studies, but the purposeful maintenance of a diverse microbiome is less common in managed systems. In our work, a trait based dynamic energy budget model was developed to explore emergent microalgal community structure under various environmental (e.g. light, temperature, nutrient availability) conditions. The complex algal community can be reduced into functional groups (guilds). Each guild (algae or bacteria) is characterized by distinct physiological traits (e.g. nutrient requirement, growth rate, substrate affinity, lipid production) constrained by biochemical trade-offs. These trait values are derived from literature and information encoded in genomic data. Metabolism of the algae and the bacterial species (symbiotic or non-symbiotic) are described within a dynamic energy budget framework. The model offers a mechanistic framework to predict the optimal microalgal community assemblage towards high productivity and resistance to invasion under prevailing environmental conditions.

  8. The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors.

    Science.gov (United States)

    Agrawal, Shelesh; Karst, Søren M; Gilbert, Eva M; Horn, Harald; Nielsen, Per H; Lackner, Susanne

    2017-03-10

    Implementation of partial nitritation anammox (PNA) in the mainstream (municipal wastewater treatment) is still under investigation. Microbial community structure and reactor type can influence the performance of PNA reactor; yet, little is known about the role of the community composition of the inoculum and the reactor configuration under mainstream conditions. Therefore, this study investigated the community structure of inocula of different origin and their consecutive community dynamics in four different lab-scale PNA reactors with 16S rRNA gene amplicon sequencing. These reactors were operated for almost 1 year and subjected to realistic seasonal temperature fluctuations as in moderate climate regions, that is, from 20°C in summer to 10°C in winter. The sequencing analysis revealed that the bacterial community in the reactors comprised: (1) a nitrifying community (consisting of anaerobic ammonium-oxidizing bacteria (AnAOB), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB)); (2) different heterotrophic denitrifying bacteria and other putative heterotrophic bacteria (HB). The nitrifying community was the same in all four reactors at the genus level, although the biomasses were of different origin. Community dynamics revealed a stable community in the moving bed biofilm reactors (MBBR) in contrast to the sequencing batch reactors (SBR) at the genus level. Moreover, the reactor design seemed to influence the community dynamics, and reactor operation significantly influenced the overall community composition. The MBBR seems to be the reactor type of choice for mainstream wastewater treatment.

  9. The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

    Directory of Open Access Journals (Sweden)

    Federico M Ibarbalz

    Full Text Available The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1 the changes occurring within the communities along fixed time intervals, 2 the slow turnover of activated sludge communities and 3 the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

  10. Data Identifiers and Citations Enable Reproducible Science

    Science.gov (United States)

    Tilmes, C.

    2011-12-01

    Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or reproduce their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for reproducibility. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

  11. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells – Influence of Acetate and Propionate Concentration

    KAUST Repository

    Rao, Hari Ananda

    2017-07-20

    Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor\\'s performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its

  12. Coding of Markov dynamics for multiscale community detection in complex networks

    CERN Document Server

    Schaub, Michael T; Barahona, Mauricio

    2011-01-01

    The detection of community structure in complex networks is intimately related to the problem of finding a concise description of the network in terms of its modules. This notion has been recently exploited by the Map equation formalism (M. Rosvall and C. T. Bergstrom, PNAS, vol. 105, no. 4, pp. 1118-1123, 2008) through an information-theoretic characterization of the process of coding the transitions of a random walker inside and between communities at stationarity. However, a thorough consideration of the relationship between a time-evolving Markov dynamics and the coding mechanism is still lacking. We show that the original one-step coding scheme used by the Map equation method neglects the internal structure of the communities and introduces an upper scale, the 'field-of-view' limit, for the communities that it can detect. Although the Map equation method is known for its good performance on clique-like graphs, the field-of-view limit can result in undesirable overpartitioning when communities are far fro...

  13. Persistence, Seasonal Dynamics and Pathogenic Potential of Vibrio Communities from Pacific Oyster Hemolymph

    Science.gov (United States)

    Wendling, Carolin C.; Batista, Frederico M.; Wegner, K. Mathias

    2014-01-01

    Bacteria of the genus Vibrio occur at a continuum from free-living to symbiotic life forms, including opportunists and pathogens, that can contribute to severe diseases, for instance summer mortality events of Pacific oysters Crassostrea gigas. While most studies focused on Vibrio isolated from moribund oysters during mortality outbreaks, investigations of the Vibrio community in healthy oysters are rare. Therefore, we characterized the persistence, diversity, seasonal dynamics, and pathogenicity of the Vibrio community isolated from healthy Pacific oysters. In a reciprocal transplant experiment we repeatedly sampled hemolymph from adult Pacific oysters to differentiate population from site-specific effects during six months of in situ incubation in the field. We characterized virulence phenotypes and genomic diversity based on multilocus sequence typing in a total of 70 Vibrio strains. Based on controlled infection experiments we could show that strains with the ability to colonize healthy adult oysters can also have the potential to induce high mortality rates on larvae. Diversity and abundance of Vibrio varied significantly over time with highest values during and after spawning season. Vibrio communities from transplanted and stationary oysters converged over time, indicating that communities were not population specific, but rather assemble from the surrounding environment forming communities, some of which can persist over longer periods. PMID:24728233

  14. Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs.

    Science.gov (United States)

    Fischer, Martin A; Güllert, Simon; Neulinger, Sven C; Streit, Wolfgang R; Schmitz, Ruth A

    2016-01-01

    The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis

  15. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network

    KAUST Repository

    El Chakhtoura, Joline

    2015-05-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic.

  16. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network.

    Science.gov (United States)

    El-Chakhtoura, Joline; Prest, Emmanuelle; Saikaly, Pascal; van Loosdrecht, Mark; Hammes, Frederik; Vrouwenvelder, Hans

    2015-05-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Reproducibility of NIF hohlraum measurements

    Science.gov (United States)

    Moody, J. D.; Ralph, J. E.; Turnbull, D. P.; Casey, D. T.; Albert, F.; Bachmann, B. L.; Doeppner, T.; Divol, L.; Grim, G. P.; Hoover, M.; Landen, O. L.; MacGowan, B. J.; Michel, P. A.; Moore, A. S.; Pino, J. E.; Schneider, M. B.; Tipton, R. E.; Smalyuk, V. A.; Strozzi, D. J.; Widmann, K.; Hohenberger, M.

    2015-11-01

    The strategy of experimentally ``tuning'' the implosion in a NIF hohlraum ignition target towards increasing hot-spot pressure, areal density of compressed fuel, and neutron yield relies on a level of experimental reproducibility. We examine the reproducibility of experimental measurements for a collection of 15 identical NIF hohlraum experiments. The measurements include incident laser power, backscattered optical power, x-ray measurements, hot-electron fraction and energy, and target characteristics. We use exact statistics to set 1-sigma confidence levels on the variations in each of the measurements. Of particular interest is the backscatter and laser-induced hot-spot locations on the hohlraum wall. Hohlraum implosion designs typically include variability specifications [S. W. Haan et al., Phys. Plasmas 18, 051001 (2011)]. We describe our findings and compare with the specifications. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

  18. Habitat dynamics, marine reserve status, and the decline and recovery of coral reef fish communities

    Science.gov (United States)

    Williamson, David H; Ceccarelli, Daniela M; Evans, Richard D; Jones, Geoffrey P; Russ, Garry R

    2014-01-01

    Severe climatic disturbance events often have major impacts on coral reef communities, generating cycles of decline and recovery, and in some extreme cases, community-level phase shifts from coral-to algal-dominated states. Benthic habitat changes directly affect reef fish communities, with low coral cover usually associated with low fish diversity and abundance. No-take marine reserves (NTRs) are widely advocated for conserving biodiversity and enhancing the sustainability of exploited fish populations. Numerous studies have documented positive ecological and socio-economic benefits of NTRs; however, the ability of NTRs to ameliorate the effects of acute disturbances on coral reefs has seldom been investigated. Here, we test these factors by tracking the dynamics of benthic and fish communities, including the important fishery species, coral trout (Plectropomus spp.), over 8 years in both NTRs and fished areas in the Keppel Island group, Great Barrier Reef, Australia. Two major disturbances impacted the reefs during the monitoring period, a coral bleaching event in 2006 and a freshwater flood plume in 2011. Both disturbances generated significant declines in coral cover and habitat complexity, with subsequent declines in fish abundance and diversity, and pronounced shifts in fish assemblage structure. Coral trout density also declined in response to the loss of live coral, however, the approximately 2:1 density ratio between NTRs and fished zones was maintained over time. The only post-disturbance refuges for coral trout spawning stocks were within the NTRs that escaped the worst effects of the disturbances. Although NTRs had little discernible effect on the temporal dynamics of benthic or fish communities, it was evident that the post-disturbance refuges for coral trout spawning stocks within some NTRs may be critically important to regional-scale population persistence and recovery. PMID:24634720

  19. Habitat dynamics, marine reserve status, and the decline and recovery of coral reef fish communities.

    Science.gov (United States)

    Williamson, David H; Ceccarelli, Daniela M; Evans, Richard D; Jones, Geoffrey P; Russ, Garry R

    2014-02-01

    Severe climatic disturbance events often have major impacts on coral reef communities, generating cycles of decline and recovery, and in some extreme cases, community-level phase shifts from coral-to algal-dominated states. Benthic habitat changes directly affect reef fish communities, with low coral cover usually associated with low fish diversity and abundance. No-take marine reserves (NTRs) are widely advocated for conserving biodiversity and enhancing the sustainability of exploited fish populations. Numerous studies have documented positive ecological and socio-economic benefits of NTRs; however, the ability of NTRs to ameliorate the effects of acute disturbances on coral reefs has seldom been investigated. Here, we test these factors by tracking the dynamics of benthic and fish communities, including the important fishery species, coral trout (Plectropomus spp.), over 8 years in both NTRs and fished areas in the Keppel Island group, Great Barrier Reef, Australia. Two major disturbances impacted the reefs during the monitoring period, a coral bleaching event in 2006 and a freshwater flood plume in 2011. Both disturbances generated significant declines in coral cover and habitat complexity, with subsequent declines in fish abundance and diversity, and pronounced shifts in fish assemblage structure. Coral trout density also declined in response to the loss of live coral, however, the approximately 2:1 density ratio between NTRs and fished zones was maintained over time. The only post-disturbance refuges for coral trout spawning stocks were within the NTRs that escaped the worst effects of the disturbances. Although NTRs had little discernible effect on the temporal dynamics of benthic or fish communities, it was evident that the post-disturbance refuges for coral trout spawning stocks within some NTRs may be critically important to regional-scale population persistence and recovery.

  20. Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Xueju; McKinley, James P.; Resch, Charles T.; Kaluzny, Rachael M.; Lauber, C.; Fredrickson, Jim K.; Knight, Robbie C.; Konopka, Allan

    2012-03-29

    Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater Bacteria and Archaea over 10 months within 3 well clusters separated by ~30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained 3 wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all 9 wells over the 10 month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated to river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (e.g.methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment, but also by top-down biological control.

  1. Socio-hydrology: understanding the dynamics of agricultural communities under water stress

    Science.gov (United States)

    Kuil, Linda; Blöschl, Günter

    2014-05-01

    At present, over 4 billion people globally face a form of water scarcity. Over the coming decades this number is expected to rise due to a combination of factors, including population growth, changing (dietary) habits and changes in climate. As agriculture is a major water user, water scarcity is of particular significance in this respect. The concept being relative and dynamic, a community can experience water scarcity at any level of demand and supply. Moreover, different communities may have followed different paths to arrive at their present situation as a consequence of the continuous, specific interactions between the hydrological and the social system present. Models studying the socio-hydrological system have traditionally started at the water cycle dynamics thereby considering human interactions as external forces to the system. Also, these models have run under the assumption of stationarity. Aim of this study is to identify the major feedbacks between the hydrological and the social system and identify the main drivers that result in these different pathways and outcomes. This is done through the development of a stylized model consisting of 3 (4) ordinary differential equations intended at capturing only those interactions between the social and the hydrological system that give rise to the long-term dynamics of a hypothetical agricultural community. The model is, through its simplicity and its emphasis on feedbacks, complementary to existing social theories and more complex, spatial explicit and often data intensive model frameworks. Having insight in the dynamics and the qualitative behavior of the state variables in this hypothetical setting is the first step in characterizing the similarities and differences between real world human-water systems and in so doing follows the path of comparative socio-hydrology.

  2. Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit.

    Science.gov (United States)

    Schaub, Michael T; Delvenne, Jean-Charles; Yaliraki, Sophia N; Barahona, Mauricio

    2012-01-01

    In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the 'right' split into communities. Although a thorough comparison of algorithms is still lacking, there has been an effort to design benchmarks, i.e., random graph models with known community structure against which algorithms can be evaluated. However, popular community detection methods and benchmarks normally assume an implicit notion of community based on clique-like subgraphs, a form of community structure that is not always characteristic of real networks. Specifically, networks that emerge from geometric constraints can have natural non clique-like substructures with large effective diameters, which can be interpreted as long-range communities. In this work, we show that long-range communities escape detection by popular methods, which are blinded by a restricted 'field-of-view' limit, an intrinsic upper scale on the communities they can detect. The field-of-view limit means that long-range communities tend to be overpartitioned. We show how by adopting a dynamical perspective towards community detection [1], [2], in which the evolution of a Markov process on the graph is used as a zooming lens over the structure of the network at all scales, one can detect both clique- or non clique-like communities without imposing an upper scale to the detection. Consequently, the performance of algorithms on inherently low-diameter, clique-like benchmarks may not always be indicative of equally good results in real networks with local, sparser connectivity. We illustrate our ideas with constructive examples and through the analysis of real-world networks from imaging, protein structures and the power grid, where a

  3. Monitoring the dynamics of an invasive emergent macrophyte community using operational remote sensing data

    Science.gov (United States)

    Albright, T.P.; Ode, D.J.

    2011-01-01

    Potamogeton crispus L. (curly pondweed) is a cosmopolitan aquatic macrophyte considered invasive in North America and elsewhere. Its range is expanding and, on individual water bodies, its coverage can be dynamic both within and among years. In this study, we evaluate the use of free and low-cost satellite remote sensing data to monitor a problematic emergent macrophyte community dominated by P. crispus. Between 2000 and 2006, we acquired eight satellite images of 24,000-ha Lake Sharpe, South Dakota (USA). During one of the dates for which satellite imagery was acquired, we sampled the lake for P. crispus and other emergent macrophytes using GPS and photography for documentation. We used cluster analysis to assist in classification of the satellite imagery and independently validated results using the field data. Resulting estimates of emergent macrophyte coverage ranged from less than 20 ha in 2002 to 245 ha in 2004. Accuracy assessment indicated 82% of image pixels were correctly classified, with errors being primarily due to failure to identify emergent macrophytes. These results emphasize the dynamic nature of P. crispus-dominated macrophyte communities and show how they can be effectively monitored over large areas using low-cost remote sensing imagery. While results may vary in other systems depending on water quality and local flora, such an approach could be applied elsewhere and for a variety of macrophyte communities. ?? Springer Science+Business Media B.V. 2010.

  4. Imaging the Population Dynamics of Bacterial Communities in the Zebrafish Gut

    Science.gov (United States)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Zac Stephens, W.; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

    2013-03-01

    The vertebrate gut is home to a diverse microbial ecosystem whose composition has a strong influence on the development and health of the host organism. While researchers are increasingly able to identify the constituent members of the microbiome, very little is known about the spatial and temporal dynamics of commensal microbial communities, including the mechanisms by which communities nucleate, grow, and interact. We address these issues using a model organism: the larval zebrafish (Danio rerio) prepared microbe-free and inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging with light sheet fluorescence microscopy enables visualization of individual bacterial cells as well as growing colonies over the entire volume of the gut over periods up to 24 hours. We analyze the structure and dynamics of imaged bacterial communities, uncovering correlations between population size, growth rates, and the timing of inoculations that suggest the existence of active changes in the host environment induced by early bacterial exposure. Our data provide the first visualizations of gut microbiota development over an extended period of time in a vertebrate.

  5. Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Yagi, J.M.; Neuhauser, E.F.; Ripp, J.A.; Mauro, D.M.; Madsen, E.L. [Cornell University, Ithaca, NY (United States). Dept. of Microbiology

    2010-01-15

    The propensity for groundwater ecosystems to recover from contamination by organic chemicals (in this case, coal-tar waste) is of vital concern for scientists and engineers who manage polluted sites. The microbially mediated cleanup processes are also of interest to ecologists because they are an important mechanism for the resilience of ecosystems. In this study we establish the long-term dynamic nature of a coal-tar waste-contaminated site and its microbial community. We present 16 years of chemical monitoring data, tracking responses of a groundwater ecosystem to organic contamination (naphthalene, xylenes, toluene, 2-methyl naphthalene and acenaphthylene) associated with coal-tar waste. In addition, we analyzed small-subunit (SSU) ribosomal RNA (rRNA) genes from two contaminated wells at multiple time points over a 2-year period. Principle component analysis of community rRNA fingerprints (terminal-restriction fragment length polymorphism (T-RFLP)) showed that the composition of native microbial communities varied temporally, yet remained distinctive from well to well. After screening and analysis of 1178 cloned SSU rRNA genes from Bacteria, Archaea and Eukarya, we discovered that the site supports a robust variety of eukaryotes (for example, alveolates (especially anaerobic and predatory ciliates), stramenopiles, fungi, even the small metazoan flatworm, Suomina) that are absent from an uncontaminated control well. This study links the dynamic microbial composition of a contaminated site with the long-term attenuation of its subsurface contaminants.

  6. Climate scaling behaviour in the dynamics of the marine interstitial ciliate community

    Science.gov (United States)

    Varotsos, Costas A.; Mazei, Yuri A.; Burkovsky, Igor; Efstathiou, Maria N.; Tzanis, Chris G.

    2016-08-01

    The present paper uses characteristics of the marine interstitial ciliate community in the White Sea intertidal sandflat during the period of 1991-2011, in order to study its long-term dynamics, investigating in particular whether it exhibits scaling behaviour into its fluctuations, which is a characteristic feature of the climate system. To this aim, a recently proposed version of the detrended fluctuation analysis is herewith employed which has been successfully applied to a wide range of simulated and physiologic time series in recent years. In case that the fluctuations of the ciliate community present self-similarity processes, an ideal field test for the currently proposed biological models will be established, allowing to evaluate their reliability. Indeed, we show for the first time that different ciliate species exhibit long-range power-law persistent correlations. This means that ciliate fluctuations in different intervals are positively correlated, obeying a power-law behaviour. Although the origin of power-law temporal evolution of ciliates should be further investigated, this finding is probably associated with the self-organized criticality of ciliates. It should be noted that the long-range correlations obtained do not imply the presence of specific cycles but rather the existence of dynamic links between long-term and short-term temporal evolution. The scaling behaviour found in marine interstitial ciliate community should be taken into account in the investigation of their response to the present or future climate change.

  7. Quantifying effects of abiotic and biotic drivers on community dynamics with multivariate autoregressive (MAR) models.

    Science.gov (United States)

    Hampton, Stephanie E; Holmes, Elizabeth E; Scheef, Lindsay P; Scheuerell, Mark D; Katz, Stephen L; Pendleton, Daniel E; Ward, Eric J

    2013-12-01

    Long-term ecological data sets present opportunities for identifying drivers of community dynamics and quantifying their effects through time series analysis. Multivariate autoregressive (MAR) models are well known in many other disciplines, such as econometrics, but widespread adoption of MAR methods in ecology and natural resource management has been much slower despite some widely cited ecological examples. Here we review previous ecological applications of MAR models and highlight their ability to identify abiotic and biotic drivers of population dynamics, as well as community-level stability metrics, from long-term empirical observations. Thus far, MAR models have been used mainly with data from freshwater plankton communities; we examine the obstacles that may be hindering adoption in other systems and suggest practical modifications that will improve MAR models for broader application. Many of these modifications are already well known in other fields in which MAR models are common, although they are frequently described under different names. In an effort to make MAR models more accessible to ecologists, we include a worked example using recently developed R packages (MAR1 and MARSS), freely available and open-access software.

  8. Dynamic systems and the role of evaluation: The case of the Green Communities project.

    Science.gov (United States)

    Anzoise, Valentina; Sardo, Stefania

    2016-02-01

    The crucial role evaluation can play in the co-development of project design and its implementation will be addressed through the analysis of a case study, the Green Communities (GC) project, funded by the Italian Ministry of Environment within the EU Interregional Operational Program (2007-2013) "Renewable Energy and Energy Efficiency". The project's broader goals included an attempt to trigger a change in Italian local development strategies, especially for mountain and inland areas, which would be tailored to the real needs of communities, and based on a sustainable exploitation and management of the territorial assets. The goal was not achieved, and this paper addresses the issues of how GC could have been more effective in fostering a vision of change, and which design adaptations and evaluation procedures would have allowed the project to better cope with the unexpected consequences and resistances it encountered. The conclusions drawn are that projects should be conceived, designed and carried out as dynamic systems, inclusive of a dynamic and engaged evaluation enabling the generation of feedbacks loops, iteratively interpreting the narratives and dynamics unfolding within the project, and actively monitoring the potential of various relationships among project participants for generating positive social change.

  9. The System Dynamics of Forest Cover in the Developing World: Researcher Versus Community Perspectives

    Directory of Open Access Journals (Sweden)

    Laura Schmitt Olabisi

    2010-06-01

    Full Text Available Efforts to increase forest cover in the developing world will only succeed if the root causes of deforestation are addressed. Researchers designing reforestation initiatives tend to emphasize macro-level drivers of deforestation, about which they have extensive data and knowledge. On the other hand, local people have contextually based knowledge of forest cover dynamics in their region—about which external researchers may be largely ignorant. This type of perception gap between researchers and community members has led to many failed or insufficiently implemented projects. An emerging tool—group model-building with system dynamics—shows promise in its ability to integrate different perspectives on a complex problem such as forest cover loss. In this study, I use system dynamics modeling methodology to compare causal loop diagrams of forest cover dynamics on Negros Island, Philippines generated by researchers working for the World Wildlife Fund with causal loop diagrams generated by community members in upland Negros. The diagrams were significantly different, with very few variables in common, but both illuminate critical aspects of the deforestation problem on the island. I conclude that reforestation initiatives in the Philippines would benefit from incorporating all relevant information into a single, coherent model.

  10. Microbial community dynamics during fermentation of doenjang-meju, traditional Korean fermented soybean.

    Science.gov (United States)

    Jung, Ji Young; Lee, Se Hee; Jeon, Che Ok

    2014-08-18

    Bacterial and fungal community dynamics, along with viable plate counts and water content, were investigated in the exterior and interior regions of doenjang-meju, traditional Korean fermented soybean, during its fermentation process. Measurement of viable cells showed that the meju molding equipment might be an important source of bacterial cells (mostly Bacillus) during doenjang-meju fermentation, whereas fungi might be mostly derived from the fermentation environment including incubation shelves, air, and rice straws. Community analysis using rRNA-targeted pyrosequencing revealed that Bacillus among bacteria and Mucor among fungi were predominant in both the exterior and interior regions of doenjang-meju during the early fermentation period. Bacteria such as Ignatzschineria, Myroides, Enterococcus, Corynebacterium, and Clostridium and fungi such as Geotrichum, Scopulariopsis, Monascus, Fusarium, and eventually Aspergillus were mainly detected as the fermentation progressed. Bacillus, an aerobic bacterial group, was predominant in the exterior regions during the entire fermentation period, while anaerobic, facultative anaerobic, and microaerobic bacteria including Enterococcus, Lactobacillus, Clostridium, Myroides, and Ignatzschineria were much more abundant in the interior regions. Principal component analysis (PCA) also indicated that the bacterial communities in the exterior and interior regions were clearly differentiated, suggesting that aeration might be an important factor in determining the bacterial communities during doenjang-meju fermentation. However, PCA showed that fungal communities were not separated in the exterior and interior regions and Pearson's correlation coefficients showed that the major fungal taxa had significantly positive (Mucor and Geotrichum) or negative (Aspergillus) correlations with the water content during doenjang-meju fermentation, indicating that water content might be a significant factor in determining the fungal

  11. Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea.

    Directory of Open Access Journals (Sweden)

    Sung-Suk Suh

    Full Text Available High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs. The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.

  12. The Cumacea community of the southeastern Brazilian Continental Shelf: structure and dynamics

    Directory of Open Access Journals (Sweden)

    Maria Fernanda L. Dos Santos

    1999-03-01

    Full Text Available Specific composition, abundance, diversity and dynamics of the Cumacea community from the southeastern Brazilian continental shelf were studied. The area is characterized by the intrusion of a cold and highly saline water mass in summer, the South Atlantic Central Water (SACW, from the slope towards the coast, changing the hydrographic structure of the shelf and the species distribution. During the other seasons the inner shelf, area shallower than 50 m, is filled with warm and low saline water, the Coastal Water (CW. The presence of the SACW seems to favor the abundance and diversity of Cumacea due to its higher primary production and stability. Three groups of species were related to the water masses. Depth and fine sand fraction were shown to be the main factors structuring the Cumacea community. The role of the SACW in maintaining the Cumacea populations in the area through the passive transport of pre-ovigerous and ovigerous females is discussed.

  13. Biological soil crusts across disturbance-recovery scenarios: effect of grazing regime on community dynamics

    Science.gov (United States)

    Concostrina-Zubiri, L.; Huber-Sannwald, E.; Martínez, I.; Flores Flores, J. L.; Reyes-Agüero, J. A.; Escudero, A.; Belnap, Jayne

    2014-01-01

    Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

  14. Estimating partial observability and nonlinear climate effects on stochastic community dynamics of migratory waterfowl.

    Science.gov (United States)

    Almaraz, Pablo; Green, Andy J; Aguilera, Eduardo; Rendón, Miguel A; Bustamante, Javier

    2012-09-01

    1. Understanding the impact of environmental variability on migrating species requires the estimation of sequential abiotic effects in different geographic areas across the life cycle. For instance, waterfowl (ducks, geese and swans) usually breed widely dispersed throughout their breeding range and gather in large numbers in their wintering headquarters, but there is a lack of knowledge on the effects of the sequential environmental conditions experienced by migrating birds on the long-term community dynamics at their wintering sites. 2. Here, we analyse multidecadal time-series data of 10 waterfowl species wintering in the Guadalquivir Marshes (SW Spain), the single most important wintering site for waterfowl breeding in Europe. We use a multivariate state-space approach to estimate the effects of biotic interactions, local environmental forcing during winter and large-scale climate during breeding and migration on wintering multispecies abundance fluctuations, while accounting for partial observability (observation error and missing data) in both population and environmental data. 3. The joint effect of local weather and large-scale climate explained 31·6% of variance at the community level, while the variability explained by interspecific interactions was negligible (observations through data augmentation increased the estimated magnitude of environmental forcing by an average 30·1% and reduced the impact of stochasticity by 39·3% when accounting for observation error. Interestingly however, the impact of environmental forcing on community dynamics was underestimated by an average 15·3% and environmental stochasticity overestimated by 14·1% when ignoring both observation error and data augmentation. 5. These results provide a salient example of sequential multiscale environmental forcing in a major migratory bird community, which suggests a demographic link between the breeding and wintering grounds operating through nonlinear environmental effects

  15. Effects of ocean acidification on population dynamics and community structure of crustose coralline algae.

    Science.gov (United States)

    Ordoñez, Alexandra; Doropoulos, Christopher; Diaz-Pulido, Guillermo

    2014-06-01

    Calcification and growth of crustose coralline algae (CCA) are affected by elevated seawater pCO2 and associated changes in carbonate chemistry. However, the effects of ocean acidification (OA) on population and community-level responses of CCA have barely been investigated. We explored changes in community structure and population dynamics (size structure and reproduction) of CCA in response to OA. Recruited from an experimental flow-through system, CCA settled onto the walls of plastic aquaria and developed under exposure to one of three pCO2 treatments (control [present day, 389±6 ppm CO2], medium [753±11 ppm], and high [1267±19 ppm]). Elevated pCO2 reduced total CCA abundance and affected community structure, in particular the density of the dominant species Pneophyllum sp. and Porolithon onkodes. Meanwhile, the relative abundance of P. onkodes declined from 24% under control CO2 to 8.3% in high CO2 (65% change), while the relative abundance of Pneophyllum sp. remained constant. Population size structure of P. onkodes differed significantly across treatments, with fewer larger individuals under high CO2. In contrast, the population size structure and number of reproductive structures (conceptacles) per crust of Pneophyllum sp. was similar across treatments. The difference in the magnitude of the response of species abundance and population size structure between species may have the potential to induce species composition changes in the future. These results demonstrate that the impacts of OA on key coral reef builders go beyond declines in calcification and growth, and suggest important changes to aspects of population dynamics and community ecology.

  16. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

    Science.gov (United States)

    Chun, Chan Lan; Peller, Julie R.; Shively, Dawn; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J.

    2017-01-01

    Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

  17. Reproducibility of a reaming test

    DEFF Research Database (Denmark)

    Pilny, Lukas; Müller, Pavel; De Chiffre, Leonardo

    2014-01-01

    The reproducibility of a reaming test was analysed to document its applicability as a performance test for cutting fluids. Reaming tests were carried out on a drilling machine using HSS reamers. Workpiece material was an austenitic stainless steel, machined using 4.75 m•min−1 cutting speed and 0...... a built–up edge occurrence hindering a robust evaluation of cutting fluid performance, if the data evaluation is based on surface finish only. Measurements of hole geometry provide documentation to recognise systematic error distorting the performance test....

  18. Reproducibility of a reaming test

    DEFF Research Database (Denmark)

    Pilny, Lukas; Müller, Pavel; De Chiffre, Leonardo

    2012-01-01

    The reproducibility of a reaming test was analysed to document its applicability as a performance test for cutting fluids. Reaming tests were carried out on a drilling machine using HSS reamers. Workpiece material was an austenitic stainless steel, machined using 4.75 m∙min-1 cutting speed and 0...... a built-up edge occurrence hindering a robust evaluation of cutting fluid performance, if the data evaluation is based on surface finish only. Measurements of hole geometry provide documentation to recognize systematic error distorting the performance test....

  19. Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

    Science.gov (United States)

    Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

    2016-01-01

    Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

  20. Microbial community structures and dynamics in the O3/BAC drinking water treatment process.

    Science.gov (United States)

    Tian, Jian; Lu, Jun; Zhang, Yu; Li, Jian-Cheng; Sun, Li-Chen; Hu, Zhang-Li

    2014-06-16

    Effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. In this investigation, the application of PCR-DGGE technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Actinobacteria Firmicutes and Cyanobacteria. α-Proteobacteria and β-Proteobacteria were the dominant bacteria during the whole process. Bacteroidetes and Firmicutes were the dominant bacteria before and after treatment, respectively. Firmicutes showed season-dependent changes in population dynamics. Importantly, γ-Proteobacteria, which is a class of medically important bacteria, was well controlled by the O3/biological activated carbon (BAC) treatment, resulting in improved effluent water bio-safety.

  1. Microbial Community Structures and Dynamics in the O3/BAC Drinking Water Treatment Process

    Directory of Open Access Journals (Sweden)

    Jian Tian

    2014-06-01

    Full Text Available Effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. In this investigation, the application of PCR-DGGE technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, Actinobacteria Firmicutes and Cyanobacteria. α-Proteobacteria and β-Proteobacteria were the dominant bacteria during the whole process. Bacteroidetes and Firmicutes were the dominant bacteria before and after treatment, respectively. Firmicutes showed season-dependent changes in population dynamics. Importantly, γ-Proteobacteria, which is a class of medically important bacteria, was well controlled by the O3/biological activated carbon (BAC treatment, resulting in improved effluent water bio-safety.

  2. Exploring the Coming Repositories of Reproducible Experiments: Challenges and Opportunities

    DEFF Research Database (Denmark)

    Freire, Juliana; Bonnet, Philippe; Shasha, Dennis

    2011-01-01

    Computational reproducibility efforts in many communities will soon give rise to validated software and data repositories of high quality. A scientist in a field may want to query the components of such repositories to build new software workflows, perhaps after adding the scientist’s own algorithm...

  3. Novel Community/Dynamic Community Optimization Algorithm%一种新的社区/动态社区优化方法

    Institute of Scientific and Technical Information of China (English)

    李亚芳; 贾彩燕; 于剑; 刘光明

    2015-01-01

    社区结构作为复杂网络的重要拓扑特性之一,成为当前的研究热点。本文提出了一种基于边排序和模块度优化的社区发现方法。该方法首先对初始的静态网络进行稀疏化,然后在稀疏化后的网络上依据边的重要程度对边进行排序,给出了一种模块度最大化、快速边合并的社区发现方法(Fast rank‐based community detection ,FRCD)。在初始网络社区划分结果的基础上,将该方法推广到动态、实时社区划分上,给出了一种快速、鲁棒的动态社区划分方法(Incremental dynamic community detec‐tion ,IDCD)。理论分析表明FRCD相对于边具有线性时间复杂度。在实际和人工网络上的实验结果均表明,本文提出的方法无论在静态网络社区划分还是在动态网络社区追踪上都优于已有方法。%Community structure is one of the most important topological characteristics in the complex network ,being a hot research area in different fields .A novel community detection algorithm is proposed based on edges rank and modularity optimization .Local graph is sparsificated and edges are ranked ac‐cording to the similarity .Therefore ,a method called the fast rank‐based community detection (FRCD) by maximizing modularity and fast mergement of edges is achieved .Meanwhile the method is also ex‐tended to dynamic and real‐time community detection on the basis of initial community structure ,and a fast and robust dynamic community detection algorithm called the incremental dynamic community detec‐tion (IDCD) is presented .Theoretical analysis exhibit that FRCD has linear complexity for network ed‐ges .Experimental results in real‐world and artificial networks demonstrate the high accuracy and good performance of the algorithm on static community detection and tracking dynamic structure of networks .

  4. Changing dynamics in the Canadian voluntary sector: challenges in sustaining organizational capacity to support healthy communities.

    Science.gov (United States)

    Steedman, Eric; Rabinowicz, Jane

    2006-11-01

    The voluntary sector is recognized, by citizens, industry and government, as an increasingly vital contributor to healthy communities within Canadian society, called upon to provide front-line service delivery in areas of community support that were in the past often served by government and or religious charity. (The voluntary sector is large, consisting of an estimated 180,000 non-profit organizations [of which 80,000 are registered as charities] and hundreds of thousands more volunteer groups that are not incorporated [Statistics Canada, 2002].) The dynamics of the sector have changed considerably over the past decade, as government has pulled back the level of core organizational funding support and the role of the church has diminished. As community health is directly related to the organizational health of service-providing non-profits and charities, these organizations are looking increasingly towards corporate and individual donors, along with new self-financing approaches that generate revenues. They are also facing challenges in attracting and retaining skilled and motivated volunteers. As the scope of the voluntary sector and its overall influence grows, so do the organizational and financial challenges it faces. This article will address in particular the issue of funding support for healthy communities and examine a number of potential and existing best practices for sustaining community health in Canada. We will also look at the issue of volunteerism and human resource capacity challenges for organizations. This is an area in which the Canadian government has decided to focus as a result of explicit policy decisions taken in the late 1990s.

  5. Climate warming and agricultural stressors interact to determine stream macroinvertebrate community dynamics.

    Science.gov (United States)

    Piggott, Jeremy J; Townsend, Colin R; Matthaei, Christoph D

    2015-05-01

    Global climate change is likely to modify the ecological consequences of currently acting stressors, but potentially important interactions between climate warming and land-use related stressors remain largely unknown. Agriculture affects streams and rivers worldwide, including via nutrient enrichment and increased fine sediment input. We manipulated nutrients (simulating agricultural run-off) and deposited fine sediment (simulating agricultural erosion) (two levels each) and water temperature (eight levels, 0-6°C above ambient) simultaneously in 128 streamside mesocosms to determine the individual and combined effects of the three stressors on macroinvertebrate community dynamics (community composition and body size structure of benthic, drift and insect emergence assemblages). All three stressors had pervasive individual effects, but in combination often produced additive or antagonistic outcomes. Changes in benthic community composition showed a complex interplay among habitat quality (with or without sediment), resource availability (with or without nutrient enrichment) and the behavioural/physiological tendency to drift or emerge as temperature rose. The presence of sediment and raised temperature both resulted in a community of smaller organisms. Deposited fine sediment strongly increased the propensity to drift. Stressor effects were most prominent in the benthic assemblage, frequently reflected by opposite patterns in individuals quitting the benthos (in terms of their propensity to drift or emerge). Of particular importance is that community measures of stream health routinely used around the world (taxon richness, EPT richness and diversity) all showed complex three-way interactions, with either a consistently stronger temperature response or a reversal of its direction when one or both agricultural stressors were also in operation. The negative effects of added fine sediment, which were often stronger at raised temperatures, suggest that streams already

  6. Moving alcohol prevention research forward-Part II: new directions grounded in community-based system dynamics modeling.

    Science.gov (United States)

    Apostolopoulos, Yorghos; Lemke, Michael K; Barry, Adam E; Lich, Kristen Hassmiller

    2017-07-25

    Given the complexity of factors contributing to alcohol misuse, appropriate epistemologies and methodologies are needed to understand and intervene meaningfully. We aimed to (1) provide an overview of computational modeling methodologies, with an emphasis on system dynamics modeling; (2) explain how community-based system dynamics modeling can forge new directions in alcohol prevention research; and (3) present a primer on how to build alcohol misuse simulation models using system dynamics modeling, with an emphasis on stakeholder involvement, data sources and model validation. Throughout, we use alcohol misuse among college students in the United States as a heuristic example for demonstrating these methodologies. System dynamics modeling employs a top-down aggregate approach to understanding dynamically complex problems. Its three foundational properties-stocks, flows and feedbacks-capture non-linearity, time-delayed effects and other system characteristics. As a methodological choice, system dynamics modeling is amenable to participatory approaches; in particular, community-based system dynamics modeling has been used to build impactful models for addressing dynamically complex problems. The process of community-based system dynamics modeling consists of numerous stages: (1) creating model boundary charts, behavior-over-time-graphs and preliminary system dynamics models using group model-building techniques; (2) model formulation; (3) model calibration; (4) model testing and validation; and (5) model simulation using learning-laboratory techniques. Community-based system dynamics modeling can provide powerful tools for policy and intervention decisions that can result ultimately in sustainable changes in research and action in alcohol misuse prevention. © 2017 Society for the Study of Addiction.

  7. Visualizing the population dynamics of microbial communities in the larval zebrafish gut

    Science.gov (United States)

    Parthasarathy, Raghuveer

    In each of our digestive tracts, trillions of microbes representing hundreds of different species colonize local environments, reproduce, and compete with one another. The resulting ecosystems influence many aspects their host's development and health. Little is known about how gut microbial communities vary in space and time: how they grow, fluctuate, and respond to various perturbations. To address this and investigate microbial colonization of the vertebrate gut, we apply light sheet fluorescence microscopy to a model system that combines a realistic in vivo environment with a high degree of experimental control: larval zebrafish with defined subsets of commensal bacterial species. Light sheet microscopy enables three-dimensional imaging with high resolution over the entire intestine, providing visualizations that would be difficult or impossible to achieve with other techniques. Quantitative analysis of image data enables measurement of bacterial abundances and distributions. I will describe this approach and focus especially on recent experiments in which a colonizing bacterial species is challenged by the invasion of a second species, which leads to the decline of the first group. Imaging reveals dramatic population collapses that differentially affect the two species due to their different biogeographies and morphologies. The collapses are driven by the peristaltic motion of the zebrafish intestine, indicating that the physical activity of the host environment can play a major role in mediating inter-species competition. role in mediating inter-species competition. Supported by the National Science Foundation under Grant No. 0922951 and the National Institutes of Health under Award Number 1P50GM098911.

  8. [Annual dynamics of cladocera community structure in Backshore Wetland of Expo Garden, Shanghai].

    Science.gov (United States)

    Chen, Li-Jing; Wu, Yan-Fang; Jing, Yu-Xiang; Wang, Cong; Zhang, Yin-Jiang

    2012-10-01

    The Backshore Wetland of Expo Garden, Shanghai was one of the key parts of the World Expo construction project in 2010. From September 2009 to August 2010, a monthly investigation was conducted to understand the spatiotemporal dynamics of cladocera community structure (including species composition and standing crop) and related main affecting factors in the Backshore Wetland. A total of 36 cladocera species in 13 genera of 5 families were identified through the year. There were 12 dominant species, mainly Chydorus sphaericus, C. ovalis, Diaphanosoma leuchtenbergianum, and Sida crystalline. The mean annual abundance and biomass of the cladocera were 5.7 ind x L(-1) and 0.3559 mg x L(-1), respectively, and the annual dynamics of the standing crop showed bimodal, with the main peak in April and July, and the second peak in July and May, respectively. The Shannon index, Pielou index, and Margelf index were high in summer and autumn, but low in winter and spring. The canonical correspondence analysis (CCA) showed that water temperature, pH, dissolved oxygen, and nitrite nitrogen were the main factors affecting the community structure of cladocera in the Backshore Wetland.

  9. Dynamics and diversity of microbial community succession in traditional fermentation of Shanxi aged vinegar.

    Science.gov (United States)

    Nie, Zhiqiang; Zheng, Yu; Du, Hongfu; Xie, Sankuan; Wang, Min

    2015-05-01

    The traditional fermentation of Shanxi aged vinegar (SAV), a well-known traditional Chinese vinegar, generally involves the preparation of starter daqu, starch saccharification, alcoholic fermentation (AF) and acetic acid fermentation (AAF). Dynamics and diversity of microbial community succession in daqu and other fermentation stages were investigated by denaturing gradient gel electrophoresis (DGGE). Results showed that eight bacterial genera and four fungal genera were found in daqu. However, Staphylococcus, Saccharopolyspora, Bacillus, Oceanobacillus, Enterobacter, Streptomyces, Eurotium, Monascus and Pichia in daqu were eradicated during AF. Four bacterial genera and three fungal genera were found in this stage. Weissella, Lactobacillus, Streptococcus, Saccharomyces, and Saccharomycopsis were the dominant microorganisms in the late stage of AF. During AAF, four bacterial genera and four fungal genera were found. Weissella, Streptococcus, Klebsiella, Escherichia, and Cladosporium gradually disappeared; the dominant microorganisms were Acetobacter, Lactobacillus, Saccharomycopsis, and Alternaria in the late stage of AAF. Alpha diversity metrics showed that fungal diversity in daqu was greater than that in AF and AAF. By contrast, bacterial diversity decreased from daqu to AF and increased in the first three days of AAF and then decreased. Hence, these results could help understand dynamics of microbial community succession in continuous fermentation of traditional Chinese vinegars.

  10. Simulations of long-term community dynamics in coral reefs--how perturbations shape trajectories.

    Directory of Open Access Journals (Sweden)

    Andreas Kubicek

    Full Text Available Tropical coral reefs feature extraordinary biodiversity and high productivity rates in oligotrophic waters. Due to increasing frequencies of perturbations--anthropogenic and natural--many reefs are under threat. Such perturbations often have devastating effects on these unique ecosystems and especially if they occur simultaneously and amplify each other's impact, they might trigger a phase shift and create irreversible conditions.We developed a generic, spatially explicit, individual-based model in which competition drives the dynamics of a virtual benthic reef community--comprised of scleractinian corals and algae--under different environmental settings. Higher system properties, like population dynamics or community composition arise through self-organization as emergent properties. The model was parameterized for a typical coral reef site at Zanzibar, Tanzania and features coral bleaching and physical disturbance regimes as major sources of perturbations. Our results show that various types and modes (intensities and frequencies of perturbations create diverse outcomes and that the switch from high diversity to single species dominance can be evoked by small changes in a key parameter. Here we extend the understanding of coral reef resilience and the identification of key processes, drivers and respective thresholds, responsible for changes in local situations. One future goal is to provide a tool which may aid decision making processes in management of coral reefs.

  11. Evaluation of guidewire path reproducibility.

    Science.gov (United States)

    Schafer, Sebastian; Hoffmann, Kenneth R; Noël, Peter B; Ionita, Ciprian N; Dmochowski, Jacek

    2008-05-01

    The number of minimally invasive vascular interventions is increasing. In these interventions, a variety of devices are directed to and placed at the site of intervention. The device used in almost all of these interventions is the guidewire, acting as a monorail for all devices which are delivered to the intervention site. However, even with the guidewire in place, clinicians still experience difficulties during the interventions. As a first step toward understanding these difficulties and facilitating guidewire and device guidance, we have investigated the reproducibility of the final paths of the guidewire in vessel phantom models on different factors: user, materials and geometry. Three vessel phantoms (vessel diameters approximately 4 mm) were constructed having tortuousity similar to the internal carotid artery from silicon tubing and encased in Sylgard elastomer. Several trained users repeatedly passed two guidewires of different flexibility through the phantoms under pulsatile flow conditions. After the guidewire had been placed, rotational c-arm image sequences were acquired (9 in. II mode, 0.185 mm pixel size), and the phantom and guidewire were reconstructed (512(3), 0.288 mm voxel size). The reconstructed volumes were aligned. The centerlines of the guidewire and the phantom vessel were then determined using region-growing techniques. Guidewire paths appear similar across users but not across materials. The average root mean square difference of the repeated placement was 0.17 +/- 0.02 mm (plastic-coated guidewire), 0.73 +/- 0.55 mm (steel guidewire) and 1.15 +/- 0.65 mm (steel versus plastic-coated). For a given guidewire, these results indicate that the guidewire path is relatively reproducible in shape and position.

  12. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

    Directory of Open Access Journals (Sweden)

    Wei Hui

    2012-04-01

    Full Text Available Abstract Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera wood-chips and mown lawn grass clippings (85:15 in dry-weight and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  13. Plankton community dynamics in a subtropical lagoonal system and related factors

    Directory of Open Access Journals (Sweden)

    LETÍCIA DONADEL

    2016-03-01

    Full Text Available ABSTRACT Changes of the plankton community in a shallow, subtropical lagoonal system and its relation to environmental conditions were investigated during an annual cycle to provide information on its spatial and seasonal variation pattern. The study carried out at four sites (three in the Peixe lagoon and one in the Ruivo lagoon, which are located in the Lagoa do Peixe National Park, southern Brazil. The system has a temporary connection to the Atlantic Ocean by a narrow channel. The phytoplankton density was higher in the Peixe lagoon whereas the specific richness was higher in the Ruivo lagoon which is also a site with the lower salinity. The phytoplankton biomass near the channel showed seasonal variation with the highest value in fall and lowest in winter. Zooplankton richness was inversely correlated with salinity, and had the highest values in the Ruivo lagoon. Ordination analysis indicated seasonal and spatial patterns in plankton community in this lagoonal system, related to variation in salinity. In addition, the wind action and precipitation were important factors on the spatial and seasonal salinity changes in the lagoon with direct influence on the plankton community dynamics.

  14. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.

  15. Water mass dynamics shape Ross Sea protist communities in mesopelagic and bathypelagic layers

    Science.gov (United States)

    Zoccarato, Luca; Pallavicini, Alberto; Cerino, Federica; Fonda Umani, Serena; Celussi, Mauro

    2016-12-01

    Deep-sea environments host the largest pool of microbes and represent the last largely unexplored and poorly known ecosystems on Earth. The Ross Sea is characterized by unique oceanographic dynamics and harbors several water masses deeply involved in cooling and ventilation of deep oceans. In this study the V9 region of the 18S rDNA was targeted and sequenced with the Ion Torrent high-throughput sequencing technology to unveil differences in protist communities (>2 μm) correlated with biogeochemical properties of the water masses. The analyzed samples were significantly different in terms of environmental parameters and community composition outlining significant structuring effects of temperature and salinity. Overall, Alveolata (especially Dinophyta), Stramenopiles and Excavata groups dominated mesopelagic and bathypelagic layers, and protist communities were shaped according to the biogeochemistry of the water masses (advection effect and mixing events). Newly-formed High Salinity Shelf Water (HSSW) was characterized by high relative abundance of phototrophic organisms that bloom at the surface during the austral summer. Oxygen-depleted Circumpolar Deep Water (CDW) showed higher abundance of Excavata, common bacterivores in deep water masses. At the shelf-break, Antarctic Bottom Water (AABW), formed by the entrainment of shelf waters in CDW, maintained the eukaryotic genetic signature typical of both parental water masses.

  16. Dynamics of prokaryotic picoplankton community in the central and southern Adriatic Sea (Croatia)

    Science.gov (United States)

    Šantić, Danijela; Krstulović, Nada; Šolić, Mladen; Ordulj, Marin; Kušpilić, Grozdan

    2013-09-01

    This paper addresses the dynamics of the prokaryotic picoplankton community in the coastal and open sea areas of the central Adriatic and in the coastal area of the southern Adriatic. This involved the study, from January to December 2005, of bacteria (total number of non-pigmented bacteria; high nucleic acid content (HNA) bacteria; low nucleic acid content (LNA) bacteria), cyanobacteria ( Synechococcus and Prochlorococcus) and heterotrophic nanoflagellates. During the warmer seasons, in the mainly oligotrophic area under investigation into the Adriatic Sea, bacterial densities and bacterial production have shown an increase in values and domination of the LNA group of the bacterial population. In contrast, in those areas influenced by karstic rivers, the domination of HNA bacteria in total abundance of non-pigmented bacteria and high values of bacterial production was estimated throughout the investigated period. Our results show the importance of both HNA and LNA bacterial groups in the total bacterial activity throughout the investigated area. The biomass of bacteria was mostly predominant in the prokaryotic community, while within the autotrophic community Synechococcus biomass mostly predominated. During the warmer seasons, an increase in autotrophic biomass was observed in relation to non-pigmented biomass. The importance of predation in controlling bacteria by heterotrophic nanoflagellates was pronounced during the warmer period and in the coastal areas.

  17. Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

    Energy Technology Data Exchange (ETDEWEB)

    Wei, H.; Tucker, M. P.; Baker, J. O.; Harris, M.; Luo, Y. H.; Xu, Q.; Himmel, M. E.; Ding, S. Y.

    2012-04-01

    Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  18. Next-generation dynamic global vegetation models: learning from community ecology.

    Science.gov (United States)

    Scheiter, Simon; Langan, Liam; Higgins, Steven I

    2013-05-01

    Dynamic global vegetation models (DGVMs) are powerful tools to project past, current and future vegetation patterns and associated biogeochemical cycles. However, most models are limited by how they define vegetation and by their simplistic representation of competition. We discuss how concepts from community assembly theory and coexistence theory can help to improve vegetation models. We further present a trait- and individual-based vegetation model (aDGVM2) that allows individual plants to adopt a unique combination of trait values. These traits define how individual plants grow and compete. A genetic optimization algorithm is used to simulate trait inheritance and reproductive isolation between individuals. These model properties allow the assembly of plant communities that are adapted to a site's biotic and abiotic conditions. The aDGVM2 simulates how environmental conditions influence the trait spectra of plant communities; that fire selects for traits that enhance fire protection and reduces trait diversity; and the emergence of life-history strategies that are suggestive of colonization-competition trade-offs. The aDGVM2 deals with functional diversity and competition fundamentally differently from current DGVMs. This approach may yield novel insights as to how vegetation may respond to climate change and we believe it could foster collaborations between functional plant biologists and vegetation modellers.

  19. Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

    2017-08-16

    Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

  20. Sourdough microbial community dynamics: An analysis during French organic bread-making processes.

    Science.gov (United States)

    Lhomme, Emilie; Urien, Charlotte; Legrand, Judith; Dousset, Xavier; Onno, Bernard; Sicard, Delphine

    2016-02-01

    Natural sourdoughs are commonly used in bread-making processes, especially for organic bread. Despite its role in bread flavor and dough rise, the stability of the sourdough microbial community during and between bread-making processes is debated. We investigated the dynamics of lactic acid bacteria (LAB) and yeast communities in traditional organic sourdoughs of five French bakeries during the bread-making process and several months apart using classical and molecular microbiology techniques. Sourdoughs were sampled at four steps of the bread-making process with repetition. The analysis of microbial density over 68 sourdough/dough samples revealed that both LAB and yeast counts changed along the bread-making process and between bread-making runs. The species composition was less variable. A total of six LAB and nine yeast species was identified from 520 and 1675 isolates, respectively. The dominant LAB species was Lactobacillus sanfranciscensis, found for all bakeries and each bread-making run. The dominant yeast species changed only once between bread-making processes but differed between bakeries. They mostly belonged to the Kazachstania clade. Overall, this study highlights the change of population density within the bread-making process and between bread-making runs and the relative stability of the sourdough species community during bread-making process.

  1. Genotypic variation in foundation species generates network structure that may drive community dynamics and evolution.

    Science.gov (United States)

    Lau, Matthew K; Keith, Arthur R; Borrett, Stuart R; Shuster, Stephen M; Whitham, Thomas G

    2016-03-01

    Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrowleaf cottonwood), in a long-term, common garden experiment using a bipartite "genotype-species" network perspective. We combine this empirical work with a simulation experiment designed to further investigate how variation among individual tree genotypes can impact network structure. Three findings emerged: (1) the empirical "genotype-species network" exhibited significant network structure with modularity being greater than the highly conservative null model; (2) as would be expected given a modular network structure, the empirical network displayed significant positive arthropod co-occurrence patterns; and (3) furthermore, the simulations of "genotype-species" networks displayed variation in network structure, with modularity in particular clearly increasing, as genotypic variation increased. These results support the conclusion that genetic variation in a single species contributes to the structure of ecological interaction networks, which could influence eco-ogical dynamics (e.g., assembly and stability) and evolution in a community context.

  2. Biological sulphide removal from anaerobically treated domestic sewage: reactor performance and microbial community dynamics.

    Science.gov (United States)

    Garcia, Graziella Patrício Pereira; Diniz, Renata Côrtes Oliveira; Bicalho, Sarah Kinaip; Franco, Vitor Araujo de Souza; Gontijo, Eider Max de Oliveira; Toscano, Rodrigo Argolo; Canhestro, Kenia Oliveira; Santos, Merly Rita Dos; Carmo, Ana Luiza Rodrigues Dias; Lobato, Livia Cristina S; Brandt, Emanuel Manfred F; Chernicharo, Carlos A L; Calabria de Araujo, Juliana

    2015-01-01

    We developed a biological sulphide oxidation system and evaluated two reactors (shaped similar to the settler compartment of an up-flow anaerobic sludge blanket [UASB] reactor) with different support materials for biomass retention: polypropylene rings and polyurethane foam. The start-up reaction was achieved using microorganisms naturally occurring on the open surface of UASB reactors treating domestic wastewater. Sulphide removal efficiencies of 65% and 90% were achieved with hydraulic retention times (HRTs) of 24 and 12 h, respectively, in both reactors. However, a higher amount of elemental sulphur was formed and accumulated in the biomass from reactor 1 (20 mg S(0) g(-1) VTS) than in that from reactor 2 (2.9 mg S(0) g(-1) VTS) with an HRT of 24 h. Denaturing gradient gel electrophoresis (DGGE) results revealed that the the pink and green biomass that developed in both reactors comprised a diverse bacterial community and had sequences related to phototrophic green and purple-sulphur bacteria such as Chlorobium sp., Chloronema giganteum, and Chromatiaceae. DGGE band patterns also demonstrated that bacterial community was dynamic over time within the same reactor and that different support materials selected for distinct bacterial communities. Taken together, these results indicated that sulphide concentrations of 1-6 mg L(-1) could be efficiently removed from the effluent of a pilot-scale UASB reactor in two sulphide biological oxidation reactors at HRTs of 12 and 24 h, showing the potential for sulphur recovery from anaerobically treated domestic wastewater.

  3. Modeling Amazon forest vegetation dynamics and community response to increased wind disturbance

    Science.gov (United States)

    Holm, J. A.; Negron Juarez, R. I.; Chambers, J. Q.; Marra, D.; Rifai, S. W.; Knox, R. G.; Riley, W. J.; Koven, C. D.; McGroddy, M. E.; Urquiza-Muñoz, J. D.; Tello-Espinoza, R.; Ribeiro, G. H. P. M.; Higuchi, N.

    2015-12-01

    Determining the drivers of tree mortality in Amazonia is a complex task, yet essential to reliable prediction of carbon storage in a warmer climate. Past studies have shown an east-west gradient of forest disturbance and rainfall amount across Amazonia. This study uses remote sensing and dynamic vegetation modeling to take a deeper look at drivers of tree mortality and community composition shifts associated with varying mortality rates. Our analysis, using 20 years of Landsat 5 images, showed that ever-wet Amazonia (located in north-west Amazonia, i.e. NWA) was more susceptible to windthrows than the Central Amazon (i.e. CA), which has a a well-defined dry season. The higher frequency of windthrows in NWA forest correlates with higher frequency and intensity of deep convection events in this region, observed using Tropical Rainfall Measuring Mission (TRMM) data. While a combination of factors including: soil characteristics (and by proxy rooting depth) and community composition exacerbate the regional gradient of disturbance, wind was the mechanistic agent of disturbance. Using an individual-based gap model for tropical forests populated with the most representative NWA tree species and increased mortality rates, we found a decrease of biomass in this region and a slight increase in NPP compared to a control simulation, a pattern that is similar to observations. The model predicted which species had the largest response in basal area change due to elevated disturbance, but there was a non-significant shift in community composition in the NWA forests. However, analysis found strong differences in community composition between the modeled NWA and CA regions, consistent with observed results. When CA forests were subject to higher mortality rate similar to the current NWA region, dissimilarity in community composition continued to persist. In addition the model identified species-specific maximum tree height and maximum diameter as the most influential predictors of

  4. Dynamics of bloggers’ communities: Bipartite networks from empirical data and agent-based modeling

    Science.gov (United States)

    Mitrović, Marija; Tadić, Bosiljka

    2012-11-01

    We present an analysis of the empirical data and the agent-based modeling of the emotional behavior of users on the Web portals where the user interaction is mediated by posted comments, like Blogs and Diggs. We consider the dataset of discussion-driven popular Diggs, in which all comments are screened by machine-learning emotion detection in the text, to determine positive and negative valence (attractiveness and aversiveness) of each comment. By mapping the data onto a suitable bipartite network, we perform an analysis of the network topology and the related time-series of the emotional comments. The agent-based model is then introduced to simulate the dynamics and to capture the emergence of the emotional behaviors and communities. The agents are linked to posts on a bipartite network, whose structure evolves through their actions on the posts. The emotional states (arousal and valence) of each agent fluctuate in time, subject to the current contents of the posts to which the agent is exposed. By an agent’s action on a post its current emotions are transferred to the post. The model rules and the key parameters are inferred from the considered empirical data to ensure their realistic values and mutual consistency. The model assumes that the emotional arousal over posts drives the agent’s action. The simulations are preformed for the case of constant flux of agents and the results are analyzed in full analogy with the empirical data. The main conclusions are that the emotion-driven dynamics leads to long-range temporal correlations and emergent networks with community structure, that are comparable with the ones in the empirical system of popular posts. In view of pure emotion-driven agents actions, this type of comparisons provide a quantitative measure for the role of emotions in the dynamics on real blogs. Furthermore, the model reveals the underlying mechanisms which relate the post popularity with the emotion dynamics and the prevalence of negative

  5. Evidence of a dynamic microbial community structure and predation through combined microbiological and stable isotope characterization

    Science.gov (United States)

    Druhan, J. L.; Bill, M.; Lim, H. C.; Wu, C.; Conrad, M. E.; Williams, K. H.; DePaolo, D. J.; Brodie, E.

    2014-12-01

    The speciation, reactivity and mobility of carbon in the near surface environment is intimately linked to the prevalence, diversity and dynamics of native microbial populations. We utilize this relationship by introducing 13C-labeled acetate to sediments recovered from a shallow aquifer system to track both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Results demonstrate a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples analyzed weekly for microbial composition by pyrosequencing of ribosomal RNA genes showed a transient microbial community structure, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identifiable in the partitioning of carbon isotopes. The impact of predator-prey relationships on subsurface microbial community dynamics and therefore the flux of carbon through a system via the microbial biomass

  6. Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping

    Directory of Open Access Journals (Sweden)

    Jessica L. Mark Welch

    2014-11-01

    Full Text Available The human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project. Our previous work established that many of these oligotypes had dramatically different distributions between individuals and across oral habitats, suggesting that they represented functionally different organisms. Here we demonstrate the presence of a consistent tongue microbiome but with rapidly fluctuating proportions of the characteristic taxa. In some cases closely related oligotypes representing strains or variants within a single species displayed fluctuating relative abundances over time, while in other cases an initially dominant oligotype was replaced by another oligotype of the same species. We use this high temporal and taxonomic level of resolution to detect correlated changes in oligotype abundance that could indicate which taxa likely interact synergistically or occupy similar habitats, and which likely interact antagonistically or prefer distinct habitats. For example, we found a strong correlation in abundance over time between two oligotypes from different families of Gamma Proteobacteria, suggesting a close functional or ecological relationship between them. In summary, the tongue is colonized by a microbial community of moderate complexity whose proportional abundance fluctuates widely on time scales of days. The drivers and functional consequences of these community dynamics are not known, but we expect they will prove tractable to future, targeted studies employing taxonomically resolved analysis of high-throughput sequencing data sampled at appropriate temporal intervals and

  7. Dynamic communities in multichannel data: an application to the foreign exchange market during the 2007-2008 credit crisis.

    Science.gov (United States)

    Fenn, Daniel J; Porter, Mason A; McDonald, Mark; Williams, Stacy; Johnson, Neil F; Jones, Nick S

    2009-09-01

    We study the cluster dynamics of multichannel (multivariate) time series by representing their correlations as time-dependent networks and investigating the evolution of network communities. We employ a node-centric approach that allows us to track the effects of the community evolution on the functional roles of individual nodes without having to track entire communities. As an example, we consider a foreign exchange market network in which each node represents an exchange rate and each edge represents a time-dependent correlation between the rates. We study the period 2005-2008, which includes the recent credit and liquidity crisis. Using community detection, we find that exchange rates that are strongly attached to their community are persistently grouped with the same set of rates, whereas exchange rates that are important for the transfer of information tend to be positioned on the edges of communities. Our analysis successfully uncovers major trading changes that occurred in the market during the credit crisis.

  8. Mouse Social Network Dynamics and Community Structure are Associated with Plasticity-Related Brain Gene Expression.

    Science.gov (United States)

    Williamson, Cait M; Franks, Becca; Curley, James P

    2016-01-01

    Laboratory studies of social behavior have typically focused on dyadic interactions occurring within a limited spatiotemporal context. However, this strategy prevents analyses of the dynamics of group social behavior and constrains identification of the biological pathways mediating individual differences in behavior. In the current study, we aimed to identify the spatiotemporal dynamics and hierarchical organization of a large social network of male mice. We also sought to determine if standard assays of social and exploratory behavior are predictive of social behavior in this social network and whether individual network position was associated with the mRNA expression of two plasticity-related genes, DNA methyltransferase 1 and 3a. Mice were observed to form a hierarchically organized social network and self-organized into two separate social network communities. Members of both communities exhibited distinct patterns of socio-spatial organization within the vivaria that was not limited to only agonistic interactions. We further established that exploratory and social behaviors in standard behavioral assays conducted prior to placing the mice into the large group was predictive of initial network position and behavior but were not associated with final social network position. Finally, we determined that social network position is associated with variation in mRNA levels of two neural plasticity genes, DNMT1 and DNMT3a, in the hippocampus but not the mPOA. This work demonstrates the importance of understanding the role of social context and complex social dynamics in determining the relationship between individual differences in social behavior and brain gene expression.

  9. Comparative summer dynamics of surface cyanobacterial communities in two connected lakes from the west of Ireland

    Energy Technology Data Exchange (ETDEWEB)

    Touzet, N., E-mail: touzet.nicolas@itsligo.ie [Centre for Environmental Research, Innovation and Sustainability, School of Science, Department of Environmental Science, Institute of Technology Sligo, Sligo (Ireland); McCarthy, D.; Gill, A.; Fleming, G.T.A. [Microbiology, School of Natural Sciences, National University of Ireland, Galway, Galway (Ireland)

    2016-05-15

    The eutrophication of lakes is typically associated with high biomass proliferations of potentially toxic cyanobacteria. At a regional level, the sustainable management of water resources necessitates an approach that recognises the interconnectivity of multiple water systems within river catchments. This study examined the dynamics in summer diversity of planktonic cyanobacterial communities and microcystin toxin concentrations in two inter-connected lakes from the west of Ireland prone to nutrient enrichment. DGGE analysis of 16S rRNA gene amplicons of genotype-I cyanobacteria (typically spherical) showed changes in the communities of both Lough Corrib and Ballyquirke Lough throughout the summer, and identified cyanobacterial genotypes both unique and shared to both lakes. Microcystin concentrations, estimated via the protein phosphatase 2A inhibition assay, were greater in August than in July and June in both lakes. This was concomitant to the increased occurrence of Microcystis as evidenced by DGGE band excision and subsequent sequencing and BLAST analysis. RFLP analysis of PCR amplified mcy-A/E genes clustered together the August samples of both lakes, highlighting a potential change in microcystin producers across the two lakes. Finally, the multiple factor analysis of the combined environmental data set for the two lakes highlighted the expected pattern opposing greater water temperature and chlorophyll concentration against macronutrient concentrations, but also indicated a negative relationship between microcystin concentration and cyanobacterial diversity, possibly underlining allelopathic interactions. Despite some element of connectivity, the dissimilarity in the composition of the cyanobacterial assemblages and the timing of community change in the two lakes likely were a reflexion of niche differences determined by meteorologically-forced variation in physico-chemical parameters in the two water bodies. - Highlights: • DGGE highlighted

  10. Seasonal Dynamics of Ant Community Structure in the Moroccan Argan Forest

    Science.gov (United States)

    Keroumi, Abderrahim El; Naamani, Khalid; Soummane, Hassna; Dahbi, Abdallah

    2012-01-01

    In this study we describe the structure and composition of ant communities in the endemic Moroccan Argan forest, using pitfall traps sampling technique throughout the four seasons between May 2006 and February 2007. The study focused on two distinct climatic habitats within the Essaouira Argan forest, a semi-continental site at Lahssinate, and a coastal site at Boutazarte. Thirteen different ant species were identified, belonging to seven genera. Monomorium subopacum Smith and Tapinoma simrothi Krausse-Heldrungen (Hymenoptera: Formicidae) were the most abundant and behaviorally dominant ant species in the arganeraie. In addition, more specimens were captured in the semi-continental site than in the coastal area. However, no significant difference was observed in species richness, evenness, or diversity between both sites. Composition and community structure showed clear seasonal dynamics. The number of species, their abundance, their diversity, and their evenness per Argan tree were significantly dissimilar among seasons. The richness (except between summer and autumn), and the abundance and the evenness of ant species among communities, showed a significant difference between the dry period (summer and spring) and the rainy period (winter and autumn). Higher abundance and richness values occurred in the dry period of the year. Ant species dominance and seasonal climatic variations in the arganeraie might be among the main factors affecting the composition, structure, and foraging activity of ant communities. This study, together with recent findings on ant predation behavior below Argan trees, highlights the promising use of dominant ant species as potential agents of Mediterranean fruit fly bio-control in the Argan forest and surrounding ecosystems. PMID:23421815

  11. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems.

    Directory of Open Access Journals (Sweden)

    Yuanyuan Qu

    Full Text Available Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control, G2 (augmented with Comamonas sp. MQ, and G3 (augmented with recombinant E. coli nagAc, were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l, followed by G2 (27.3 ± 1.3 mg/l and G1 (19.2 ± 1.2 mg/l. The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc from both inoculated strains was strongly correlated with indigo yields in early stages (0-30 days (P 0.10 of operation. Based on detrended correspondence analysis (DCA and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average, the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05 based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05. This study should provide new insights into our understanding of indigo bio-production by microbial communities.

  12. The Spatiotemporal Dynamics of Forest–Heathland Communities over 60 Years in Fontainebleau, France

    Directory of Open Access Journals (Sweden)

    Samira Mobaied

    2015-06-01

    Full Text Available According to the EU Habitats Directive, heathlands are “natural habitats of community interest”. Heathland management aims at conserving these habitats threatened by various changes, including successional processes leading to forest vegetation. We investigate the dynamics of woody species to the detriment of heathland over a period of 60 years in the Fontainebleau forest and we examine the effects of soil types, soil depth and topography parameters on heathland stability. We assess changes in forest cover between 1946 and 2003 by comparing vegetation maps derived from aerial photographs coupled to GIS analyses. The results show the loss of more than 75% of heathland during 1946–2003 due to tree colonisation of abandoned heathland. We detected differences in the dynamics of colonisation between coniferous and deciduous trees. The colonisation of heathland by coniferous species was faster over the last 20 years of our study period. Tree encroachment was faster in north-facing areas and in areas of acidic luvisols. While this dynamic was very slow in acid sandstone soils, heathland stability was more important in shallow soils on flat and south facing areas. Our study has the potential to assist land managers in selecting those heathland areas that will be easier to conserve and/or to restore by focusing on areas and spatial conditions that prevent forest colonisation and hence favour the long-term stability of heathland.

  13. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie

    2017-03-17

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  14. The Community Surface Dynamics Modeling System: Experiences on Building a Collaborative Modeling Platform

    Science.gov (United States)

    Overeem, I.; Hutton, E.; Kettner, A.; Peckham, S. D.; Syvitski, J. P.

    2012-12-01

    The Community Surface Dynamics Modeling System - CSDMS- develops a software platform with shared and coupled modules for modeling earth surface processes as a community resource. The framework allows prediction of water, sediment and nutrient transport through the landscape and seacape. The underlying paradigm is that the Earth surface we live on is a dynamic system; topography changes with seasons, with landslides and earthquakes, with erosion and deposition. The Earth Surface changes due to storms and floods, and important boundaries, like the coast, are ever-moving features. CSDMS sets out to make better predictions of these changes. Earth surface process modeling bridges the terrestrial, coastal and marine domains and requires understanding of the system over a range of time scales, which inherently needs interdisciplinarity. Members of CSDMS (~830 in July 2012) are largely from academic institutions (˜75%), followed by federal agencies (˜17%), and oil and gas companies (˜5%). Members and governmental bodies meet once annually and rely additionally on web-based information for communication. As an organization that relies on volunteer participation, CSDMS faces challenges to scientific collaboration. Encouraging volunteerism among its members to provide and adapt metadata and model code to be sufficiently standardized for coupling is crucial to building an integrated community modeling system. We here present CSDMS strategies aimed at providing the appropriate technical tools and cyberinfrastructure to support a variety of user types, ranging from advanced to novice modelers. Application of these advances in science is key, both into the educational realm and for managers and decision-makers. We discuss some of the implemented ideas to further organizational transparency and user engagement in small-scale governance, such as advanced trackers and voting systems for model development prioritization through the CSDMS wiki. We analyzed data on community

  15. Interplay of community dynamics, temperature, and productivity on the hydrogen isotope signatures of lipid biomarkers

    Science.gov (United States)

    Nemiah Ladd, S.; Dubois, Nathalie; Schubert, Carsten J.

    2017-09-01

    The hydrogen isotopic composition (δ2H) of lipid biomarkers has diverse applications in the fields of paleoclimatology, biogeochemistry, and microbial community dynamics. Large changes in hydrogen isotope fractionation have been observed among microbes with differing core metabolisms, while environmental factors including temperature and nutrient availability can affect isotope fractionation by photoautotrophs. Much effort has gone into studying these effects under laboratory conditions with single species cultures. Moving beyond controlled environments and quantifying the natural extent of these changes in freshwater lacustrine settings and identifying their causes is essential for robust application of δ2H values of common short-chain fatty acids as a proxy of net community metabolism and of phytoplankton-specific biomarkers as a paleohydrologic proxy. This work targets the effect of community dynamics, temperature, and productivity on 2H/1H fractionation in lipid biomarkers through a comparative time series in two central Swiss lakes: eutrophic Lake Greifen and oligotrophic Lake Lucerne. Particulate organic matter was collected from surface waters at six time points throughout the spring and summer of 2015, and δ2H values of short-chain fatty acids, as well as chlorophyll-derived phytol and the diatom biomarker brassicasterol, were measured. We paired these measurements with in situ incubations conducted with NaH13CO3, which were used to calculate the production rates of individual lipids in lake surface water. As algal productivity increased from April to June, net discrimination against 2H in Lake Greifen increased by as much as 148 ‰ for individual fatty acids. During the same time period in Lake Lucerne, net discrimination against 2H increased by as much as 58 ‰ for individual fatty acids. A large portion of this signal is likely due to a greater proportion of heterotrophically derived fatty acids in the winter and early spring, which are displaced by

  16. Stability in a changing world - palm community dynamics in the hyperdiverse western Amazon over 17 years.

    Science.gov (United States)

    Olivares, Ingrid; Svenning, Jens-Christian; van Bodegom, Peter M; Valencia, Renato; Balslev, Henrik

    2017-03-01

    Are the hyperdiverse local forests of the western Amazon undergoing changes linked to global and local drivers such as climate change, or successional dynamics? We analyzed local climatic records to assess potential climatic changes in Yasuní National Park, Ecuador, and compared two censuses (1995, 2012) of a palm community to assess changes in community structure and composition. Over 17 years, the structure and composition of this palm community remained remarkably stable. Soil humidity was significantly lower and canopy conditions were significantly more open in 2012 compared to 1995, but local climatic records showed that no significant changes in precipitation, temperature or river level have occurred during the last decade. Thus, we found no evidence of recent directional shifts in climate or the palm community in Yasuní. The absence of changes in local climate and plant community dynamics in Yasuní contrasts with recent findings from eastern Amazon, where environmental change is driving significant changes in ecosystem dynamics. Our findings suggest that until now, local forests in the northwest Amazon may have escaped pressure from climate change. The stability of this rich palm community embedded in the hyperdiverse Yasuní National Park underlines its uniqueness as a sanctuary for the protection of Amazonian diversity from global change impacts.

  17. Nitrogen Effects on Organic Dynamics and Soil Communities in Forest and Agricultural Systems

    Science.gov (United States)

    Grandy, S.; Neff, J.; Sinsabaugh, B.; Wickings, K.

    2008-12-01

    Human activities have doubled the global flux of biologically available N to terrestrial ecosystems but the effects of N on soil organic matter dynamics and soil communities remain difficult to predict. We examined soil organic matter chemistry and enzyme kinetics in three soil fractions (>250, 63-250, and lignin derivatives to total polysaccharides in the >250 μm fraction of the sugar maple/basswood system but there were no changes in other size classes or in the black oak/white oak system. We also measured significant increases in the ratio of lignin derivatives to N-bearing compounds in the 63-250 and >250 μm fractions in both ecosystems but not in the corn-based cropping system. Our results demonstrate that changes in soil organic matter chemistry resulting from atmospheric N deposition or fertilization are directly linked to variation in enzyme responses to increased N availability across ecosystems and soil size fractions.

  18. Fuel cell adventures. Dynamics of a technological community in a quasi-market of technological options

    Science.gov (United States)

    Schaeffer, G. J.; Uyterlinde, M. A.

    In this paper some insights from a social science perspective in the dynamics of the fuel cell community will be provided. An important concept used in the analysis is that of a `quasi'-market of technological options. The strategic choices of actors for certain technological options can be regarded as analogous to choices of consumers made on a market. A scientometric research approach has been used to investigate the aggregate effects of this and other variations of strategic behaviour. These concepts and analyses are shown to be helpful in answering questions such as why fuel cells are so popular today whereas they have not always been, and why preferences for different types of fuel cells shift over time. At the end of the paper the relevance of these kind of analyses for technology forecasting and management practices is briefly discussed.

  19. One hundred and six years of population and community dynamics of Sonoran Desert Laboratory perennials

    Science.gov (United States)

    Rodriguez-Buritica, Susana; Raichle, Helen; Webb, Robert H.; Turner, Raymond M.; Venable, Larry

    2013-01-01

    This data set constitutes all information associated with the Spalding-Shreve permanent vegetation plots from 1906 through 2012, which is the longest-running plant monitoring program in the world. The program consists of detailed maps of all Sonoran Desert perennial plants in 30 permanent plots located on Tumamoc Hill, near Tucson, Arizona, USA. Most of these plots are 10 m × 10 m quadrats that were established by Volney Spalding and Forrest Shreve between 1906 and 1928. Analyses derived from these data have been pivotal in testing early theories on plant community succession, plant life history traits, plant longevity, and population dynamics. One of the major contributions of this data set is the species-specific demographic traits that derived from estimating individual plant trajectories for more than 106 years. Further use of these data might shed light on spatially explicit population and community dynamics, as well as long-term changes attributable to global change. Data presented here consist of digital versions of original maps created between 1906 and 1984 and digital data from recent censuses between 1993 and 2012. Attributes associated with these maps include location and coverage of all shrubs, and in some cases, plant height. In addition, we present plot-specific summaries of plant cover and density for each census year and all other information collected, including seedling counts, grass coverage, and annual species enumerations. We reference the repeat photography of these plots, which began in 1906; these images are stored at the Desert Laboratory Collection of Repeat Photography in Tucson. Initial data collection consisted of grid-mapping the plots manually on graph paper; starting in 1993, Total Stations (which allow a direct digitalization, and more accurate mapping) were used to survey root crowns and canopies.

  20. Do ecohydrology and community dynamics feed back to banded-ecosystem structure and productivity?

    Science.gov (United States)

    Callegaro, Chiara; Ursino, Nadia

    2016-04-01

    Mixed communities including grass, shrubs and trees are often reported to populate self-organized vegetation patterns. Patterns of survey data suggest that species diversity and complementarity strengthen the dynamics of banded environments. Resource scarcity and local facilitation trigger self organization, whereas coexistence of multiple species in vegetated self-organizing patches, implying competition for water and nutrients and favorable reproduction sites, is made possible by differing adaptation strategies. Mixed community spatial self-organization has so far received relatively little attention, compared with local net facilitation of isolated species. We assumed that soil moisture availability is a proxy for the environmental niche of plant species according to Ursino and Callegaro (2016). Our modelling effort was focused on niche differentiation of coexisting species within a tiger bush type ecosystem. By minimal numerical modelling and stability analysis we try to answer a few open scientific questions: Is there an adaptation strategy that increases biodiversity and ecosystem functioning? Does specific adaptation to environmental niches influence the structure of self-organizing vegetation pattern? What specific niche distribution along the environmental gradient gives the highest global productivity?

  1. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes.

    Science.gov (United States)

    Chun, Chan Lan; Peller, Julie R; Shively, Dawn; Byappanahalli, Muruleedhara N; Whitman, Richard L; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J

    2017-01-01

    Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (Great Lakes shorelines. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Phytoplankton community dynamics in an intermittently open hypereutrophic coastal lagoon in southern Portugal

    Science.gov (United States)

    Coelho, Susana; Pérez-Ruzafa, Angel; Gamito, Sofia

    2015-12-01

    Phytoplankton community' dynamics were studied in Salgados coastal lagoon in order to evaluate the effects of excessive organic loads and also physical stress caused by the irregular opening of the lagoon. Salgados is a hypereutrophic intermittently open coastal lagoon, which received freshwater inputs from small rivers and from a wastewater treatment plant. Cyanophyceae dominated the phytoplankton communities most of the time; Bacillariophyceae became the main taxonomic group in winter when the lagoon was closed; Chlorophyceae was the major class in early summer; pico-nano flagellate algae accounted for a high percentage of total phytoplankton during spring. Potentially harmful taxa were observed during most of the sampling periods, forming blooms and accounting for a considerable percentage of total phytoplankton abundance. A strong differentiation among dry and wet seasons could be noticed. The dry season was dominated by Microsystis aeruginosa, Rhodomonas sp., pico-nano flagellate algae, Cyclotella spp. and Planktothrix sp., while the wet season, although still with the presence of Microsystis aeruginosa, was dominated by Dolichospermum spiroides. The best environmental variables explaining stations patterns and based on phytoplankton taxa were days of isolation, pH, and salinity. Temperature, cumulative rain and total phosphorus were also related with species and stations patterns. The high nutrient load in Salgados lagoon promoted the development and persistence of harmful algae blooms. Proper management of coastal lagoons involves not only the control of direct discharges of nutrients, but also of other factors, including water level and communication with the sea.

  3. Detrital microbial community development and phosphorus dynamics in a stream ecosystem

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, R.E.; Elwood, J.W.; Sayler, G.S.

    1986-06-01

    Detrital microbial community development and phosphorus dynamics in a lotic system were investigated in non-recirculating laboratory streams contains leaf detritus. Temporal patterns of microbial colonization, as determined by scanning electron microscopy, indicate leaf species dependency and that bacteria were the first colonizers followed by fungi. An extensive glycocalyx layer developed. Phosphorus incorporation rates of both the whole community and intracellular components were determined by time-course measurements of /sup 33/PO/sub 4/ or /sup 32/PO/sub 4/. Phosphorus turnover rates were determined by a sequential double-labeling procedure using /sup 33/PO/sub 4/ and /sup 32/PO/sub 4/, in which the microbiota were labeled with /sup 33/P until in isotopic equilibrium, then /sup 32/P was added. The turnover rate was determined by time-course measurements of the ratio /sup 32/P to /sup 33/P. Snail grazing resulted in an increase in phosphorus metabolism per unit microbial biomass; however, per unit area of leaf surface no increase was observed. Grazing also caused a two-fold reduction in microbial biomass. The results indicate that microbiota associated with decomposing leaves slowly recycle phosphorus, are slowly growing, and have a low metabolic activity. The spiraling length is shortened by microbiota on a short-term basis; however, it may increase on a long-term basis due to hydrological transport of detritus downstream.

  4. Methanotrophic community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

    Directory of Open Access Journals (Sweden)

    Mónica Torres-Beltrán

    2016-12-01

    Full Text Available Marine oxygen minimum zones (OMZs play disproportionate roles in nutrient and climate active trace gas cycling including nitrous oxide and methane, in the ocean. OMZs are currently expanding due to climate change making it increasingly important to identify microbial controls on trace gas cycling at the individual, population and community levels. Here we present a two-year survey of the microbial community along seasonal redox gradients in Saanich Inlet focused on identifying microbial agents driving methane oxidation. Although methanotrophs were rare, we identified three uncultivated groups affiliated with particulate methane monooxygenase (pMMO encoding phylogenetic groups (OPU, and methanotrophic symbionts as primary drivers of methane oxidation in Saanich Inlet. Distribution and activity patterns for these three groups were consistent with niche partitioning that became increasingly resolved during water column stratification. Moreover co-occurrence analysis combined with multi-level indicator species analysis revealed significant correlations between operational taxonomic units affiliated with Methylophaga, Methylophilales, SAR324, Verrucomicrobia, and Planctomycetes with OPUs and methanotrophic symbiont groups. Taken together these observations shed new light on the composition, dynamics, and potential interspecific interactions of microbes associated with CH4 cycling in the Saanich Inlet water column, provide a baseline for comparison between coastal and open ocean OMZs and support the potential role of OPUs, and methanotrophic symbiont groups as a widely distributed pelagic sink for CH4 along continental margins.

  5. Report on the EU-US Environmental Biotechnology Workshop on Microbial Community Dynamics: Cooperation and Competition

    Energy Technology Data Exchange (ETDEWEB)

    Wall, Judy D. [University of Missouri-Columbia

    2013-07-01

    The Workshop on Microbial Community Dynamics: Cooperation and Competition to be held in the fall of 2012 in St. Louis, Missouri, USA, is an initiative of the Environmental Biotechnology Working Group of the EU-US Taskforce on Biotechnology Research, a cooperative program between the European Commission and the United States of America. The activities of the Environmental Biotechnology Working Group have as their goals to provide a forum for early career scientists from the US and EU to meet, to learn cutting edge research in the area of microbial biotechnology from world experts and to set the groundwork for future cooperation and collaboration. Workshop topics will address fundamental physiology and genetics of microbial communities that will contribute to advances in bioremediation, bioenergy conversion and carbon sequestration. Senior scientist participants will be world renowned experts who will present the current status of their fields and forecast research challenges and opportunities. It is a goal of the Environmental Biotechnology Working Group to facilitate the formation of direct collaborations among US and European scientists in programs of mutual interest and benefit. Therefore, the workshop will also provide an opportunity for members of the Working Group and attendees to identify areas where advancement is necessary and plan the steps necessary for realizing future research collaborations. In addition, time will be provided for mentoring of the early career scientists by the senior scientists on an individual basis.

  6. Spatial-temporal feeding dynamics of benthic communities in an estuary-marine gradient

    Science.gov (United States)

    Antonio, Emily S.; Kasai, Akihide; Ueno, Masahiro; Ishihi, Yuka; Yokoyama, Hisashi; Yamashita, Yoh

    2012-10-01

    We investigated the fluctuations of carbon and nitrogen stable isotope ratios in benthic consumers and their potential food sources to determine the spatial and temporal variations in the utilization of available organic matter, indicating the origin and pathways of energy from Yura Estuary to Tango Sea, Japan. Field samplings were conducted from the upper estuary to offshore with sampling frequency of twice per season from April (spring) 2006 to February (winter) 2007. The δ13C signatures of the upper and lower estuary benthos showed depleted and in wide range (-28.9‰ to -13.5‰) compared to the enriched and within narrow range signatures of marine benthos (-20.6‰ to -14.0‰) in all seasons. On the contrary, the δ15N signatures of benthic communities showed decreasing trend seaward and summer values were different from the other seasons. Using the dual isotope and multisource mixing models, we estimated the relative contributions of potential food sources to the benthos diet. River POM played an important source of energy for the estuarine benthos, especially in winter when river discharge was high. Marine POM served as an important alternative food for the estuarine benthos from spring to autumn when seawater intruded the bottom estuary. Benthic microalgae were the major food source at the shallow coast throughout the year, while marine POM fueled the deep coast and offshore benthic food webs. Spatial and temporal feeding variations in estuarine benthic communities were driven by the hydrology of the estuary, whereas primary production and transport of food source dictated diet variations of marine benthic communities. The elucidation of the dynamic energy subsidy among aquatic systems highlights the importance of the land-sea transition zones that is crucial for benthic secondary productions.

  7. Phytoplankton community structure and dynamics in the North Atlantic subtropical gyre

    Science.gov (United States)

    Cáceres, Carlos; Rivera, Antonella; González, Sonia; Anadón, Ricardo

    2017-02-01

    Phytoplankton fuel epipelagic ecosystems and affect global biogeochemical cycles. Nevertheless, there is still a lack of quantitative information about the factors that determine both phytoplankton community structure and dynamics, particularly in subtropical gyres. Here, we estimated size fractionated phytoplankton growth (μ) and microzooplankton grazing rates (m) along a transect in the subtropical North Atlantic, from the island of Hispaniola to the Iberian Peninsula, by conducting dilution experiments and fitting mixed models. We also examined the relationship between nutrient availability and the differences in both phytoplankton community structure and size fractionated phytoplankton growth rates at two spatial scales (i.e. subtropical gyre and within-province spatial scale). Our results revealed high values for both phytoplankton growth and microzooplankton grazing rates. Phytoplankton growth (0.00-1.19 d-1) displayed higher variability among stations, biogeochemical provinces and size fractions than the microzooplankton grazing rate (0.32-0.74 d-1). Differences in phytoplankton community structure were associated with dissolved inorganic nitrogen (0.72-5.85 μM; R2 = 0.19) and squared Brunt-Väisälä frequency (R2 = 0.21) at the whole gyre scale. Conversely, the differences in phytoplankton growth rate showed a weak relationship with those properties (R2 ⩽ 0.05) at that scale, but a stronger relationship at the within province scale (R2 ⩾ 0.07). These results support the idea that phytoplankton grow at high rates in oligotrophic subtropical gyres, this is likely due to the selection of phytoplankton groups with functional traits suited to exploit low nutrient availability. Thus, shedding new, multi-scale knowledge on the commonly misunderstood "ocean deserts".

  8. Effect of a high strength chemical industry wastewater on microbial community dynamics and mesophilic methane generation.

    Science.gov (United States)

    Venkatakrishnan, Harish; Tan, Youming; Majid, Maszenan Bin Abdul; Pathak, Santosh; Sendjaja, Antonius Yudi; Li, Dongzhe; Liu, Jerry Jian Lin; Zhou, Yan; Ng, Wun Jern

    2014-04-01

    A high strength chemical industry wastewater was assessed for its impact on anaerobic microbial community dynamics and consequently mesophilic methane generation. Cumulative methane production was 251 mL/g total chemical oxygen demand removed at standard temperature and pressure at the end of 30 days experimental period with a highest recorded methane percentage of 80.6% of total biogas volume. Volatile fatty acids (VFAs) analysis revealed that acetic acid was the major intermediate VFAs produced with propionic acid accumulating over the experimental period. Quantitative analysis of microbial communities in the test and control groups with quantitative real time polymerase chain reaction highlighted that in the test group, Eubacteria (96.3%) was dominant in comparison with methanogens (3.7%). The latter were dominated by Methanomicrobiales and Methanobacteriales while Methanosarcinaceae in test groups increased over the experimental period, reaching a maximum on day 30. Denaturing gradient gel electrophoresis profile was performed, targeting the 16S rRNA gene of Eubacteria and Archaea, with the DNA samples extracted at 3 different time points from the test groups. A phylogenetic tree was constructed for the sequences using the neighborhood joining method. The analysis revealed that the presence of organisms resembling Syntrophomonadaceae could have contributed to increased production of acetic and propionic acid intermediates while decrease of organisms resembling Pelotomaculum sp. could have most likely contributed to accumulation of propionic acid. This study suggested that the degradation of organic components within the high strength industrial wastewater is closely linked with the activity of certain niche microbial communities within eubacteria and methanogens.

  9. Functional diversity and dynamics of bacterial communities in a membrane bioreactor for the treatment of metal-working fluid wastewater.

    Science.gov (United States)

    Grijalbo, Lucía; Garbisu, Carlos; Martín, Iker; Etxebarria, Javier; Gutierrez-Mañero, F Javier; Lucas Garcia, Jose Antonio

    2015-12-01

    An extensive microbiological study has been carried out in a membrane bioreactor fed with activated sludge and metal-working fluids. Functional diversity and dynamics of bacterial communities were studied with different approaches. Functional diversity of culturable bacterial communities was studied with different Biolog™ plates. Structure and dynamics of bacterial communities were studied in culturable and in non-culturable fractions using a 16S rRNA analysis. Among the culturable bacteria, Alphaproteobacteria and Gammaproteobacteria were the predominant classes. However, changes in microbial community structure were detected over time. Culture-independent analysis showed that Betaproteobacteria was the most frequently detected class in the membrane bioreactor (MBR) community with Zoogloea and Acidovorax as dominant genera. Also, among non-culturable bacteria, a process of succession was observed. Longitudinal structural shifts observed were more marked for non-culturable than for culturable bacteria, pointing towards an important role in the MBR performance. Microbial community metabolic abilities assessed with Biolog™ Gram negative, Gram positive and anaerobic plates also showed differences over time for Shannon's diversity index, kinetics of average well colour development, and the intensely used substrates by bacterial community in each plate.

  10. A dynamic modelling approach for estimating critical loads of nitrogen based on plant community changes under a changing climate

    Energy Technology Data Exchange (ETDEWEB)

    Belyazid, Salim, E-mail: salim@belyazid.com [Belyazid Consulting and Communication, Stationsvaegen 13, SE-517 34 Bollebygd (Sweden); Kurz, Dani [EKG Geoscience, Maulbeerstrasse 14, CH-3011 Bern (Switzerland); Braun, Sabine [Institut fuer Angewandte Planzenbiologie, Sandgrubenstrasse 25, CH-4124 Schoenenbuch (Switzerland); Sverdrup, Harald [Department of Chemical Engineering, Lund University, PO Box 124, SE-221 00 Lund (Sweden); Rihm, Beat [Meteotest, Fabrikstrasse 14, CH-3012 Bern (Switzerland); Hettelingh, Jean-Paul [Coordination Centre for Effects, PO Box 303, NL-3720 AH Bilthoven (Netherlands)

    2011-03-15

    A dynamic model of forest ecosystems was used to investigate the effects of climate change, atmospheric deposition and harvest intensity on 48 forest sites in Sweden (n = 16) and Switzerland (n = 32). The model was used to investigate the feasibility of deriving critical loads for nitrogen (N) deposition based on changes in plant community composition. The simulations show that climate and atmospheric deposition have comparably important effects on N mobilization in the soil, as climate triggers the release of organically bound nitrogen stored in the soil during the elevated deposition period. Climate has the most important effect on plant community composition, underlining the fact that this cannot be ignored in future simulations of vegetation dynamics. Harvest intensity has comparatively little effect on the plant community in the long term, while it may be detrimental in the short term following cutting. This study shows: that critical loads of N deposition can be estimated using the plant community as an indicator; that future climatic changes must be taken into account; and that the definition of the reference deposition is critical for the outcome of this estimate. - Research highlights: > Plant community changes can be used to estimate critical loads of nitrogen. > Climate change is decisive for future changes of geochemistry and plant communities. > Climate change cannot be ignored in estimates of critical loads. > The model ForSAFE-Veg was successfully used to set critical loads of nitrogen. - Plant community composition can be used in dynamic modelling to estimate critical loads of nitrogen deposition, provided the appropriate reference deposition, future climate and target plant communities are defined.

  11. Linking Activity and Function to Ecosystem Dynamics in a Coastal Bacterioplankton Community

    Directory of Open Access Journals (Sweden)

    Scott Michael Gifford

    2014-04-01

    Full Text Available For bacterial communities containing hundreds to thousands of distinct populations, connecting functional processes and environmental dynamics at high taxonomic resolution has remained challenging. Here we use the expression of ribosomal proteins (%RP as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in a coastal ocean time series encompassing both seasonal variability and diel dynamics. %RP patterns grouped the taxa into seven activity clusters with distinct profiles in functional gene expression and correlations with environmental gradients. Clusters 1-3 had their highest potential activity in the winter and fall, and included some of the most active taxa, while Clusters 4-7 had their highest potential activity in the spring and summer. Cluster 1 taxa were characterized by gene expression for motility and complex carbohydrate degradation (dominated by Gammaproteobacteria and Bacteroidetes, and Cluster 2 taxa by transcription of genes for amino acid and aromatic compound metabolism and aerobic anoxygenic phototrophy (Roseobacter. Other activity clusters were enriched in transcripts for proteorhodopsin and methylotrophy (Cluster 4; SAR11 and methylotrophs, photosynthesis and attachment (Clusters 5 and 7; Synechococcus, picoeukaryotes, Verucomicrobia, and Planctomycetes, and sulfur oxidation (Cluster 7; Gammaproteobacteria. The seasonal patterns in activity were overlain, and sometimes obscured, by large differences in %RP over shorter day-night timescales. Seventy-eight taxa, many of them heterotrophs, had a higher %RP activity index during the day than night, indicating strong diel activity at this coastal site. Emerging from these taxonomically- and time-resolved estimates of in situ microbial activity are predictions of specific ecological groupings of microbial taxa in a dynamic coastal environment.

  12. The role of universities in innovation networks: the role of proximity on innovation dynamics in knowledge community precints

    NARCIS (Netherlands)

    Korotka, M.; Benneworth, Paul; Ratinho, Tiago

    2014-01-01

    This paper critically analyses the recent fad for using technopoles and as key economic growth drivers stimulating innovation dynamics in particular territories. Conceptualising technopoles as “knowledge community precincts” creating science-park style benefits, we characterise these benefits as cr

  13. Synchrony, compensatory dynamics, and the functional trait basis of phenological diversity in a tropical dry forest tree community

    DEFF Research Database (Denmark)

    Lasky, Jesse R.; Uriarte, Maria; Muscarella, Robert

    2016-01-01

    among species), while biotic interactions can favor synchrony or compensatory dynamics (negative covariance). We used wavelet analyses to examine phenology of community flower and seed production for 45 tree species across multiple temporal scales in a tropical dry forest in Puerto Rico with marked...

  14. Beyond Learner Autonomy: A Dynamic Systems View of the Informal Learning of English in Virtual Online Communities

    Science.gov (United States)

    Sockett, Geoffrey; Toffoli, Denyze

    2012-01-01

    This article discusses the informal learning of English by non-native speakers with particular reference to the role of virtual communities. The concept of informal learning is presented and related to current areas of interest in the literature such as incidental learning, and dynamic systems theory. Our research investigates how non-specialist…

  15. Reproducibility in density functional theory calculations of solids

    OpenAIRE

    2016-01-01

    This is the author accepted manuscript.The final version is available from the American Association for the Advancement of Science via http://dx.doi.org/10.1126/science.aad3000 The widespread popularity of density-functional theory has given rise to a vast range of dedicated codes to predict molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions on the reproducibility of such predictions. We report the results of a community-...

  16. Age-Structure and Dynamic of Dominant Population of Castanopsis carlesii Community in Dujiangyan City,Sichuan, China

    Institute of Scientific and Technical Information of China (English)

    CAI Xiao-hu; ZHONG Xiang-hao; WANG Jin-xi; HE Fei; LIU Xing-liang

    2005-01-01

    It analyses the Castanopsis carlesii, Camellia oleifera and Symplocos laurina populations' status and role in the Castanopsis carlesii community basing on the study on the dominant population size structure, survival curve and dynamic. It reveals the Castanopsis carlesi population acts as a main role in the community which maintains the stabilization and renovation of the community. The populations of Camellia oleifera and Symplocos laurina act as a secondary position. The development and succession dynamics of dominant populations is also discussed. The management method is preliminary drawn out which offers a theoretical basis for the evergreen broad-leaved forest restoration and reconstruction in the lower hilly of the west edge of the Sichuan basin.

  17. Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis.

    Science.gov (United States)

    Liu, An-Chi; Chou, Chu-Yang; Chen, Ling-Ling; Kuo, Chih-Horng

    2015-01-20

    Anaerobic digestion is a microbiological process of converting organic wastes into digestate and biogas in the absence of oxygen. In practice, disturbance to the system (e.g., organic shock loading) may cause imbalance of the microbial community and lead to digester failure. To examine the bacterial community dynamics after a disturbance, this study simulated an organic shock loading that doubled the chemical oxygen demand (COD) loading using a 4.5L swine wastewater anaerobic completely stirred tank reactor (CSTR). Before the shock (loading rate=0.65gCOD/L/day), biogas production rate was about 1-2L/L/day. After the shock, three periods representing increased biogas production rates were observed during days 1-7 (∼4.0L/L/day), 13 (3.3L/L/day), and 21-23 (∼6.1L/L/day). For culture-independent assessments of the bacterial community composition, the 454 pyrosequencing results indicated that the community contained >2500 operational taxonomic units (OTUs) and was dominated by three phyla: Bacteroidetes, Firmicutes, and Proteobacteria. The shock induced dynamic changes in the community composition, which was re-stabilized after approximately threefold hydraulic retention time (HRT). Intriguingly, upon restabilization, the community composition became similar to that observed before the shock, rather than reaching a new equilibrium.

  18. Effective Form of Reproducing the Total Financial Potential of Ukraine

    Directory of Open Access Journals (Sweden)

    Portna Oksana V.

    2015-03-01

    Full Text Available Development of scientific principles of reproducing the total financial potential of the country and its effective form is an urgent problem both in theoretical and practical aspects of the study, the solution of which is intended to ensure the active mobilization and effective use of the total financial potential of Ukraine, and as a result — its expanded reproduction as well, which would contribute to realization of the internal capacities for stabilization of the national economy. The purpose of the article is disclosing the essence of the effective form of reproducing the total financial potential of the country, analyzing the results of reproducing the total financial potential of Ukraine. It has been proved that the basis for the effective form of reproducing the total financial potential of the country is the volume and flow of resources, which are associated with the «real» economy, affect the dynamics of GDP and define it, i.e. resource and process forms of reproducing the total financial potential of Ukraine (which precede the effective one. The analysis of reproducing the total financial potential of Ukraine has shown that in the analyzed period there was an increase in the financial possibilities of the country, but steady dynamics of reduction of the total financial potential was observed. If we consider the amount of resources involved in production, creating a net value added and GDP, it occurs on a restricted basis. Growth of the total financial potential of Ukraine is connected only with extensive quantitative factors rather than intensive qualitative changes.

  19. The role of transient dynamics in biological pest control: insights from a host-parasitoid community.

    Science.gov (United States)

    Kidd, David; Amarasekare, Priyanga

    2012-01-01

    1. Identifying natural enemies that can maintain pests at low abundances is a priority in biological control. Here, we show that experiments combined with models generate new insights into identifying effective control agents prior to their release in the field. Using a host-parasitoid community (the harlequin bug and its egg parasitoids) as a model system, we report three key findings. 2. The interplay between the host's self-limitation and the parasitoids' saturating functional response causes the long-term (steady-state) outcomes for pest suppression to differ from those of short-term (transient) dynamics. When the bug's self-limitation is moderately strong, the parasitoid with the higher attack rate and conversion efficiency (Ooencyrtus) achieves greater host suppression in the long term, but its longer handling time causes long periods of transient dynamics during which the bug can reach high abundances; when the bug's self-limitation is weak, host fluctuations amplify over time and Ooencyrtus fails at host suppression altogether. In contrast, the parasitoid with the lower attack rate and conversion efficiency but the shorter handling time (Trissolcus) induces only weak transient fluctuations of short duration and can maintain the host at low abundances regardless of the strength of the bug's self-limitation. 3. Release of multiple enemy species can compromise host suppression if an enemy that induces stronger transient fluctuations excludes one that induces weaker fluctuations. For instance, Ooencyrtus excludes Trissolcus despite having a longer handling time because of its higher conversion efficiency. The model correctly predicts the time to exclusion observed in experiments, suggesting that it captures the key biological features of the host-parasitoid interaction. 4. Intraspecific interference reduces long-term pest suppression but improves short-term pest control by reducing the magnitude and duration of transient fluctuations. 5. These results highlight

  20. Theory of reproducing kernels and applications

    CERN Document Server

    Saitoh, Saburou

    2016-01-01

    This book provides a large extension of the general theory of reproducing kernels published by N. Aronszajn in 1950, with many concrete applications. In Chapter 1, many concrete reproducing kernels are first introduced with detailed information. Chapter 2 presents a general and global theory of reproducing kernels with basic applications in a self-contained way. Many fundamental operations among reproducing kernel Hilbert spaces are dealt with. Chapter 2 is the heart of this book. Chapter 3 is devoted to the Tikhonov regularization using the theory of reproducing kernels with applications to numerical and practical solutions of bounded linear operator equations. In Chapter 4, the numerical real inversion formulas of the Laplace transform are presented by applying the Tikhonov regularization, where the reproducing kernels play a key role in the results. Chapter 5 deals with ordinary differential equations; Chapter 6 includes many concrete results for various fundamental partial differential equations. In Chapt...

  1. Filters, reproducing kernel, and adaptive meshfree method

    Science.gov (United States)

    You, Y.; Chen, J.-S.; Lu, H.

    Reproducing kernel, with its intrinsic feature of moving averaging, can be utilized as a low-pass filter with scale decomposition capability. The discrete convolution of two nth order reproducing kernels with arbitrary support size in each kernel results in a filtered reproducing kernel function that has the same reproducing order. This property is utilized to separate the numerical solution into an unfiltered lower order portion and a filtered higher order portion. As such, the corresponding high-pass filter of this reproducing kernel filter can be used to identify the locations of high gradient, and consequently serves as an operator for error indication in meshfree analysis. In conjunction with the naturally conforming property of the reproducing kernel approximation, a meshfree adaptivity method is also proposed.

  2. Dynamics in cyanobacterial communities from a relatively stable environment in an urbanised area (ambient springs in Central Poland).

    Science.gov (United States)

    Nowicka-Krawczyk, Paulina; Żelazna-Wieczorek, Joanna

    2017-02-01

    Ambient springs are often cited as an example of an ecosystem with stable environmental conditions. A static biotope fosters the development of constant communities with a stable qualitative and relatively stable quantitative structure. Two years of studying cyanobacteria in different microhabitats of the rheocrenic and limnocrenic ambient springs located in urban areas showed that there is a high degree of cyanobacterial diversity and spatial and seasonal dynamics in communities. Spatial heterogeneity in relation to the type of spring and the type of microhabitat is reflected not only by a change in the quantitative structure (the number of species and their biomass), but also by a change in the composition of species. Seasonal changes depended on the type of spring and the type of microhabitat, where weather conditions influenced the communities by different degrees. Cyanobacterial communities of limnocrenes were more diverse in terms of composition and biomass, but they revealed a low seasonal dynamic in contrast to the communities of rheocrenes. The classification of springs based on their environmental conditions revealed that some springs were similar. The resemblance stemmed from the origin of human impact, which was reflected to a high degree in changes in the natural hydrochemical conditions of the springs. For the purpose of understanding which environmental factors had the greatest influence on cyanobacterial communities, a BIO-ENV procedure was performed. The procedure revealed that of most importance was a group of ions not related to the nature of the spring environment - NH4(+), NO2(-), NO3(-), and PO4(3-). The presence of these ions in groundwater was a result of direct and indirect human activity in the area of aquifers. The dynamics in communities in the studied springs were accelerated by human impact and weather conditions.

  3. Examination of reproducibility in microbiological degredation experiments

    DEFF Research Database (Denmark)

    Sommer, Helle Mølgaard; Spliid, Henrik; Holst, Helle

    1998-01-01

    Experimental data indicate that certain microbiological degradation experiments have a limited reproducibility. Nine identical batch experiments were carried out on 3 different days to examine reproducibility. A pure culture, isolated from soil, grew with toluene as the only carbon and energy sou....... The limited reproducibility may be caused by variability in the preculture, or more precisely, variations in the physiological state of the bacteria in the precultures just before used as inoculum....

  4. Using prediction markets to estimate the reproducibility of scientific research.

    Science.gov (United States)

    Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus

    2015-12-15

    Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants' individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a "statistically significant" finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.

  5. Dynamics of the microfauna community in a full-scale municipal wastewater treatment plant experiencing sludge bulking.

    Science.gov (United States)

    Hu, Bo; Qi, Rong; An, Wei; Xu, Muqi; Zhang, Yu; Bai, Xue; Bao, Haipeng; Wen, Yang; Gu, Jian; Yang, Min

    2013-11-01

    We investigated the dynamics of the microfauna community in activated sludge, with special reference to sludge bulking, in two parallel municipal wastewater treatment systems in Beijing, China over a period of 14 months. Annual cyclic changes in microfauna community structures occurred in both systems. RELATE analysis based on Spearman's Rank correlation indicated that microfauna community structures were highly correlated with the sludge volume index (SVI) (pVorticella striata increased significantly with an increase in SVI (p<0.001) and decrease in water temperature (p<0.001), suggesting that sludge bulking may have created favorable conditions for the two species, even under unfavorable temperature conditions. Sludge de-flocculation primarily due to the excessive growth of Microthrix parvicella-like filaments could be an important driving force for the microfauna community changes. The release of flocculated non-filamentous bacteria may represent a suitable food source for these species. The two species may be considered as potential bioindicators for sludge bulking.

  6. Seasonal dynamics of crustacean zooplankton community structure in Erhai Lake, a plateau lake, with reference to phytoplankton and environmental factors

    Science.gov (United States)

    Yang, Wei; Deng, Daogui; Zhang, Sai; Hu, Cuilin

    2014-09-01

    The seasonal dynamics of a crustacean zooplankton community in Erhai Lake was investigated from May 2010 to April 2011. In total, 11 species were recorded, including six (6 genera) cladoceran and five (5 genera) copepod species. The crustacean zooplankton densities ranged from 24.3 to 155.4 ind./L. In winter and spring, the large-bodied cladoceran Daphnia galeata dominated the crustacean plankton community. In summer and autumn, when the colonial or filamentous algae dominated the phytoplankton communities, the small-bodied species (e.g. B osmina fatalis, Ceriodaphnia quadrangular, and Mesocyclops leuckarti) replaced the large-bodied ones. One-way ANOVA and redundancy analysis revealed that community structure was dependent upon total nitrogen, total phosphorus, water temperature, transparency, and the biomass of small algae. The variation in both phytoplankton structure and environmental variables were important factors in the seasonal succession of crustacean zooplankton structure in Erhai Lake.

  7. The Rise and Fall of a Central Contributor: Dynamics of Social Organization and Performance in the Gentoo Community

    CERN Document Server

    Zanetti, Marcelo Serrano; Tessone, Claudio Juan; Schweitzer, Frank

    2013-01-01

    Social organization and division of labor crucially influence the performance of collaborative software engineering efforts. In this paper, we provide a quantitative analysis of the relation between social organization and performance in Gentoo, an Open Source community developing a Linux distribution. We study the structure and dynamics of collaborations as recorded in the project's bug tracking system over a period of ten years. We identify a period of increasing centralization after which most interactions in the community were mediated by a single central contributor. In this period of maximum centralization, the central contributor unexpectedly left the project, thus posing a significant challenge for the community. We quantify how the rise, the activity as well as the subsequent sudden dropout of this central contributor affected both the social organization and the bug handling performance of the Gentoo community. We analyze social organization from the perspective of network theory and augment our qua...

  8. Bacterial community dynamics over successional stages of Australian biological soil crusts

    Science.gov (United States)

    Chilton, Angela; Woodhouse, Jason; Neilan, Brett

    2015-04-01

    A key aspect for successful ecological rehabilitation is understanding the naturally occurring ecosystem and landscape function which is to be restored. This allows for recovery indicators to be identified and criteria to be developed to assess progress and outcomes. In arid rangelands, environmental stresses result in characteristically heterogeneous landscapes where biological soil crusts (BSCs) cover large expanses of inter-plant areas. Here, BSCs perform crucial roles in nutrient cycling and re-distribution, affect hydrological patterns and stabilise the soil surface. They also serve as a large reservoir of microbial and avascular plant biodiversity. The recognition of these important roles has resulted in increased global arid rehabilitation efforts employing BSCs. Within Australia, research has focused on the macro components of BSCs including lichens and mosses, however, there have been insufficient studies examining the BSC bacterial communities and their dynamics over different successional stages. This project surveyed the bacterial community of crust-free soil and three successional stages of undisturbed BSCs from New South Wales (NSW), Australia, in order to provide reference standards of naturally occurring Australian BSCs. Visual assessments were conducted and BSCs were categorised as Early, Mid or Late stage depending on colour, thickness, topography and presence of lichens and mosses. The crust-free soil and different stages were sampled within three 50 m2 plots of the same edaphic conditions near the town of Cobar, NSW. High throughput sequencing using the Illumina MiSeq platform was performed targeting the V2 region of the 16S rRNA gene. Preliminary analysis has revealed a clear distinction between the crust-free and crusted soil while Canonical Analysis of Principal Co-ordinates (CAP) suggests the presence of two distinct BSC microbial communities despite three stages being sampled. Across all sample types, the dominant phyla were Actinobacteria

  9. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill.

    Science.gov (United States)

    Bernhard, Anne E; Sheffer, Roberta; Giblin, Anne E; Marton, John M; Roberts, Brian J

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain.

  10. Random walk in genome space: A key ingredient of intermittent dynamics of community assembly on evolutionary time scales

    KAUST Repository

    Murase, Yohsuke

    2010-06-01

    Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species, while migrants have no correlation with the resident species. It is found that the dynamics of community assembly with mutations are quite different from the case with migrations. In contrast to mutation models, which show intermittent dynamics of quasi-steady states interrupted by sudden reorganizations of the community, migration models show smooth and gradual renewal of the community. As a consequence, instead of the 1/f diversity fluctuations found for the mutation models, 1/f2, random-walk like fluctuations are observed for the migration models. In addition, a characteristic species-lifetime distribution is found: a power law that is cut off by a "skewed" distribution in the long-lifetime regime. The latter has a longer tail than a simple exponential function, which indicates an age-dependent species-mortality function. Since this characteristic profile has been observed, both in fossil data and in several other mathematical models, we conclude that it is a universal feature of macroevolution. © 2010 Elsevier Ltd.

  11. Time lags and the balance of positive and negative interactions in driving grassland community dynamics.

    Science.gov (United States)

    Farrer, Emily C; Goldberg, Deborah E; King, Aaron A

    2010-02-01

    Both facilitative and competitive interactions occur simultaneously among plants, and the net balance between them can vary over time. Despite this, recent model-fitting studies have found that negative interactions predominate. This suggests that more complex models may be necessary to uncover facilitation. Here we fitted models including seasonality, interannual variation, and time lags to survey data to test for patterns in positive and negative interactions among plants in a Michigan dry sand prairie. We hypothesized that interactions would be generally facilitative in this dry environment. Results indicate that most immediate (direct) interactions among dominant species are actually competitive, although interactions were more facilitative over the drier summer season. Interestingly, lagged density dependence was strong for all species in both seasons; it was positive for conspecific interactions and both positive and negative for heterospecific interactions. Observed lagged density dependence is likely due to effects from litter and/or past storage in rhizomes. Conspecific immediate and lagged interactions tended to be stronger than heterospecific interactions, suggesting that population dynamics in this community are driven mostly by conspecifics. Overall, the presence of strong lagged density dependence in this system suggests that it may be more widespread in plants than previously thought.

  12. Bacterial community dynamics in a rotating biological contactor treating 2-fluorophenol-containing wastewater.

    Science.gov (United States)

    Duque, Anouk F; Bessa, Vânia S; Castro, Paula M L

    2014-01-01

    One of the main factors affecting the performance of rotating biological contactors (RBC) is the biofilm characteristics. Therefore, a deep understanding of the microbial population dynamics and structure of the biofilm is mandatory if optimization of organic matter and nutrients removal is targeted. This study focused on the effects of organic shock loads of 2-fluorophenol (2-FP) on the microbial diversity present in an RBC biofilm. The RBC was seeded with activated sludge from a conventional wastewater treatment plant and was operated during 496 days. During the first 126 days, the RBC was subjected to intermittent 2-FP shocks of 25 mg l(-1) and no degradation occurred. Therefore, the reactor was subsequently augmented with a 2-FP-degrading strain (FP1). Afterwards, the RBC had a stable performance when subjected to 2-FP shocks up to 50 mg l(-1) and to a starvation period, as indicated by removal of the compound. Denaturing gradient gel electrophoresis (DGGE) revealed large shifts in microbial communities present in the first and fifth stages, although no clear relation between the sample collection time and spatial factor was found. Phylogenetic affiliation of some predominant members was assessed by direct sequencing of correspondent DGGE bands. Affiliations to α-, β- and δ-Proteobacteria were found. Several bacterial strains isolated from the reactor showed capacity for 2-FP degradation. Strain FP1 was successfully recovered from the biofilm by plating and by DGGE, reinforcing that bioaugmentation was successfully achieved.

  13. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

    Science.gov (United States)

    Laureys, David; De Vuyst, Luc

    2014-04-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product.

  14. Transmission dynamics of Simulium damnosum in rural communities of Akwa Ibom State, Nigeria

    Directory of Open Access Journals (Sweden)

    K.N. Opara

    2008-08-01

    Full Text Available Background & objectives: Onchocerciasis is endemic in some parts of Akwa Ibom State, Nigeria. This study describes the entomological parameters of transmission in three rural communities of Akwa Ibom State, prior to ivermectin intervention in 2004. Methods: Blackflies were caught using human bait and 90% of the flies were dissected for parity. All parous flies were further dissected for the presence of filaria larvae. Monthly and annual biting rate, and transmission potential were calculated using standard methods.Results: A total of 4296 adult Simulium damnosum were caught on human bait, 4119 were dissected of which 208 (5.1% were infected with Onchocerca volvulus larvae. Transmission parameters varied significantly (p < 0.05 in the three villages. Annual biting rates, ranged from 9490 to 11,218 bites per person per year. The annual transmission potential ranged from 131 to 189 infective larvae per person per year, monthly biting rate and monthly transmission potential varied significantly (p < 0.05 in the three villages. Transmission was highly seasonal occurring during the peak of rainy season from August to October. There was no transmission during the dry periods — November to March, and the early rainy periods — April to May. The diurnal biting activity of the fly exhibited a bimodal pattern with a morning peak (0900–1000 hrs and a more marked evening peak (1600–1700 hrs. Interpretation & conclusion: The results indicate that there is a temporal and spatial variation in the transmission dynamics of S. damnosum in the study area.

  15. Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

    Science.gov (United States)

    Laureys, David

    2014-01-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  16. Reproducibility principles, problems, practices, and prospects

    CERN Document Server

    Maasen, Sabine

    2016-01-01

    Featuring peer-reviewed contributions from noted experts in their fields of research, Reproducibility: Principles, Problems, Practices, and Prospects presents state-of-the-art approaches to reproducibility, the gold standard sound science, from multi- and interdisciplinary perspectives. Including comprehensive coverage for implementing and reflecting the norm of reproducibility in various pertinent fields of research, the book focuses on how the reproducibility of results is applied, how it may be limited, and how such limitations can be understood or even controlled in the natural sciences, computational sciences, life sciences, social sciences, and studies of science and technology. The book presents many chapters devoted to a variety of methods and techniques, as well as their epistemic and ontological underpinnings, which have been developed to safeguard reproducible research and curtail deficits and failures. The book also investigates the political, historical, and social practices that underlie repro...

  17. Explorations in statistics: statistical facets of reproducibility.

    Science.gov (United States)

    Curran-Everett, Douglas

    2016-06-01

    Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This eleventh installment of Explorations in Statistics explores statistical facets of reproducibility. If we obtain an experimental result that is scientifically meaningful and statistically unusual, we would like to know that our result reflects a general biological phenomenon that another researcher could reproduce if (s)he repeated our experiment. But more often than not, we may learn this researcher cannot replicate our result. The National Institutes of Health and the Federation of American Societies for Experimental Biology have created training modules and outlined strategies to help improve the reproducibility of research. These particular approaches are necessary, but they are not sufficient. The principles of hypothesis testing and estimation are inherent to the notion of reproducibility in science. If we want to improve the reproducibility of our research, then we need to rethink how we apply fundamental concepts of statistics to our science.

  18. Emotional insecurity about the community: A dynamic, within-person mediator of child adjustment in contexts of political violence.

    Science.gov (United States)

    Cummings, E Mark; Merrilees, Christine; Taylor, Laura K; Goeke-Morey, Marcie; Shirlow, Peter

    2017-02-01

    Over 1 billion children worldwide are exposed to political violence and armed conflict. The current conclusions are qualified by limited longitudinal research testing sophisticated process-oriented explanatory models for child adjustment outcomes. In this study, consistent with a developmental psychopathology perspective emphasizing the value of process-oriented longitudinal study of child adjustment in developmental and social-ecological contexts, we tested emotional insecurity about the community as a dynamic, within-person mediating process for relations between sectarian community violence and child adjustment. Specifically, this study explored children's emotional insecurity at a person-oriented level of analysis assessed over 5 consecutive years, with child gender examined as a moderator of indirect effects between sectarian community violence and child adjustment. In the context of a five-wave longitudinal research design, participants included 928 mother-child dyads in Belfast (453 boys, 475 girls) drawn from socially deprived, ethnically homogenous areas that had experienced political violence. Youth ranged in age from 10 to 20 years and were 13.24 (SD = 1.83) years old on average at the initial time point. Greater insecurity about the community measured over multiple time points mediated relations between sectarian community violence and youth's total adjustment problems. The pathway from sectarian community violence to emotional insecurity about the community was moderated by child gender, with relations to emotional insecurity about the community stronger for girls than for boys. The results suggest that ameliorating children's insecurity about community in contexts of political violence is an important goal toward improving adolescents' well-being and adjustment. These results are discussed in terms of their translational research implications, consistent with a developmental psychopathology model for the interface between basic and intervention

  19. Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics.

    Science.gov (United States)

    Drigo, Barbara; Kowalchuk, George A; Knapp, Brigitte A; Pijl, Agata S; Boschker, Henricus T S; van Veen, Johannes A

    2013-02-01

    Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and diversity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by (13) C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the (13) C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.

  20. Doing "Business as Usual": Dynamics of Voice in Community Organizing Talk

    Science.gov (United States)

    O'Connor, Kevin; Hanny, Courtney; Lewis, Cameron

    2011-01-01

    This article examines discourse in a community change project committed to undoing "business as usual"--attempts to "fix" problems within the community without involvement of residents in the process. We show how, despite commitments to recognizing community "voice," participants' orientation to powerful "centering institutions" (Jan Blommaert…

  1. Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

    Science.gov (United States)

    Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

    2015-08-01

    Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

  2. Biomass dynamics of Quercus aliena var.acutesrata Community on Mountain Xiaolong in Gansu Province,China

    Institute of Scientific and Technical Information of China (English)

    Suo Anning; Ju Tianzhen; Zhang Junhua; Ge Jianping

    2006-01-01

    The dynamics of tree layer biomass was studied by combining 35 sample plots of field census with biomass model estimation in a natural Quercus aliena var.acutesrata community on Mountain Xiaolong in Gansu Province,China.The tree layer biomass of Quercus aliena var.acutesrata community was 183 660 kg/ha,in which the slow growth group accounted for 64.89% of the total biomass.The fast-medium growth group accounted for 33.40% and the coniferous group accounted for 1.38%.The organs biomass was found to be in the following order:trunk>root>branch>leaf.The total biomass accumulated with the development of the community.The total biomass and the biomass of the organs were highest in the mature community and became stable as the community developed.The relative growth rate of organs was in the following order:trunk>branch>root>leaf.The biomass ratio of the slow growth group trees tended to increase and the fast-medium group trees tended to decrease as the community developed,which was reveresed in the decline development stage.The biomass of the coniferous group was very small throughout the development process.

  3. Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center

    Science.gov (United States)

    Prussin, Aaron J.; Vikram, Amit; Bibby, Kyle J.; Marr, Linsey C.

    2016-01-01

    Children’s daycare centers appear to be hubs of respiratory infectious disease transmission, yet there is only limited information about the airborne microbial communities that are present in daycare centers. We have investigated the microbial community of the air in a daycare center, including seasonal dynamics in the bacterial community and the presence of specific viral pathogens. We collected filters from the heating, ventilation, and air conditioning (HVAC) system of a daycare center every two weeks over the course of a year. Amplifying and sequencing the 16S rRNA gene revealed that the air was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes that are commonly associated with the human skin flora. Clear seasonal differences in the microbial community were not evident; however, the community structure differed when the daycare center was closed and unoccupied for a 13-day period. These results suggest that human occupancy, rather than the environment, is the major driver in shaping the microbial community structure in the air of the daycare center. Using PCR for targeted viruses, we detected a seasonal pattern in the presence of respiratory syncytial virus that included the period of typical occurrence of the disease related to the virus; however, we did not detect the presence of adenovirus or rotavirus at any time. PMID:26942410

  4. The Rise and Fall of a Central Contributor: Dynamics of Social Organization and Performance in the Gentoo Community

    OpenAIRE

    Zanetti, Marcelo Serrano; Scholtes, Ingo; Tessone, Claudio Juan; Schweitzer, Frank

    2013-01-01

    Social organization and division of labor crucially influence the performance of collaborative software engineering efforts. In this paper, we provide a quantitative analysis of the relation between social organization and performance in Gentoo, an Open Source community developing a Linux distribution. We study the structure and dynamics of collaborations as recorded in the project's bug tracking system over a period of ten years. We identify a period of increasing centralization after which ...

  5. Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms

    DEFF Research Database (Denmark)

    Klausen, M.; Gjermansen, Morten; Kreft, J.-U.;

    2006-01-01

    Surface-associated microbial communities in many cases display dynamic developmental patterns. Model biofilms formed by Pseudomonas aeruginosa and Pseudomonas putida in laboratory flow-chamber setups represent examples of such behaviour. Dependent on the experimental conditions the bacteria...... organisms do not possess comprehensive genetic programs for biofilm development. Instead the bacteria appear to have evolved a number of different mechanisms to optimize surface colonization, of which they express a subset in response to the prevailing environmental conditions. These mechanisms include...

  6. The Economics of Reproducibility in Preclinical Research.

    Directory of Open Access Journals (Sweden)

    Leonard P Freedman

    2015-06-01

    Full Text Available Low reproducibility rates within life science research undermine cumulative knowledge production and contribute to both delays and costs of therapeutic drug development. An analysis of past studies indicates that the cumulative (total prevalence of irreproducible preclinical research exceeds 50%, resulting in approximately US$28,000,000,000 (US$28B/year spent on preclinical research that is not reproducible-in the United States alone. We outline a framework for solutions and a plan for long-term improvements in reproducibility rates that will help to accelerate the discovery of life-saving therapies and cures.

  7. Comparing Metabolic Functionalities, Community Structures, and Dynamics of Herbicide-Degrading Communities Cultivated with Different Substrate Concentrations

    DEFF Research Database (Denmark)

    Gözdereliler, Erkin; Boon, Nico; Aamand, Jens

    2013-01-01

    Two 4-chloro-2-methylphenoxyacetic acid (MCPA)-degrading enrichment cultures selected from an aquifer on low (0.1 mg liter−1) or high (25 mg liter−1) MCPA concentrations were compared in terms of metabolic activity, community composition, population growth, and single cell physiology. Different....... The enrichments selected on low concentrations mineralized MCPA with shorter lag phases than those selected on high concentrations. Flow cytometry measurements revealed that mineralization led to cell growth. The presence of low-nucleic acid-content bacteria (LNA bacteria) was correlated with mineralization...

  8. Mosquito community composition in dynamic landscapes from the Atlantic Forest biome (Diptera, Culicidae

    Directory of Open Access Journals (Sweden)

    Mário Luís Pessôa Guedes

    2014-03-01

    Full Text Available Mosquito community composition in dynamic landscapes from the Atlantic Forest biome (Diptera, Culicidae. Considering that some species of Culicidae are vectors of pathogens, both the knowledge of the diversity of the mosquito fauna and how some environment factors influence in it, are important subjects. In order to address the composition of Culicidae species in a forest reserve in southern Atlantic Forest, we compared biotic and abiotic environmental determinants and how they were associated with the occurrence of species between sunset and sunrise. The level of conservation of the area was also considered. The investigation was carried out at Reserva Natural do Morro da Mina, in Antonina, state of Paraná, Brazil. We performed sixteen mosquito collections employing Shannon traps at three-hour intervals, from July 2008 to June 2009. The characterization of the area was determined using ecological indices of diversity, evenness, dominance and similarity. We compared the frequency of specimens with abiotic variables, i.e., temperature, relative humidity and pluviosity. Seven thousand four hundred ten mosquito females were captured. They belong to 48 species of 12 genera. The most abundant genera were Anopheles, Culex, Coquillettidia, Aedes and Runchomyia. Among the species, the most abundant was Anopheles cruzii, the primary vector of Plasmodium spp. in the Atlantic Forest. Results of the analyses showed that the abiotic variables we tested did not influence the occurrence of species, although certain values suggested that there was an optimum range for the occurrence of culicid species. It was possible to detect the presence of species of Culicidae with different epidemiologic profiles and habitat preference.

  9. Structure and dynamics of the phytoplankton community within a maturation pond in a semiarid region

    Directory of Open Access Journals (Sweden)

    E. A. Pastich

    Full Text Available Abstract In northeastern Brazil, stabilization ponds are very suitable for wastewater treatment because of the relative great land availability and environmental conditions (e.g., high temperature favorable for microorganism optimal development. However, blooms of potentially toxic cyanobacteria may affect the use of these treatment ponds due to resulting effluent poor quality. The objective of this study was to evaluate the dynamics of phytoplankton communities and the occurrence of cyanobacteria in a maturation pond located immediately after a series of two ponds. Temperature, dissolved oxygen, pH, BOD, N, and P were measured during a period of four months when samples were collected from the surface and the bottom of 7 sampling points distributed inside the pond. The phytoplankton of collected samples was also identified and classified using a conventional optical microscopy. Analysis of variance and Tukey test were used to evaluate the results. The three phytoplankton divisions found (Cyanophyta, Chlorophyta, and Euglenophyta did not change considerably through surface and bottom. However, they changed greatly over the sampled months; great dominance of Cyanophyta was found at April and October, while Chlorophyta dominated the lagoon in September. Low superficial organic loads (between 78 and 109 kg BOD.ha–1.d–1 and N:P ≤ 10 were the determinant factors that favored the predominance of Cyanophyta. The presence of two potentially toxic species of Cyanophyta, Oscillatoria sp. and Microcystis aeruginosa, indicates that caution is required when considering the final destination of treated effluent and suggests a need to assess the risks and benefits associated with the use of the treatment technology.

  10. Permafrost dynamics structure species compositions of oribatid mite (Acari: Oribatida communities in sub-Arctic palsa mires

    Directory of Open Access Journals (Sweden)

    Inkeri Markkula

    2014-10-01

    Full Text Available Palsa mires are sub-Arctic peatland complexes, vulnerable ecosystems with patches of permafrost. Permafrost thawing in palsa mires occurs throughout Fennoscandia, probably due to local climatic warming. In palsa mires, permafrost thaw alters hydrological conditions, vegetation structure and microhabitat composition with unknown consequences for invertebrate fauna. This study's objectives were to examine the role of microhabitat heterogeneity and the effects of permafrost dynamics and thaw on oribatid mite communities in palsa mires. Oribatid mites were sampled in two palsa mires in Finland and Norway. Three different types of microhabitats were examined: graminoid-dominated wet sites, herb-dominated small hummocks and evergreen shrub-dominated permafrost-underlain palsa hummocks. The results indicate that permafrost dynamics are an important factor structuring oribatid mite communities in palsa mires. The community composition of oribatid mites differed remarkably among microhabitats. Six species were significantly more abundant in permafrost-underlain microhabitats in relation to non-permafrost microhabitats. None of the species identified occurred exclusively in permafrost-underlain microhabitats. Findings suggest that permafrost thaw may not have an impact on species diversity but may alter community composition of oribatid mites in palsa mire ecosystems.

  11. The Effect of Initial Inoculum Source on the Microbial Community Structure and Dynamics in Laboratory-Scale Sequencing Batch Reactors

    KAUST Repository

    Hernandez, Susana

    2011-07-01

    Understanding the factors that shapes the microbial community assembly in activated sludge wastewater treatment processes provide a conceptual foundation for improving process performance. The aim of this study was to compare two major theories (deterministic theory and neutral theory) regarding the assembly of microorganisms in activated sludge: Six lab-scale activated sludge sequencing batch reactors were inoculated with activated sludge collected from three different sources (domestic, industrial, and sugar industry WWTP). Additionally, two reactors were seeded with equal proportion of sludge from the three WWTPs. Duplicate reactors were used for each sludge source (i.e. domestic, industrial, sugar and mix). Reactors were operated in parallel for 11 weeks under identical conditions. Bacterial diversity and community structure in the eight SBRs were assessed by 16S rRNA gene pyrosequencing. The 16S rRNA gene sequences were analyzed using taxonomic and clustering analysis and by measuring diversity indices (Shannon-weaver and Chao1 indices). Cluster analysis revealed that the microbial community structure was dynamic and that replicate reactors evolved differently. Also the microbial community structure in the SBRs seeded with a different sludge did not converge after 11 weeks of operation under identical conditions. These results suggest that history and distribution of taxa in the source inoculum were stronger regulating factors in shaping bacterial community structure than environmental factors. This supports the neutral theory which states that the assembly of the local microbial community from the metacommunity is random and is regulated by the size and diversity of the metacommunity. Furthermore, sludge performance, measured by COD and ammonia removal, confirmed that broad-scale functions (e.g. COD removal) are not influenced by dynamics in the microbial composition, while specific functions (e.g. nitrification) are more susceptible to these changes.

  12. Reproducibility Experiment of OSL and TL Dosimeter

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>Reproducibility is an important property of personal dosimeter. It not only can indicate the stability of dosimeter, appraise the precision and accuracy of measured value, but also can evaluate the

  13. Reproducible statistical analysis with multiple languages

    DEFF Research Database (Denmark)

    Lenth, Russell; Højsgaard, Søren

    2011-01-01

    This paper describes the system for making reproducible statistical analyses. differs from other systems for reproducible analysis in several ways. The two main differences are: (1) Several statistics programs can be in used in the same document. (2) Documents can be prepared using OpenOffice or ......This paper describes the system for making reproducible statistical analyses. differs from other systems for reproducible analysis in several ways. The two main differences are: (1) Several statistics programs can be in used in the same document. (2) Documents can be prepared using Open......Office or \\LaTeX. The main part of this paper is an example showing how to use and together in an OpenOffice text document. The paper also contains some practical considerations on the use of literate programming in statistics....

  14. Reproducible research in vadose zone sciences

    Science.gov (United States)

    A significant portion of present-day soil and Earth science research is computational, involving complex data analysis pipelines, advanced mathematical and statistical models, and sophisticated computer codes. Opportunities for scientific progress are greatly diminished if reproducing and building o...

  15. Reproducible Research in the Geosciences at Scale: Achievable Goal or Elusive Dream?

    Science.gov (United States)

    Wyborn, L. A.; Evans, B. J. K.

    2016-12-01

    Reproducibility is a fundamental tenant of the scientific method: it implies that any researcher, or a third party working independently, can duplicate any experiment or investigation and produce the same results. Historically computationally based research involved an individual using their own data and processing it in their own private area, often using software they wrote or inherited from close collaborators. Today, a researcher is likely to be part of a large team that will use a subset of data from an external repository and then process the data on a public or private cloud or on a large centralised supercomputer, using a mixture of their own code, third party software and libraries, or global community codes. In 'Big Geoscience' research it is common for data inputs to be extracts from externally managed dynamic data collections, where new data is being regularly appended, or existing data is revised when errors are detected and/or as processing methods are improved. New workflows increasingly use services to access data dynamically to create subsets on-the-fly from distributed sources, each of which can have a complex history. At major computational facilities, underlying systems, libraries, software and services are being constantly tuned and optimised, or as new or replacement infrastructure being installed. Likewise code used from a community repository is continually being refined, re-packaged and ported to the target platform. To achieve reproducibility, today's researcher increasingly needs to track their workflow, including querying information on the current or historical state of facilities used. Versioning methods are standard practice for software repositories or packages, but it is not common for either data repositories or data services to provide information about their state, or for systems to provide query-able access to changes in the underlying software. While a researcher can achieve transparency and describe steps in their workflow so

  16. Reproducibility of AMPLICOR enterovirus PCR test results.

    OpenAIRE

    1997-01-01

    The reproducibility of AMPLICOR enterovirus PCR test results was determined with clinical samples of cerebrospinal fluid, serum, urine, and throat and rectal swabs. Among 608 samples from which duplicate aliquots were run simultaneously, only seven pairs gave discordant results. Among 104 samples from which duplicate aliquots were run in separate assays, no discordance was seen. Overall, the reproducibility of test kit results was 99% (705 of 712).

  17. A time-course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities.

    Science.gov (United States)

    Pycke, B F G; Etchebehere, C; Van de Caveye, P; Negroni, A; Verstraete, W; Boon, N

    2011-01-01

    This study describes the microbial community richness, -dynamics, and -organization of four full-scale anaerobic digesters during a time-course study of 45 days. The microbial community was analyzed using a Bacteria- and Archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism approach. Clustering analysis separated meso- and thermophilic reactors for both archaeal and bacterial communities. Regardless of the operating temperature, each installation possessed a distinct community profile. For both microbial domains, about 8 dominant terminal-restriction fragments could be observed, with a minimum of 4 and a maximum of 14. The bacterial community organization (a coefficient which describes the specific degree of evenness) showed a factor 2 more variation in the mesophilic reactors, compared with the thermophilic ones. The archaeal community structure of the mesophilic UASB reactor was found to be more stable. The community composition was highly dynamic for Bacteria and Archaea, with a rate of change between 20-50% per 15 days. This study illustrated that microbial communities in full-scale anaerobic digesters are unique to the installation and that community properties are dynamic. Converging complex microbial processes such as anaerobic digestion which rely on a multitude of microbial teams apparently can be highly dynamic.

  18. Dynamics of microbial community in a mesophilic anaerobic digester treating food waste: Relationship between community structure and process stability.

    Science.gov (United States)

    Li, Lei; He, Qin; Ma, Yao; Wang, Xiaoming; Peng, Xuya

    2015-01-01

    Organic loading rate (OLR) disturbances were introduced into a mesophilic anaerobic digester treating food waste (FW) to induce stable and deteriorative phases. The microbial community of each phase was investigated using 454-pyrosequencing. Results show that the relative abundance of acid-producing bacteria and syntrophic volatile fatty acid (VFA) oxidizers increased dramatically at deteriorative phase, while the dominant methanogens did not shift from acetoclastic to hydrogenotrophic groups. The mismatching between bacteria and methanogens may partially be responsible for the process deterioration. Moreover, the succession of predominant hydrogenotrophic methanogens reduced the consumption efficiency of hydrogen; meanwhile, the dominant Methanosaeta with low acetate degradation rate, and the increase of inhibitors concentrations further decreased its activity, which may be the other causes for the process failure. These results improve the understanding of the microbial mechanisms of process instability, and provide theoretical basis for the efficient and stable operation of anaerobic digester treating FW.

  19. Seasonal dynamics of fungal communities in a temperate oak forest soil

    National Research Council Canada - National Science Library

    Voříšková, Jana; Brabcová, Vendula; Cajthaml, Tomáš; Baldrian, Petr

    2014-01-01

    .... Vertical stratification of and seasonal changes in fungal abundance, activity and community composition were investigated in the litter, organic and upper mineral soils of a temperate Quercus petraea...

  20. GMR biosensor arrays: correction techniques for reproducibility and enhanced sensitivity.

    Science.gov (United States)

    Hall, D A; Gaster, R S; Osterfeld, S J; Murmann, B; Wang, S X

    2010-05-15

    Giant magnetoresistive biosensors possess great potential in biomedical applications for quantitatively detecting magnetically tagged biomolecules. Magnetic sensing does not suffer from the high background levels found in optical sensing modalities such as the enzyme linked immunosorbent assay translating into a technology with higher sensitivity. However, to reveal the full potential of these sensors and compensate for non-idealities such as temperature dependence, digital correction and calibration techniques are not only useful but imperative. Using these calibration techniques to correct for process variations and dynamic changes in the sensing environment (such as temperature and magnetic field), we are able to obtain extremely sensitive and, more importantly, reproducible results for quantifiable biomolecular reorganization. The reproducibility of the system was improved by over 3 x using digital correction techniques and the sensors are made temperature independent by using a novel background correction technique. 2010 Elsevier B.V. All rights reserved.

  1. Reproducible Ultrahigh Electromagnetic SERS Enhancement in Nanosphere-Plane Junctions

    CERN Document Server

    Long, Jing; Li, Hongquan; Yang, Tian

    2015-01-01

    Surface enhanced Raman scattering (SERS) in nanoscale hotspots has been placed great hopes upon for identification of minimum chemical traces and in-situ investigation of single molecule structures and dynamics. However, previous work consists of either irreproducible enhancement factors (EF) from random aggregates, or moderate EFs despite better reproducibility. Consequently, systematic study of SERS at the single and few molecules level is still very limited, and the promised applications are far from being realized. Here we report EFs as high as the most intense hotspots in previous work yet achieved in a reproducible and well controlled manner, that is, electromagnetic EFs (EMEF) of 10^9~10 with an error down to 10^+/-0.08 from gold nanospheres on atomically flat gold planes under radially polarized (RP) laser excitation. In addition, our experiment reveals the EF's unexpected nonlinearity under as low as hundreds of nanowatts of laser power.

  2. Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ping [Univ. of Oklahoma, Norman, OK (United States); He, Zhili [Univ. of Oklahoma, Norman, OK (United States); Van Nostrand, Joy D. [Univ. of Oklahoma, Norman, OK (United States); Qin, Yujia [Univ. of Oklahoma, Norman, OK (United States); Deng, Ye [Univ. of Oklahoma, Norman, OK (United States); Chinese Academy of Sciences (CAS), Beijing (China); Wu, Liyou [Univ. of Oklahoma, Norman, OK (United States); Tu, Qichao [Univ. of Oklahoma, Norman, OK (United States); Zhejiang Univ., Hangzhou (China); Wang, Jianjun [Univ. of Oklahoma, Norman, OK (United States); Chinese Academy of Sciences (CAS), Nanjing (China); Schadt, Christopher W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); W. Fields, Matthew [Montana State Univ., Bozeman, MT (United States); Hazen, Terry C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Arkin, Adam P. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Stahl, David A. [Univ. of Washington, Seattle, WA (United States); Zhou, Jizhong [Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)

    2017-03-16

    To further understand the diversity and dynamics of SRB in response to substrate amendment, we sequenced in this paper genes coding for the dissimilatory sulfite reductase (dsrA) in groundwater samples collected after an emulsified vegetable oil (EVO) amendment, which sustained U(VI)-reducing conditions for one year in a fast-flowing aquifer. EVO amendment significantly altered the composition of groundwater SRB communities. Sequences having no closely related-described species dominated (80%) the indigenous SRB communities in nonamended wells. After EVO amendment, Desulfococcus, Desulfobacterium, and Desulfovibrio, known for long-chain-fatty-acid, short-chain-fatty-acid and H2 oxidation and U(VI) reduction, became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ± 8% of the SRB communities, respectively. Succession of these SRB at different bioactivity stages based on redox substrates/products (acetate, SO4–2, U(VI), NO3, Fe(II), and Mn(II)) was observed. Desulfovibrio and Desulfococcus dominated SRB communities at 4–31 days, whereas Desulfobacterium became dominant at 80–140 days. By the end of the experiment (day 269), the abundance of these SRB decreased but the overall diversity of groundwater SRB was still higher than non-EVO controls. Up to 62% of the SRB community changes could be explained by groundwater geochemical variables, including those redox substrates/products. A significant (P < 0.001) correlation was observed between groundwater U(VI) concentrations and Desulfovibrio abundance. Finally, our results showed that the members of SRB and their dynamics were correlated significantly with slow EVO biodegradation, electron donor production and maintenance of U(VI)-reducing conditions in the aquifer.

  3. Community dynamics of coagulase-negative staphylococci during spontaneous artisan-type meat fermentations differ between smoking and moulding treatments.

    Science.gov (United States)

    Janssens, M; Myter, N; De Vuyst, L; Leroy, F

    2013-08-16

    Coagulase-negative staphylococci (CNS) that are naturally present in the raw meat batter of fermented sausages or that originate from the addition of a starter culture play a role in flavour development. A wide species diversity of CNS can be present in fermented meats, but it is not fully clear yet how specific process parameters select for specific CNS by affecting their community dynamics. Therefore, the influence of smoking and moulding treatments on the CNS community dynamics in spontaneously fermented, artisan-type sausages was investigated. During the fermentation stage, the meat batter was in all cases dominated by Staphylococcus saprophyticus, in addition to Lactobacillus sakei as governing lactic acid bacterium. Following fermentation, the bacterial communities were not perturbed by the smoking treatment, since both L. sakei and S. saprophyticus remained dominant throughout the ripening stage and prevailed in the end-products. Yet, when fermentation was followed by a moulding step with Penicillium nalgiovense, a shift of the CNS communities towards dominance by Staphyloccocus equorum was seen, despite a similar evolution of L. sakei. This effect was possibly due to a pH rise caused by the mould, a hypothesis which was reinforced by the finding that the isolated strain S. equorum DBX-S-17 was more sensitive to low pH than the isolated strain S. saprophyticus DFL-S-12 during growth experiments in brain heart infusion (BHI). Differences in CNS communities may affect sausage flavour, due to intraspecies variations in metabolic conversions of, for instance, amino acids. The fact that 3-methyl-butanal was only found in the moulded sausage, which was dominated by S. equorum, may be related to the finding that the isolated strain of this species was able to produce this compound in BHI medium, whereas the isolated strain of S. saprophyticus was not.

  4. Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

    Directory of Open Access Journals (Sweden)

    Erica N Spotswood

    Full Text Available Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species, temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

  5. Exploring the locus of invention : The dynamics of network communities and firms’ invention productivity

    NARCIS (Netherlands)

    Sytch, M.; Tatarynowicz, A.

    2014-01-01

    Departing from prior research analyzing the implications of social structure for actors' outcomes by applying either an ego network or a global network perspective, this study examines the implications of network communities for the invention productivity of firms. Network communities represent

  6. Dynamic Simulation of Crime Perpetration and Reporting to Examine Community Intervention Strategies

    Science.gov (United States)

    Yonas, Michael A.; Burke, Jessica G.; Brown, Shawn T.; Borrebach, Jeffrey D.; Garland, Richard; Burke, Donald S.; Grefenstette, John J.

    2013-01-01

    Objective: To develop a conceptual computational agent-based model (ABM) to explore community-wide versus spatially focused crime reporting interventions to reduce community crime perpetrated by youth. Method: Agents within the model represent individual residents and interact on a two-dimensional grid representing an abstract nonempirically…

  7. Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation test

    NARCIS (Netherlands)

    Diepens, N.J.; Dimitrov, M.R.; Koelmans, A.A.; Smidt, H.

    2015-01-01

    Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in

  8. The biggest fish in the sea? Dynamic Kenyan labour migration in the East African community

    NARCIS (Netherlands)

    Ong'ayo, A.O.O.; Oucho, J.O.; Oucho, L.A.

    2013-01-01

    This study assesses the Kenyan policy and institutional framework concerning South–South labour migration with particular focus on the East African Community (EAC) countries. It focuses mainly on one particular policy instrument, the East African Community Common Market framework. The research furth

  9. Association of running manner with bacterial community dynamics in a partial short-term nitrifying bioreactor for treatment of piggery wastewater with high ammonia content

    OpenAIRE

    Du, Wei-Li; Huang, Qiang; Miao, Li-Li; Liu,Ying; Liu, Zhi-Pei

    2016-01-01

    Optimization of running parameters in a bioreactor requires detailed understanding of microbial community dynamics during the startup and running periods. Using a novel piggery wastewater treatment system termed “UASB + SHARON + ANAMMOX” constructed in our laboratory, we investigated microbial community dynamics using the Illumina MiSeq method, taking activated sludge samples at ~2-week intervals during a ~300-day period. Ammonia-oxidizing bacteria (AOB) were further investigated by quantific...

  10. Effects of community succession dynamics on forest biodiversity in eastern mountainous area of Heilongjiang Province

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Plant, insect and forest structures of 25 forest communities were investigated in Mao'ershan Experimental Forest Farm and Liangshui Experimental Forest Farm during 1994-1995. The paper used continuum index (Ci) as a parameter, to quantitatively describe forest community succession stage. Relationships between the biodiversity and continuum index of forest community were studied. The annual species and family diversities in forest plant community showed nonlinear correlation with continuum index, and the largest diversities were during the middle stage of succession. The diversities of total insect community and herbivorous insect group were negatively related with Ci, that of spide group and parasitic insect group was positively related. The pattern diversity and coverage weight diversity index foliage height increased with continuum index.

  11. Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment.

    Science.gov (United States)

    Gekenidis, M-T; Gossin, D; Schmelcher, M; Schöner, U; Remus-Emsermann, M N P; Drissner, D

    2017-10-01

    Investigate dynamics of culturable mesophilic bacteria and selected food-contaminating bacteria from three herbs and their production environment. Marjoram, basil and thyme were investigated during one growing season by sampling plants, organic fertilizers, soil, irrigation water and marketed products. Mesophilic bacteria and selected food-contaminating bacteria (Escherichia coli, Enterococcus spp., Bacillus cereus group) were cultured and identified by MALDI biotyping. Culturable mesophilic bacteria on marjoram and basil plants decreased over time by two orders of magnitude starting at above 10(6) colony forming units per gram (CFU per g), while they remained constant on thyme (~10(4)  CFU per g). Compared to the last field sample, mesophilic bacteria were increased on all market-ready products by one order of magnitude. Marjoram and basil were dominated by B. cereus group, Enterobacter spp. and Pseudomonas spp., thyme by Bacillus spp. and Pseudomonas spp. All selected food-contaminating bacteria were detected in soil and reservoir-sourced irrigation water, whereas in municipal water, only B. cereus group and rarely Enterococcus spp. were found. Escherichia coli was detected only on young marjoram and basil plants (5 × 10(2) and 5 × 10(1)  CFU per g, respectively), whereas Enterococcus spp. and B. cereus group were consistently detected on these two herbs. Thyme plants only contained B. cereus group consistently (above 10(3) CFU per g). Marketed marjoram and thyme contained Enterococcus spp. (5 × 10(2) and 10(4) CFU per g) and B. cereus group (~5 × 10(2) CFU per g), while no selected food-contaminating bacteria were found on marketed basil. Overall, culturable mesophilic bacteria were dominated by Pseudomonas spp. and Bacillus spp., with increased numbers on market-ready products. Selected food-contaminating bacteria were readily detectable, however, only the B. cereus group was found throughout in all systems. Insight into composition and

  12. A new multi-tracer transport scheme for the dynamical core of NCAR's Community Atmosphere Model

    Science.gov (United States)

    Erath, C.

    2012-04-01

    The integration of a conservative semi-Lagrangian multi-tracer transport scheme (CSLAM) in NCAR's High-Order Method Modeling Environment (HOMME) is considered here. HOMME is a highly scalable atmospheric modeling framework, and its current horizontal discretization relies on spectral element (SE) and/or discontinuous Galerkin (DG) methods on the cubed-sphere. It is one dynamical core of NCAR's Community Atmosphere Model (CAM). The main advantage of CSLAM is that the upstream cell (trajectories) information and computation of weights of integrals can be reused for each additional tracer. This makes CSLAM particularly interesting for global atmospheric modeling with growing number of tracers, e.g. more than 100 tracers for the chemistry version of CAM. An algorithm specifically designed for multiple processors and on the cubed-sphere grid for CSLAM in HOMME is a challenging task. HOMME is running on an element ansatz on the six cube faces. Inside these elements we create an Eulerian finite volume grid of equiangular gnomonic type, which represents the arrival grid in the scheme. But CSLAM relies on backward trajectories, which entails a departure grid. That means departure and arrival grid don't necessary have to be on the same element and certainly not on the same cube face. Also the reconstruction for higher order modeling needs a patch of tracer values which extend the element. Here we consider a third order reconstruction method. Therefore, we introduce a halo for the tracer values in the cell centers of a cube-element. The size of this halo depends on the Courant number (CFL condition) and the reconstruction type. Note that for a third order scheme and CFL number communication can be limited to one per time step. This data structure allows us to consider an element with its halo as one task where we have to be extra carful for elements which share a cube edge due to projection and orientation reasons. We stress that the reconstruction coefficients for elements

  13. Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species

    Science.gov (United States)

    Ruiz-Gutierrez, Viviana; Zipkin, Elise F.; Dhondt, Andre A.

    2010-01-01

    1. Worldwide loss of biodiversity necessitates a clear understanding of the factors driving population declines as well as informed predictions about which species and populations are at greatest risk. The biggest threat to the long-term persistence of populations is the reduction and changes in configuration of their natural habitat. 2. Inconsistencies have been noted in the responses of populations to the combined effects of habitat loss and fragmentation. These have been widely attributed to the effects of the matrix habitats in which remnant focal habitats are typically embedded. 3. We quantified the potential effects of the inter-patch matrix by estimating occupancy and colonization of forest and surrounding non-forest matrix (NF). We estimated species-specific parameters using a dynamic, multi-species hierarchical model on a bird community in southwestern Costa Rica. 4. Overall, we found higher probabilities of occupancy and colonization of forest relative to the NF across bird species, including those previously categorized as open habitat generalists not needing forest to persist. Forest dependency was a poor predictor of occupancy dynamics in our study region, largely predicting occupancy and colonization of only non-forest habitats. 5. Our results indicate that the protection of remnant forest habitats is key for the long-term persistence of all members of the bird community in this fragmented landscape, including species typically associated with open, non-forest habitats. 6.Synthesis and applications. We identified 39 bird species of conservation concern defined by having high estimates of forest occupancy, and low estimates of occupancy and colonization of non-forest. These species survive in forest but are unlikely to venture out into open, non-forested habitats, therefore, they are vulnerable to the effects of habitat loss and fragmentation. Our hierarchical community-level model can be used to estimate species-specific occupancy dynamics for focal

  14. Metabolic and microbial community dynamics during the hydrolytic and acidogenic fermentation in a leach-bed process

    Energy Technology Data Exchange (ETDEWEB)

    Straeuber, Heike; Kleinsteuber, Sabine [UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Bioenergy; UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Environmental Microbiology; Schroeder, Martina [UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Bioenergy

    2012-12-15

    Biogas production from lignocellulosic feedstock not competing with food production can contribute to a sustainable bioenergy system. The hydrolysis is the rate-limiting step in the anaerobic digestion of solid substrates such as straw. Hence, a detailed understanding of the metabolic processes during the steps of hydrolysis and acidogenesis is required to improve process control strategies. The fermentation products formed during the acidogenic fermentation of maize silage as a model substrate in a leach-bed process were determined by gas and liquid chromatography. The bacterial community dynamics was monitored by terminal restriction fragment length polymorphism analysis. The community profiles were correlated with the process data using multivariate statistics. The batch process comprised three metabolic phases characterized by different fermentation products. The bacterial community dynamics correlated with the production of the respective metabolites. In phase 1, lactic and acetic acid fermentations dominated. Accordingly, bacteria of the genera Lactobacillus and Acetobacter were detected. In phase 2, the metabolic pathways shifted to butyric acid fermentation, accompanied by the production of hydrogen and carbon dioxide and a dominance of the genus Clostridium. In phase 3, phylotypes affiliated with Ruminococcaceae and Lachnospiraceae prevailed, accompanied by the formation of caproic and acetic acids, and a high gas production rate. A clostridial butyric type of fermentation was predominant in the acidogenic fermentation of maize silage, whereas propionic-type fermentation was marginal. As the metabolite composition resulting from acidogenesis affects the subsequent methanogenic performance, process control should focus on hydrolysis/acidogenesis when solid substrates are digested. (orig.)

  15. Dynamics of bacterial community development in the reef coral Acropora muricata following experimental antibiotic treatment

    Science.gov (United States)

    Sweet, M. J.; Croquer, A.; Bythell, J. C.

    2011-12-01

    Development of the bacterial community associated with the coral Acropora muricata (= formosa) was monitored using 16S rRNA gene-based techniques and abundance counts over time following experimental modification of the existing microbial community using the antibiotic ciprofloxacin. Abundance of bacteria was reduced >99% by the treatment, resulting in significant changes in bacterial community structure. Following redeployment to their natural environment, some settlement and re-growth of bacteria took place within a few hours, including ribosomal types that were not present, or in low abundance, in the natural microbiota. However, complete recovery of the bacterial community required longer than 96 h, which indicates a relatively slow settlement and growth of bacteria from the water column and suggests that turnover of the natural community is similarly slow. The early developing community was dominated by antibiotic-resistant bacteria from the natural microbiota that survived the treatment and proliferated in the absence of natural competitors, but also included some non-resident ribotypes colonizing from the water column. Almost, all these opportunists were significantly reduced or eliminated within 96 h after treatment, demonstrating a high resilience in the natural bacterial community. Potential pathogens, including a Clostridium sp., inhabited the coral at low abundances, only becoming prevalent when the natural microbiota was disturbed by the treatment. The healthy coral-associated microbiota appears to be strongly controlled by microbial interactions.

  16. Reproducing Kernel for D2(Ω, ρ) and Metric Induced by Reproducing Kernel

    Institute of Scientific and Technical Information of China (English)

    ZHAO Zhen Gang

    2009-01-01

    An important property of the reproducing kernel of D2(Ω, ρ) is obtained and the reproducing kernels for D2(Ω, ρ) are calculated when Ω = Bn × Bn and ρ are some special functions. A reproducing kernel is used to construct a semi-positive definite matrix and a distance function defined on Ω×Ω. An inequality is obtained about the distance function and the pseudodistance induced by the matrix.

  17. Complex, dynamic combination of physical, chemical and nutritional variables controls spatio-temporal variation of sandy beach community structure.

    Science.gov (United States)

    Ortega Cisneros, Kelly; Smit, Albertus J; Laudien, Jürgen; Schoeman, David S

    2011-01-01

    Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy

  18. Complex, Dynamic Combination of Physical, Chemical and Nutritional Variables Controls Spatio-Temporal Variation of Sandy Beach Community Structure

    Science.gov (United States)

    Ortega Cisneros, Kelly; Smit, Albertus J.; Laudien, Jürgen; Schoeman, David S.

    2011-01-01

    Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy

  19. Reproducibility, controllability, and optimization of LENR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Nagel, David J. [The George Washington University, Washington DC 20052 (United States)

    2006-07-01

    Low-energy nuclear reaction (LENR) measurements are significantly, and increasingly reproducible. Practical control of the production of energy or materials by LENR has yet to be demonstrated. Minimization of costly inputs and maximization of desired outputs of LENR remain for future developments. The paper concludes by underlying that it is now clearly that demands for reproducible experiments in the early years of LENR experiments were premature. In fact, one can argue that irreproducibility should be expected for early experiments in a complex new field. As emphasized in the paper and as often happened in the history of science, experimental and theoretical progress can take even decades. It is likely to be many years before investments in LENR experiments will yield significant returns, even for successful research programs. However, it is clearly that a fundamental understanding of the anomalous effects observed in numerous experiments will significantly increase reproducibility, improve controllability, enable optimization of processes, and accelerate the economic viability of LENR.

  20. Reproducibility of surface roughness in reaming

    DEFF Research Database (Denmark)

    Müller, Pavel; De Chiffre, Leonardo

    concentration of the oil in water-based cutting fluid (or when using a straight mineral oil) results in surface profiles that are more reproducible at higher cutting speed. Moreover, it can be seen that three cutting fluids (two water-based cutting fluids with different oil concentration and a straight mineral......An investigation on the reproducibility of surface roughness in reaming was performed to document the applicability of this approach for testing cutting fluids. Austenitic stainless steel was used as a workpiece material and HSS reamers as cutting tools. Reproducibility of the results was evaluated...... oil) used in connection with a low cutting speed result in "identical" surface profiles. Biggest uncertainty contributors were due to the process repeatability and repeatability around the hole circumference. This was however only in the case of high cutting speeds and low degree of oil concentration...

  1. Most computational hydrology is not reproducible, so is it really science?

    Science.gov (United States)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

    2016-10-01

    Reproducibility is a foundational principle in scientific research. Yet in computational hydrology the code and data that actually produces published results are not regularly made available, inhibiting the ability of the community to reproduce and verify previous findings. In order to overcome this problem we recommend that reuseable code and formal workflows, which unambiguously reproduce published scientific results, are made available for the community alongside data, so that we can verify previous findings, and build directly from previous work. In cases where reproducing large-scale hydrologic studies is computationally very expensive and time-consuming, new processes are required to ensure scientific rigor. Such changes will strongly improve the transparency of hydrological research, and thus provide a more credible foundation for scientific advancement and policy support.

  2. Reproducibility of operator processing for radiation dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Sui Shen; DeNardo, Gerald L.; DeNardo, Sally J.; Aina, Yuan; DeNardo, Diane A.; Lamborn, Kathleen R

    1997-01-01

    Reproducibility of operator processing for radiation dose and biological half-life was assessed for radioimmunotherapy. Mean coefficient of variation for intra-operator consecutive processing and for inter-operator processing was less than 15% for all tissues. The mean coefficient of variation for intra-operator processing over 2 wk or inter-operator processing comparing an experienced and less experienced operator was generally greater, and particularly so for tumors. Satisfactory reproducibility was achievable using visual determination of regions of interests after 80 h of training.

  3. Archiving Reproducible Research with R and Dataverse

    DEFF Research Database (Denmark)

    Leeper, Thomas

    2014-01-01

    Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...... Network online repositories, an open-source data archiving project sponsored by Harvard University. In this article I review the importance of data archiving in the context of reproducible research, introduce the Dataverse Network, explain the implementation of the dvn package, and provide example code...... for archiving and releasing data using the package....

  4. Archiving Reproducible Research with R and Dataverse

    DEFF Research Database (Denmark)

    Leeper, Thomas

    2014-01-01

    Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...... Network online repositories, an open-source data archiving project sponsored by Harvard University. In this article I review the importance of data archiving in the context of reproducible research, introduce the Dataverse Network, explain the implementation of the dvn package, and provide example code...

  5. Population dynamics of iron-oxidizing communities in pilot plants for the treatment of acid mine waters.

    Science.gov (United States)

    Heinzel, Elke; Janneck, Eberhard; Glombitza, Franz; Schlömann, Michael; Seifert, Jana

    2009-08-15

    The iron-oxidizing microbial community in two pilot plants for the treatment of acid mine water was monitored to investigate the influence of different process parameters such as pH, iron concentration, and retention time on the stability of the system to evaluate the applicability of this treatment technology on an industrial scale. The dynamics of the microbial populations were followed using T-RFLP (terminal restriction fragment length polymorphism) over a period of several months. For a more precise quantification, two TaqMan assays specific for the two prominent groups were developed and the relative abundance of these taxa in the iron-oxidizing community was verified by real-time PCR. The investigations revealed that the iron-oxidizing community was clearly dominated by two groups of Betaproteobacteria affiliated with the poorly known and not yet recognized species "Ferrovum myxofaciens" and with strains related to Gallionella ferruginea, respectively. These taxa dominated the microbial community during the whole investigation period and accelerated the oxidation of ferrous iron despite the changing characteristics of mine waters flowing into the plants. Thus, it is assumed that the treatment technology can also be applied to other mine sites and that these organisms play a crucial role in such treatment systems.

  6. Population dynamics of iron-oxidizing communities in pilot plants for the treatment of acid mine waters

    Energy Technology Data Exchange (ETDEWEB)

    Elke Heinzel; Eberhard Janneck; Franz Glombitza; Michael Schlmann; Jana Seifert [TU Bergakademie Freiberg, Freiberg (Germany). Interdisciplinary Ecological Center

    2009-08-15

    The iron-oxidizing microbial community in two pilot plants for the treatment of acid mine water was monitored to investigate the influence of different process parameters such as pH, iron concentration, and retention time on the stability of the system to evaluate the applicability of this treatment technology on an industrial scale. The dynamics of the microbial populations were followed using T-RFLP (terminal restriction fragment length polymorphism) over a period of several months. For a more precise quantification, two TaqMan assays specific for the two prominent groups were developed and the relative abundance of these taxa in the iron-oxidizing community was verified by real-time PCR. The investigations revealed that the iron-oxidizing community was clearly dominated by two groups of Betaproteobacteria affiliated with the poorly known and not yet recognized species 'Ferrovum myxofaciens' and with strains related to Gallionella ferruginea, respectively. These taxa dominated the microbial community during the whole investigation period and accelerated the oxidation of ferrous iron despite the changing characteristics of mine waters flowing into the plants. Thus, it is assumed that the treatment technology can also be applied to other mine sites and that these organisms play a crucial role in such treatment systems. 32 refs., 4 figs. 1 tab.

  7. Remote Sensing observations of Cecropia communities along Amazonian rivers: Mapping and monitoring habitat dynamics with time series datasets

    Science.gov (United States)

    Quinteros Casaverde, N. L.; McDonald, K.

    2016-12-01

    Riverine habitats host more than 14% of non-aquatic birds in the Amazon basin, some of them considered vulnerable by the UICN due to habitat destruction. Plant species of the genus Cecropia are known for being a late pioneer species in these riverine habitats creating monospecific stands along the Amazonian rivers. Cecropia biomes are thought to have significant impacts on the avifauna communities and their diversity. Nowadays, these habitats are threatened by the on-going development in the Amazonian countries. There are plans to build hydroelectric facilities, damming important tributaries of the Amazon river. Such large scale land cover change threatens Cecropia communities and the habitats they support and associated biodiversity. Thus, it is imperative to understand the fragility of these ecosystems, their extent and spatial distribution, and seasonal influences to their environments. We employ multiple sources of remote sensing data to assess the ability to use high resolution imagery to map Cecropia communities and multi-temporal observations to assess their seasonal dynamics. This research aims to facilitate the understanding of these communities through time series analyses using remote sensing products such as high resolution images from Synthetic Aperture Radar (SAR) and Landsat to identify the Cecropia stands along the rivers and lower resolution products such as satellite-borne radiometers and scatterometers to assess seasonality. Our goal is to employ combined remote sensing data sources at map and monitor these important habitats.

  8. Poverty and fatalism: Impacts on the community dynamics and on hope in Brazilian residents.

    Science.gov (United States)

    Cidade, Elívia Camurça; Moura, James Ferreira; Nepomuceno, Bárbara Barbosa; Ximenes, Verônica Morais; Sarriera, Jorge Castellá

    2016-01-01

    The aim of this study was to analyze the consequences of poverty on expressions of fatalism, hope, and sense of community of two Brazilian States: Ceará and Rio Grande do Sul. Seven-hundred and thirty-one people, divided in four groups (extreme poverty, poverty, median income, and adequate income) answered a questionnaire. The variables sense of community and hope were found to be predictors of fatalism. Individuals in situations of poverty and extreme poverty showed high indices of fatalism, pessimism, divinity control, and luck, and low indices of hope and sense of community. Individuals with adequate income have low levels of fatalism, pessimism, and divinity control. It is concluded that poverty has consequences on the life of those who experience it, and that attitudes of pessimism, hopelessness, and belief in luck as well as the weakening of community networks, articulate and support the maintenance of the status quo.

  9. Biofilm Community Dynamics in Bench-Scale Annular Reactors Simulating Arrestment of Chloraminated Drinking Water Nitrification

    Science.gov (United States)

    Annular reactors (ARs) were used to study biofilm community succession and provide an ecological insight during nitrification arrestment through simultaneously increasing monochloramine (NH2Cl) and chlorine to nitrogen mass ratios, resulting in four operational periods (I to IV)....

  10. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)

    National Research Council Canada - National Science Library

    Loudon, Andrew H; Woodhams, Douglas C; Parfrey, Laura Wegener; Archer, Holly; Knight, Rob; McKenzie, Valerie; Harris, Reid N

    2014-01-01

    .... We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing...

  11. Exploring the Role of Information Professionals in Improving Research Reproducibility:A Case Study in Geosciences

    Science.gov (United States)

    Yan, A.; West, J.

    2016-12-01

    The validity of Geosciences research is of great significance to general public and policy-makers. In an earlier study, we surveyed 136 faculty and graduate students in geosciences. The result indicated that nearly 80% of respondents who had ever reproduced a published study had failed at least one time in reproducing, suggesting a general lack of research reproducibility in geosciences. Although there is much enthusiasm for creation of technologies such as workflow system, literate programming, and cloud-based system to facilitate reproducibility, much less emphasis has been placed on the information services essential for meaningful use of these tools. Library and Information Science (LIS) has a rich tradition of providing customized service for research communities. LIS professionals such as academic librarians have made strong contribution to resources locating, software recommending, data curation, metadata guidance, project management, submission review and author training. In particular, university libraries have been actively developing tools and offering guidelines, consultations, and trainings on Data Management Plan (DMP) required by National Science Foundation (NSF). And effective data management is a significant first step towards reproducible research. Hereby we argue that LIS professionals may be well-positioned to assist researchers to make their research reproducible. In this study, we aim to answer the question: how can LIS professionals assist geoscience researchers in making their research capable of being reproduced? We first synthesize different definitions of "reproducibility" and provide a conceptual framework of "reproducibility" in geosciences to resolve some of the misunderstandings around related terminology. Using a case study approach, we then examine 1) university librarians' technical skills, domain knowledge, professional activities, together with their awareness of, readiness for, and attitudes towards research reproducibility and

  12. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

    DEFF Research Database (Denmark)

    Nagarajan, Harish; Embree, Mallory; Rotaru, Amelia-Elena

    2013-01-01

    Syntrophic associations are central to microbial communities and thus have a fundamental role in the global carbon cycle. Despite biochemical approaches describing the physiological activity of these communities, there has been a lack of a mechanistic understanding of the relationship between...... metallireducens and Geobacter sulfurreducens. Genome-scale modelling of direct interspecies electron transfer reveals insights into the energetics of electron transfer mechanisms. While G. sulfurreducens adapts to rapid syntrophic growth by changes at the genomic and transcriptomic level, G. metallireducens...

  13. Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage.

    Science.gov (United States)

    Biswas, Kristi; Turner, Susan J

    2012-02-01

    Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.

  14. Temporal dynamics of a fish community in the lower portion of a tidal creek, Pando sub-estuarine system, Uruguay

    Directory of Open Access Journals (Sweden)

    Rodrigo Gurdek

    Full Text Available ABSTRACT Estuaries are highly dynamic ecosystems subjected to variability of their fish communities over different time scales. The nearshore fish community of the lower Pando estuary, a temperate sub-system of the Río de la Plata estuary, was sampled from May 2002 to June 2003. A total of 2,165 fishes, represented by 16 species were caught by seine netting. Captures were dominated by juveniles (>90%, as well as by the sciaenid Micropogonias furnieri (Desmarest, 1823 (82.8%. The fish community showed high seasonal variability, with the greatest diversity and biomass in summer and spring and the highest species richness during summer. Lowest values of all community parameters occurred in winter and autumn, seasons that presented the highest similarity in fish composition. Number of species was correlated with water temperature and salinity. The ichthyofaunal composition showed significant diel differences in summer and spring. Diel changes were observed in the density of M. furnieri and Odontesthes argentinensis (Valenciennes, 1835, occurring mainly during the day, and of Mugil liza Valenciennes, 1836, Parapimelodus valenciennis (Lütken, 1874 and Brevoortia aurea (Spix & Agassiz, 1829, caught mostly during the night. Temporal variability was attributed to environmental fluctuations, life cycle of species as well as to feeding patterns and small-scale displacements. Presented findings in the Pando sub-estuary denote similar juvenile use and seasonal patterns to those found in estuaries. Further studies in the nursery function and juvenile dynamics over the year are recommended in order to better understand the ecological role of sub-estuaries.

  15. Reproducing wavelet kernel method in nonlinear system identification

    Institute of Scientific and Technical Information of China (English)

    WEN Xiang-jun; XU Xiao-ming; CAI Yun-ze

    2008-01-01

    By combining the wavelet decomposition with kernel method, a practical approach of universal multi-scale wavelet kernels constructed in reproducing kernel Hilbert space (RKHS) is discussed, and an identifica-tion scheme using wavelet support vector machines ( WSVM ) estimator is proposed for nonlinear dynamic sys-tems. The good approximating properties of wavelet kernel function enhance the generalization ability of the pro-posed method, and the comparison of some numerical experimental results between the novel approach and some existing methods is encouraging.

  16. Assessment of Modeling Capability for Reproducing Storm Impacts on TEC

    Science.gov (United States)

    Shim, J. S.; Kuznetsova, M. M.; Rastaetter, L.; Bilitza, D.; Codrescu, M.; Coster, A. J.; Emery, B. A.; Foerster, M.; Foster, B.; Fuller-Rowell, T. J.; Huba, J. D.; Goncharenko, L. P.; Mannucci, A. J.; Namgaladze, A. A.; Pi, X.; Prokhorov, B. E.; Ridley, A. J.; Scherliess, L.; Schunk, R. W.; Sojka, J. J.; Zhu, L.

    2014-12-01

    During geomagnetic storm, the energy transfer from solar wind to magnetosphere-ionosphere system adversely affects the communication and navigation systems. Quantifying storm impacts on TEC (Total Electron Content) and assessment of modeling capability of reproducing storm impacts on TEC are of importance to specifying and forecasting space weather. In order to quantify storm impacts on TEC, we considered several parameters: TEC changes compared to quiet time (the day before storm), TEC difference between 24-hour intervals, and maximum increase/decrease during the storm. We investigated the spatial and temporal variations of the parameters during the 2006 AGU storm event (14-15 Dec. 2006) using ground-based GPS TEC measurements in the selected 5 degree eight longitude sectors. The latitudinal variations were also studied in two longitude sectors among the eight sectors where data coverage is relatively better. We obtained modeled TEC from various ionosphere/thermosphere (IT) models. The parameters from the models were compared with each other and with the observed values. We quantified performance of the models in reproducing the TEC variations during the storm using skill scores. This study has been supported by the Community Coordinated Modeling Center (CCMC) at the Goddard Space Flight Center. Model outputs and observational data used for the study will be permanently posted at the CCMC website (http://ccmc.gsfc.nasa.gov) for the space science communities to use.

  17. Hyperbolic L2-modules with Reproducing Kernels

    Institute of Scientific and Technical Information of China (English)

    David EELPODE; Frank SOMMEN

    2006-01-01

    Abstract In this paper, the Dirac operator on the Klein model for the hyperbolic space is considered. A function space containing L2-functions on the sphere Sm-1 in (R)m, which are boundary values of solutions for this operator, is defined, and it is proved that this gives rise to a Hilbert module with a reproducing kernel.

  18. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël|info:eu-repo/dai/nl/298811855; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel|info:eu-repo/dai/nl/407629971; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf; Echeverría, Alejandro Vásquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

    2015-01-01

    Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Rep

  19. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël|info:eu-repo/dai/nl/298811855; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel|info:eu-repo/dai/nl/407629971; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf

    2015-01-01

    Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available.

  20. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Aarts, Alexander A.; Anderson, Joanna E.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahnik, Stepan; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Bruening, Jovita; Calhoun-Sauls, Ann; Chagnon, Elizabeth; Callahan, Shannon P.; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Cillessen, Linda; Christopherson, Cody D.; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Cohn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D. Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Della Penna, Nicolas; den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernandez-Castilla, Belen; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Gloeckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O. -Y.; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jaekel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knezevic, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniel; Lane, Kristin A.; Lassetter, Bethany; Lazarevic, Ljiljana B.; LeBel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, M.; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; Mackinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Moeschl, Marcus; Motyl, Matt; Mueller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michele B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima-Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schmidt, Kathleen; Schlegelmilch, Rene; Seibel, Larissa; Scholz, Sabine; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L. M.; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valasek, Milan; van 't Veer, Anna E.; Van Aert, Robbie; van Assen, M.A.L.M.; van Bork, Riet; van de Ven, Mathijs; van den Bergh, Don; van der Hulst, Marije; van Dooren, Roel; van Doorn, Johnny; van Renswoude, Daan R.; van Rijn, Hedderik; Vanpaemel, Wolf; Echeverria, Alejandro Vasquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark

    2015-01-01

    INTRODUCTION Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research

  1. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf; Echeverría, Alejandro Vásquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

    2015-01-01

    Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Rep

  2. Estimating the reproducibility of psychological science

    NARCIS (Netherlands)

    Aarts, Alexander A.; Anderson, Joanna E.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahnik, Stepan; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Bruening, Jovita; Calhoun-Sauls, Ann; Chagnon, Elizabeth; Callahan, Shannon P.; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Cillessen, Linda; Christopherson, Cody D.; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Cohn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D. Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Della Penna, Nicolas; den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernandez-Castilla, Belen; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Gloeckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O. -Y.; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jaekel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knezevic, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniel; Lane, Kristin A.; Lassetter, Bethany; Lazarevic, Ljiljana B.; LeBel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, M.; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; Mackinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Moeschl, Marcus; Motyl, Matt; Mueller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michele B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima-Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schmidt, Kathleen; Schlegelmilch, Rene; Seibel, Larissa; Scholz, Sabine; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L. M.; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valasek, Milan; van 't Veer, Anna E.; Van Aert, Robbie; van Assen, M.A.L.M.; van Bork, Riet; van de Ven, Mathijs; van den Bergh, Don; van der Hulst, Marije; van Dooren, Roel; van Doorn, Johnny; van Renswoude, Daan R.; van Rijn, Hedderik; Vanpaemel, Wolf; Echeverria, Alejandro Vasquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric-Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

    2015-01-01

    INTRODUCTION Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research

  3. Towards reproducible descriptions of neuronal network models.

    Directory of Open Access Journals (Sweden)

    Eilen Nordlie

    2009-08-01

    Full Text Available Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use. We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages. We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing--and thinking about--complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain.

  4. Spatial and temporal dynamics of microbial communities in a human-perturbed estuary of China

    Science.gov (United States)

    Hu, A.; Yu, C. P.; Hou, L.

    2015-12-01

    Estuaries are responsible for the transport and transformation of nutrients and organic matters from the continent to the adjacent coastal zone, and therefore play critical roles in global biogeochemical cycles. They are under increasing stress from human activities, especially in China, yet we still know little about the responses of microbial communities that mediate biogeochemical processes. Here, we investigated planktonic and benthic microbial communities in the human-perturbed Jiulong River estuary (JRE), southern China by using Illumina 16S ribosomal RNA amplicon sequencing. The results of taxonomic assignments indicated that Beta- (23.32%), Alpha- (22.21%), Gammaproteobacteria (14.83%), Actinobacteria (8.67%), and Flavobacteria (7.56%) were the five most abundant classes in estuarine surface waters, while benthic microbial communities were dominated by Gamma- (20.09%), Delta- (14.68%), Beta- (9.82%), Alphaproteobacteria (7.63%), and Anaerolineae (7.25%). The results of Adnois and ANOSIM tests confirmed that the compositions of microbial communities from waters and sediments of the JRE were significantly different from each other, and then salinity may be the primary factor controlling spatial distributions of planktonic and benthic microbial communities in this estuary. At the temporal scale, planktonic communities showed a more clear variation pattern. Remarkably, the ratios of Thaumarchaeota (putative ammonia-oxidizing archaea) to Nitrosomonadales (ammonia-oxidizing bacteria) either in water or sediments of the JRE increased from freshwater to marine end, suggesting that bacterial and archaeal nitrifiers occupy low-salinity and high-salinity niches, respectively. The nutrient concentrations and salinity might be the most important factors which are responsible for this niche diversification. Overall, this study shed light on our understanding of the biogeographic patterns and its ecological drivers of estuarine microbial communities.

  5. Dynamics and associations of microbial community types across the human body.

    Science.gov (United States)

    Ding, Tao; Schloss, Patrick D

    2014-05-15

    A primary goal of the Human Microbiome Project (HMP) was to provide a reference collection of 16S ribosomal RNA gene sequences collected from sites across the human body that would allow microbiologists to better associate changes in the microbiome with changes in health. The HMP Consortium has reported the structure and function of the human microbiome in 300 healthy adults at 18 body sites from a single time point. Using additional data collected over the course of 12-18 months, we used Dirichlet multinomial mixture models to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. Our results demonstrate that even with the considerable intra- and interpersonal variation in the human microbiome, this variation can be partitioned into community types that are predictive of each other and are probably the result of life-history characteristics. Understanding the diversity of community types and the mechanisms that result in an individual having a particular type or changing types, will allow us to use their community types to assess disease risk and to personalize therapies.

  6. Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge.

    Science.gov (United States)

    Westerholm, Maria; Crauwels, Sam; Houtmeyers, Sofie; Meerbergen, Ken; Van Geel, Maarten; Lievens, Bart; Appels, Lise

    2016-10-01

    The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the

  7. A PHYSICAL ACTIVITY QUESTIONNAIRE: REPRODUCIBILITY AND VALIDITY

    Directory of Open Access Journals (Sweden)

    Nicolas Barbosa

    2007-12-01

    Full Text Available This study evaluates the Quantification de L'Activite Physique en Altitude chez les Enfants (QAPACE supervised self-administered questionnaire reproducibility and validity on the estimation of the mean daily energy expenditure (DEE on Bogotá's schoolchildren. The comprehension was assessed on 324 students, whereas the reproducibility was studied on a different random sample of 162 who were exposed twice to it. Reproducibility was assessed using both the Bland-Altman plot and the intra-class correlation coefficient (ICC. The validity was studied in a sample of 18 girls and 18 boys randomly selected, which completed the test - re-test study. The DEE derived from the questionnaire was compared with the laboratory measurement results of the peak oxygen uptake (Peak VO2 from ergo-spirometry and Leger Test. The reproducibility ICC was 0.96 (95% C.I. 0.95-0.97; by age categories 8-10, 0.94 (0.89-0. 97; 11-13, 0.98 (0.96- 0.99; 14-16, 0.95 (0.91-0.98. The ICC between mean TEE as estimated by the questionnaire and the direct and indirect Peak VO2 was 0.76 (0.66 (p<0.01; by age categories, 8-10, 11-13, and 14-16 were 0.89 (0.87, 0.76 (0.78 and 0.88 (0.80 respectively. The QAPACE questionnaire is reproducible and valid for estimating PA and showed a high correlation with the Peak VO2 uptake

  8. Community dynamics of intertidal soft-bottom mussel beds over two decades

    Science.gov (United States)

    Büttger, Heike; Asmus, Harald; Asmus, Ragnhild; Buschbaum, Christian; Dittmann, Sabine; Nehls, Georg

    2008-03-01

    Macrozoobenthos communities in the North Sea showed pronounced changes over the past decade in relation to an increasing number of invasive species and climate change. We analysed data sets spanning 22 years on abundance, biomass and species composition of intertidal soft bottom mussel beds near the island of Sylt (German Bight) in the Northern Wadden Sea, based on surveys from 1983/1984, 1990, 1993 and from 1999 to 2005. Mussel bed area and blue mussel biomass decreased, and a change in the dominance structure in the associated community comparing 1984 to mid-1990s with the period from 1999 to 2005 was observed. Coverage of the mussel beds with the algae Fucus vesiculosus decreased since the end of the 1990s. Within the study period biomass and densities of the associated community increased significantly. Dominance structure changed mainly because of increasing abundances of associated epibenthic taxa. Apart from the Pacific oyster C rassostrea gigas all other alien species were already present in the area during the study period. Community changes already started before Pacific oysters became abundant. An attempt is made to evaluate effects on the observed changes of decreasing mussel biomass, ageing of mussel beds, decreasing fucoid coverage and increasing abundances of invader. All four factors are assumed to contribute to changing community structure of intertidal mussel beds.

  9. Zooplankton community dynamics in the N. Aegean front (E. Mediterranean in the winter spring period

    Directory of Open Access Journals (Sweden)

    I. SIOKOU

    2015-01-01

    Full Text Available Zooplankton community composition was studied in the North Aegean frontal area in the winter-spring period along a trophic gradient going from the less saline and cold modified Black Sea water to the high salinity and temperature waters of Levantine origin. Samples were collected at the upper 100 m of three stations positioned along this gradient by using three nets with different mesh sizes (45 μm, 200 μm and 500 μm. Τhe community composition (all sizes was differentiated along the gradient with smoother seasonal succession and higher diversity with increasing oligotrophy and salinity. The temporal variability of the community composition revealed significant changes in the January-April period as well as gradual decrease of diversity index values at the station positioned within the front.  The major characteristic at this station was the abrupt increment and dominance of Centropages typicus in April, especially within the layer occupied by the modified Black Sea water. Significant difference in the community composition between March and April was a common feature in the whole study area and for all zooplankton fractions, though not of the same strength. The inflow of the Black Sea water and the trophic gradient were found to be important factors for the observed temporal variability and its spatial differentiation, while changes in the phytoplankton and protozoa abundance and community composition could account for the seasonal succession in species dominance.

  10. Advances in Global Magnetosphere Modeling at the Community Coordinated Modeling Center.

    Science.gov (United States)

    Kuznetsova, Maria

    2016-07-01

    The Community Coordinated Modeling Center (CCMC) hosts a set of state-of-the-art global magnetosphere models that are capable to reproduce a broad range of physical phenomena in Earth's magnetosphere. We will discuss successes and challenges in global magnetosphere modeling and the role of non-MHD effects on global dynamics.

  11. Influence of dynamic vegetation on carbon-nitrogen cycle feedback in the Community Land Model (CLM4)

    Science.gov (United States)

    Sakaguchi, K.; Zeng, X.; Leung, LR; Shao, P.

    2016-12-01

    Land carbon sensitivity to atmospheric CO2 concentration (βL) and climate warming (γL) is a crucial part of carbon-climate feedbacks that affect the magnitude of future warming. Although these sensitivities can be estimated by earth system models, their dependence on model representation of land carbon dynamics and the inherent model assumptions has rarely been investigated. Using the widely used Community Land Model version 4 as an example, we examine how βL and γL vary with prescribed versus dynamic vegetation covers. Both sensitivities are found to be larger with dynamic compared to prescribed vegetation on decadal timescale in the late twentieth century, with a more robust difference in γL. The latter is a result of dynamic vegetation model deficiencies in representing the competitions between deciduous versus evergreen trees and tree versus grass over the tropics and subtropics. The biased vegetation cover changes the regional characteristics of carbon-nitrogen cycles such that plant productivity responds less strongly to the enhancement of nitrogen mineralization with warming, so more carbon is lost to the atmosphere with rising temperature. The result calls for systematic evaluations of land carbon sensitivities with varying assumptions for land cover representations to help prioritize development effort and constrain uncertainties in carbon-climate feedbacks.

  12. Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation.

    Science.gov (United States)

    Röling, Wilfred F M; Milner, Michael G; Jones, D Martin; Lee, Kenneth; Daniel, Fabien; Swannell, Richard J P; Head, Ian M

    2002-11-01

    Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% +/- 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% +/- 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% +/- 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although

  13. Coupled Spatiotemporal Dynamics of Microbial Community Ecology, Biogeochemistry, and Hydrologic Mixing

    Science.gov (United States)

    Stegen, J.; Johnson, T. C.; Fredrickson, J.; Wilkins, M.; Konopka, A.; Nelson, W.; Arntzen, E.; Chrisler, W.; Chu, R. K.; Fansler, S.; Kennedy, D.; Resch, T.; Tfaily, M. M.

    2015-12-01

    The hyporheic zone (HZ) is a critical ecosystem component that links terrestrial, surface water, and groundwater ecosystems. A dominant feature of the HZ is groundwater-surface water mixing and the input of terrestrially—as well as aquatically—derived organic carbon. In many systems the HZ has a relatively small spatial extent, but in larger riverine systems groundwater-surface water mixing can occur 100s of meters beyond the surface water shoreline; we consider these more distal locations to be within the 'subsurface interaction zone' (SIZ) as they are beyond the traditional HZ. Microbial communities in the HZ and SIZ drive biogeochemical processes in these system components, yet relatively little is known about the ecological processes that drive HZ and SIZ microbial communities. Here, we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected through space (400m spatial extent) and time (7 month temporal extent) within the Hanford Site 300 Area. These data streams were integrated to evaluate how the influence of groundwater-surface water mixing on microbial communities changes when moving from the HZ to the broader SIZ. Our results indicate that groundwater-surface water mixing (i) consistently stimulated heterotrophic respiration, but only above a threshold of surface water intrusion, (ii) did not stimulate denitrification, (iii) caused deterministic shifts in HZ microbial communities due to changes in organic carbon composition, and (iv) did not cause shifts in SIZ microbial communities. These results suggest that microbial communities and the biogeochemical processes they drive are impacted by groundwater-surface water mixing primarily in the HZ and to a lesser extent in the SIZ.

  14. Bacterial Community Structure and Dynamics During Corn-Based Bioethanol Fermentation.

    Science.gov (United States)

    Li, Qing; Heist, E Patrick; Moe, Luke A

    2016-02-01

    Corn-based fuel ethanol facilities mix enzymatically treated, gelatinized corn starch with water to generate a "mash" that is used as the substrate in large-scale (∼500,000 gallon) yeast-based fermentations. In contrast to other food and beverage fermentations (e.g., cheese, wine), bioethanol production is presumed to be optimal when bacteria are absent from the fermentation-thus maximizing conversion of glucose to ethanol-yet the facilities are not sterilized. Culture-based analysis has suggested that lactic acid bacteria occupy this niche and, under certain circumstances, can outcompete the dedicated fermentation yeast for nutrients. Here, we use 16S rRNA gene amplicon sequencing to probe bacterial community structure during bioethanol fermentation. Nineteen total batches from five corn-based fuel ethanol fermentation facilities were analyzed. From each batch, five samples were taken. This includes the contents of the yeast propagation tank at inoculation, three samples taken at intervals during the fermentation, and a sample taken at the end of fermentation. Bacterial community structure was compared with time, between facility, between fermentor, between batches from the same fermentor, and against environmental variables within each fermentation. Communities were dominated by members of the Firmicutes and Proteobacteria phyla, with lactic acid bacteria dominating the communities in two of the five facilities. In the other facilities, Proteobacteria (largely members of the Pseudomonas and Escherichia-Shigella genera) outcompete the lactic acid bacteria. In most cases, the yeast propagation tank inoculum imparted a rich bacterial community, but the batches vary regarding whether this inoculum was the primary driver of the fermentation community structure.

  15. Fish community dynamics following dam removal in a fragmented agricultural stream

    Science.gov (United States)

    Kornis, Matthew; Weidel, Brian C.; Powers, Stephens; Diebel, Matthew W.; Cline, Timpthy; Fox, Justin; Kitchell, James F.

    2014-01-01

    Habitat fragmentation impedes dispersal of aquatic fauna, and barrier removal is increasingly used to increase stream network connectivity and facilitate fish dispersal. Improved understanding of fish community response to barrier removal is needed, especially in fragmented agricultural streams where numerous antiquated dams are likely destined for removal. We examined post-removal responses in two distinct fish communities formerly separated by a small aging mill dam. The dam was removed midway through the 6 year study, enabling passage for downstream fishes affiliated with a connected reservoir into previously inaccessible habitat, thus creating the potential for taxonomic homogenization between upstream and downstream communities. Both communities changed substantially post-removal. Two previously excluded species (white sucker, yellow perch) established substantial populations upstream of the former dam, contributing to a doubling of total fish biomass. Meanwhile, numerical density of pre-existing upstream fishes declined. Downstream, largemouth bass density was inversely correlated with prey fish density throughout the study, while post-removal declines in bluegill density coincided with cooler water temperature and increased suspended and benthic fine sediment. Upstream and downstream fish communities became more similar post-removal, represented by a shift in Bray-Curtis index from 14 to 41 % similarity. Our findings emphasize that barrier removal in highly fragmented stream networks can facilitate the unintended and possibly undesirable spread of species into headwater streams, including dispersal of species from remaining reservoirs. We suggest that knowledge of dispersal patterns for key piscivore and competitor species in both the target system and neighboring systems may help predict community outcomes following barrier removal.

  16. Response of macroinvertebrate communities to temporal dynamics of pesticide mixtures: A case study from the Sacramento River watershed, California.

    Science.gov (United States)

    Chiu, Ming-Chih; Hunt, Lisa; Resh, Vincent H

    2016-12-01

    Pesticide pollution from agricultural field run-off or spray drift has been documented to impact river ecosystems worldwide. However, there is limited data on short- and long-term effects of repeated pulses of pesticide mixtures on biotic assemblages in natural systems. We used reported pesticide application data as input to a hydrological fate and transport model (Soil and Water Assessment Tool) to simulate spatiotemporal dynamics of pesticides mixtures in streams on a daily time-step. We then applied regression models to explore the relationship between macroinvertebrate communities and pesticide dynamics in the Sacramento River watershed of California during 2002-2013. We found that both maximum and average pesticide toxic units were important in determining impacts on macroinvertebrates, and that the compositions of macroinvertebrates trended toward taxa having higher resilience and resistance to pesticide exposure, based on the Species at Risk pesticide (SPEARpesticides) index. Results indicate that risk-assessment efforts can be improved by considering both short- and long-term effects of pesticide mixtures on macroinvertebrate community composition.

  17. Projected Effects of CO2 Enrichment on Community Dynamics and Carbon Cycling in an Early-successional Forest

    Science.gov (United States)

    Miller, A. D.; Dietze, M.; DeLucia, E. H.; Anderson-Teixeira, K. J.

    2013-12-01

    Early-successional forests are strong carbon (C) sinks that play an important role in the global C cycle. Elevated CO2 may alter C cycling in regenerating forests both directly through ecophysiological mechanisms and indirectly through altered community dynamics, which may be particularly important in early successional forests with high community turnover. Thus, to discriminate impacts of CO2 enrichment on C cycles in regenerating forests it is necessary to characterize how the physiological and successional mechanisms that regulate the C cycle are altered by climate change. Because species are known to display differential growth stimulus under CO2 enrichment, and these species-specific effects are grouped by classic plant functional type, we hypothesize that successional trajectories will be altered in high CO2 forests, compared to forests regenerating under historic climatic conditions. To test this hypothesis, we use the Ecosystem Demography model (ED2), a height- and successional-structured terrestrial biosphere model to predict possible effects of elevated CO2 on forest succession. Using data from the Duke Free Air CO2 Enrichment (FACE) experiment and a nearby chronosequence of pine forests to parameterize and evaluate the model, we use ED2 to project how plant demography and competition will react to elevated CO2 over a 50-100 year time frame. We evaluate the sensitivity of model results to a variety of model configurations, and demonstrate that the outcomes are largely robust to structural uncertainty regarding assumptions about nitrogen limitation and water availability. The model predicts that elevated CO2 will alter C cycling directly through ecophysiological effect and indirectly through altered community dynamics, which in turn affect C cycling. For instance, late-successional hardwood species will receive more benefit on average from elevated CO2, than early-successional hardwoods. After 50 years of 550 ppm CO2, late-successional hardwoods experience

  18. Prior Experience as a Predictor for Institutional Performance: An Emerging Dynamic for the Community College Presidency

    Science.gov (United States)

    King, Matteel Deneen

    2010-01-01

    For the past several years, community college presidents have retired at alarming rates. At the same time, institutional needs have shifted and new skill sets are often desired. These changes, coupled with a lack of leader succession plans, budget cuts, and an increased emphasis on accountability, created opportunities for candidates with…

  19. Feminist Community Psychology: The Dynamic Co-Creation of Identities in Multilayered Contexts

    Science.gov (United States)

    Angelique, Holly; Mulvey, Anne

    2012-01-01

    In this special issue, we view the development of feminist community psychology (FCP) as an ongoing project that must be co-created. This is reflected in articles that focus on authors' unique social locations inside and outside organizations in which they work, critical reflections on their multilayered identities, feminist methodological and…

  20. Positive Workplace Dynamics: A Qualitative Exploration of Exceptional Performance in Community College Units

    Science.gov (United States)

    Stapleton, R. Michael

    2013-01-01

    This companion dissertation reports the findings of applied case study research on four community college organizational units that consistently meet or exceed standard performance measures. In addition, prior ample evidence confirmed that performance extended significantly beyond what might be explained by available tangible resources alone. The…

  1. Distributed Storage Management Using Dynamic Pricing in a Self-Organized Energy Community

    NARCIS (Netherlands)

    Negeri, E.; Baken, N.

    2012-01-01

    We consider a future self-organized energy community that is composed of “prosumer” households that can autonomously generate, store, import and export power, and also selfishly strive to minimize their cost by adjusting their load profiles using the flexibly of their distributed storage. In such

  2. Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.

    Science.gov (United States)

    Rubio-Portillo, Esther; Santos, Fernando; Martínez-García, Manuel; de Los Ríos, Asunción; Ascaso, Carmen; Souza-Egipsy, Virginia; Ramos-Esplá, Alfonso A; Anton, Josefa

    2016-12-01

    Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  3. Feminist Community Psychology: The Dynamic Co-Creation of Identities in Multilayered Contexts

    Science.gov (United States)

    Angelique, Holly; Mulvey, Anne

    2012-01-01

    In this special issue, we view the development of feminist community psychology (FCP) as an ongoing project that must be co-created. This is reflected in articles that focus on authors' unique social locations inside and outside organizations in which they work, critical reflections on their multilayered identities, feminist methodological and…

  4. Team Learning: Through the Relational Dynamics of Co-operation and Rivalry in Team Communities

    Science.gov (United States)

    Lotz, Maja

    2010-01-01

    This paper explores the constructive links between cooperation, rivalry, and learning within the structure of team communities. Drawing upon social learning theory and qualitative data from case studies conducted in Danish team-based firms, the main purpose is to argue that both cooperation and rivalry are important triggers for mobilizing…

  5. Team Learning: Through the Relational Dynamics of Co-operation and Rivalry in Team Communities

    Science.gov (United States)

    Lotz, Maja

    2010-01-01

    This paper explores the constructive links between cooperation, rivalry, and learning within the structure of team communities. Drawing upon social learning theory and qualitative data from case studies conducted in Danish team-based firms, the main purpose is to argue that both cooperation and rivalry are important triggers for mobilizing…

  6. The Microbial Community Dynamics during the Vitex Honey Ripening Process in the Honeycomb

    Directory of Open Access Journals (Sweden)

    Yaqin Wen

    2017-08-01

    Full Text Available The bacterial and fungal communities of vitex honey were surveyed by sequencing the 16S rRNA gene and the internal transcribed spacer region of ribosomal DNA. Vitex honey samples were analyzed at different stage of ripening; the vitex flower was also analyzed, and the effect of the chemical composition in the experimental setup was assessed. The results confirmed the presence of dominant Bacillus spp. as the dominant bacterial in honey, and yeast related genera was the main fungal in the honey, respectively. Lactococcus and Enterococcus were detected for the first time in honey. The proportion of most of the fungal community decreased during the honey ripening process. Multivariate analyses also showed that the fungal community of 5, 10, and 15 days honey samples tended to cluster together and were completely separated from the 1 day honey sample. The change in the fungal community showed a correlation with the variation in the chemical components, such as moisture and phenolic compounds. Together, these results suggest that ripening of honey could change its microbial composition, and decrease the potential risk of microbiology.

  7. Dynamics of bacterial and fungal communities associated with eggshells during incubation

    NARCIS (Netherlands)

    Grizard, Stephanie; Dini Andreote, Francisco; Tieleman, B. Irene; Falcao Salles, Joana

    Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and

  8. The impact of atrazine on lake periphyton communities, including carbon uptake dynamics using track autoradiography.

    Science.gov (United States)

    Hamilton, P B; Jackson, G S; Kaushik, N K; Solomon, K R

    1987-01-01

    Chlorophyll a, freshweight biomass, ash-free dry weight, cell numbers, species richness, community carbon uptake and species-specific carbon uptake were used to monitor the impact of atrazine (2 chloro-4-ethylamino-6-isopropylamino-s-triazine) on an in situ, enclosed periphyton community. Atrazine concentrations ranging from 0.08 to 1.56 mg litre(-1) were used during the 2 years of study. In both 1982 and 1983, there was a shift from a chlorophyte- to a diatom-dominated community. In 1982 the cyanobacterium Cylindrospermum stagnale and the chlorophyte Tetraspora cylindrica developed isolated colonies in the 1.56 mg litre(-1) treatment, indicating resistance to atrazine at this concentration. After atrazine exposure, community productivity was reduced by 21% to 82% in the low to high exposures, respectively. After day 21 productivity returned to control levels. It was shown, using track autoradiography, that the productivities of the larger algae Mougeotia sp., Oedogonium sp., Tolypothrix limbata and Epithemia turgida were the most affected, with reductions of 74.3% to 93.1% that of the controls. All the biotic measures indicated reduced growth after herbicide exposure.

  9. Microbial community dynamics in continuous microbial fuel cells fed with synthetic wastewater and pig slurry.

    Science.gov (United States)

    Sotres, Ana; Tey, Laura; Bonmatí, August; Viñas, Marc

    2016-10-01

    Two-chambered microbial fuel cells (MFCs) operating with synthetic wastewater and pig slurry were assessed. Additionally, the use of 2-bromoethanesulfonate (BES-Inh) was studied. The synthetic wastewater-fed MFC (MFCSW) showed a maximum power density (PDmax) of 2138mWm(-3), and the addition of BES-Inh (10mM) did not show any improvement in its performance (PDmax=2078mWm(-3)). When pig slurry was used as feed (MFCPS), PDmax increased up to 5623mWm(-3). The microbial community composition was affected by the type of substrate used. While, Pseudomonadaceae and Clostridiaceae were the most representative families within the acetate-based medium, Flavobacteriaceae, Chitinophagaceae, Comamonadaceae and Nitrosomonadaceae were predominant when pig slurry was used as feed. Otherwise, only the Eubacterial microbial community composition was strongly modified when adding BES-Inh, thus leading to an enrichment of the Bacteroidetes phylum. Oppositely, the Archaeal community was less affected by the addition of BES-Inh, and Methanosarcina sp., arose as the predominant family in both situations. Despite all the differences in microbial communities, 6 operational taxonomic units (OTUs) belonging to Bacteroidetes (Porphyromonadaceae and Marinilabiaceae) and Firmicutes (Clostridiales) were found to be common to both MFCs, also for different contents of COD and N-NH4(+), and therefore could be considered as the bioanode core microbiome.

  10. Towards science educational spaces as dynamic and coauthored communities of practice

    Science.gov (United States)

    Dhingra, Koshi

    2008-04-01

    In this essay review, four studies around the themes of identity and globalization are summarized and analyzed. The researchers' perspectives are generally grounded in Brown and Campione's ideas on situated knowledge ( Classroom lessons: Integrating cognitive theory and classroom practice (pp. 229-270). Cambridge: The MIT Press/Bradford Books, 1994) and Lave and Wenger's definition of learning as an activity fostered through participation in communities of practice ( Situated learning. Legitimate peripheral participation. Cambridge: University of Cambridge Press, 1991). Questions about the goals of science education spaces, the nature of globalization in relation to practices in schools, the role of identities-in-practice in relation to participation in communities of practice such as classrooms are explored. Recommendations for key design features in effective science educational spaces, based upon the findings presented in the collection of four studies, are offered. School, it is suggested here, functions best as a clearing house for the myriad science-related stories student participants generate in their various communities of practice (e.g., within popular culture, family, community, informal educational sites). In this way, school has the potential to construct bridges between multiple student experiences and identities-in-practice.

  11. Rapid and Specific Method for Evaluating Streptomyces Competitive Dynamics in Complex Soil Communities

    Science.gov (United States)

    Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative real-time PCR (qPCR) offers a rapid and specific means to assess populations of target microorganisms. SYBR Green and TaqMan-based qPCR assays were de...

  12. Rural Poverty Dynamics and Refugee Communities in South Africa: A Spatial-Temporal Model.

    Science.gov (United States)

    Sartorius, Kurt; Sartorius, Benn; Tollman, Stephen; Schatz, Enid; Kirsten, Johann; Collinson, Mark

    2013-01-01

    The assimilation of refugees into their host community economic structures is often problematic. The paper investigates the ability of refugees in rural South Africa to accumulate assets over time relative to their host community. Bayesian spatial-temporal modelling was employed to analyse a longitudinal database that indicated that the asset accumulation rate of former Mozambican refugee households was similar to their host community; however, they were unable to close the wealth gap. A series of geo-statistical wealth maps illustrate that there is a spatial element to the higher levels of absolute poverty in the former refugee villages. The primary reason for this is their physical location in drier conditions that are established further away from facilities and infrastructure. Neighbouring South African villages in close proximity, however, display lower levels of absolute poverty, suggesting that the spatial location of the refugees only partially explains their disadvantaged situation. In this regard, the results indicate that the wealth of former refugee households continues to be more compromised by higher mortality levels, poorer education, and less access to high-return employment opportunities. The long-term impact of low initial asset status appears to be perpetuated in this instance by difficulties in obtaining legal status in order to access state pensions, facilities, and opportunities. The usefulness of the results is that they can be used to sharpen the targeting of differentiated policy in a given geographical area for refugee communities in rural Africa. Copyright © 2011 John Wiley & Sons, Ltd.

  13. Soil microbial community and its interaction with soil carbon and nitrogen dynamics following afforestation in central China.

    Science.gov (United States)

    Deng, Qi; Cheng, Xiaoli; Hui, Dafeng; Zhang, Qian; Li, Ming; Zhang, Quanfa

    2016-01-15

    Afforestation may alter soil microbial community structure and function, and further affect soil carbon (C) and nitrogen (N) dynamics. Here we investigated soil microbial carbon and nitrogen (MBC and MBN) and microbial community [e.g. bacteria (B), fungi (F)] derived from phospholipid fatty acids (PLFAs) analysis in afforested (implementing woodland and shrubland plantations) and adjacent croplands in central China. Relationships of microbial properties with biotic factors [litter, fine root, soil organic carbon (SOC), total nitrogen (TN) and inorganic N], abiotic factors (soil temperature, moisture and pH), and major biological processes [basal microbial respiration, microbial metabolic quotient (qCO2), net N mineralization and nitrification] were developed. Afforested soils had higher mean MBC, MBN and MBN:TN ratios than the croplands due to an increase in litter input, but had lower MBC:SOC ratio resulting from low-quality (higher C:N ratio) litter. Afforested soils also had higher F:B ratio, which was probably attributed to higher C:N ratios in litter and soil, and shifts of soil inorganic N forms, water, pH and disturbance. Alterations in soil microbial biomass and community structure following afforestation were associated with declines in basal microbial respiration, qCO2, net N mineralization and nitrification, which likely maintained higher soil carbon and nitrogen storage and stability.

  14. Bacterial community dynamics during cold storage of minced meat packaged under modified atmosphere and supplemented with different preservatives.

    Science.gov (United States)

    Stoops, J; Ruyters, S; Busschaert, P; Spaepen, R; Verreth, C; Claes, J; Lievens, B; Van Campenhout, L

    2015-06-01

    Since minced meat is very susceptible for microbial growth, characterisation of the bacterial community dynamics during storage is important to optimise preservation strategies. The purpose of this study was to investigate the effect of different production batches and the use of different preservatives on the composition of the bacterial community in minced meat during 9 days of cold storage under modified atmosphere (66% O2, 25% CO2 and 9% N2). To this end, both culture-dependent (viable aerobic and anaerobic counts) and culture-independent (454 pyrosequencing) analyses were performed. Initially, microbial counts of fresh minced meat showed microbial loads between 3.5 and 5.0 log cfu/g. The observed microbial diversity was relatively high, and the most abundant bacteria differed among the samples. During storage an increase of microbial counts coincided with a dramatic decrease in bacterial diversity. At the end of the storage period, most samples showed microbial counts above the spoilage level of 7 log cfu/g. A relatively similar bacterial community was obtained regardless of the manufacturing batch and the preservative used, with Lactobacillus algidus and Leuconostoc sp. as the most dominant microorganisms. This suggests that both bacteria played an important role in the spoilage of minced meat packaged under modified atmosphere. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics

    Directory of Open Access Journals (Sweden)

    Elliot S. Friedman

    2016-01-01

    Full Text Available Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale. Here, we elucidated the effect of an inexhaustible, ferrous-iron and humic-substance mimicking terminal electron acceptor by deploying potentiostatically poised electrodes in the sediment of a very specific stream riparian zone in Upstate New York state. At two sites within the same stream riparian zone during the course of six weeks in the spring of 2013, we measured CH4 and N2/N2O emissions from soil chambers containing either poised or unpoised electrodes, and we harvested biofilms from the electrodes to quantify microbial community dynamics. At the upstream site, which had a lower vegetation cover and highest soil temperatures, the poised electrodes inhibited CH4 emissions by ~45% (when normalized to remove temporal effects. CH4 emissions were not significantly impacted at the downstream site. N2/N2O emissions were generally low at both sites and were not impacted by poised electrodes. We did not find a direct link between bioelectrochemical treatment and microbial community membership; however, we did find a correspondence between environment/function and microbial community dynamics.

  16. Bacterial Community and “Candidatus Accumulibacter” Population Dynamics in Laboratory-Scale Enhanced Biological Phosphorus Removal Reactors ▿ †

    Science.gov (United States)

    He, Shaomei; Bishop, Forrest I.; McMahon, Katherine D.

    2010-01-01

    “Candidatus Accumulibacter” and total bacterial community dynamics were studied in two lab-scale enhanced biological phosphorus removal (EBPR) reactors by using a community fingerprint technique, automated ribosomal intergenic spacer analysis (ARISA). We first evaluated the quantitative capability of ARISA compared to quantitative real-time PCR (qPCR). ARISA and qPCR provided comparable relative quantification of the two dominant “Ca. Accumulibacter” clades (IA and IIA) detected in our reactors. The quantification of total “Ca. Accumulibacter” 16S rRNA genes relative to that from the total bacterial community was highly correlated, with ARISA systematically underestimating “Ca. Accumulibacter” abundance, probably due to the different normalization techniques applied. During 6 months of normal (undisturbed) operation, the distribution of the two clades within the total “Ca. Accumulibacter” population was quite stable in one reactor while comparatively dynamic in the other reactor. However, the variance in the clade distribution did not appear to affect reactor performance. Instead, good EBPR activity was positively associated with the abundance of total “Ca. Accumulibacter.” Therefore, we concluded that the different clades in the system provided functional redundancy. We disturbed the reactor operation by adding nitrate together with acetate feeding in the anaerobic phase to reach initial reactor concentrations of 10 mg/liter NO3-N for 35 days. The reactor performance deteriorated with a concomitant decrease in the total “Ca. Accumulibacter” population, suggesting that a population shift was the cause of performance upset after a long exposure to nitrate in the anaerobic phase. PMID:20601516

  17. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).

    Science.gov (United States)

    Loudon, Andrew H; Woodhams, Douglas C; Parfrey, Laura Wegener; Archer, Holly; Knight, Rob; McKenzie, Valerie; Harris, Reid N

    2014-04-01

    Beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus Batrachochytrium dendrobatidis. We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing. After field sampling, salamanders were housed with soil from the field or sterile media. The captive conditions led to different trajectories of bacterial communities. Eight OTUs present on >90% of salamanders in the field, through time, and in both treatments were defined as the core community, suggesting that some bacteria are closely associated with the host and are independent of an environmental reservoir. One of these taxa, a Pseudomonas sp., was previously cultured from amphibians and found to be antifungal. As all host-associated bacteria were found in the soil reservoir, environmental microbes strongly influence host-microbial diversity and likely regulate the core community. Using PICRUSt, an exploratory bioinformatics tool to predict gene functions, we found that core skin bacteria provided similar gene functions to the entire community. We suggest that future experiments focus on testing whether core bacteria on salamander skin contribute to the observed resistance to chytridiomycosis in this species even under hygenic captive conditions. For disease-susceptible hosts, providing an environmental reservoir with defensive bacteria in captive-rearing programs may improve outcomes by increasing bacterial diversity on threatened amphibians or increasing the likelihood that defensive bacteria are available for colonization.

  18. Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine.

    Directory of Open Access Journals (Sweden)

    Guo-Chun Ding

    Full Text Available Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.

  19. Additive Manufacturing: Reproducibility of Metallic Parts

    Directory of Open Access Journals (Sweden)

    Konda Gokuldoss Prashanth

    2017-02-01

    Full Text Available The present study deals with the properties of five different metals/alloys (Al-12Si, Cu-10Sn and 316L—face centered cubic structure, CoCrMo and commercially pure Ti (CP-Ti—hexagonal closed packed structure fabricated by selective laser melting. The room temperature tensile properties of Al-12Si samples show good consistency in results within the experimental errors. Similar reproducible results were observed for sliding wear and corrosion experiments. The other metal/alloy systems also show repeatable tensile properties, with the tensile curves overlapping until the yield point. The curves may then follow the same path or show a marginal deviation (~10 MPa until they reach the ultimate tensile strength and a negligible difference in ductility levels (of ~0.3% is observed between the samples. The results show that selective laser melting is a reliable fabrication method to produce metallic materials with consistent and reproducible properties.

  20. Reproducibility of scoring emphysema by HRCT

    Energy Technology Data Exchange (ETDEWEB)

    Malinen, A.; Partanen, K.; Rytkoenen, H.; Vanninen, R. [Kuopio Univ. Hospital (Finland). Dept. of Clinical Radiology; Erkinjuntti-Pekkanen, R. [Kuopio Univ. Hospital (Finland). Dept. of Pulmonary Diseases

    2002-04-01

    Purpose: We evaluated the reproducibility of three visual scoring methods of emphysema and compared these methods with pulmonary function tests (VC, DLCO, FEV1 and FEV%) among farmer's lung patients and farmers. Material and Methods: Three radiologists examined high-resolution CT images of farmer's lung patients and their matched controls (n=70) for chronic interstitial lung diseases. Intraobserver reproducibility and interobserver variability were assessed for three methods: severity, Sanders' (extent) and Sakai. Pulmonary function tests as spirometry and diffusing capacity were measured. Results: Intraobserver -values for all three methods were good (0.51-0.74). Interobserver varied from 0.35 to 0.72. The Sanders' and the severity methods correlated strongly with pulmonary function tests, especially DLCO and FEV1. Conclusion: The Sanders' method proved to be reliable in evaluating emphysema, in terms of good consistency of interpretation and good correlation with pulmonary function tests.

  1. Reproducibility of electroretinograms recorded with DTL electrodes.

    Science.gov (United States)

    Hébert, M; Lachapelle, P; Dumont, M

    The purpose of this study was to examine whether the use of the DTL fiber electrode yields stable and reproducible electroretinographic recordings. To do so, luminance response function, derived from dark-adapted electroretinograms, was obtained from both eyes of 10 normal subjects at two recording sessions spaced by 7-14 days. The data thus generated was used to calculate Naka-Rushton Vmax and k parameters and values obtained at the two recording sessions were compared. Our results showed that there was no significant difference in the values of Vmax and k calculated from the data generated at the two recording sessions. The above clearly demonstrate that the use of the DTL fiber electrode does not jeopardize, in any way, the stability and reproducibility of ERG responses.

  2. Repeatability and Reproducibility of Virtual Subjective Refraction.

    Science.gov (United States)

    Perches, Sara; Collados, M Victoria; Ares, Jorge

    2016-10-01

    To establish the repeatability and reproducibility of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and reproducibility of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding reproducibility, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in reproducibility and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.

  3. Tissue Doppler imaging reproducibility during exercise.

    Science.gov (United States)

    Bougault, V; Nottin, S; Noltin, S; Doucende, G; Obert, P

    2008-05-01

    Tissue Doppler imaging (TDI) is an echocardiographic technique used during exercising to improve the accuracy of a cardiovascular diagnostic. The validity of TDI requires its reproducibility, which has never been challenged during moderate to maximal intensity exercising. The present study was specifically designed to assess the transmitral Doppler and pulsed TDI reproducibility in 19 healthy men, who had undergone two identical semi-supine maximal exercise tests on a cycle ergometer. Systolic (S') and diastolic (E') tissue velocities at the septal and lateral walls as well as early transmitral velocities (E) were assessed during exercise up to maximal effort. The data were compared between the two tests at 40 %, 60 %, 80 % and 100 % of maximal aerobic power. Despite upper body movements and hyperventilation, good quality echocardiographic images were obtained in each case. Regardless of exercise intensity, no differences were noticed between the two tests for all measurements. The variation coefficients for Doppler variables ranged from 3 % to 9 % over the transition from rest to maximal exercise. The random measurement error was, on average, 5.8 cm/s for E' and 4.4 cm/s for S'. Overall, the reproducibility of TDI was acceptable. Tissue Doppler imaging can be used to accurately evaluate LV diastolic and/or systolic function for this range of exercise intensity.

  4. How to Write a Reproducible Paper

    Science.gov (United States)

    Irving, D. B.

    2016-12-01

    The geosciences have undergone a computational revolution in recent decades, to the point where almost all modern research relies heavily on software and code. Despite this profound change in the research methods employed by geoscientists, the reporting of computational results has changed very little in academic journals. This lag has led to something of a reproducibility crisis, whereby it is impossible to replicate and verify most of today's published computational results. While it is tempting to decry the slow response of journals and funding agencies in the face of this crisis, there are very few examples of reproducible research upon which to base new communication standards. In an attempt to address this deficiency, this presentation will describe a procedure for reporting computational results that was employed in a recent Journal of Climate paper. The procedure was developed to be consistent with recommended computational best practices and seeks to minimize the time burden on authors, which has been identified as the most important barrier to publishing code. It should provide a starting point for geoscientists looking to publish reproducible research, and could be adopted by journals as a formal minimum communication standard.

  5. Tools and techniques for computational reproducibility.

    Science.gov (United States)

    Piccolo, Stephen R; Frampton, Michael B

    2016-07-11

    When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will